[gmx-users] New problem GROMACS 4.6.7 in Intel Cluster

Justin Lemkul jalemkul at vt.edu
Wed Nov 12 03:08:21 CET 2014

On 11/11/14 8:59 PM, Agnivo Gosai wrote:
> Dear Users
> I thought that using MPI OFF commands in cmake will solve my problem. So I
> used the following command :
> -bash-4.1$ /work/gb_lab/agosai/GROMACS/cmake-2.8.11/bin/cmake ..
> -DCMAKE_INSTALL_PREFIX=/work/gb_lab/agosai/gmx465serial
> -DGMX_MPI=off
> However "genbox" is still failing with the same error i.e.
> OMP: Error #178: Function pthread_getattr_np failed:
> OMP: System error #12: Cannot allocate memory
> Aborted
> I read Dr. Mark 's comments and Dr Justin's comments in the trailing mail.
> But I am not sure what is to be done. Can anyone lay down a procedure for
> fixing this. I am sorry if I am asking too much but it will be of great
> help.

This is probably a question best asked of your sysadmin, who should know how to 
execute jobs on your cluster (so please ask your sysadmin).  But if you want any 
advice from this community, you'll need to provide the exact command you're 
trying to issue, and the full job script if it's being submitted to a queuing 
system.  Something is wrong with the environment or the invocation of the 
command.  Serial commands like preprocessing and analysis tools should be 
totally independent of any type of configured parallelization.



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


More information about the gromacs.org_gmx-users mailing list