make[2]: Entering directory '/home/samanta/build/amber20/test' export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd nonper && ./Run.egb6 diffing mdout.egb6.save with mdout.egb6 PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd 4096wat && ./Run.pure_wat diffing mdout.pure_wat.save with mdout.pure_wat PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd 4096wat && ./Run.pure_wat_nmr_temp_reg diffing mdout.pure_wat_nmr_temp.save with mdout.pure_wat_nmr_temp PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd 4096wat && ./Run.vrand diffing mdout.vrand.save with mdout.vrand PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd 4096wat && ./Run.frcdmp export TESTsander='/home/samanta/build/amber20///bin/pmemd'; 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='/home/samanta/build/amber20///bin/pmemd'; cd 4096wat && ./Run.pure_wat_fswitch diffing mdout.pure_wat_fswitch.save with mdout.pure_wat_fswitch PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd 4096wat && ./Run.pure_wat_efield diffing mdout.pure_wat_efield.save with mdout.pure_wat_efield PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd alp && ./Run.alp diffing mdout.alp.save with mdout.alp PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd cytosine && ./Run.cytosine diffing cytosine.out.save with cytosine.out PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd dhfr && ./Run.dhfr diffing mdout.dhfr.save with mdout.dhfr PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd dhfr && ./Run.dhfr.min diffing mdout.dhfr.min.save with mdout.dhfr.min PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd dhfr && ./Run.dhfr.noshake diffing mdout.dhfr.noshake.save with mdout.dhfr.noshake PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd dhfr && ./Run.dhfr.bussi STOP PMEMD Terminated Abnormally! diffing mdout.dhfr.bussi.save with mdout.dhfr.bussi possible FAILURE: (ignored) check mdout.dhfr.bussi.dif ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd dhfr && ./Run.dhfr_reweight At line 717 of file /home/samanta/build/amber20_src/src/pmemd/src/mdin_ctrl_dat.F90 (unit = 5, file = 'gbin') Fortran runtime error: Cannot match namelist object name reweight Error termination. Backtrace: #0 0x7f045ce9ad0a #1 0x7f045ce9b819 #2 0x7f045ce9c4ef #3 0x7f045d0d752d #4 0x7f045d0e09a7 #5 0x7f045d0e0bcc #6 0x7f045d0e0d27 #7 0x55c8beec7c8b #8 0x55c8befafbab #9 0x55c8bef96670 #10 0x55c8beeb778e #11 0x7f045cc930b2 #12 0x55c8beeb77cd #13 0xffffffffffffffff ./Run.dhfr_reweight: Program error make[2]: [Makefile:1082: test.serial.pmemd.basic] Error 1 (ignored) export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd ff14ipq && ./Run.ff14ipq diffing mdout.ff14ipq.save with mdout.ff14ipq PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd variable_14 && ./Run.variable_14_ntb1 diffing variable_14_ntb1.mdout.save with variable_14_ntb1.mdout PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd variable_14 && ./Run.variable_14_igb1 diffing variable_14_igb1.mdout.save with variable_14_igb1.mdout PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd trx && ./Run.trx diffing mdout.trx.save with mdout.trx PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd trx && ./Run.trx.cpln.pmemd diffing mdout.trx.cpln.pmemd.save with mdout.trx.cpln.pmemd PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gb_rna && ./Run.gbrna diffing mdout.gbrna.save with mdout.gbrna PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gb_rna && ./Run.gbrna.min diffing mdout.gbrna.min.save with mdout.gbrna.min PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gb_rna && ./Run.gbrna.ln diffing mdout.gbrna.ln.save with mdout.gbrna.ln PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd circ_dna && ./Run.circdna diffing mdout.circdna.save with mdout.circdna PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gb2_trx && ./Run.trxox.nogbsa && ./Run.trxox.nogbsa prmtop_an diffing mdout.trxox.nogbsa.save with mdout.trxox.nogbsa PASSED ============================================================== diffing mdout.trxox.nogbsa.save with mdout.trxox.nogbsa PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gb7_trx && ./Run.trxox_md diffing mdout.trxox_md.save with mdout.trxox_md PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gb8_trx && ./Run.trxox diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; 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='/home/samanta/build/amber20///bin/pmemd'; cd mcwat && ./Run.mcwat diffing mdout.mcwat.save with mdout.mcwat possible FAILURE: check mdout.mcwat.dif ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd RAMD && ./Run.ramd At line 717 of file /home/samanta/build/amber20_src/src/pmemd/src/mdin_ctrl_dat.F90 (unit = 5, file = 'gbin') Fortran runtime error: Cannot match namelist object name ramdboost Error termination. Backtrace: #0 0x7fb299c3fd0a #1 0x7fb299c40819 #2 0x7fb299c414ef #3 0x7fb299e7c52d #4 0x7fb299e859a7 #5 0x7fb299e85bcc #6 0x7fb299e85d27 #7 0x5645f4132c8b #8 0x5645f421abab #9 0x5645f4201670 #10 0x5645f412278e #11 0x7fb299a380b2 #12 0x5645f41227cd #13 0xffffffffffffffff ./Run.ramd: Program error make[2]: [Makefile:1097: test.serial.pmemd.basic] Error 1 (ignored) export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd ff19SB && ./Run.pmemd diffing mdout.save.pmemd with mdout file ddtmp.mdout is short possible FAILURE: check mdout.dif ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gbneck2nu/1hji && ./Run.1hji_md diffing mdout.1hji_md.save with mdout.1hji_md PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gbneck2nu/modified_nu/3p4a/ && ./Run.3p4a diffing mdout.3p4a.save with mdout.3p4a PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd alpb_trx && ./Run.trxox.nogbsa diffing mdout.trxox.nogbsa.save with mdout.trxox.nogbsa PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gbsa_xfin && ./Run.gbsa1 diffing mdout.gbsa1.save with mdout.gbsa1 PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gbsa_xfin && ./Run.gbsa3 STOP PMEMD Terminated Abnormally! diffing mdout.gbsa3.save with mdout.gbsa3 possible FAILURE: (ignored) check mdout.gbsa3.dif ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd tip4p && ./Run.tip4p diffing mdout.tip4p.save with mdout.tip4p PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; 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='/home/samanta/build/amber20///bin/pmemd'; cd tip4p && ./Run.tip4p_nve diffing mdout.tip4p_nve.save with mdout.tip4p_nve PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd tip5p && ./Run.tip5p diffing mdout.tip5p.save with mdout.tip5p PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd tip5p && ./Run.tip5p_nve diffing mdout.tip5p_nve.save with mdout.tip5p_nve PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd cnstph/implicit && ./Run.cnstph diffing mdout.save with mdout possible FAILURE: check mdout.dif ============================================================== diffing cpout.save with cpout PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd cnstph/explicit && ./Run.cnstph diffing mdout.pmemd.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd phmd/implicit && ./Run.phmd Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL diffing mdout.save with mdout possible FAILURE: (ignored) check mdout.dif ============================================================== diffing phmdout.save with phmdout possible FAILURE: (ignored) check phmdout.dif ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd cnste/implicit && ./Run.cnste diffing mdout.pmemd.save with mdout possible FAILURE: check mdout.dif ============================================================== diffing ceout.save with ceout PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd cnste/explicit && ./Run.cnste diffing mdout.pmemd.save with mdout PASSED ============================================================== diffing ceout.save with ceout PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd cnstphe/implicit && ./Run.cnstphe diffing mdout.pmemd.save with mdout possible FAILURE: check mdout.dif ============================================================== diffing cpout.save with cpout PASSED ============================================================== diffing ceout.save with ceout PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd cnstphe/explicit && ./Run.cnstphe diffing mdout.pmemd.save with mdout PASSED ============================================================== diffing cpout.pmemd.save with cpout PASSED ============================================================== diffing ceout.pmemd.save with ceout PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd cnstphe_merged/implicit && ./Run.cnstphe unknown flag: -cpein usage: pmemd [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt [-ref refc -x mdcrd -v mdvel -frc mdfrc -e mden -inf mdinfo -l logfile] [-amd amdlog_name -gamd gamdlog_name -scaledMD scaledMDlog_name -suffix output_files_suffix] STOP PMEMD Terminated Abnormally! possible FAILURE: file mdout does not exist. ============================================================== possible FAILURE: file cpeout does not exist. ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd cnstphe_merged/explicit && ./Run.cnstphe unknown flag: -cpein usage: pmemd [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt [-ref refc -x mdcrd -v mdvel -frc mdfrc -e mden -inf mdinfo -l logfile] [-amd amdlog_name -gamd gamdlog_name -scaledMD scaledMDlog_name -suffix output_files_suffix] STOP PMEMD Terminated Abnormally! possible FAILURE: file mdout does not exist. ============================================================== possible FAILURE: file cpeout does not exist. ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.min diffing mdout.dhfr_charmm.min.save with mdout.dhfr_charmm.min PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.md diffing mdout.dhfr_charmm.save with mdout.dhfr_charmm PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd chamber/md_engine/dhfr_cmap && ./Run.dhfr_charmm.md diffing mdout.dhfr_charmm.save with mdout.dhfr_charmm PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; 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='/home/samanta/build/amber20///bin/pmemd'; 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='/home/samanta/build/amber20///bin/pmemd'; 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='/home/samanta/build/amber20///bin/pmemd'; 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='/home/samanta/build/amber20///bin/pmemd'; cd gact_ips && ./Run.ips Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL diffing mdout.ips.save with mdout.ips PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd csurften && ./Run.csurften_z-dir diffing mdout.csurften_z-dir.save with mdout.csurften_z-dir PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd lj_12-6-4 && ./Run.12-6-4 diffing mdout.save with mdout PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; 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='/home/samanta/build/amber20///bin/pmemd'; cd nmropt && make pmemd_compat make[3]: Entering directory '/home/samanta/build/amber20/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 gb/angle_torsion_com/ && ./Run.angdihCOM_gb STOP PMEMD Terminated Abnormally! diffing mdout.save with mdout file ddtmp.mdout is short possible FAILURE: check mdout.dif ============================================================== possible FAILURE: file angtorCOM_gb does not exist. ============================================================== 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 ./Run.nmropt_1tautp_pbc: 42: [: pmemd: unexpected operator diffing mdout.save with mdout PASSED ============================================================== cd pme/temp && ./Run.nmropt_1temp_pbc diffing mdout.save with mdout PASSED ============================================================== cd pme/angle_torsion_com/ && ./Run.angdihCOM STOP PMEMD Terminated Abnormally! diffing mdout.save with mdout file ddtmp.mdout is short possible FAILURE: check mdout.dif ============================================================== possible FAILURE: file angtorCOM does not exist. ============================================================== make[3]: Leaving directory '/home/samanta/build/amber20/test/nmropt' export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd rdc && ./Run.nmr diffing gcg.nmr.o.save with gcg.nmr.o PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd netcdf && make -k test OPT=yes make[3]: Entering directory '/home/samanta/build/amber20/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/samanta/build/amber20/test/netcdf' export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd baroscalingdir && ./Run.baroscalingdir_z-dir At line 717 of file /home/samanta/build/amber20_src/src/pmemd/src/mdin_ctrl_dat.F90 (unit = 5, file = 'mdin') Fortran runtime error: Cannot match namelist object name baroscalingdir Error termination. Backtrace: #0 0x7f7a37bf3d0a #1 0x7f7a37bf4819 #2 0x7f7a37bf54ef #3 0x7f7a37e3052d #4 0x7f7a37e399a7 #5 0x7f7a37e39bcc #6 0x7f7a37e39d27 #7 0x561eea2e5c8b #8 0x561eea3cdbab #9 0x561eea3b4670 #10 0x561eea2d578e #11 0x7f7a379ec0b2 #12 0x561eea2d57cd #13 0xffffffffffffffff ./Run.baroscalingdir_z-dir: Program error make[2]: [Makefile:1132: test.serial.pmemd.basic] Error 1 (ignored) export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd velocity_write && ./Run.vel1 diffing vel1.vel.save with vel1.vel PASSED ============================================================== diffing vel1.crd.save with vel1.crd PASSED ============================================================== diffing vel1.frc.save with vel1.frc PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd velocity_write && ./Run.vel2 At line 717 of file /home/samanta/build/amber20_src/src/pmemd/src/mdin_ctrl_dat.F90 (unit = 5, file = 'vel2.in') Fortran runtime error: Cannot match namelist object name ionstepvelocities Error termination. Backtrace: #0 0x7f0fd0a4dd0a #1 0x7f0fd0a4e819 #2 0x7f0fd0a4f4ef #3 0x7f0fd0c8a52d #4 0x7f0fd0c939a7 #5 0x7f0fd0c93bcc #6 0x7f0fd0c93d27 #7 0x555c8c19ac8b #8 0x555c8c282bab #9 0x555c8c269670 #10 0x555c8c18a78e #11 0x7f0fd08460b2 #12 0x555c8c18a7cd #13 0xffffffffffffffff ./Run.vel2: Program error make[2]: [Makefile:1135: test.serial.pmemd.basic] Error 1 (ignored) export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd pmemdTI/gasphase && ./Run.gasphase STOP PMEMD Terminated Abnormally! diffing mdout.gasphase.save with mdout.gasphase file ddtmp.mdout.gasphase is short possible FAILURE: check mdout.gasphase.dif ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd pmemdTI/campTI && ./Run.campTI diffing campTI.out.save with campTI.out PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd pmemdTI/pheMTI && ./Run.0 diffing out.0.save with out.0 PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd pmemdTI/pheMTI && ./Run.1 diffing out.1.save with out.1 PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd pmemdTI/pheMTI && ./Run.lambda0 diffing pheMTI0.out.save with pheMTI0.out PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd pmemdTI/pheMTI && ./Run.lambda1 diffing pheMTI1.out.save with pheMTI1.out PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd pmemdTI/sodium && ./Run.sodium diffing md1.o.save with md1.o PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; 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='/home/samanta/build/amber20///bin/pmemd'; 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='/home/samanta/build/amber20///bin/pmemd'; 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 Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 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 Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL diffing out.0.save with out.0 PASSED ============================================================== diffing restrt.0.save with restrt.0 PASSED ============================================================== ============================================================== Soft core test suite complete ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gact_ips && ./Run.ips_sgld Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL diffing mdout.ips_sgld.save with mdout.ips_sgld PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gact_ips && ./Run.ips_sgldfp Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL diffing mdout.ips_sgldfp.save with mdout.ips_sgldfp PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gact_ips && ./Run.ips_sgldg Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL diffing mdout.ips_sgldg.save with mdout.ips_sgldg PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gact_ips && ./Run.ips_sgmdg Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL diffing mdout.ips_sgmdg.save with mdout.ips_sgmdg PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gb_rna && ./Run.gbrna.sgld diffing mdout.gbrna.sgld.save with mdout.gbrna.sgld PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gb_rna && ./Run.gbrna.sgldfp diffing mdout.gbrna.sgldfp.save with mdout.gbrna.sgldfp PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gb_rna && ./Run.gbrna.sgldg diffing mdout.gbrna.sgldg.save with mdout.gbrna.sgldg PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gb_rna && ./Run.gbrna.sgmdg diffing mdout.gbrna.sgmdg.save with mdout.gbrna.sgmdg PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd emap/ && ./Run.emap Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL diffing mdout.emap.save with mdout.emap PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; unset DO_PARALLEL; cd emil/emil_pmemd_gbsa && ./Run.emil EMIL DO_PARALLEL not set... testing emil in serial. 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='/home/samanta/build/amber20///bin/pmemd'; unset DO_PARALLEL; cd emil/emil_pmemd_tip3p && ./Run.emil EMIL DO_PARALLEL not set... testing emil in serial. diffing mdout.emil.0.9.save with mdout.emil.0.9 possible FAILURE: check mdout.emil.0.9.dif ============================================================== diffing emil.log.0.9.save with emil.log.0.9 possible FAILURE: check emil.log.0.9.dif ============================================================== cd nfe && ./run-pmemd-serial.sh >>>>>>> doing 'abmd_ANALYSIS' diffing save.pmemd/mdout with mdout possible FAILURE: check mdout.dif ============================================================== diffing save.pmemd/monitor.txt with monitor.txt PASSED ============================================================== >>>>>>> doing 'abmd_FLOODING' diffing save.pmemd/mdout with mdout possible FAILURE: check mdout.dif ============================================================== diffing save.pmemd/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.pmemd/mdout with mdout possible FAILURE: check mdout.dif ============================================================== diffing save.pmemd/monitor.txt with monitor.txt PASSED ============================================================== >>>>>>> doing 'smd' diffing save.pmemd/mdout with mdout possible FAILURE: check mdout.dif ============================================================== diffing save.pmemd/smd.txt with smd.txt PASSED ============================================================== >>>>>>> doing 'smd2' diffing save.pmemd/mdout with mdout possible FAILURE: check mdout.dif ============================================================== diffing save.pmemd/work.txt with work.txt PASSED ============================================================== >>>>>>> doing 'pmd' diffing save.pmemd/mdout with mdout possible FAILURE: check mdout.dif ============================================================== diffing save.pmemd/pmd.txt with pmd.txt PASSED ============================================================== export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd gamd && make -k test OPT=pmemd make[3]: Entering directory '/home/samanta/build/amber20/test/gamd' Testing GaMD with PME diffing pmemd.pme.gamd1.save with pmemd.pme.gamd1 file ddtmp.pmemd.pme.gamd1.save is short possible FAILURE: check pmemd.pme.gamd1.dif ============================================================== diffing pmemd.pme.gamd2.save with pmemd.pme.gamd2 file ddtmp.pmemd.pme.gamd2.save is short possible FAILURE: check pmemd.pme.gamd2.dif ============================================================== diffing pmemd.pme.gamd3.save with pmemd.pme.gamd3 file ddtmp.pmemd.pme.gamd3.save is short possible FAILURE: check pmemd.pme.gamd3.dif ============================================================== Testing GaMD with GB diffing pmemd.gb.gamd1.save with pmemd.gb.gamd1 file ddtmp.pmemd.gb.gamd1.save is short possible FAILURE: check pmemd.gb.gamd1.dif ============================================================== diffing pmemd.gb.gamd2.save with pmemd.gb.gamd2 possible FAILURE: check pmemd.gb.gamd2.dif ============================================================== diffing pmemd.gb.gamd3.save with pmemd.gb.gamd3 file ddtmp.pmemd.gb.gamd3.save is short possible FAILURE: check pmemd.gb.gamd3.dif ============================================================== make[3]: Leaving directory '/home/samanta/build/amber20/test/gamd' export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd amd && make -k test OPT=pmemd make[3]: Entering directory '/home/samanta/build/amber20/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 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/samanta/build/amber20/test/amd' export TESTsander='/home/samanta/build/amber20///bin/pmemd'; cd scaledMD && make -k test OPT=pmemd make[3]: Entering directory '/home/samanta/build/amber20/test/scaledMD' Testing scaledMD with PME diffing mdout.save with mdout PASSED ============================================================== make[3]: Leaving directory '/home/samanta/build/amber20/test/scaledMD' make[2]: Leaving directory '/home/samanta/build/amber20/test' make[2]: Entering directory '/home/samanta/build/amber20/test' Finished serial test suite for Amber 20 at czw, 21 maj 2020, 11:15:53 CEST. make[2]: Leaving directory '/home/samanta/build/amber20/test' 158 file comparisons passed 32 file comparisons failed (4 of which can be ignored) 4 tests experienced errors Test log file saved as /home/samanta/build/amber20/logs/test_amber_serial/2020-05-21_11-11-29.log Test diffs file saved as /home/samanta/build/amber20/logs/test_amber_serial/2020-05-21_11-11-29.diff