branches/newcdf/run-escript.in

#!/usr/bin/env sh

##############################################################################
#
# Copyright (c) 2003-2014 by University of Queensland
# http://www.uq.edu.au
#
# Primary Business: Queensland, Australia
# Licensed under the Open Software License version 3.0
# http://www.opensource.org/licenses/osl-3.0.php
#
# Development until 2012 by Earth Systems Science Computational Center (ESSCC)
# Development 2012-2013 by School of Earth Sciences
# Development from 2014 by Centre for Geoscience Computing (GeoComp)
#
##############################################################################

# Escript 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 this is a standalone build and ../../pkg 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.$USER.$$

die () {
    echo "Error: $@" 1>&2
    exit 1
}

#Begin finding ESCRIPT_ROOT
if [ $STDLOCATION -ne 0 ]
then
    ESCRIPT_ROOT=/usr/lib/python-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 $(echo $0|grep -q /)
  then
      # We are not using the PATH to find the script
      cd "$(dirname $0)"
      scriptdir=$(pwd)
      cd "$CURDIR"
  else
      # name does not contain / therefore we are using
      tscriptdir=$(which $0)
      if [ $? -ne 0 ]
      then
          die "Unable to determine script directory!"
      fi
      scriptdir=$(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

if [ $STDLOCATION -eq 1 ]
then
    EXTRA_LD_LIBRARY_PATH=/usr/lib/python-escript
else
    EXTRA_LD_LIBRARY_PATH=$ESCRIPT_ROOT/lib
fi


if [ $STANDALONE -eq 1 ]
then
    EXTRA_PATH=$ESCRIPT_PARENT/pkg/python/bin:$ESCRIPT_PARENT/pkg/scons/bin:$EXTRA_PATH
    EXTRA_LD_LIBRARY_PATH=$ESCRIPT_PARENT/pkg/boost/lib:$ESCRIPT_PARENT/pkg/netcdf/lib/:$EXTRA_LD_LIBRARY_PATH
    EXTRA_LD_LIBRARY_PATH=$EXTRA_LD_LIBRARY_PATH
    EXTRA_LD_LIBRARY_PATH=$ESCRIPT_PARENT/pkg/python/lib:$EXTRA_LD_LIBRARY_PATH
    EXTRA_PYTHONPATH=$ESCRIPT_PARENT/pkg/numpy/lib/python2.6/site-packages:$ESCRIPT_PARENT/pkg/matplotlib/lib/python2.6/site-packages:$EXTRA_PYTHONPATH
fi


BUILDINFO_FILE="$ESCRIPT_ROOT/lib/buildvars"
if [ "$STDLOCATION" = "1" ]
then
    BUILDINFO_FILE=/usr/lib/python-escript/buildvars
fi
if [ ! -r "$BUILDINFO_FILE" ]; then
    if [ "$1" = "-e" ]; then
        echo "export LD_LIBRARY_PATH=$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
    fi
    die "Unable to read escript build information!"
fi

get_buildvar () {
    echo $(grep "^$1=" "$BUILDINFO_FILE" |cut -d= -f2)
}

HELP_TEXT="
Usage: run-escript [options] script.py [arguments...]
    -n nn       number of nodes to use
    -p np       number of MPI processes to spawn per node
    -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      run in new xterm instance
    -m tool     run with valgrind {tool=m[emcheck]/c[allgrind]/[cac]h[egrind]}
    script.py   Your python script
    arguments...    The optional command-line arguments to your script
"

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

# Parse the command-line options
while getopts 'bn:p:t:f:echim:oVvx' option
do
    case "$option" in
      "b")  DO_BINARY=y
        ;;
      "m")  DO_VALGRIND=$OPTARG
        ;;
      "n")  ESCRIPT_NUM_NODES=$OPTARG
        ;;
      "p")  ESCRIPT_NUM_PROCS=$OPTARG
        ;;
      "t")  ESCRIPT_NUM_THREADS=$OPTARG
        ;;
      "f")  ESCRIPT_HOSTFILE=$OPTARG
        ;;
      "c")  cat "$BUILDINFO_FILE"
        exit 0
        ;;
      "V")  echo "escript-development(build "$(get_buildvar svn_revision)")"
        exit 0
        ;;
      "h")  echo "$HELP_TEXT"
        exit 0
        ;;
      "i")  DO_INTERACTIVE=y
        ;;
      "e")  echo "export LD_LIBRARY_PATH=$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:$EXTRA_LD_LIBRARY_PATH:\$DYLD_LIBRARY_PATH"
        fi
        exit 0
        ;;
      "o")  ESCRIPT_CREATESTDFILES=y
        ;;
      "v")  ESCRIPT_VERBOSE=y
        ;;
      "x")  DO_XTERM=y
        ;;
      ?)    echo "$HELP_TEXT"
        exit 1
        ;;
    esac
done
shift $(($OPTIND - 1))

vlog () {
    if [ ! -z $ESCRIPT_VERBOSE ]; then
        echo "$@"
    fi
}

#==============================================
#
#   Read MPI_FLAVOUR and WITH_OPENMP from the buildvars
#
MPI_FLAVOUR=$(get_buildvar mpi)
WITH_OPENMP=$(get_buildvar openmp)

vlog "MPI flavour is $MPI_FLAVOUR."
if [ "$WITH_OPENMP" = "1" ]; then
    vlog "OpenMP enabled."
else
    vlog "OpenMP disabled."
fi

#
#   Add VisIt paths if required
#
WITH_VISIT=$(get_buildvar visit)
if [ "$WITH_VISIT" = "1" ]; then
    VISIT_BIN=$(which visit 2>/dev/null)
    if [ $? -eq 0 ]; then
        VISIT_PY_PATH=$($VISIT_BIN -env | grep LIBPATH | cut -d= -f2)
        EXTRA_PYTHONPATH=$EXTRA_PYTHONPATH:$VISIT_PY_PATH
        EXTRA_LD_LIBRARY_PATH=$EXTRA_LD_LIBRARY_PATH:$VISIT_PY_PATH
    else
        vlog "Warning: VisIt module enabled but VisIt not in path!"
    fi
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
vlog "PATH = $PATH
LD_LIBRARY_PATH = $LD_LIBRARY_PATH
PYTHONPATH = $PYTHONPATH"
if [ ! -z $DYLD_LIBRARY_PATH ]; then
    vlog "DYLD_LIBRARY_PATH = $DYLD_LIBRARY_PATH"
fi

#==============================================
#
#  Ensure the variables have sensible values
#
if [ "$MPI_FLAVOUR" = "none" ]
then
    if [ ! -z "$ESCRIPT_NUM_NODES" ]; then
        if [ $ESCRIPT_NUM_NODES -gt 1 ]; then
            echo "Warning: MPI disabled but number of nodes set. Option ignored."
        fi
    fi
    if [ ! -z "$ESCRIPT_NUM_PROCS" ]; then
        if [ $ESCRIPT_NUM_PROCS -gt 1 ]; then
            echo "Warning: MPI disabled but number of processors per node set. Option ignored."
        fi
    fi
    if [ ! -z "$ESCRIPT_HOSTFILE" ]
    then
        echo "Warning: MPI disabled but host file is given. Option ignored."
    fi
    ESCRIPT_NUM_NODES=1
    ESCRIPT_NUM_PROCS=1
else
    # use the PBS_NODEFILE if not otherwise specified
    if [ ! -z "$PBS_NODEFILE" ] && [ -z "$ESCRIPT_HOSTFILE" ]
    then
        ESCRIPT_HOSTFILE=$PBS_NODEFILE
    fi

    if [ ! -z "$ESCRIPT_HOSTFILE" ]
    then
        if [ -f "$ESCRIPT_HOSTFILE" ]
        then
            sort -u "${ESCRIPT_HOSTFILE}" > $HOSTFILE
            HOSTLIST=$(awk 'BEGIN{S=""}{if (S == "") { S = $0 } else {S = S "," $0}}END{print S}' "$HOSTFILE")

            NUM_HOSTS=$(cat "$HOSTFILE" | wc -l)
            if [ ! -z $ESCRIPT_NUM_NODES ]
            then
                if [ $NUM_HOSTS -ne $ESCRIPT_NUM_NODES ]
                then
                    die "Number of hosts selected in the host file $ESCRIPT_HOSTFILE needs to match the requested number of nodes $ESCRIPT_NUM_NODES!"
                fi
             else
                ESCRIPT_NUM_NODES=$NUM_HOSTS
             fi
        else
           die "Cannot find hostfile $ESCRIPT_HOSTFILE!"
        fi
    else
        echo "localhost" > $HOSTFILE
        HOSTLIST="localhost"
    fi

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

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

    vlog "ESCRIPT_NUM_NODES = $ESCRIPT_NUM_NODES\nESCRIPT_NUM_PROCS = $ESCRIPT_NUM_PROCS"
fi

if [ "$WITH_OPENMP" = "1" ]
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
    vlog "ESCRIPT_NUM_THREADS = $ESCRIPT_NUM_THREADS"
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. Option ignored."
    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
    die "Expression of total number of processors = $ESCRIPT_NUM_NODES * $ESCRIPT_NUM_PROCS is not numerical!"
fi

# set up thread binding if unset -- disabled by default because it interfers
# with MPI binding
#if [ "$OMP_PROC_BIND" = "" ]; then
#    #Force OpenMP binding for Intel (and GCC, though GCC is on by default)
#    export OMP_PROC_BIND=true
#fi
#if [ "$KMP_AFFINITY" = "" ]; then
#    #Set the style of binding (overrides OMP_PROC_BIND in many cases)
#    export KMP_AFFINITY=verbose,compact
#fi

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

if [ $TOTPROC -gt 1 ]
then
    if [ "$ESCRIPT_CREATESTDFILES" = "y" ]
    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 $DO_BINARY ]
    then
        die "No program to run was specified!"
    else
        DO_INTERACTIVE=y
    fi
fi

#==============================================================================

if [ ! -z $DO_XTERM ]
then
    EXEC_CMD="xterm -e"
else
    EXEC_CMD=""
fi

if [ ! -z "$DO_VALGRIND" ]
then
    VALGRIND_BIN=$(which valgrind 2>/dev/null)
    if [ $? -eq 0 ]; then
        LOGDIR=$ESCRIPT_ROOT/valgrind_logs
        [ -d $LOGDIR ] || mkdir $LOGDIR
        VG_TOOL=$(echo $DO_VALGRIND | awk '{ s=substr($0,1,1);print s;}')
        if [ $VG_TOOL = "c" ];
        then
            # run callgrind
            LOGFILE=${LOGDIR}/callgrind.%p.xml
            VALGRIND="valgrind --tool=callgrind --callgrind-out-file=$LOGFILE"
            EXEC_CMD="$EXEC_CMD $VALGRIND"
        elif [ $VG_TOOL = "h" ];
        then
            # run cachegrind
            LOGFILE=${LOGDIR}/cachegrind.%p.xml
            VALGRIND="valgrind --tool=cachegrind --cachegrind-out-file=$LOGFILE"
            EXEC_CMD="$EXEC_CMD $VALGRIND"
        else
            # run memcheck by default
            LAST_N=$(ls -1 $LOGDIR|grep "^memcheck"|tail -1|cut -d. -f2)
            NEW_N=$(printf "%04d" $((LAST_N + 1)))
            LOGFILE=${LOGDIR}/memcheck.${NEW_N}.xml
            VALGRIND="valgrind --tool=memcheck --xml=yes --show-reachable=yes --error-limit=no --gen-suppressions=all --suppressions=$ESCRIPT_ROOT/scripts/escript.supp --leak-check=full --xml-file=$LOGFILE"
            EXEC_CMD="$EXEC_CMD $VALGRIND"
        fi
    else
        die "Execution with valgrind requested but valgrind not in path!"
    fi
fi

if [ ! -z $DO_BINARY ]
then
    EXEC_CMD="$EXEC_CMD $@"
else
    # Check to see if the python version we were compiled with matches the
    # one of PYTHON_CMD.
    compfull=$(get_buildvar python_version)
    compversion=$(echo $compfull | cut -d. -f1,2)
    compmajor=$(echo $compfull | cut -d. -f1)
    if [ "$PYTHON_CMD" = "python" ] # if people have customised the command they
    then                                # might not want us changing it
        if [ "$compmajor" = "3" ]
        then
            PYTHON_CMD=python3
        fi
    fi
    intversion=$($PYTHON_CMD -c 'from __future__ import print_function;import sys;print("%d.%d"%(sys.version_info[0], sys.version_info[1]))')
    if [ "$compversion" != "$intversion" ]
    then
        die "Python versions do not match. Escript was compiled for '$compversion'.
Current version of Python appears to be '$intversion'."
    fi
    if [ "$MPI_FLAVOUR" = "none" ]
    then
        if [ ! -z $DO_INTERACTIVE ]
        then
           EXEC_CMD="$EXEC_CMD $PYTHON_CMD -i $@"
        else
           EXEC_CMD="$EXEC_CMD $PYTHON_CMD $@"
        fi
    else
        if [ ! -z $DO_INTERACTIVE ]
        then
           EXEC_CMD="$EXEC_CMD $PYTHON_MPI -i $@"
        else
           EXEC_CMD="$EXEC_CMD $PYTHON_MPI $@"
        fi
    fi
fi
vlog "Command to be executed is \"$EXEC_CMD\""
#==============================================================================
#
#   now we start to spawn things:
#
if [ "$WITH_OPENMP" = "1" ]
then
   export OMP_NUM_THREADS=$ESCRIPT_NUM_THREADS
   EXPORT_ENV="$EXPORT_ENV,OMP_NUM_THREADS"
fi

vlog "Pre-launch command: \"@@PRELAUNCH\""
@@PRELAUNCH
vlog "Launch command: \"@@LAUNCH\""
@@LAUNCH
EXIT_CODE=$?
vlog "Post-launch command: \"@@POSTLAUNCH\""
@@POSTLAUNCH

if [ ! -z "$DO_VALGRIND" ]; then
   echo "Valgrind log file written to ${LOGFILE}"
fi

rm -f $HOSTFILE

exit $EXIT_CODE

1	caltinay	4927	#!/usr/bin/env sh
2	jfenwick	2409
3	caltinay	5266	##############################################################################
4			#
5			# Copyright (c) 2003-2014 by University of Queensland
6			# http://www.uq.edu.au
7			#
8			# Primary Business: Queensland, Australia
9			# Licensed under the Open Software License version 3.0
10			# http://www.opensource.org/licenses/osl-3.0.php
11			#
12			# Development until 2012 by Earth Systems Science Computational Center (ESSCC)
13			# Development 2012-2013 by School of Earth Sciences
14			# Development from 2014 by Centre for Geoscience Computing (GeoComp)
15			#
16			##############################################################################
17	jfenwick	2409
18	caltinay	5266	# Escript wrapper for python
19			# Sets LD_LIBRARY_PATH and PYTHONPATH and then runs either python or the MPI
20			# launcher.
21	jfenwick	2409
22	caltinay	5266	# Extra paths can be configured about a page further down
23			# Search for EXTRA_PATH=""
24
25			# set to 1 if this is a standalone build and ../../pkg contains the relevant
26			# tools
27	caltinay	4362	STANDALONE=0
28	jfenwick	2409
29	caltinay	5266	# set to 1 if this is part of a packaged build (.deb) and files will be
30			# installed in standard locations rather than everything in a single directory
31			# Do not use this together with STANDALONE
32	jfenwick	2409	STDLOCATION=0
33
34	caltinay	5266	# Now we find the location of this script
35			# Note that this location should be absolute but does not need to be unique
36	jfenwick	2409	scriptdir=""
37	caltinay	4970	CURDIR=$(pwd)
38	jfenwick	2409
39	caltinay	5266	# Environment vars which control operations:
40	jfenwick	2409	# ESCRIPT_NUM_NODES, ESCRIPT_NUM_PROCS, ESCRIPT_NUM_THREADS, ESCRIPT_HOSTFILE, ESCRIPT_CREATESTDFILES
41
42	jfenwick	3047	HOSTFILE=/tmp/escript.$USER.$$
43	jfenwick	2409
44	caltinay	5266	die () {
45			echo "Error: $@" 1>&2
46			exit 1
47			}
48
49	jfenwick	2409	#Begin finding ESCRIPT_ROOT
50	caltinay	2806	if [ $STDLOCATION -ne 0 ]
51	jfenwick	2409	then
52	caltinay	4491	ESCRIPT_ROOT=/usr/lib/python-escript
53	jfenwick	2409	else
54	caltinay	4031	# We don't know the escript root so we need to work it out from the invocation
55			# Need to match if the name contains /
56	caltinay	4927	if $(echo $0\|grep -q /)
57	jfenwick	2409	then
58			# We are not using the PATH to find the script
59	caltinay	4970	cd "$(dirname $0)"
60			scriptdir=$(pwd)
61	caltinay	3388	cd "$CURDIR"
62	jfenwick	2409	else
63	caltinay	4927	# name does not contain / therefore we are using
64	caltinay	4970	tscriptdir=$(which $0)
65	caltinay	3096	if [ $? -ne 0 ]
66	jfenwick	2409	then
67	caltinay	5266	die "Unable to determine script directory!"
68	jfenwick	2409	fi
69	caltinay	4970	scriptdir=$(dirname $tscriptdir)
70	jfenwick	2409	fi
71
72	caltinay	3388	cd "$scriptdir/.."
73	caltinay	4970	ESCRIPT_ROOT=$(pwd)
74	jfenwick	2409	cd ..
75	caltinay	4970	ESCRIPT_PARENT=$(pwd)
76	caltinay	3388	cd "$CURDIR"
77	jfenwick	2409
78			fi
79	caltinay	4031	##### End finding ESCRIPT_ROOT ########
80	jfenwick	2409
81			PYTHON_MPI_NULL="$ESCRIPT_ROOT/lib/pythonMPI"
82			PYTHON_MPI_REDIRECT="$ESCRIPT_ROOT/lib/pythonMPIredirect"
83			PYTHON_CMD=python
84
85			# if possible please express paths relative to $ESCRIPT_ROOT unless
86			# they are in an unrelated location
87
88			EXTRA_DYLD_LIBRARY_PATH=""
89			EXTRA_PATH=$ESCRIPT_ROOT/bin
90			EXTRA_PYTHONPATH=$ESCRIPT_ROOT
91
92	jfenwick	4078	if [ $STDLOCATION -eq 1 ]
93			then
94	caltinay	4491	EXTRA_LD_LIBRARY_PATH=/usr/lib/python-escript
95	jfenwick	4078	else
96			EXTRA_LD_LIBRARY_PATH=$ESCRIPT_ROOT/lib
97			fi
98
99
100	caltinay	2806	if [ $STANDALONE -eq 1 ]
101	jfenwick	2409	then
102	jfenwick	3335	EXTRA_PATH=$ESCRIPT_PARENT/pkg/python/bin:$ESCRIPT_PARENT/pkg/scons/bin:$EXTRA_PATH
103	jfenwick	2530	EXTRA_LD_LIBRARY_PATH=$ESCRIPT_PARENT/pkg/boost/lib:$ESCRIPT_PARENT/pkg/netcdf/lib/:$EXTRA_LD_LIBRARY_PATH
104	jfenwick	2541	EXTRA_LD_LIBRARY_PATH=$EXTRA_LD_LIBRARY_PATH
105	jfenwick	2530	EXTRA_LD_LIBRARY_PATH=$ESCRIPT_PARENT/pkg/python/lib:$EXTRA_LD_LIBRARY_PATH
106	jfenwick	2541	EXTRA_PYTHONPATH=$ESCRIPT_PARENT/pkg/numpy/lib/python2.6/site-packages:$ESCRIPT_PARENT/pkg/matplotlib/lib/python2.6/site-packages:$EXTRA_PYTHONPATH
107	jfenwick	2409	fi
108
109	jfenwick	3335
110	jfenwick	4342	BUILDINFO_FILE="$ESCRIPT_ROOT/lib/buildvars"
111	jfenwick	4078	if [ "$STDLOCATION" = "1" ]
112			then
113	caltinay	4491	BUILDINFO_FILE=/usr/lib/python-escript/buildvars
114	jfenwick	4078	fi
115	jfenwick	4342	if [ ! -r "$BUILDINFO_FILE" ]; then
116	caltinay	4031	if [ "$1" = "-e" ]; then
117			echo "export LD_LIBRARY_PATH=$EXTRA_LD_LIBRARY_PATH:\$LD_LIBRARY_PATH"
118			echo "export PYTHONPATH=$EXTRA_PYTHONPATH:\$PYTHONPATH"
119			echo "export PATH=$EXTRA_PATH:\$PATH"
120	caltinay	4970	if [ "$(uname)" = "Darwin" ]
121	caltinay	4031	then
122			echo "export DYLD_LIBRARY_PATH=$EXTRA_DYLD_LIBRARY_PATH:$EXTRA_LD_LIBRARY_PATH:\$DYLD_LIBRARY_PATH"
123	caltinay	4927	fi
124	jfenwick	3335	exit 0
125			fi
126	caltinay	5266	die "Unable to read escript build information!"
127	jfenwick	3335	fi
128
129	caltinay	4031	get_buildvar () {
130	caltinay	4970	echo $(grep "^$1=" "$BUILDINFO_FILE" \|cut -d= -f2)
131	jfenwick	3335	}
132
133	jfenwick	2409	HELP_TEXT="
134	caltinay	4031	Usage: run-escript [options] script.py [arguments...]
135	jfenwick	2409	-n nn number of nodes to use
136	gross	3193	-p np number of MPI processes to spawn per node
137	jfenwick	2409	-t nt number of OpenMP threads to use
138			-f file name of MPI hostfile
139	caltinay	4031	-c print compile information for escript and exit
140	jfenwick	2409	-V print escript version and exit
141	caltinay	4927	-i interactive mode
142	jfenwick	2409	-b do not invoke python (run non-python programs)
143			-e print export statements for environment and exit
144			-o redirect output from MPI to files
145			-v print diagnostics
146	caltinay	4031	-x run in new xterm instance
147	caltinay	5239	-m tool run with valgrind {tool=m[emcheck]/c[allgrind]/[cac]h[egrind]}
148	jfenwick	2409	script.py Your python script
149			arguments... The optional command-line arguments to your script
150			"
151
152			if [ "$1" = "--help" ]; then
153			echo "$HELP_TEXT"
154			exit 0
155			fi
156	caltinay	4031	#==============================================================================
157	jfenwick	2409
158			# Parse the command-line options
159	caltinay	4506	while getopts 'bn:p:t:f:echim:oVvx' option
160	jfenwick	2409	do
161	caltinay	4031	case "$option" in
162			"b") DO_BINARY=y
163			;;
164	caltinay	4506	"m") DO_VALGRIND=$OPTARG
165	caltinay	4483	;;
166	caltinay	4031	"n") ESCRIPT_NUM_NODES=$OPTARG
167			;;
168			"p") ESCRIPT_NUM_PROCS=$OPTARG
169			;;
170			"t") ESCRIPT_NUM_THREADS=$OPTARG
171			;;
172			"f") ESCRIPT_HOSTFILE=$OPTARG
173			;;
174	jfenwick	4342	"c") cat "$BUILDINFO_FILE"
175	caltinay	4031	exit 0
176			;;
177	caltinay	4970	"V") echo "escript-development(build "$(get_buildvar svn_revision)")"
178	caltinay	4031	exit 0
179			;;
180			"h") echo "$HELP_TEXT"
181			exit 0
182			;;
183			"i") DO_INTERACTIVE=y
184			;;
185			"e") echo "export LD_LIBRARY_PATH=$EXTRA_LD_LIBRARY_PATH:\$LD_LIBRARY_PATH"
186			echo "export PYTHONPATH=$EXTRA_PYTHONPATH:\$PYTHONPATH"
187			echo "export PATH=$EXTRA_PATH:\$PATH"
188	caltinay	4970	if [ "$(uname)" = "Darwin" ]
189	caltinay	4031	then
190			echo "export DYLD_LIBRARY_PATH=$EXTRA_DYLD_LIBRARY_PATH:$EXTRA_LD_LIBRARY_PATH:\$DYLD_LIBRARY_PATH"
191			fi
192			exit 0
193			;;
194			"o") ESCRIPT_CREATESTDFILES=y
195			;;
196			"v") ESCRIPT_VERBOSE=y
197			;;
198			"x") DO_XTERM=y
199			;;
200			?) echo "$HELP_TEXT"
201			exit 1
202			;;
203			esac
204	jfenwick	2409	done
205	caltinay	4970	shift $(($OPTIND - 1))
206	caltinay	5266
207			vlog () {
208			if [ ! -z $ESCRIPT_VERBOSE ]; then
209			echo "$@"
210			fi
211			}
212
213	jfenwick	2409	#==============================================
214			#
215	caltinay	3178	# Read MPI_FLAVOUR and WITH_OPENMP from the buildvars
216	jfenwick	2409	#
217	caltinay	4970	MPI_FLAVOUR=$(get_buildvar mpi)
218			WITH_OPENMP=$(get_buildvar openmp)
219	jfenwick	2409
220	caltinay	5266	vlog "MPI flavour is $MPI_FLAVOUR."
221			if [ "$WITH_OPENMP" = "1" ]; then
222			vlog "OpenMP enabled."
223			else
224			vlog "OpenMP disabled."
225	caltinay	2806	fi
226
227	jfenwick	2409	#
228	caltinay	5266	# Add VisIt paths if required
229			#
230			WITH_VISIT=$(get_buildvar visit)
231			if [ "$WITH_VISIT" = "1" ]; then
232			VISIT_BIN=$(which visit 2>/dev/null)
233			if [ $? -eq 0 ]; then
234			VISIT_PY_PATH=$($VISIT_BIN -env \| grep LIBPATH \| cut -d= -f2)
235			EXTRA_PYTHONPATH=$EXTRA_PYTHONPATH:$VISIT_PY_PATH
236			EXTRA_LD_LIBRARY_PATH=$EXTRA_LD_LIBRARY_PATH:$VISIT_PY_PATH
237			else
238			vlog "Warning: VisIt module enabled but VisIt not in path!"
239			fi
240			fi
241
242			#
243	jfenwick	2409	# extend path variables
244			#
245			export PATH=$EXTRA_PATH:$PATH
246			export LD_LIBRARY_PATH=$EXTRA_LD_LIBRARY_PATH:$LD_LIBRARY_PATH
247			export PYTHONPATH=$EXTRA_PYTHONPATH:$PYTHONPATH
248			EXPORT_ENV="PATH,LD_LIBRARY_PATH,PYTHONPATH"
249	caltinay	4970	if [ "$(uname)" = "Darwin" ]
250	jfenwick	2409	then
251			export DYLD_LIBRARY_PATH=$EXTRA_DYLD_LIBRARY_PATH:$EXTRA_LD_LIBRARY_PATH:$DYLD_LIBRARY_PATH
252			EXPORT_ENV="$EXPORT_ENV,DYLD_LIBRARY_PATH"
253			fi
254	caltinay	5266	vlog "PATH = $PATH
255			LD_LIBRARY_PATH = $LD_LIBRARY_PATH
256			PYTHONPATH = $PYTHONPATH"
257			if [ ! -z $DYLD_LIBRARY_PATH ]; then
258			vlog "DYLD_LIBRARY_PATH = $DYLD_LIBRARY_PATH"
259	jfenwick	2409	fi
260	caltinay	5266
261	jfenwick	2409	#==============================================
262			#
263			# Ensure the variables have sensible values
264			#
265	caltinay	4927	if [ "$MPI_FLAVOUR" = "none" ]
266	jfenwick	2409	then
267	caltinay	4664	if [ ! -z "$ESCRIPT_NUM_NODES" ]; then
268			if [ $ESCRIPT_NUM_NODES -gt 1 ]; then
269			echo "Warning: MPI disabled but number of nodes set. Option ignored."
270			fi
271	jfenwick	2409	fi
272	caltinay	4664	if [ ! -z "$ESCRIPT_NUM_PROCS" ]; then
273			if [ $ESCRIPT_NUM_PROCS -gt 1 ]; then
274			echo "Warning: MPI disabled but number of processors per node set. Option ignored."
275			fi
276	jfenwick	2409	fi
277	jfenwick	4342	if [ ! -z "$ESCRIPT_HOSTFILE" ]
278	jfenwick	2409	then
279			echo "Warning: MPI disabled but host file is given. Option ignored."
280			fi
281			ESCRIPT_NUM_NODES=1
282			ESCRIPT_NUM_PROCS=1
283			else
284	jfenwick	3056	# use the PBS_NODEFILE if not otherwise specified
285	jfenwick	4342	if [ ! -z "$PBS_NODEFILE" ] && [ -z "$ESCRIPT_HOSTFILE" ]
286	jfenwick	3056	then
287	caltinay	3178	ESCRIPT_HOSTFILE=$PBS_NODEFILE
288	jfenwick	3056	fi
289
290	caltinay	4927	if [ ! -z "$ESCRIPT_HOSTFILE" ]
291	jfenwick	2409	then
292	jfenwick	4342	if [ -f "$ESCRIPT_HOSTFILE" ]
293	jfenwick	2409	then
294	caltinay	5266	sort -u "${ESCRIPT_HOSTFILE}" > $HOSTFILE
295			HOSTLIST=$(awk 'BEGIN{S=""}{if (S == "") { S = $0 } else {S = S "," $0}}END{print S}' "$HOSTFILE")
296
297	caltinay	5275	NUM_HOSTS=$(cat "$HOSTFILE" \| wc -l)
298	caltinay	4927	if [ ! -z $ESCRIPT_NUM_NODES ]
299	jfenwick	2409	then
300			if [ $NUM_HOSTS -ne $ESCRIPT_NUM_NODES ]
301			then
302	caltinay	5266	die "Number of hosts selected in the host file $ESCRIPT_HOSTFILE needs to match the requested number of nodes $ESCRIPT_NUM_NODES!"
303	jfenwick	2409	fi
304			else
305			ESCRIPT_NUM_NODES=$NUM_HOSTS
306			fi
307			else
308	caltinay	5266	die "Cannot find hostfile $ESCRIPT_HOSTFILE!"
309	jfenwick	2409	fi
310			else
311	caltinay	5266	echo "localhost" > $HOSTFILE
312			HOSTLIST="localhost"
313	jfenwick	2409	fi
314
315			if [ -z $ESCRIPT_NUM_NODES ]
316			then
317	caltinay	3178	ESCRIPT_NUM_NODES=1
318	jfenwick	2409	fi
319
320			if [ -z $ESCRIPT_NUM_PROCS ]
321			then
322	caltinay	3178	ESCRIPT_NUM_PROCS=1
323	jfenwick	2409	fi
324
325	caltinay	5266	vlog "ESCRIPT_NUM_NODES = $ESCRIPT_NUM_NODES\nESCRIPT_NUM_PROCS = $ESCRIPT_NUM_PROCS"
326	jfenwick	2409	fi
327
328	jfenwick	3259	if [ "$WITH_OPENMP" = "1" ]
329	jfenwick	2409	then
330	caltinay	5266	if [ -z $ESCRIPT_NUM_THREADS ]
331			then
332	jfenwick	2409	ESCRIPT_NUM_THREADS=$OMP_NUM_THREADS
333			if [ -z $ESCRIPT_NUM_THREADS ]
334			then
335	caltinay	5266	ESCRIPT_NUM_THREADS=1
336	jfenwick	2409	fi
337	caltinay	5266	fi
338			vlog "ESCRIPT_NUM_THREADS = $ESCRIPT_NUM_THREADS"
339	jfenwick	2409	else
340	caltinay	5266	if [ ! -z $ESCRIPT_NUM_THREADS ] && [ $ESCRIPT_NUM_THREADS != 1 ]
341			then
342			echo "Warning: OpenMP is disabled but number of threads requested is $ESCRIPT_NUM_THREADS!=1. Option ignored."
343			fi
344			ESCRIPT_NUM_THREADS=1
345	jfenwick	2409	fi
346	caltinay	5266
347	jfenwick	2409	#
348			# Now we compute total number of Processes
349			#
350	caltinay	4031	TOTPROC=$((ESCRIPT_NUM_NODES * ESCRIPT_NUM_PROCS))
351	caltinay	5266	if [ $? -ne 0 ] #Some compute error
352	caltinay	4031	then #This could happen if the args were not a number
353	caltinay	5266	die "Expression of total number of processors = $ESCRIPT_NUM_NODES * $ESCRIPT_NUM_PROCS is not numerical!"
354	jfenwick	2409	fi
355
356	caltinay	5404	# set up thread binding if unset -- disabled by default because it interfers
357			# with MPI binding
358			#if [ "$OMP_PROC_BIND" = "" ]; then
359			# #Force OpenMP binding for Intel (and GCC, though GCC is on by default)
360			# export OMP_PROC_BIND=true
361			#fi
362			#if [ "$KMP_AFFINITY" = "" ]; then
363			# #Set the style of binding (overrides OMP_PROC_BIND in many cases)
364			# export KMP_AFFINITY=verbose,compact
365			#fi
366	caltinay	5266
367	jfenwick	2409	#
368			# Test to ensure people aren't trying to combine interactive and multi-process
369			#
370	caltinay	4058	if ([ ! -z $DO_INTERACTIVE ] \|\| [ $# -eq 0 ]) && ([ $TOTPROC -gt 1 ])
371	jfenwick	2409	then
372	caltinay	5266	die "Interactive mode cannot be used with more than one process!"
373	jfenwick	2409	fi
374
375	caltinay	4927	if [ $TOTPROC -gt 1 ]
376	jfenwick	2409	then
377	caltinay	4322	if [ "$ESCRIPT_CREATESTDFILES" = "y" ]
378	caltinay	3178	then
379			PYTHON_MPI=$PYTHON_MPI_REDIRECT
380			else
381			PYTHON_MPI=$PYTHON_MPI_NULL
382			fi
383	jfenwick	2409	else
384			PYTHON_MPI=$PYTHON_MPI_NULL
385			fi
386	caltinay	4031	#==============================================================================
387	jfenwick	2409	# Must have at least one command-line arg: the python script
388			if [ $# -eq 0 ]
389			then
390	caltinay	4031	if [ ! -z $DO_BINARY ]
391	caltinay	3178	then
392	caltinay	5266	die "No program to run was specified!"
393	caltinay	3178	else
394	caltinay	4031	DO_INTERACTIVE=y
395	caltinay	3178	fi
396	jfenwick	2409	fi
397
398	caltinay	4031	#==============================================================================
399	caltinay	4483
400	caltinay	4031	if [ ! -z $DO_XTERM ]
401	jfenwick	2409	then
402	caltinay	4031	EXEC_CMD="xterm -e"
403	jfenwick	2409	else
404	caltinay	4031	EXEC_CMD=""
405			fi
406
407	caltinay	4483	if [ ! -z "$DO_VALGRIND" ]
408			then
409	caltinay	4970	VALGRIND_BIN=$(which valgrind 2>/dev/null)
410	caltinay	4483	if [ $? -eq 0 ]; then
411	caltinay	4506	LOGDIR=$ESCRIPT_ROOT/valgrind_logs
412	caltinay	4483	[ -d $LOGDIR ] \|\| mkdir $LOGDIR
413	caltinay	4970	VG_TOOL=$(echo $DO_VALGRIND \| awk '{ s=substr($0,1,1);print s;}')
414			if [ $VG_TOOL = "c" ];
415	caltinay	4506	then
416			# run callgrind
417			LOGFILE=${LOGDIR}/callgrind.%p.xml
418			VALGRIND="valgrind --tool=callgrind --callgrind-out-file=$LOGFILE"
419			EXEC_CMD="$EXEC_CMD $VALGRIND"
420	caltinay	5239	elif [ $VG_TOOL = "h" ];
421			then
422			# run cachegrind
423			LOGFILE=${LOGDIR}/cachegrind.%p.xml
424			VALGRIND="valgrind --tool=cachegrind --cachegrind-out-file=$LOGFILE"
425			EXEC_CMD="$EXEC_CMD $VALGRIND"
426	caltinay	4506	else
427			# run memcheck by default
428	caltinay	4970	LAST_N=$(ls -1 $LOGDIR\|grep "^memcheck"\|tail -1\|cut -d. -f2)
429			NEW_N=$(printf "%04d" $((LAST_N + 1)))
430	caltinay	4506	LOGFILE=${LOGDIR}/memcheck.${NEW_N}.xml
431			VALGRIND="valgrind --tool=memcheck --xml=yes --show-reachable=yes --error-limit=no --gen-suppressions=all --suppressions=$ESCRIPT_ROOT/scripts/escript.supp --leak-check=full --xml-file=$LOGFILE"
432			EXEC_CMD="$EXEC_CMD $VALGRIND"
433			fi
434	caltinay	4483	else
435	caltinay	5266	die "Execution with valgrind requested but valgrind not in path!"
436	caltinay	4483	fi
437			fi
438
439	caltinay	4031	if [ ! -z $DO_BINARY ]
440			then
441			EXEC_CMD="$EXEC_CMD $@"
442			else
443	caltinay	3178	# Check to see if the python version we were compiled with matches the
444			# one of PYTHON_CMD.
445	caltinay	4970	compfull=$(get_buildvar python_version)
446			compversion=$(echo $compfull \| cut -d. -f1,2)
447			compmajor=$(echo $compfull \| cut -d. -f1)
448	caltinay	4031	if [ "$PYTHON_CMD" = "python" ] # if people have customised the command they
449	jfenwick	3892	then # might not want us changing it
450			if [ "$compmajor" = "3" ]
451			then
452			PYTHON_CMD=python3
453			fi
454			fi
455	caltinay	4970	intversion=$($PYTHON_CMD -c 'from __future__ import print_function;import sys;print("%d.%d"%(sys.version_info[0], sys.version_info[1]))')
456	caltinay	3178	if [ "$compversion" != "$intversion" ]
457			then
458	caltinay	5266	die "Python versions do not match. Escript was compiled for '$compversion'.
459			Current version of Python appears to be '$intversion'."
460	caltinay	3178	fi
461	caltinay	2806	if [ "$MPI_FLAVOUR" = "none" ]
462	jfenwick	2409	then
463	caltinay	4031	if [ ! -z $DO_INTERACTIVE ]
464	jfenwick	2409	then
465	caltinay	4031	EXEC_CMD="$EXEC_CMD $PYTHON_CMD -i $@"
466	jfenwick	2409	else
467	caltinay	4031	EXEC_CMD="$EXEC_CMD $PYTHON_CMD $@"
468	jfenwick	2409	fi
469			else
470	caltinay	4031	if [ ! -z $DO_INTERACTIVE ]
471	gross	2865	then
472	caltinay	4031	EXEC_CMD="$EXEC_CMD $PYTHON_MPI -i $@"
473	gross	2865	else
474	caltinay	4031	EXEC_CMD="$EXEC_CMD $PYTHON_MPI $@"
475	gross	2865	fi
476	jfenwick	2409	fi
477			fi
478	caltinay	5266	vlog "Command to be executed is \"$EXEC_CMD\""
479	caltinay	4031	#==============================================================================
480	jfenwick	2409	#
481	caltinay	4031	# now we start to spawn things:
482	jfenwick	2409	#
483	jfenwick	3259	if [ "$WITH_OPENMP" = "1" ]
484	jfenwick	2409	then
485			export OMP_NUM_THREADS=$ESCRIPT_NUM_THREADS
486			EXPORT_ENV="$EXPORT_ENV,OMP_NUM_THREADS"
487			fi
488
489	caltinay	5266	vlog "Pre-launch command: \"@@PRELAUNCH\""
490			@@PRELAUNCH
491			vlog "Launch command: \"@@LAUNCH\""
492			@@LAUNCH
493			EXIT_CODE=$?
494			vlog "Post-launch command: \"@@POSTLAUNCH\""
495			@@POSTLAUNCH
496	gross	2510
497	caltinay	4970	if [ ! -z "$DO_VALGRIND" ]; then
498			echo "Valgrind log file written to ${LOGFILE}"
499			fi
500
501	caltinay	5266	rm -f $HOSTFILE
502
503	jfenwick	2409	exit $EXIT_CODE
504	caltinay	4031