This file is indexed.

/usr/bin/run-escript2-mpi is in python-escript-mpi 5.1-5.

This file is owned by root:root, with mode 0o755.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
#!/usr/bin/env sh

##############################################################################
#
# Copyright (c) 2003-2017 by The University of Queensland
# http://www.uq.edu.au
#
# Primary Business: Queensland, Australia
# Licensed under the Apache License, version 2.0
# http://www.apache.org/licenses/LICENSE-2.0
#
# 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 part of a packaged build (.deb) and files will be
# installed in standard locations rather than everything in a single directory
STDLOCATION=1

# 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
    #Package building scripts will replace this line
    ESCRIPT_ROOT=/usr/lib/python-escript-mpi 
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 ########

# 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 [ $STDLOCATION -eq 1 ]
then
    EXTRA_LD_LIBRARY_PATH=$ESCRIPT_ROOT/lib
else
    EXTRA_LD_LIBRARY_PATH=$ESCRIPT_ROOT/lib
fi

BUILDINFO_FILE="$ESCRIPT_ROOT/lib/buildvars"
if [ ! -r "$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)
}

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

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 -lt $ESCRIPT_NUM_NODES ]
                then
		   die "Number of requested nodes must not exceed the number of entries selected in the host file $ESCRIPT_HOSTFILE.  You asked for $ESCRIPT_NUM_NODES from $NUM_HOSTS."
                fi
             else
                ESCRIPT_NUM_NODES=$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.${NEW_N}.%p.xml
            VALGRIND="valgrind --tool=memcheck --xml=yes --show-reachable=yes --error-limit=no --suppressions=$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

if [ "$MPI_FLAVOUR" = "OPENMPI" ]
then
    if [ -z `which rsh``which ssh` ]
    then
        AGENTOVERRIDE="--gmca plm_rsh_agent /bin/false"
    fi
fi 

vlog "Pre-launch command: \"EE=$(echo -x ${EXPORT_ENV}|sed -e 's/,/ -x /g')\""
EE=$(echo -x ${EXPORT_ENV}|sed -e 's/,/ -x /g')
vlog "Launch command: \"mpirun ${AGENTOVERRIDE} --gmca mpi_warn_on_fork 0 ${EE} --host ${HOSTLIST} --map-by node:pe=${ESCRIPT_NUM_THREADS} -bind-to core -np ${TOTPROC} ${EXEC_CMD}\""
mpirun ${AGENTOVERRIDE} --gmca mpi_warn_on_fork 0 ${EE} --host ${HOSTLIST} --map-by node:pe=${ESCRIPT_NUM_THREADS} -bind-to core -np ${TOTPROC} ${EXEC_CMD}
EXIT_CODE=$?
vlog "Post-launch command: \"\""


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

rm -f $HOSTFILE

exit $EXIT_CODE