FinisterraePbs

qsub -l num_proc=1,s_rt=20:00:00,s_vmem=32G,h_fsize=2G -pe mpi 16 /home/csic/eda/msp/xmipp_example.pbs

Corresponding pbs file:

#PBS -o $HOME/OUTPUT/
#PBS -e $HOME/OUTPUT/
module load hp-mpi
source /home/csic/eda/msp/.bashrc
cd /home/csic/eda/msp/xmipp_test/
echo "PBS_FILE," $PBS_NODEFILE
echo "NSLOTS," $NSLOTS
echo "$TMPDIR/machines," $TMPDIR/machines 

### For Xmipp protocols:
export PBS_NODEFILE=$TMPDIR/machines
export XMIPP_MACHINEFILE_FLAG=hostfile

echo "PBS_FILE," $PBS_NODEFILE

### The actual command goes here:
mpirun -hostfile $TMPDIR/machines -np $NSLOTS /home/csic/fam/mcg/bin/TS < NDR.fdf
### OR:
python xmipp_protocol_projmatch.py

Note 1: if the two first lines are deleted no error output is generated. If left the output is in $HOME and not in $HOME/OUTPUT/.

Note 2: The following three lines are only needed in finisterrae and not in other computers. Do not forget to add them

module load hp-mpi
export PBS_NODEFILE=$TMPDIR/machines
export XMIPP_MACHINEFILE_FLAG=hostfile

Note 3: In case you want to run your personal copy of Xmipp, that is an Xmipp that is not in the PATH defined in .bashrc, then you need to explicitely pass to the mpirun command the correct $PATH and $LD_LIBRARY_PATH environmental variables like:

export PATH=/my/Xmipp/install/bin:$PATH
export LD_LIBRARY_PATH=/my/Xmipp/install/lib:$LD_LIBRARY_PATH

mpirun ... -e PATH=$PATH -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH

Note 4: In case you want to run Xmipp compiled using Intel C Compiler, then you need to explicitely pass to the mpirun command the correct $PATH and $LD_LIBRARY_PATH environmental variables like (change the Intel C compiler version to the correct one):

export PATH=/my/Xmipp/install/bin:/opt/cesga/intel/intel10.0/cc/10.1.012/bin:$PATH
export LD_LIBRARY_PATH=/my/Xmipp/install/lib:/opt/cesga/intel/intel10.0/cc/10.1.012/lib:$LD_LIBRARY_PATH

mpirun ... -e PATH=$PATH -e LD_LIBRARY_PATH=$LD_LIBRARY_PATH

-- Main.RobertoMarabini - 12 Dec 2008