make[2]: Entering directory '/home/pharmacy/amber18/AmberTools/test' ./test_at_clean.sh cd antechamber && make -k clean make[3]: Entering directory '/home/pharmacy/amber18/AmberTools/test/antechamber' Cleaning all antechamber test subdirectories: find . -name "*.dif" -print0 | xargs -0 /bin/rm -f /bin/rm -f \ ash/antechamber.out \ ash/sqm.in \ ash/sqm.out \ ash/sqm.pdb \ bondtype/antechamber.out \ c60/antechamber.out \ charmm/antechamber.out \ fluorescein/antechamber.out \ fluorescein/sqm.in \ fluorescein/sqm.out \ fpph/antechamber.out \ guanine_amber/antechamber.out \ guanine_amber/sqm.in \ guanine_amber/sqm.out \ guanine_amber/sqm.pdb \ residuegen/ala_conf1.esp \ residuegen/ala_conf2.esp \ residuegen/ANTECHAMBER_AC.AC \ residuegen/ANTECHAMBER_AC.AC0 \ residuegen/ANTECHAMBER_BOND_TYPE.AC \ residuegen/ANTECHAMBER_BOND_TYPE.AC0 \ residuegen/antechamber.out \ residuegen/ATOMTYPE.INF \ residuegen/esout \ residuegen/espgen.out \ residuegen/NEWPDB.PDB \ residuegen/PREP.INF \ residuegen/punch \ residuegen/QIN \ residuegen/qout \ residuegen/RESIDUE_GEN_MAINCHAIN.DAT \ residuegen/RESIDUE_GEN_RESP.INPUT1 \ residuegen/RESIDUE_GEN_RESP.INPUT2 \ residuegen/RESIDUE_GEN_RESP.OUTPUT1 \ residuegen/RESIDUE_GEN_RESP.OUTPUT2 \ residuegen/RESIDUE_GEN_RESPGEN.DAT \ residuegen/RESIDUE_GEN.AC \ residuegen/residuegen.out \ sustiva/antechamber.out \ sustiva/leap.log \ sustiva/prmtop \ sustiva/sqm.in \ sustiva/sqm.out \ tp/antechamber.out \ tp/sqm.out make[3]: Leaving directory '/home/pharmacy/amber18/AmberTools/test/antechamber' cd mmpbsa_py && make -k clean make[3]: Entering directory '/home/pharmacy/amber18/AmberTools/test/mmpbsa_py' cd EstRAL_Files && /bin/rm -f ?.top _AnteMMPBSA_* *.dif cd 01_Generalized_Born && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 02_Poisson_Boltzmann && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 03_Alanine_Scanning && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 04_Per_Residue_Decomp && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 05_Pairwise_Decomp && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 06_NAB_Nmode && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 07_Comprehensive && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA*.dat *.dif *.csv cd 08_Stability && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA*.dat *.dif *.csv cd 09_APBS_Poisson_Boltzmann && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 10_QM_MMGBSA && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 11_3D-RISM && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 12_Membrane_Channel && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv make[3]: Leaving directory '/home/pharmacy/amber18/AmberTools/test/mmpbsa_py' cd /home/pharmacy/amber18/AmberTools/src/mm_pbsa/Examples && ./Run.mmpbsa.clean cd /home/pharmacy/amber18/AmberTools/src/FEW/examples/test && ./Run.few.clean cd /home/pharmacy/amber18/AmberTools/src/cpptraj/test && make -k clean make[3]: Entering directory '/home/pharmacy/amber18/AmberTools/src/cpptraj/test' Cleaning all test directories: make test.complete test.libcpptraj OPT=clean make[4]: Entering directory '/home/pharmacy/amber18/AmberTools/src/cpptraj/test' make[5]: Entering directory '/home/pharmacy/amber18/AmberTools/src/cpptraj/test' make[5]: Leaving directory '/home/pharmacy/amber18/AmberTools/src/cpptraj/test' make[4]: Leaving directory '/home/pharmacy/amber18/AmberTools/src/cpptraj/test' make[3]: Leaving directory '/home/pharmacy/amber18/AmberTools/src/cpptraj/test' cd leap && make -k clean make[3]: Entering directory '/home/pharmacy/amber18/AmberTools/test/leap' Cleaning all test directories: (find . -name 'leap.log' -o -name 'leap.out' | \ while read dif ;\ do \ rm -f $dif ;\ done ;\ ) make test.complete OPT=clean make[4]: Entering directory '/home/pharmacy/amber18/AmberTools/test/leap' make[4]: Nothing to be done for 'test.complete'. make[4]: Leaving directory '/home/pharmacy/amber18/AmberTools/test/leap' make[3]: Leaving directory '/home/pharmacy/amber18/AmberTools/test/leap' cd leap/glycam/06j && ./Run.glycam clean cd leap/glycam/06EPb && ./Run.glycam clean cd leap/glycam/06j_10 && ./Run.glycam clean cd leap/glycam/06j_12SB && ./Run.glycam clean cd nab && make -k test make[3]: Entering directory '/home/pharmacy/amber18/AmberTools/test/nab' Running test to do simple minimization (this tests the molecular mechanics interface) diffing ltest.out.check with ltest.out possible FAILURE: check ltest.out.dif ============================================================== Running test to do simple minimization with shake (this tests the molecular mechanics interface) diffing rattle_min.out.check with rattle_min.out possible FAILURE: check rattle_min.out.dif ============================================================== Running test to do simple minimization (this tests the generalized Born implementation) diffing gbrna.out.check with gbrna.out possible FAILURE: check gbrna.out.dif ============================================================== Running test to do simple minimization (this tests the generalized Born implementation) diffing xfin_sa.out.check with xfin_sa.out possible FAILURE: check xfin_sa.out.dif ============================================================== Running test to do simple minimization (this tests the LCPO surface area) diffing gbrna_sa.out.check with gbrna_sa.out possible FAILURE: check gbrna_sa.out.dif ============================================================== Running test to do simple minimization (this tests the ao generalized Born implementation) diffing gbtrx.out.check with gbtrx.out possible FAILURE: check gbtrx.out.dif ============================================================== Running test to do simple minimization (this tests the ao-2 generalized Born implementation) diffing gb5trx.out.check with gb5trx.out possible FAILURE: check gb5trx.out.dif ============================================================== Running test to do simple minimization (this tests the GB Neck implementation; gb==8) diffing gb8trx.out.check with gb8trx.out possible FAILURE: check gb8trx.out.dif ============================================================== Running test to do simple minimization (this tests the GB Neck implementation; gb==7) diffing gb7trx.out.check with gb7trx.out possible FAILURE: check gb7trx.out.dif ============================================================== Running test to do molecular dynamics with rattle diffing rattle_md.out.check with rattle_md.out possible FAILURE: check rattle_md.out.dif ============================================================== Running test to compute NAB energy of 3dfr minus waters. Compare the NAB energy with the previously computed Amber energy: Amber8 total energy is 5184.0880 NAB total energy is 5184.0880 NAB total energy is 5184.0880 NAB total energy is 5184.0880 NAB total energy is 5184.0880 diffing dhfrndpmtx.out.check with dhfrndpmtx.out file ddtmp.dhfrndpmtx.out.check is short possible FAILURE: check dhfrndpmtx.out.dif ============================================================== Running test to compute GB Newton-Raphson and normal modes: Note: Very small differences between asp.out and the saved file are common and do not necessarily indicate a problem. diffing asp.out.check with asp.out PASSED ============================================================== Running test to compute non-GB Newton-Raphson and normal modes: Note: Small differences are common and do not necessarily indicate a problem. diffing aspnb.out.check with aspnb.out PASSED ============================================================== Running test to create Amber force-field description Assertion failed in file src/mpi/coll/helper_fns.c at line 84: FALSE memcpy argument memory ranges overlap, dst_=0x5654ba5bdd70 src_=0x5654ba5bdd90 len_=15360 internal ABORT - process 0 [unset]: Assertion failed in file src/mpi/coll/helper_fns.c at line 84: FALSE memcpy argument memory ranges overlap, dst_=0x564ac44a4d70 src_=0x564ac44a4d90 len_=15360 internal ABORT - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor system msg for write_line failure : Bad file descriptor ./Run.prm: Program error Makefile:95: recipe for target 'prm_test' failed make[3]: *** [prm_test] Error 1 Running test to do simple xmin minimization diffing txmin.out.check with txmin.out file ddtmp.txmin.out.check is short possible FAILURE: check txmin.out.dif ============================================================== Running test to do md with netcdf diffing gbnetcdf.out.check with gbnetcdf.out possible FAILURE: check gbnetcdf.out.dif ============================================================== Running test on netcdf files diffing tnetcdf.out.check with tnetcdf.out possible FAILURE: check tnetcdf.out.dif ============================================================== Running test for variable 1-4 scaled nonbonded interactions diffing variable_14scale.out.check with variable_14scale.out possible FAILURE: check variable_14scale.out.dif ============================================================== Running test to compute GB normal modes using DSYEVD: diffing asp_nm1.out.check with asp_nm1.out PASSED ============================================================== Running test to compute GB normal modes using DSAUPD: diffing asp_nm2.out.check with asp_nm2.out PASSED ============================================================== Running test to compute Langevin modes: diffing asp_nm3.out.check with asp_nm3.out PASSED ============================================================== Running test of the isotropic periodic sum technique diffing dhfr_ips.out.check with dhfr_ips.out file ddtmp.dhfr_ips.out.check is short possible FAILURE: check dhfr_ips.out.dif ============================================================== Running test to do simple minimization (libpbsa) (this tests the PBSA implementation) Please note that PARALLEL PBSA is not implemented in nab. ============================================================================ make[3]: Target 'test' not remade because of errors. make[3]: Leaving directory '/home/pharmacy/amber18/AmberTools/test/nab' Makefile:98: recipe for target 'test.nab' failed make[2]: *** [test.nab] Error 2 cd /home/pharmacy/amber18/AmberTools/src/cpptraj/test && make -k test make[3]: Entering directory '/home/pharmacy/amber18/AmberTools/src/cpptraj/test' make test.complete summary make[4]: Entering directory '/home/pharmacy/amber18/AmberTools/src/cpptraj/test' 1 1 1 1 MPI threads. make[5]: Entering directory '/home/pharmacy/amber18/AmberTools/src/cpptraj/test' ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_General General tests cannot be run in parallel. SKIP: General tests ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Parallel CPPTRAJ: Parallel tests. diffing d1-12.dat.save with d1-12.dat PASSED ============================================================== diffing a1-6-12.dat.save with a1-6-12.dat PASSED ============================================================== diffing phi2.dat.save with phi2.dat PASSED ============================================================== diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing avg.rst7.save with avg.rst7 PASSED ============================================================== Parallel test with trajectory offset requires Parallel NetCDF. Cpptraj was compiled without Parallel NetCDF support. Skipped test: Parallel test with trajectory offset ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Strip ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: One frame strip command test diffing dummy.pdb.save with dummy.pdb.1 PASSED ============================================================== diffing dummy.rst7.save with dummy.rst7 PASSED ============================================================== diffing strip.tz2.truncoct.parm7.save with strip.tz2.truncoct.parm7 PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Unstrip (Lig/Rec/Complex) command test diffing strip.tz2.truncoct.parm7.save with complex.tz2.truncoct.parm7 PASSED ============================================================== diffing receptor.tz2.truncoct.parm7.save with receptor.tz2.truncoct.parm7 PASSED ============================================================== diffing ligand.tz2.truncoct.parm7.save with ligand.tz2.truncoct.parm7 PASSED ============================================================== diffing Ligand.crd.save with Ligand.crd PASSED ============================================================== diffing Receptor.crd.save with Receptor.crd PASSED ============================================================== diffing Complex.crd.save with Complex.crd PASSED ============================================================== CPPTRAJ: Multi frame strip command test. diffing res1.tz2.crd.save with res1.tz2.crd PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_BrokenTraj Broken trajectory tests cannot be run in parallel. SKIP: Broken trajectory tests ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_TrajinOffset CPPTRAJ: Normal trajectory read with offsets. diffing rem.crd.save with rem.crd.combined PASSED ============================================================== CPPTRAJ: Gzipped trajectory read with offsets diffing rem.crd.save with gzip.rem.crd.combined PASSED ============================================================== CPPTRAJ: Bzip2ed trajectory read with offsets. diffing rem.crd.save with bzip2.rem.crd.combined PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_RemdTraj ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: CRD Replica Trajectory Run with offset diffing d1.offset.dat.save with d1.offset.dat PASSED ============================================================== CPPTRAJ: CRD Replica Trajectory Run diffing d1.crd.dat.save with d1.crd.dat PASSED ============================================================== CPPTRAJ: NetCDF Replica Trajectory Run test diffing d1.nc.dat.save with d1.nc.dat PASSED ============================================================== expr: syntax error ../MasterTest.sh: line 971: [: too many arguments CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj CPPTRAJ: CRD Replica Trajectory Run with remdout Error: Fewer threads than groups currently not allowed. Error: Could not set up input ensemble 'rem.crd.000'. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: Fewer threads than groups currently not allowed. Error: Could not set up input ensemble 'rem.crd.000'. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: Fewer threads than groups currently not allowed. Error: Could not set up input ensemble 'rem.crd.000'. 1 errors encountered reading input. Error: Error(s) occurred during execution. /home/pharmacy/amber18/bin/cpptraj.MPI: Program error cat: 'd1.ensemble.dat.?': No such file or directory diffing all.dat.save with all.dat possible FAILURE: check all.dat.dif ============================================================== possible FAILURE: file temp.crd.0 does not exist. ============================================================== possible FAILURE: file temp.crd.1 does not exist. ============================================================== possible FAILURE: file temp.crd.2 does not exist. ============================================================== possible FAILURE: file temp.crd.3 does not exist. ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_trajout_framerange Trajout frame range cannot be run in parallel. SKIP: Trajout frame range ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_PerResRMSD ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Per-Residue RMSD Test. diffing PerResRMSD.agr.save with PerResRMSD.agr PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Per-Residue RMSD Test with averaging diffing perresavg.dat.save with perresavg.dat PASSED ============================================================== CPPTRAJ: Per-Residue RMSD Test with residue centering. diffing center.agr.save with center.agr PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_DSSP CPPTRAJ: Secstruct (DSSP) command test. diffing dssp.gnu.save with dssp.gnu PASSED ============================================================== diffing dssp.sum.agr.save with dssp.sum.agr PASSED ============================================================== diffing total.agr.save with total.agr PASSED ============================================================== diffing DSSP.assign.dat.save with DSSP.assign.dat PASSED ============================================================== CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. diffing dssp.dat.save with dssp.dat PASSED ============================================================== diffing dssp.dat.sum.save with dssp.dat.sum PASSED ============================================================== Secstruct (DSSP) command with changing number of residues. cannot be run in parallel. Skipped test: Secstruct (DSSP) command with changing number of residues. ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Secstruct (DSSP): SS assign output test diffing assign.4.dat.save with assign.4.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Center ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Center command test. diffing centered.crd.save with centered.crd PASSED ============================================================== CPPTRAJ: Center origin command test. diffing origin.centered.crd.save with origin.centered.crd PASSED ============================================================== CPPTRAJ: Center origin mass command test. diffing origin.mass.centered.crd.save with origin.mass.centered.crd PASSED ============================================================== CPPTRAJ: Center reference command test. diffing ref.centered.crd.save with ref.centered.crd PASSED ============================================================== CPPTRAJ: Center point test. diffing point.centered.crd.save with point.centered.crd PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Hbond CPPTRAJ: Solute Hbond test diffing nhb.dat.save with nhb.dat PASSED ============================================================== diffing avghb.dat.save with avghb.dat PASSED ============================================================== diffing nbb.dat.save with nbb.dat PASSED ============================================================== diffing hbavg.dat.save with hbavg.dat PASSED ============================================================== diffing solutehb.agr.save with solutehb.agr PASSED ============================================================== diffing lifehb.gnu.save with lifehb.gnu PASSED ============================================================== diffing avg.lifehb.gnu.save with avg.lifehb.gnu PASSED ============================================================== diffing max.lifehb.gnu.save with max.lifehb.gnu PASSED ============================================================== diffing crv.lifehb.gnu.save with crv.lifehb.gnu PASSED ============================================================== CPPTRAJ: Solute-solvent hbond test diffing solvhb.dat.save with solvhb.dat PASSED ============================================================== diffing solvavg.dat.save with solvavg.dat PASSED ============================================================== CPPTRAJ: Hbond, no intramolecular hydrogen bonds test diffing hbond.mol.dat.save with hbond.mol.dat PASSED ============================================================== diffing mol.avg.dat.save with mol.avg.dat PASSED ============================================================== CPPTRAJ: Hbond, specified solute masks diffing ud.dat.save with ud.dat PASSED ============================================================== diffing uh.dat.save with uh.dat PASSED ============================================================== diffing ua.dat.save with ua.dat PASSED ============================================================== CPPTRAJ: Hbond, no angle cutoff test diffing noacut.dat.save with noacut.dat PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Hbond, Bridge nointramol test diffing bridgeintermol.dat.save with bridgeintermol.dat PASSED ============================================================== diffing avgbridgeintermol.dat.save with avgbridgeintermol.dat PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Hbond with imaging diffing hb1.dat.save with hb1.dat PASSED ============================================================== diffing hb2.dat.save with hb2.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_NCrestart ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: NetCDF Restart Test - TXT->NetCDF CPPTRAJ: NetCDF Restart Test - NetCDF->TXT diffing ../tz2.rst7 with text.rst7 PASSED ============================================================== CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt diffing ../tz2.ortho.rst7 with text.rst7 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Image ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Orthorhombic imaged distance test. diffing ortho.dat.save with ortho.dat PASSED ============================================================== CPPTRAJ: Non-orthorhombic imaged distance test. diffing nonortho.dat.save with nonortho.dat PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Orthorhombic coordinate imaging test diffing image.crd.save with image.crd PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Nonorthorhombic coordinate imaging test diffing image2.crd.save with image2.crd PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar diffing image3.crd.save with image3.crd PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM diffing image4.crd.save with image4.crd PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Surf CPPTRAJ: Surface calculation test diffing surf.dat.save with surf.dat PASSED ============================================================== CPPTRAJ: Partial Surface calculation test diffing tsurf.dat.save with tsurf.dat PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: LCPO test with GAFF atom types diffing ral.surf.dat.save with ral.surf.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Radgyr ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Radius of gyration command test diffing radgyr.dat.save with radgyr.dat PASSED ============================================================== diffing radgyr.mass.dat.save with radgyr.mass.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Mask ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Mask single frame test diffing mask.out.save with mask.out PASSED ============================================================== diffing mask.pdb.1.save with mask.pdb.1 PASSED ============================================================== diffing mask.mol2.1.save with mask.mol2.1 PASSED ============================================================== CPPTRAJ: Mask longer command test. diffing M.dat.save with M.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Jcoupling ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: J-Coupling single frame test diffing Jcoupling.dat.save with Jcoupling.dat PASSED ============================================================== CPPTRAJ: J-Coupling extended test. diffing jc.dat.save with jc.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Diffusion CPPTRAJ: Diffusion test, no imaging. diffing noimage.dat.save with noimage.dat PASSED ============================================================== diffing noimage.agr.save with noimage.agr PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Diffusion test, old syntax. diffing diff_a.xmgr.save with diff_a.xmgr PASSED ============================================================== diffing diff_r.xmgr.save with diff_r.xmgr PASSED ============================================================== diffing diff_x.xmgr.save with diff_x.xmgr PASSED ============================================================== diffing diff_y.xmgr.save with diff_y.xmgr PASSED ============================================================== diffing diff_z.xmgr.save with diff_z.xmgr PASSED ============================================================== CPPTRAJ: Diffusion test, new syntax. diffing WAT_O.agr.save with WAT_O.agr PASSED ============================================================== diffing DC.dat.save with DC.dat PASSED ============================================================== CPPTRAJ: Diffusion test, nonorthogonal box diffing Nonortho.dat.save with Nonortho.dat PASSED ============================================================== diffing Nonortho.agr.save with Nonortho.agr PASSED ============================================================== STFC diffusion tests cannot be run in parallel. Skipped test: STFC diffusion tests ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Outtraj CPPTRAJ: RMSD Test with outtraj. diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing T1.crd with T2.crd PASSED ============================================================== diffing ../tz2.truncoct.crd with test.crd PASSED ============================================================== Outtraj Test with maxmin. cannot be run in parallel. Skipped test: Outtraj Test with maxmin. ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Charmm ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: CHARMM PSF/DCD test diffing test.ala3.pdb.save with test.ala3.pdb.1 PASSED ============================================================== CPPTRAJ: CHARMM DCD Write, step 1. CPPTRAJ: CHARMM DCD Write, step 2. diffing first.ala3.crd with second.ala3.crd PASSED ============================================================== CPPTRAJ: CHAMBER topology read/strip test. diffing strip.chamber.parm7.save with strip.chamber.parm7 PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Charmm DCD tests diffing run0.res_0.mol2.save with run0.res_0.mol2 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Rotdif CPPTRAJ: Rotational diffusion calculation test diffing rvecs.dat.save with rvecs.dat PASSED ============================================================== diffing matrices.dat.save with matrices.dat PASSED ============================================================== diffing deffs.dat.save with deffs.dat PASSED ============================================================== diffing rotdif.out.save with rotdif.out PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_NetcdfTraj NetCDF tests requires Parallel NetCDF. Cpptraj was compiled without Parallel NetCDF support. SKIP: NetCDF tests ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Runavg CPPTRAJ: Coordinate Running Average test. diffing R1.dat.save with R1.dat PASSED ============================================================== Coordinate Running Average Traj Write cannot be run in parallel. Skipped test: Coordinate Running Average Traj Write ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_RMSD ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Basic RMSD tests diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing rmsd.mass.dat.save with rmsd.mass.dat PASSED ============================================================== diffing vecs.dat.save with vecs.dat PASSED ============================================================== diffing rmsd.reftraj.dat.save with rmsd.reftraj.dat PASSED ============================================================== diffing rmsd.reftraj.dat.save with rmsd.refcoords.dat PASSED ============================================================== CPPTRAJ: RMS coordinate rotation/rotation matrices test. diffing tz2.norotate.crd.save with tz2.norotate.crd PASSED ============================================================== diffing tz2.rotate.crd.save with tz2.rotate.crd PASSED ============================================================== diffing rmatrices.dat.save with rmatrices.dat PASSED ============================================================== CPPTRAJ: RMS fit with no coordinates modification test. diffing NoMod.dat.save with NoMod.dat PASSED ============================================================== diffing NoMod.crd.save with NoMod.crd PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_2DRMS CPPTRAJ: 2D RMSD Test. diffing rmsd.dat.save with rmsd2.dat PASSED ============================================================== CPPTRAJ: 2D RMSD Test, mass-weighted. diffing rmsd.mass.dat.save with rmsd.mass.dat PASSED ============================================================== 2D RMSD Test with reference trajectory requires Parallel NetCDF. Cpptraj was compiled without Parallel NetCDF support. Skipped test: 2D RMSD Test with reference trajectory CPPTRAJ: 2D DME Test. diffing dme.dat.save with dme.dat PASSED ============================================================== CPPTRAJ: 2D RMSD with reference mask test. diffing trp.dat.save with trp.dat PASSED ============================================================== CPPTRAJ: 2D RMSD test, no fitting. diffing nofit.dat.save with nofit.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Mol2 Mol2 tests cannot be run in parallel. SKIP: Mol2 tests ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_NAstruct ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: NAstruct command test. diffing BP.adh026.dat.save with BP.adh026.dat PASSED ============================================================== diffing BPstep.adh026.dat.save with BPstep.adh026.dat PASSED ============================================================== diffing Helix.adh026.dat.save with Helix.adh026.dat PASSED ============================================================== diffing BP.adh026.dat.save with BP.baseref.dat PASSED ============================================================== diffing BPstep.adh026.dat.save with BPstep.baseref.dat PASSED ============================================================== diffing Helix.adh026.dat.save with Helix.baseref.dat PASSED ============================================================== diffing BPstep.groove.dat.save with BPstep.groove.dat PASSED ============================================================== diffing BP.adh026.dat.save with BP.GuessBP.dat PASSED ============================================================== diffing BPstep.adh026.dat.save with BPstep.GuessBP.dat PASSED ============================================================== diffing Helix.adh026.dat.save with Helix.GuessBP.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Average CPPTRAJ: Average Test. diffing test.pdb.save with test.pdb PASSED ============================================================== diffing test.pdb.save with test2.pdb PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Pucker ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Pucker command test diffing pucker.dat.save with pucker.dat PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test diffing CremerF.dat.save with CremerF.dat PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. diffing CremerP.dat.save with CremerP.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_AtomMap ../MasterTest.sh: line 961: [: too many arguments ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: AtomMap Test diffing initial.mol2.save with initial.mol2 PASSED ============================================================== diffing atommap.dat.save with atommap.dat PASSED ============================================================== diffing reordered.pdb.save with reordered.pdb PASSED ============================================================== diffing reordered.mol2.save with reordered.mol2 PASSED ============================================================== diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing fit.mol2.save with fit.mol2 PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: AtomMap with 'rmsfit' diffing rmsd.dat.save with rmsout.dat PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Atom map charmm->amber atom order diffing map.chm_to_amb.dat.save with map.chm_to_amb.dat PASSED ============================================================== CPPTRAJ: Atom map charmm->amber atom order, by residue diffing map.chm_to_amb.dat.save with map.byres.chm_to_amb.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Datafile CPPTRAJ: Data file output precision test diffing prec.dat.save with prec.dat PASSED ============================================================== CPPTRAJ: Standard -> Grace Data CPPTRAJ: Grace -> Standard Data diffing ../Test_General/a1.dat.save with a1.dat PASSED ============================================================== CPPTRAJ: X column format/precision test. diffing xprec.dat.save with xprec.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Radial ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Radial test diffing Radial.agr.save with Radial.agr PASSED ============================================================== diffing cRadial.agr.save with cRadial.agr PASSED ============================================================== diffing WatO-Trp4.agr.save with WatO-Trp4.agr PASSED ============================================================== diffing WatO-Trp4.raw.agr.save with WatO-Trp4.raw.agr PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Hist CPPTRAJ: 1D/2D Histogram Analysis test diffing hist.gnu.save with hist.gnu PASSED ============================================================== diffing hist.agr.save with hist.agr PASSED ============================================================== diffing freeE.gnu.save with freeE.gnu PASSED ============================================================== diffing norm.gnu.save with norm.gnu PASSED ============================================================== diffing phipsihist.agr.save with phipsihist.agr PASSED ============================================================== diffing phipsikde.agr.save with phipsikde.agr PASSED ============================================================== CPPTRAJ: 3D histogram test. diffing hist.dx.save with hist.dx PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Closest ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Closest command test using first solvent atom. diffing first.Closest.pdb.save with first.Closest.pdb.1 PASSED ============================================================== diffing closestmols.dat.save with closestmols.dat PASSED ============================================================== diffing closest.tz2.truncoct.parm7.save with closest.tz2.truncoct.parm7 PASSED ============================================================== CPPTRAJ: Closest command test using all solvent atoms. diffing all.Closest.pdb.save with all.Closest.pdb.1 PASSED ============================================================== CPPTRAJ: Closest command test, using mask center diffing closest10.center2_4.crd.save with closest10.center2_4.crd PASSED ============================================================== diffing closest10.mols.dat.save with closest10.mols.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_DRMSD CPPTRAJ: Distance RMSD test diffing drmsd.dat.save with drmsd.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Cluster CPPTRAJ: Cluster command test, in-memory pairwise distances. diffing cnumvtime.dat.save with cnumvtime.dat PASSED ============================================================== diffing avg.summary.dat.save with avg.summary.dat PASSED ============================================================== diffing summary.dat.save with summary.dat PASSED ============================================================== diffing cpop.agr.save with cpop.agr PASSED ============================================================== CPPTRAJ: Cluster command test, read pairwise distances. diffing summary.dat.save with summary2.dat PASSED ============================================================== CPPTRAJ: Cluster command test, read NetCDF pairwise distances. diffing summary.dat.save with summary3.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Cluster_Sieve CPPTRAJ: Cluster, nosieve diffing nosieve.info.dat.save with nosieve.info.dat PASSED ============================================================== diffing nosieve.half.dat.save with nosieve.half.dat PASSED ============================================================== diffing nosieve.sil.cluster.dat.save with nosieve.sil.cluster.dat PASSED ============================================================== CPPTRAJ: Cluster, sieve5 Error: Opening Netcdf file sieve5.nc.c3 for Write. Error: Could not set up cluster trajectory sieve5.nc.c3 for write. diffing sieve5.info.dat.save with sieve5.info.dat PASSED ============================================================== diffing sieve5.half.dat.save with sieve5.half.dat PASSED ============================================================== diffing sieve5.sil.cluster.dat.save with sieve5.sil.cluster.dat PASSED ============================================================== CPPTRAJ: Cluster, nosieve savepairdist diffing nosieve.info.dat.save with nosieve.info.dat PASSED ============================================================== diffing nosieve.half.dat.save with nosieve.half.dat PASSED ============================================================== diffing nosieve.sil.cluster.dat.save with nosieve.sil.cluster.dat PASSED ============================================================== CPPTRAJ: Cluster, nosieve loadpairdist diffing nosieve.info.dat.save with nosieve.info.dat PASSED ============================================================== diffing nosieve.half.dat.save with nosieve.half.dat PASSED ============================================================== diffing nosieve.sil.cluster.dat.save with nosieve.sil.cluster.dat PASSED ============================================================== CPPTRAJ: Cluster, sieve5 savepairdist diffing sieve5.info.dat.save with sieve5.info.dat PASSED ============================================================== diffing sieve5.half.dat.save with sieve5.half.dat PASSED ============================================================== diffing sieve5.sil.cluster.dat.save with sieve5.sil.cluster.dat PASSED ============================================================== diffing nc0.save with nc0 PASSED ============================================================== CPPTRAJ: Cluster, sieve5 loadpairdist diffing sieve5.info.dat.save with sieve5.info.dat PASSED ============================================================== diffing sieve5.half.dat.save with sieve5.half.dat PASSED ============================================================== diffing sieve5.sil.cluster.dat.save with sieve5.sil.cluster.dat PASSED ============================================================== CPPTRAJ: Cluster, nosieve pairwisecache none diffing nosieve.info.dat.save with nosieve.info.dat PASSED ============================================================== diffing nosieve.half.dat.save with nosieve.half.dat PASSED ============================================================== diffing nosieve.sil.cluster.dat.save with nosieve.sil.cluster.dat PASSED ============================================================== CPPTRAJ: Cluster, sieve5 pairwisecache none diffing sieve5.info.dat.save with sieve5.info.dat PASSED ============================================================== diffing sieve5.half.dat.save with sieve5.half.dat PASSED ============================================================== diffing sieve5.sil.cluster.dat.save with sieve5.sil.cluster.dat PASSED ============================================================== CPPTRAJ: Cluster, random diffing random.info.dat.save with random.info.dat PASSED ============================================================== diffing random.half.dat.save with random.half.dat PASSED ============================================================== diffing random.sil.cluster.dat.save with random.sil.cluster.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Cluster_RandomSieve CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). diffing random.info.dat.save with random.info.dat PASSED ============================================================== diffing random.summary.dat.save with random.summary.dat PASSED ============================================================== CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). diffing random.info.dat.save with random.info.dat PASSED ============================================================== diffing random.summary.dat.save with random.summary.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Cluster_DataSet CPPTRAJ: Clustering, One DataSet diffing oneds.info.dat.save with oneds.info.dat PASSED ============================================================== diffing eps_v_n.dat.save with eps_v_n.dat PASSED ============================================================== diffing cvt.dat.save with cvt.dat PASSED ============================================================== CPPTRAJ: Clustering, Two DataSets diffing twods.info.dat.save with twods.info.dat PASSED ============================================================== CPPTRAJ: Clustering, dihedral DataSet diffing onedihds.info.dat.save with onedihds.info.dat PASSED ============================================================== CPPTRAJ: Clustering, two dihedral DataSets diffing twodihds.info.dat.save with twodihds.info.dat PASSED ============================================================== CPPTRAJ: Clustering, dihedral DataSet, K-means diffing onedihds.kmeans.info.dat.save with onedihds.kmeans.info.dat PASSED ============================================================== CPPTRAJ: Clustering, two dihedral DataSets, K-means diffing twodihds.kmeans.info.dat.save with twodihds.kmeans.info.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Cluster_DBSCAN CPPTRAJ: DBSCAN test diffing rvc.dat.save with rvc.dat PASSED ============================================================== CPPTRAJ: DBSCAN automatic parameter determination test. diffing Kdist.dat.save with Kdist.4.dat PASSED ============================================================== CPPTRAJ: DBSCAN kdist map test diffing Kmatrix.gnu.save with Kmatrix.gnu PASSED ============================================================== CPPTRAJ: DBSCAN with sieve diffing sieveinfo.dat.2.save with sieveinfo.dat.2 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Cluster_Kmeans CPPTRAJ: Cpptraj Kmeans diffing summary.dat.save with summary.dat PASSED ============================================================== diffing info.dat.save with info.dat PASSED ============================================================== diffing cpptraj.crd.c0.save with cpptraj.crd.c0 PASSED ============================================================== CPPTRAJ: Cpptraj Kmeans random diffing random.dat.save with random.dat PASSED ============================================================== diffing info.dat.save with rinfo.dat PASSED ============================================================== diffing cpptraj.crd.c0.save with random.crd.c0 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Cluster_SymmRMSD CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) diffing rms.summary.dat.save with rms.summary.dat PASSED ============================================================== diffing rms.info.dat.save with rms.info.dat PASSED ============================================================== diffing srmsd.summary.dat.save with srmsd.summary.dat PASSED ============================================================== diffing srmsd.info.dat.save with srmsd.info.dat PASSED ============================================================== diffing 2drms.gnu.save with 2drms.gnu PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Cluster_TrajWrites CPPTRAJ: Cluster command test, coordinate writes. CPPTRAJ: Cluster command test, coordinate writes using info file. diffing clusterinfo.txt.save with clusterinfo.txt PASSED ============================================================== diffing cluster.c0.save with cluster.c0 PASSED ============================================================== diffing rep.1.crd.save with rep.c8.1.crd PASSED ============================================================== diffing single.save with single PASSED ============================================================== diffing avg.summary.dat.save with avg.summary.dat PASSED ============================================================== diffing lifetime.dat.save with lifetime.dat PASSED ============================================================== diffing Avg.c0.rst7.save with Avg.c0.rst7 PASSED ============================================================== diffing cluster.c0.save with fromInfo.c0 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Cluster_Dpeaks CPPTRAJ: Density peaks clustering test diffing dpeaks.dat.save with dpeaks.dat PASSED ============================================================== diffing summary.dat.save with summary.dat PASSED ============================================================== diffing info.dat.save with info.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_IRED CPPTRAJ: IRED vector/matrix test diffing ired.vec.save with ired.vec PASSED ============================================================== diffing v0.cmt.new.norm.save with v0.cmt PASSED ============================================================== diffing plateau.norm.dat.save with plateau.norm.dat PASSED ============================================================== diffing v0.cjt.new.save with v0.cjt PASSED ============================================================== diffing orderparam.save with orderparam PASSED ============================================================== diffing matrix_ds2.dat.save with matrix_ds2.dat PASSED ============================================================== diffing noe.save with noe PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_RandomizeIons ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: randomizeions test diffing random.crd.save with random.crd PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Molsurf CPPTRAJ: Molsurf test diffing msurf.dat.save with msurf.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Corr CPPTRAJ: Correlation test diffing corr.dat.save with corr.dat PASSED ============================================================== diffing cross.dat.save with cross.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_CheckStructure ../MasterTest.sh: line 961: [: too many arguments ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Structure Check diffing report.dat.save with report.dat PASSED ============================================================== diffing nprob.dat.save with nprob.dat PASSED ============================================================== CPPTRAJ: Structure Check with Around and Skip diffing skip.dat.save with skip.dat PASSED ============================================================== diffing d1.dat.save with d1.dat PASSED ============================================================== CPPTRAJ: Structure Check with PBC diffing tz2.dat.save with tz2.dat PASSED ============================================================== CPPTRAJ: Structure Check with Around diffing around.dat.save with around.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_RmsAvgCorr CPPTRAJ: RmsAvgCorr Reference diffing rmscorr.dat.save with rmscorr.dat PASSED ============================================================== diffing rmscorr.10.dat.save with rmscorr.10.dat PASSED ============================================================== CPPTRAJ: RmsAvgCorr First diffing rmscorr.first.dat.save with rmscorr.first.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Contacts Contacts test cannot be run in parallel. SKIP: Contacts test ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Principal CPPTRAJ: Principal Test diffing Ctest.crd.save with Ctest.crd PASSED ============================================================== diffing eigen.dat.save with eigen.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_ClusterDihedral clusterdihedral test cannot be run in parallel. SKIP: clusterdihedral test ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Vector ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Basic vector tests diffing vtest.dat.0.save with vtest.dat.0 PASSED ============================================================== diffing vtest.dat.1.save with vtest.dat.1 PASSED ============================================================== diffing vtest.dat.2.save with vtest.dat.2 PASSED ============================================================== diffing vtest.dat.3.save with vtest.dat.3 PASSED ============================================================== diffing vtest.dat.4.save with vtest.dat.4 PASSED ============================================================== diffing vtest.dat.5.save with vtest.dat.5 PASSED ============================================================== diffing vtest.dat.6.save with vtest.dat.6 PASSED ============================================================== diffing vtest.dat.7.save with vtest.dat.7 PASSED ============================================================== diffing v8.mol2.save with v8.mol2 PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Test vector center with magnitude diffing avgcoord.out.save with avgcoord.out PASSED ============================================================== diffing res5.out.save with res5.out PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Momentum vector test. diffing vtest.dat.9.save with vtest.dat.9 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Matrix CPPTRAJ: Matrix Tests. diffing mtest.dat.0.save with mtest.0.dat PASSED ============================================================== diffing mtest.dat.1.save with mtest.1.dat PASSED ============================================================== diffing mtest.dat.2.save with mtest.2.dat PASSED ============================================================== diffing mtest.dat.3.save with mtest.3.dat PASSED ============================================================== diffing mtest.dat.4.save with mtest.4.dat PASSED ============================================================== diffing mtest.dat.5.save with mtest.5.dat PASSED ============================================================== diffing mtest.dat.6.save with mtest.6.dat PASSED ============================================================== diffing mtest.dat.7.save with mtest.7.dat PASSED ============================================================== diffing mtest.dat.8.save with mtest.8.dat PASSED ============================================================== diffing mtest.dat.9.save with mtest.9.dat PASSED ============================================================== diffing mtest.dat.10.save with mtest.10.dat PASSED ============================================================== diffing mtest.dat.11.save with mtest.11.dat PASSED ============================================================== diffing mtest.dat.12.save with mtest.12.dat PASSED ============================================================== diffing mtest.dat.13.save with mtest.13.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_AtomicFluct CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. diffing fluct.1.dat.save with fluct.1.dat PASSED ============================================================== CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. diffing fluct.2.dat.save with fluct.2.dat PASSED ============================================================== CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. diffing fluct.3.dat.save with fluct.3.dat PASSED ============================================================== CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. diffing fluct.4.dat.save with fluct.4.dat PASSED ============================================================== CPPTRAJ: Atomicfluct test with ADP output diffing dpdp.fluct.dat.save with dpdp.fluct.dat PASSED ============================================================== diffing dpdp.adp.dat.save with dpdp.adp.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Grid ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Dipole test diffing out.dipole.save with out.dipole PASSED ============================================================== CPPTRAJ: Grid test diffing out.xplor.save with out.xplor PASSED ============================================================== diffing out.dx.save with out.dx PASSED ============================================================== CPPTRAJ: OpenDX Grid read test diffing out.dx.2.save with out.dx.2 PASSED ============================================================== CPPTRAJ: Grid with specified center test. diffing test.dx.save with test.dx PASSED ============================================================== CPPTRAJ: Grid with box center offset test. diffing box.dx.save with box.dx PASSED ============================================================== CPPTRAJ: Grid with mask center offset test. diffing mask.dx.save with mask.dx PASSED ============================================================== CPPTRAJ: Non-orthogonal grid test. diffing nonortho.dx.save with nonortho.dx PASSED ============================================================== CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test diffing nonortho_wrap.dx.save with nonortho_wrap.dx PASSED ============================================================== CPPTRAJ: Grid generation from 'bounds' test. diffing bounds.dat.save with bounds.dat PASSED ============================================================== diffing bounds.xplor.save with bounds.xplor PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Unwrap Unwrap tests cannot be run in parallel. SKIP: Unwrap tests ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Project CPPTRAJ: Projection diffing project.dat.save with project.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Analyze_Modes CPPTRAJ: Modes analysis, RMS fluctuations diffing fluct.dat.save with fluct.dat PASSED ============================================================== CPPTRAJ: Modes analysis, displacements diffing displ.dat.save with displ.dat PASSED ============================================================== CPPTRAJ: Modes analysis, dipole correlation diffing corr.dat.save with corr.dat PASSED ============================================================== CPPTRAJ: Modes analysis, pseudo trajectory creation test diffing modestest.2.crd.save with modestest.2.crd PASSED ============================================================== CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test diffing rmsip.dat.save with rmsip.dat PASSED ============================================================== diffing eigenval.dat.save with eigenval.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Watershell CPPTRAJ: Watershell Test, non-orthorhombic imaging. diffing ws.agr.save with ws.agr PASSED ============================================================== CPPTRAJ: Watershell Test, orthorhombic imaging. diffing ws.ortho.agr.save with ws.ortho.agr PASSED ============================================================== CPPTRAJ: Watershell Test, no imaging. diffing ws.noimage.agr.save with ws.noimage.agr PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_AnalysisRunAvg CPPTRAJ: Analysis Running Average diffing running_avg.dat.save with running_avg.dat PASSED ============================================================== diffing cumulative_avg.dat.save with cumulative_avg.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Volmap ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: VMD VolMap Algorithm test diffing volmap3.dx.save with volmap3.dx PASSED ============================================================== diffing peaks1.xyz.save with peaks1.xyz PASSED ============================================================== VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. Skipped test: VMD VolMap Algorithm longer tests ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_SPAM CPPTRAJ: SPAM Test diffing summary.dat.save with summary.dat PASSED ============================================================== diffing spam.info.save with spam.info PASSED ============================================================== diffing spam.dat.save with spam.dat PASSED ============================================================== CPPTRAJ: SPAM Pure Solvent Test diffing spampure.dat.save with spampure.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_LIE CPPTRAJ: LIE test diffing TCL.out.save with TCL.out PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Density Density test cannot be run in parallel. SKIP: Density test ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_LipidOrder Lipid Order Parameter Test cannot be run in parallel. SKIP: Lipid Order Parameter Test ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_LipidSCD ../MasterTest.sh: line 961: [: too many arguments ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Basic lipid order parameter test diffing ol1.dat.save with ol1.dat PASSED ============================================================== diffing ol2.dat.save with ol2.dat PASSED ============================================================== diffing ol3.agr.save with ol3.agr PASSED ============================================================== CPPTRAJ: New Lipid Order Parameter Test, DOPC. diffing dopc.agr.save with dopc.agr PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_PairDist CPPTRAJ: PairDist Test. diffing Pr.dat.save with Pr.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_ReadData CPPTRAJ: Read vector data test diffing v6and7.dat.save with v6and7.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_GIST GIST tests cannot be run in parallel. SKIP: GIST tests ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_GIST_Order GIST tetrahedral water cluster test cannot be run in parallel. SKIP: GIST tetrahedral water cluster test ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_AmbPDB AMBPDB: AmbPDB tests. diffing out.pdb.save with out.pdb PASSED ============================================================== diffing out.pdb.save with out1.pdb PASSED ============================================================== diffing fabi.pdb.save with fabi.pdb PASSED ============================================================== diffing ../Test_Mol2/test2.mol2.save with out.mol2 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_systemVF Amber NetCDF trajectory with Velocity/Force test requires Parallel NetCDF. Cpptraj was compiled without Parallel NetCDF support. SKIP: Amber NetCDF trajectory with Velocity/Force test ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_AtomicCorr CPPTRAJ: Atomic Correlation test diffing acorr.gnu.save with acorr.gnu PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_AutoCorr CPPTRAJ: AutoCorr test. diffing ac.agr.save with ac.agr PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Box ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Box Test (Add box info) diffing addbox.rst7.1.save with addbox.rst7.1 PASSED ============================================================== diffing addbox.rst7.10.save with addbox.rst7.10 PASSED ============================================================== CPPTRAJ: Box test (Modify box length) diffing modX.rst7.1.save with modX.rst7.1 PASSED ============================================================== diffing modX.rst7.10.save with modX.rst7.10 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_AtomTypeSelect CPPTRAJ: Selection by atom type test. diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_AvgRef CPPTRAJ: Parallel, average reference coordinates. CPPTRAJ: Parallel, RMSD Test with averaged reference coordinates. diffing rmsavg.dat.save with rmsavg.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Crank_Stat CPPTRAJ: Crankshaft test diffing crank.dat.save with crank.dat PASSED ============================================================== diffing results.dat.save with results.dat PASSED ============================================================== diffing stat.dat.save with stat.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_CreateCrd CPPTRAJ: COORDS data set creation and CRDFLUCT test. diffing crd1.dat.save with crd1.dat PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: COORDS data set creation with velocities test diffing crd0.rst7 with crd.rst7 PASSED ============================================================== diffing crd1.rst7.save with crd1.rst7 PASSED ============================================================== CPPTRAJ: TRAJ data set creation and CRDFLUCT test. diffing crd1.dat.save with crd1.dat PASSED ============================================================== CPPTRAJ: TRAJ data set creation with velocities test. diffing crd1.rst7.save with crd2.rst7 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_AutoImage ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: AutoImage test (split DNA duplex) diffing reimage.mdcrd.save with reimage.mdcrd PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: AutoImage test, use anchor mask diffing image.G3_3A.rst7.save with image.G3_3A.rst7 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_LoadCrd CPPTRAJ: LoadCrd test. diffing d1-10.dat.save with d1-10.dat PASSED ============================================================== CPPTRAJ: LoadTraj test. diffing d1-10.dat.save with d1-10.dat PASSED ============================================================== CPPTRAJ: LoadTraj from trajin test. diffing d1-10.dat.save with d1-10.dat PASSED ============================================================== CPPTRAJ: LoadCrd append from multiple files test diffing d1-12.dat.save with d1-12.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_MultiVector CPPTRAJ: Multivector test diffing NH.dat.save with NH.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Lifetime CPPTRAJ: Lifetime test. diffing avg.life.5.gnu.save with avg.life.5.gnu PASSED ============================================================== diffing max.life.5.gnu.save with max.life.5.gnu PASSED ============================================================== diffing life.5.gnu.save with life.5.gnu PASSED ============================================================== diffing crv.life.5.gnu.save with crv.life.5.gnu PASSED ============================================================== diffing solutehb.gnu.save with solutehb.gnu PASSED ============================================================== CPPTRAJ: Lifetime average and cumulative average test. diffing perres.avg.gnu.save with perres.avg.gnu PASSED ============================================================== diffing perres.cumulative.gnu.save with perres.cumulative.gnu PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_FFT CPPTRAJ: FFT test. diffing fft.agr.save with fft.agr PASSED ============================================================== diffing fft1.agr.save with fft1.agr PASSED ============================================================== diffing fft2.agr.save with fft2.agr PASSED ============================================================== diffing fft3.agr.save with fft3.agr PASSED ============================================================== diffing fft4.agr.save with fft4.agr PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Timecorr CPPTRAJ: Timecorr test. diffing v1.auto.dat.save with v1.auto.dat PASSED ============================================================== diffing v1v2.cross.dat.save with v1v2.cross.dat PASSED ============================================================== diffing v1.dplr.auto.dat.save with v1.dplr.auto.dat PASSED ============================================================== diffing v1v2.dplr.cross.dat.save with v1v2.dplr.cross.dat PASSED ============================================================== diffing v1.o0.auto.dat.save with v1.o0.auto.dat PASSED ============================================================== diffing v1.o1.auto.dat.save with v1.o1.auto.dat PASSED ============================================================== diffing tz2.2.3.cross.dat.save with tz2.2.3.cross.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_CrossCorr CPPTRAJ: CrossCorr test diffing cc.gnu.save with cc.gnu PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_SymmRmsd ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: SymmRmsd diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: ASP symmetry-corrected RMSD test diffing ASP.rmsd.dat.save with ASP.rmsd.dat PASSED ============================================================== diffing ASP.remap.crd.save with ASP.remap.crd PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: GLU symmetry-corrected RMSD test diffing GLU.rmsd.dat.save with GLU.rmsd.dat PASSED ============================================================== diffing GLU.remap.crd.save with GLU.remap.crd PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: TYR symmetry-corrected RMSD test diffing TYR.rmsd.dat.save with TYR.rmsd.dat PASSED ============================================================== diffing TYR.remap.crd.save with TYR.remap.crd PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Multidihedral CPPTRAJ: Multidihedral test diffing dihedral.dat with multidih.dat PASSED ============================================================== diffing dihedral2.dat with custom.dat PASSED ============================================================== diffing all.dat.save with all.dat PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Multidihedral Nucleotide CHI test diffing chin.dat.save with chin.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Ensemble_MREMD expr: syntax error ../MasterTest.sh: line 971: [: too many arguments CPPTRAJ: M-REMD sort test. Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. /home/pharmacy/amber18/bin/cpptraj.MPI: Program error possible FAILURE: file Strip.sorted.crd.0 does not exist. ============================================================== possible FAILURE: file Strip.sorted.crd.1 does not exist. ============================================================== possible FAILURE: file Strip.sorted.crd.2 does not exist. ============================================================== possible FAILURE: file Strip.sorted.crd.3 does not exist. ============================================================== possible FAILURE: file Strip.sorted.crd.4 does not exist. ============================================================== possible FAILURE: file Strip.sorted.crd.5 does not exist. ============================================================== possible FAILURE: file Strip.sorted.crd.6 does not exist. ============================================================== possible FAILURE: file Strip.sorted.crd.7 does not exist. ============================================================== CPPTRAJ: M-REMD actions test. Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. /home/pharmacy/amber18/bin/cpptraj.MPI: Program error cat: 'rmsd.dat.?': No such file or directory cat: 'nhbond.dat.?': No such file or directory cat: 'hbavg.dat.?': No such file or directory possible FAILURE: file avg.rst7.2 does not exist. ============================================================== possible FAILURE: file avg.rst7.5 does not exist. ============================================================== CPPTRAJ: M-REMD ensemble outtraj test. Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. /home/pharmacy/amber18/bin/cpptraj.MPI: Program error possible FAILURE: file Outtraj.crd.0 does not exist. ============================================================== possible FAILURE: file Outtraj.crd.1 does not exist. ============================================================== CPPTRAJ: M-REMD no sort, running average test Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. /home/pharmacy/amber18/bin/cpptraj.MPI: Program error cat: 'RA.dat.?': No such file or directory CPPTRAJ: M-REMD, generate RMS data Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: Fewer threads than groups currently not allowed. 1 errors encountered reading input. Error: Error(s) occurred during execution. /home/pharmacy/amber18/bin/cpptraj.MPI: Program error CPPTRAJ: M-REMD, meltcurve analysis Error: 'RmsToRep1.dat.?': No such file or directory Error: Could not read data file 'RmsToRep1.dat.?'. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: 'RmsToRep1.dat.?': No such file or directory Error: Could not read data file 'RmsToRep1.dat.?'. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: 'RmsToRep1.dat.?': No such file or directory Error: Could not read data file 'RmsToRep1.dat.?'. 1 errors encountered reading input. Error: Error(s) occurred during execution. /home/pharmacy/amber18/bin/cpptraj.MPI: Program error possible FAILURE: file melt.dat does not exist. ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_MakeStructure ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Basic makestructure test diffing pp2.rst7.save with pp2.rst7 PASSED ============================================================== diffing dihedrals.dat.save with dihedrals.dat PASSED ============================================================== diffing dihedrals2.dat.save with dihedrals2.dat PASSED ============================================================== diffing dihedrals3.dat.save with dihedrals3.dat PASSED ============================================================== CPPTRAJ: Makestructure test with reference. diffing fromref.pdb.save with fromref.pdb.1 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Rotate CPPTRAJ: Rotation (and inverse) of coords from matrices diffing fromMatrices.crd.save with fromMatrices.crd PASSED ============================================================== diffing ../Test_RMSD/tz2.norotate.crd.save with inverse.crd PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Rotate with defined axis diffing TCS.rotated.mol2.save with TCS.rotated.mol2 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Integrate CPPTRAJ: Integration test. diffing curve.dat.save with curve.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_NativeContacts CPPTRAJ: NativeContacts test. diffing nc.hp1.ca.dat.save with nc.hp1.ca.dat PASSED ============================================================== diffing nc1.pdb.save with nc1.pdb PASSED ============================================================== diffing nc.hp2.ca.dat.save with nc.hp2.ca.dat PASSED ============================================================== diffing nc2.contacts.dat.save with nc2.contacts.dat PASSED ============================================================== diffing nc2.res.dat.save with nc2.res.dat PASSED ============================================================== diffing NC2.series.dat.save with NC2.series.dat PASSED ============================================================== diffing nc.all.res.dat.save with nc.all.res.dat PASSED ============================================================== diffing native.resmap.gnu.save with native.resmap.gnu PASSED ============================================================== diffing nonnative.resmap.gnu.save with nonnative.resmap.gnu PASSED ============================================================== NativeContacts test, save non-native contacts, residue time series cannot be run in parallel. Skipped test: NativeContacts test, save non-native contacts, residue time series ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_CheckChiral CPPTRAJ: Check chirality test diffing chiral.dat.save with chiral.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Energy CPPTRAJ: Simple energy tests diffing ene.agr.save with ene.agr PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Test kinetic energy calculation diffing short.dat.save with short.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_LESsplit ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: LES split/average test diffing splittraj.0.save with splittraj.0 PASSED ============================================================== diffing avg.crd.save with avg.crd PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_PermuteDihedrals ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: PermuteDihedrals interval -120, phi psi diffing rotations.mdcrd.save with rotations.mdcrd PASSED ============================================================== CPPTRAJ: PermuteDihedrals, random rotations diffing random.mol2.save with random.mol2.1 PASSED ============================================================== diffing random.mol2.save with RAND.mol2 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_CCP4 CPPTRAJ: CCP4 read/write and DX conversion test. diffing fav8.dx.save with fav8.dx PASSED ============================================================== diffing fav8.guv.O.1.ccp4 with fav8.ccp4 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_DihCovar CPPTRAJ: Dihedral Covariance Matrix Test (parallel, create matrix) CPPTRAJ: Dihedral Covariance Matrix Test (parallel, projection) diffing dihcovar.dat.save with dihcovar.dat PASSED ============================================================== diffing modes.dihcovar.dat.save with modes.dihcovar.dat PASSED ============================================================== diffing dih.project.dat.save with dih.project.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_CurveFit CPPTRAJ: Curve fitting test. diffing curve.dat.save with curve.dat PASSED ============================================================== CPPTRAJ: Curve fitting multi-exponential tests. diffing curve.dat.save with curve1.dat PASSED ============================================================== diffing Kcurve.dat.save with Kcurve.dat PASSED ============================================================== diffing PKcurve.dat.save with PKcurve.dat PASSED ============================================================== diffing Results.dat.save with Results.dat PASSED ============================================================== CPPTRAJ: Curve fitting, custom output range. diffing curve2.dat.save with curve2.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Multicurve CPPTRAJ: Multicurve test diffing curves.agr.save with curves.agr PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_DataSetAverage CPPTRAJ: Data set averaging and averaging over all sets test. diffing output.dat.save with output.dat PASSED ============================================================== diffing avg.dat.save with avg.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_VectorMath CPPTRAJ: Vector dot/cross product test diffing dotproduct.dat.save with dotproduct.dat PASSED ============================================================== diffing v1init_dot_v1.dat.save with v1init_dot_v1.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Esander SANDER energy tests (long) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. SKIP: SANDER energy tests (long) ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Esander_Short Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. ../MasterTest.sh: line 961: [: too many arguments SKIP: Energy via sander API short tests (GB/PME) ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Temperature CPPTRAJ: Temperature test. diffing T.dat.save with T.dat PASSED ============================================================== CPPTRAJ: Temperature with SHAKE on hydrogens. diffing T2.dat.save with T2.dat PASSED ============================================================== CPPTRAJ: Temperature with SHAKE on all atoms. diffing T3.dat.save with T3.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Spline CPPTRAJ: Spline test diffing spline.dat.save with spline.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_KDE CPPTRAJ: KDE test. diffing kde.dat.save with kde.dat PASSED ============================================================== CPPTRAJ: KDE with Kullback-Leibler divergence test diffing kl.dat.save with kl.dat PASSED ============================================================== diffing final.dat.save with final.dat PASSED ============================================================== diffing divergence.dat.save with divergence.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Wavelet CPPTRAJ: Wavelet analysis test diffing wavelet.gnu.save with wavelet.gnu PASSED ============================================================== CPPTRAJ: Wavelet WAFEX test diffing cluster.gnu.save with cluster.gnu PASSED ============================================================== diffing cluster.dat.save with cluster.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_CIF ../MasterTest.sh: line 961: [: too many arguments CIF read test cannot be run in parallel. Skipped test: CIF read test CPPTRAJ: Generate offset traj from PDB CPPTRAJ: Generate offset traj from CIF diffing temp1.crd with temp2.crd PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_PDB ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: PDB format read/write test diffing test.pdb.save with test.pdb PASSED ============================================================== diffing chainA.dat.save with chainA.dat PASSED ============================================================== diffing oresnum.dat.save with oresnum.dat PASSED ============================================================== PQR file write with various radii cannot be run in parallel. Skipped test: PQR file write with various radii ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Align CPPTRAJ: Align Tests. diffing ../Test_RMSD/rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing ../Test_RMSD/rmsd.mass.dat.save with rmsd.mass.dat PASSED ============================================================== diffing ../Test_RMSD/rmsd.reftraj.dat.save with rmsd.reftraj.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_VelocityAutoCorr ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Velocity autocorrelation test diffing VAC.agr.save with VAC.agr PASSED ============================================================== diffing diff.dat.save with diff.dat PASSED ============================================================== diffing VAC2.dat.save with VAC2.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_VelFrc Read separate velocity/force trajectory data tests cannot be run in parallel. SKIP: Read separate velocity/force trajectory data tests ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_RotateDihedral CPPTRAJ: Rotate dihedral to target value. diffing tz2.rotate.1.mol2.save with tz2.rotate.1.mol2 PASSED ============================================================== CPPTRAJ: Rotate dihedral by increment diffing tz2.rotate.1.mol2.save with tz2.rotate.2.mol2 PASSED ============================================================== CPPTRAJ: Rotate dihedral in TRAJ data set diffing tz2.rotate.1.mol2.save with tz2.rotate.3.mol2 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_DataSetCmd CPPTRAJ: Data Set commands test diffing avg.dat.save with avg.dat PASSED ============================================================== diffing D4.dat.save with D4.dat PASSED ============================================================== diffing matrix.dat.save with matrix.dat PASSED ============================================================== diffing matrix.dat.save with matrix2.dat PASSED ============================================================== diffing Keep1.dat.save with Keep1.dat PASSED ============================================================== diffing Keep2.dat.save with Keep2.dat PASSED ============================================================== diffing Keep1.dat.save with Drop1.dat PASSED ============================================================== diffing Keep2.dat.save with Drop2.dat PASSED ============================================================== diffing VXYZ.dat.save with VXYZ.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Remap ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Remap Test diffing ../Test_AtomMap/reordered.mol2.save with reordered.mol2 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_CompareTop Compare topology test cannot be run in parallel. SKIP: Compare topology test ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Filter Filter tests cannot be run in parallel. SKIP: Filter tests ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_CombineCrd Combine COORDS tests cannot be run in parallel. SKIP: Combine COORDS tests ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_TopInfo CPPTRAJ: Topology info print test. diffing atoms.dat.save with atoms.dat PASSED ============================================================== diffing residues.dat.save with residues.dat PASSED ============================================================== diffing bonds.dat.save with bonds.dat PASSED ============================================================== diffing angles.dat.save with angles.dat PASSED ============================================================== diffing dihedrals.dat.save with dihedrals.dat PASSED ============================================================== diffing masscharge.dat.save with masscharge.dat PASSED ============================================================== diffing molecules.dat.save with molecules.dat PASSED ============================================================== diffing molshort.dat.save with molshort.dat PASSED ============================================================== diffing molselect.dat.save with molselect.dat PASSED ============================================================== diffing molselect2.dat.save with molselect2.dat PASSED ============================================================== CPPTRAJ: Topology info with reference coords test diffing values.dat.save with values.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_GromacsTrr ../MasterTest.sh: line 961: [: too many arguments TRR force/velocity read/write test requires Parallel NetCDF. Cpptraj was compiled without Parallel NetCDF support. Skipped test: TRR force/velocity read/write test CPPTRAJ: CRD => TRR CPPTRAJ: TRR => CRD diffing ../tz2.truncoct.crd with temp.crd PASSED ============================================================== GMX TRR append test cannot be run in parallel. Skipped test: GMX TRR append test ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: GMX: CRD with offset CPPTRAJ: GMX: TRR with offset diffing total1.out with total2.out PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_GromacsXtc ../MasterTest.sh: line 961: [: too many arguments XTC read test requires Parallel NetCDF. Cpptraj was compiled without Parallel NetCDF support. Skipped test: XTC read test XTC write test cannot be run in parallel. Skipped test: XTC write test GMX XTC append test cannot be run in parallel. Skipped test: GMX XTC append test GMX XTC offset test cannot be run in parallel. Skipped test: GMX XTC offset test ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Ewald ../MasterTest.sh: line 961: [: too many arguments ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Direct sum test diffing directsum.0.save with directsum.0 PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Ewald test (NaCl crystal) diffing ewald.dat.save with ewald.dat PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Ewald test (trunc. oct) diffing ew_tz2.dat.save with ew_tz2.dat PASSED ============================================================== Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: Ewald test (trunc. oct), 10 frames Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: Ewald test (ortho), 10 frames ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_LibPME ../MasterTest.sh: line 961: [: too many arguments ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Particle mesh Ewald test (NaCl crystal) diffing nacl.dat.save with nacl.dat PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Particle mesh Ewald test (trunc. oct) diffing tz2n.dat.save with tz2n.dat PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Particle mesh Ewald test (ortho) diffing tz2o.dat.save with tz2o.dat PASSED ============================================================== ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Particle mesh Ewald test (ortho, with mask) diffing mtz2o.dat.save with mtz2o.dat PASSED ============================================================== PME test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: PME test (trunc. oct), 10 frames ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_TI CPPTRAJ: TI analysis test. diffing skip.agr.save with skip.agr PASSED ============================================================== diffing curve.agr.save with curve.agr PASSED ============================================================== diffing avg.dat.save with avg.dat PASSED ============================================================== diffing bs.dat.save with bs.dat PASSED ============================================================== diffing incr.crv.agr.save with incr.crv.agr PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_FixImagedBonds ../MasterTest.sh: line 961: [: too many arguments ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Fix imaged bonds test (Ortho.) diffing fixed.rst7.save with fixed.rst7 PASSED ============================================================== CPPTRAJ: Fix imaged bonds test (Non-ortho.) diffing unimage.crd.save with unimage.crd PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Distance CPPTRAJ: Distance tests diffing dist.dat.save with dist.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Volume CPPTRAJ: Volume tests diffing vol.dat.save with vol.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_SetVelocity ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Set Velocity test Error: Could not determine trajectory tz2.vel.rst7 format. Error: Could not set up input trajectory 'tz2.vel.rst7'. 1 errors encountered reading input. Error: Error(s) occurred during execution. /home/pharmacy/amber18/bin/cpptraj.MPI: Program error diffing tz2.vel.rst7.save with tz2.vel.rst7 PASSED ============================================================== diffing V1.dat.save with V1.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Remlog CPPTRAJ: Replica log read/analyze test. diffing trepidx.agr.save with trepidx.agr PASSED ============================================================== diffing accept.dat.save with accept.dat PASSED ============================================================== diffing mremdreptime.dat.save with mremdreptime.dat PASSED ============================================================== diffing ph.repidx.agr.save with ph.repidx.agr PASSED ============================================================== diffing ph.stats.dat.save with ph.stats.dat PASSED ============================================================== diffing tcharmm.accept.dat.save with tcharmm.accept.dat PASSED ============================================================== diffing tcharmm.edata.dat.save with tcharmm.edata.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_AreaPerMol ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Area per molecule test diffing apm.dat.save with apm.dat PASSED ============================================================== diffing apm.dat.save with areaxy.dat PASSED ============================================================== diffing apm.dat.save with mask.dat PASSED ============================================================== diffing apm.dat.save with mask2.dat PASSED ============================================================== diffing areaxz.dat with xz.dat PASSED ============================================================== diffing areayz.dat with yz.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_DistBasedMask ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Distance-based atom mask tests (atom, residue) diffing First.pdb.1.save with First.pdb.1 PASSED ============================================================== diffing Second.pdb.1.save with Second.pdb.1 PASSED ============================================================== diffing Third.pdb.1.save with Third.pdb.1 PASSED ============================================================== diffing Fourth.pdb.1.save with Fourth.pdb.1 PASSED ============================================================== CPPTRAJ: Distance-based atom mask tests (molecule) diffing Fifth.pdb.1.save with Fifth.pdb.1 PASSED ============================================================== diffing Sixth.pdb.1.save with Sixth.pdb.1 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Calc CPPTRAJ: Calc test diffing calc.dat.save with calc.dat PASSED ============================================================== CPPTRAJ: Calc test with data sets diffing mag.dat.save with mag.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_CalcState CPPTRAJ: Calcstate test diffing state.dat.save with state.dat PASSED ============================================================== diffing curve.dat.save with curve.dat PASSED ============================================================== diffing states.dat.save with states.dat PASSED ============================================================== diffing trans.dat.save with trans.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Change ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Change command test diffing ala3.mod.pdb.save with ala3.mod.pdb PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_CreateReservoir ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Create RREMD NetCDF reservoir test diffing nc0.save with nc0 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_FixAtomOrder CPPTRAJ: Out of order molecules test (will print error messages) Error: Atom 45 was assigned a lower molecule # than previous atom. Error: This can happen if bond information is incorrect or missing, or if the Error: atom numbering in molecules is not sequential. Try one of the Error: following: Error: - If this is a PDB file, try using the 'noconect' keyword. Error: - If this topology did not have bond info, try increasing the bond Error: search cutoff above 0.2 Ang. ('bondsearch '). Error: - Use the 'fixatomorder' command to reorder the topology and any Error: associated coordinates. Error: - Use the 'setMolecules' command in parmed to reorder only the Error: topology. Error: Could not determine molecule information for outoforder.parm7. Error: SetSolventInfo: No molecule information. Error: Could not determine solvent information for outoforder.parm7. Error: Atom 45 was assigned a lower molecule # than previous atom. Error: This can happen if bond information is incorrect or missing, or if the Error: atom numbering in molecules is not sequential. Try one of the Error: following: Error: - If this is a PDB file, try using the 'noconect' keyword. Error: - If this topology did not have bond info, try increasing the bond Error: search cutoff above 0.2 Ang. ('bondsearch '). Error: - Use the 'fixatomorder' command to reorder the topology and any Error: associated coordinates. Error: - Use the 'setMolecules' command in parmed to reorder only the Error: topology. Error: Could not determine molecule information for outoforder.parm7. Error: SetSolventInfo: No molecule information. Error: Could not determine solvent information for outoforder.parm7. Error: Atom 45 was assigned a lower molecule # than previous atom. Error: This can happen if bond information is incorrect or missing, or if the Error: atom numbering in molecules is not sequential. Try one of the Error: following: Error: - If this is a PDB file, try using the 'noconect' keyword. Error: - If this topology did not have bond info, try increasing the bond Error: search cutoff above 0.2 Ang. ('bondsearch '). Error: - Use the 'fixatomorder' command to reorder the topology and any Error: associated coordinates. Error: - Use the 'setMolecules' command in parmed to reorder only the Error: topology. Error: Could not determine molecule information for outoforder.parm7. Error: SetSolventInfo: No molecule information. Error: Could not determine solvent information for outoforder.parm7. Error: Atom 45 was assigned a lower molecule # than previous atom. Error: This can happen if bond information is incorrect or missing, or if the Error: atom numbering in molecules is not sequential. Try one of the Error: following: Error: - If this is a PDB file, try using the 'noconect' keyword. Error: - If this topology did not have bond info, try increasing the bond Error: search cutoff above 0.2 Ang. ('bondsearch '). Error: - Use the 'fixatomorder' command to reorder the topology and any Error: associated coordinates. Error: - Use the 'setMolecules' command in parmed to reorder only the Error: topology. Error: Could not determine molecule information for outoforder.parm7. Error: SetSolventInfo: No molecule information. Error: Could not determine solvent information for outoforder.parm7. diffing reorder.outoforder.parm7.save with reorder.outoforder.parm7 PASSED ============================================================== diffing reorder.mdcrd.save with reorder.mdcrd PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_LowestCurve CPPTRAJ: LowestCurve test diffing All.agr.save with All.agr PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_MinImage ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Minimum Image test. diffing min.dat.save with min.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Regress ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Linear regression test. diffing statsout.dat.save with statsout.dat PASSED ============================================================== diffing regress.dat.save with regress.dat PASSED ============================================================== diffing Y.dat.save with Y.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Rst CPPTRAJ: Generate restraints (rst) test diffing output.save with output PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Pairwise ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Pairwise test diffing pair.dat.save with pair.dat PASSED ============================================================== diffing energy.dat.save with energy.dat PASSED ============================================================== diffing avg.dat.save with avg.dat PASSED ============================================================== diffing map.vdw.gnu.save with map.vdw.gnu PASSED ============================================================== diffing map.elec.gnu.save with map.elec.gnu PASSED ============================================================== diffing ref.cut.mol2.eelec.mol2.1.save with ref.cut.mol2.eelec.mol2.1 PASSED ============================================================== diffing ref.cut.mol2.evdw.mol2.1.save with ref.cut.mol2.evdw.mol2.1 PASSED ============================================================== diffing ref.ene.pdb.save with ref.ene.pdb PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_ParmBox CPPTRAJ: Parmbox test diffing out.parm7.save with out.parm7 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Solvent ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Test solvent command with closest diffing closest10.mol2.save with closest10.mol2 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Translate ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Translate test diffing translate.2.11.mol2.save with translate.2.11.mol2 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_ReplicateCell ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Replicate cell test diffing cell.mol2.save with cell.mol2 PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_ScaleDihedralK CPPTRAJ: Scale dihedral force constant test diffing scale.res1.0.5.dat.save with scale.res1.0.5.dat PASSED ============================================================== CPPTRAJ: Scale dihedral force constant with 'useall' diffing scale.N.C.CA.0.5.dat.save with scale.N.C.CA.0.5.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_PhiPsi CPPTRAJ: Phipsi test diffing phipsi.dat.save with phipsi.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Control ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Loop tests diffing TRP.vec.dat.save with TRP.vec.dat PASSED ============================================================== diffing TRP.rms.dat.save with TRP.rms.dat PASSED ============================================================== diffing TRP.CA.dist.dat.save with TRP.CA.dist.dat PASSED ============================================================== diffing TRP.tocenter.dat.save with TRP.tocenter.dat PASSED ============================================================== diffing nh.dat.save with nh.dat PASSED ============================================================== diffing rms.nofit.dat.save with rms.nofit.dat PASSED ============================================================== diffing last10.dat.save with last10.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_InfraredSpec ../MasterTest.sh: line 961: [: too many arguments CPPTRAJ: Infrared spectrum calculation test diffing irspec.dat.save with irspec.dat PASSED ============================================================== diffing raw.dat.save with raw.dat PASSED ============================================================== ******************************************************************************** TEST: /home/pharmacy/amber18/AmberTools/src/cpptraj/test/Test_Cphstats ./RunTest.sh: line 14: [: too many arguments CPPTRAJ: Explicit pH REMD ensemble data read / sort diffing sorted.pH_1.00.save with sorted.pH_1.00 PASSED ============================================================== diffing sorted.pH_2.00.save with sorted.pH_2.00 PASSED ============================================================== diffing sorted.pH_3.00.save with sorted.pH_3.00 PASSED ============================================================== diffing sorted.pH_4.00.save with sorted.pH_4.00 PASSED ============================================================== diffing sorted.pH_5.00.save with sorted.pH_5.00 PASSED ============================================================== diffing sorted.pH_6.00.save with sorted.pH_6.00 PASSED ============================================================== CPPTRAJ: Constant pH stats test diffing stats.dat.save with stats.dat PASSED ============================================================== diffing frac.agr.save with frac.agr PASSED ============================================================== CPPTRAJ: Sorted implicit constant pH stats test diffing implicit.sorted.dat.save with implicit.sorted.dat PASSED ============================================================== ./RunTest.sh: line 79: [: too many arguments CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats diffing smallimplicit.sorted.0.cpout.save with smallimplicit.sorted.0.cpout PASSED ============================================================== diffing smallimplicit.sorted.1.cpout.save with smallimplicit.sorted.1.cpout PASSED ============================================================== diffing smallimplicit.sorted.2.cpout.save with smallimplicit.sorted.2.cpout PASSED ============================================================== diffing smallimplicit.sorted.3.cpout.save with smallimplicit.sorted.3.cpout PASSED ============================================================== diffing smallimplicit.stats.dat.save with smallimplicit.stats.dat PASSED ============================================================== CPPTRAJ: Unsorted pH read/write test diffing ExplicitRemd/cpout.004 with explicit.004.cpout PASSED ============================================================== diffing SmallImplicitRemd/run0.cpout.001 with implicit.001.cpout PASSED ============================================================== make[5]: Leaving directory '/home/pharmacy/amber18/AmberTools/src/cpptraj/test' 1 1 1 1 MPI threads. make[4]: Leaving directory '/home/pharmacy/amber18/AmberTools/src/cpptraj/test' make[3]: Leaving directory '/home/pharmacy/amber18/AmberTools/src/cpptraj/test' cd mmpbsa_py && make test make[3]: Entering directory '/home/pharmacy/amber18/AmberTools/test/mmpbsa_py' cd 07_Comprehensive && ./Run.comprehensive ./Run.comprehensive: 20: [: 1: unexpected operator ./Run.comprehensive: Program error Makefile:23: recipe for target 'COMPREHENSIVE' failed make[3]: [COMPREHENSIVE] Error 1 (ignored) make[3]: Leaving directory '/home/pharmacy/amber18/AmberTools/test/mmpbsa_py' cd rism3d.periodic/PH4+ && ./Run.PH4+.kh.pme DO_PARALLEL set to mpirun -np 4; max is 2 cd rism3d.periodic/imidazoleH+ && ./Run.imidazoleH+.kh.pme DO_PARALLEL set to mpirun -np 4; max is 2 cd rism3d.periodic/PH4+_triclinic && ./Run.PH4+_triclinic.kh.pme DO_PARALLEL set to mpirun -np 4; max is 2 cd rism3d.periodic/4lzta && ./Run.4lzta_5.kh.pme DO_PARALLEL set to mpirun -np 4; max is 2 cd rism3d.periodic/2igd && ./Run.2igd.kh.pme DO_PARALLEL set to mpirun -np 4; max is 2 cd rism3d.periodic/1d23 && ./Run.1d23.kh.pme DO_PARALLEL set to mpirun -np 4; max is 2 make[2]: Target 'test.parallel2' not remade because of errors. make[2]: Leaving directory '/home/pharmacy/amber18/AmberTools/test' make[2]: Entering directory '/home/pharmacy/amber18/test' export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; make -k test.sander.BASIC make[3]: Entering directory '/home/pharmacy/amber18/test' cd cytosine && ./Run.cytosine diffing cytosine.out.save with cytosine.out PASSED ============================================================== cd nonper && ./Run.nonper diffing mdout.nonper.save with mdout.nonper PASSED ============================================================== cd nonper && ./Run.egb6 diffing mdout.egb6.save with mdout.egb6 PASSED ============================================================== cd nonper && ./Run.nonper.belly diffing mdout.belly.save with mdout.belly PASSED ============================================================== cd nonper && ./Run.nonper.belly.mask diffing mdout.belly.mask.save with mdout.belly.mask PASSED ============================================================== cd nonper && ./Run.nonper.min diffing mdout.min.save with mdout.min PASSED ============================================================== cd nonper && ./Run.cap diffing mdout.cap.save with mdout.cap PASSED ============================================================== cd nonper && ./Run.nonper.nocut diffing mdout.nocut.save with mdout.nocut PASSED ============================================================== cd tip4p && ./Run.tip4p diffing mdout.tip4p.save with mdout.tip4p possible FAILURE: check mdout.tip4p.dif ============================================================== cd tip4p && ./Run.tip4p_mcbar diffing mdout.mcbar.tip4p.sander.save with mdout.mcbar.tip4p.sander PASSED ============================================================== diffing mdout.mcbar_aniso.tip4p.sander.save with mdout.mcbar_aniso.tip4p.sander PASSED ============================================================== cd tip4p && ./Run.tip4p_nve diffing mdout.tip4p_nve.save with mdout.tip4p_nve possible FAILURE: check mdout.tip4p_nve.dif ============================================================== cd tip5p && ./Run.tip5p diffing mdout.tip5p.save with mdout.tip5p PASSED ============================================================== cd tip5p && ./Run.tip5p_nve diffing mdout.tip5p_nve.save with mdout.tip5p_nve PASSED ============================================================== cd 4096wat && ./Run.pure_wat diffing mdout.pure_wat.save with mdout.pure_wat PASSED ============================================================== cd 4096wat && ./Run.pure_wat_fswitch diffing mdout.pure_wat_fswitch.save with mdout.pure_wat_fswitch PASSED ============================================================== cd 4096wat && ./Run.pure_wat_nmr_temp_reg diffing mdout.pure_wat_nmr_temp.save with mdout.pure_wat_nmr_temp PASSED ============================================================== cd 4096wat && ./Run.vrand diffing mdout.vrand.save with mdout.vrand PASSED ============================================================== cd 4096wat && ./Run.frcdmp cd 4096wat_oct && ./Run.pure_wat_oct diffing mdout.pure_wat_oct.save with mdout.pure_wat_oct PASSED ============================================================== diffing mdcrd.pure_wat_oct.save with mdcrd.pure_wat_oct PASSED ============================================================== cd dhfr && ./Run.dhfr && ./Run.dhfr prmtop_an diffing mdout.dhfr.save with mdout.dhfr PASSED ============================================================== diffing mdout.dhfr.save with mdout.dhfr possible FAILURE: check mdout.dhfr.dif ============================================================== cd dhfr && ./Run.dhfr.noboxinfo diffing mdout.dhfr.noboxinfo.save with mdout.dhfr.noboxinfo PASSED ============================================================== cd dhfr && ./Run.dhfr.noshake diffing mdout.dhfr.noshake.save with mdout.dhfr.noshake possible FAILURE: check mdout.dhfr.noshake.dif ============================================================== cd dhfr && ./Run.dhfr.min diffing mdout.dhfr.min.save with mdout.dhfr.min PASSED ============================================================== cd dhfr && ./Run.dhfr.min_prcg diffing mdout.dhfr.min_prcg.save with mdout.dhfr.min_prcg PASSED ============================================================== cd dhfr && ./Run.dhfr.xmin diffing mdout.dhfr.xmin.save with mdout.dhfr.xmin possible FAILURE: check mdout.dhfr.xmin.dif ============================================================== cd ff14ipq && ./Run.ff14ipq diffing mdout.ff14ipq.save with mdout.ff14ipq PASSED ============================================================== cd variable_14 && ./Run.variable_14_ntb1 diffing variable_14_ntb1.mdout.save with variable_14_ntb1.mdout possible FAILURE: check variable_14_ntb1.mdout.dif ============================================================== cd gact_ips && ./Run.ips diffing mdout.ips.save with mdout.ips PASSED ============================================================== cd gact_ips && ./Run.ipsnve diffing mdout.ipsnve.save with mdout.ipsnve PASSED ============================================================== cd gact_ips && ./Run.ips_dfft diffing mdout.ips_dfft.save with mdout.ips_dfft PASSED ============================================================== cd gact_ips && ./Run.ips_vacuum diffing mdout.ips_vacuum.save with mdout.ips_vacuum PASSED ============================================================== cd polarizable_water && ./Run.pol_wat diffing mdout.polwat.save with mdout.polwat PASSED ============================================================== cd ubiquitin && ./Run.ubiquitin diffing mdout.ubiquitin.save with mdout.ubiquitin PASSED ============================================================== diffing mden.save with mden PASSED ============================================================== diffing mdcrd.save with mdcrd PASSED ============================================================== diffing mdvel.save with mdvel PASSED ============================================================== cd dna_pol && ./Run.dna_pol diffing mdout.dna_pol.save with mdout.dna_pol PASSED ============================================================== cd trx && ./Run.trx diffing mdout.trx.save with mdout.trx PASSED ============================================================== cd trx && ./Run.trx.cpln diffing mdout.trx.cpln.save with mdout.trx.cpln PASSED ============================================================== cd rdc && ./Run.dip diffing gcg.dip.o.save with gcg.dip.o PASSED ============================================================== cd rdc && ./Run.csa diffing gcg.csa.o.save with gcg.csa.o PASSED ============================================================== cd rdc && ./Run.csa_min diffing gcg.csa_min.o.save with gcg.csa_min.o PASSED ============================================================== cd rdc && ./Run.nmr diffing gcg.nmr.o.save with gcg.nmr.o PASSED ============================================================== cd pcsa && ./Run.dip diffing stem.dip.o.save with stem.dip.o PASSED ============================================================== cd pcsa && ./Run.csa diffing stem.csa.o.save with stem.csa.o PASSED ============================================================== cd pcsa && ./Run.csa2 diffing stem.csa2.o.save with stem.csa2.o PASSED ============================================================== cd pcsa && ./Run.csa_min diffing stem.csa_min.o.save with stem.csa_min.o PASSED ============================================================== cd tgtmd/change_target && ./Run.tgtmd diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/change_target.rms && ./Run.tgtmd diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/change_target.ntr && ./Run.tgtmd DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting (Max = 2) ============================================================ cd tgtmd/conserve_ene && ./Run.tgtmd diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/minimize && ./Run.tgtmin diffing tgtmin.out.save with tgtmin.out PASSED ============================================================== cd tgtmd/PME && ./Run.tgtPME diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd mtmdtest && ./Run.mtmdtest SANDER: Multiply-targeted MD, new to AMBER 11 Tested on an RNA duplex. diffing mtmdtest.out.save with mtmdtest.out PASSED ============================================================== diffing mtmdtest.mdcrd.save with mtmdtest.mdcrd PASSED ============================================================== cd trajene && ./Run.trajene diffing trajene.out.save with trajene.out PASSED ============================================================== diffing mdcrd.out.save with mdcrd.out PASSED ============================================================== cd trajene_box && ./Run.trajene DO_PARALLEL set to mpirun -np 4 This test cannot be run with more than 1 processor, exiting. ============================================================ cd trajene_netcdf && ./Run.trajene /home/pharmacy/amber18/include/netcdf.mod diffing trajene.out.save with trajene.out PASSED ============================================================== diffing mdcrd.out.nc.save with mdcrd.out.nc PASSED ============================================================== cd alp && ./Run.alp diffing mdout.alp.save with mdout.alp PASSED ============================================================== cd umbrella && ./Run.umbrella diffing mdout.umbrella.save with mdout.umbrella PASSED ============================================================== diffing chi_vs_t.save with chi_vs_t PASSED ============================================================== cd noesy && ./Run.noesy diffing noesy.out.mpi.save with noesy.out PASSED ============================================================== cd jar && ./Run.jarz diffing mdout.jar.save with mdout.jar PASSED ============================================================== diffing dist_vs_t.save with dist_vs_t PASSED ============================================================== cd plane_plane_restraint && ./Run.dinuc_plpt SANDER: Dinucleoside restrained with new plane-point angle restraint that was defined with new natural language restraint input. DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting (Max = 2) ============================================================ cd plane_plane_restraint && ./Run.dinuc_pln SANDER: Dinucleoside restrained with new plane-plane angle restraint that was defined with new natural language restraint input. DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting (Max = 2) ============================================================ cd iwrap2 && ./Run.iwrap2 diffing mdout.iw2.save with mdout.iw2 PASSED ============================================================== diffing mdcrd.iw2.save with mdcrd.iw2 PASSED ============================================================== diffing rstrt.iw2.save with rstrt.iw2 PASSED ============================================================== cd idecomp1 && ./run_idecomp1.sh diffing decomp.out.save with decomp.out PASSED ============================================================== cd idecomp4 && ./run_idecomp4.sh diffing decomp.out.save with decomp.out PASSED ============================================================== cd bintraj && ./Run.bintraj /home/pharmacy/amber18/include/netcdf.mod diffing nc_headers.save with nc_headers PASSED ============================================================== cd netcdf && make -k test OPT=/home/pharmacy/amber18/include/netcdf.mod make[4]: Entering directory '/home/pharmacy/amber18/test/netcdf' Netcdf MD Restart Write Test diffing textmd.rst7.save with textmd.rst7 PASSED ============================================================== Netcdf Minimization Restart Write Test diffing textmin.rst7.save with textmin.rst7 PASSED ============================================================== Restrained MD with netcdf Restart Reference Coords Test diffing md.rst7.save with md.rst7 PASSED ============================================================== diffing ene.dat.save with ene.dat PASSED ============================================================== Netcdf MD restart read test, ntx=5 diffing md1.rst7 with md2.rst7 PASSED ============================================================== diffing ene1 with ene2 PASSED ============================================================== diffing md.crd.save with md.crd PASSED ============================================================== Netcdf MD restart read test, ntx=1 diffing md1.rst7 with md2.rst7 PASSED ============================================================== diffing ene1 with ene2 PASSED ============================================================== diffing md.crd.save with md.crd PASSED ============================================================== make[4]: Leaving directory '/home/pharmacy/amber18/test/netcdf' cd csurften && ./Run.csurften_z-dir diffing mdout.csurften_z-dir.save with mdout.csurften_z-dir PASSED ============================================================== cd csurften && ./Run.csurften_z-dir_npt_3 diffing mdout.csurften_z-dir_npt_3.save with mdout.csurften_z-dir_npt_3 PASSED ============================================================== cd linear_interaction_energy && ./Run.lie This test not set up for parallel cannot run in parallel with #residues < #pes ============================================================== cd nmropt && make all make[4]: Entering directory '/home/pharmacy/amber18/test/nmropt' cd gb/angle && ./Run.nmropt_1angle_gb diffing mdout.save with mdout PASSED ============================================================== diffing angle_gb_vs_t.save with angle_gb_vs_t PASSED ============================================================== cd gb/distance && ./Run.dist_gb diffing mdout.save with mdout PASSED ============================================================== diffing dist_gb_vs_t.save with dist_gb_vs_t PASSED ============================================================== cd gb/distance_COM && ./Run.distCOM_gb diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_gb_vs_t.save with distCOM_gb_vs_t PASSED ============================================================== cd gb/jar_distance && ./Run.jar_gb diffing mdout.save with mdout PASSED ============================================================== diffing dist_gb_vs_t.save with dist_gb_vs_t PASSED ============================================================== cd gb/jar_distance_COM && ./Run.jar_gb diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_gb_vs_t.save with distCOM_gb_vs_t PASSED ============================================================== cd gb/jar_torsion && ./Run.jar_torsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_gb.dat.save with jartorsion_gb.dat PASSED ============================================================== cd gb/nmropt_1_torsion && ./Run.nmropt_1_torsion diffing mdout.save with mdout PASSED ============================================================== diffing torsion_gb.dat.save with torsion_gb.dat PASSED ============================================================== cd gb/tautp && ./Run.nmropt_1tautp_gb diffing mdout.save with mdout PASSED ============================================================== cd gb/temp && ./Run.nmropt_1temp_gb diffing mdout.save with mdout PASSED ============================================================== cd pme/angle && ./Run.nmropt_1angle_pbc diffing mdout.save with mdout possible FAILURE: check mdout.dif ============================================================== diffing angle_pbc_vs_t.save with angle_pbc_vs_t PASSED ============================================================== cd pme/distance && ./Run.dist_pbc diffing mdout.save with mdout PASSED ============================================================== diffing dist_pbc_vs_t.save with dist_pbc_vs_t PASSED ============================================================== cd pme/distance_COM && ./Run.distCOM_pbc diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_pbc_vs_t.save with distCOM_pbc_vs_t PASSED ============================================================== cd pme/jar_torsion && ./Run.jar_torsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_pbc.dat.save with jartorsion_pbc.dat PASSED ============================================================== cd pme/jar_distance && ./Run.jar_pbc diffing mdout.save with mdout PASSED ============================================================== diffing dist_pbc_vs_t.save with dist_pbc_vs_t PASSED ============================================================== cd pme/jar_distance_COM && ./Run.jar_pbc diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_pbc_vs_t.save with distCOM_pbc_vs_t PASSED ============================================================== cd pme/nmropt_1_torsion && ./Run.nmropt_1_torsion diffing mdout.save with mdout possible FAILURE: check mdout.dif ============================================================== diffing torsion_pbc.dat.save with torsion_pbc.dat PASSED ============================================================== cd pme/tautp && ./Run.nmropt_1tautp_pbc ./Run.nmropt_1tautp_pbc: 42: [: sander.MPI: unexpected operator diffing mdout.save with mdout possible FAILURE: check mdout.dif ============================================================== cd pme/temp && ./Run.nmropt_1temp_pbc diffing mdout.save with mdout possible FAILURE: check mdout.dif ============================================================== cd gb/2xangle && ./Run.nmropt_1_2xangle_gb diffing mdout.save with mdout PASSED ============================================================== diffing 2xangle_gb_vs_t.save with 2xangle_gb_vs_t PASSED ============================================================== cd gb/jar_comtorsion && ./Run.jar_comtorsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_com_gb.dat.save with jartorsion_com_gb.dat PASSED ============================================================== cd gb/jar_lcod && ./Run.lcod_jar diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/jar_lcod_dist && ./Run.jar_lcod diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/lcod && ./Run.lcod diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/lcod_com && ./Run.lcod_com diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/nmropt_1_2xtorsion && ./Run.nmropt_1_2xtorsion diffing mdout.save with mdout PASSED ============================================================== diffing 2xtorsion_gb.dat.save with 2xtorsion_gb.dat PASSED ============================================================== cd pme/2xangle && ./Run.nmropt_1_2xangle_pbc diffing mdout.save with mdout PASSED ============================================================== diffing 2xangle_pbc_vs_t.save with 2xangle_pbc_vs_t PASSED ============================================================== cd pme/jar_comtorsion && ./Run.jar_comtorsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_com_pbc.dat.save with jartorsion_com_pbc.dat PASSED ============================================================== cd pme/jar_lcod && ./Run.jar_lcod diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/jar_lcod_dist && ./Run.lcod_dist diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/lcod && ./Run.lcod_pme diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/lcod_com && ./Run.lcod_com diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/nmropt_1_2xtorsion && ./Run.nmropt_1_2xtorsion diffing mdout.save with mdout PASSED ============================================================== diffing 2xtorsion_pbc.dat.save with 2xtorsion_pbc.dat PASSED ============================================================== make[4]: Leaving directory '/home/pharmacy/amber18/test/nmropt' cd lj_12-6-4 && ./Run.12-6-4 diffing mdout.save with mdout PASSED ============================================================== cd MD_Constr_Andersen_VVMiddle_water && ./Run.ADS_VV AMBERHOME is /home/pharmacy/amber18 Testing MD with Andersen thermostat diffing md_ADS.out.save with md_ADS.out PASSED ============================================================== cd MD_Constr_Langevin_LFMiddle_water && ./Run.LGV_LF AMBERHOME is /home/pharmacy/amber18 Testing MD with langevin dynamics diffing md_LGV.out.save with md_LGV.out PASSED ============================================================== make[3]: Leaving directory '/home/pharmacy/amber18/test' export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd 4096wat && ./Run.column_fft diffing mdout.column_fft.save with mdout.column_fft PASSED ============================================================== export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd jar_multi && ./Run.jarz if: Expression Syntax. Makefile:210: recipe for target 'test.sander.BASIC.MPI' failed make[2]: [test.sander.BASIC.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd ti_eth2meth_gas && ./Run.test1 DO_PARALLEL set to mpirun -np 4 number of processors for this test > 2, exiting... ============================================================ export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd ti_eth2meth_gas && ./Run.test2 DO_PARALLEL set to mpirun -np 4 number of processors for this test > 2, exiting... ============================================================ export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd ti_ggcc && ./Run.test1 if: Expression Syntax. Makefile:210: recipe for target 'test.sander.BASIC.MPI' failed make[2]: [test.sander.BASIC.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd ti_ggcc && ./Run.test2 if: Expression Syntax. Makefile:210: recipe for target 'test.sander.BASIC.MPI' failed make[2]: [test.sander.BASIC.MPI] Error 1 (ignored) cd PIMD_Langevin_LFMiddle_water && ./Run.LGV_LF AMBERHOME is /home/pharmacy/amber18 Testing PIMD with langevin dynamics application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ./Run.LGV_LF: Program error Makefile:210: recipe for target 'test.sander.BASIC.MPI' failed make[2]: [test.sander.BASIC.MPI] Error 1 (ignored) cd PIMD_Constr_Andersen_LFMiddle_water && ./Run.ADS_LF AMBERHOME is /home/pharmacy/amber18 Testing PIMD with Andersen thermostat application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ./Run.ADS_LF: Program error Makefile:210: recipe for target 'test.sander.BASIC.MPI' failed make[2]: [test.sander.BASIC.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; make -k test.sander.GB make[3]: Entering directory '/home/pharmacy/amber18/test' cd gb_rna && ./Run.gbrna diffing mdout.gbrna.save with mdout.gbrna PASSED ============================================================== cd gb_rna && ./Run.gbrna.min diffing mdout.gbrna.min.save with mdout.gbrna.min PASSED ============================================================== cd gb_rna && ./Run.gbrna.ln diffing mdout.gbrna.ln.save with mdout.gbrna.ln PASSED ============================================================== cd gb_rna && ./Run.gbrna.ips diffing mdout.gbrna.ips.save with mdout.gbrna.ips PASSED ============================================================== cd gbsa_xfin && ./Run.gbsa diffing mdout.gbsa.save with mdout.gbsa PASSED ============================================================== cd circ_dna && ./Run.circdna diffing mdout.circdna.save with mdout.circdna PASSED ============================================================== cd gb2_trx && ./Run.trxox diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== cd gb7_trx && ./Run.trxox && ./Run.trxox prmtop_an diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== diffing mdout.trxox.save with mdout.trxox possible FAILURE: check mdout.trxox.dif ============================================================== cd gb7_trx && ./Run.trxox_md diffing mdout.trxox_md.save with mdout.trxox_md PASSED ============================================================== cd gb8_trx && ./Run.trxox diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== cd gb8_trx && ./Run.trxox_md && ./Run.trxox_md prmtop_an diffing mdout.trxox_md.save with mdout.trxox_md PASSED ============================================================== diffing mdout.trxox_md.save with mdout.trxox_md possible FAILURE: check mdout.trxox_md.dif ============================================================== cd gbneck2nu/1hji && ./Run.1hji_md diffing mdout.1hji_md.save with mdout.1hji_md PASSED ============================================================== cd gbneck2nu/modified_nu/3p4a/ && ./Run.3p4a diffing mdout.3p4a.save with mdout.3p4a PASSED ============================================================== cd alpb_trx && ./Run.trxox diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== make[3]: Leaving directory '/home/pharmacy/amber18/test' export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd rem_gb_2rep && ./Run.rem application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[24034,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.rem: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd rem_gb_4rep && ./Run.rem ./Run.rem: 22: [: 1: unexpected operator Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23980,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.rem: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd rxsgld_4rep && ./Run.rxsgld ./Run.rxsgld: 26: [: 1: unexpected operator Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23875,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.rxsgld: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd rem_wat && ./Run.rem application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23915,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.rem: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd rem_hybrid && ./Run.rem if: Expression Syntax. Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd h_rem && ./Run.rem ./Run.rem: 22: [: 1: unexpected operator Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23820,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.rem: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd multid_remd && ./Run.multirem ./Run.multirem: 22: [: 1: unexpected operator application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23825,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.multirem: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnstph_remd/TempRem && ./Run.cnstph_remd ./Run.cnstph_remd: 30: [: 1: unexpected operator application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23864,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.cnstph_remd: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnstph_remd/pHREM && ./Run.pHremd ./Run.pHremd: 20: [: 1: unexpected operator Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23775,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.pHremd: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnstph_remd/pHREMrst && ./Run.pHremdrst ./Run.pHremdrst: 20: [: 1: unexpected operator Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23806,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.pHremdrst: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnstph_remd/Explicit_pHREM && ./Run.pHremd File "", line 2 1 ^ SyntaxError: invalid syntax File "", line 1 print( and 1 ^ SyntaxError: invalid syntax Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23699,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.pHremd: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnste_remd/TempRem && ./Run.cnste_remd ./Run.cnste_remd: 30: [: 1: unexpected operator Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23733,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.cnste_remd: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnste_remd/EREM && ./Run.Eremd ./Run.Eremd: 20: [: 1: unexpected operator Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23638,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.Eremd: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnste_remd/EREMrst && ./Run.Eremdrst ./Run.Eremdrst: 20: [: 1: unexpected operator Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23567,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.Eremdrst: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnste_remd/Explicit_EREM && ./Run.Eremd File "", line 2 1 ^ SyntaxError: invalid syntax File "", line 1 print( and 1 ^ SyntaxError: invalid syntax Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23496,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.Eremd: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd phtremd/implicit && ./Run.phtremd ./Run.phtremd: 22: [: 1: unexpected operator Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23448,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.phtremd: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd phtremd/explicit && ./Run.phtremd ./Run.phtremd: 22: [: 1: unexpected operator Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23367,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.phtremd: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd phtremd/explicitRst && ./Run.phtremdRst ./Run.phtremdRst: 22: [: 1: unexpected operator application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23393,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.phtremdRst: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd ephtremd/implicit && ./Run.ephtremd ./Run.ephtremd: 22: [: 1: unexpected operator application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 8 ) than the number of processors ( 1 ) ! ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 8 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23299,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.ephtremd: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd ephtremd/explicit && ./Run.ephtremd ./Run.ephtremd: 22: [: 1: unexpected operator Error: specified more groups ( 8 ) than the number of processors ( 1 ) ! Error: specified more groups ( 8 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 8 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[23328,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.ephtremd: Program error Makefile:767: recipe for target 'test.sander.REM' failed make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd sodium && ./Run.sodium if: Expression Syntax. Makefile:336: recipe for target 'test.sander.TI' failed make[2]: [test.sander.TI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd pheMTI && ./Run.0 diffing out.0.save with out.0 PASSED ============================================================== export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd pheMTI && ./Run.1 diffing out.1.save with out.1 PASSED ============================================================== export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd pheMTI && ./Run.lambda0 if: Expression Syntax. Makefile:336: recipe for target 'test.sander.TI' failed make[2]: [test.sander.TI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd pheMTI && ./Run.lambda1 if: Expression Syntax. Makefile:336: recipe for target 'test.sander.TI' failed make[2]: [test.sander.TI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd campTI && ./Run.campTI if: Expression Syntax. Makefile:336: recipe for target 'test.sander.TI' failed make[2]: [test.sander.TI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd softcore && ./Run_sc Running the Softcore potential tests ============================================================== Minimization test DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ Protein-Ligand complex test if: Expression Syntax. ============================================================== Solvation free energy test if: Expression Syntax. if: Expression Syntax. ============================================================== Dynamic lambda test if: Expression Syntax. ============================================================== Restrained complex test if: Expression Syntax. ============================================================== Using softcore electrostatics if: Expression Syntax. ============================================================== Soft core test suite complete ============================================================== export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd ti_decomp; ./Run.ti_decomp if: Expression Syntax. Makefile:336: recipe for target 'test.sander.TI' failed make[2]: [test.sander.TI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd ti_decomp; ./Run.ti_decomp_sc DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ export TESTsanderLES=/home/pharmacy/amber18/bin/sander.LES.MPI; make -k test.sander.LES make[3]: Entering directory '/home/pharmacy/amber18/test' cd LES_noPME && ./Run.LESmd SANDER: LES MD gas phase diffing md.out.save with md.out PASSED ============================================================== cd LES_noPME && ./Run.LESmd.rdiel SANDER: LES MD gas phase rdiel diffing md.rdiel.out.save with md.rdiel.out PASSED ============================================================== cd LES && ./Run.PME_LES ADDLES and SANDER.LES test: addles: diffing output_addles.save with output_addles PASSED ============================================================== diffing LES.crd.save with LES.crd PASSED ============================================================== diffing LES.prmtop.save with LES.prmtop PASSED ============================================================== sander.LES: diffing md.LES.out.save with md.LES.out possible FAILURE: check md.LES.out.dif ============================================================== cd LES_CUT && ./Run.LES SANDER.LES test, no PME diffing md.LES.out.save with md.LES.out PASSED ============================================================== cd LES_TEMP && ./Run.2temp SANDER: LES T coupling diffing 2temp.out.save with 2temp.out PASSED ============================================================== cd LES_GB && ./Run.LES SANDER: LES+GB 1: GB/LES GB1 diffcoords application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[22644,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.LES: Program error Makefile:397: recipe for target 'test.sander.LES' failed make[3]: [test.sander.LES] Error 1 (ignored) make[3]: Leaving directory '/home/pharmacy/amber18/test' cd neb-testcases/neb_gb_partial && ./Run.neb_gb_partial application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[22535,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.neb_gb_partial: Program error Makefile:1442: recipe for target 'test.neb' failed make[2]: [test.neb] Error 1 (ignored) cd neb-testcases/neb_gb_full && ./Run.neb_gb_full Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[22545,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.neb_gb_full: Program error Makefile:1442: recipe for target 'test.neb' failed make[2]: [test.neb] Error 1 (ignored) cd neb-testcases/neb_explicit && ./Run.neb_explicit application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[22563,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.neb_explicit: Program error Makefile:1442: recipe for target 'test.neb' failed make[2]: [test.neb] Error 1 (ignored) cd nfe && ./run-parallel.sh >>>>>>> doing 'abmd_ANALYSIS' diffing save.sander/mdout with mdout possible FAILURE: check mdout.dif ============================================================== possible FAILURE: file monitor.txt does not exist. ============================================================== >>>>>>> doing 'abmd_FLOODING' diffing save.sander/mdout with mdout possible FAILURE: check mdout.dif ============================================================== possible FAILURE: file monitor.txt does not exist. ============================================================== /home/pharmacy/amber18/bin/ncdump: umbrella.nc: No such file or directory ncgen: - line 1: syntax error, unexpected $end, expecting NETCDF /home/pharmacy/amber18/bin/ncdump: ncdump.tmp: No such file or directory diffing umbrella.save.ncdump with umbrella.ncdump possible FAILURE: check umbrella.ncdump.dif ============================================================== /home/pharmacy/amber18/bin/ncdump: wt_umbrella.nc: No such file or directory ncgen: - line 1: syntax error, unexpected $end, expecting NETCDF /home/pharmacy/amber18/bin/ncdump: ncdump.tmp: No such file or directory diffing wt_umbrella.save.ncdump with wt_umbrella.ncdump possible FAILURE: check wt_umbrella.ncdump.dif ============================================================== >>>>>>> doing 'abmd_UMBRELLA' diffing save.sander/mdout with mdout possible FAILURE: check mdout.dif ============================================================== possible FAILURE: file monitor.txt does not exist. ============================================================== >>>>>>> doing 'smd' diffing save.sander/mdout with mdout PASSED ============================================================== diffing save.sander/smd.txt with smd.txt PASSED ============================================================== >>>>>>> doing 'pmd' diffing save.sander/mdout with mdout PASSED ============================================================== diffing save.sander/pmd.txt with pmd.txt PASSED ============================================================== >>>>>>> doing 'smd2' diffing save.sander/mdout with mdout PASSED ============================================================== diffing save.sander/work.txt with work.txt PASSED ============================================================== >>>>>>> doing 'bbmd' ./run-sander.sh: 60: ./run-sander.sh: 4: not found ./run-sander.sh: 65: ./run-sander.sh: [[: not found ./run-sander.sh: 67: ./run-sander.sh: [[: not found ./run-sander.sh: 71: ./run-sander.sh: cannot open : No such file ./run-sander.sh: 71: ./run-sander.sh: 4: not found This test case (/home/pharmacy/amber18/test/nfe/bbmd) requires a least mpi threads. The number of mpi threads must also be a multiple of 4 and not more than 256. Not running test, exiting ..... >>>>>>> doing 'abremd' ./run-sander.sh: 60: ./run-sander.sh: 4: not found ./run-sander.sh: 65: ./run-sander.sh: [[: not found ./run-sander.sh: 67: ./run-sander.sh: [[: not found ./run-sander.sh: 71: ./run-sander.sh: cannot open : No such file ./run-sander.sh: 71: ./run-sander.sh: 4: not found This test case (/home/pharmacy/amber18/test/nfe/abremd) requires a least mpi threads. The number of mpi threads must also be a multiple of 4 and not more than 256. Not running test, exiting ..... >>>>>>> doing 'mwabmd' ./run-sander.sh: 60: ./run-sander.sh: 4: not found ./run-sander.sh: 65: ./run-sander.sh: [[: not found ./run-sander.sh: 67: ./run-sander.sh: [[: not found ./run-sander.sh: 71: ./run-sander.sh: cannot open : No such file ./run-sander.sh: 71: ./run-sander.sh: 4: not found This test case (/home/pharmacy/amber18/test/nfe/mwabmd) requires a least mpi threads. The number of mpi threads must also be a multiple of 4 and not more than 256. Not running test, exiting ..... >>>>>>> doing 'premd' ./run-sander.sh: 60: ./run-sander.sh: 4: not found ./run-sander.sh: 65: ./run-sander.sh: [[: not found ./run-sander.sh: 67: ./run-sander.sh: [[: not found ./run-sander.sh: 71: ./run-sander.sh: cannot open : No such file ./run-sander.sh: 71: ./run-sander.sh: 4: not found This test case (/home/pharmacy/amber18/test/nfe/premd) requires a least mpi threads. The number of mpi threads must also be a multiple of 4 and not more than 256. Not running test, exiting ..... export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; make -k test.sander.CHARMM make[3]: Entering directory '/home/pharmacy/amber18/test' cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.min diffing mdout.dhfr_charmm.min.save with mdout.dhfr_charmm.min PASSED ============================================================== cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.md diffing mdout.dhfr_charmm.save with mdout.dhfr_charmm PASSED ============================================================== cd chamber/md_engine/dhfr_cmap && ./Run.dhfr_charmm.min diffing mdout.dhfr_charmm.min.save with mdout.dhfr_charmm.min PASSED ============================================================== cd chamber/md_engine/dhfr_cmap && ./Run.dhfr_charmm.md diffing mdout.dhfr_charmm.save with mdout.dhfr_charmm PASSED ============================================================== cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm_noshake.min diffing mdout.dhfr_charmm_noshake.min.save with mdout.dhfr_charmm_noshake.min PASSED ============================================================== cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm_noshake.md diffing mdout.dhfr_charmm_noshake.md.save with mdout.dhfr_charmm_noshake.md PASSED ============================================================== cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm.min diffing mdout.dhfr_charmm.min.save with mdout.dhfr_charmm.min PASSED ============================================================== cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm.md diffing mdout.dhfr_charmm.md.save with mdout.dhfr_charmm.md PASSED ============================================================== make[3]: Leaving directory '/home/pharmacy/amber18/test' export TESTsander=/home/pharmacy/amber18/bin/sander.LES.MPI; make -k test.sander.PIMD.partial make[3]: Entering directory '/home/pharmacy/amber18/test' cd PIMD/part_pimd_water && ./Run.pimd This test not set up for parallel cannot run in parallel with #residues < #pes cd PIMD/part_nmpimd_water && ./Run.nmpimd This test not set up for parallel cannot run in parallel with #residues < #pes cd PIMD/part_pimd_helium && ./Run.pimd diffing hef_pimd.out.save with hef_pimd.out PASSED ============================================================== cd PIMD/part_nmpimd_helium && ./Run.nmpimd diffing hef_pimd.out.save with hef_pimd.out PASSED ============================================================== cd PIMD/part_nmpimd_ntp && ./Run.nmpimd diffing ntp_nmpimd.out.save with ntp_nmpimd.out PASSED ============================================================== diffing NHC.dat.save with NHC.dat PASSED ============================================================== cd PIMD/part_pimd_spcfw && ./Run.pimd diffing spcfw_pimd.top.save with spcfw_pimd.top PASSED ============================================================== diffing spcfw_pimd.xyz.save with spcfw_pimd.xyz PASSED ============================================================== diffing spcfw_pimd.out.save with spcfw_pimd.out possible FAILURE: check spcfw_pimd.out.dif ============================================================== cd PIMD/part_rpmd_water && ./Run.rpmd diffing spcfw_rpmd.top.save with spcfw_rpmd.top PASSED ============================================================== diffing spcfw_rpmd.xyz.save with spcfw_rpmd.xyz PASSED ============================================================== diffing spcfw_rpmd.out.save with spcfw_rpmd.out PASSED ============================================================== cd ti_mass/pent_LES_PIMD && ./Run.pentadiene This test not set up for parallel cannot run in parallel with #residues < #pes make[3]: Leaving directory '/home/pharmacy/amber18/test' cd PIMD/full_cmd_water/equilib && ./Run.full_cmd Testing Centroid MD application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ./Run.full_cmd: Program error Makefile:756: recipe for target 'test.sander.PIMD.MPI.full' failed make[2]: *** [test.sander.PIMD.MPI.full] Error 1 export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnstph/implicit && ./Run.cnstph diffing mdout.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnstph/explicit && ./Run.cnstph diffing mdout.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnstph_remd/TempRem && ./Run.cnstph_remd ./Run.cnstph_remd: 30: [: 1: unexpected operator Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[21179,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.cnstph_remd: Program error Makefile:299: recipe for target 'test.sander.constph.MPI' failed make[2]: [test.sander.constph.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnstph_remd/pHREM && ./Run.pHremd ./Run.pHremd: 20: [: 1: unexpected operator application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[21058,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.pHremd: Program error Makefile:299: recipe for target 'test.sander.constph.MPI' failed make[2]: [test.sander.constph.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnstph_remd/pHREMrst && ./Run.pHremdrst ./Run.pHremdrst: 20: [: 1: unexpected operator Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[21077,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.pHremdrst: Program error Makefile:299: recipe for target 'test.sander.constph.MPI' failed make[2]: [test.sander.constph.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnstph_remd/Explicit_pHREM && ./Run.pHremd File "", line 2 1 ^ SyntaxError: invalid syntax File "", line 1 print( and 1 ^ SyntaxError: invalid syntax application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[21106,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.pHremd: Program error Makefile:299: recipe for target 'test.sander.constph.MPI' failed make[2]: [test.sander.constph.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnste/implicit && ./Run.cnste diffing mdout.save with mdout PASSED ============================================================== diffing ceout.save with ceout PASSED ============================================================== export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnste/explicit && ./Run.cnste diffing mdout.save with mdout PASSED ============================================================== diffing ceout.save with ceout PASSED ============================================================== export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnste_remd/TempRem && ./Run.cnste_remd ./Run.cnste_remd: 30: [: 1: unexpected operator Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 2 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[20880,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.cnste_remd: Program error Makefile:307: recipe for target 'test.sander.conste.MPI' failed make[2]: [test.sander.conste.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnste_remd/EREM && ./Run.Eremd ./Run.Eremd: 20: [: 1: unexpected operator Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[20923,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.Eremd: Program error Makefile:307: recipe for target 'test.sander.conste.MPI' failed make[2]: [test.sander.conste.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnste_remd/EREMrst && ./Run.Eremdrst ./Run.Eremdrst: 20: [: 1: unexpected operator application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[20803,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.Eremdrst: Program error Makefile:307: recipe for target 'test.sander.conste.MPI' failed make[2]: [test.sander.conste.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnste_remd/Explicit_EREM && ./Run.Eremd File "", line 2 1 ^ SyntaxError: invalid syntax File "", line 1 print( and 1 ^ SyntaxError: invalid syntax Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- Error: specified more groups ( 4 ) than the number of processors ( 1 ) ! application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[20840,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.Eremd: Program error Makefile:307: recipe for target 'test.sander.conste.MPI' failed make[2]: [test.sander.conste.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnstphe/implicit && ./Run.cnstphe diffing mdout.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== diffing ceout.save with ceout PASSED ============================================================== export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd cnstphe/explicit && ./Run.cnstphe diffing mdout.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== diffing ceout.save with ceout PASSED ============================================================== export TESTsander='/home/pharmacy/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala /home/pharmacy/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/pharmacy/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.min /home/pharmacy/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/pharmacy/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.imin5 /home/pharmacy/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/pharmacy/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.mdiis0 /home/pharmacy/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/pharmacy/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.mdiis1 /home/pharmacy/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/pharmacy/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.resize /home/pharmacy/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/pharmacy/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.dist /home/pharmacy/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/pharmacy/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.dist.xyzv /home/pharmacy/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/pharmacy/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.hnc /home/pharmacy/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/pharmacy/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.pse1 /home/pharmacy/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/pharmacy/amber18/bin/sander.MPI' && cd crg_reloc/water && ./Run.water.min application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[20478,1],0] Exit code: 1 -------------------------------------------------------------------------- ./Run.water.min: Program error Makefile:938: recipe for target 'test.sander.crgreloc.MPI' failed make[2]: [test.sander.crgreloc.MPI] Error 1 (ignored) export TESTsander='/home/pharmacy/amber18/bin/sander.MPI' && cd crg_reloc/water && ./Run.water.md diffing md.out.save with md.out PASSED ============================================================== export TESTsander='/home/pharmacy/amber18/bin/sander.MPI'; cd amd && make -k test make[3]: Entering directory '/home/pharmacy/amber18/test/amd' Testing AMD with PME diffing mdout.pme.amd1.save with mdout.pme.amd1 PASSED ============================================================== diffing mdout.pme.amd2.save with mdout.pme.amd2 PASSED ============================================================== diffing mdout.pme.amd3.save with mdout.pme.amd3 PASSED ============================================================== Testing AMD with IPS diffing mdout.ips.amd1.save with mdout.ips.amd1 PASSED ============================================================== diffing mdout.ips.amd2.save with mdout.ips.amd2 PASSED ============================================================== diffing mdout.ips.amd3.save with mdout.ips.amd3 PASSED ============================================================== Testing AMD with GB diffing mdout.gb.amd1.save with mdout.gb.amd1 PASSED ============================================================== diffing mdout.gb.amd2.save with mdout.gb.amd2 PASSED ============================================================== diffing mdout.gb.amd3.save with mdout.gb.amd3 PASSED ============================================================== make[3]: Leaving directory '/home/pharmacy/amber18/test/amd' export TESTsander='/home/pharmacy/amber18/bin/sander.MPI'; cd scaledMD && make -k test make[3]: Entering directory '/home/pharmacy/amber18/test/scaledMD' Testing scaledMD with PME diffing mdout.save with mdout PASSED ============================================================== make[3]: Leaving directory '/home/pharmacy/amber18/test/scaledMD' export TESTsander='/home/pharmacy/amber18/bin/sander.MPI'; cd gact_ips && ./Run.ips_sgld diffing mdout.ips_sgld.save with mdout.ips_sgld PASSED ============================================================== export TESTsander='/home/pharmacy/amber18/bin/sander.MPI'; cd gact_ips && ./Run.ips_sgldfp diffing mdout.ips_sgldfp.save with mdout.ips_sgldfp PASSED ============================================================== export TESTsander='/home/pharmacy/amber18/bin/sander.MPI'; cd gact_ips && ./Run.ips_sgldg diffing mdout.ips_sgldg.save with mdout.ips_sgldg PASSED ============================================================== export TESTsander='/home/pharmacy/amber18/bin/sander.MPI'; cd gact_ips && ./Run.ips_sgmdg diffing mdout.ips_sgmdg.save with mdout.ips_sgmdg PASSED ============================================================== export TESTsander='/home/pharmacy/amber18/bin/sander.MPI'; cd gb_rna && ./Run.gbrna.sgld diffing mdout.gbrna.sgld.save with mdout.gbrna.sgld PASSED ============================================================== export TESTsander='/home/pharmacy/amber18/bin/sander.MPI'; cd gb_rna && ./Run.gbrna.sgldfp diffing mdout.gbrna.sgldfp.save with mdout.gbrna.sgldfp PASSED ============================================================== export TESTsander='/home/pharmacy/amber18/bin/sander.MPI'; cd gb_rna && ./Run.gbrna.sgldg diffing mdout.gbrna.sgldg.save with mdout.gbrna.sgldg PASSED ============================================================== export TESTsander='/home/pharmacy/amber18/bin/sander.MPI'; cd gb_rna && ./Run.gbrna.sgmdg diffing mdout.gbrna.sgmdg.save with mdout.gbrna.sgmdg PASSED ============================================================== export TESTsander='/home/pharmacy/amber18/bin/sander.MPI'; cd emap/ && ./Run.emap diffing mdout.emap.save with mdout.emap PASSED ============================================================== export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd sander_OIN_MPI && ./Run.sander.OIN.MPI diffing mdout.sander.OIN.MPI.save with mdout.sander.OIN.MPI file ddtmp.mdout.sander.OIN.MPI.save is short possible FAILURE: check mdout.sander.OIN.MPI.dif ============================================================== export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd sinr_MPI && ./RUN.sander.SINR.MPI DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting (Max = 2) ============================================================ export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd sander_music/pt-water-gal17 && ./Run.md diffing mdout.save with mdout PASSED ============================================================== export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd sander_music/pt-water-vsgal17 && ./Run.md diffing mdout.save with mdout PASSED ============================================================== export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; make -k test.sander.QMMM make[3]: Entering directory '/home/pharmacy/amber18/test' cd qmmm2/xcrd_build_test/ && ./Run.oct_nma_imaged diffing mdout.oct_nma_imaged.save with mdout.oct_nma_imaged PASSED ============================================================== cd qmmm2/xcrd_build_test/ && ./Run.oct_nma_noimage diffing mdout.oct_nma_noimage.save with mdout.oct_nma_noimage PASSED ============================================================== cd qmmm2/xcrd_build_test/ && ./Run.ortho_qmewald0 diffing mdout.ortho_qmewald0.save with mdout.ortho_qmewald0 PASSED ============================================================== cd qmmm2/xcrd_build_test/ && ./Run.truncoct_qmewald0 diffing mdout.truncoct_qmewald0.save with mdout.truncoct_qmewald0 PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_calc_mulliken diffing crambin_md_calc_mulliken.out.save with crambin_md_calc_mulliken.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2 diffing crambin_md_qmgb2.out.save with crambin_md_qmgb2.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_alpb diffing crambin_md_qmgb2_alpb.out.save with crambin_md_qmgb2_alpb.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_aq1 diffing crambin_md_qmgb2_aq1.out.save with crambin_md_qmgb2_aq1.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_aq2 diffing crambin_md_qmgb2_aq2.out.save with crambin_md_qmgb2_aq2.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_saltcon diffing crambin_md_qmgb2_saltcon.out.save with crambin_md_qmgb2_saltcon.out PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_internal diffing mdout.1NLN_internal.save with mdout.1NLN_internal PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dspev diffing mdout.1NLN_dspev.save with mdout.1NLN_dspev PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dspevd diffing mdout.1NLN_dspevd.save with mdout.1NLN_dspevd PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dspevx diffing mdout.1NLN_dspevx.save with mdout.1NLN_dspevx PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyev diffing mdout.1NLN_dsyev.save with mdout.1NLN_dsyev possible FAILURE: check mdout.1NLN_dsyev.dif ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyevd diffing mdout.1NLN_dsyevd.save with mdout.1NLN_dsyevd PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyevr diffing mdout.1NLN_dsyevr.save with mdout.1NLN_dsyevr PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_auto diffing mdout.1NLN_auto.save with mdout.1NLN_auto possible FAILURE: check mdout.1NLN_auto.dif ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_min diffing mdout.1NLN_min.save with mdout.1NLN_min PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1 diffing mdout.1NLN_MD_ntb1.save with mdout.1NLN_MD_ntb1 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_aq1 diffing mdout.1NLN_MD_ntb1_aq1.save with mdout.1NLN_MD_ntb1_aq1 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_aq2 diffing mdout.1NLN_MD_ntb1_aq2.save with mdout.1NLN_MD_ntb1_aq2 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_mmcorr diffing mdout.1NLN_MD_ntb1_mmcorr.save with mdout.1NLN_MD_ntb1_mmcorr PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_qmewald2 diffing mdout.1NLN_MD_ntb1_qmewald2.save with mdout.1NLN_MD_ntb1_qmewald2 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb2 diffing mdout.1NLN_MD_ntb2.save with mdout.1NLN_MD_ntb2 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_aq2_NUMER_DERIV diffing mdout.1NLN_MD_ntb1_aq2_NUMER_DERIV.save with mdout.1NLN_MD_ntb1_aq2_NUMER_DERIV PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_lnk_dis_neg diffing mdout.1NLN_MD_ntb1_lnk_dis_neg.save with mdout.1NLN_MD_ntb1_lnk_dis_neg possible FAILURE: check mdout.1NLN_MD_ntb1_lnk_dis_neg.dif ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_lnk_method2 diffing mdout.1NLN_MD_ntb1_lnk_method2.save with mdout.1NLN_MD_ntb1_lnk_method2 PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged diffing mdout.notimaged.save with mdout.notimaged PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md diffing mdout.notimaged_md.save with mdout.notimaged_md PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md_pme diffing mdout.notimaged_md_pme.save with mdout.notimaged_md_pme PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md_pme_qmewald diffing mdout.notimaged_md_pme_qmewald.save with mdout.notimaged_md_pme_qmewald PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md_pme_qmewald_lowmem diffing mdout.notimaged_md_pme_qmewald_lowmem.save with mdout.notimaged_md_pme_qmewald_lowmem PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.imaged diffing mdout.imaged.save with mdout.imaged PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.imaged_md diffing mdout.imaged_md.save with mdout.imaged_md PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.img_center diffing mdout.img_center.save with mdout.img_center PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.img_center_md diffing mdout.img_center_md.save with mdout.img_center_md PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.img_center_bigqmcut_md diffing mdout.img_center_bigqmcut_md.save with mdout.img_center_bigqmcut_md PASSED ============================================================== cd qmmm2/crambin && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm2/crambin && ./Run.crambin_md_hot_start diffing crambin_md_hot_start.out.save with crambin_md_hot_start.out PASSED ============================================================== cd qmmm2/crambin && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out PASSED ============================================================== diffing mdcrd.save with mdcrd PASSED ============================================================== diffing mdvel.save with mdvel PASSED ============================================================== diffing restrt.save with restrt PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap diffing tip3p_cap.out.save with tip3p_cap.out PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap_md diffing tip3p_cap_md.out.save with tip3p_cap_md.out PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap_md.shake diffing tip3p_cap_md_shake.out.save with tip3p_cap_md_shake.out PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap_md.shake_qmshakeoff diffing tip3p_cap_md_shake_qmshake_off.out.save with tip3p_cap_md_shake_qmshake_off.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut && ./Run.MG_QM_water_MM diffing MG_QM_water_MM.out.save with MG_QM_water_MM.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut_lowmem && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut_ADDMM && ./Run.MG_QM_water_MM diffing MG_QM_water_MM.out.save with MG_QM_water_MM.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut_ADDMM && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm2/variable_solvent && ./Run.mg_periodic_vsolv_wat diffing mg_periodic_vsolv_wat.out.save with mg_periodic_vsolv_wat.out file ddtmp.mg_periodic_vsolv_wat.out.save is short possible FAILURE: check mg_periodic_vsolv_wat.out.dif ============================================================== cd qmmm2/variable_solvent && ./Run.1NLN_MD_ntb1_vsolv diffing mdout.1NLN_MD_ntb1_vsolv.save with mdout.1NLN_MD_ntb1_vsolv possible FAILURE: check mdout.1NLN_MD_ntb1_vsolv.dif ============================================================== cd qmmm2/PM3-MMX && ./Run.crambin_md_pm3mmx diffing crambin_md_pm3mmx.out.save with crambin_md_pm3mmx.out PASSED ============================================================== cd qmmm2/PM3-MMX2 && ./Run.crambin_md_pm3mmx2 diffing crambin_md_pm3mmx2.out.save with crambin_md_pm3mmx2.out possible FAILURE: check crambin_md_pm3mmx2.out.dif ============================================================== cd qmmm2/crambin_PM6 && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm2/crambin_PM6 && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out PASSED ============================================================== diffing mdcrd.save with mdcrd PASSED ============================================================== diffing mdvel.save with mdvel PASSED ============================================================== diffing restrt.save with restrt PASSED ============================================================== cd qmmm2/PM3-MAIS && ./Run.zundel if: Expression Syntax. Makefile:500: recipe for target 'test.sander.QMMM' failed make[3]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/PM3-MAIS && ./Run.hcl_wat if: Expression Syntax. Makefile:500: recipe for target 'test.sander.QMMM' failed make[3]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MechEm_nma-spcfwbox && ./Run.MechEm_PDDGPM3 diffing mdout.MechEm_PDDGPM3.save with mdout.MechEm_PDDGPM3 possible FAILURE: check mdout.MechEm_PDDGPM3.dif ============================================================== cd qmmm2/qmmm_switching_func && ./Run.nma_md_switching diffing nma.out.save with nma.out PASSED ============================================================== make[3]: Leaving directory '/home/pharmacy/amber18/test' export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; make -k test.sander.DFTB make[3]: Entering directory '/home/pharmacy/amber18/test' cd qmmm_DFTB/crambin_DFTB && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm_DFTB/crambin_DFTB && ./Run.crambin_md_hot_start diffing crambin_md_hot_start.out.save with crambin_md_hot_start.out PASSED ============================================================== cd qmmm_DFTB/crambin_DFTB && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out PASSED ============================================================== diffing mdcrd.save with mdcrd PASSED ============================================================== diffing mdvel.save with mdvel PASSED ============================================================== diffing restrt.save with restrt PASSED ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out possible FAILURE: check crambin_md.out.dif ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_calc_mulliken diffing crambin_md_calc_mulliken.out.save with crambin_md_calc_mulliken.out PASSED ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2 diffing crambin_md_qmgb2.out.save with crambin_md_qmgb2.out PASSED ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_alpb diffing crambin_md_qmgb2_alpb.out.save with crambin_md_qmgb2_alpb.out PASSED ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_aq1 diffing crambin_md_qmgb2_aq1.out.save with crambin_md_qmgb2_aq1.out PASSED ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_aq2 diffing crambin_md_qmgb2_aq2.out.save with crambin_md_qmgb2_aq2.out PASSED ============================================================== cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_saltcon diffing crambin_md_qmgb2_saltcon.out.save with crambin_md_qmgb2_saltcon.out PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1 diffing mdout.aladip_ewald_ntb1.save with mdout.aladip_ewald_ntb1 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1_link_atoms diffing mdout.aladip_ewald_ntb1_link_atoms.save with mdout.aladip_ewald_ntb1_link_atoms possible FAILURE: check mdout.aladip_ewald_ntb1_link_atoms.dif ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1_qmewald2 diffing mdout.aladip_ewald_ntb1_qmewald2.save with mdout.aladip_ewald_ntb1_qmewald2 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb2 diffing mdout.aladip_ewald_ntb2.save with mdout.aladip_ewald_ntb2 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb1 diffing mdout.aladip_pme_ntb1.save with mdout.aladip_pme_ntb1 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2 diffing mdout.aladip_pme_ntb2.save with mdout.aladip_pme_ntb2 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms diffing mdout.aladip_pme_ntb2_link_atoms.save with mdout.aladip_pme_ntb2_link_atoms PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms_aq1 diffing mdout.aladip_pme_ntb2_link_atoms_aq1.save with mdout.aladip_pme_ntb2_link_atoms_aq1 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms_aq2 diffing mdout.aladip_pme_ntb2_link_atoms_aq2.save with mdout.aladip_pme_ntb2_link_atoms_aq2 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_qmewald2 diffing mdout.aladip_pme_ntb2_qmewald2.save with mdout.aladip_pme_ntb2_qmewald2 PASSED ============================================================== cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_telec diffing mdout.aladip_pme_ntb2_telec.save with mdout.aladip_pme_ntb2_telec PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut && ./Run.MG_QM_water_MM diffing MG_QM_water_MM.out.save with MG_QM_water_MM.out PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged diffing mdout.notimaged.save with mdout.notimaged PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md diffing mdout.notimaged_md.save with mdout.notimaged_md PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md_pme diffing mdout.notimaged_md_pme.save with mdout.notimaged_md_pme PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md_pme_qmewald diffing mdout.notimaged_md_pme_qmewald.save with mdout.notimaged_md_pme_qmewald PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.imaged diffing mdout.imaged.save with mdout.imaged PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.imaged_md diffing mdout.imaged_md.save with mdout.imaged_md PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center diffing mdout.img_center.save with mdout.img_center PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center_md diffing mdout.img_center_md.save with mdout.img_center_md PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center_bigqmcut_md diffing mdout.img_center_bigqmcut_md.save with mdout.img_center_bigqmcut_md PASSED ============================================================== cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut_lowmem && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap diffing tip3p_cap.out.save with tip3p_cap.out PASSED ============================================================== cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md diffing tip3p_cap_md.out.save with tip3p_cap_md.out PASSED ============================================================== cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md.shake diffing tip3p_cap_md_shake.out.save with tip3p_cap_md_shake.out PASSED ============================================================== cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md.shake_qmshakeoff diffing tip3p_cap_md_shake_qmshake_off.out.save with tip3p_cap_md_shake_qmshake_off.out PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_min diffing mdout.1NLN_min.save with mdout.1NLN_min PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1 diffing mdout.1NLN_MD_ntb1.save with mdout.1NLN_MD_ntb1 PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_lnk_dis_neg diffing mdout.1NLN_MD_ntb1_lnk_dis_neg.save with mdout.1NLN_MD_ntb1_lnk_dis_neg PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_lnk_method2 diffing mdout.1NLN_MD_ntb1_lnk_method2.save with mdout.1NLN_MD_ntb1_lnk_method2 PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq1 diffing mdout.1NLN_MD_ntb1_aq1.save with mdout.1NLN_MD_ntb1_aq1 PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq1_disp diffing mdout.1NLN_MD_ntb1_aq1_disp.save with mdout.1NLN_MD_ntb1_aq1_disp PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq2 diffing mdout.1NLN_MD_ntb1_aq2.save with mdout.1NLN_MD_ntb1_aq2 PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_qmewald2 diffing mdout.1NLN_MD_ntb1_qmewald2.save with mdout.1NLN_MD_ntb1_qmewald2 PASSED ============================================================== cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb2 diffing mdout.1NLN_MD_ntb2.save with mdout.1NLN_MD_ntb2 PASSED ============================================================== cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PA diffing mdout_PA.save with mdout_PA PASSED ============================================================== cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PR diffing mdout_PR.save with mdout_PR PASSED ============================================================== cd qmmm2/MechEm_nma-spcfwbox && ./Run.MechEm_DFTB diffing mdout.MechEm_DFTB.save with mdout.MechEm_DFTB PASSED ============================================================== cd qmmm_DFTB/dftb3/nma-h2o-box && ./Run.nma-spcfw-15.md diffing nma-spcfw-15.md.out.save with nma-spcfw-15.md.out PASSED ============================================================== make[3]: Leaving directory '/home/pharmacy/amber18/test' export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_ADF_PIMD && ./Run.h2o.blyp_sz.pimd ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF dftb executable is called dftb.exe export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_ADF_REMD && ./Run.h2o.blyp_sz.remd ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_GAMESS_PIMD && ./Run.h2o.hf_sto-3g.pimd GAMESS not installed - Skipping Test... Check your GAMESS installation and make sure that the GAMESS executable is called rungms export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_GAMESS_REMD && ./Run.h2o.hf_sto-3g.remd GAMESS not installed - Skipping Test... Check your GAMESS installation and make sure that the GAMESS executable is called rungms export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN_PIMD && ./Run.h2o.hf_sto-3g.pimd GAUSSIAN not installed - Skipping Test... Check your GAUSSIAN installation and make sure that the GAUSSIAN executable is called g16 or g09 or g03. export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN_REMD && ./Run.h2o.hf_sto-3g.remd GAUSSIAN not installed - Skipping Test... Check your GAUSSIAN installation and make sure that the GAUSSIAN executable is called g16 or g09 or g03. export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_Q-Chem_PIMD && ./Run.h2o.hf_sto-3g.pimd Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_TeraChem_PIMD && ./Run.h2o.hf_sto-3g.pimd TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_TeraChem_PIMD && ./Run.h2o.hf_sto-3g.pimd mpi TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_TeraChem_REMD && ./Run.h2o.hf_sto-3g.remd TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_TeraChem_REMD && ./Run.h2o.hf_sto-3g.remd mpi TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd qmmm_EXTERN/adqmmm_na+28water_TeraChem && ./Run.adqmmm TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem export TESTsander=/home/pharmacy/amber18/bin/sander.MPI && cd qmmm2/adqmmm_na+28water && ./Run.adqmmm if: Expression Syntax. Makefile:660: recipe for target 'test.sander.ADQMMM.MPI' failed make[2]: [test.sander.ADQMMM.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI && cd qmmm2/adqmmm_na+28water && ./Run.adqmmm-calc_wbk2 if: Expression Syntax. Makefile:660: recipe for target 'test.sander.ADQMMM.MPI' failed make[2]: [test.sander.ADQMMM.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI && cd qmmm2/adqmmm_na+28water && ./Run.adqmmm-fixedR if: Expression Syntax. Makefile:660: recipe for target 'test.sander.ADQMMM.MPI' failed make[2]: [test.sander.ADQMMM.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI && cd qmmm2/adqmmm_h2o-box && ./Run.adqmmm if: Expression Syntax. Makefile:660: recipe for target 'test.sander.ADQMMM.MPI' failed make[2]: [test.sander.ADQMMM.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI && cd qmmm2/adqmmm_h2o-box && ./Run.adqmmm-fixedR-calc_wbk2 if: Expression Syntax. Makefile:660: recipe for target 'test.sander.ADQMMM.MPI' failed make[2]: [test.sander.ADQMMM.MPI] Error 1 (ignored) export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; make -k test.sander.ABFQMMM make[3]: Entering directory '/home/pharmacy/amber18/test' cd abfqmmm/abfqmmm_water_sp && ./Run.abfqmmm_water_sp diffing abfqmmm_water_sp.out.save with abfqmmm_water_sp.out PASSED ============================================================== diffing abfqmmm_water_sp.frc.save with abfqmmm_water_sp.frc PASSED ============================================================== diffing abfqmmm_water_sp.pdb.save with abfqmmm_water_sp.pdb PASSED ============================================================== diffing abfqmmm_water_sp.idrst.save with abfqmmm_water_sp.idrst PASSED ============================================================== cd abfqmmm/abfqmmm_water_md && ./Run.abfqmmm_water_md diffing abfqmmm_water_md.out.save with abfqmmm_water_md.out PASSED ============================================================== diffing abfqmmm_water_md.frc.save with abfqmmm_water_md.frc PASSED ============================================================== diffing abfqmmm_water_md.pdb.save with abfqmmm_water_md.pdb PASSED ============================================================== diffing abfqmmm_water_md.idrst.save with abfqmmm_water_md.idrst PASSED ============================================================== cd abfqmmm/abfqmmm_dmpoh_md && ./Run.abfqmmm_dmpoh_md diffing abfqmmm_dmpoh_md.out.save with abfqmmm_dmpoh_md.out PASSED ============================================================== diffing abfqmmm_dmpoh_md.frc.save with abfqmmm_dmpoh_md.frc PASSED ============================================================== diffing abfqmmm_dmpoh_md.pdb.save with abfqmmm_dmpoh_md.pdb PASSED ============================================================== diffing abfqmmm_dmpoh_md.idrst.save with abfqmmm_dmpoh_md.idrst PASSED ============================================================== diffing abfqmmm_dmpoh_md.rst.save with abfqmmm_dmpoh_md.rst PASSED ============================================================== cd abfqmmm/abfqmmm_lysozyme_md && ./Run.abfqmmm_lysozyme_md diffing abfqmmm_lysozyme_md.out.save with abfqmmm_lysozyme_md.out PASSED ============================================================== diffing abfqmmm_lysozyme_md.frc.save with abfqmmm_lysozyme_md.frc PASSED ============================================================== diffing abfqmmm_lysozyme_md.pdb.save with abfqmmm_lysozyme_md.pdb PASSED ============================================================== diffing abfqmmm_lysozyme_md.idrst.save with abfqmmm_lysozyme_md.idrst PASSED ============================================================== cd abfqmmm/adqmmm_water_md && ./Run.adqmmm_water_md diffing adqmmm_water_md.out.save with adqmmm_water_md.out PASSED ============================================================== diffing adqmmm_water_md.frc.save with adqmmm_water_md.frc PASSED ============================================================== diffing adqmmm_water_md.pdb.save with adqmmm_water_md.pdb PASSED ============================================================== diffing adqmmm_water_md.idrst.save with adqmmm_water_md.idrst PASSED ============================================================== cd abfqmmm/hotspot_water_md && ./Run.hotspot_water_md diffing hotspot_water_md.out.save with hotspot_water_md.out PASSED ============================================================== diffing hotspot_water_md.frc.save with hotspot_water_md.frc PASSED ============================================================== diffing hotspot_water_md.pdb.save with hotspot_water_md.pdb PASSED ============================================================== diffing hotspot_water_md.idrst.save with hotspot_water_md.idrst PASSED ============================================================== make[3]: Leaving directory '/home/pharmacy/amber18/test' cd evb/malon_bond_umb_GAFF && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_GAFF_MORSIFY && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_GAFF_MORSIFY_XVDW && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_nmpimd_full && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_pimd_ld_full && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_pimd_nhc_full && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_EXP-XCH && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_EXP-XCH_pimd_ld_full && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_EXP-XCH_pimd_nhc_full && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_EXP-XCH_nmpimd_full && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_GAUSS-XCH && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_GAUSS-XCH_pimd_ld_full && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_GAUSS-XCH_pimd_nhc_full && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_GAUSS-XCH_nmpimd_full && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_emap_GAFF_MORSIFY && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_emap_GAFF_MORSIFY_XVDW && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_dg_UFF_3DG && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_dg_UFF_3DG_nmpimd_full && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_dg_UFF_3DG_pimd_ld_full && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_dg_UFF_3DG_pimd_nhc_full && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_dg_UFF_3DG_pimd_nhc_full_TI-MASS && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbond_umb_dg_UFF_3DG_pimd_nhc_full_TI-MASS && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_dg_UFF_3DG_qi_full_2D-PMF && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_dg_UFF_3DG_qi_full_corrF && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/poh_dbonds_umb_dg_UFF_3DG && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/poh_dbonds_umb_dg_UFF_9DG && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/poh_dbonds_umb_dg_UFF_9DG_pimd_ld_full && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/poh_dbonds_umb_dg_UFF_9DG_pimd_nhc_full && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/poh_dbonds_umb_dg_UFF_9DG_nmpimd_full && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/poh_dbonds_umb_dg_UFF_9DG_nmpimd_full_TST-freqf && ./Run.evb DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ export TESTsander=/home/pharmacy/amber18/bin/sander.MPI; cd sebomd/DC/water32 && ./min.csh && ./md.csh diffing min.out.save with min.out PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== make[2]: Target 'test.parallel.at' not remade because of errors. make[2]: Leaving directory '/home/pharmacy/amber18/test' make[2]: Entering directory '/home/pharmacy/amber18/AmberTools/test' Finished test suite for AmberTools at Tue Apr 2 22:02:58 IST 2019. make[2]: Leaving directory '/home/pharmacy/amber18/AmberTools/test' 924 file comparisons passed 66 file comparisons failed 45 tests experienced errors Test log file saved as /home/pharmacy/amber18/logs/test_at_parallel/2019-04-02_21-28-55.log Test diffs file saved as /home/pharmacy/amber18/logs/test_at_parallel/2019-04-02_21-28-55.diff