[gmx-users] GROMACS with MPICH on Sun Cluster

[Alok]

Thanks again to your help.
I will discuss these issues with my system administrator.
I am really grateful for being a part of this excellent mailing list.
Warm regards,
Alok Jain

----- Original Message ----- 
From: "David van der Spoel" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Friday, June 09, 2006 5:12 PM
Subject: Re: [gmx-users] GROMACS with MPICH on Sun Cluster


> Alok wrote:
>> Thanks a lot Dr. David Spoel :)
>>
>> I compiled GROMACS again with CFLAGS=-g , after that i ran mdrun_mpi. It 
>> is running fine though with some warning. This time I specified the full 
>> path of mdrun_mpi  binary.
>> But now I am having one strange problem. Sometimes it runs smoothly and 
>> sometimes it does not. I am not able to pin point this problem.Actually i 
>> am running mdrun_mpi by using one wrapper script as follows:
>>
>>
>> ######################################################################################################## 
>> #!/bin/csh -f
>> #
>> #
>> # (c) 2004 Sun Microsystems, Inc. Use is subject to license terms.
>>
>> # ---------------------------
>> # our name
>> #$ -N MPI_Job
>> #
>> # pe request
>> #$ -pe mpich* 2-20
>> #
>> # MPIR_HOME from submitting environment
>> #$ -v MPIR_HOME=/opt/mpichdefault-1.2.6
>> # ---------------------------
>>
>> #
>> # needs in
>> #   $NSLOTS
>> #       the number of tasks to be used
>> #   $TMPDIR/machines
>> #       a valid machine file to be passed to mpirun
>>
>> echo "Got $NSLOTS slots."
>>
>> # enables $TMPDIR/rsh to catch rsh calls if available
>> set path=($TMPDIR $path)
>>
>> $MPIR_HOME/bin/mpirun -np $NSLOTS -machinefile $TMPDIR/machines
>> -nolocal  /to/install/gromacs/x86_64-unknown-linux-gnu/bin/mdrun_mpi -v
>> -s full -o full -x full -c after_full -e full -g full  >& full.job &
>>
>>
>> ################################################################################################################### 
>> Then I have to execute this script by following commands
>>
>> qsub -pe mpichpar <no of nodes> -q  par.q  <file name of above script>
>>
>>
>> But the problem is: sometimes it works well and sometimes it gives me the 
>> following error message:
>>
>> ***********************************************
>> Cannot read /tmp/28015.1.par.q/machines.
>> Looked for files with extension LINUX in
>> directory /opt/mpichdefault-1.2.6//share .
>> ***********************************************
>>
>>
>> It seems that there is some problem in reading machines.LINUX file, but 
>> if there is some problem then it should not work sometimes, as it does, 
>> so I am very much confused now !!!
>>
>> I have also installed some other software package but they are running 
>> fine with same script.
>>
>> I also talked with my system adminstrator he told me there is some 
>> problem in installing the GROMACS that why it is behaving so strangely.
>>
>> Could you suggest me something about what am I doing wrong or where am I 
>> going wrong????
>>
>> Thanks again for your kind help (Atleast now I am able to run mdrun_mpi 
>> in the SUN CLUSTER)
>>
>> Warm regards,
>> Alok Jain
>>
> These messages come either from the queuing system or from MPICH or fro 
> both but not from GROMACS.
> If it works sometimes but not otherwise, I suspect some of the nodes in 
> your cluster are confused or broken.
>
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org   http://folding.bmc.uu.se
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