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SSAGESproject / SSAGES

Software Suite for Advanced General Ensemble Simulations
GNU General Public License v3.0
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Segmentation fault: address not mapped to object at address 0xffffffffff56cd50 #53

Open momodoucamara opened 3 weeks ago

momodoucamara commented 3 weeks ago

I am trying to run FTS, but I keep getting this Segmentation fault error. Any help on how to get past this error or what might be wrong?

Back Off! I just backed up step1b.pdb to ./#step1b.pdb.6#

Back Off! I just backed up step1c.pdb to ./#step1c.pdb.4#

Back Off! I just backed up step1c.pdb to ./#step1c.pdb.5#

Back Off! I just backed up step1c.pdb to ./#step1c.pdb.6#

Back Off! I just backed up step1c.pdb to ./#step1c.pdb.7# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates [c1214:4078953:0:4078953] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xffffffffff56cd50) ==== backtrace (tid:4078953) ==== 0 /util/opt/ucx/1.12.1/gcc/8.5.0/lib/libucs.so.0(ucs_handle_error+0x2a4) [0x14ab19f8dc94] 1 /util/opt/ucx/1.12.1/gcc/8.5.0/lib/libucs.so.0(+0x2ee94) [0x14ab19f8de94] 2 /util/opt/ucx/1.12.1/gcc/8.5.0/lib/libucs.so.0(+0x2f138) [0x14ab19f8e138] 3 /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(+0x1fd49b) [0x14ab3414349b] 4 /util/comp/intel/19/lib/intel64_lin/libiomp5.so(GOMP_parallel+0x148) [0x14ab2aefc988] 5 /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(_Z14spread_on_gridPK9gmx_pme_tPK14pme_atomcomm_tPK10pmegrids_tiiPdii+0x107) [0x14ab34144ef7] 6 /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(_Z10gmx_pme_doP9gmx_pme_tiiPA3_dS2_PdS3_S3_S3_S3_S3_S2_P9t_commreciiP6t_nrnbP13gmx_wallcycleS2_S2_S3_S3_ddS3_S3_i+0x64c) [0x14ab3414858c] 7 /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(_Z17do_force_lowlevelP10t_forcerecP10t_inputrecP6t_idefP9t_commrecP6t_nrnbP13gmx_wallcycleP9t_mdatomsPA3_dP9history_tSE_PN3gmx15ForceWithVirialEP14gmx_enerdata_tP8t_fcdataP14gmx_localtop_tP13gmx_genborn_tiSE_P8t_lambdaPdP7t_graphP8t_blockaSE_iPf+0x12bf) [0x14ab3477b50f] 8 /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(+0x93ae45) [0x14ab34880e45] 9 /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(_Z8do_forceP8_IO_FILEP9t_commrecP10t_inputreclP6t_nrnbP13gmx_wallcycleP14gmx_localtop_tP12gmx_groups_tPA3_dN3gmx8ArrayRefINSF_11BasicVectorIdEEEEP9history_tSJ_SE_P9t_mdatomsP14gmx_enerdata_tP8t_fcdataNSG_IdEEP7t_graphP10t_forcerecP11gmx_vsite_tPddP9gmx_edsamii41DdOpenBalanceRegionBeforeForceComputation41DdCloseBalanceRegionAfterForceComputation+0x261) [0x14ab348828c1] 10 /util/opt/ssages/0.9/openmpi/4.0/gcc/9/bin/ssages(_ZN3gmx5do_mdEP8_IO_FILEP9t_commrecRKNS_8MDLoggerEiPK8t_filenmPK16gmx_output_env_tRK12MdrunOptionsP11gmx_vsite_tP10gmx_constrPNS_17IMDOutputProviderEP10t_inputrecP10gmx_mtop_tP8t_fcdataP7t_stateP18ObservablesHistoryPNS_7MDAtomsEP6t_nrnbP13gmx_wallcycleP10t_forcerecRK25ReplicaExchangeParametersP12gmx_membed_tP23gmx_walltime_accounting+0x3463) [0x43fc53] 11 /util/opt/ssages/0.9/openmpi/4.0/gcc/9/bin/ssages(_ZN3gmx8Mdrunner8mdrunnerEv+0x2f99) [0x43a689] 12 /util/opt/ssages/0.9/openmpi/4.0/gcc/9/bin/ssages(_ZN3gmx8Mdrunner12mainFunctionEiPPc+0xfc7) [0x436917] 13 /util/opt/ssages/0.9/openmpi/4.0/gcc/9/bin/ssages(_Z9gmx_mdruniPPc+0x7a5) [0x437285] 14 /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x252) [0x14ab340c4012] 15 /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(_ZN3gmx24CommandLineModuleManager21runAsMainSingleModuleEiPPcPNS_18ICommandLineModuleE+0x4d) [0x14ab340c41ed] 16 /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(_ZN3gmx24CommandLineModuleManager14runAsMainCMainEiPPcPFiiS2_E+0x36) [0x14ab340c4256] 17 /util/opt/ssages/0.9/openmpi/4.0/gcc/9/bin/ssages(main+0x3d4) [0x41b3a4] 18 /lib64/libc.so.6(__libc_start_main+0xe5) [0x14ab32cd0d85] 19 /util/opt/ssages/0.9/openmpi/4.0/gcc/9/bin/ssages(_start+0x2e) [0x41b57e]

[c1214:4078953] Process received signal [c1214:4078953] Signal: Segmentation fault (11) [c1214:4078953] Signal code: (-6) [c1214:4078953] Failing at address: 0x1873003e3d69 [c1214:4078953] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x14ab3306dcf0] [c1214:4078953] [ 1] /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(+0x1fd49b)[0x14ab3414349b] [c1214:4078953] [ 2] /util/comp/intel/19/lib/intel64_lin/libiomp5.so(GOMP_parallel+0x148)[0x14ab2aefc988] [c1214:4078953] [ 3] /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(_Z14spread_on_gridPK9gmx_pme_tPK14pme_atomcomm_tPK10pmegrids_tiiPdii+0x107)[0x14ab34144ef7] [c1214:4078953] [ 4] /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(_Z10gmx_pme_doP9gmx_pme_tiiPA3_dS2_PdS3_S3_S3_S3_S3_S2_P9t_commreciiP6t_nrnbP13gmx_wallcycleS2_S2_S3_S3_ddS3_S3_i+0x64c)[0x14ab3414858c] [c1214:4078953] [ 5] /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(_Z17do_force_lowlevelP10t_forcerecP10t_inputrecP6t_idefP9t_commrecP6t_nrnbP13gmx_wallcycleP9t_mdatomsPA3_dP9history_tSE_PN3gmx15ForceWithVirialEP14gmx_enerdata_tP8t_fcdataP14gmx_localtop_tP13gmx_genborn_tiSE_P8t_lambdaPdP7t_graphP8t_blockaSE_iPf+0x12bf)[0x14ab3477b50f] [c1214:4078953] [ 6] /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(+0x93ae45)[0x14ab34880e45] [c1214:4078953] [ 7] /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(_Z8do_forceP8_IO_FILEP9t_commrecP10t_inputreclP6t_nrnbP13gmx_wallcycleP14gmx_localtop_tP12gmx_groups_tPA3_dN3gmx8ArrayRefINSF_11BasicVectorIdEEEEP9history_tSJ_SE_P9t_mdatomsP14gmx_enerdata_tP8t_fcdataNSG_IdEEP7t_graphP10t_forcerecP11gmx_vsite_tPddP9gmx_edsamii41DdOpenBalanceRegionBeforeForceComputation41DdCloseBalanceRegionAfterForceComputation+0x261)[0x14ab348828c1] [c1214:4078953] [ 8] /util/opt/ssages/0.9/openmpi/4.0/gcc/9/bin/ssages(_ZN3gmx5do_mdEP8_IO_FILEP9t_commrecRKNS_8MDLoggerEiPK8t_filenmPK16gmx_output_env_tRK12MdrunOptionsP11gmx_vsite_tP10gmx_constrPNS_17IMDOutputProviderEP10t_inputrecP10gmx_mtop_tP8t_fcdataP7t_stateP18ObservablesHistoryPNS_7MDAtomsEP6t_nrnbP13gmx_wallcycleP10t_forcerecRK25ReplicaExchangeParametersP12gmx_membed_tP23gmx_walltime_accounting+0x3463)[0x43fc53] [c1214:4078953] [ 9] /util/opt/ssages/0.9/openmpi/4.0/gcc/9/bin/ssages(_ZN3gmx8Mdrunner8mdrunnerEv+0x2f99)[0x43a689] [c1214:4078953] [10] /util/opt/ssages/0.9/openmpi/4.0/gcc/9/bin/ssages(_ZN3gmx8Mdrunner12mainFunctionEiPPc+0xfc7)[0x436917] [c1214:4078953] [11] /util/opt/ssages/0.9/openmpi/4.0/gcc/9/bin/ssages(_Z9gmx_mdruniPPc+0x7a5)[0x437285] [c1214:4078953] [12] /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x252)[0x14ab340c4012] [c1214:4078953] [13] /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(_ZN3gmx24CommandLineModuleManager21runAsMainSingleModuleEiPPcPNS_18ICommandLineModuleE+0x4d)[0x14ab340c41ed] [c1214:4078953] [14] /util/opt/ssages/0.9/openmpi/4.0/gcc/9/lib64/libgromacs_ssages.so.3(_ZN3gmx24CommandLineModuleManager14runAsMainCMainEiPPcPFiiS2_E+0x36)[0x14ab340c4256] [c1214:4078953] [15] /util/opt/ssages/0.9/openmpi/4.0/gcc/9/bin/ssages(main+0x3d4)[0x41b3a4] [c1214:4078953] [16] /lib64/libc.so.6(__libc_start_main+0xe5)[0x14ab32cd0d85] [c1214:4078953] [17] /util/opt/ssages/0.9/openmpi/4.0/gcc/9/bin/ssages(_start+0x2e)[0x41b57e] [c1214:4078953] End of error message