make[2]: Entering directory `/home/21cy91r03/amber18/AmberTools/test' ./test_at_clean.sh cd antechamber && make -k clean make[3]: Entering directory `/home/21cy91r03/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/21cy91r03/amber18/AmberTools/test/antechamber' cd mmpbsa_py && make -k clean make[3]: Entering directory `/home/21cy91r03/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/21cy91r03/amber18/AmberTools/test/mmpbsa_py' cd ../src/mm_pbsa/Examples && ./Run.mmpbsa.clean cd ../src/FEW/examples/test && ./Run.few.clean cd ../src/cpptraj/test && make -k clean make[3]: Entering directory `/home/21cy91r03/amber18/AmberTools/src/cpptraj/test' Cleaning all test directories: make test.complete test.libcpptraj OPT=clean make[4]: Entering directory `/home/21cy91r03/amber18/AmberTools/src/cpptraj/test' make[5]: Entering directory `/home/21cy91r03/amber18/AmberTools/src/cpptraj/test' make[5]: Leaving directory `/home/21cy91r03/amber18/AmberTools/src/cpptraj/test' make[4]: Leaving directory `/home/21cy91r03/amber18/AmberTools/src/cpptraj/test' make[3]: Leaving directory `/home/21cy91r03/amber18/AmberTools/src/cpptraj/test' cd leap && make -k clean make[3]: Entering directory `/home/21cy91r03/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/21cy91r03/amber18/AmberTools/test/leap' make[4]: Nothing to be done for `test.complete'. make[4]: Leaving directory `/home/21cy91r03/amber18/AmberTools/test/leap' make[3]: Leaving directory `/home/21cy91r03/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/21cy91r03/amber18/AmberTools/test/nab' Running test to do simple minimization (this tests the molecular mechanics interface) diffing ltest.out.check with ltest.out PASSED ============================================================== Running test to do simple minimization with shake (this tests the molecular mechanics interface) diffing rattle_min.out.check with rattle_min.out PASSED ============================================================== Running test to do simple minimization (this tests the generalized Born implementation) diffing gbrna.out.check with gbrna.out PASSED ============================================================== Running test to do simple minimization (this tests the generalized Born implementation) diffing xfin_sa.out.check with xfin_sa.out PASSED ============================================================== Running test to do simple minimization (this tests the LCPO surface area) diffing gbrna_sa.out.check with gbrna_sa.out PASSED ============================================================== Running test to do simple minimization (this tests the ao generalized Born implementation) diffing gbtrx.out.check with gbtrx.out PASSED ============================================================== Running test to do simple minimization (this tests the ao-2 generalized Born implementation) diffing gb5trx.out.check with gb5trx.out PASSED ============================================================== Running test to do simple minimization (this tests the GB Neck implementation; gb==8) diffing gb8trx.out.check with gb8trx.out PASSED ============================================================== Running test to do simple minimization (this tests the GB Neck implementation; gb==7) diffing gb7trx.out.check with gb7trx.out PASSED ============================================================== Running test to do molecular dynamics with rattle diffing rattle_md.out.check with rattle_md.out PASSED ============================================================== 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 diffing dhfrndpmtx.out.check with dhfrndpmtx.out PASSED ============================================================== 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 diffing prm.out.check with prm.out PASSED ============================================================== checking the prmtop file: diffing tprmtop.check with tprmtop PASSED ============================================================== Running test to do simple xmin minimization diffing txmin.out.check with txmin.out PASSED ============================================================== Running test to do md with netcdf diffing gbnetcdf.out.check with gbnetcdf.out PASSED ============================================================== Running test on netcdf files diffing tnetcdf.out.check with tnetcdf.out PASSED ============================================================== Running test for variable 1-4 scaled nonbonded interactions diffing variable_14scale.out.check with variable_14scale.out PASSED ============================================================== 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 PASSED ============================================================== Running test to do simple minimization (libpbsa) (this tests the PBSA implementation) Please note that PARALLEL PBSA is not implemented in nab. ============================================================================ make[3]: Leaving directory `/home/21cy91r03/amber18/AmberTools/test/nab' cd ../src/cpptraj/test && make -k test make[3]: Entering directory `/home/21cy91r03/amber18/AmberTools/src/cpptraj/test' make test.complete summary make[4]: Entering directory `/home/21cy91r03/amber18/AmberTools/src/cpptraj/test' 8 MPI threads. make[5]: Entering directory `/home/21cy91r03/amber18/AmberTools/src/cpptraj/test' ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_General General tests cannot be run in parallel. SKIP: General tests ******************************************************************************** TEST: /home/21cy91r03/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 ============================================================== CPPTRAJ: Parallel test with trajectory offset diffing offset.dat.save with offset.dat PASSED ============================================================== diffing nc0.save with nc0 PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Strip One frame strip command test can only run with 1 or fewer parallel threads. Skipped test: One frame strip command test Unstrip (Lig/Rec/Complex) command test can only run with 1 or fewer parallel threads. Skipped test: Unstrip (Lig/Rec/Complex) command test CPPTRAJ: Multi frame strip command test. diffing res1.tz2.crd.save with res1.tz2.crd PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_BrokenTraj Broken trajectory tests cannot be run in parallel. SKIP: Broken trajectory tests ******************************************************************************** TEST: /home/21cy91r03/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 ============================================================== CPPTRAJ: Start argument offset [6] Error: Process is handling less than 1 frame. Try reducing # processes. [7] Error: Process is handling less than 1 frame. Try reducing # processes. 1 errors encountered reading input. Error: Error(s) occurred during execution. /home/21cy91r03/amber18/bin/cpptraj.MPI: Program error possible FAILURE: file phi.dat.save does not exist. ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_RemdTraj CRD Replica Trajectory Run with offset can only run with 5 or fewer parallel threads. Skipped test: CRD Replica Trajectory Run with offset 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 ============================================================== 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 diffing all.dat.save with all.dat PASSED ============================================================== diffing temp0.crd.300.00 with temp.crd.0 PASSED ============================================================== diffing temp0.crd.384.30 with temp.crd.1 PASSED ============================================================== diffing temp0.crd.492.20 with temp.crd.2 PASSED ============================================================== diffing temp0.crd.630.50 with temp.crd.3 PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_trajout_framerange Trajout frame range cannot be run in parallel. SKIP: Trajout frame range ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_PerResRMSD CPPTRAJ: Per-Residue RMSD Test. diffing PerResRMSD.agr.save with PerResRMSD.agr PASSED ============================================================== Per-Residue RMSD Test with averaging can only run with 3 or fewer parallel threads. Skipped test: Per-Residue RMSD Test with averaging CPPTRAJ: Per-Residue RMSD Test with residue centering. diffing center.agr.save with center.agr PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/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. Secstruct (DSSP): SS assign output test can only run with 1 or fewer parallel threads. Skipped test: Secstruct (DSSP): SS assign output test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Center Center tests can only run with 2 or fewer parallel threads. SKIP: Center tests ******************************************************************************** TEST: /home/21cy91r03/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 ============================================================== Solute Hbond test with disk caching cannot be run in parallel. Skipped test: Solute Hbond test with disk caching 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 ============================================================== Hbond, Bridge nointramol test can only run with 2 or fewer parallel threads. Skipped test: Hbond, Bridge nointramol test Hbond with imaging can only run with 1 or fewer parallel threads. Skipped test: Hbond with imaging ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_NCrestart NetCDF restart tests can only run with 1 or fewer parallel threads. SKIP: NetCDF restart tests ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Image 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 ============================================================== Orthorhombic coordinate imaging test can only run with 2 or fewer parallel threads. Skipped test: Orthorhombic coordinate imaging test Nonorthorhombic coordinate imaging test can only run with 2 or fewer parallel threads. Skipped test: Nonorthorhombic coordinate imaging test Nonorthorhombic coordinate imaging test with familiar can only run with 2 or fewer parallel threads. Skipped test: Nonorthorhombic coordinate imaging test with familiar Nonorthorhombic coordinate imaging test with familiar and COM can only run with 2 or fewer parallel threads. Skipped test: Nonorthorhombic coordinate imaging test with familiar and COM ******************************************************************************** TEST: /home/21cy91r03/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 ============================================================== LCPO test with GAFF atom types can only run with 1 or fewer parallel threads. Skipped test: LCPO test with GAFF atom types ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Radgyr 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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Mask Mask single frame test can only run with 1 or fewer parallel threads. Skipped test: Mask single frame test CPPTRAJ: Mask longer command test. diffing M.dat.save with M.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Jcoupling J-Coupling single frame test can only run with 1 or fewer parallel threads. Skipped test: J-Coupling single frame test CPPTRAJ: J-Coupling extended test. diffing jc.dat.save with jc.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/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 ============================================================== Imaged diffusion tests can only run with 1 or fewer parallel threads. Skipped test: Imaged diffusion tests STFC diffusion tests cannot be run in parallel. Skipped test: STFC diffusion tests ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Charmm 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 ============================================================== Read CHARMM restart can only run with 1 or fewer parallel threads. Skipped test: Read CHARMM restart ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_NetcdfTraj CPPTRAJ: Convert mdcrd -> NetCDF CPPTRAJ: Convert NetCDF -> mdcrd diffing ../tz2.truncoct.crd with trajectory_test.mdcrd PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_RMSD 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/21cy91r03/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 ============================================================== CPPTRAJ: 2D RMSD Test with reference trajectory diffing rmsd.dat.save with rmsd1.dat PASSED ============================================================== 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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Mol2 Mol2 tests cannot be run in parallel. SKIP: Mol2 tests ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_NAstruct NAstruct tests can only run with 3 or fewer parallel threads. SKIP: NAstruct tests ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Pucker Pucker tests can only run with 3 or fewer parallel threads. SKIP: Pucker tests ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_AtomMap Atom map tests can only run with 3 or fewer parallel threads. SKIP: Atom map tests ******************************************************************************** TEST: /home/21cy91r03/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 ============================================================== CPPTRAJ: Data file group by name test diffing byname.dat.save with byname.dat PASSED ============================================================== CPPTRAJ: Data file group by aspect test diffing dssp.dat.save with dssp.dat PASSED ============================================================== diffing byidx.dat.save with byidx.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Radial 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 ============================================================== diffing WatO-Trp4.agr.save with WatO-Trp4.byres.agr PASSED ============================================================== diffing WatO-Trp.agr.save with WatO-Trp.agr PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Closest Closest command tests using first/all solvent atoms can only run with 1 or fewer parallel threads. Skipped test: Closest command tests using first/all solvent atoms 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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_DRMSD CPPTRAJ: Distance RMSD test diffing drmsd.dat.save with drmsd.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/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 ============================================================== diffing normpop.agr.save with normpop.agr PASSED ============================================================== CPPTRAJ: Cluster command test, read NetCDF pairwise distances. diffing summary.dat.save with summary3.dat PASSED ============================================================== diffing normframe.agr.save with normframe.agr PASSED ============================================================== CPPTRAJ: Cluster command test, write ASCII pairwise distances. CPPTRAJ: Cluster command test, read ASCII pairwise distances. diffing cascii.dat.save with cascii.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/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 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/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Cluster_Nreps CPPTRAJ: Clustering with specified # reps diffing clusters.2.dat.save with clusters.2.dat PASSED ============================================================== diffing summary.2.dat.save with summary.2.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_RandomizeIons randomizeions test can only run with 1 or fewer parallel threads. SKIP: randomizeions test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Molsurf CPPTRAJ: Molsurf test diffing msurf.dat.save with msurf.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_CheckStructure Basic structure check can only run with 1 or fewer parallel threads. Skipped test: Basic structure check 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/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Contacts Contacts test cannot be run in parallel. SKIP: Contacts test ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_ClusterDihedral clusterdihedral test cannot be run in parallel. SKIP: clusterdihedral test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Vector 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 ============================================================== CPPTRAJ: Test vector center with magnitude diffing avgcoord.out.save with avgcoord.out PASSED ============================================================== diffing res5.out.save with res5.out PASSED ============================================================== Momentum/velocity vector test. can only run with 1 or fewer parallel threads. Skipped test: Momentum/velocity vector test. Force vector test. can only run with 1 or fewer parallel threads. Skipped test: Force vector test. ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Grid 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 ============================================================== diffing byres.dx.save with byres.dx PASSED ============================================================== diffing byres.dx.save with bymol.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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Unwrap Unwrap tests cannot be run in parallel. SKIP: Unwrap tests ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Project CPPTRAJ: Projection diffing project.dat.save with project.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Volmap 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/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_LIE CPPTRAJ: LIE test diffing TCL.out.save with TCL.out PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Density Density along axis tests can only run with 1 or fewer parallel threads. Skipped test: Density along axis tests CPPTRAJ: Multi-frame density along axis test diffing tz2.wato.agr.save with tz2.wato.agr PASSED ============================================================== CPPTRAJ: Total system density test diffing total.dat.save with total.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_LipidOrder Lipid Order Parameter Test cannot be run in parallel. SKIP: Lipid Order Parameter Test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_LipidSCD Basic lipid order parameter test can only run with 1 or fewer parallel threads. Skipped test: Basic lipid order parameter test CPPTRAJ: New Lipid Order Parameter Test, DOPC. diffing dopc.agr.save with dopc.agr PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_PairDist CPPTRAJ: PairDist Test. diffing Pr.dat.save with Pr.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_ReadData CPPTRAJ: Read vector data test diffing v6and7.dat.save with v6and7.dat PASSED ============================================================== CPPTRAJ: Read Amber output test diffing MD.ene.dat.save with MD.ene.dat PASSED ============================================================== CPPTRAJ: Read CHARMM output test diffing rex-d.dat.save with rex-d.dat PASSED ============================================================== CPPTRAJ: 3D data read/write test diffing ../Test_Grid/out.dx.save with out.dx PASSED ============================================================== CPPTRAJ: Standard 3D data write test CPPTRAJ: Standard 3D data read test diffing ../Test_Grid/out.dx.save with out2.dx PASSED ============================================================== CPPTRAJ: Standard 3D data read/append test diffing append.dat.save with append.dat PASSED ============================================================== CPPTRAJ: Standard 3D data, sparse diffing ../Test_Grid/out.dx.save with out3.dx PASSED ============================================================== Nonorthogonal grid standard write/read tests. can only run with 1 or fewer parallel threads. Skipped test: Nonorthogonal grid standard write/read tests. CPPTRAJ: Read specific columns test. diffing xyz.dat.save with xyz.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_GIST GIST tests cannot be run in parallel. SKIP: GIST tests ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_systemVF CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test diffing nc0.save with nc0 PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_AtomicCorr CPPTRAJ: Atomic Correlation test diffing acorr.gnu.save with acorr.gnu PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_AutoCorr CPPTRAJ: AutoCorr test. diffing ac.agr.save with ac.agr PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Box 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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_AtomTypeSelect CPPTRAJ: Selection by atom type test. diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_CreateCrd CPPTRAJ: COORDS data set creation and CRDFLUCT test. diffing crd1.dat.save with crd1.dat PASSED ============================================================== COORDS data set creation with velocities test can only run with 1 or fewer parallel threads. Skipped test: COORDS data set creation with velocities test 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 ============================================================== COORDS data set append test can only run with 1 or fewer parallel threads. Skipped test: COORDS data set append test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_AutoImage AutoImage tests can only run with 2 or fewer parallel threads. SKIP: AutoImage tests ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_MultiVector CPPTRAJ: Multivector test diffing NH.dat.save with NH.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/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 ============================================================== Lifetime test with data set caching cannot be run in parallel. Skipped test: Lifetime test with data set caching 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/21cy91r03/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/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_CrossCorr CPPTRAJ: CrossCorr test diffing cc.gnu.save with cc.gnu PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_SymmRmsd Symmetry-corrected RMSD tests can only run with 3 or fewer parallel threads. SKIP: Symmetry-corrected RMSD tests ******************************************************************************** TEST: /home/21cy91r03/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 ============================================================== Multidihedral Nucleotide CHI test can only run with 3 or fewer parallel threads. Skipped test: Multidihedral Nucleotide CHI test Multidihedral protein dihedrals test can only run with 1 or fewer parallel threads. Skipped test: Multidihedral protein dihedrals test Multidihedral cyclic molecule test can only run with 1 or fewer parallel threads. Skipped test: Multidihedral cyclic molecule test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Ensemble_MREMD CPPTRAJ: M-REMD sort test. diffing Strip.sorted.crd.0.save with Strip.sorted.crd.0 PASSED ============================================================== diffing Strip.sorted.crd.1.save with Strip.sorted.crd.1 PASSED ============================================================== diffing Strip.sorted.crd.2.save with Strip.sorted.crd.2 PASSED ============================================================== diffing Strip.sorted.crd.3.save with Strip.sorted.crd.3 PASSED ============================================================== diffing Strip.sorted.crd.4.save with Strip.sorted.crd.4 PASSED ============================================================== diffing Strip.sorted.crd.5.save with Strip.sorted.crd.5 PASSED ============================================================== diffing Strip.sorted.crd.6.save with Strip.sorted.crd.6 PASSED ============================================================== diffing Strip.sorted.crd.7.save with Strip.sorted.crd.7 PASSED ============================================================== CPPTRAJ: M-REMD actions test. diffing all.rmsd.dat.save with all.rmsd.dat PASSED ============================================================== diffing all.nhbond.dat.save with all.nhbond.dat PASSED ============================================================== diffing all.hbavg.dat.save with all.hbavg.dat PASSED ============================================================== diffing avg.rst7.2.save with avg.rst7.2 PASSED ============================================================== diffing avg.rst7.5.save with avg.rst7.5 PASSED ============================================================== CPPTRAJ: M-REMD ensemble outtraj test. diffing Outtraj.crd.0.save with Outtraj.crd.0 PASSED ============================================================== diffing Outtraj.crd.1.save with Outtraj.crd.1 PASSED ============================================================== CPPTRAJ: M-REMD no sort, running average test diffing all.RA.dat.save with all.RA.dat PASSED ============================================================== CPPTRAJ: M-REMD, generate RMS data CPPTRAJ: M-REMD, meltcurve analysis diffing melt.dat.save with melt.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_MakeStructure Make structure tests can only run with 1 or fewer parallel threads. SKIP: Make structure tests ******************************************************************************** TEST: /home/21cy91r03/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 ============================================================== Rotate with defined axis can only run with 1 or fewer parallel threads. Skipped test: Rotate with defined axis ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Integrate CPPTRAJ: Integration test. diffing curve.dat.save with curve.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_CheckChiral CPPTRAJ: Check chirality test diffing chiral.dat.save with chiral.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Energy CPPTRAJ: Simple energy tests diffing ene.agr.save with ene.agr PASSED ============================================================== Test kinetic energy calculation can only run with 2 or fewer parallel threads. Skipped test: Test kinetic energy calculation Test total energy calculation can only run with 2 or fewer parallel threads. Skipped test: Test total energy calculation ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_LESsplit LES split/average test can only run with 5 or fewer parallel threads. SKIP: LES split/average test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_PermuteDihedrals PermuteDihedrals tests can only run with 1 or fewer parallel threads. SKIP: PermuteDihedrals tests ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Multicurve CPPTRAJ: Multicurve test diffing curves.agr.save with curves.agr PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/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. Energy via sander API short tests (GB/PME) can only run with 1 or fewer parallel threads. SKIP: Energy via sander API short tests (GB/PME) ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Spline CPPTRAJ: Spline test diffing spline.dat.save with spline.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_CIF CIF tests can only run with 6 or fewer parallel threads. SKIP: CIF tests ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_PDB PDB format tests can only run with 1 or fewer parallel threads. SKIP: PDB format tests ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_VelocityAutoCorr Velocity autocorrelation test can only run with 5 or fewer parallel threads. SKIP: Velocity autocorrelation test ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/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/21cy91r03/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 ============================================================== diffing Invert.dat.save with Invert.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Remap Remap test can only run with 1 or fewer parallel threads. SKIP: Remap test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_CompareTop Compare topology test cannot be run in parallel. SKIP: Compare topology test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Filter Filter tests cannot be run in parallel. SKIP: Filter tests ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_CombineCrd Combine COORDS tests cannot be run in parallel. SKIP: Combine COORDS tests ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_GromacsTrr TRR force/velocity read/write test can only run with 2 or fewer parallel threads. 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 GMX offset test can only run with 5 or fewer parallel threads. Skipped test: GMX offset test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_GromacsXtc XTC tests can only run with 2 or fewer parallel threads. SKIP: XTC tests ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Ewald Direct sum test can only run with 1 or fewer parallel threads. Skipped test: Direct sum test Ewald test (NaCl crystal) can only run with 1 or fewer parallel threads. Skipped test: Ewald test (NaCl crystal) Ewald test (trunc. oct) can only run with 1 or fewer parallel threads. Skipped test: Ewald test (trunc. oct) 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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_LibPME Particle mesh Ewald test (NaCl crystal) can only run with 1 or fewer parallel threads. Skipped test: Particle mesh Ewald test (NaCl crystal) Particle mesh Ewald test (trunc. oct) can only run with 1 or fewer parallel threads. Skipped test: Particle mesh Ewald test (trunc. oct) Particle mesh Ewald test (ortho) can only run with 1 or fewer parallel threads. Skipped test: Particle mesh Ewald test (ortho) Particle mesh Ewald test (ortho, with mask) can only run with 1 or fewer parallel threads. Skipped test: Particle mesh Ewald test (ortho, with mask) 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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_LJ_PME LJ PME tests. can only run with 1 or fewer parallel threads. SKIP: LJ PME tests. ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_FixImagedBonds Fix imaged bonds test (Ortho.) can only run with 1 or fewer parallel threads. Skipped test: Fix imaged bonds test (Ortho.) CPPTRAJ: Fix imaged bonds test (Non-ortho.) diffing unimage.crd.save with unimage.crd PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Distance CPPTRAJ: Distance tests diffing dist.dat.save with dist.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Volume CPPTRAJ: Volume tests diffing vol.dat.save with vol.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_SetVelocity Set Velocity tests can only run with 1 or fewer parallel threads. SKIP: Set Velocity tests ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_AreaPerMol Area per molecule test can only run with 1 or fewer parallel threads. SKIP: Area per molecule test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_DistBasedMask Distance-based atom mask tests can only run with 1 or fewer parallel threads. SKIP: Distance-based atom mask tests ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Change Change command test can only run with 1 or fewer parallel threads. SKIP: Change command test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_CreateReservoir Create RREMD NetCDF reservoir test can only run with 1 or fewer parallel threads. SKIP: Create RREMD NetCDF reservoir test ******************************************************************************** TEST: /home/21cy91r03/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 # (1) than previous atom (2). 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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_LowestCurve CPPTRAJ: LowestCurve test diffing All.agr.save with All.agr PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_MinImage CPPTRAJ: Minimum Image test. diffing min.dat.save with min.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Regress Linear regression test. can only run with 1 or fewer parallel threads. SKIP: Linear regression test. ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Rst CPPTRAJ: Generate restraints (rst) test diffing output.save with output PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Pairwise Pairwise test can only run with 1 or fewer parallel threads. SKIP: Pairwise test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_ParmBox CPPTRAJ: Parmbox test diffing out.parm7.save with out.parm7 PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Solvent Solvent test can only run with 1 or fewer parallel threads. SKIP: Solvent test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Translate Translate test can only run with 1 or fewer parallel threads. SKIP: Translate test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_ReplicateCell Replicate cell test can only run with 1 or fewer parallel threads. SKIP: Replicate cell test ******************************************************************************** TEST: /home/21cy91r03/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/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_PhiPsi CPPTRAJ: Phipsi test diffing phipsi.dat.save with phipsi.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Control CPPTRAJ: Loop tests [4] Error: Process is handling less than 1 frame. Try reducing # processes. [5] Error: Process is handling less than 1 frame. Try reducing # processes. [6] Error: Process is handling less than 1 frame. Try reducing # processes. [7] Error: Process is handling less than 1 frame. Try reducing # processes. 1 errors encountered reading input. Error: Error(s) occurred during execution. /home/21cy91r03/amber18/bin/cpptraj.MPI: Program error 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 ============================================================== possible FAILURE: file distance.dat does not exist. ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_InfraredSpec CPPTRAJ: Infrared spectrum calculation test diffing irspec.dat.save with irspec.dat PASSED ============================================================== diffing raw.dat.save with raw.dat PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Cphstats Explicit pH REMD ensemble data read / sort can only run with 6 or fewer parallel threads. Skipped test: Explicit pH REMD ensemble data read / sort 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 ============================================================== Implicit pH REMD ensemble data read / sort / stats can only run with 4 or fewer parallel threads. Skipped test: Implicit pH REMD ensemble data read / sort / stats 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 ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_CmdLine CPPTRAJ: Command line trajectory args test, part 1 CPPTRAJ: Command line test trajectory args test, part 2 diffing test1.crd.save with test1.crd PASSED ============================================================== CPPTRAJ: Command line wildcard test, part 1 CPPTRAJ: Command line wildcard test, part 2 diffing res.save with res PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_XYZformat XYZ format tests cannot be run in parallel. SKIP: XYZ format tests ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_Hausdorff CPPTRAJ: Simple Hausdorff distance test. diffing hd.dat.save with hd.dat PASSED ============================================================== CPPTRAJ: Hausdorff distance of 2D rms output test. diffing hausdorff.matrix.gnu.save with hausdorff.matrix.gnu PASSED ============================================================== CPPTRAJ: Hausdorff distance of 2D rms output test. diffing hausdorff.matrix.gnu.save with hausdorff.fullmatrix.gnu PASSED ============================================================== ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_CatCrd Concatenate COORDS data set test can only run with 1 or fewer parallel threads. SKIP: Concatenate COORDS data set test ******************************************************************************** TEST: /home/21cy91r03/amber18/AmberTools/src/cpptraj/test/Test_XtalSymm XtalSymm tests cannot be run in parallel. SKIP: XtalSymm tests make[5]: Leaving directory `/home/21cy91r03/amber18/AmberTools/src/cpptraj/test' 8 MPI threads. make[4]: Leaving directory `/home/21cy91r03/amber18/AmberTools/src/cpptraj/test' make[3]: Leaving directory `/home/21cy91r03/amber18/AmberTools/src/cpptraj/test' cd mmpbsa_py && make test make[3]: Entering directory `/home/21cy91r03/amber18/AmberTools/test/mmpbsa_py' cd 07_Comprehensive && ./Run.comprehensive Skipping test: Cannot have more than 2 processors. make[3]: Leaving directory `/home/21cy91r03/amber18/AmberTools/test/mmpbsa_py' cd rism3d.periodic/4lzta && ./Run.4lzta.kh.pme Running mpirun -np 8 /home/21cy91r03/amber18/bin/rism3d.snglpnt.MPI /home/21cy91r03/amber18/bin/rism3d.snglpnt.MPI not found... skipping test cd rism3d.periodic/1ahoa && ./Run.1ahoa.kh.pme Running mpirun -np 8 /home/21cy91r03/amber18/bin/rism3d.snglpnt.MPI /home/21cy91r03/amber18/bin/rism3d.snglpnt.MPI not found... skipping test make[2]: Leaving directory `/home/21cy91r03/amber18/AmberTools/test' make[2]: Entering directory `/home/21cy91r03/amber18/test' export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; make -k test.sander.BASIC make[3]: Entering directory `/home/21cy91r03/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 PASSED ============================================================== 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 PASSED ============================================================== 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 PASSED ============================================================== 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 PASSED ============================================================== 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 PASSED ============================================================== 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 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 8 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 ============================================================== diffing mdfrc.out.save with mdfrc.out PASSED ============================================================== cd trajene_box && ./Run.trajene DO_PARALLEL set to mpirun -np 8 This test cannot be run with more than 1 processor, exiting. ============================================================ cd trajene_netcdf && ./Run.trajene /home/21cy91r03/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 8 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 8 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/21cy91r03/amber18/include/netcdf.mod diffing nc_headers.save with nc_headers PASSED ============================================================== cd netcdf && make -k test OPT=/home/21cy91r03/amber18/include/netcdf.mod make[4]: Entering directory `/home/21cy91r03/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/21cy91r03/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/21cy91r03/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 PASSED ============================================================== 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 PASSED ============================================================== diffing torsion_pbc.dat.save with torsion_pbc.dat PASSED ============================================================== cd pme/tautp && ./Run.nmropt_1tautp_pbc diffing mdout.save with mdout PASSED ============================================================== cd pme/temp && ./Run.nmropt_1temp_pbc diffing mdout.save with mdout PASSED ============================================================== 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/21cy91r03/amber18/test/nmropt' cd lj_12-6-4 && ./Run.12-6-4 diffing mdout.save with mdout PASSED ============================================================== cd baroscalingdir && ./Run.baroscalingdir_z-dir cd ff19SB && ./Run.sander diffing mdout.save.sander with mdout PASSED ============================================================== make[3]: Leaving directory `/home/21cy91r03/amber18/test' export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd 4096wat && ./Run.column_fft diffing mdout.column_fft.save with mdout.column_fft PASSED ============================================================== export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd jar_multi && ./Run.jarz Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "gbin.001" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.jarz: Program error make[2]: [test.sander.BASIC.MPI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd ti_eth2meth_gas && ./Run.test1 DO_PARALLEL set to mpirun -np 8 number of processors for this test > 2, exiting... ============================================================ export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd ti_eth2meth_gas && ./Run.test2 DO_PARALLEL set to mpirun -np 8 number of processors for this test > 2, exiting... ============================================================ export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd ti_ggcc && ./Run.test1 Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "mdin" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.test1: Program error make[2]: [test.sander.BASIC.MPI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd ti_ggcc && ./Run.test2 Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "mdin" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.test2: Program error make[2]: [test.sander.BASIC.MPI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; make -k test.sander.GB make[3]: Entering directory `/home/21cy91r03/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 gbsa_xfin && ./Run.gbsa1 diffing mdout.gbsa1.save with mdout.gbsa1 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 PASSED ============================================================== 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 PASSED ============================================================== 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/21cy91r03/amber18/test' export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd rem_gb_2rep && ./Run.rem Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "./rem.in.001" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.rem: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd rrem_gb_2rep_boltzmann && ./Run.rem Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "./rem.in.001" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.rem: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd rrem_gb_2rep_nonboltzmann && ./Run.rem Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "./rem.in.001" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.rem: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd rem_gb_4rep && ./Run.rem Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "./rem.in.001" is missing or unreadable Error opening unit 5: File "./rem.in.003" is missing or unreadable Abort(1) on node 6 (rank 6 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.rem: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd rrem_gb_4rep_boltzmann && ./Run.rem Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "./rem.in.003" is missing or unreadable Abort(1) on node 6 (rank 6 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 ./Run.rem: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd rrem_gb_4rep_nonboltzmann && ./Run.rem Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "./rem.in.001" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.rem: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd rxsgld_4rep && ./Run.rxsgld Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "./rxsgld.in.001" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.rxsgld: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd rem_wat && ./Run.rem Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "./rem.in.001" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.rem: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd rem_wat_pv && ./Run.rem Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "./rem.in.001" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.rem: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd hrem_wat_pv && ./Run.rem Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "./rem.in.001" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.rem: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd rem_hybrid && ./Run.rem Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "./rem.in.001" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.rem: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd h_rem && ./Run.rem Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.rem: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd multid_remd && ./Run.multirem Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "remd.mdin2" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 Error opening unit 5: File "remd.mdin2" is missing or unreadable Abort(1) on node 6 (rank 6 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 Error opening unit 5: File "remd.mdin1" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.multirem: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnstph_remd/TempRem && ./Run.cnstph_remd Constant pH REMD test needs 2 or 4 processors to run (you selected 8) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnstph_remd/pHREM && ./Run.pHremd Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "phremd.pH2.5.mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.pHremd: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnstph_remd/pHREMrst && ./Run.pHremdrst Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "phremd.pH2.5.mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.pHremdrst: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnstph_remd/Explicit_pHREM && ./Run.pHremd Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "1AKI_mdin.1" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.pHremd: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnste_remd/TempRem && ./Run.cnste_remd Constant E REMD test needs 2 or 4 processors to run (you selected 8) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnste_remd/EREM && ./Run.Eremd Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "eremd.E0.84.mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.Eremd: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnste_remd/EREMrst && ./Run.Eremdrst Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "eremd.E0.84.mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.Eremdrst: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnste_remd/Explicit_EREM && ./Run.Eremd Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "mdin.1" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.Eremd: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd phtremd/implicit && ./Run.phtremd Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "mdin.rep.002" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 Error opening unit 5: File "mdin.rep.003" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 Error opening unit 5: File "mdin.rep.004" is missing or unreadable Abort(1) on node 6 (rank 6 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 ./Run.phtremd: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd phtremd/explicit && ./Run.phtremd Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "mdin.rep.003" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.phtremd: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd phtremd/explicitRst && ./Run.phtremdRst Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "mdin.rep.002" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.phtremdRst: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd ephtremd/implicit && ./Run.ephtremd Running multisander version of sander Amber18 Total processors = 8 Number of groups = 8 Error opening unit 5: File "mdin.rep.003" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.ephtremd: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd ephtremd/explicit && ./Run.ephtremd Running multisander version of sander Amber18 Total processors = 8 Number of groups = 8 Error opening unit 5: File "mdin.rep.004" is missing or unreadable Abort(1) on node 3 (rank 3 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3 ./Run.ephtremd: Program error make[2]: [test.sander.REM] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd sodium && ./Run.sodium Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "mdin" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.sodium: Program error make[2]: [test.sander.TI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd pheMTI && ./Run.0 diffing out.0.save with out.0 PASSED ============================================================== export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd pheMTI && ./Run.1 diffing out.1.save with out.1 PASSED ============================================================== export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd pheMTI && ./Run.lambda0 Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "mdin" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.lambda0: Program error make[2]: [test.sander.TI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd pheMTI && ./Run.lambda1 Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "mdin" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.lambda1: Program error make[2]: [test.sander.TI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd campTI && ./Run.campTI Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "mdin" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.campTI: Program error make[2]: [test.sander.TI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd softcore && ./Run_sc Running the Softcore potential tests ============================================================== Minimization test DO_PARALLEL set to mpirun -np 8 too many processors for this test, exiting ============================================================ Protein-Ligand complex test Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "mdin.1" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.complex: Program error ============================================================== Solvation free energy test Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "mdin.1" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.toluene: Program error Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "mdin.1" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.toluene2: Program error ============================================================== Dynamic lambda test Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "mdin.1" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.dynlmb: Program error ============================================================== Restrained complex test Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "mdin.1" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.complex_rst: Program error ============================================================== Using softcore electrostatics Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "mdin.1" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.ethanol: Program error ============================================================== Soft core test suite complete ============================================================== export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd ti_decomp; ./Run.ti_decomp Running multisander version of sander Amber18 Total processors = 8 Number of groups = 2 Error opening unit 5: File "mdin" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.ti_decomp: Program error make[2]: [test.sander.TI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd ti_decomp; ./Run.ti_decomp_sc DO_PARALLEL set to mpirun -np 8 too many processors for this test, exiting ============================================================ export TESTsanderLES=/home/21cy91r03/amber18/bin/sander.LES.MPI; make -k test.sander.LES make[3]: Entering directory `/home/21cy91r03/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 PASSED ============================================================== 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 DO_PARALLEL set to mpirun -np 8 too many processors for this test, exiting ============================================================ make[3]: Leaving directory `/home/21cy91r03/amber18/test' cd neb-testcases/neb_gb_partial && ./Run.neb_gb_partial Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.neb_gb_partial: Program error make[2]: [test.neb] Error 1 (ignored) cd neb-testcases/neb_gb_full && ./Run.neb_gb_full Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.neb_gb_full: Program error make[2]: [test.neb] Error 1 (ignored) cd neb-testcases/neb_explicit && ./Run.neb_explicit Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "mdin" is missing or unreadable Abort(1) on node 6 (rank 6 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 Error opening unit 5: File "mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.neb_explicit: Program error make[2]: [test.neb] Error 1 (ignored) cd nfe && ./run-parallel.sh >>>>>>> doing 'abmd_ANALYSIS' diffing save.sander/mdout with mdout PASSED ============================================================== diffing save.sander/monitor.txt with monitor.txt PASSED ============================================================== >>>>>>> doing 'abmd_FLOODING' diffing save.sander/mdout with mdout PASSED ============================================================== diffing save.sander/monitor.txt with monitor.txt PASSED ============================================================== diffing umbrella.save.ncdump with umbrella.ncdump PASSED ============================================================== diffing wt_umbrella.save.ncdump with wt_umbrella.ncdump PASSED ============================================================== >>>>>>> doing 'abmd_UMBRELLA' diffing save.sander/mdout with mdout PASSED ============================================================== diffing save.sander/monitor.txt with monitor.txt PASSED ============================================================== >>>>>>> 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' This test requires six or fewer processors. Skipping. >>>>>>> doing 'bbmd' ../common.sh: line 60: [: too many arguments This test case (/home/21cy91r03/amber18/test/nfe/bbmd) requires a least 4 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' ../common.sh: line 60: [: too many arguments This test case (/home/21cy91r03/amber18/test/nfe/abremd) requires a least 4 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' ../common.sh: line 60: [: too many arguments This test case (/home/21cy91r03/amber18/test/nfe/mwabmd) requires a least 4 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' ../common.sh: line 60: [: too many arguments This test case (/home/21cy91r03/amber18/test/nfe/premd) requires a least 4 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/21cy91r03/amber18/bin/sander.MPI; make -k test.sander.CHARMM make[3]: Entering directory `/home/21cy91r03/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/21cy91r03/amber18/test' export TESTsander=/home/21cy91r03/amber18/bin/sander.LES.MPI; make -k test.sander.PIMD.partial make[3]: Entering directory `/home/21cy91r03/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 PASSED ============================================================== 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/21cy91r03/amber18/test' cd PIMD/full_cmd_water/equilib && ./Run.full_cmd Testing Centroid MD Error opening unit 5: File "cmd.in" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.full_cmd: Program error make[2]: *** [test.sander.PIMD.MPI.full] Error 1 export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnstph/implicit && ./Run.cnstph diffing mdout.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnstph/explicit && ./Run.cnstph diffing mdout.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnstph_remd/TempRem && ./Run.cnstph_remd Constant pH REMD test needs 2 or 4 processors to run (you selected 8) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnstph_remd/pHREM && ./Run.pHremd Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "phremd.pH2.5.mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 Error opening unit 5: File "phremd.pH3.mdin" is missing or unreadable Error opening unit 5: File "phremd.pH3.5.mdin" is missing or unreadable Abort(1) on node 6 (rank 6 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 ./Run.pHremd: Program error make[2]: [test.sander.constph.MPI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnstph_remd/pHREMrst && ./Run.pHremdrst Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "phremd.pH2.5.mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.pHremdrst: Program error make[2]: [test.sander.constph.MPI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnstph_remd/Explicit_pHREM && ./Run.pHremd Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "1AKI_mdin.1" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.pHremd: Program error make[2]: [test.sander.constph.MPI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnste/implicit && ./Run.cnste DO_PARALLEL set to mpirun -np 8 too many MPI ranks for this test, exiting (Max MPI ranks = 6) ============================================================ export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnste/explicit && ./Run.cnste diffing mdout.save with mdout PASSED ============================================================== diffing ceout.save with ceout PASSED ============================================================== export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnste_remd/TempRem && ./Run.cnste_remd Constant E REMD test needs 2 or 4 processors to run (you selected 8) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnste_remd/EREM && ./Run.Eremd Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "eremd.E0.84.mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 Error opening unit 5: File "eremd.E0.90.mdin" is missing or unreadable Abort(1) on node 6 (rank 6 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 ./Run.Eremd: Program error make[2]: [test.sander.conste.MPI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnste_remd/EREMrst && ./Run.Eremdrst Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "eremd.E0.84.mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 Error opening unit 5: File "eremd.E0.87.mdin" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 ./Run.Eremdrst: Program error make[2]: [test.sander.conste.MPI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnste_remd/Explicit_EREM && ./Run.Eremd Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "mdin.1" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.Eremd: Program error make[2]: [test.sander.conste.MPI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnstphe/implicit && ./Run.cnstphe DO_PARALLEL set to mpirun -np 8 too many MPI ranks for this test, exiting (Max MPI ranks = 6) ============================================================ export TESTsander=/home/21cy91r03/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/21cy91r03/amber18/bin/sander.MPI; cd cnstphe_merged/implicit && ./Run.cnstphe DO_PARALLEL set to mpirun -np 8 too many MPI ranks for this test, exiting (Max MPI ranks = 6) ============================================================ export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd cnstphe_merged/explicit && ./Run.cnstphe diffing mdout.save with mdout PASSED ============================================================== diffing cpeout.save with cpeout PASSED ============================================================== export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala /home/21cy91r03/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.min /home/21cy91r03/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.imin5 /home/21cy91r03/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.mdiis0 /home/21cy91r03/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.mdiis1 /home/21cy91r03/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.resize /home/21cy91r03/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.dist /home/21cy91r03/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.dist.xyzv /home/21cy91r03/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.hnc /home/21cy91r03/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.pse1 /home/21cy91r03/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.tree /home/21cy91r03/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.nacl /home/21cy91r03/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' \ && cd rism3d/1ahoa && ./Run.1ahoa.pme SANDER: 3D-RISM: PME potential - orthorhombic /home/21cy91r03/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' \ && cd rism3d/4lzt && ./Run.4lzt.pme SANDER: 3D-RISM: PME potential - triclinic /home/21cy91r03/amber18/bin/sander.MPI compiled without RISM support. export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' && cd crg_reloc/water && ./Run.water.min diffing min.out.save with min.out PASSED ============================================================== export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI' && cd crg_reloc/water && ./Run.water.md diffing md.out.save with md.out PASSED ============================================================== export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI'; cd amd && make -k test make[3]: Entering directory `/home/21cy91r03/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 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/21cy91r03/amber18/test/amd' export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI'; cd scaledMD && make -k test make[3]: Entering directory `/home/21cy91r03/amber18/test/scaledMD' Testing scaledMD with PME diffing mdout.save with mdout PASSED ============================================================== make[3]: Leaving directory `/home/21cy91r03/amber18/test/scaledMD' export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI'; cd gb_rna && ./Run.gbrna.sgld diffing mdout.gbrna.sgld.save with mdout.gbrna.sgld PASSED ============================================================== export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI'; cd gb_rna && ./Run.gbrna.sgldfp diffing mdout.gbrna.sgldfp.save with mdout.gbrna.sgldfp PASSED ============================================================== export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI'; cd gb_rna && ./Run.gbrna.sgldg diffing mdout.gbrna.sgldg.save with mdout.gbrna.sgldg PASSED ============================================================== export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI'; cd gb_rna && ./Run.gbrna.sgmdg diffing mdout.gbrna.sgmdg.save with mdout.gbrna.sgmdg PASSED ============================================================== export TESTsander='/home/21cy91r03/amber18/bin/sander.MPI'; cd emap/ && ./Run.emap diffing mdout.emap.save with mdout.emap PASSED ============================================================== export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd sander_OIN_MPI && ./Run.sander.OIN.MPI diffing mdout.sander.OIN.MPI.save with mdout.sander.OIN.MPI PASSED ============================================================== export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd sinr_MPI && ./RUN.sander.SINR.MPI DO_PARALLEL set to mpirun -np 8 too many processors for this test, exiting (Max = 2) ============================================================ export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd sander_music/pt-water-gal17 && ./Run.md diffing mdout.save with mdout PASSED ============================================================== export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd sander_music/pt-water-vsgal17 && ./Run.md diffing mdout.save with mdout PASSED ============================================================== cd middle-scheme/MD_Unconstr_Langevin_water && ./Run.LGV_LF.MPI AMBERHOME is /home/21cy91r03/amber18 Testing mpirun MD with Langevin thermostat diffing md_LGV.out.save with md_LGV.out PASSED ============================================================== cd middle-scheme/MD_Constr_Langevin_water && ./Run.LGV_LF.MPI AMBERHOME is /home/21cy91r03/amber18 Testing mpirun MD with Langevin thermostat diffing md_LGV.out.save with md_LGV.out PASSED ============================================================== cd middle-scheme/QMMM_Constr_ALA_Methol && ./Run.qmmm.MPI Testing mpirun MD with qmmm mpirun -np 8 /home/21cy91r03/amber18/bin/sander.MPI diffing qmmm.out.save with qmmm.out PASSED ============================================================== cd middle-scheme/REMD_Constr_ALA && ./Run.rem Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "./rem.in.002" is missing or unreadable Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 Error opening unit 5: File "./rem.in.003" is missing or unreadable Abort(1) on node 6 (rank 6 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 Error opening unit 5: File "./rem.in.001" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.rem: line 44: error: command not found possible FAILURE: file rem.log does not exist. ============================================================== diffing rem.out.000.save with rem.out.000 possible FAILURE: check rem.out.000.dif ============================================================== export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; make -k test.sander.QMMM make[3]: Entering directory `/home/21cy91r03/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 PASSED ============================================================== 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 PASSED ============================================================== 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 PASSED ============================================================== 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 PASSED ============================================================== cd qmmm2/variable_solvent && ./Run.1NLN_MD_ntb1_vsolv diffing mdout.1NLN_MD_ntb1_vsolv.save with mdout.1NLN_MD_ntb1_vsolv PASSED ============================================================== 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 PASSED ============================================================== 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 DO_PARALLEL set to mpirun -np 8 too many processors for this test cd qmmm2/PM3-MAIS && ./Run.hcl_wat DO_PARALLEL set to mpirun -np 8 too many processors for this test cd qmmm2/MechEm_nma-spcfwbox && ./Run.MechEm_PDDGPM3 diffing mdout.MechEm_PDDGPM3.save with mdout.MechEm_PDDGPM3 PASSED ============================================================== cd qmmm2/qmmm_switching_func && ./Run.nma_md_switching diffing nma.out.save with nma.out PASSED ============================================================== make[3]: Leaving directory `/home/21cy91r03/amber18/test' export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; make -k test.sander.DFTB make[3]: Entering directory `/home/21cy91r03/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 PASSED ============================================================== 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 PASSED ============================================================== 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/21cy91r03/amber18/test' export TESTsander=/home/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/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/21cy91r03/amber18/bin/sander.MPI; cd qmmm_EXTERN/QMMM_Fireball/min && ./Run.min Not compiled with Fireball - Skipping Test... export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; cd qmmm_EXTERN/QMMM_Fireball/md && ./Run.md Not compiled with Fireball - Skipping Test... export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI && cd qmmm2/adqmmm_na+28water && ./Run.adqmmm Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "adqmmm-6-4.mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.adqmmm: Program error make[2]: [test.sander.ADQMMM.MPI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI && cd qmmm2/adqmmm_na+28water && ./Run.adqmmm-calc_wbk2 Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "adqmmm-calc_wbk2-6-4.mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.adqmmm-calc_wbk2: Program error make[2]: [test.sander.ADQMMM.MPI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI && cd qmmm2/adqmmm_na+28water && ./Run.adqmmm-fixedR Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "adqmmm-fixedR-6-4.mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 Error opening unit 5: File "adqmmm-fixedR-6-4.mdin" is missing or unreadable ./Run.adqmmm-fixedR: Program error make[2]: [test.sander.ADQMMM.MPI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI && cd qmmm2/adqmmm_h2o-box && ./Run.adqmmm Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "adqmmm-6-4.mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.adqmmm: Program error make[2]: [test.sander.ADQMMM.MPI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI && cd qmmm2/adqmmm_h2o-box && ./Run.adqmmm-fixedR-calc_wbk2 Running multisander version of sander Amber18 Total processors = 8 Number of groups = 4 Error opening unit 5: File "adqmmm-fixedR-calc_wbk2-6-4.mdin" is missing or unreadable Abort(1) on node 2 (rank 2 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 ./Run.adqmmm-fixedR-calc_wbk2: Program error make[2]: [test.sander.ADQMMM.MPI] Error 1 (ignored) export TESTsander=/home/21cy91r03/amber18/bin/sander.MPI; make -k test.sander.ABFQMMM make[3]: Entering directory `/home/21cy91r03/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/21cy91r03/amber18/test' cd evb/malon_bond_umb_GAFF && ./Run.evb DO_PARALLEL set to mpirun -np 8 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_GAFF_MORSIFY && ./Run.evb DO_PARALLEL set to mpirun -np 8 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_GAFF_MORSIFY_XVDW && ./Run.evb DO_PARALLEL set to mpirun -np 8 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF && ./Run.evb DO_PARALLEL set to mpirun -np 8 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY && ./Run.evb DO_PARALLEL set to mpirun -np 8 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_nmpimd_full && ./Run.evb DO_PARALLEL set to mpirun -np 8 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 8 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 8 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW && ./Run.evb DO_PARALLEL set to mpirun -np 8 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 8 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 8 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 8 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 8 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 8 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 8 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 8 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 8 too many processors for this test, exiting ============================================================ cd evb/malon_emap_GAFF_MORSIFY && ./Run.evb DO_PARALLEL set to mpirun -np 8 too many processors for this test, exiting ============================================================ cd evb/malon_emap_GAFF_MORSIFY_XVDW && ./Run.evb DO_PARALLEL set to mpirun -np 8 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_dg_UFF_3DG && ./Run.evb DO_PARALLEL set to mpirun -np 8 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 8 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 8 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 8 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 8 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 8 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 8 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 8 too many processors for this test, exiting ============================================================ cd evb/poh_dbonds_umb_dg_UFF_3DG && ./Run.evb DO_PARALLEL set to mpirun -np 8 too many processors for this test, exiting ============================================================ cd evb/poh_dbonds_umb_dg_UFF_9DG && ./Run.evb DO_PARALLEL set to mpirun -np 8 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 8 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 8 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 8 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 8 too many processors for this test, exiting ============================================================ export TESTsander=/home/21cy91r03/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/21cy91r03/amber18/test' make[2]: Entering directory `/home/21cy91r03/amber18/AmberTools/test' Finished test suite for AmberTools at Sat Nov 12 00:59:31 IST 2022. make[2]: Leaving directory `/home/21cy91r03/amber18/AmberTools/test' 852 file comparisons passed 4 file comparisons failed (0 ignored) 55 tests experienced errors Test log file saved as /home/21cy91r03/amber18/logs/test_at_parallel/2022-11-12_00-21-45.log No test diffs to save!