[gmx-users] Problem in mdrun_mpi using MPICH

[Erik Lindahl]

Hi,

I'm not too familiar with SGE (which I assume is your batch system),  
but for Torque (also uses 'qsub') you cannot provide arguments after  
the command. The suggested workaround there is to create a batch  
script with the exact commands (and args) you need.

It's also worth trying to request an interactive session from the  
queue system and debug it that way...

Cheers,

Erik


On Oct 20, 2005, at 11:41 AM, Alok wrote:

> Hello Dr. Eric & Dr. David,
>
> Thanks for your reply. I have set the path for MPICH compilers and  
> then
> compiled for MPICH parallel environment. Now I am not getting that  
> warning
> related to "lamboot". Still I am not able to run the script. I am  
> getting
> following error message when tried tu run mdrun_mpi
> ______________________________________________________________
> Warning: no access to tty (Bad file descriptor).
> Thus no job control in this shell.
> Got 2 slots.
> Unrecognized argument mdrun_mpi ignored.        "
>
> _________________________________________________________________
>
> So I am not sure that it is compiled for MPICH or not. Is there a  
> way by
> which we may know for what it is compiled of is there a problem in my
> script ?
>
>
> I was using following script and command
>
> ---------------------------------------------------------------------- 
> -----
>
> #!/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 *
>
> ---------------------------------------------------------------------- 
> -----
>
>
> and start the job by using following command.
> qsub -pe mpichpar <no of nodes> -q par.q <script_name>
>
> where * is Path of the input file including parallel program name  
> (in my
> case it is /users/alokjain/mdrun_mpi -s full.tpr -o full -x full -c
> after_full -e full -g full)
>
> Best regards,
> Alok Jain
>
>
>
>
>
>
>
>
>
>>
>> On Oct 19, 2005, at 5:05 PM, Alok wrote:
>>
>>
>>> Hello Dr. David,
>>>                        Thanks for your kind reply. Can you guide me
>>> how can I compile it with MPICH, previously I used --enable mpi
>>> flag for both fftw & groamacs 3.3.
>>> Thanking you,
>>> Best Regards,
>>> Alok
>>>
>>
>> ./configure looks for the first instance of "mpicc" in your path,
>> which apparently was lam. If you want to use a different compiler
>> (e.g. MPICH script) you'll need to set it with the MPICC environment
>> variable prior to running configure.
>>
>> Cheers,
>>
>> Erik
>>
>> -----------------------------------------------------------
>> Erik Lindahl  <lindahl at sbc.su.se>
>> Assistant Professor, Stockholm Bioinformatics Center
>> Stockholm University, SE 106 91 Stockholm
>> Phone: +46 8 5537 8564     Fax: +46 8 5537 8214
>>
>>
>>
>>
>> _______________________________________________
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>>
>
>
> ---------------------------------------------
> Alok Jain
> Graduate Student
> C/o Dr. R. sankararamakrishnan
> Bioinformatics & Biomolecule Simulation Lab
> Dept. of Biological Sciences & Bioengineering
> Indian Institute of Technology,
> Kanpur (U.P.) - India
> Lab: - +91-512-259-4025
> Cell: - 9415540594
> http://www.iitk.ac.in/bsbe/
> ----------------------------------------------
>
>
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>

-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214