[gmx-users] segmentation fault - orientation restraints - mdrun_mpi(init_orires+0x7f8) [0x7abdf8]

[Alistair Bailey]

Dear all,

I originally posted this a couple of weeks ago, but haven't had much luck
fixing in myself or finding a solution from the forums or elsewhere so I'm
re-posting it in the hope someone will have an idea. Apologies for posting
multiple times.

Originally I tried to extend a protein simulation using RDC derived
orientation restraints using gromacs 4.5.3 and it failed and I then found
this bug relating to extending a distance restraint simulation that was
giving a similar error to mine: http://bugzilla.gromacs.org/issues/1174
which Mark has posted as resolved in the latest version.

So I requested an upgrade to gromacs 4.6.4 on our cluster. This has been
compiled using:

Intel compilers: v13.1.2
MKL Libraries: v11.1
fftw v3.3.3
OpenMPI library version v1.6.4

When I run an initial test with this command, where nprocs = 4, it works
fine:

mpirun -np $nprocs mdrun_mpi -pd -deffnm pr_test_md -s pr_test_md -cpi
pr_test_md.cpt -nice 0 >& pr_test_md.out

But when I try to extend it, I get this segmentation fault in my log file
pr_test_md.out :

Reading file pr_test_md.tpr, VERSION 4.6.4 (single precision)

[green0069:28137] * Process received signal *
[green0069:28137] Signal: Segmentation fault (11)
[green0069:28137] Signal code: Address not mapped (1)
[green0069:28137] Failing at address: 0xc0
[green0069:28137] [ 0] /lib64/libpthread.so.0(+0xf500) [0x7fd91a329500]
[green0069:28137] [ 1] /lib64/libc.so.6(_IO_vfprintf+0x39) [0x7fd918efcd49]
[green0069:28137] [ 2] /lib64/libc.so.6(_IO_fprintf+0x88) [0x7fd918f07a28]
[green0069:28137] [ 3] mdrun_mpi(init_orires+0x7f8) [0x7abdf8]
[green0069:28137] [ 4] mdrun_mpi(mdrunner+0x1e74) [0x433c74]
[green0069:28137] [ 5] mdrun_mpi(cmain+0xdea) [0x446f1a]
[green0069:28137] [ 6] mdrun_mpi(main+0x4b) [0x44da1b]
[green0069:28137] [ 7] /lib64/libc.so.6(__libc_start_main+0xfd)
[0x7fd918ed7cdd]
[green0069:28137] [ 8] mdrun_mpi() [0x42d419]
[green0069:28137] * End of error message *

My understanding is that the first error  "Address not mapped" means that
the program tried to access a memory location that is not part of the
process' address space (e.g. a null pointer). What follows is a backtrace of
the functions currently being executed (in reverse order, as found on the
stack). I would suspect that the problem relates to Gromacs rather than
OpenMPI -- looking at the origin of the trace.

So I'm guessing that it's this error that is the issue:

mdrun_mpi(init_orires+0x7f8) [0x7abdf8]

Would anyone be able to help me with this or know whether I should report
this as a bug?  The simulation I need to run uses about 180 hours of
walltime and I am only allowed 60 hours for one job, hence I need to extend
my initial run.

Many thanks,

Alistair


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