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 ***
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 ***