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run maker using qsub

Sobel-Sorenson, Chandler - (scar)
How could we run maker using qsub with our Sun Grid Engine?  We have it working with mpiexec but this does not show slots used on the grid, so can lead to over loading our cluster.
Currently we are using command like this with mpich: mpiexec -f /opt/machinelist -n 192 maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl -fix_nucleotides

Thanks
Chandler
Arizona Genomics Institute

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Re: run maker using qsub

Carson Holt-2
You will have to look up documentation for Sun Grid Engine and the MPI flavor you wish to use. This is not a MAKER configuration issue, rather you need to setup Sun Grid for MPI according to it’s documentation. When Sun Grid is configured for MPI, it should automatically sets environmental variables and files for jobs. When set up correctly you should not even have to use the -n or -f option with mpiexec as it will be detected from values Sun Grid configures for you.

Then a command like the following will work in your batch job
—> mpiexec maker

—Carson



> On Apr 11, 2017, at 6:21 PM, Sobel-Sorenson, Chandler - (scar) <[hidden email]> wrote:
>
> How could we run maker using qsub with our Sun Grid Engine?  We have it working with mpiexec but this does not show slots used on the grid, so can lead to over loading our cluster.
> Currently we are using command like this with mpich: mpiexec -f /opt/machinelist -n 192 maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl -fix_nucleotides
>
> Thanks
> Chandler
> Arizona Genomics Institute
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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