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

[Mark Abraham]

Hi,

That looks suspiciously like a bug, perhaps of the same type as 1174.
Please do open a new issue on Redmine, with the above content, so that your
report does not get lost. If you are able to do cmake
-DCMAKE_BUILD_TYPE=RelWithDebInfo and run with that mdrun, then the above
stack trace should have some line numbers and perhaps that will be enough
information for a quick fix. Otherwise, the developers are all busy with
the 5.0 release cycle right now!

Mark


On Tue, Dec 10, 2013 at 3:10 AM, Alistair Bailey <ab604 at soton.ac.uk> wrote:

> 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
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/segmentation-fault-orientation-restraints-mdrun-mpi-init-orires-0x7f8-0x7abdf8-tp5013211.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>