[gmx-users] REMD: mdrun_mpi crash with segmentation fault (but mpi is working)

[Justin Lemkul]

On 2/10/15 7:35 AM, Felipe Villanelo wrote:
> Absolutely nothing is written in the log file, just the citations
>

That indicates that the simulation systems are totally unstable and crash 
immediately.  Test by running each job individually (not as part of REMD) and 
see if you can do any diagnosis and troubleshooting based on 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up.

-Justin

> Felipe Villanelo Lizana
> Bioquímico
> Laboratorio de Biología Estructural y Molecular
> Universidad de Chile
>
> 2015-02-03 10:01 GMT-03:00 Felipe Villanelo <el.maestrox at gmail.com>:
>
>> Hi,
>>
>> I trying to learn REMD following the tutorial on gromacs page
>> <http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B> on
>> a 4-cores computer.
>> However when I try to use the command:
>> mpirun -np 4 mdrun_mpi -v -multidir equil[0123] (as the tutorial says)
>> the program crashed with the following error:
>> mpirun noticed that process rank 2 with PID 13013 on node debian exited on
>> signal 11 (Segmentation fault).
>>
>> The mpi is running fine with the 4 cores if I run a simple gromacs
>> simulation (NPT equil) in the same machine.
>> So I think it is not a problem of mpi configuration (as I read in another
>> thread)
>>
>> These with gromacs version is 5.0.2
>>
>> If I try to run the same with an older version of gromacs (4.5.5) the
>> error is different (previously adjusting the options on the mdp file to
>> match changes in syntaxis betweeen versions):
>>
>> [debian:23526] *** An error occurred in MPI_comm_size
>> [debian:23526] *** on communicator MPI_COMM_WORLD
>> [debian:23526] *** MPI_ERR_COMM: invalid communicator
>> [debian:23526] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
>>
>> But this version also work fine with mpi using the 4 cores on a simple
>> simulation
>>
>> Thanks
>> Bye
>>
>> Felipe Villanelo Lizana
>> Bioquímico
>> Laboratorio de Biología Estructural y Molecular
>> Universidad de Chile
>>

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

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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