normal A system with the number of beasd > 3,000,000

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2 years 9 months ago #9160 by Jinyoung
I have tried to run a transmembrane protein system with the martini force field.
My system has more than 3,700,000 beads (There are more than 3,700,000 lines in the structure gro file)

But when I try to run NVT equilibration simulation, I met the error as below (Sorry for long error message...)
[cpu7:97508] *** Process received signal ***
[cpu7:97508] Signal: Segmentation fault (11)
[cpu7:97508] Signal code: Address not mapped (1)
[cpu7:97508] Failing at address: 0x1de81b9c0
[cpu7:97508] [ 0] /lib64/libpthread.so.0(+0xf5f0)[0x7ff975bae5f0]
[cpu7:97508] [ 1] /home/byun/apps/GROMACS/gromacs_cpu-2020.2_gcc-7.5.0_openmpi-4.0.2/lib64/libgromacs_mpi.so.5(+0xb8d0fa)[0x7ff976e8c0fa]
[cpu7:97508] [ 2] /appl/compiler/gcc-7.5.0/lib64/libgomp.so.1(GOMP_parallel+0x3f)[0x7ff975dc8acf]
[cpu7:97508] [ 3] /home/byun/apps/GROMACS/gromacs_cpu-2020.2_gcc-7.5.0_openmpi-4.0.2/lib64/libgromacs_mpi.so.5(_Z14spread_on_gridPK9gmx_pme_t\
P11PmeAtomCommPK10pmegrids_tbbPfbi+0x73c)[0x7ff976e8ce7c]
[cpu7:97508] [ 4] /home/byun/apps/GROMACS/gromacs_cpu-2020.2_gcc-7.5.0_openmpi-4.0.2/lib64/libgromacs_mpi.so.5(_Z10gmx_pme_doP9gmx_pme_tN3gmx\
8ArrayRefIKNS1_11BasicVectorIfEEEENS2_IS4_EEPfS8_S8_S8_S8_S8_PA3_KfPK9t_commreciiP6t_nrnbP13gmx_wallcyclePA3_fSK_S8_S8_ffS8_S8_i+0x746)[0x7ff\
976e6d866]
[cpu7:97508] [ 5] /home/byun/apps/GROMACS/gromacs_cpu-2020.2_gcc-7.5.0_openmpi-4.0.2/lib64/libgromacs_mpi.so.5(_Z17do_force_lowlevelP10t_forc\
erecPK10t_inputrecPK6t_idefPK9t_commrecPK14gmx_multisim_tP6t_nrnbP13gmx_wallcyclePK9t_mdatomsN3gmx19ArrayRefWithPaddingINSK_11BasicVectorIfEE\
EEP9history_tPNSK_12ForceOutputsEP14gmx_enerdata_tP8t_fcdataPA3_KfPSX_PK7t_graphSZ_RKNSK_12StepWorkloadERK22DDBalanceRegionHandler+0x8f5)[0x7\
ff976dafb75]
[cpu7:97508] [ 6] /home/byun/apps/GROMACS/gromacs_cpu-2020.2_gcc-7.5.0_openmpi-4.0.2/lib64/libgromacs_mpi.so.5(_Z8do_forceP8_IO_FILEPK9t_comm\
recPK14gmx_multisim_tPK10t_inputrecPN3gmx3AwhEP10gmx_enfrotPNSA_10ImdSessionEP6pull_tlP6t_nrnbP13gmx_wallcyclePK14gmx_localtop_tPA3_KfNSA_19A\
rrayRefWithPaddingINSA_11BasicVectorIfEEEEP9history_tSW_PA3_fPK9t_mdatomsP14gmx_enerdata_tP8t_fcdataNSA_8ArrayRefIfEEP7t_graphP10t_forcerecPN\
SA_21MdrunScheduleWorkloadEPK11gmx_vsite_tPfdP9gmx_edsamiRK22DDBalanceRegionHandler+0x1170)[0x7ff976df06f0]
[cpu7:97508] [ 7] /home/byun/apps/GROMACS/gromacs_cpu-2020.2_gcc-7.5.0_openmpi-4.0.2/lib64/libgromacs_mpi.so.5(_ZN3gmx15LegacySimulator5do_md\
Ev+0x4162)[0x7ff976eac212]
[cpu7:97508] [ 8] /home/byun/apps/GROMACS/gromacs_cpu-2020.2_gcc-7.5.0_openmpi-4.0.2/lib64/libgromacs_mpi.so.5(_ZN3gmx15LegacySimulator3runEv\
+0x7d)[0x7ff976ea77ad]
[cpu7:97508] [ 9] /home/byun/apps/GROMACS/gromacs_cpu-2020.2_gcc-7.5.0_openmpi-4.0.2/lib64/libgromacs_mpi.so.5(_ZN3gmx8Mdrunner8mdrunnerEv+0x\
48f4)[0x7ff976edff84]
[cpu7:97508] [10] gmx_mpi[0x408443]
[cpu7:97508] [11] /home/byun/apps/GROMACS/gromacs_cpu-2020.2_gcc-7.5.0_openmpi-4.0.2/lib64/libgromacs_mpi.so.5(_ZN3gmx24CommandLineModuleMana\
ger3runEiPPc+0x237)[0x7ff9768f0f57]
[cpu7:97508] [12] gmx_mpi[0x404f6c]
[cpu7:97508] [13] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7ff974f57505]
[cpu7:97508] [14] gmx_mpi[0x405031]
[cpu7:97508] *** End of error message ***
/var/spool/slurmd/job937846/slurm_script: line 179: 97508 Segmentation fault      (core dumped) gmx_mpi mdrun -v -deffnm eq_nvt > _eq_nvt_mdr\
un.log 2>&1

As I found, this error is from the number of beads in the system…
Is that right?
How can I run a simulation this system with beads > 3,000,000 ??

Best regards,
Jinyoung

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2 years 9 months ago #9161 by Jinyoung
Replied by Jinyoung on topic A system with the number of beasd > 3,000,000
ps. My email address is This email address is being protected from spambots. You need JavaScript enabled to view it. If there are some problem, please let me know that. Thank you:)

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2 years 8 months ago #9209 by riccardo
Replied by riccardo on topic A system with the number of beasd > 3,000,000
Not clear how you conclude that the problem is with the number of beads. Looks like your system is not well energy minimized/equilibrated.

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