Manual machinefile script example

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 (.bashrc) 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