make[2]: Entering directory `/home/amber16/test' export TESTsander='../../bin/pmemd.MPI'; cd nonper && ./Run.egb6 diffing mdout.egb6.save with mdout.egb6 PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd 4096wat && ./Run.pure_wat diffing mdout.pure_wat.save with mdout.pure_wat PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd 4096wat && ./Run.pure_wat_fswitch diffing mdout.pure_wat_fswitch.save with mdout.pure_wat_fswitch PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd 4096wat && ./Run.pure_wat_efield diffing mdout.pure_wat_efield.save with mdout.pure_wat_efield PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd 4096wat && ./Run.pure_wat_nmr_temp_reg diffing mdout.pure_wat_nmr_temp.save with mdout.pure_wat_nmr_temp PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd 4096wat && ./Run.vrand diffing mdout.vrand.save with mdout.vrand PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd 4096wat && ./Run.frcdmp export TESTsander='../../bin/pmemd.MPI'; 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 ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd alp && ./Run.alp diffing mdout.alp.save with mdout.alp PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd cytosine && ./Run.cytosine diffing cytosine.out.save with cytosine.out PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd dhfr && ./Run.dhfr diffing mdout.dhfr.save with mdout.dhfr PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd dhfr && ./Run.dhfr.min diffing mdout.dhfr.min.save with mdout.dhfr.min PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd dhfr && ./Run.dhfr.noshake diffing mdout.dhfr.noshake.save with mdout.dhfr.noshake PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd ff14ipq && ./Run.ff14ipq diffing mdout.ff14ipq.save with mdout.ff14ipq PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd variable_14 && ./Run.variable_14_ntb1 diffing variable_14_ntb1.mdout.save with variable_14_ntb1.mdout PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd trx && ./Run.trx diffing mdout.trx.save with mdout.trx PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd trx && ./Run.trx.cpln.pmemd diffing mdout.trx.cpln.pmemd.save with mdout.trx.cpln.pmemd PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gb_rna && ./Run.gbrna diffing mdout.gbrna.save with mdout.gbrna PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gb_rna && ./Run.gbrna.min diffing mdout.gbrna.min.save with mdout.gbrna.min PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gb_rna && ./Run.gbrna.ln diffing mdout.gbrna.ln.save with mdout.gbrna.ln PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd circ_dna && ./Run.circdna diffing mdout.circdna.save with mdout.circdna PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gb2_trx && ./Run.trxox.nogbsa diffing mdout.trxox.nogbsa.save with mdout.trxox.nogbsa PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gb7_trx && ./Run.trxox_md diffing mdout.trxox_md.save with mdout.trxox_md PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gb8_trx && ./Run.trxox diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; 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 ============================================================== export TESTsander='../../../bin/pmemd.MPI'; cd gbneck2nu/1hji && ./Run.1hji_md diffing mdout.1hji_md.save with mdout.1hji_md PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd alpb_trx && ./Run.trxox.nogbsa diffing mdout.trxox.nogbsa.save with mdout.trxox.nogbsa PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gb1_cox2 && ./Run.cox2 diffing cox2.out.save with cox2.out PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gbsa_xfin && ./Run.gbsa diffing mdout.gbsa.save with mdout.gbsa PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd tip4p && ./Run.tip4p diffing mdout.tip4p.save with mdout.tip4p PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd tip4p && ./Run.tip4p_mcbar diffing mdout.mcbar.tip4p.save with mdout.mcbar.tip4p PASSED ============================================================== diffing mdout.mcbar_aniso.tip4p.save with mdout.mcbar_aniso.tip4p PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd tip4p && ./Run.tip4p_nve diffing mdout.tip4p_nve.save with mdout.tip4p_nve PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd tip5p && ./Run.tip5p diffing mdout.tip5p.save with mdout.tip5p PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd tip5p && ./Run.tip5p_nve diffing mdout.tip5p_nve.save with mdout.tip5p_nve PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI'; cd cnstph/implicit && ./Run.cnstph diffing mdout.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI'; cd cnstph/explicit && ./Run.cnstph diffing mdout.pmemd.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== export TESTsander='../../../../bin/pmemd.MPI'; cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.min diffing mdout.dhfr_charmm.min.save with mdout.dhfr_charmm.min PASSED ============================================================== export TESTsander='../../../../bin/pmemd.MPI'; cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.md diffing mdout.dhfr_charmm.save with mdout.dhfr_charmm PASSED ============================================================== export TESTsander='../../../../bin/pmemd.MPI'; cd chamber/md_engine/dhfr_cmap && ./Run.dhfr_charmm.md diffing mdout.dhfr_charmm.save with mdout.dhfr_charmm PASSED ============================================================== export TESTsander='../../../../bin/pmemd.MPI'; 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 ============================================================== export TESTsander='../../../../bin/pmemd.MPI'; 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 ============================================================== export TESTsander='../../../../bin/pmemd.MPI'; 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 ============================================================== export TESTsander='../../../../bin/pmemd.MPI'; 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='../../../bin/pmemd.MPI'; cd amd && make -k test OPT=pmemd make[3]: Entering directory `/home/amber16/test/amd' Testing AMD with PME diffing pmemd.pme.amd1.save with pmemd.pme.amd1 PASSED ============================================================== diffing pmemd.pme.amd2.save with pmemd.pme.amd2 PASSED ============================================================== diffing pmemd.pme.amd3.save with pmemd.pme.amd3 PASSED ============================================================== Testing AMD with IPS diffing pmemd.ips.amd1.save with pmemd.ips.amd1 PASSED ============================================================== diffing pmemd.ips.amd2.save with pmemd.ips.amd2 PASSED ============================================================== diffing pmemd.ips.amd3.save with pmemd.ips.amd3 PASSED ============================================================== Testing AMD with GB diffing pmemd.gb.amd1.save with pmemd.gb.amd1 PASSED ============================================================== diffing pmemd.gb.amd2.save with pmemd.gb.amd2 PASSED ============================================================== diffing pmemd.gb.amd3.save with pmemd.gb.amd3 PASSED ============================================================== make[3]: Leaving directory `/home/amber16/test/amd' export TESTsander='../../bin/pmemd.MPI'; cd scaledMD && make -k test OPT=pmemd make[3]: Entering directory `/home/amber16/test/scaledMD' Testing scaledMD with PME diffing mdout.save with mdout PASSED ============================================================== make[3]: Leaving directory `/home/amber16/test/scaledMD' export TESTsander='../../bin/pmemd.MPI'; cd gact_ips && ./Run.ips diffing mdout.ips.save with mdout.ips PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd csurften && ./Run.csurften_z-dir diffing mdout.csurften_z-dir.save with mdout.csurften_z-dir PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd lj_12-6-4 && ./Run.12-6-4 diffing mdout.save with mdout PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd csurften && ./Run.csurften_z-dir_npt_3 diffing mdout.csurften_z-dir_npt_3.save with mdout.csurften_z-dir_npt_3 PASSED ============================================================== export TESTsander='../../../../bin/pmemd.MPI'; cd nmropt && make pmemd_compat make[3]: Entering directory `/home/amber16/test/nmropt' cd gb/angle && ./Run.nmropt_1angle_gb diffing mdout.save with mdout PASSED ============================================================== diffing angle_gb_vs_t.save with angle_gb_vs_t PASSED ============================================================== cd gb/distance && ./Run.dist_gb diffing mdout.save with mdout PASSED ============================================================== diffing dist_gb_vs_t.save with dist_gb_vs_t PASSED ============================================================== cd gb/distance_COM && ./Run.distCOM_gb diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_gb_vs_t.save with distCOM_gb_vs_t PASSED ============================================================== cd gb/jar_distance && ./Run.jar_gb diffing mdout.save with mdout PASSED ============================================================== diffing dist_gb_vs_t.save with dist_gb_vs_t PASSED ============================================================== cd gb/jar_distance_COM && ./Run.jar_gb diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_gb_vs_t.save with distCOM_gb_vs_t PASSED ============================================================== cd gb/jar_torsion && ./Run.jar_torsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_gb.dat.save with jartorsion_gb.dat PASSED ============================================================== cd gb/nmropt_1_torsion && ./Run.nmropt_1_torsion diffing mdout.save with mdout PASSED ============================================================== diffing torsion_gb.dat.save with torsion_gb.dat PASSED ============================================================== cd gb/tautp && ./Run.nmropt_1tautp_gb diffing mdout.save with mdout PASSED ============================================================== cd gb/temp && ./Run.nmropt_1temp_gb diffing mdout.save with mdout PASSED ============================================================== cd pme/angle && ./Run.nmropt_1angle_pbc diffing mdout.save with mdout PASSED ============================================================== diffing angle_pbc_vs_t.save with angle_pbc_vs_t PASSED ============================================================== cd pme/distance && ./Run.dist_pbc diffing mdout.save with mdout PASSED ============================================================== diffing dist_pbc_vs_t.save with dist_pbc_vs_t PASSED ============================================================== cd pme/distance_COM && ./Run.distCOM_pbc diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_pbc_vs_t.save with distCOM_pbc_vs_t PASSED ============================================================== cd pme/jar_torsion && ./Run.jar_torsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_pbc.dat.save with jartorsion_pbc.dat PASSED ============================================================== cd pme/jar_distance && ./Run.jar_pbc diffing mdout.save with mdout PASSED ============================================================== diffing dist_pbc_vs_t.save with dist_pbc_vs_t PASSED ============================================================== cd pme/jar_distance_COM && ./Run.jar_pbc diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_pbc_vs_t.save with distCOM_pbc_vs_t PASSED ============================================================== cd pme/nmropt_1_torsion && ./Run.nmropt_1_torsion diffing mdout.save with mdout PASSED ============================================================== diffing torsion_pbc.dat.save with torsion_pbc.dat PASSED ============================================================== cd pme/tautp && ./Run.nmropt_1tautp_pbc diffing mdout.save with mdout PASSED ============================================================== cd pme/temp && ./Run.nmropt_1temp_pbc diffing mdout.save with mdout PASSED ============================================================== make[3]: Leaving directory `/home/amber16/test/nmropt' export TESTsander='../../bin/pmemd.MPI'; cd rdc && ./Run.nmr diffing gcg.nmr.o.save with gcg.nmr.o PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI'; cd netcdf && make -k test OPT=/home/amber16/include/netcdf.mod make[3]: Entering directory `/home/amber16/test/netcdf' Netcdf MD Restart Write Test diffing textmd.rst7.save with textmd.rst7 PASSED ============================================================== Netcdf Minimization Restart Write Test diffing textmin.rst7.save with textmin.rst7 PASSED ============================================================== Restrained MD with netcdf Restart Reference Coords Test diffing md.rst7.save with md.rst7 PASSED ============================================================== diffing ene.dat.save with ene.dat PASSED ============================================================== Netcdf MD restart read test, ntx=5 diffing md1.rst7 with md2.rst7 PASSED ============================================================== diffing ene1 with ene2 PASSED ============================================================== diffing md.crd.save with md.crd PASSED ============================================================== Netcdf MD restart read test, ntx=1 diffing md1.rst7 with md2.rst7 PASSED ============================================================== diffing ene1 with ene2 PASSED ============================================================== diffing md.crd.save with md.crd PASSED ============================================================== make[3]: Leaving directory `/home/amber16/test/netcdf' export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/campTI && ./Run.campTI diffing campTI.out.save with campTI.out PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/pheMTI && ./Run.0 diffing out.0.save with out.0 PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/pheMTI && ./Run.1 diffing out.1.save with out.1 PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/pheMTI && ./Run.lambda0 diffing pheMTI0.out.save with pheMTI0.out PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/pheMTI && ./Run.lambda1 diffing pheMTI1.out.save with pheMTI1.out PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/sodium && ./Run.sodium diffing md1.o.save with md1.o PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/ti_ggcc && ./Run.test1 diffing out_icfe1_klambda_1_clambda_0.5.p1.save with out_icfe1_klambda_1_clambda_0.5.p1 PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/ti_ggcc && ./Run.test2 diffing out_icfe1_klambda_6_clambda_0.5.p1.save with out_icfe1_klambda_6_clambda_0.5.p1 PASSED ============================================================== export TESTsander='../../../../bin/pmemd.MPI'; cd pmemdTI/softcore && ./Run_sc Running the Softcore potential tests ============================================================== Minimization test diffing out.0.save with out.0 PASSED ============================================================== diffing restrt.0.save with restrt.0 PASSED ============================================================== Protein-Ligand complex test diffing out.save with out PASSED ============================================================== diffing restrt.save with restrt PASSED ============================================================== ============================================================== Solvation free energy test diffing out.0.save with out.0 PASSED ============================================================== diffing restrt.0.save with restrt.0 PASSED ============================================================== diffing out2.0.save with out2.0 PASSED ============================================================== diffing restrt2.0.save with restrt2.0 PASSED ============================================================== ============================================================== Dynamic lambda test diffing out.0.save with out.0 PASSED ============================================================== diffing restrt.0.save with restrt.0 PASSED ============================================================== ============================================================== Restrained complex test diffing out.0.save with out.0 PASSED ============================================================== diffing restrt.0.save with restrt.0 PASSED ============================================================== ============================================================== Using softcore electrostatics diffing out.0.save with out.0 PASSED ============================================================== diffing restrt.0.save with restrt.0 PASSED ============================================================== ============================================================== Soft core test suite complete ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gact_ips && ./Run.ips_sgld diffing mdout.ips_sgld.save with mdout.ips_sgld PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gact_ips && ./Run.ips_sgldfp diffing mdout.ips_sgldfp.save with mdout.ips_sgldfp PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gact_ips && ./Run.ips_sgldg diffing mdout.ips_sgldg.save with mdout.ips_sgldg PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gact_ips && ./Run.ips_sgmdg diffing mdout.ips_sgmdg.save with mdout.ips_sgmdg PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gb_rna && ./Run.gbrna.sgld diffing mdout.gbrna.sgld.save with mdout.gbrna.sgld PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gb_rna && ./Run.gbrna.sgldfp diffing mdout.gbrna.sgldfp.save with mdout.gbrna.sgldfp PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gb_rna && ./Run.gbrna.sgldg diffing mdout.gbrna.sgldg.save with mdout.gbrna.sgldg PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd gb_rna && ./Run.gbrna.sgmdg diffing mdout.gbrna.sgmdg.save with mdout.gbrna.sgmdg PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI'; cd emap/ && ./Run.emap diffing mdout.emap.save with mdout.emap PASSED ============================================================== cd nfe && ./run-pmemd-parallel.sh /bin/sh: ./run-pmemd-parallel.sh: Permission denied make[2]: [test.parallel.pmemd.nfe] Error 126 (ignored) export TESTsander='../../../bin/pmemd.MPI'; cd emil/emil_pmemd_gbsa && ./Run.emil EMIL DO_PARALLEL is set: mpirun -np 2 diffing mdout.emil.0.0.save with mdout.emil.0.0 PASSED ============================================================== diffing emil.log.0.0.save with emil.log.0.0 PASSED ============================================================== diffing mdout.emil.0.1.save with mdout.emil.0.1 PASSED ============================================================== diffing emil.log.0.1.save with emil.log.0.1 PASSED ============================================================== diffing mdout.emil.0.9.save with mdout.emil.0.9 PASSED ============================================================== diffing emil.log.0.9.save with emil.log.0.9 PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI'; cd emil/emil_pmemd_tip3p && ./Run.emil EMIL DO_PARALLEL is set: mpirun -np 2 diffing mdout.emil.0.1.save with mdout.emil.0.1 PASSED ============================================================== diffing emil.log.0.1.save with emil.log.0.1 PASSED ============================================================== diffing mdout.emil.0.5.save with mdout.emil.0.5 PASSED ============================================================== diffing emil.log.0.5.save with emil.log.0.5 PASSED ============================================================== diffing mdout.emil.0.9.save with mdout.emil.0.9 PASSED ============================================================== diffing emil.log.0.9.save with emil.log.0.9 PASSED ============================================================== export TESTsander='../../bin/pmemd.MPI' && cd rem_gb_2rep && ./Run.rem REM with pmemd.MPI requires 4 or 8 processors! Only using 2 export TESTsander='../../bin/pmemd.MPI' && cd rem_wat && ./Run.rem REM with pmemd.MPI or pmemd.mic_offload.MPI requires a multiple of 2 processors, but at least 4! Only using 2 export TESTsander='../../bin/pmemd.MPI' && cd rem_gb_4rep && ./Run.rem This test case requires 8, 12, or 16 MPI threads! export TESTsander='../../bin/pmemd.MPI' && cd h_rem && ./Run.rem This test case requires 8, 12, or 16 MPI threads! export TESTsander='../../bin/pmemd.MPI' && cd multid_remd && ./Run.multirem This test case requires 8 or 16 MPI threads! export TESTsander='../../bin/pmemd.MPI'; cd rxsgld_4rep && ./Run.rxsgld This test case requires 8, 12, or 16 MPI threads! export TESTsander='../../../bin/pmemd.MPI'; cd cnstph_remd/pHREM && ./Run.pHremd This test requires 4, 8, or 12 processors! export TESTsander='../../../bin/pmemd.MPI'; cd cnstph_remd/TempRem && ./Run.cnstph_remd Constant pH REMD test needs 4 processors to run (you selected 2) export TESTsander='../../../bin/pmemd.MPI'; cd cnstph_remd/Explicit_pHREM && ./Run.pHremd This test requires a multiple of 4 processors! Only detected 2 -- skipping test Finished parallel test suite for Amber 16 at Sat Jan 28 01:33:58 EST 2017. Some tests require 4 threads to run, while some will not run with more than 2. Please run further parallel tests with the appropriate number of processors. See /home/amber16/test/README. make[2]: Leaving directory `/home/amber16/test' 147 file comparisons passed 0 file comparisons failed 0 tests experienced an error Test log file saved as /home/amber16/logs/test_amber_parallel/2017-01-28_01-27-03.log No test diffs to save!