Palm.sge

#!/bin/bash

##############################################################################
#                   Sun Grid Engine (SGE) Batch Job Script                   #
#                  Example for submitting a PALM job to FLOW                 #
#                  (BW, Unversity of Oldenburg, January 2013)                #
##############################################################################


##############################################################################
#                SGE directives (options to the qsub command)                #
##############################################################################

### NOTE: All lines containing SGE directives have to start with "#$" ###

###################
# General options #
###################

### Write stdout and stderr in only one file: ###
#$ -j y

### PALM requires the Korn-shell: ###
#$ -S /bin/ksh

### name of the job ###
#$ -N palm

### change to directory where job was submitted from: ###
#$ -cwd

### extend PATH-variable to use PALM scripts ###
### and set environment variable PALM_BIN    ###
export PALM_BIN=$HOME/palm/current_version/trunk/SCRIPTS
export PATH=$PALM_BIN:$PATH

####################################
# Resource requirements of the job #
####################################

### maximum walltime of the job (hh:mm:ss): ###
#$ -l h_rt=0:10:0

### memory per job slot (maximum: ca. 1800M for low-memory nodes, ###
### ca. 3750M for high-memory nodes):                             ###
### Usuallay on FLOW you can use per defaul 1800M because the     ###
### the node will be used exclusively by the job                  ###
#$ -l h_vmem=1800M

### uncomment line if high-memory node is needed (>23 GB per node): ###
##$ -l highmem=true

### disk space - default: 50 GB (if too low, job aborts!)    ###
### if job generates data larger than 50G --> increase value ###
#$ -l h_fsize=50G


######################################
# Specific options for parallel jobs #
######################################

### which parallel environment to use, and number of slots ###
#$ -pe impi41 8

### enable resource reservation (to prevent starving of parallel jobs) ###
#$ -R y


##############################################################################
#                     Commands to be executed by the job                     #
##############################################################################

echo `date`
echo

### it's useful (and nice) to see on which machines the job is running ###
echo "Contents of PE_HOSTFILE:"
cat $PE_HOSTFILE
echo

### load required modules / unload conflicting modules ###
module unload gcc
module load netcdf/4.2.1.1/intel/64/2011.0.013
module load netcdf-fortran/4.2/intel/64/2011.0.013
module load intel/ics/64/2011.0.013
module load intel/impi/64/4.1.0.024
module load hdf5/1.8.9/intel/64/2011.0.013
module load qt4

### call script which starts palm ###
mrun -z -d example_cbl -h lcflow -K parallel -X 8 -t 600 -r "d3# pr#"

exit