make[2]: Entering directory `/home/gc603449/APPLICATIONS/amber12/test' export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; make -k test.sander.BASIC make[3]: Entering directory `/home/gc603449/APPLICATIONS/amber12/test' cd cytosine && ./Run.cytosine diffing cytosine.out.save with cytosine.out PASSED ============================================================== cd nonper && ./Run.nonper diffing mdout.nonper.save with mdout.nonper PASSED ============================================================== cd nonper && ./Run.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_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_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_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.lmodxmin diffing mdout.dhfr.lmodxmin.save with mdout.dhfr.lmodxmin 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_sgld diffing mdout.ips_sgld.save with mdout.ips_sgld PASSED ============================================================== cd gact_ips && ./Run.ips_sgldfp diffing mdout.ips_sgldfp.save with mdout.ips_sgldfp 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 possible FAILURE: check gcg.dip.o.dif ============================================================== 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 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 /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/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 /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 This test cannot be run with more than 1 processor, exiting. ============================================================ cd trajene_netcdf && ./Run.trajene /home/gc603449/APPLICATIONS/amber12/include/netcdf.mod diffing trajene.out.save with trajene.out PASSED ============================================================== diffing mdcrd.out.nc.save with mdcrd.out.nc PASSED ============================================================== cd alp && ./Run.alp diffing mdout.alp.save with mdout.alp PASSED ============================================================== cd umbrella && ./Run.umbrella diffing mdout.umbrella.save with mdout.umbrella PASSED ============================================================== diffing chi_vs_t.save with chi_vs_t PASSED ============================================================== cd noesy && ./Run.noesy diffing noesy.out.mpi.save with noesy.out PASSED ============================================================== cd jar && ./Run.jarz diffing mdout.jar.save with mdout.jar PASSED ============================================================== diffing dist_vs_t.save with dist_vs_t PASSED ============================================================== cd plane_plane_restraint && ./Run.dinuc_plpt SANDER: Dinucleoside restrained with new plane-point angle restraint that was defined with new natural language restraint input. DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/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 /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting (Max = 2) ============================================================ cd iwrap2 && ./Run.iwrap2 diffing mdout.save with mdout.iw2 PASSED ============================================================== diffing mdcrd.save with mdcrd.iw2 PASSED ============================================================== diffing rstrt.save with rstrt.iw2 PASSED ============================================================== /bin/rm: No match. 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 diffing nc_headers.save with nc_headers PASSED ============================================================== cd nc_restart && make -k test make[4]: Entering directory `/home/gc603449/APPLICATIONS/amber12/test/nc_restart' 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 md.out.save with md.out PASSED ============================================================== Netcdf MD restart read test, ntx=5 diffing md1.rst7 with md2.rst7 PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== Netcdf MD restart read test, ntx=1 diffing md1.rst7 with md2.rst7 PASSED ============================================================== diffing md.out.save with md.out PASSED ============================================================== make[4]: Leaving directory `/home/gc603449/APPLICATIONS/amber12/test/nc_restart' 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 nmropt && make all make[4]: Entering directory `/home/gc603449/APPLICATIONS/amber12/test/nmropt' cd gb/angle && ./Run.nmropt_1angle_gb diffing mdout.save with mdout PASSED ============================================================== diffing angle_gb_vs_t.save with angle_gb_vs_t PASSED ============================================================== cd gb/distance && ./Run.dist_gb diffing mdout.save with mdout PASSED ============================================================== diffing dist_gb_vs_t.save with dist_gb_vs_t PASSED ============================================================== cd gb/distance_COM && ./Run.distCOM_gb diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_gb_vs_t.save with distCOM_gb_vs_t PASSED ============================================================== cd gb/jar_distance && ./Run.jar_gb diffing mdout.save with mdout PASSED ============================================================== diffing dist_gb_vs_t.save with dist_gb_vs_t PASSED ============================================================== cd gb/jar_distance_COM && ./Run.jar_gb diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_gb_vs_t.save with distCOM_gb_vs_t PASSED ============================================================== cd gb/jar_torsion && ./Run.jar_torsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_gb.dat.save with jartorsion_gb.dat PASSED ============================================================== cd gb/nmropt_1_torsion && ./Run.nmropt_1_torsion diffing mdout.save with mdout PASSED ============================================================== diffing torsion_gb.dat.save with torsion_gb.dat PASSED ============================================================== cd gb/tautp && ./Run.nmropt_1tautp_gb diffing mdout.save with mdout PASSED ============================================================== cd gb/temp && ./Run.nmropt_1temp_gb diffing mdout.save with mdout PASSED ============================================================== cd pme/angle && ./Run.nmropt_1angle_pbc diffing mdout.save with mdout PASSED ============================================================== diffing angle_pbc_vs_t.save with angle_pbc_vs_t PASSED ============================================================== cd pme/distance && ./Run.dist_pbc diffing mdout.save with mdout PASSED ============================================================== diffing dist_pbc_vs_t.save with dist_pbc_vs_t PASSED ============================================================== cd pme/distance_COM && ./Run.distCOM_pbc diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_pbc_vs_t.save with distCOM_pbc_vs_t PASSED ============================================================== cd pme/jar_torsion && ./Run.jar_torsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_pbc.dat.save with jartorsion_pbc.dat PASSED ============================================================== cd pme/jar_distance && ./Run.jar_pbc diffing mdout.save with mdout PASSED ============================================================== diffing dist_pbc_vs_t.save with dist_pbc_vs_t PASSED ============================================================== cd pme/jar_distance_COM && ./Run.jar_pbc diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_pbc_vs_t.save with distCOM_pbc_vs_t PASSED ============================================================== cd pme/nmropt_1_torsion && ./Run.nmropt_1_torsion diffing mdout.save with mdout PASSED ============================================================== diffing torsion_pbc.dat.save with torsion_pbc.dat PASSED ============================================================== cd pme/tautp && ./Run.nmropt_1tautp_pbc diffing mdout.save with mdout PASSED ============================================================== cd pme/temp && ./Run.nmropt_1temp_pbc diffing mdout.save with mdout PASSED ============================================================== cd gb/2xangle && ./Run.nmropt_1_2xangle_gb diffing mdout.save with mdout PASSED ============================================================== diffing 2xangle_gb_vs_t.save with 2xangle_gb_vs_t PASSED ============================================================== cd gb/jar_comtorsion && ./Run.jar_comtorsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_com_gb.dat.save with jartorsion_com_gb.dat PASSED ============================================================== cd gb/jar_lcod && ./Run.lcod_jar diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/jar_lcod_dist && ./Run.jar_lcod diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/lcod && ./Run.lcod diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/lcod_com && ./Run.lcod_com diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/nmropt_1_2xtorsion && ./Run.nmropt_1_2xtorsion diffing mdout.save with mdout PASSED ============================================================== diffing 2xtorsion_gb.dat.save with 2xtorsion_gb.dat PASSED ============================================================== cd pme/2xangle && ./Run.nmropt_1_2xangle_pbc diffing mdout.save with mdout PASSED ============================================================== diffing 2xangle_pbc_vs_t.save with 2xangle_pbc_vs_t PASSED ============================================================== cd pme/jar_comtorsion && ./Run.jar_comtorsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_com_pbc.dat.save with jartorsion_com_pbc.dat PASSED ============================================================== cd pme/jar_lcod && ./Run.jar_lcod diffing mdout.save with mdout possible FAILURE: check mdout.dif ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/jar_lcod_dist && ./Run.lcod_dist diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/lcod && ./Run.lcod_pme diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/lcod_com && ./Run.lcod_com diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/nmropt_1_2xtorsion && ./Run.nmropt_1_2xtorsion diffing mdout.save with mdout PASSED ============================================================== diffing 2xtorsion_pbc.dat.save with 2xtorsion_pbc.dat PASSED ============================================================== make[4]: Leaving directory `/home/gc603449/APPLICATIONS/amber12/test/nmropt' make[3]: Leaving directory `/home/gc603449/APPLICATIONS/amber12/test' export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd 4096wat && ./Run.column_fft diffing mdout.column_fft.save with mdout.column_fft PASSED ============================================================== export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd jar_multi && ./Run.jarz Running multisander version of sander Amber12 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=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd ti_eth2meth_gas && ./Run.test1 DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 number of processors for this test > 2, exiting... ============================================================ export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd ti_eth2meth_gas && ./Run.test2 DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 number of processors for this test > 2, exiting... ============================================================ export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd ti_ggcc && ./Run.test1 Running multisander version of sander Amber12 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=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd ti_ggcc && ./Run.test2 Running multisander version of sander Amber12 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=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd csurften && ./Run.csurften_z-dir diffing mdout.csurften_z-dir.save with mdout.csurften_z-dir PASSED ============================================================== export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.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=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; make -k test.sander.GB make[3]: Entering directory `/home/gc603449/APPLICATIONS/amber12/test' cd gb_rna && ./Run.gbrna diffing mdout.gbrna.save with mdout.gbrna PASSED ============================================================== cd gb_rna && ./Run.gbrna.min diffing mdout.gbrna.min.save with mdout.gbrna.min PASSED ============================================================== cd gb_rna && ./Run.gbrna.ln diffing mdout.gbrna.ln.save with mdout.gbrna.ln PASSED ============================================================== cd gb_rna && ./Run.gbrna.ips diffing mdout.gbrna.ips.save with mdout.gbrna.ips PASSED ============================================================== cd gb_rna && ./Run.gbrna.sgld diffing mdout.gbrna.sgld.save with mdout.gbrna.sgld PASSED ============================================================== cd gb_rna && ./Run.gbrna.sgldfp diffing mdout.gbrna.sgldfp.save with mdout.gbrna.sgldfp 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 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 ============================================================== make[3]: Leaving directory `/home/gc603449/APPLICATIONS/amber12/test' export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd rem_gb_2rep && ./Run.rem Running multisander version of sander Amber12 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=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd rem_gb_4rep && ./Run.rem Running multisander version of sander Amber12 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=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd rem_wat && ./Run.rem Running multisander version of sander Amber12 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=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd rem_hybrid && ./Run.rem /bin/rm: No match. Running multisander version of sander Amber12 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=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd h_rem && ./Run.rem Running multisander version of sander Amber12 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=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd sodium && ./Run.sodium Running multisander version of sander Amber12 Total processors = 4 Number of groups = 2 diffing md1.o.save with md1.o PASSED ============================================================== export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd pheMTI && ./Run.0 diffing out.0.save with out.0 PASSED ============================================================== export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd pheMTI && ./Run.1 diffing out.1.save with out.1 PASSED ============================================================== export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd pheMTI && ./Run.lambda0 Running multisander version of sander Amber12 Total processors = 4 Number of groups = 2 diffing out.lambda0.p0.save with out.lambda0.p0 PASSED ============================================================== export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd pheMTI && ./Run.lambda1 Running multisander version of sander Amber12 Total processors = 4 Number of groups = 2 diffing out.lambda1.p0.save with out.lambda1.p0 PASSED ============================================================== export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd campTI && ./Run.campTI Running multisander version of sander Amber12 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=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd softcore && ./Run_sc Running the Softcore potential tests ============================================================== Minimization test DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ Protein-Ligand complex test Running multisander version of sander Amber12 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 Amber12 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 Amber12 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 Amber12 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 Amber12 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 Amber12 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=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd ti_decomp; ./Run.ti_decomp Running multisander version of sander Amber12 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=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd ti_decomp; ./Run.ti_decomp_sc DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ export TESTsanderLES=/home/gc603449/APPLICATIONS/amber12/bin/sander.LES.MPI; make -k test.sander.LES make[3]: Entering directory `/home/gc603449/APPLICATIONS/amber12/test' cd LES_noPME && ./Run.LESmd SANDER: LES MD gas phase diffing md.out.save with md.out PASSED ============================================================== cd LES_noPME && ./Run.LESmd.rdiel SANDER: LES MD gas phase rdiel diffing md.rdiel.out.save with md.rdiel.out PASSED ============================================================== cd LES && ./Run.PME_LES Amber 8 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 Amber 10 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 ============================================================== make[3]: Leaving directory `/home/gc603449/APPLICATIONS/amber12/test' cd neb-testcases/neb_gb_partial && ./Run.neb_gb_partial Running multisander version of sander Amber12 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 Amber12 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 Amber12 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 ncsu && ./run-parallel.sh >>>>>>> doing 'abmd_ANALYSIS' >>>>>>> doing 'abmd_FLOODING' >>>>>>> doing 'abmd_UMBRELLA' >>>>>>> doing 'smd' diffing save/mdout with mdout PASSED ============================================================== diffing save/smd.txt with smd.txt PASSED ============================================================== >>>>>>> doing 'pmd' diffing save/mdout with mdout PASSED ============================================================== diffing save/pmd.txt with pmd.txt PASSED ============================================================== >>>>>>> doing 'smd2' diffing save/mdout with mdout PASSED ============================================================== diffing save/work.txt with work.txt PASSED ============================================================== >>>>>>> doing 'bbmd' >>>>>>> doing 'abremd' >>>>>>> doing 'mwabmd' >>>>>>> doing 'premd' diffing save/rem.log with rem.log PASSED ============================================================== diffing save/ncsu-pmd.log with ncsu-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=/home/gc603449/APPLICATIONS/amber12/bin/sander.LES.MPI; make -k test.sander.PIMD.partial make[3]: Entering directory `/home/gc603449/APPLICATIONS/amber12/test' cd PIMD/part_pimd_water && ./Run.pimd This test not set up for parallel cannot run in parallel with #residues < #pes cd PIMD/part_nmpimd_water && ./Run.nmpimd This test not set up for parallel cannot run in parallel with #residues < #pes cd PIMD/part_pimd_helium && ./Run.pimd diffing hef_pimd.out.save with hef_pimd.out PASSED ============================================================== cd PIMD/part_nmpimd_helium && ./Run.nmpimd diffing hef_pimd.out.save with hef_pimd.out PASSED ============================================================== cd PIMD/part_nmpimd_ntp && ./Run.nmpimd diffing ntp_nmpimd.out.save with ntp_nmpimd.out PASSED ============================================================== diffing NHC.dat.save with NHC.dat PASSED ============================================================== cd PIMD/part_pimd_spcfw && ./Run.pimd diffing spcfw_pimd.top.save with spcfw_pimd.top PASSED ============================================================== diffing spcfw_pimd.xyz.save with spcfw_pimd.xyz PASSED ============================================================== diffing spcfw_pimd.out.save with spcfw_pimd.out PASSED ============================================================== cd PIMD/part_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 make[3]: Leaving directory `/home/gc603449/APPLICATIONS/amber12/test' 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 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 2 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. -------------------------------------------------------------------------- forrtl: error (78): process killed (SIGTERM) Image PC Routine Line Source libintlc.so.5 00002B29B2A561F9 Unknown Unknown Unknown libintlc.so.5 00002B29B2A54B70 Unknown Unknown Unknown libifcore.so.5 00002B29B27DADDF Unknown Unknown Unknown libifcore.so.5 00002B29B27424CF Unknown Unknown Unknown libifcore.so.5 00002B29B2753B8E Unknown Unknown Unknown libpthread.so.0 0000003CE760ECA0 Unknown Unknown Unknown libc.so.6 0000003CE6A9681B Unknown Unknown Unknown libc.so.6 0000003CE6A96258 Unknown Unknown Unknown libmpi.so.1 00002B29B1B01C94 Unknown Unknown Unknown libmpi.so.1 00002B29B1B01BA2 Unknown Unknown Unknown libmpi.so.1 00002B29B1A80B43 Unknown Unknown Unknown libmpi.so.1 00002B29B1A9488B Unknown Unknown Unknown libmpi.so.1 00002B29B1A304F2 Unknown Unknown Unknown libmpi_f77.so.1 00002B29B17B972A Unknown Unknown Unknown sander.MPI 0000000000658EEF Unknown Unknown Unknown sander.MPI 0000000000547B37 Unknown Unknown Unknown sander.MPI 00000000004FE9A8 Unknown Unknown Unknown sander.MPI 00000000004FD331 Unknown Unknown Unknown sander.MPI 0000000000451AA6 Unknown Unknown Unknown libc.so.6 0000003CE6A1D9C4 Unknown Unknown Unknown sander.MPI 00000000004519A9 Unknown Unknown Unknown -------------------------------------------------------------------------- mpirun has exited due to process rank 2 with PID 24429 on node uptwolx420.corpnet2.com exiting improperly. There are two reasons this could occur: 1. this process did not call "init" before exiting, but others in the job did. This can cause a job to hang indefinitely while it waits for all processes to call "init". By rule, if one process calls "init", then ALL processes must call "init" prior to termination. 2. this process called "init", but exited without calling "finalize". By rule, all processes that call "init" MUST call "finalize" prior to exiting or it will be considered an "abnormal termination" This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------- [uptwolx420.corpnet2.com:24426] 3 more processes have sent help message help-mpi-api.txt / mpi-abort [uptwolx420.corpnet2.com:24426] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages program error. 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 /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 This test can be run only with two processes, exiting... export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd cnstph/implicit && ./Run.cnstph diffing mdout.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd cnstph_remd && ./Run.cnstph_remd /home/gc603449/APPLICATIONS/amber12/bin/sander.MPI Running multisander version of sander Amber12 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 ============================================================== if [ -n "" ]; then \ export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala; \ fi if [ -n "" ]; then \ export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.mdiis0; \ fi if [ -n "" ]; then \ export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.mdiis1; \ fi if [ -n "" ]; then \ export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.resize; \ fi if [ -n "" ]; then \ export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.dist; \ fi if [ -n "" ]; then \ export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.dist.xyzv; \ fi if [ -n "" ]; then \ export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.hnc; \ fi if [ -n "" ]; then \ export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' \ && cd rism3d/ala && ./Run.ala.pse1; \ fi export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd rxsgld_4rep && ./Run.rxsgld Running multisander version of sander Amber12 Total processors = 4 Number of groups = 4 diffing rxsgld.log.save with rxsgld.log PASSED ============================================================== diffing rxsgld.out.000.save with rxsgld.out.000 PASSED ============================================================== export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' && cd crg_reloc/water && ./Run.water.min diffing min.out.save with min.out PASSED ============================================================== export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' && cd crg_reloc/water && ./Run.water.md diffing md.out.save with md.out PASSED ============================================================== export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' && cd crg_reloc/cyt && ./Run.cyt.min diffing min.out.save with min.out PASSED ============================================================== export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' && cd crg_reloc/cyt && ./Run.cyt.md diffing md.out.save with md.out PASSED ============================================================== export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' && cd crg_reloc/misc && ./Run.dist.type1 diffing dist.type1.out.save with dist.type1.out PASSED ============================================================== export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' && cd crg_reloc/misc && ./Run.dist.type3 diffing dist.type3.out.save with dist.type3.out PASSED ============================================================== export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' && cd crg_reloc/misc && ./Run.dist.type4 diffing dist.type4.out.save with dist.type4.out PASSED ============================================================== export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' && cd crg_reloc/misc && ./Run.dist.type5 diffing dist.type5.out.save with dist.type5.out PASSED ============================================================== export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' && cd crg_reloc/misc && ./Run.angle.type1 diffing angle.type1.out.save with angle.type1.out PASSED ============================================================== export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' && cd crg_reloc/misc && ./Run.angle.type2 diffing angle.type2.out.save with angle.type2.out PASSED ============================================================== export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' && cd crg_reloc/misc && ./Run.angle.type3 diffing angle.type3.out.save with angle.type3.out PASSED ============================================================== export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' && cd crg_reloc/misc && ./Run.angle.type4 diffing angle.type4.out.save with angle.type4.out PASSED ============================================================== export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' && cd crg_reloc/misc && ./Run.mix diffing mix.out.save with mix.out PASSED ============================================================== export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' && cd crg_reloc/1-4elec && ./Run.opt0 diffing min.opt0.out.save with min.opt0.out PASSED ============================================================== export TESTsander='/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI' && cd crg_reloc/1-4elec && ./Run.opt1 diffing min.opt1.out.save with min.opt1.out PASSED ============================================================== export TESTsander='../../../bin/sander.MPI'; cd amd/dhfr_pme && ./Run.pme.amd1 diffing mdout.pme.amd1.save with mdout.pme.amd1 PASSED ============================================================== export TESTsander='../../../bin/sander.MPI'; cd amd/dhfr_pme && ./Run.pme.amd2 diffing mdout.pme.amd2.save with mdout.pme.amd2 PASSED ============================================================== export TESTsander='../../../bin/sander.MPI'; cd amd/dhfr_pme && ./Run.pme.amd3 diffing mdout.pme.amd3.save with mdout.pme.amd3 PASSED ============================================================== export TESTsander='../../../bin/sander.MPI'; cd amd/gact_ips && ./Run.ips.amd1 diffing mdout.ips.amd1.save with mdout.ips.amd1 PASSED ============================================================== export TESTsander='../../../bin/sander.MPI'; cd amd/gact_ips && ./Run.ips.amd2 diffing mdout.ips.amd2.save with mdout.ips.amd2 PASSED ============================================================== export TESTsander='../../../bin/sander.MPI'; cd amd/gact_ips && ./Run.ips.amd3 diffing mdout.ips.amd3.save with mdout.ips.amd3 PASSED ============================================================== export TESTsander='../../../bin/sander.MPI'; cd amd/rna_gb && ./Run.gb.amd1 diffing mdout.gb.amd1.save with mdout.gb.amd1 PASSED ============================================================== export TESTsander='../../../bin/sander.MPI'; cd amd/rna_gb && ./Run.gb.amd2 diffing mdout.gb.amd2.save with mdout.gb.amd2 PASSED ============================================================== export TESTsander='../../../bin/sander.MPI'; cd amd/rna_gb && ./Run.gb.amd3 diffing mdout.gb.amd3.save with mdout.gb.amd3 PASSED ============================================================== export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; make -k test.sander.QMMM make[3]: Entering directory `/home/gc603449/APPLICATIONS/amber12/test' cd qmmm2/xcrd_build_test/ && ./Run.oct_nma_imaged diffing mdout.oct_nma_imaged.save with mdout.oct_nma_imaged PASSED ============================================================== cd qmmm2/xcrd_build_test/ && ./Run.oct_nma_noimage diffing mdout.oct_nma_noimage.save with mdout.oct_nma_noimage PASSED ============================================================== cd qmmm2/xcrd_build_test/ && ./Run.ortho_qmewald0 diffing mdout.ortho_qmewald0.save with mdout.ortho_qmewald0 PASSED ============================================================== cd qmmm2/xcrd_build_test/ && ./Run.truncoct_qmewald0 diffing mdout.truncoct_qmewald0.save with mdout.truncoct_qmewald0 PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_calc_mulliken diffing crambin_md_calc_mulliken.out.save with crambin_md_calc_mulliken.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2 diffing crambin_md_qmgb2.out.save with crambin_md_qmgb2.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_alpb diffing crambin_md_qmgb2_alpb.out.save with crambin_md_qmgb2_alpb.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_aq1 diffing crambin_md_qmgb2_aq1.out.save with crambin_md_qmgb2_aq1.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_aq2 diffing crambin_md_qmgb2_aq2.out.save with crambin_md_qmgb2_aq2.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_saltcon diffing crambin_md_qmgb2_saltcon.out.save with crambin_md_qmgb2_saltcon.out PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_internal diffing mdout.1NLN_internal.save with mdout.1NLN_internal PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dspev diffing mdout.1NLN_dspev.save with mdout.1NLN_dspev PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dspevd diffing mdout.1NLN_dspevd.save with mdout.1NLN_dspevd PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dspevx diffing mdout.1NLN_dspevx.save with mdout.1NLN_dspevx PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyev diffing mdout.1NLN_dsyev.save with mdout.1NLN_dsyev PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyevd diffing mdout.1NLN_dsyevd.save with mdout.1NLN_dsyevd PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyevr diffing mdout.1NLN_dsyevr.save with mdout.1NLN_dsyevr PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_auto diffing mdout.1NLN_auto.save with mdout.1NLN_auto PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_min diffing mdout.1NLN_min.save with mdout.1NLN_min PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1 diffing mdout.1NLN_MD_ntb1.save with mdout.1NLN_MD_ntb1 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_aq1 diffing mdout.1NLN_MD_ntb1_aq1.save with mdout.1NLN_MD_ntb1_aq1 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_aq2 diffing mdout.1NLN_MD_ntb1_aq2.save with mdout.1NLN_MD_ntb1_aq2 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_mmcorr diffing mdout.1NLN_MD_ntb1_mmcorr.save with mdout.1NLN_MD_ntb1_mmcorr PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_qmewald2 diffing mdout.1NLN_MD_ntb1_qmewald2.save with mdout.1NLN_MD_ntb1_qmewald2 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb2 diffing mdout.1NLN_MD_ntb2.save with mdout.1NLN_MD_ntb2 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_aq2_NUMER_DERIV diffing mdout.1NLN_MD_ntb1_aq2_NUMER_DERIV.save with mdout.1NLN_MD_ntb1_aq2_NUMER_DERIV PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_lnk_dis_neg diffing mdout.1NLN_MD_ntb1_lnk_dis_neg.save with mdout.1NLN_MD_ntb1_lnk_dis_neg PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_lnk_method2 diffing mdout.1NLN_MD_ntb1_lnk_method2.save with mdout.1NLN_MD_ntb1_lnk_method2 PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged diffing mdout.notimaged.save with mdout.notimaged PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md diffing mdout.notimaged_md.save with mdout.notimaged_md PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md_pme diffing mdout.notimaged_md_pme.save with mdout.notimaged_md_pme PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md_pme_qmewald diffing mdout.notimaged_md_pme_qmewald.save with mdout.notimaged_md_pme_qmewald PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md_pme_qmewald_lowmem diffing mdout.notimaged_md_pme_qmewald_lowmem.save with mdout.notimaged_md_pme_qmewald_lowmem PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.imaged diffing mdout.imaged.save with mdout.imaged PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.imaged_md diffing mdout.imaged_md.save with mdout.imaged_md PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.img_center diffing mdout.img_center.save with mdout.img_center PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.img_center_md diffing mdout.img_center_md.save with mdout.img_center_md PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.img_center_bigqmcut_md diffing mdout.img_center_bigqmcut_md.save with mdout.img_center_bigqmcut_md PASSED ============================================================== cd qmmm2/crambin && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm2/crambin && ./Run.crambin_md_hot_start diffing crambin_md_hot_start.out.save with crambin_md_hot_start.out PASSED ============================================================== cd qmmm2/crambin && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out PASSED ============================================================== diffing mdcrd.save with mdcrd PASSED ============================================================== diffing mdvel.save with mdvel PASSED ============================================================== diffing restrt.save with restrt PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap diffing tip3p_cap.out.save with tip3p_cap.out PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap_md diffing tip3p_cap_md.out.save with tip3p_cap_md.out PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap_md.shake diffing tip3p_cap_md_shake.out.save with tip3p_cap_md_shake.out PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap_md.shake_qmshakeoff diffing tip3p_cap_md_shake_qmshake_off.out.save with tip3p_cap_md_shake_qmshake_off.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut && ./Run.MG_QM_water_MM diffing MG_QM_water_MM.out.save with MG_QM_water_MM.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut_lowmem && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut_ADDMM && ./Run.MG_QM_water_MM diffing MG_QM_water_MM.out.save with MG_QM_water_MM.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut_ADDMM && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm2/variable_solvent && ./Run.mg_periodic_vsolv_wat diffing mg_periodic_vsolv_wat.out.save with mg_periodic_vsolv_wat.out PASSED ============================================================== cd qmmm2/variable_solvent && ./Run.1NLN_MD_ntb1_vsolv diffing mdout.1NLN_MD_ntb1_vsolv.save with mdout.1NLN_MD_ntb1_vsolv PASSED ============================================================== cd qmmm2/PM3-MMX && ./Run.crambin_md_pm3mmx diffing crambin_md_pm3mmx.out.save with crambin_md_pm3mmx.out PASSED ============================================================== cd qmmm2/PM3-MMX2 && ./Run.crambin_md_pm3mmx2 diffing crambin_md_pm3mmx2.out.save with crambin_md_pm3mmx2.out PASSED ============================================================== cd qmmm2/crambin_PM6 && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm2/crambin_PM6 && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out PASSED ============================================================== diffing mdcrd.save with mdcrd PASSED ============================================================== diffing mdvel.save with mdvel PASSED ============================================================== diffing restrt.save with restrt PASSED ============================================================== cd qmmm2/PM3-MAIS && ./Run.zundel DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test cd qmmm2/PM3-MAIS && ./Run.hcl_wat DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test cd qmmm2/MechEm_nma-spcfwbox && ./Run.MechEm_PDDGPM3 diffing mdout.MechEm_PDDGPM3.save with mdout.MechEm_PDDGPM3 PASSED ============================================================== cd qmmm2/qmmm_switching_func && ./Run.nma_md_switching diffing nma.out.save with nma.out PASSED ============================================================== make[3]: Leaving directory `/home/gc603449/APPLICATIONS/amber12/test' export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; make -k test.sander.DFTB make[3]: Entering directory `/home/gc603449/APPLICATIONS/amber12/test' cd qmmm_DFTB/crambin_DFTB && ./Run.crambin DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_DFTB && ./Run.crambin_md_hot_start DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_DFTB && ./Run.crambin_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_calc_mulliken DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_alpb DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_aq1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_aq2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_saltcon DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1_link_atoms DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1_qmewald2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms_aq1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms_aq2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_qmewald2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_telec DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut && ./Run.MG_QM_water_MM DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut && ./Run.MG_QM_water_MM_MD DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md_pme DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md_pme_qmewald DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.imaged DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.imaged_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center_bigqmcut_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut_lowmem && ./Run.MG_QM_water_MM_MD DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md.shake DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md.shake_qmshakeoff DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_min DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_lnk_dis_neg DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_lnk_method2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq1_disp DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_qmewald2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PA DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PR DFTB SLKO files not found - Skipping Test... cd qmmm2/MechEm_nma-spcfwbox && ./Run.MechEm_DFTB DFTB SLKO files not found - Skipping Test... make[3]: Leaving directory `/home/gc603449/APPLICATIONS/amber12/test' export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_ADF_PIMD && ./Run.h2o.blyp_sz.pimd ADF dftb program not installed - Skipping Test... export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_ADF_REMD && ./Run.h2o.blyp_sz.remd ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_GAMESS_PIMD && ./Run.h2o.hf_sto-3g.pimd GAMESS not installed - Skipping Test... Check your GAMESS installation and make sure that the GAMESS executable is called rungms export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_GAMESS_REMD && ./Run.h2o.hf_sto-3g.remd GAMESS not installed - Skipping Test... Check your GAMESS installation and make sure that the GAMESS executable is called rungms export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN_PIMD && ./Run.h2o.hf_sto-3g.pimd Error: This test needs to run in parallel on 2 processors. Exiting. export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN_REMD && ./Run.h2o.hf_sto-3g.remd Error: This test needs to run in parallel on 2 processors. Exiting. export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_TeraChem_PIMD && ./Run.h2o.hf_sto-3g.pimd TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_TeraChem_PIMD && ./Run.h2o.hf_sto-3g.pimd mpi TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_TeraChem_PIMD && ./Run.h2o.hf_sto-3g.pimd mpi TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem export TESTsander=/home/gc603449/APPLICATIONS/amber12/bin/sander.MPI; cd qmmm_EXTERN/pure_QM_MD_TeraChem_REMD && ./Run.h2o.hf_sto-3g.remd /bin/sh: ./Run.h2o.hf_sto-3g.remd: No such file or directory make[2]: *** [test.sander.EXTERN.MPI] Error 127 cd evb/malon_bond_umb_GAFF && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_GAFF_MORSIFY && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_GAFF_MORSIFY_XVDW && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_nmpimd_full && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_pimd_ld_full && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_pimd_nhc_full && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_EXP-XCH && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_EXP-XCH_pimd_ld_full && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_EXP-XCH_pimd_nhc_full && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_EXP-XCH_nmpimd_full && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_GAUSS-XCH && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_GAUSS-XCH_pimd_ld_full && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_GAUSS-XCH_pimd_nhc_full && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_GAFF_MORSIFY_XVDW_GAUSS-XCH_nmpimd_full && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_emap_GAFF_MORSIFY && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_emap_GAFF_MORSIFY_XVDW && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_dg_UFF_3DG && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_dg_UFF_3DG_nmpimd_full && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_dg_UFF_3DG_pimd_ld_full && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_dg_UFF_3DG_pimd_nhc_full && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_bond_umb_dg_UFF_3DG_pimd_nhc_full_TI-MASS && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbond_umb_dg_UFF_3DG_pimd_nhc_full_TI-MASS && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_dg_UFF_3DG_qi_full_2D-PMF && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/malon_dbonds_umb_dg_UFF_3DG_qi_full_corrF && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/poh_dbonds_umb_dg_UFF_3DG && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/poh_dbonds_umb_dg_UFF_9DG && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/poh_dbonds_umb_dg_UFF_9DG_pimd_ld_full && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/poh_dbonds_umb_dg_UFF_9DG_pimd_nhc_full && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/poh_dbonds_umb_dg_UFF_9DG_nmpimd_full && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ cd evb/poh_dbonds_umb_dg_UFF_9DG_nmpimd_full_TST-freqf && ./Run.evb DO_PARALLEL set to /home/gc603449/APPLICATIONS/openmpi-1.6.5/bin/mpirun -np 4 too many processors for this test, exiting ============================================================ 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_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_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 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 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_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 possible FAILURE: check mdout.tip5p.dif ============================================================== 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 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/dhfr_pme && ./Run.pme.amd1 diffing mdout.pme.amd1.save with mdout.pme.amd1 PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI' && cd amd/dhfr_pme && ./Run.pme.amd2 diffing mdout.pme.amd2.save with mdout.pme.amd2 PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI' && cd amd/dhfr_pme && ./Run.pme.amd3 diffing mdout.pme.amd3.save with mdout.pme.amd3 PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI' && cd amd/gact_ips && ./Run.ips.amd1 diffing mdout.ips.amd1.save with mdout.ips.amd1 PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI' && cd amd/gact_ips && ./Run.ips.amd2 diffing mdout.ips.amd2.save with mdout.ips.amd2 PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI' && cd amd/gact_ips && ./Run.ips.amd3 diffing mdout.ips.amd3.save with mdout.ips.amd3 PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI' && cd amd/rna_gb && ./Run.gb.amd1 diffing mdout.gb.amd1.save with mdout.gb.amd1 PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI' && cd amd/rna_gb && ./Run.gb.amd2 diffing mdout.gb.amd2.save with mdout.gb.amd2 PASSED ============================================================== export TESTsander='../../../bin/pmemd.MPI' && cd amd/rna_gb && ./Run.gb.amd3 diffing mdout.gb.amd3.save with mdout.gb.amd3 PASSED ============================================================== 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 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/gc603449/APPLICATIONS/amber12/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/gc603449/APPLICATIONS/amber12/test/nmropt' export TESTsander='../../bin/pmemd.MPI'; cd rem_gb_2rep && ./Run.rem Running multipmemd version of pmemd Amber12 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='../../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 rem_wat && ./Run.rem Running multipmemd version of pmemd Amber12 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 ============================================================== Finished parallel test suite for Amber 12 at Thu Nov 21 15:02:01 EST 2013. 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/gc603449/APPLICATIONS/amber12/test/README. make[2]: Target `test.parallel2' not remade because of errors. make[2]: Leaving directory `/home/gc603449/APPLICATIONS/amber12/test' 459 file comparisons passed 3 file comparisons failed 0 tests experienced an error Test log file saved as /home/gc603449/APPLICATIONS/amber12/logs/test_amber_parallel/2013-11-21_14-40-30.log Test diffs file saved as /home/gc603449/APPLICATIONS/amber12/logs/test_amber_parallel/2013-11-21_14-40-30.diff