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" <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users" <gmx-users@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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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