[gmx-users] Core Dump

[Justin Lemkul]

On 3/18/15 8:51 PM, BAOLIN HUANG wrote:
> Hi,
> Thanks for help.
> It was not grommp fault. The command line was mdrun_mpi -ntomp 1 -s relaxation.tp -deffnm relaxation -c HAP_relaxation.pdb
> Hope following can help.
> MPT: On host cl2n109, Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 0, Process 220661: Dumping core on signal SIGBUS(7) into directory /home/huangb2/test
> MPT: Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 1, Process 220662: Core dump on signal SIGBUS(7) suppressed.
> MPT: Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 2, Process 220663: Core dump on signal SIGBUS(7) suppressed.
> MPT: Program /pkg/suse11/gromacs/5.0.4/bin/gmx_mpi, Rank 3, Process 220664: Core dump on signal SIGBUS(7) suppressed.
> MPT: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
> 	aborting job
> MPT: Received signal 7
>

Nope, that's just a generic failure.  Check the .log file for any specific 
message from GROMACS.  Likely there's some immediate, catastrophic failure.  If 
you're lucky, mdrun will have printed the initial conditions, which can be used 
to spot the problem.

-Justin

> Kind regards,
> Alex
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
> Sent: Thursday, 19 March 2015 10:05 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Core Dump
>
>
>
> On 3/18/15 7:48 PM, BAOLIN HUANG wrote:
>> Hi All,
>>
>> I am using GRMACS 5.0.4, I got and error: Core dump on signal SIGBUS (7) suppressed.
>> There was a warning: This run will generate roughly 3298 Mb of data.
>>
>
> So grompp seg faults?  You're going to have to provide real information, like what your command was, relevant output, etc.  There's nothing that can be diagnosed here.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul
>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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