Running MAKER using MPI over SGE scheduler with multiple nodes

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Running MAKER using MPI over SGE scheduler with multiple nodes

Lior Glick
Dear MAKER users,

I am running MAKER in order to annotate a large plant genome. To improve performance, I use the MPI option as described in the documentation (specifically openMPI). The machines I currently have access to are part of a cluster on which SGE is used as the job scheduler. There are about 15 machines, each with 20 cores. Therefore, in order to run, I create files that look something like this:

#!/bin/bash
#$ -N try_MAKER
#$ -S /bin/bash
#$ -e /path/to/err
#$ -o /path/to/out
#$ -pe openmpi-x86_64 20
cd /path/to/run_dir
mpiexec -n 20 --mca btl tcp,self maker

I then just qsub the file.
This works fine, but I'd like to use more than 20 cores, which means I need to use multiple nodes of the cluster. Simply increasing the number of requested cores (e.g.  mpiexec -n 100) does not work - it keeps using 20 cores of a single node.
I see this is possible when the scheduler used is PBS (using the nodes:ppn option), but couldn't find any examples/instructions regarding SGE.
Can anyone help me figure it out? Has anyone done this on SGE?

Thanks a lot and best regards,
Lior


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