#!/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=2

# shared directory for application installation 
application_base_path=/home/opt/

case "$1" in
0 )
    # Here we can reserve a whole node (with $num_thread cores) for running HMMer threaded.
    # This can be done for example by reserving memory worth of one node, if no
    # more elegant ways are available.

    # The reservation is done below by using a parallel environment 'threaded'
    # Requires ARC with new SGE backend (0.6.1 or newer) 
    if [ "xxx$CONFIG_sge_jobopts" = "xxx" ]; then
      CONFIG_sge_jobopts="-pe threaded $num_threads"
    else
      CONFIG_sge_jobopts="$CONFIG_sge_jobopts -pe threaded $num_threads"
    fi

    # Append a stack option to the SGE job script needed for running threaded.
    if [ "xxx$CONFIG_sge_jobopts" = "xxx" ]; then
      CONFIG_sge_jobopts="-l h_stack=10M"
    else
      CONFIG_sge_jobopts="$CONFIG_sge_jobopts -l h_stack=10M"
    fi
;;

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!" 1>&2 ; exit 1; fi
    fi
    
    # export the database directory location
    export HMMER_DB_DIR=$TMPDIR/database
;;

2 )
    # Nothing here
;;

* )
    # 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