Manual machinefile script example: Difference between revisions
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== The environment setup == | == The environment setup == | ||
The cluster at Columbia does not use any queue. Multiple jobs get nodes assigned by manual editing of an MPI machinefile. The location of this machinefile may be accessible from the GUI through the use of the XXXextra1XXX variable. In their environment (.cshrc) one includes: | The cluster at Columbia does not use any queue. Multiple jobs get nodes assigned by manual editing of an MPI machinefile. The location of this machinefile may be accessible from the GUI through the use of the XXXextra1XXX variable. In their environment (.cshrc) one includes: | ||
setenv RELION_QSUB_TEMPLATE "/home/hstau/relion-0.9/bin/qsub.csh" | setenv RELION_QSUB_TEMPLATE "/home/hstau/relion-0.9/bin/qsub.csh" | ||
setenv RELION_QSUB_EXTRA1 "MPI machinefile" | setenv RELION_QSUB_EXTRA1 "MPI machinefile" | ||
setenv RELION_QSUB_EXTRA1_DEFAULT "/home/hstau/machinefile.dat" | setenv RELION_QSUB_EXTRA1_DEFAULT "/home/hstau/machinefile.dat" | ||
Note that the (perhaps unusual) command used for job submission (to be given in the GUI) is <code>csh</code>. | Note that the (perhaps unusual) command used for job submission (to be given in the GUI) is <code>csh</code>. | ||
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The following script is saved as /home/hstau/relion-0.9/bin/qsub.csh: | The following script is saved as /home/hstau/relion-0.9/bin/qsub.csh: | ||
#!/usr/bin/env csh | #!/usr/bin/env csh | ||
# | # | ||
mpirun -n XXXmpinodesXXX -machinefile XXXextra1XXX XXXcommandXXX | mpirun -n XXXmpinodesXXX -machinefile XXXextra1XXX XXXcommandXXX | ||
Latest revision as of 13:23, 13 November 2017
The environment setup
The cluster at Columbia does not use any queue. Multiple jobs get nodes assigned by manual editing of an MPI machinefile. The location of this machinefile may be accessible from the GUI through the use of the XXXextra1XXX variable. In their environment (.cshrc) one includes:
setenv RELION_QSUB_TEMPLATE "/home/hstau/relion-0.9/bin/qsub.csh" setenv RELION_QSUB_EXTRA1 "MPI machinefile" setenv RELION_QSUB_EXTRA1_DEFAULT "/home/hstau/machinefile.dat"
Note that the (perhaps unusual) command used for job submission (to be given in the GUI) is csh.
The template script
The following script is saved as /home/hstau/relion-0.9/bin/qsub.csh:
#!/usr/bin/env csh # mpirun -n XXXmpinodesXXX -machinefile XXXextra1XXX XXXcommandXXX