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

Justin Lemkul jalemkul at vt.edu
Mon Nov 10 02:18:09 CET 2014

On 11/9/14 8:15 PM, Agnivo Gosai wrote:
> Dear Users
> Firstly thanks (specially Drs. Szilard and Mark ) for helping me out with
> the installation of GROMACS 4.6.7 on my university Intel cluster. However I
> ran into a new problem while using it.
> 1. Firstly I used pdb2gmx to process a pdb file.
> 2. Then I used editconf.
> 3. Then I used genbox.
> But I encountered with the following error.
> Initialising van der waals distances...
> Will generate new solvent configuration of 5x5x9 boxes
> Generating configuration
> Sorting configuration
> Found 1 molecule type:
>      SOL (   3 atoms): 48600 residues
> Calculating Overlap...
> box_margin = 0.315
> Removed 53454 atoms that were outside the box
> OMP: Error #178: Function pthread_getattr_np failed:
> OMP: System error #12: Cannot allocate memory
> Aborted
> Now upon searching on the web it seems to be an OpenMP error. Again I am in
> a fix which I have little or no idea about.

Preprocessing tools (and most analysis tools) are not parallelized in any way. 
They run on one core only.  Generally you do not carry out these sorts of 
operations on a cluster, as there is no benefit to doing so.



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


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