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

[Mark Abraham]

On Mon, Nov 10, 2014 at 2:17 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
>

True, and the particular problem is likely that Agnivo has not prepared the
environment correctly, e.g. by sourcing Intel's compilervars.sh script,
and/or following the cluster's usage guide for loading its Intel module.

Mark


> -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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