#!/bin/bash
#
# HMMER runtime environment script for Nordugrid ARC
#
# Runtime environment scripts are called (bash source)
#   from NorduGrid ARC with argument 0,1 or 2.
# First call with argument "0" is made before the the batch
#   job submission script is written.
# Second call is made with argument "1" just prior to execution of the
#   user specified executable.
# Third "clean-up" call is made with argument "2" after the user
#   specified executable has returned.
#
# author: Olli Tourunen <olli.tourunen@csc.fi>
#

# internal variable for setting the number of threads
num_threads=8

# shared directory for application installation 
application_base_path=/grid/nordugrid-arc/appl/

case "$1" in
0 )
    # Here we can reserve a whole node (with $num_thread cores) for running HMMer threaded.

    # append the number of cores to the joboptions
    i=0
    # we need indirect reference here so this looks a bit nasty
    eval jonp=\${joboption_nodeproperty_$i}
    while [ ! -z $jonp ] ; do
        (( i++ ))
        eval jonp=\${joboption_nodeproperty_$i}
    done

    declare joboption_nodeproperty_$i="ppn=$num_threads"
;;

1 )
    # no TMPDIR set up by PBS? Create one here and clean it up in stage 2
    export TMPDIR=`mktemp -d -p /scratch`

    # include HMMer binaries in the path
    export PATH=$PATH:$application_base_path/hmmer/3.0/bin

    # set the number of threads used by HMMer
    # NOTE: if HMMER_NCPU is not set, HMMer will run on all CPUs on the node, 
    # so set this even if you intend to allow serial jobs only!
    export HMMER_NCPU=$num_threads
    
    # create the database directory to local scratch
    if [ ! -d $TMPDIR/database ]; then
      mkdir $TMPDIR/database
      if [ $? != 0 ]; then 
      	echo "ERROR: Can't create database directory, TMPDIR=$TMPDIR" 1>&2
      	df -h 1>&2
      	exit 1
      fi
    fi
    
    # export the database directory location
    export HMMER_DB_DIR=$TMPDIR/database
        
;;

2 )
    # clean up the temporary directory
    if [ -d $TMPDIR ]; then
      rm -rf $TMPDIR
    fi
;;
* )
    # Now, calling argument is wrong or missing.
    # If call was made from NorduGrid ARC, it is considered
    # an error. If this script is to be used also to initialize
    # MPI environment for local jobs in cluster, raising error here
    # could be improper.
    return 1
;;
esac