[gmx-users] question about Gromacs4.0.7: parallel run

[Yi Peng]

Hi, Justin,

Thank you so much. Now it works well.

Yi

On Mon, May 24, 2010 at 7:59 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Yi Peng wrote:
>
>> Hi, everyone,
>>
>> Recently our school upgraded the clusters for us. And they install the
>> Gromacs-4.0.7 for us.  Before I always used Gromacs-4.0.3, the scripts used
>> for parallel running works well.
>>
>> My script is as follows:
>>
>> #PBS -l nodes=4:ppn=2
>> #PBS -N pr-impd1-wt
>> #PBS -j oe
>> module load gromacs
>> module load openmpi-intel
>> cd $PBS_O_WORKDIR
>> NPROCS=`wc -l < $PBS_NODEFILE`
>> /usr/local/bin/pbsdcp -s pr.tpr $TMPDIR
>> cd $TMPDIR
>> mpiexec mdrun -multi $NPROCS -maxh 100 -s pr.tpr -e pr.edr -o pr.trr -g
>> pr.log -c pr.gro
>> /usr/local/bin/pbsdcp -g '*' $PBS_O_WORKDIR
>> cd $PBS_O_WORKDIR
>>
>> But today I tried to use Gromacs-4.0.7 for this. It always has the error
>> message as follows:
>> -------------------------------------------------------
>> Program mdrun, VERSION 4.0.7
>> Source code file: gmxfio.c, line: 737
>>
>> Can not open file:
>> pr7.tpr
>> -------------------------------------------------------
>>
>> "Your Bones Got a Little Machine" (Pixies)
>>
>> Error on node 7, will try to stop all the nodes
>> Halting parallel program mdrun on CPU 7 out of 8
>>
>> gcq#212: "Your Bones Got a Little Machine" (Pixies)
>>
>>
>> -------------------------------------------------------
>> Program mdrun, VERSION 4.0.7
>> Source code file: gmxfio.c, line: 737
>>
>> Can not open file:
>> pr5.tpr
>> -------------------------------------------------------
>>
>> "Your Bones Got a Little Machine" (Pixies)
>>
>>
>> gcq#212: "Your Bones Got a Little Machine" (Pixies)
>>
>> Error on node 5, will try to stop all the nodes
>> Halting parallel program mdrun on CPU 5 out of 8
>>
>> -------------------------------------------------------
>> Program mdrun, VERSION 4.0.7
>> Source code file: gmxfio.c, line: 737
>>
>> Can not open file:
>> pr4.tpr
>> -------------------------------------------------------
>>
>> "Your Bones Got a Little Machine" (Pixies)
>>
>>
>> gcq#212: "Your Bones Got a Little Machine" (Pixies)
>>
>> Error on node 4, will try to stop all the nodes
>> Halting parallel program mdrun on CPU 4 out of 8
>> --------------------------------------------------------------------------
>> MPI_ABORT was invoked on rank 6 in communicator MPI_COMM_WORLD
>> with errorcode -1.
>>
>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> You may or may not see output from other processes, depending on
>> exactly when Open MPI kills them.
>> --------------------------------------------------------------------------
>>
>> How can I solve this problem. Where can I add number to each input  file
>> for pr.tpr?
>>
>>
> The use of -multi implies that you have a series of .tpr files beginning
> with zero, i.e. pr0.tpr, pr1.tpr, etc.  So the input files have to be named
> as mdrun expects them to be.  The name given to the -s flag is a prefix.
>  See, for instance:
>
> http://www.gromacs.org/Documentation/How-tos/REMD#Execution_Steps
>
> -Justin
>
>  Thanks!
>>
>> Yi
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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