start-meme.txt

来自「EM算法的改进」· 文本 代码 · 共 145 行

#!/bin/sh
#
# $Id: start-meme.txt 1339 2006-09-21 19:46:28Z tbailey $
# $Log$
# Revision 1.10  2005/10/07 05:33:55  nadya
# keep uniform name MEME_LOGS throughout scripts.
#
# Revision 1.9  2005/10/05 23:10:43  nadya
# revert to previous version. For now the exit case is used for all the
# unknown and untested mopicc and queing combinations.
#
# Revision 1.8  2005/10/05 08:43:57  wilfred
# commented out the exit for meme server start up process if mpicc isn't found.
# configure should indicate whether serial or parallel will be installed.
#
# Revision 1.7  2005/10/05 06:18:35  nadya
# use full path for "rm". Asssume everybody has /bin/rm.
#
# Revision 1.6  2005/10/02 05:48:07  nadya
# use variable to call meme-client
#
# Revision 1.5  2005/08/25 21:04:41  nadya
# check for config file existance
#
# Revision 1.4  2005/08/25 20:22:11  nadya
# -add -V to get all the shell variables when using qsub
#
# Revision 1.3  2005/08/24 00:32:55  nadya
# use csh scripts for now when starting the servers
#
# Revision 1.2  2005/08/12 17:51:03  nadya
# use meme_config file to set variables
#
# Revision 1.1.1.1  2005/07/28 23:56:39  nadya
# Importing from meme-3.0.14, and adding configure/make
#

# load localization variables configured during install
if [ -f @MEMEDIR@/etc/meme_config ] ; then
    . @MEMEDIR@/etc/meme_config
else
    echo "@MEMEDIR@/etc/meme_config does not exist. Meme installation is incomplete"
    exit 1
fi


#######################################################
#            define functions
#######################################################

# Set up the MEME command
func_set_mpi () {
    if [ $nprocs == 1 ] ; then
      mpiargs=""
      return
    fi
    case "$mpi" in
        mpich)
            mpiargs="-p $nprocs -nolocal -machinefile $tmpdir/machines"
            ;;
        mpich_mpd)
            mpiargs="-p $nprocs -1 -m $tmpdir/machines"
            ;;
        lam)
            mpiargs="-p $nprocs" 
            ;;
        *)
            echo "Unknown type of MPI: $mpi"
            exit 1
    esac
}

# Set queueing command
func_set_queue () {
    case "$qsystem" in
        sge)
            qsub="qsub -pe mpich $nprocs -l h_rt=$maxtime $queue -j y -o $jobout -S $shell -V %s"
            ;;
        pbs)
            qsub="qsub -lncpus=$nprocs -l walltime=$maxtime $queue -j oe -o $jobout -S $shell %s" 
            ;;
        shell)
            qsub="$shell %s &"
            ;;
        *)
            echo "Unknown queueing system"
            exit 1
    esac
}

# Set logfile
func_log () {
    log=$MEME_LOGS/meme.startup.log
}

# Print usage info
func_usage () {
    func_log
    echo "Uses meme-client to check if server is running."
    echo "If not, starts the meme-server and updates"
    echo "file $log"
}

# Check if server is alive   
func_ping() {
    tmpfile=/tmp/start-meme.$$
    echo "ping" > $tmpfile
    $MEME_BIN/$MEME_CLIENT_EXEC $MEME_PORT $HOST $tmpfile 1
    ALIVE=$?
    if [ -f $tmpfile ] ; then
       /bin/rm -f $tmpfile
    fi
}

# If server is already running do nothing, otherwise
# start the server, and update the server log
func_start () {
    if [ $ALIVE -eq 0 ] ; then
        echo "Meme-server is already running"
    else
        func_log
        func_set_mpi
        func_set_queue
        echo "Starting meme-server ..."
        touch $log
        echo "" >> $log
        date >> $log
        nohup $MEME_BIN/meme-server $MEME_PORT "$MEME_BIN/$MEME_SH $mpiargs" "$qsub" >> $log 2>&1 &
        echo "Meme-server started"
      fi
}

#######################################################
#            main
#######################################################

if [ $# -gt 1 ] ; then
    func_usage 1>&2
    exit 1
else
    func_ping
    func_start
fi