[gmx-users] Gromacs mpi error while running REMD

[Justin Lemkul]

On 5/1/13 7:50 PM, bharat gupta wrote:
> Dear gmx-users,
>
> I got the following error after issuing the final command for running 12
> replicas :-
>
> [bme:42039] *** Process received signal ***
> [bme:42039] Signal: Segmentation fault (11)
> [bme:42039] Signal code: Invalid permissions (2)
> [bme:42039] Failing at address: 0x7f093b655340
> [bme:42039] [ 0] /lib64/libpthread.so.0() [0x329220f500]
> [bme:42039] [ 1]
> /opt/bio/gromacs/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x2337)
> [0x7f093c281fa7]
> [bme:42039] [ 2] /opt/bio/gromacs/lib/libgmx_mpi.so.6(do_nonbonded+0xa96)
> [0x7f093c2175d6]
> [bme:42039] [ 3] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force_lowlevel+0x2fa)
> [0x7f093ca47b3a]
> [bme:42039] [ 4] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force+0xeb7)
> [0x7f093cadc6f7]
> [bme:42039] [ 5] mdrun(do_md+0x6a45) [0x42c245]
> [bme:42039] [ 6] mdrun(mdrunner+0xa59) [0x421309]
> [bme:42039] [ 7] mdrun(main+0x12fd) [0x4317dd]
> [bme:42039] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x329161ecdd]
> [bme:42039] [ 9] mdrun() [0x405a29]
> [bme:42039] *** End of error message ***
> Wrote pdb files with previous and current coordinates
> [bme:42036] *** Process received signal ***
> [bme:42036] Signal: Segmentation fault (11)
> [bme:42036] Signal code: Invalid permissions (2)
> [bme:42036] Failing at address: 0x7f794bbe3800
> [bme:42036] [ 0] /lib64/libpthread.so.0() [0x329220f500]
> [bme:42036] [ 1]
> /opt/bio/gromacs/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x13e2)
> [0x7f794c4b8052]
> [bme:42036] [ 2] /opt/bio/gromacs/lib/libgmx_mpi.so.6(do_nonbonded+0xa96)
> [0x7f794c44e5d6]
> [bme:42036] [ 3] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force_lowlevel+0x2fa)
> [0x7f794cc7eb3a]
> [bme:42036] [ 4] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force+0xeb7)
> [0x7f794cd136f7]
> [bme:42036] [ 5] mdrun(do_md+0x6a45) [0x42c245]
> [bme:42036] [ 6] mdrun(mdrunner+0xa59) [0x421309]
> [bme:42036] [ 7] mdrun(main+0x12fd) [0x4317dd]
> [bme:42036] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x329161ecdd]
> [bme:42036] [ 9] mdrun() [0x405a29]
> [bme:42036] *** End of error message ***
> [bme:42042] *** Process received signal ***
> [bme:42042] Signal: Segmentation fault (11)
> [bme:42042] Signal code: Address not mapped (1)
> [bme:42042] Failing at address: 0x7f119c3b96b0
> [bme:42042] [ 0] /lib64/libpthread.so.0() [0x329220f500]
> [bme:42042] [ 1]
> /opt/bio/gromacs/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x1345)
> [0x7f11972e2fb5]
> [bme:42042] [ 2] /opt/bio/gromacs/lib/libgmx_mpi.so.6(do_nonbonded+0xa96)
> [0x7f11972795d6]
> [bme:42042] [ 3] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force_lowlevel+0x2fa)
> [0x7f1197aa9b3a]
> [bme:42042] [ 4] /opt/bio/gromacs/lib/libmd_mpi.so.6(do_force+0xeb7)
> [0x7f1197b3e6f7]
> [bme:42042] [ 5] mdrun(do_md+0x6a45) [0x42c245]
> [bme:42042] [ 6] mdrun(mdrunner+0xa59) [0x421309]
> [bme:42042] [ 7] mdrun(main+0x12fd) [0x4317dd]
> [bme:42042] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd) [0x329161ecdd]
> [bme:42042] [ 9] mdrun() [0x405a29]
> [bme:42042] *** End of error message ***
>
>

Check your .log file and/or stderr for more informative, Gromacs-specific error 
messages.  The backtrace suggests your system is probably blowing up.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================