[gmx-users] Problem in mdrun_mpi using MPICH

Alok alokjain at iitk.ac.in
Thu Oct 20 11:41:06 CEST 2005

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
#       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

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