Manual machinefile script example: Difference between revisions
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(Created page with "== The environment setup == Because the TORQUE queue at the CNB-CSIC requires a maximum wall-clock-time, one needs to define the XXXextra1XXX variable. In their environment (.bas...") |
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== The environment setup == | == The environment setup == | ||
Because the TORQUE queue at the CNB-CSIC requires a maximum wall-clock-time, one needs to define the XXXextra1XXX variable. In their environment (. | Because the TORQUE queue at the CNB-CSIC requires a maximum wall-clock-time, one needs to define the XXXextra1XXX variable. In their environment (.cshrc) one includes: | ||
<code> | <code> | ||
setenv RELION_QSUB_TEMPLATE "/home/hstau/relion-0.9/bin/qsub.csh" | setenv RELION_QSUB_TEMPLATE "/home/hstau/relion-0.9/bin/qsub.csh" | ||
Revision as of 17:11, 4 October 2011
The environment setup
Because the TORQUE queue at the CNB-CSIC requires a maximum wall-clock-time, one needs to define 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"
The command used for job submission (to be given in the GUI) is qsub.
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