./test_at_clean.sh cd antechamber && /Applications/Xcode.app/Contents/Developer/usr/bin/make -k clean 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 cd mmpbsa_py && /Applications/Xcode.app/Contents/Developer/usr/bin/make -k clean 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 cd /Users/blaine-mooers/software/Amber16/AmberTools/src/mm_pbsa/Examples && ./Run.mmpbsa.clean cd /Users/blaine-mooers/software/Amber16/AmberTools/src/FEW/examples/test && ./Run.few.clean cd /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test && /Applications/Xcode.app/Contents/Developer/usr/bin/make -k clean Cleaning all test directories: (find . -name 'test.out' -o -name 'valgrind.out' -o -name 'Thread.*' \ -o -name 'Test_Results.dat' -o -name 'Test_Error.dat' | \ while read dif ;\ do \ rm -f $dif ;\ done ;\ ) /Applications/Xcode.app/Contents/Developer/usr/bin/make test.complete test.libcpptraj OPT=clean cd leap && /Applications/Xcode.app/Contents/Developer/usr/bin/make -k clean Cleaning all test directories: (find . -name 'leap.log' -o -name 'leap.out' | \ while read dif ;\ do \ rm -f $dif ;\ done ;\ ) /Applications/Xcode.app/Contents/Developer/usr/bin/make test.complete OPT=clean 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 && /Applications/Xcode.app/Contents/Developer/usr/bin/make -k test 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 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 do simple lmod optimization diffing tlmod.out.check with tlmod.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: [blaine:12280] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed! [blaine:12281] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed! [blaine:12279] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed! ./Run.nmode3: Program error make[3]: *** [nmode3_test] Error 1 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]: Target `test' not remade because of errors. make[2]: *** [test.nab] Error 2 cd /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test && /Applications/Xcode.app/Contents/Developer/usr/bin/make -k test /Applications/Xcode.app/Contents/Developer/usr/bin/make test.complete summary ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_General CPPTRAJ: General tests This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Strip CPPTRAJ: Strip tests Warning: Test can only run with 1 or fewer parallel threads. Skipping. CPPTRAJ: Multi frame strip command test. diffing res1.tz2.crd.save with res1.tz2.crd PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_BrokenTraj CPPTRAJ: Broken Traj This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_TrajinOffset CPPTRAJ: Normal trajectory read with offsets. diffing rem.crd.save with rem.crd.combined PASSED ============================================================== CPPTRAJ: Gzipped trajectory read with offsets. diffing rem.crd.save with gzip.rem.crd.combined PASSED ============================================================== CPPTRAJ: Bzip2ed trajectory read with offsets. diffing rem.crd.save with bzip2.rem.crd.combined PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_RemdTraj CPPTRAJ: CRD Replica Trajectory Run with offset diffing d1.offset.dat.save with d1.offset.dat PASSED ============================================================== CPPTRAJ: CRD Replica Trajectory Run diffing d1.crd.dat.save with d1.crd.dat PASSED ============================================================== CPPTRAJ: NETCDF Replica Trajectory Run 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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_trajout_framerange CPPTRAJ: Trajout Frame Range This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_PerResRMSD CPPTRAJ: Per-Residue RMSD Test. diffing PerResRMSD.agr.save with PerResRMSD.agr PASSED ============================================================== CPPTRAJ: Per-Residue RMSD Test with averaging. Warning: Test can only run with 3 or fewer parallel threads. Skipping. CPPTRAJ: Per-Residue RMSD Test with residue centering. diffing center.agr.save with center.agr PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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 ============================================================== CPPTRAJ: Secstruct (DSSP) command with changing number of residues. This test cannot be run in parallel. Skipping test. CPPTRAJ: Secstruct (DSSP): SS assign output test Warning: Test can only run with 1 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Center CPPTRAJ: Center tests. Warning: Test can only run with 2 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Hbond CPPTRAJ: Solute Hbond test. diffing nhb.dat.save with nhb.dat PASSED ============================================================== diffing avghb.dat.save with avghb.dat PASSED ============================================================== diffing nbb.dat.save with nbb.dat PASSED ============================================================== diffing hbavg.dat.save with hbavg.dat PASSED ============================================================== diffing solutehb.agr.save with solutehb.agr PASSED ============================================================== diffing lifehb.gnu.save with lifehb.gnu PASSED ============================================================== diffing avg.lifehb.gnu.save with avg.lifehb.gnu PASSED ============================================================== diffing max.lifehb.gnu.save with max.lifehb.gnu PASSED ============================================================== diffing crv.lifehb.gnu.save with crv.lifehb.gnu PASSED ============================================================== CPPTRAJ: Solvent Hbond test. diffing solvhb.dat.save with solvhb.dat PASSED ============================================================== diffing solvavg.dat.save with solvavg.dat PASSED ============================================================== CPPTRAJ: Hbond with imaging Warning: Test can only run with 1 or fewer parallel threads. Skipping. 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 ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_NCrestart CPPTRAJ: NetCDF restart tests Warning: Test can only run with 1 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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 ============================================================== CPPTRAJ: Coordinate imaging tests. Warning: Test can only run with 2 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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 ============================================================== CPPTRAJ: LCPO test with GAFF atom types. Warning: Test can only run with 1 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Mask CPPTRAJ: Mask single frame tests Warning: Test can only run with 1 or fewer parallel threads. Skipping. CPPTRAJ: Mask longer command test. diffing M.dat.save with M.dat PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Jcoupling CPPTRAJ: J-Coupling single frame test. Warning: Test can only run with 1 or fewer parallel threads. Skipping. CPPTRAJ: J-Coupling extended test. diffing jc.dat.save with jc.dat PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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 ============================================================== CPPTRAJ: Imaged diffusion tests Warning: Test can only run with 1 or fewer parallel threads. Skipping. CPPTRAJ: STFC diffusion tests. This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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 ============================================================== CPPTRAJ: Outtraj Test with maxmin. This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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 ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Rotdif CPPTRAJ: Rotdif 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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_NetcdfTraj CPPTRAJ: Convert mdcrd -> netcdf. CPPTRAJ: Convert netcdf -> mdcrd. diffing ../tz2.truncoct.crd with trajectory_test.mdcrd PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Runavg CPPTRAJ: Coordinate Running Average test. diffing R1.dat.save with R1.dat PASSED ============================================================== CPPTRAJ: Coordinate Running Average Traj Write This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_RMSD CPPTRAJ: RMSD Tests. diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing rmsd.mass.dat.save with rmsd.mass.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: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Mol2 CPPTRAJ: Mol2 tests. This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_NAstruct CPPTRAJ: NAstruct tests Warning: Test can only run with 3 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Pucker CPPTRAJ: Pucker command test Warning: Test can only run with 3 or fewer parallel threads. Skipping. CPPTRAJ: Pyranoid/furanoid pucker tests. Warning: Test can only run with 1 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_AtomMap CPPTRAJ: AtomMap Test Warning: Test can only run with 1 or fewer parallel threads. Skipping. CPPTRAJ: AtomMap with 'rmsfit' Warning: Test can only run with 2 or fewer parallel threads. Skipping. CPPTRAJ: Atom map charmm->amber atom order Warning: Test can only run with 3 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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 ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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 ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Hist CPPTRAJ: 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 ============================================================== CPPTRAJ: 3D histogram test. diffing hist.dx.save with hist.dx PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Closest CPPTRAJ: Closest command test using first solvent atom. Warning: Test can only run with 1 or fewer parallel threads. Skipping. CPPTRAJ: Closest command test using all solvent atoms. Warning: Test can only run with 1 or fewer parallel threads. Skipping. 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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_DRMSD CPPTRAJ: Distance RMSD test. diffing drmsd.dat.save with drmsd.dat PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Cluster CPPTRAJ: Cluster command test, in-memory pairwise distances. diffing cnumvtime.dat.save with cnumvtime.dat PASSED ============================================================== diffing avg.summary.dat.save with avg.summary.dat PASSED ============================================================== diffing summary.dat.save with summary.dat PASSED ============================================================== diffing cpop.agr.save with cpop.agr PASSED ============================================================== CPPTRAJ: Cluster command test, read pairwise distances. diffing summary.dat.save with summary2.dat PASSED ============================================================== CPPTRAJ: Cluster command test, read NetCDF pairwise distances. diffing summary.dat.save with summary3.dat PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_RandomizeIons CPPTRAJ: randomizeions test Warning: Test can only run with 1 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Molsurf CPPTRAJ: Molsurf test. diffing msurf.dat.save with msurf.dat PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_CheckStructure CPPTRAJ: Structure check test Warning: Test can only run with 1 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Contacts CPPTRAJ: Contacts test. This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_ClusterDihedral CPPTRAJ: clusterdihedral test This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Vector CPPTRAJ: 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: AvgCoord test. diffing avgcoord.out.save with avgcoord.out PASSED ============================================================== diffing res5.out.save with res5.out PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/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 ============================================================== 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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Unwrap CPPTRAJ: Unwrap tests. This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Project CPPTRAJ: Projection diffing project.dat.save with project.dat PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Volmap CPPTRAJ: VMD VolMap Algorithm test diffing volmap.dx.save with volmap.dx PASSED ============================================================== diffing volmap.dx.save with volmap2.dx PASSED ============================================================== diffing peaks.xyz.save with peaks.xyz PASSED ============================================================== diffing volmap3.dx.save with volmap3.dx PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_LIE CPPTRAJ: LIE test, TCL diffing TCL.out.save with TCL.out PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Density CPPTRAJ: Density test. This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_LipidOrder CPPTRAJ: Lipid Order Parameter Test. This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_PairDist CPPTRAJ: PairDist Test. diffing Pr.dat.save with Pr.dat PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_GIST CPPTRAJ: GIST test. This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_GIST_Order CPPTRAJ: GIST tetrahedral water cluster test. This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_AmbPDB AMBPDB: AmbPDB tests. diffing out.pdb.save with out.pdb PASSED ============================================================== diffing out.pdb.save with out1.pdb PASSED ============================================================== diffing fabi.pdb.save with fabi.pdb PASSED ============================================================== diffing ../Test_Mol2/test2.mol2.save with out.mol2 PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_systemVF CPPTRAJ: Amber Netcdf with Velocity/Force test diffing nc0.save with nc0 PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_AtomicCorr CPPTRAJ: Atomic Correlation test. diffing acorr.gnu.save with acorr.gnu PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_AutoCorr CPPTRAJ: AutoCorr test. diffing ac.agr.save with ac.agr PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_AtomTypeSelect CPPTRAJ: Selection by atom type test. diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_CreateCrd CPPTRAJ: COORDS data set creation and CRDFLUCT test. diffing crd1.dat.save with crd1.dat PASSED ============================================================== CPPTRAJ: COORDS data set creation with velocities test. Warning: Test can only run with 1 or fewer parallel threads. Skipping. CPPTRAJ: TRAJ data set creation and CRDFLUCT test. diffing crd1.dat.save with crd1.dat PASSED ============================================================== CPPTRAJ: TRAJ data set creation with velocities test. diffing crd1.rst7.save with crd2.rst7 PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_AutoImage CPPTRAJ: AutoImage test Warning: Test can only run with 2 or fewer parallel threads. Skipping. CPPTRAJ: AutoImage test, use anchor mask Warning: Test can only run with 1 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_MultiVector CPPTRAJ: Multivector test. diffing NH.dat.save with NH.dat PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Lifetime CPPTRAJ: Lifetime test. diffing avg.life.5.gnu.save with avg.life.5.gnu PASSED ============================================================== diffing max.life.5.gnu.save with max.life.5.gnu PASSED ============================================================== diffing life.5.gnu.save with life.5.gnu PASSED ============================================================== diffing crv.life.5.gnu.save with crv.life.5.gnu PASSED ============================================================== diffing solutehb.gnu.save with solutehb.gnu PASSED ============================================================== CPPTRAJ: Lifetime average and cumulative average test. diffing perres.avg.gnu.save with perres.avg.gnu PASSED ============================================================== diffing perres.cumulative.gnu.save with perres.cumulative.gnu PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_CrossCorr CPPTRAJ: CrossCorr test. diffing cc.gnu.save with cc.gnu PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_SymmRmsd CPPTRAJ: Symmetry-corrected RMSD tests Warning: Test can only run with 3 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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 ============================================================== CPPTRAJ: Multidihedral Nucleotide CHI test. Warning: Test can only run with 3 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Ensemble_MREMD CPPTRAJ: M-REMD ensemble tests Warning: Test requires a multiple of 8 parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_MakeStructure CPPTRAJ: Makestructure test Warning: Test can only run with 1 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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 ============================================================== CPPTRAJ: Rotate with defined axis. Warning: Test can only run with 1 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Integrate CPPTRAJ: Integration test. diffing curve.dat.save with curve.dat PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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 ============================================================== CPPTRAJ: NativeContacts test, save non-native contacts, residue time series This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_CheckChiral CPPTRAJ: Check chirality test. diffing chiral.dat.save with chiral.dat PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Energy CPPTRAJ: Simple Energy test diffing ene.agr.save with ene.agr PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_LESsplit CPPTRAJ: LES split test diffing splittraj.0.save with splittraj.0 PASSED ============================================================== diffing avg.crd.save with avg.crd PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_PermuteDihedrals CPPTRAJ: PermuteDihedrals tests Warning: Test can only run with 1 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_CCP4 CPPTRAJ: CCP4 read/write and DX conversion test. diffing fav8.dx.save with fav8.dx PASSED ============================================================== sed: RE error: illegal byte sequence sed: RE error: illegal byte sequence diffing fav8.guv.O.1.ccp4 with fav8.ccp4 PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Multicurve CPPTRAJ: Multicurve test diffing curves.agr.save with curves.agr PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Esander SANDER energy tests requires compilation with the Sander API from AmberTools. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Spline CPPTRAJ: Spline test diffing spline.dat.save with spline.dat PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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 ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_CIF CPPTRAJ: CIF read test. This test cannot be run in parallel. Skipping test. CPPTRAJ: Generate offset traj from PDB CPPTRAJ: Generate offset traj from CIF diffing temp1.crd with temp2.crd PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_PDB CPPTRAJ: PDB format read/write test. Warning: Test can only run with 1 or fewer parallel threads. Skipping. CPPTRAJ: PQR file write with various radii This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_VelocityAutoCorr CPPTRAJ: Velocity autocorrelation test diffing VAC.agr.save with VAC.agr PASSED ============================================================== diffing diff.dat.save with diff.dat PASSED ============================================================== diffing VAC2.dat.save with VAC2.dat PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_VelFrc CPPTRAJ: Separate velocity/force This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_DataSetCmd CPPTRAJ: Data Set commands test diffing avg.dat.save with avg.dat PASSED ============================================================== diffing matrix.dat.save with matrix.dat PASSED ============================================================== diffing matrix.dat.save with matrix2.dat PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Remap CPPTRAJ: Remap Test Warning: Test can only run with 1 or fewer parallel threads. Skipping. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_CompareTop CPPTRAJ: Compare topology test. This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Filter CPPTRAJ: Filter test. This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_CombineCrd CPPTRAJ: Combine COORDS tests. This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/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 values.dat.save with values.dat PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_GromacsTrr CPPTRAJ: TRR force/velocity read/write Warning: Test can only run with 2 or fewer parallel threads. Skipping. CPPTRAJ: CRD => TRR CPPTRAJ: TRR => CRD diffing ../tz2.truncoct.crd with temp.crd PASSED ============================================================== CPPTRAJ: GMX TRR append This test cannot be run in parallel. Skipping test. CPPTRAJ: GMX: CRD with offset CPPTRAJ: GMX: TRR with offset diffing total1.out with total2.out PASSED ============================================================== ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_GromacsXtc CPPTRAJ: XTC read/write Warning: Test can only run with 2 or fewer parallel threads. Skipping. CPPTRAJ: XTC write test This test cannot be run in parallel. Skipping test. CPPTRAJ: GMX XTC append This test cannot be run in parallel. Skipping test. CPPTRAJ: GMX XTC offset test This test cannot be run in parallel. Skipping test. ************************************************************** TEST: /Users/blaine-mooers/software/Amber16/AmberTools/src/cpptraj/test/Test_Ewald CPPTRAJ: Direct sum test Warning: Test can only run with 1 or fewer parallel threads. Skipping. CPPTRAJ: Ewald test (NaCl crystal) Warning: Test can only run with 1 or fewer parallel threads. Skipping. CPPTRAJ: Ewald test (trunc. oct) Warning: Test can only run with 1 or fewer parallel threads. Skipping. CPPTRAJ: Ewald test (trunc. oct), 10 frames diffing ew_tz2_10.dat.save with ew_tz2_10.dat PASSED ============================================================== CPPTRAJ: Ewald test (Ortho), 10 frames diffing tz2_ortho.dat.save with tz2_ortho.dat PASSED ============================================================== ===================== TEST SUMMARY ====================== No Test Results files (./*/Test_Results.dat) found. ========================================================= cd mmpbsa_py && /Applications/Xcode.app/Contents/Developer/usr/bin/make test cd 07_Comprehensive && ./Run.comprehensive Skipping test: Cannot have more than 2 processors. cd rism3d.periodic/PH4+ && ./Run.PH4+.kh.pme DO_PARALLEL set to mpirun -np 4; max is 2 cd rism3d.periodic/imidazoleH+ && ./Run.imidazoleH+.kh.pme DO_PARALLEL set to mpirun -np 4; max is 2 cd rism3d.periodic/PH4+_triclinic && ./Run.PH4+_triclinic.kh.pme DO_PARALLEL set to mpirun -np 4; max is 2 cd rism3d.periodic/4lzta && ./Run.4lzta_5.kh.pme DO_PARALLEL set to mpirun -np 4; max is 2 cd rism3d.periodic/2igd && ./Run.2igd.kh.pme DO_PARALLEL set to mpirun -np 4; max is 2 cd rism3d.periodic/1d23 && ./Run.1d23.kh.pme DO_PARALLEL set to mpirun -np 4; max is 2 make[2]: Target `test.parallel2' not remade because of errors. export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; /Applications/Xcode.app/Contents/Developer/usr/bin/make -k test.sander.BASIC 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 gact_ips && ./Run.ips diffing mdout.ips.save with mdout.ips PASSED ============================================================== cd gact_ips && ./Run.ipsnve diffing mdout.ipsnve.save with mdout.ipsnve PASSED ============================================================== cd gact_ips && ./Run.ips_dfft diffing mdout.ips_dfft.save with mdout.ips_dfft PASSED ============================================================== cd gact_ips && ./Run.ips_vacuum diffing mdout.ips_vacuum.save with mdout.ips_vacuum PASSED ============================================================== cd polarizable_water && ./Run.pol_wat diffing mdout.polwat.save with mdout.polwat PASSED ============================================================== cd ubiquitin && ./Run.ubiquitin diffing mdout.ubiquitin.save with mdout.ubiquitin PASSED ============================================================== diffing mden.save with mden PASSED ============================================================== diffing mdcrd.save with mdcrd PASSED ============================================================== diffing mdvel.save with mdvel PASSED ============================================================== cd dna_pol && ./Run.dna_pol diffing mdout.dna_pol.save with mdout.dna_pol PASSED ============================================================== cd trx && ./Run.trx diffing mdout.trx.save with mdout.trx PASSED ============================================================== cd trx && ./Run.trx.cpln diffing mdout.trx.cpln.save with mdout.trx.cpln PASSED ============================================================== cd rdc && ./Run.dip diffing gcg.dip.o.save with gcg.dip.o PASSED ============================================================== cd rdc && ./Run.csa diffing gcg.csa.o.save with gcg.csa.o PASSED ============================================================== cd rdc && ./Run.csa_min diffing gcg.csa_min.o.save with gcg.csa_min.o PASSED ============================================================== cd rdc && ./Run.nmr diffing gcg.nmr.o.save with gcg.nmr.o PASSED ============================================================== cd pcsa && ./Run.dip diffing stem.dip.o.save with stem.dip.o PASSED ============================================================== cd pcsa && ./Run.csa diffing stem.csa.o.save with stem.csa.o PASSED ============================================================== cd pcsa && ./Run.csa2 diffing stem.csa2.o.save with stem.csa2.o PASSED ============================================================== cd pcsa && ./Run.csa_min diffing stem.csa_min.o.save with stem.csa_min.o PASSED ============================================================== cd tgtmd/change_target && ./Run.tgtmd SANDER: Targeted MD with changing target diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/change_target.rms && ./Run.tgtmd SANDER: Targeted MD with changing target and fit/rmsd to different regions diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/change_target.ntr && ./Run.tgtmd SANDER: Targeted MD with changing target and restraints DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting (Max = 2) ============================================================ cd tgtmd/conserve_ene && ./Run.tgtmd SANDER: Targeted MD energy conservation test diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/minimize && ./Run.tgtmin SANDER: Targeted minimization diffing tgtmin.out.save with tgtmin.out PASSED ============================================================== cd tgtmd/PME && ./Run.tgtPME SANDER: Targeted MD with PME diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd mtmdtest && ./Run.mtmdtest SANDER: Multiply-targeted MD, new to AMBER 11 Tested on an RNA duplex. diffing mtmdtest.out.save with mtmdtest.out PASSED ============================================================== diffing mtmdtest.mdcrd.save with mtmdtest.mdcrd PASSED ============================================================== cd trajene && ./Run.trajene diffing trajene.out.save with trajene.out PASSED ============================================================== diffing mdcrd.out.save with mdcrd.out PASSED ============================================================== cd trajene_box && ./Run.trajene DO_PARALLEL set to mpirun -np 4 This test cannot be run with more than 1 processor, exiting. ============================================================ cd trajene_netcdf && ./Run.trajene /Users/blaine-mooers/software/Amber16/include/netcdf.mod diffing trajene.out.save with trajene.out PASSED ============================================================== sed: RE error: illegal byte sequence sed: RE error: illegal byte sequence diffing mdcrd.out.nc.save with mdcrd.out.nc PASSED ============================================================== cd alp && ./Run.alp diffing mdout.alp.save with mdout.alp PASSED ============================================================== cd umbrella && ./Run.umbrella diffing mdout.umbrella.save with mdout.umbrella PASSED ============================================================== diffing chi_vs_t.save with chi_vs_t PASSED ============================================================== cd noesy && ./Run.noesy diffing noesy.out.mpi.save with noesy.out PASSED ============================================================== cd jar && ./Run.jarz diffing mdout.jar.save with mdout.jar PASSED ============================================================== diffing dist_vs_t.save with dist_vs_t PASSED ============================================================== cd plane_plane_restraint && ./Run.dinuc_plpt SANDER: Dinucleoside restrained with new plane-point angle restraint that was defined with new natural language restraint input. DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting (Max = 2) ============================================================ cd plane_plane_restraint && ./Run.dinuc_pln SANDER: Dinucleoside restrained with new plane-plane angle restraint that was defined with new natural language restraint input. DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting (Max = 2) ============================================================ cd iwrap2 && ./Run.iwrap2 diffing mdout.iw2.save with mdout.iw2 PASSED ============================================================== diffing mdcrd.iw2.save with mdcrd.iw2 PASSED ============================================================== diffing rstrt.iw2.save with rstrt.iw2 PASSED ============================================================== cd idecomp1 && ./run_idecomp1.sh diffing decomp.out.save with decomp.out PASSED ============================================================== cd idecomp4 && ./run_idecomp4.sh diffing decomp.out.save with decomp.out PASSED ============================================================== cd bintraj && ./Run.bintraj /Users/blaine-mooers/software/Amber16/include/netcdf.mod diffing nc_headers.save with nc_headers PASSED ============================================================== cd netcdf && /Applications/Xcode.app/Contents/Developer/usr/bin/make -k test OPT=/Users/blaine-mooers/software/Amber16/include/netcdf.mod 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 ============================================================== 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 && /Applications/Xcode.app/Contents/Developer/usr/bin/make all 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 ============================================================== cd lj_12-6-4 && ./Run.12-6-4 diffing mdout.save with mdout PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd 4096wat && ./Run.column_fft diffing mdout.column_fft.save with mdout.column_fft PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd jar_multi && ./Run.jarz Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing mdout.jar.000.save with mdout.jar.000 PASSED ============================================================== diffing mdout.jar.001.save with mdout.jar.001 PASSED ============================================================== diffing dist_vs_t.000.save with dist_vs_t.000 PASSED ============================================================== diffing dist_vs_t.001.save with dist_vs_t.001 PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd ti_eth2meth_gas && ./Run.test1 DO_PARALLEL set to mpirun -np 4 number of processors for this test > 2, exiting... ============================================================ export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd ti_eth2meth_gas && ./Run.test2 DO_PARALLEL set to mpirun -np 4 number of processors for this test > 2, exiting... ============================================================ export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd ti_ggcc && ./Run.test1 Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing out_icfe1_klambda_1_clambda_0.5.p1.save with out_icfe1_klambda_1_clambda_0.5.p1 PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd ti_ggcc && ./Run.test2 Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing out_icfe1_klambda_6_clambda_0.5.p1.save with out_icfe1_klambda_6_clambda_0.5.p1 PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; /Applications/Xcode.app/Contents/Developer/usr/bin/make -k test.sander.GB cd gb_rna && ./Run.gbrna diffing mdout.gbrna.save with mdout.gbrna PASSED ============================================================== cd gb_rna && ./Run.gbrna.min diffing mdout.gbrna.min.save with mdout.gbrna.min PASSED ============================================================== cd gb_rna && ./Run.gbrna.ln diffing mdout.gbrna.ln.save with mdout.gbrna.ln PASSED ============================================================== cd gb_rna && ./Run.gbrna.ips diffing mdout.gbrna.ips.save with mdout.gbrna.ips PASSED ============================================================== cd gbsa_xfin && ./Run.gbsa diffing mdout.gbsa.save with mdout.gbsa PASSED ============================================================== cd circ_dna && ./Run.circdna diffing mdout.circdna.save with mdout.circdna PASSED ============================================================== cd gb2_trx && ./Run.trxox diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== cd gb7_trx && ./Run.trxox && ./Run.trxox prmtop_an diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== diffing mdout.trxox.save with mdout.trxox 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 ============================================================== cd gb1_cox2 && ./Run.cox2 diffing cox2.out.save with cox2.out PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd rem_gb_2rep && ./Run.rem Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing rem.log.save with rem.log PASSED ============================================================== diffing rem.out.000.save with rem.out.000 PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd rem_gb_4rep && ./Run.rem Running multisander version of sander Amber16 Total processors = 4 Number of groups = 4 diffing rem.log.save with rem.log PASSED ============================================================== diffing rem.out.000.save with rem.out.000 PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd rxsgld_4rep && ./Run.rxsgld Running multisander version of sander Amber16 Total processors = 4 Number of groups = 4 diffing rxsgld.log.save with rxsgld.log PASSED ============================================================== diffing rxsgld.crd.000.save with rxsgld.crd.000 PASSED ============================================================== diffing rxsgld.out.000.save with rxsgld.out.000 PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd rem_wat && ./Run.rem Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing rem.log.save with rem.log PASSED ============================================================== diffing rem.out.000.save with rem.out.000 PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd rem_hybrid && ./Run.rem Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing rem.log.save with rem.log PASSED ============================================================== diffing rem.out.000.save with rem.out.000 PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd h_rem && ./Run.rem Running multisander version of sander Amber16 Total processors = 4 Number of groups = 4 diffing rem.log.save with rem.log PASSED ============================================================== diffing rem.out.000.save with rem.out.000 PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd multid_remd && ./Run.multirem Running multisander version of sander Amber16 Total processors = 4 Number of groups = 4 diffing rem.log.1.save with rem.log.1 PASSED ============================================================== diffing rem.log.2.save with rem.log.2 PASSED ============================================================== diffing ala4_ash.rep1.mdout.save with ala4_ash.rep1.mdout PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd sodium && ./Run.sodium Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing md1.o.save with md1.o PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd pheMTI && ./Run.0 diffing out.0.save with out.0 PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd pheMTI && ./Run.1 diffing out.1.save with out.1 PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd pheMTI && ./Run.lambda0 Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing out.lambda0.p0.save with out.lambda0.p0 PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd pheMTI && ./Run.lambda1 Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing out.lambda1.p0.save with out.lambda1.p0 PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd campTI && ./Run.campTI Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing camp.p0.save with camp.p0 PASSED ============================================================== diffing camp.p1.save with camp.p1 PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd softcore && ./Run_sc Running the Softcore potential tests ============================================================== Minimization test DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ Protein-Ligand complex test Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing out.0.save with out.0 PASSED ============================================================== diffing out.1.save with out.1 PASSED ============================================================== diffing restrt.0.save with restrt.0 PASSED ============================================================== diffing restrt.1.save with restrt.1 PASSED ============================================================== ============================================================== Solvation free energy test Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing out.0.save with out.0 PASSED ============================================================== diffing out.1.save with out.1 PASSED ============================================================== diffing restrt.0.save with restrt.0 PASSED ============================================================== diffing restrt.1.save with restrt.1 PASSED ============================================================== Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing out2.0.save with out2.0 PASSED ============================================================== diffing out2.1.save with out2.1 PASSED ============================================================== diffing restrt2.0.save with restrt2.0 PASSED ============================================================== diffing restrt2.1.save with restrt2.1 PASSED ============================================================== ============================================================== Dynamic lambda test Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing out.0.save with out.0 PASSED ============================================================== diffing out.1.save with out.1 PASSED ============================================================== diffing restrt.0.save with restrt.0 PASSED ============================================================== diffing restrt.1.save with restrt.1 PASSED ============================================================== ============================================================== Restrained complex test Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing out.0.save with out.0 PASSED ============================================================== diffing out.1.save with out.1 PASSED ============================================================== diffing restrt.0.save with restrt.0 PASSED ============================================================== diffing restrt.1.save with restrt.1 PASSED ============================================================== ============================================================== Using softcore electrostatics Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing out.0.save with out.0 PASSED ============================================================== diffing out.1.save with out.1 PASSED ============================================================== diffing restrt.0.save with restrt.0 PASSED ============================================================== diffing restrt.1.save with restrt.1 PASSED ============================================================== ============================================================== Soft core test suite complete ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd ti_decomp; ./Run.ti_decomp Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing ti_decomp_1.out.save with ti_decomp_1.out PASSED ============================================================== diffing ti_decomp_2.out.save with ti_decomp_2.out PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd ti_decomp; ./Run.ti_decomp_sc DO_PARALLEL set to mpirun -np 4 too many processors for this test, exiting ============================================================ export TESTsanderLES=/Users/blaine-mooers/software/Amber16/bin/sander.LES.MPI; /Applications/Xcode.app/Contents/Developer/usr/bin/make -k test.sander.LES 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 1: GB/LES GB1 diffcoords diffing les.gb1.diffcrd.out.save with les.gb1.diffcrd.out PASSED ============================================================== 1: GB/LES GB1 samecoords diffing les.gb1.samecrd.out.save with les.gb1.samecrd.out PASSED ============================================================== 1: GB/LES GB5 samecoords diffing les.gb5.samecrd.out.save with les.gb5.samecrd.out PASSED ============================================================== 1: GB/LES GB7 samecoords diffing les.gb7.samecrd.out.save with les.gb7.samecrd.out PASSED ============================================================== 1: GB/LES GB7 diffcoords w/RDT diffing les.gb7.rdt.out.save with les.gb7.rdt.out PASSED ============================================================== cd neb-testcases/neb_gb_partial && ./Run.neb_gb_partial Running multisander version of sander Amber16 Total processors = 4 Number of groups = 4 diffing neb_gb_partial_01.out.save with neb_gb_partial_01.out PASSED ============================================================== diffing neb_gb_partial_02.out.save with neb_gb_partial_02.out PASSED ============================================================== diffing neb_gb_partial_03.out.save with neb_gb_partial_03.out PASSED ============================================================== diffing neb_gb_partial_04.out.save with neb_gb_partial_04.out PASSED ============================================================== cd neb-testcases/neb_gb_full && ./Run.neb_gb_full Running multisander version of sander Amber16 Total processors = 4 Number of groups = 4 diffing neb_gb_full_01.out.save with neb_gb_full_01.out PASSED ============================================================== diffing neb_gb_full_02.out.save with neb_gb_full_02.out PASSED ============================================================== diffing neb_gb_full_03.out.save with neb_gb_full_03.out PASSED ============================================================== diffing neb_gb_full_04.out.save with neb_gb_full_04.out PASSED ============================================================== cd neb-testcases/neb_explicit && ./Run.neb_explicit Running multisander version of sander Amber16 Total processors = 4 Number of groups = 4 diffing neb_explicit_01.out.save with neb_explicit_01.out PASSED ============================================================== diffing neb_explicit_02.out.save with neb_explicit_02.out PASSED ============================================================== diffing neb_explicit_03.out.save with neb_explicit_03.out PASSED ============================================================== diffing neb_explicit_04.out.save with neb_explicit_04.out PASSED ============================================================== 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' diffing save.sander/mdout with mdout PASSED ============================================================== diffing save.sander/work.txt with work.txt PASSED ============================================================== >>>>>>> doing 'bbmd' diffing save.sander/bbmd.log with bbmd.log PASSED ============================================================== sed: RE error: illegal byte sequence sed: RE error: illegal byte sequence diffing save.sander/mt19937.nc with mt19937.nc PASSED ============================================================== diffing save.sander/bbmd.1.txt with bbmd.1.txt PASSED ============================================================== diffing save.sander/mdout.1 with mdout.1 PASSED ============================================================== diffing save.sander/bbmd.2.txt with bbmd.2.txt PASSED ============================================================== diffing save.sander/mdout.2 with mdout.2 PASSED ============================================================== diffing save.sander/bbmd.3.txt with bbmd.3.txt PASSED ============================================================== diffing save.sander/mdout.3 with mdout.3 PASSED ============================================================== diffing save.sander/bbmd.4.txt with bbmd.4.txt PASSED ============================================================== diffing save.sander/mdout.4 with mdout.4 PASSED ============================================================== diffing umbrella.1.save.ncdump with umbrella.1.ncdump PASSED ============================================================== diffing umbrella.2.save.ncdump with umbrella.2.ncdump PASSED ============================================================== diffing umbrella.3.save.ncdump with umbrella.3.ncdump PASSED ============================================================== >>>>>>> doing 'abremd' diffing save/rem.log with rem.log PASSED ============================================================== diffing save/nfe-abmd.log with nfe-abmd.log PASSED ============================================================== diffing save/abmd.1.txt with abmd.1.txt PASSED ============================================================== diffing save/mdout.1 with mdout.1 PASSED ============================================================== diffing save/abmd.2.txt with abmd.2.txt PASSED ============================================================== diffing save/mdout.2 with mdout.2 PASSED ============================================================== diffing save/abmd.3.txt with abmd.3.txt PASSED ============================================================== diffing save/mdout.3 with mdout.3 PASSED ============================================================== diffing save/abmd.4.txt with abmd.4.txt PASSED ============================================================== diffing save/mdout.4 with mdout.4 PASSED ============================================================== diffing umbrella.1.save.ncdump with umbrella.1.ncdump PASSED ============================================================== diffing umbrella.2.save.ncdump with umbrella.2.ncdump PASSED ============================================================== diffing umbrella.3.save.ncdump with umbrella.3.ncdump PASSED ============================================================== diffing umbrella.4.save.ncdump with umbrella.4.ncdump PASSED ============================================================== >>>>>>> doing 'mwabmd' This test case (/Users/blaine-mooers/software/Amber16/test/nfe/mwabmd) requires 8 mpi threads. Not running test, exiting ..... >>>>>>> doing 'premd' diffing save/rem.log with rem.log PASSED ============================================================== diffing save/nfe-pmd.log with nfe-pmd.log PASSED ============================================================== diffing save/pmd.1.txt with pmd.1.txt PASSED ============================================================== diffing save/mdout.1 with mdout.1 PASSED ============================================================== diffing save/pmd.2.txt with pmd.2.txt PASSED ============================================================== diffing save/mdout.2 with mdout.2 PASSED ============================================================== diffing save/pmd.3.txt with pmd.3.txt PASSED ============================================================== diffing save/mdout.3 with mdout.3 PASSED ============================================================== diffing save/pmd.4.txt with pmd.4.txt PASSED ============================================================== diffing save/mdout.4 with mdout.4 PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; /Applications/Xcode.app/Contents/Developer/usr/bin/make -k test.sander.CHARMM 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 ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.LES.MPI; /Applications/Xcode.app/Contents/Developer/usr/bin/make -k test.sander.PIMD.partial 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_cmd_water/equilib && ./Run.cmdyn diffing h2o_les.top.save with h2o_les.top PASSED ============================================================== diffing h2o_les.crd.save with h2o_les.crd PASSED ============================================================== diffing cmd.out.save with cmd.out PASSED ============================================================== cd PIMD/part_cmd_water/start && ./Run.cmdyn diffing cmd.out.save with cmd.out PASSED ============================================================== cd PIMD/part_cmd_water/restart && ./Run.cmdyn diffing cmd.out.save with cmd.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 cd PIMD/full_cmd_water/equilib && ./Run.full_cmd Testing Centroid MD diffing cmd.out.save with cmd.out PASSED ============================================================== diffing cmd_bead1.out.save with cmd_bead1.out PASSED ============================================================== diffing cmd_bead2.out.save with cmd_bead2.out PASSED ============================================================== diffing cmd_bead3.out.save with cmd_bead3.out PASSED ============================================================== diffing cmd_bead4.out.save with cmd_bead4.out PASSED ============================================================== cd PIMD/full_cmd_water/start && ./Run.full_cmd Testing Centroid MD diffing cmd.out.save with cmd.out PASSED ============================================================== diffing cmd_bead1.out.save with cmd_bead1.out PASSED ============================================================== diffing cmd_bead2.out.save with cmd_bead2.out PASSED ============================================================== diffing cmd_bead3.out.save with cmd_bead3.out PASSED ============================================================== diffing cmd_bead4.out.save with cmd_bead4.out PASSED ============================================================== cd PIMD/full_cmd_water/restart && ./Run.full_cmd Testing Centroid MD diffing cmd.out.save with cmd.out PASSED ============================================================== diffing cmd_bead1.out.save with cmd_bead1.out PASSED ============================================================== diffing cmd_bead2.out.save with cmd_bead2.out PASSED ============================================================== diffing cmd_bead3.out.save with cmd_bead3.out PASSED ============================================================== diffing cmd_bead4.out.save with cmd_bead4.out PASSED ============================================================== cd PIMD/full_nmpimd_water && ./Run.full_pimd Testing Normal Mode PIMD diffing nmpimd.out.save with nmpimd.out PASSED ============================================================== cd PIMD/full_pimd_amoeba && ./Run.full_pimd_amoeba Testing PIMD with amoeba force field diffing pimd_amoeba.out.save with pimd_amoeba.out PASSED ============================================================== cd PIMD/full_pimd_ln_water && ./Run.full_pimd_ln Testing PIMD with langevin dynamics diffing pimd_ln.out.save with pimd_ln.out PASSED ============================================================== cd PIMD/full_pimd_nhc_water && ./Run.full_pimd_nhc Testing PIMD with Nose-Hoover-Chain thermostat diffing pimd_nhc.out.save with pimd_nhc.out PASSED ============================================================== cd PIMD/full_pimd_ntp_water && ./Run.full_pimd_ntp Testing constant pressure PIMD diffing pimd_ntp.out.save with pimd_ntp.out PASSED ============================================================== diffing NHC.dat.save with NHC.dat PASSED ============================================================== cd PIMD/full_rpmd_water && ./Run.full_rpmd Testing RPMD diffing rpmd.out.save with rpmd.out PASSED ============================================================== cd ti_mass/pentadiene && ./Run.pentadiene DO_PARALLEL set to mpirun -np 4 This test can be run only with two processes, exiting... export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd cnstph/implicit && ./Run.cnstph diffing mdout.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd cnstph_remd/TempRem && ./Run.cnstph_remd Running multisander version of sander Amber16 Total processors = 4 Number of groups = 2 diffing ph4.cpout.000.save with ph4.cpout.000 PASSED ============================================================== diffing ph4.out.000.save with ph4.out.000 PASSED ============================================================== diffing rem.log.save with rem.log PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd cnstph_remd/pHREM && ./Run.pHremd Running multisander version of sander Amber16 Total processors = 4 Number of groups = 4 diffing mdout.pH2.save with mdout.pH2 PASSED ============================================================== diffing cpout.pH2.5.save with cpout.pH2.5 PASSED ============================================================== diffing rem.log.save with rem.log PASSED ============================================================== export TESTsander=/Users/blaine-mooers/software/Amber16/bin/sander.MPI; cd cnstph_remd/Explicit_pHREM && ./Run.pHremd Running multisander version of sander Amber16 Total processors = 4 Number of groups = 4 diffing 1AKI.solv10.md1.mdout.0.save with 1AKI.solv10.md1.mdout.0 PASSED ============================================================== diffing cpout.001.save with cpout.001 PASSED ============================================================== diffing rem.log.save with rem.log PASSED ============================================================== export TESTsander='/Users/blaine-mooers/software/Amber16/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala SANDER: 3D-RISM /Users/blaine-mooers/software/Amber16/bin/sander.MPI compiled without RISM support. export TESTsander='/Users/blaine-mooers/software/Amber16/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.min SANDER: 3D-RISM /Users/blaine-mooers/software/Amber16/bin/sander.MPI compiled without RISM support. export TESTsander='/Users/blaine-mooers/software/Amber16/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.imin5 SANDER: 3D-RISM /Users/blaine-mooers/software/Amber16/bin/sander.MPI compiled without RISM support. export TESTsander='/Users/blaine-mooers/software/Amber16/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.mdiis0 SANDER: 3D-RISM /Users/blaine-mooers/software/Amber16/bin/sander.MPI compiled without RISM support. export TESTsander='/Users/blaine-mooers/software/Amber16/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.mdiis1 SANDER: 3D-RISM /Users/blaine-mooers/software/Amber16/bin/sander.MPI compiled without RISM support. export TESTsander='/Users/blaine-mooers/software/Amber16/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.resize SANDER: 3D-RISM w/ Force Extrapolation & dynamic solvation box /Users/blaine-mooers/software/Amber16/bin/sander.MPI compiled without RISM support. export TESTsander='/Users/blaine-mooers/software/Amber16/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.dist SANDER: 3D-RISM: KH distributions /Users/blaine-mooers/software/Amber16/bin/sander.MPI compiled without RISM support. export TESTsander='/Users/blaine-mooers/software/Amber16/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.dist.xyzv SANDER: 3D-RISM /Users/blaine-mooers/software/Amber16/bin/sander.MPI compiled without RISM support. export TESTsander='/Users/blaine-mooers/software/Amber16/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.hnc SANDER: 3D-RISM /Users/blaine-mooers/software/Amber16/bin/sander.MPI compiled without RISM support. export TESTsander='/Users/blaine-mooers/software/Amber16/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.pse1 SANDER: 3D-RISM /Users/blaine-mooers/software/Amber16/bin/sander.MPI compiled without RISM support. export TESTsander='/Users/blaine-mooers/software/Amber16/bin/sander.MPI' && cd crg_reloc/water && ./Run.water.min diffing min.out.save with min.out PASSED ============================================================== export TESTsander='/Users/blaine-mooers/software/Amber16/bin/sander.MPI' && cd crg_reloc/water && ./Run.water.md diffing md.out.save with md.out PASSED ============================================================== export TESTsander='../../../bin/sander.MPI'; cd amd && /Applications/Xcode.app/Contents/Developer/usr/bin/make -k test Testing AMD with PME diffing mdout.pme.amd1.save with mdout.pme.amd1 PASSED ============================================================== diffing mdout.pme.amd2.save with mdout.pme.amd2 PASSED ============================================================== diffing mdout.pme.amd3.save with mdout.pme.amd3 PASSED ============================================================== Testing AMD with IPS -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- Finished test suite for AmberTools at Wed Apr 19 16:38:07 CDT 2017. 731 file comparisons passed 0 file comparisons failed 1 tests experienced errors Test log file saved as /Users/blaine-mooers/software/Amber16/logs/test_at_parallel/2017-04-19_10-36-17.log No test diffs to save!