[gmx-users] Using MPI gromacs with CONDOR

[Sara Campos]

Hi Arthur,

In our group we do use Gromacs, MPI and Condor. I will leave you some 
tips of how to use it but if you still have some doubts you can contact 
me off the list.

Sara Campos

####################
Submission script:

Universe = parallel
Executable = exec.sh
# 2 processors will be used
machine_count = 2
output = $(NODE).out
error = $(NODE).error
log = run.log
#To choose 2 processors from the same machine
#(ParallelSchedulingGroup="$(HOSTNAME)" must be defined in machine local 
configuration files):
+WantParallelSchedulingGroups = True
Queue

######################
Executable script (exec.sh from previous example):

#!/bin/sh -e

# Do nothing if this is not the first process:
if [ $_CONDOR_PROCNO -ne 0 ]
then
wait
exit 0
fi
# to allow multiple lam jobs running on a single machine,
# we have to give somewhat unique value
export LAM_MPI_SESSION_SUFFIX=$$
# start LAM
echo "$HOSTNAME cpu=2" | lamboot
#running GROMACS
GROMACS=<you_gromacs_path>
${GROMACS}/grompp -np 2 <your_options>
${GROMACS}/mdrun_mpi -np 2 <your_options>
# Halt LAM
lamhalt

###################

Try also to see etc/examples/lamscript in condor installation directory. 
You may want to add some of that stuff  to your executable file.

 

Arthur Roberts wrote:

> Hi, all,
>
> I was wondering if there was anyone out there that has successfully  
> used Gromacs, MPI, and CONDOR.  One thing that would be particularly  
> useful would be submit scripts.  I have installed MPI on my own  
> account, but I haven't figured out how to use MPI with condor.  I  
> would appreciate your help.
>
> Best wishes,
> Art
>
>
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