Annotation of /trunk/bin/run-escript

#!/bin/bash

# Escript/Finley wrapper for python
# Sets LD_LIBRARY_PATH and PYTHONPATH and then runs either python or the MPI launcher

#Extra paths can be configured about a page further down
#Search for EXTRA_PATH=""

#set to 1 if performing this is a standalone build and /packages contains the relevant tools
STANDALONE=0

#set to 1 if this is part of a packaged build (.deb) and files will be installed in standard locations
#rather than everything in a single directory
#Do not use this together with $STANDALONE
STDLOCATION=0

#Now we find the location of this script
#Note that this location should be absolute but does not need to be unique
scriptdir=""
CURDIR=`pwd`

#Environment vars which control operations:
# ESCRIPT_NUM_NODES, ESCRIPT_NUM_PROCS, ESCRIPT_NUM_THREADS, ESCRIPT_HOSTFILE, ESCRIPT_CREATESTDFILES

HOSTFILE=/tmp/escript.$$
HOSTFILE2=/tmp/escript2.$$

#Begin finding ESCRIPT_ROOT
if [ $STDLOCATION != 0 ]
then
    ESCRIPT_ROOT=/usr/lib/escript
else
  #We don't know the escript root so we need to work it out from the invocation
  #Need to match if the name contains /
  if [[ $0 =~ / ]]
  then
      # We are not using the PATH to find the script
      cd `dirname $0`
      scriptdir=`pwd`
      cd $CURDIR
  else
      # name does not contain / therefore we are using 
      tscriptdir=`which $0`
      if [ $? != 0 ]
      then
          echo "Error unable to determine script directory. Exiting."
      exit 1
      fi
      scriptdir=`dirname $tscriptdir`
  fi

  cd $scriptdir/..
  ESCRIPT_ROOT=`pwd`
  cd ..
  ESCRIPT_PARENT=`pwd`
  cd $CURDIR

fi
##### End finding ESCRIPT_ROOT  ########

PYTHON_MPI_NULL="$ESCRIPT_ROOT/lib/pythonMPI"
PYTHON_MPI_REDIRECT="$ESCRIPT_ROOT/lib/pythonMPIredirect"
PYTHON_CMD=python

# if possible please express paths relative to $ESCRIPT_ROOT unless
# they are in an unrelated location

EXTRA_DYLD_LIBRARY_PATH=""
EXTRA_PATH=$ESCRIPT_ROOT/bin
EXTRA_PYTHONPATH=$ESCRIPT_ROOT
EXTRA_LD_LIBRARY_PATH=$ESCRIPT_ROOT/lib

if [ $STANDALONE == 1 ]
then
    EXTRA_PATH=$ESCRIPT_PARENT/packages/python/bin:$EXTRA_PATH
    EXTRA_LD_LIBRARY_PATH=$ESCRIPT_PARENT/packages/boost/lib:$ESCRIPT_PARENT/packages/netcdf/lib/:$EXTRA_LD_LIBRARY_PATH
    EXTRA_LD_LIBRARY_PATH=$ESCRIPT_PARENT/packages/vtk/lib/vtk-5.2:$ESCRIPT_PARENT/packages/mesa/lib:$EXTRA_LD_LIBRARY_PATH
    EXTRA_LD_LIBRARY_PATH=$ESCRIPT_PARENT/packages/python/lib:$EXTRA_LD_LIBRARY_PATH
    EXTRA_PYTHONPATH=$ESCRIPT_PARENT/packages/numpy/lib/python2.6/site-packages:$ESCRIPT_PARENT/packages/vtk/lib/python2.6/site-packages:$EXTRA_PYTHONPATH
fi


HELP_TEXT="
Usage: escript [options] script.py [arguments...]
    -n nn       number of nodes to use
    -p np       number of MPI processes to spawn
    -t nt       number of OpenMP threads to use
    -f file     name of MPI hostfile
    -c      print compile information for escript and exit
    -V      print escript version and exit
    -i      interactive mode 
    -b      do not invoke python (run non-python programs)
    -e      print export statements for environment and exit
    -o      redirect output from MPI to files
    -v      print diagnostics
    -x      ..reserved for future use ..
    script.py   Your python script
    arguments...    The optional command-line arguments to your script
"

if [ "$1" = "--help" ]; then
  echo "$HELP_TEXT"
  exit 0
fi
#=======================================================================================

# Avoid bug in hybrid runs with MPT MPI


# Parse the command-line options
# option e should not be followed by a :
while getopts 'bn:p:t:f:h:ecVviox' option
do
    case "$option" in
      "b")  DOBINARY=yes
        ;;
      "n")  ESCRIPT_NUM_NODES=$OPTARG
        ;;
      "p")  ESCRIPT_NUM_PROCS=$OPTARG
        ;;
      "t")  ESCRIPT_NUM_THREADS=$OPTARG
        ;;
      "f")  ESCRIPT_HOSTFILE=$OPTARG
        ;;
      "c")  cat $ESCRIPT_ROOT/lib/buildvars
        exit 0
        ;;
      "V")  echo "escript-pre2.0(build "`grep svn_revision $ESCRIPT_ROOT/lib/buildvars |cut -d= -f2`")"
        exit 0
        ;;
      "h")  echo "$HELPTEXT"
        exit 0
        ;;
      "i")  DOINTERACTIVE=yes
        ;;
      "e")  echo "export LD_LIBRARY_PATH=$EXTRA_LD_LIBRARY_PATH:\$LD_LIBRARY_PATH"
        echo "export PYTHONPATH=$EXTRA_PYTHONPATH:\$PYTHONPATH"
        echo "export PATH=$EXTRA_PATH:\$PATH"
        if [ `uname` == Darwin ]
        then
            echo "export DYLD_LIBRARY_PATH=$EXTRA_DYLD_LIBRARY_PATH:$EXTRA_LD_LIBRARY_PATH:\$DYLD_LIBRARY_PATH"
        fi
        exit 0
        ;;
      "o")  ESCRIPT_CREATESTDFILES="yes"
        ;;
      "v")  ESCRIPT_VERBOSE="yes"
        ;;
      "x")  echo "-x not implemented yet"
        exit 1
        ;;
      ?)    echo "$HELP_TEXT"
        exit 1
        ;;
    esac
done
shift `expr $OPTIND - 1`
#==============================================
#
#   Read the MPI_FLAVOUR from the buildvars
#
MPI_FLAVOUR=`grep mpi_flavour $ESCRIPT_ROOT/lib/buildvars |cut -d= -f2`
WITH_OPENMP=`grep useopenmp $ESCRIPT_ROOT/lib/buildvars |cut -d= -f2`

if [ ! -z $ESCRIPT_VERBOSE  ]; then echo "MPI flavor is $MPI_FLAVOUR."; fi
if [ ! -z $ESCRIPT_VERBOSE ] && [  $WITH_OPENMP == "y"  ]; then echo "OpenMP enabled."; fi
#
#  extend path variables
#
export PATH=$EXTRA_PATH:$PATH
export LD_LIBRARY_PATH=$EXTRA_LD_LIBRARY_PATH:$LD_LIBRARY_PATH
export PYTHONPATH=$EXTRA_PYTHONPATH:$PYTHONPATH
EXPORT_ENV="PATH,LD_LIBRARY_PATH,PYTHONPATH"
if [ `uname` == Darwin ]
then
    export DYLD_LIBRARY_PATH=$EXTRA_DYLD_LIBRARY_PATH:$EXTRA_LD_LIBRARY_PATH:$DYLD_LIBRARY_PATH
    EXPORT_ENV="$EXPORT_ENV,DYLD_LIBRARY_PATH"
fi
if [ ! -z $ESCRIPT_VERBOSE  ] 
then 
    echo "PATH = $PATH "
    echo "LD_LIBRARY_PATH = $LD_LIBRARY_PATH "
    echo "PYTHONPATH = $PYTHONPATH "
    if [ ! -z $DYLD_LIBRARY_PATH ]; then echo "DYLD_LIBRARY_PATH = $DYLD_LIBRARY_PATH "; fi
fi
#==============================================
#
#  Ensure the variables have sensible values
#
if [ $MPI_FLAVOUR  == "none" ] 
then
    if [ ! -z $ESCRIPT_NUM_NODES ]
    then
        echo "Warning: MPI disabled but number of nodes set. Option ignored."
    fi
    if [ ! -z $ESCRIPT_NUM_PROCS ]
    then
        echo "Warning: MPI disabled but number of processors per node set. Option ignored."
    fi
    if [ ! -z $ESCRIPT_HOSTFILE ]
    then
        echo "Warning: MPI disabled but host file is given. Option ignored."
    fi
    ESCRIPT_NUM_NODES=1
    ESCRIPT_NUM_PROCS=1
else
    if [ ! -z $ESCRIPT_HOSTFILE ] 
    then
        if [ -f $ESCRIPT_HOSTFILE ]
        then
            cat $ESCRIPT_HOSTFILE | sort -u > $HOSTFILE
            NUM_HOSTS=`cat $HOSTFILE | wc -l`
            if [ ! -z $ESCRIPT_NUM_NODES ] 
            then
                if [ $NUM_HOSTS -ne $ESCRIPT_NUM_NODES ]
                then
                    echo "number of hosts selected in the host file $ESCRIPT_HOSTFILE needs to match the requested number of nodes $ESCRIPT_NUM_NODES."
                    exit 1
                fi
             else
                ESCRIPT_NUM_NODES=$NUM_HOSTS
             fi
        else
           echo "cannot find hostfile $ESCRIPT_HOSTFILE."
           exit 1
        fi
    else
        HOSTFILE=''
    fi

    if [ -z $ESCRIPT_NUM_NODES ]
    then
      ESCRIPT_NUM_NODES=1
    fi

    if [ -z $ESCRIPT_NUM_PROCS ]
    then
      ESCRIPT_NUM_PROCS=1
    fi

    if [ ! -z $ESCRIPT_VERBOSE  ]
    then 
          echo "ESCRIPT_NUM_NODES = $ESCRIPT_NUM_NODES "
          echo "ESCRIPT_NUM_PROCS = $ESCRIPT_NUM_PROCS "
    fi
fi

if [  $WITH_OPENMP == "y"  ]
then
   if [ -z $ESCRIPT_NUM_THREADS ]
   then
        ESCRIPT_NUM_THREADS=$OMP_NUM_THREADS
        if [ -z $ESCRIPT_NUM_THREADS ]
        then
           ESCRIPT_NUM_THREADS=1
        fi
   fi
   if [ ! -z $ESCRIPT_VERBOSE ]
   then
        echo "ESCRIPT_NUM_THREADS is $ESCRIPT_NUM_THREADS."
   fi
else
   if [[ ( ! -z $ESCRIPT_NUM_THREADS ) && ( $ESCRIPT_NUM_THREADS != 1 ) ]]
   then
       echo "Warning: OpenMP is disabled but number of threads requested is $ESCRIPT_NUM_THREADS!=1. Running without threads."
   fi
   ESCRIPT_NUM_THREADS=1
fi
#
# Now we compute total number of Processes
#
(( TOTPROC=$ESCRIPT_NUM_NODES * $ESCRIPT_NUM_PROCS))
if [ $? -ne 0 ]     #Some compute error 
then            #This could happen if the args were not a number
  echo "expression of total number of processors = $ESCRIPT_NUM_NODES * $ESCRIPT_NUM_PROCS is not numerical."
  exit 1
fi

#
# Test to ensure people aren't trying to combine interactive and multi-process
#
if [[ ( ( ! -z $DOINTERACTIVE ) || ( $# -eq 0 ) ) && ( $TOTPROC -gt 1) ]]
then
  echo "Interactive mode cannot be used with more than one process"
  exit 1
fi

if [ $TOTPROC -gt 1 ] 
then
   if [ "$ESCRIPT_CREATESTDFILES" == "yes" ]
   then
       PYTHON_MPI=$PYTHON_MPI_REDIRECT
   else
       PYTHON_MPI=$PYTHON_MPI_NULL
   fi
else
    PYTHON_MPI=$PYTHON_MPI_NULL
fi
#=========================================================================================================
# Must have at least one command-line arg: the python script
if [ $# -eq 0 ]
then
  if [ ! -z $DOBINARY ]
  then
    echo "No program to run was specified. Exiting."
    exit 1
  fi
fi

#=========================================================================================================
if [ ! -z $DOBINARY ]
then
    EXEC_CMD="$@"
else
    if [ $MPI_FLAVOUR  == "none" ]
    then
        # Check to see if the python version we were compiled with matches the one of EXEC_CMD
        # We should only do this check if they are running a python script
        if [ -f $ESCRIPT_ROOT/lib/pyversion ]
        then
           compversion=`cat $ESCRIPT_ROOT/lib/pyversion`
           intversion=`$PYTHON_CMD -V 2>&1`
           if [ "$compversion" != "$intversion" ]
           then
              echo "Python versions do not match. Escript was compiled for "$compversion"."
              echo "Current version of Python appears to be "$intversion"."
              exit 1
           fi
        fi
    if [ ! -z $DOINTERACTIVE ]
        then
           EXEC_CMD="$PYTHON_CMD -i $@"
        else
           EXEC_CMD="$PYTHON_CMD $@"
        fi
    else
        EXEC_CMD="$PYTHON_MPI $@"
    fi
fi
if [ ! -z $ESCRIPT_VERBOSE ]; then echo "Command to be executed is \"$EXEC_CMD\"."; fi
#===============================================================================================
#
#   now we start to spwan things:
#
if [  $WITH_OPENMP == "y"  ]
then
   export OMP_NUM_THREADS=$ESCRIPT_NUM_THREADS
   EXPORT_ENV="$EXPORT_ENV,OMP_NUM_THREADS"
fi
EXIT_CODE=1
#=============== no MPI ===================================
if [ $MPI_FLAVOUR  == "none" ] 
then
   $EXEC_CMD 
   EXIT_CODE=$?
#=============== OpenMPI ===================================
elif [ $MPI_FLAVOUR == "OPENMPI" ] 
then 
   if [ ! -z $HOSTFILE ] 
   then
      HOST_LIST=`awk 'BEGIN{S=""}{if (S == "") { S = $0 } else {S = S "," $0}}END{print S}' $HOSTFILE`
      CMD="mpirun -x ${EXPORT_ENV//,/ -x } --bynode -np $TOTPROC --host $HOST_LIST $EXEC_CMD"
   else
      CMD="mpirun -x ${EXPORT_ENV//,/ -x } -np $TOTPROC $EXEC_CMD"
   fi 
   if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI command is \"$CMD\"."; fi
   $CMD
   EXIT_CODE=$?

#=============== Intel MPI ===================================
elif [ $MPI_FLAVOUR == "INTELMPI" ]
then

   if [  $WITH_OPENMP == "y"  ]
   then
       export I_MPI_PIN_DOMAIN=omp
       EXPORT_ENV="$EXPORT_ENV, I_MPI_PIN_DOMAIN"
   fi

   if [ ! -z $HOSTFILE ] 
   then
      mpdboot -n $ESCRIPT_NUM_NODES -r ssh -f $HOSTFILE
      if [ $? -ne 0 ] 
      then
         echo "mpdboot with host file $ESCRIPT_HOSTFILE for $ESCRIPT_NUM_NODES nodes failed."
         exit 1
      else 
          if [ ! -z $ESCRIPT_VERBOSE ]; then echo "mpdboot was started with host file $ESCRIPT_HOSTFILE for $ESCRIPT_NUM_NODES nodes."; fi
      fi
   fi
   CMD="mpiexec -perhost $ESCRIPT_NUM_PROCS -envall -n $TOTPROC $EXEC_CMD"
   if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI command is \"$CMD\"."; fi
   $CMD
   EXIT_CODE=$?
   if [ ! -z $HOSTFILE ]
   then
       mpdallexit
       if [ ! -z $ESCRIPT_VERBOSE ]; then echo "mpdallexit executed."; fi
   fi 
#=============== SGI's MPIMPT ===================================
elif [ $MPI_FLAVOUR == "MPT" ]
then
   export MPI_NUM_MEMORY_REGIONS=0
   EXPORT_ENV="$EXPORT_ENV,MPI_NUM_MEMORY_REGIONS"
   if [ ! -z $HOSTFILE ] 
   then
      HOST_LIST=`awk 'BEGIN{S=""}{if (S == "") { S = $0 } else {S = S "," $0}}END{print S}' $HOSTFILE`
      CMD="mpirun $HOST_LIST $ESCRIPT_NUM_PROCS $EXEC_CMD"
   else
      CMD="mpirun -np $TOTPROC $EXEC_CMD"
   fi 
   if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI command is \"$CMD\"."; fi
   $CMD
   EXIT_CODE=$?
#=============== MPICH ===================================
elif [ $MPI_FLAVOUR == "MPICH" ]
then
   if [ ! -z $HOSTFILE ] 
   then
      touch $HOSTFILE2
      for (( i=1;i<=$ESCRIPT_NUM_PROCS;i+=1 )) ; do cat $HOSTFILE >> $HOSTFILE2  ; done
      CMD="mpirun -machinefile $HOSTFILE2  -np $TOTPROC $EXEC_CMD"
   else
      CMD="mpirun -np $TOTPROC $EXEC_CMD"
   fi 
   if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI command is \"$CMD\"."; fi
   $CMD
   EXIT_CODE=$?
#=============== MPICH2 ===================================
elif [ $MPI_FLAVOUR == "MPICH2" ]
then
   if [ ! -z $HOSTFILE ] 
   then
         mpdboot -n $ESCRIPT_NUM_NODES -r ssh -f $HOSTFILE
         if [ $? -ne 0 ] 
         then
            echo "mpdboot with host file $ESCRIPT_HOSTFILE for $ESCRIPT_NUM_NODES nodes failed."
            exit 1
         else 
             if [ ! -z $ESCRIPT_VERBOSE ]; then echo "mpdboot was started with host file $ESCRIPT_HOSTFILE for $ESCRIPT_NUM_NODES nodes."; fi
         fi
   fi
   CMD="mpiexec -genvlist $EXPORT_ENV -np $TOTPROC $EXEC_CMD"
   if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI command is \"$CMD\"."; fi
   $CMD
   EXIT_CODE=$?
   if [ ! -z $HOSTFILE ]
   then
       mpdallexit
       if [ ! -z $ESCRIPT_VERBOSE ]; then echo "mpdallexit executed."; fi
   fi 
else
   echo "unknown MPI falvour $MPI_FLAVOUR."
fi
exit $EXIT_CODE
1	jfenwick	2409	#!/bin/bash
2
3			# Escript/Finley wrapper for python
4			# Sets LD_LIBRARY_PATH and PYTHONPATH and then runs either python or the MPI launcher
5
6			#Extra paths can be configured about a page further down
7			#Search for EXTRA_PATH=""
8
9			#set to 1 if performing this is a standalone build and /packages contains the relevant tools
10			STANDALONE=0
11
12			#set to 1 if this is part of a packaged build (.deb) and files will be installed in standard locations
13			#rather than everything in a single directory
14			#Do not use this together with $STANDALONE
15			STDLOCATION=0
16
17			#Now we find the location of this script
18			#Note that this location should be absolute but does not need to be unique
19			scriptdir=""
20			CURDIR=`pwd`
21
22			#Environment vars which control operations:
23			# ESCRIPT_NUM_NODES, ESCRIPT_NUM_PROCS, ESCRIPT_NUM_THREADS, ESCRIPT_HOSTFILE, ESCRIPT_CREATESTDFILES
24
25			HOSTFILE=/tmp/escript.$$
26			HOSTFILE2=/tmp/escript2.$$
27
28			#Begin finding ESCRIPT_ROOT
29			if [ $STDLOCATION != 0 ]
30			then
31			ESCRIPT_ROOT=/usr/lib/escript
32			else
33			#We don't know the escript root so we need to work it out from the invocation
34			#Need to match if the name contains /
35			if [[ $0 =~ / ]]
36			then
37			# We are not using the PATH to find the script
38			cd `dirname $0`
39			scriptdir=`pwd`
40			cd $CURDIR
41			else
42			# name does not contain / therefore we are using
43			tscriptdir=`which $0`
44			if [ $? != 0 ]
45			then
46			echo "Error unable to determine script directory. Exiting."
47			exit 1
48			fi
49			scriptdir=`dirname $tscriptdir`
50			fi
51
52			cd $scriptdir/..
53			ESCRIPT_ROOT=`pwd`
54			cd ..
55			ESCRIPT_PARENT=`pwd`
56			cd $CURDIR
57
58			fi
59			##### End finding ESCRIPT_ROOT ########
60
61			PYTHON_MPI_NULL="$ESCRIPT_ROOT/lib/pythonMPI"
62			PYTHON_MPI_REDIRECT="$ESCRIPT_ROOT/lib/pythonMPIredirect"
63			PYTHON_CMD=python
64
65			# if possible please express paths relative to $ESCRIPT_ROOT unless
66			# they are in an unrelated location
67
68			EXTRA_DYLD_LIBRARY_PATH=""
69			EXTRA_PATH=$ESCRIPT_ROOT/bin
70			EXTRA_PYTHONPATH=$ESCRIPT_ROOT
71			EXTRA_LD_LIBRARY_PATH=$ESCRIPT_ROOT/lib
72
73			if [ $STANDALONE == 1 ]
74			then
75			EXTRA_PATH=$ESCRIPT_PARENT/packages/python/bin:$EXTRA_PATH
76			EXTRA_LD_LIBRARY_PATH=$ESCRIPT_PARENT/packages/boost/lib:$ESCRIPT_PARENT/packages/netcdf/lib/:$EXTRA_LD_LIBRARY_PATH
77			EXTRA_LD_LIBRARY_PATH=$ESCRIPT_PARENT/packages/vtk/lib/vtk-5.2:$ESCRIPT_PARENT/packages/mesa/lib:$EXTRA_LD_LIBRARY_PATH
78			EXTRA_LD_LIBRARY_PATH=$ESCRIPT_PARENT/packages/python/lib:$EXTRA_LD_LIBRARY_PATH
79	jfenwick	2462	EXTRA_PYTHONPATH=$ESCRIPT_PARENT/packages/numpy/lib/python2.6/site-packages:$ESCRIPT_PARENT/packages/vtk/lib/python2.6/site-packages:$EXTRA_PYTHONPATH
80	jfenwick	2409	fi
81
82
83
84			HELP_TEXT="
85			Usage: escript [options] script.py [arguments...]
86			-n nn number of nodes to use
87			-p np number of MPI processes to spawn
88			-t nt number of OpenMP threads to use
89			-f file name of MPI hostfile
90			-c print compile information for escript and exit
91			-V print escript version and exit
92			-i interactive mode
93			-b do not invoke python (run non-python programs)
94			-e print export statements for environment and exit
95			-o redirect output from MPI to files
96			-v print diagnostics
97			-x ..reserved for future use ..
98			script.py Your python script
99			arguments... The optional command-line arguments to your script
100			"
101
102			if [ "$1" = "--help" ]; then
103			echo "$HELP_TEXT"
104			exit 0
105			fi
106			#=======================================================================================
107
108			# Avoid bug in hybrid runs with MPT MPI
109
110
111			# Parse the command-line options
112			# option e should not be followed by a :
113			while getopts 'bn:p:t:f:h:ecVviox' option
114			do
115			case "$option" in
116			"b") DOBINARY=yes
117			;;
118			"n") ESCRIPT_NUM_NODES=$OPTARG
119			;;
120			"p") ESCRIPT_NUM_PROCS=$OPTARG
121			;;
122			"t") ESCRIPT_NUM_THREADS=$OPTARG
123			;;
124			"f") ESCRIPT_HOSTFILE=$OPTARG
125			;;
126			"c") cat $ESCRIPT_ROOT/lib/buildvars
127			exit 0
128			;;
129			"V") echo "escript-pre2.0(build "`grep svn_revision $ESCRIPT_ROOT/lib/buildvars \|cut -d= -f2`")"
130			exit 0
131			;;
132			"h") echo "$HELPTEXT"
133			exit 0
134			;;
135			"i") DOINTERACTIVE=yes
136			;;
137			"e") echo "export LD_LIBRARY_PATH=$EXTRA_LD_LIBRARY_PATH:\$LD_LIBRARY_PATH"
138			echo "export PYTHONPATH=$EXTRA_PYTHONPATH:\$PYTHONPATH"
139			echo "export PATH=$EXTRA_PATH:\$PATH"
140			if [ `uname` == Darwin ]
141			then
142			echo "export DYLD_LIBRARY_PATH=$EXTRA_DYLD_LIBRARY_PATH:$EXTRA_LD_LIBRARY_PATH:\$DYLD_LIBRARY_PATH"
143			fi
144			exit 0
145			;;
146			"o") ESCRIPT_CREATESTDFILES="yes"
147			;;
148			"v") ESCRIPT_VERBOSE="yes"
149			;;
150			"x") echo "-x not implemented yet"
151			exit 1
152			;;
153			?) echo "$HELP_TEXT"
154			exit 1
155			;;
156			esac
157			done
158			shift `expr $OPTIND - 1`
159			#==============================================
160			#
161			# Read the MPI_FLAVOUR from the buildvars
162			#
163			MPI_FLAVOUR=`grep mpi_flavour $ESCRIPT_ROOT/lib/buildvars \|cut -d= -f2`
164			WITH_OPENMP=`grep useopenmp $ESCRIPT_ROOT/lib/buildvars \|cut -d= -f2`
165
166			if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI flavor is $MPI_FLAVOUR."; fi
167			if [ ! -z $ESCRIPT_VERBOSE ] && [ $WITH_OPENMP == "y" ]; then echo "OpenMP enabled."; fi
168			#
169			# extend path variables
170			#
171			export PATH=$EXTRA_PATH:$PATH
172			export LD_LIBRARY_PATH=$EXTRA_LD_LIBRARY_PATH:$LD_LIBRARY_PATH
173			export PYTHONPATH=$EXTRA_PYTHONPATH:$PYTHONPATH
174			EXPORT_ENV="PATH,LD_LIBRARY_PATH,PYTHONPATH"
175			if [ `uname` == Darwin ]
176			then
177			export DYLD_LIBRARY_PATH=$EXTRA_DYLD_LIBRARY_PATH:$EXTRA_LD_LIBRARY_PATH:$DYLD_LIBRARY_PATH
178			EXPORT_ENV="$EXPORT_ENV,DYLD_LIBRARY_PATH"
179			fi
180			if [ ! -z $ESCRIPT_VERBOSE ]
181			then
182			echo "PATH = $PATH "
183			echo "LD_LIBRARY_PATH = $LD_LIBRARY_PATH "
184			echo "PYTHONPATH = $PYTHONPATH "
185			if [ ! -z $DYLD_LIBRARY_PATH ]; then echo "DYLD_LIBRARY_PATH = $DYLD_LIBRARY_PATH "; fi
186			fi
187			#==============================================
188			#
189			# Ensure the variables have sensible values
190			#
191			if [ $MPI_FLAVOUR == "none" ]
192			then
193			if [ ! -z $ESCRIPT_NUM_NODES ]
194			then
195			echo "Warning: MPI disabled but number of nodes set. Option ignored."
196			fi
197			if [ ! -z $ESCRIPT_NUM_PROCS ]
198			then
199			echo "Warning: MPI disabled but number of processors per node set. Option ignored."
200			fi
201			if [ ! -z $ESCRIPT_HOSTFILE ]
202			then
203			echo "Warning: MPI disabled but host file is given. Option ignored."
204			fi
205			ESCRIPT_NUM_NODES=1
206			ESCRIPT_NUM_PROCS=1
207			else
208			if [ ! -z $ESCRIPT_HOSTFILE ]
209			then
210			if [ -f $ESCRIPT_HOSTFILE ]
211			then
212			cat $ESCRIPT_HOSTFILE \| sort -u > $HOSTFILE
213			NUM_HOSTS=`cat $HOSTFILE \| wc -l`
214			if [ ! -z $ESCRIPT_NUM_NODES ]
215			then
216			if [ $NUM_HOSTS -ne $ESCRIPT_NUM_NODES ]
217			then
218			echo "number of hosts selected in the host file $ESCRIPT_HOSTFILE needs to match the requested number of nodes $ESCRIPT_NUM_NODES."
219			exit 1
220			fi
221			else
222			ESCRIPT_NUM_NODES=$NUM_HOSTS
223			fi
224			else
225			echo "cannot find hostfile $ESCRIPT_HOSTFILE."
226			exit 1
227			fi
228			else
229			HOSTFILE=''
230			fi
231
232			if [ -z $ESCRIPT_NUM_NODES ]
233			then
234			ESCRIPT_NUM_NODES=1
235			fi
236
237			if [ -z $ESCRIPT_NUM_PROCS ]
238			then
239			ESCRIPT_NUM_PROCS=1
240			fi
241
242			if [ ! -z $ESCRIPT_VERBOSE ]
243			then
244			echo "ESCRIPT_NUM_NODES = $ESCRIPT_NUM_NODES "
245			echo "ESCRIPT_NUM_PROCS = $ESCRIPT_NUM_PROCS "
246			fi
247			fi
248
249			if [ $WITH_OPENMP == "y" ]
250			then
251			if [ -z $ESCRIPT_NUM_THREADS ]
252			then
253			ESCRIPT_NUM_THREADS=$OMP_NUM_THREADS
254			if [ -z $ESCRIPT_NUM_THREADS ]
255			then
256			ESCRIPT_NUM_THREADS=1
257			fi
258			fi
259			if [ ! -z $ESCRIPT_VERBOSE ]
260			then
261			echo "ESCRIPT_NUM_THREADS is $ESCRIPT_NUM_THREADS."
262			fi
263			else
264			if [[ ( ! -z $ESCRIPT_NUM_THREADS ) && ( $ESCRIPT_NUM_THREADS != 1 ) ]]
265			then
266			echo "Warning: OpenMP is disabled but number of threads requested is $ESCRIPT_NUM_THREADS!=1. Running without threads."
267			fi
268			ESCRIPT_NUM_THREADS=1
269			fi
270			#
271			# Now we compute total number of Processes
272			#
273			(( TOTPROC=$ESCRIPT_NUM_NODES * $ESCRIPT_NUM_PROCS))
274			if [ $? -ne 0 ] #Some compute error
275			then #This could happen if the args were not a number
276			echo "expression of total number of processors = $ESCRIPT_NUM_NODES * $ESCRIPT_NUM_PROCS is not numerical."
277			exit 1
278			fi
279
280			#
281			# Test to ensure people aren't trying to combine interactive and multi-process
282			#
283			if [[ ( ( ! -z $DOINTERACTIVE ) \|\| ( $# -eq 0 ) ) && ( $TOTPROC -gt 1) ]]
284			then
285			echo "Interactive mode cannot be used with more than one process"
286			exit 1
287			fi
288
289			if [ $TOTPROC -gt 1 ]
290			then
291			if [ "$ESCRIPT_CREATESTDFILES" == "yes" ]
292			then
293			PYTHON_MPI=$PYTHON_MPI_REDIRECT
294			else
295			PYTHON_MPI=$PYTHON_MPI_NULL
296			fi
297			else
298			PYTHON_MPI=$PYTHON_MPI_NULL
299			fi
300			#=========================================================================================================
301			# Must have at least one command-line arg: the python script
302			if [ $# -eq 0 ]
303			then
304			if [ ! -z $DOBINARY ]
305			then
306			echo "No program to run was specified. Exiting."
307			exit 1
308			fi
309			fi
310
311			#=========================================================================================================
312			if [ ! -z $DOBINARY ]
313			then
314			EXEC_CMD="$@"
315			else
316			if [ $MPI_FLAVOUR == "none" ]
317			then
318			# Check to see if the python version we were compiled with matches the one of EXEC_CMD
319			# We should only do this check if they are running a python script
320			if [ -f $ESCRIPT_ROOT/lib/pyversion ]
321			then
322			compversion=`cat $ESCRIPT_ROOT/lib/pyversion`
323			intversion=`$PYTHON_CMD -V 2>&1`
324			if [ "$compversion" != "$intversion" ]
325			then
326			echo "Python versions do not match. Escript was compiled for "$compversion"."
327			echo "Current version of Python appears to be "$intversion"."
328			exit 1
329			fi
330			fi
331			if [ ! -z $DOINTERACTIVE ]
332			then
333			EXEC_CMD="$PYTHON_CMD -i $@"
334			else
335			EXEC_CMD="$PYTHON_CMD $@"
336			fi
337			else
338			EXEC_CMD="$PYTHON_MPI $@"
339			fi
340			fi
341			if [ ! -z $ESCRIPT_VERBOSE ]; then echo "Command to be executed is \"$EXEC_CMD\"."; fi
342			#===============================================================================================
343			#
344			# now we start to spwan things:
345			#
346			if [ $WITH_OPENMP == "y" ]
347			then
348			export OMP_NUM_THREADS=$ESCRIPT_NUM_THREADS
349			EXPORT_ENV="$EXPORT_ENV,OMP_NUM_THREADS"
350			fi
351			EXIT_CODE=1
352			#=============== no MPI ===================================
353			if [ $MPI_FLAVOUR == "none" ]
354			then
355			$EXEC_CMD
356			EXIT_CODE=$?
357			#=============== OpenMPI ===================================
358			elif [ $MPI_FLAVOUR == "OPENMPI" ]
359			then
360			if [ ! -z $HOSTFILE ]
361			then
362			HOST_LIST=`awk 'BEGIN{S=""}{if (S == "") { S = $0 } else {S = S "," $0}}END{print S}' $HOSTFILE`
363	gross	2491	CMD="mpirun -x ${EXPORT_ENV//,/ -x } --bynode -np $TOTPROC --host $HOST_LIST $EXEC_CMD"
364	jfenwick	2409	else
365	gross	2491	CMD="mpirun -x ${EXPORT_ENV//,/ -x } -np $TOTPROC $EXEC_CMD"
366	jfenwick	2409	fi
367			if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI command is \"$CMD\"."; fi
368			$CMD
369			EXIT_CODE=$?
370
371			#=============== Intel MPI ===================================
372			elif [ $MPI_FLAVOUR == "INTELMPI" ]
373			then
374	gross	2510
375			if [ $WITH_OPENMP == "y" ]
376			then
377			export I_MPI_PIN_DOMAIN=omp
378			EXPORT_ENV="$EXPORT_ENV, I_MPI_PIN_DOMAIN"
379			fi
380
381	jfenwick	2409	if [ ! -z $HOSTFILE ]
382			then
383			mpdboot -n $ESCRIPT_NUM_NODES -r ssh -f $HOSTFILE
384			if [ $? -ne 0 ]
385			then
386			echo "mpdboot with host file $ESCRIPT_HOSTFILE for $ESCRIPT_NUM_NODES nodes failed."
387			exit 1
388			else
389			if [ ! -z $ESCRIPT_VERBOSE ]; then echo "mpdboot was started with host file $ESCRIPT_HOSTFILE for $ESCRIPT_NUM_NODES nodes."; fi
390			fi
391			fi
392			CMD="mpiexec -perhost $ESCRIPT_NUM_PROCS -envall -n $TOTPROC $EXEC_CMD"
393			if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI command is \"$CMD\"."; fi
394			$CMD
395			EXIT_CODE=$?
396			if [ ! -z $HOSTFILE ]
397			then
398			mpdallexit
399			if [ ! -z $ESCRIPT_VERBOSE ]; then echo "mpdallexit executed."; fi
400			fi
401			#=============== SGI's MPIMPT ===================================
402			elif [ $MPI_FLAVOUR == "MPT" ]
403			then
404			export MPI_NUM_MEMORY_REGIONS=0
405			EXPORT_ENV="$EXPORT_ENV,MPI_NUM_MEMORY_REGIONS"
406			if [ ! -z $HOSTFILE ]
407			then
408			HOST_LIST=`awk 'BEGIN{S=""}{if (S == "") { S = $0 } else {S = S "," $0}}END{print S}' $HOSTFILE`
409			CMD="mpirun $HOST_LIST $ESCRIPT_NUM_PROCS $EXEC_CMD"
410			else
411			CMD="mpirun -np $TOTPROC $EXEC_CMD"
412			fi
413			if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI command is \"$CMD\"."; fi
414			$CMD
415			EXIT_CODE=$?
416			#=============== MPICH ===================================
417			elif [ $MPI_FLAVOUR == "MPICH" ]
418			then
419			if [ ! -z $HOSTFILE ]
420			then
421			touch $HOSTFILE2
422			for (( i=1;i<=$ESCRIPT_NUM_PROCS;i+=1 )) ; do cat $HOSTFILE >> $HOSTFILE2 ; done
423			CMD="mpirun -machinefile $HOSTFILE2 -np $TOTPROC $EXEC_CMD"
424			else
425			CMD="mpirun -np $TOTPROC $EXEC_CMD"
426			fi
427			if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI command is \"$CMD\"."; fi
428			$CMD
429			EXIT_CODE=$?
430			#=============== MPICH2 ===================================
431			elif [ $MPI_FLAVOUR == "MPICH2" ]
432			then
433			if [ ! -z $HOSTFILE ]
434			then
435			mpdboot -n $ESCRIPT_NUM_NODES -r ssh -f $HOSTFILE
436			if [ $? -ne 0 ]
437			then
438			echo "mpdboot with host file $ESCRIPT_HOSTFILE for $ESCRIPT_NUM_NODES nodes failed."
439			exit 1
440			else
441			if [ ! -z $ESCRIPT_VERBOSE ]; then echo "mpdboot was started with host file $ESCRIPT_HOSTFILE for $ESCRIPT_NUM_NODES nodes."; fi
442			fi
443			fi
444			CMD="mpiexec -genvlist $EXPORT_ENV -np $TOTPROC $EXEC_CMD"
445			if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI command is \"$CMD\"."; fi
446			$CMD
447			EXIT_CODE=$?
448			if [ ! -z $HOSTFILE ]
449			then
450			mpdallexit
451			if [ ! -z $ESCRIPT_VERBOSE ]; then echo "mpdallexit executed."; fi
452			fi
453			else
454			echo "unknown MPI falvour $MPI_FLAVOUR."
455			fi
456			exit $EXIT_CODE