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

Agnivo Gosai agnivogromacs14 at gmail.com
Wed Nov 12 02:59:30 CET 2014

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 ..

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

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

---------- Forwarded message ----------
From: Mark Abraham <mark.j.abraham at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Mon, 10 Nov 2014 02:26:09 +0100
Subject: Re: [gmx-users] New problem GROMACS 4.6.7 in Intel Cluster
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
> 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.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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