Howdy, a user of a cluster that I manage sent me an output file of their Gromacs 3.3.1 job. It looks like the job runs for approx 11 hours and then abruptly terminates with a SEGV_MAPERR. What could cause this (gromacs, or a system config / resource?).
The output of the log file is below, thanks for any suggestions. Mike ######################################################################## ############# STARTED AT: Wed Jan 17 11:40:03 CST 2007 NSLOTS: 16 :-) /share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi (-: Option Filename Type Description ------------------------------------------------------------ -s production-Npt-300K_16CPU.tpr Input Generic run input: tpr tpb tpa xml -o production-Npt-300K_16CPU.trr Output Full precision trajectory: trr trj -x production-Npt-300K_16CPU.xtc Output, Opt! Compressed trajectory (portable xdr format) -c production-Npt-300K_16CPU.gro Output Generic structure: gro g96 pdb xml -e ener.edr Output Generic energy: edr ene Getting Loaded... Reading file production-Npt-300K_16CPU.tpr, VERSION 3.3.1 (single precision) Loaded with Money Back Off! I just backed up ener.edr to ./#ener.edr.1# starting mdrun 'Protein in water' 2500000 steps, 2500.0 ps. ...... steps ...... step 650170, will finish at Fri Jan 19 06:52:24 2007 step 650180, will finish at Fri Jan 19 06:52:21 2007 Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR) Failing at addr:0x7c3fefc [0] func:/share/apps/openmpi/intel/openmpi-1.1.2-64/lib/libopal.so.0 [0x2a966102a5] [1] func:/lib64/tls/libpthread.so.0 [0x3793b0c430] [2] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi( spread_q_bsplines+0x1c0) [0x45c80c] [3] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi( do_pme+0xb5a) [0x45dfea] [4] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi( force+0x9ac) [0x43eac2] [5] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi( do_force+0xa10) [0x46e69a] [6] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi( do_md+0x1a42) [0x429bfe] [7] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi( mdrunner+0xc0f) [0x427f87] [8] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi( main+0x2d6) [0x42b62a] [9] func:/lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x379321c3fb] [10] func:/share/apps/gromacs/intel/gromacs-3.3.1-s64-openmpi/bin/mdrun_ompi [0x418b8a] *** End of error message *** 11 additional processes aborted (not shown) ENDED AT: Wed Jan 17 22:54:32 CST 2007 ######################################################################## ############# _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php