source: CONFIG_DEVT/IPSLCM6.5_work_ENSEMBLES/libIGCM/libIGCM_sys/libIGCM_sys_iitm.ksh @ 5899

Last change on this file since 5899 was 5899, checked in by aclsce, 3 years ago

Modified libIGCM and configuration to run XIOS ensembles.
File size: 33.2 KB
Line 
1#!/bin/ksh
2
3#**************************************************************
4# Author: Sébastien Denvil
5# Contact: Sebastien.Denvil__at__ipsl.jussieu.fr
6# $Revision:: 1459                                     $ Revision of last commit
7# $Author:: jgipsl                                     $ Author of last commit
8# $Date:: 2018-06-22 11:42:05 +0200 (Fri, 22 Jun 2018) $ Date of last commit
9# IPSL (2006)
10#  This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC
11#
12#**************************************************************
13
14#=========================================================
15# The documentation of this file can be automatically generated
16# if you use the prefix #D- for comments to be extracted.
17# Extract with command: cat lib* | grep "^#D-" | cut -c "4-"
18#=========================================================
19
20#D-#==================================================
21#D-LibIGCM_sys for IITM IBM machine
22#D-#==================================================
23#D-
24#D- This ksh library if a layer under some usefull
25#D-environment variables and shell commands.
26#D-All those definitions depend on host particularities.
27#D-It manages a stack mechanism and test validity of operations.
28#D-All function described bellow must be prefixed by IGCM_sys.
29
30#====================================================
31# libIGCM_sys PARAMETERS
32#====================================================
33
34#====================================================
35# set DEBUG_sys to true to output calls of function
36typeset -r DEBUG_sys=${DEBUG_sys:=true}
37
38#====================================================
39# Turn in dry run mode ? (sys_Put_Rest, sys_Put_Out, sys_Get)
40typeset -r DRYRUN=${DRYRUN:=0}
41
42# YOU MUST COMPILE YOUR EXE FILES FOR DRYRUN MODE !
43# -------------------------------------------------------------------------------------
44# | DRYRUN=  |  Date computations, | sys_Get    |  Exe    | sys_Put_Out; sys_Put_Rest |
45# |          |  Cp/Exe/param/files |            |         |                           |
46# |          |  Chmod Qsub         |            |         |                           |
47# -------------------------------------------------------------------------------------
48# |    0     |       yes           |    yes     |  yes    |      yes                  |
49# -------------------------------------------------------------------------------------
50# |    1     |       yes           |    yes     |  yes    |      no                   |
51# -------------------------------------------------------------------------------------
52# |    2     |       yes           |    yes     |  no     |      no                   |
53# -------------------------------------------------------------------------------------
54# |    3     |       yes           |    no      |  no     |      no                   |
55# -------------------------------------------------------------------------------------
56
57#=====================================================
58# Global Variables :
59#=====================================================
60# Language : "fr" or "en"
61typeset -r MYLANG="fr"
62
63#=====================================================
64# Host and user names
65# $hostname ou hostname
66typeset HOST=${HOST:=$( hostname )}
67# $username ou whoami
68typeset LOGIN=${LOGIN:=$( whoami )}
69# $hostname of the MASTER job
70typeset MASTER=iitm01
71# project name
72typeset PROJECT=NONE
73# jobWarningDelay in seconds
74typeset jobWarningDelay=NONE
75
76#D-
77#D-#==================================================
78#D-Program used in libIGCM
79#D-#==================================================
80
81# Submit command
82typeset SUBMIT=${SUBMIT:=/usr/lpp/LoadL/full/bin/llsubmit}
83# rsync with path
84typeset -r RSYNC=/usr/bin/rsync
85# RSYNC_opt args to rsync
86typeset -r RSYNC_opt="-va"
87# ie storage filesystem
88typeset -r STOREHOST=iitm01
89typeset -r REMOTE_RSYNC=/usr/bin/rsync
90
91#====================================================
92# Set environment tools (ferret, nco, cdo, rebuild, ...)
93#====================================================
94# Not applicable here. Only rebuild path
95export export PATH=${PATH}:/gpfs1/home/sebastien/REBUILD/
96
97#====================================================
98# Host specific DIRECTORIES
99#====================================================
100
101#====================================================
102#- MirrorlibIGCM for frontend
103typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false}
104
105#====================================================
106#- libIGCM_POST for frontend
107typeset -r libIGCM_POST=${libIGCM}
108
109#====================================================
110#- R_EXE   (==> BIN_DIR = ${MODIPSL}/bin )
111typeset -r R_EXE="${MODIPSL}/bin"
112
113#====================================================
114#- SUBMIT_DIR : submission dir
115typeset SUBMIT_DIR=${SUBMIT_DIR:=${LOADL_STEP_INITDIR}}
116
117#====================================================
118#- IN
119typeset -r R_IN=${R_IN:=/gpfs1/home/sabin}
120
121#====================================================
122#- RUN_DIR_PATH : Temporary working directory (=> TMP)
123typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=$( echo ${HOME} | sed -e "s/gpfs1/gpfs3/" )/RUN/${LOADL_STEP_ID}}
124
125#====================================================
126#- OUTCOMMAND_PATH : tmp place to store command lines standard error and outputs
127typeset -r OUTCOMMAND_PATH=/tmp
128
129#====================================================
130#- HOST_MPIRUN_COMMAND
131typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="/usr/bin/time poe"}
132
133#====================================================
134#- Max number of arguments passed to nco operator or demigration command
135UNIX_MAX_LIMIT=360
136
137#====================================================
138#- set PackDefault to false on iitm
139PackDefault=false
140
141#====================================================
142#- Number of core per node (max number of OpenMP task)
143NUM_COREPERNODE=2
144
145#====================================================
146#- Default number of MPI task for IPSL coupled model
147#- required for backward compatibility
148#-
149DEFAULT_NUM_PROC_OCE=5
150DEFAULT_NUM_PROC_CPL=1
151(( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL ))
152
153#D-#==================================================
154#D-function IGCM_sys_defineArchives
155#D-* Purpose:
156#D-* Define ARCHIVE : Dedicated to large files
157#D-* Define STORAGE : Dedicated to small/medium files
158#D-* Define R_OUT   : Output tree located on ARCHIVE
159#D-* Define R_FIG   : Output tree located on STORAGE hosting figures (monitoring and atlas, and/or small files)
160#D-* Define R_BUF   : Output tree located on STORAGE hosting files waiting for rebuild or pack processes
161#D-* if SpaceName=TEST nothing special will hapen
162#D-* Examples:
163#D-
164function IGCM_sys_defineArchives {
165  IGCM_debug_PushStack "IGCM_sys_defineArchives"
166
167  if [ ! X${config_UserChoices_ARCHIVE} = X ]; then
168    #====================================================
169    #- ARCHIVE (dedicated to large files)
170    ARCHIVE=${config_UserChoices_ARCHIVE}
171  else
172    #====================================================
173    #- ARCHIVE (dedicated to large files)
174    ARCHIVE=$( echo ${HOME} | sed -e "s/gpfs1/gpfs3/" )
175  fi
176
177  if [ ! X${config_UserChoices_STORAGE} = X ]; then
178    #====================================================
179    #- STORAGE (dedicated to small/medium files)
180    STORAGE=${config_UserChoices_STORAGE}
181  else
182    #====================================================
183    #- STORAGE (dedicated to small/medium files)
184    STORAGE=${ARCHIVE}
185  fi
186
187  # ON OBELIX NO SPECIAL CASE WHEN X${config_UserChoices_SpaceName} = XTEST
188
189  #====================================================
190  #- R_OUT
191  R_OUT=${ARCHIVE}/IGCM_OUT
192
193  #====================================================
194  #- R_FIG (hosting figures : monitoring and atlas, and/or small files)
195  R_FIG=${WORKDIR}/IGCM_OUT
196
197  #====================================================
198  #- CMIP6 (hosting CMIP6 files produced by XIOS2 and configured by dr2xml)
199  CMIP6_BUF=${STORAGE}/IGCM_OUT
200
201  #====================================================
202  #- R_BUF (ONLY FOR double copy an scratch)
203  R_BUF=${WORKDIR}/IGCM_OUT
204
205  IGCM_debug_Print 1 "R_OUT has been defined = ${R_OUT}"
206  IGCM_debug_Print 1 "R_BUF has been defined = ${R_BUF}"
207  IGCM_debug_Print 1 "R_FIG has been defined = ${R_FIG}"
208
209  IGCM_debug_PopStack "IGCM_sys_defineArchives"
210}
211
212#D-#==================================================
213#D-function IGCM_sys_RshArchive
214#D-* Purpose: Archive rsh command
215#D-* Examples:
216#D-
217function IGCM_sys_RshArchive {
218  IGCM_debug_PushStack "IGCM_sys_RshArchive" $@
219  /bin/ksh <<-EOF
220    ${@}
221EOF
222  status=$?
223  if [ ${status} -gt 0 ] ; then
224    IGCM_debug_Print 2 "IGCM_sys_RshArchive : command failed error code ${status}"
225    IGCM_debug_Exit "IGCM_sys_RshArchive"
226  fi
227  IGCM_debug_PopStack "IGCM_sys_RshArchive"
228}
229
230#D-#==================================================
231#D-function IGCM_sys_RshArchive_NoError
232#D-* Purpose: Archive rsh command, without error
233#D-*          used only in monitoring.job
234#D-* Examples:
235#D-
236function IGCM_sys_RshArchive_NoError {
237  IGCM_debug_PushStack "IGCM_sys_RshArchive_NoError" $@
238  /bin/ksh <<-EOF
239    ${@} 2> /dev/null
240EOF
241  IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError"
242}
243
244#D-#==================================================
245#D-function IGCM_sys_MkdirArchive
246#D-* Purpose: Mkdir on Archive
247#D-* Examples:
248#D-
249function IGCM_sys_MkdirArchive {
250  IGCM_debug_PushStack "IGCM_sys_MkdirArchive" $@
251  if ( $DEBUG_sys ) ; then
252    echo "IGCM_sys_MkdirArchive :" $@
253  fi
254  #- creation de repertoire sur le serveur fichier
255  if [ ! -d ${1} ]; then
256    \mkdir -p $1
257    status=$?
258
259    if [ ${status} -gt 0 ] ; then
260      IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : mkdir failed error code ${status}"
261      IGCM_debug_Exit "IGCM_sys_MkdirArchive"
262    fi
263  fi
264  IGCM_debug_PopStack "IGCM_sys_MkdirArchive"
265}
266
267#D-#==================================================
268#D-function IGCM_sys_TestDirArchive
269#D-* Purpose: Test Directory that must exists on Archive
270#D-* Examples:
271#D-
272function IGCM_sys_TestDirArchive {
273  IGCM_debug_PushStack "IGCM_sys_TestDirArchive" $@
274  if ( $DEBUG_sys ) ; then
275    echo "IGCM_sys_TestDirArchive :" $@
276  fi
277  typeset ExistFlag
278  ExistFlag=$( IGCM_sys_RshArchive "[ -d $1 ] && echo 0 || echo 1" )
279  IGCM_debug_PopStack "IGCM_sys_TestDirArchive"
280  return ${ExistFlag}
281}
282
283#D-#==================================================
284#D-function IGCM_sys_IsFileArchived
285#D-* Purpose: Test file that must NOT EXISTS on Archive based on filename only
286#D-* Examples:
287#D-
288function IGCM_sys_IsFileArchived {
289  IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@
290  if ( $DEBUG_sys ) ; then
291    echo "IGCM_sys_IsFileArchived :" $@
292  fi
293  typeset IsArchivedFlag
294  IsArchivedFlag=$( [ "X$( echo $@ | grep \/gpfs3 )" != "X" ] && echo 0 || echo 1 )
295  IGCM_debug_PopStack "IGCM_sys_IsFileArchived"
296
297  return ${IsArchivedFlag}
298}
299
300#D-#==================================================
301#D-function IGCM_sys_TestFileArchive
302#D-* Purpose: Test file that must NOT EXISTS on Archive
303#D-* Examples:
304#D-
305function IGCM_sys_TestFileArchive {
306  IGCM_debug_PushStack "IGCM_sys_TestFileArchive" $@
307  typeset ExistFlag
308  ExistFlag=$( IGCM_sys_RshArchive "[ -f $1 ] && echo 0 || echo 1" )
309  IGCM_debug_PopStack "IGCM_sys_TestFileArchive"
310
311  return ${ExistFlag}
312}
313
314#D-#==================================================
315#D-function IGCM_sys_CountFileArchive
316#D-* Purpose: Count files on Archive filesystem
317#D-* Examples:
318#D-
319function IGCM_sys_CountFileArchive {
320  IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@
321  #Command depends on targeted file system
322  DEBUG_sys=false IGCM_sys_IsFileArchived $1
323  if [ $? = 0 ] ; then
324    IGCM_sys_RshArchive "ls ${@} 2>/dev/null | wc -l"
325    status=$?
326  else
327    ls ${@} 2>/dev/null | wc -l
328    status=$?
329  fi
330  if [ ${status} -gt 0 ] ; then
331    echo "IGCM_sys_CountFileArchive : erreur."
332  fi
333  IGCM_debug_PopStack "IGCM_sys_CountFileArchive"
334}
335
336#D-#==================================================
337#D-function IGCM_sys_Qsub
338#D-* Purpose: Qsub new job
339#D-* Examples:
340#D-
341function IGCM_sys_Qsub {
342  IGCM_debug_PushStack "IGCM_sys_Qsub" $@
343
344  typeset status
345
346  if ( $DEBUG_sys ) ; then
347    echo "IGCM_sys_Qsub :" $@
348  fi
349  # We have to change output/error file
350  [ ${#@} = 1 ] &&  REP_FOR_JOB=${SUBMIT_DIR}
351  [ ${#@} = 2 ] &&  REP_FOR_JOB=${2}
352  sed -e "s:\# \@ output *= .*:\# \@ output = ${Script_Output}:" \
353    -e "s:\# \@ error *= .*:\# \@ error = ${Script_Output}:"   \
354    $1 > ${REP_FOR_JOB}/JOB_FOR_IGCM
355  cd $REP_FOR_JOB ; /usr/lpp/LoadL/full/bin/llsubmit JOB_FOR_IGCM > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 ; status=$? ; cd - ;
356
357  cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
358  if [ ${status} -gt 0 ] ; then
359    IGCM_debug_Print 2 "IGCM_sys_Qsub $1 : error code ${status}"
360    IGCM_debug_Exit "IGCM_sys_Qsub"
361  else
362    JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ | tail -1 | sed -e s/\"//g )
363    IGCM_sys_Rm ${REP_FOR_JOB}/JOB_FOR_IGCM
364  fi
365  IGCM_debug_PopStack "IGCM_sys_Qsub"
366}
367
368#D-#==================================================
369#D-function IGCM_sys_QsubPost
370#D-* Purpose: Qsub new job on scalaire
371#D-* Examples:
372#D-
373function IGCM_sys_QsubPost {
374  IGCM_debug_PushStack "IGCM_sys_QsubPost" $@
375
376  typeset status
377
378  if ( $DEBUG_sys ) ; then
379    echo "IGCM_sys_QsubPost :" $@
380  fi
381  # We have to change output/error file
382  [ ${#@} = 1 ] &&  REP_FOR_JOB=${POST_DIR}
383  [ ${#@} = 2 ] &&  REP_FOR_JOB=${2}
384
385  sed -e "s:\# \@ output *= .*:\# \@ output = ${Script_Post_Output}.out:" \
386    -e "s:\# \@ error *= .*:\# \@ error = ${Script_Post_Output}.out:"   \
387    ${libIGCM_POST}/$1.job > ${REP_FOR_JOB}/JOB_FOR_IGCM
388
389  cd $REP_FOR_JOB ; /usr/lpp/LoadL/full/bin/llsubmit JOB_FOR_IGCM > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 ; status=$? ; cd - ;
390
391  cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
392  if [ ${status} -gt 0 ] ; then
393    IGCM_debug_Print 2 "IGCM_sys_QsubPost $1 : error code ${status}"
394    IGCM_debug_Exit "IGCM_sys_QsubPost"
395  else
396    JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ | tail -1 | sed -e s/\"//g )
397    IGCM_sys_Rm ${REP_FOR_JOB}/JOB_FOR_IGCM
398  fi
399  IGCM_debug_PopStack "IGCM_sys_QsubPost"
400}
401
402#D-*************************
403#D- File transfer functions
404#D-*************************
405#D-
406
407#D-#==================================================
408#D-function IGCM_sys_RmRunDir
409#D-* Purpose: rm tmpdir (dummy function most of the time batch
410#D-                      scheduler will do the job)
411#D-* Examples:
412#D-
413function IGCM_sys_RmRunDir {
414  IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@
415  if ( $DEBUG_sys ) ; then
416    echo "IGCM_sys_RmRunDir :" $@
417  fi
418
419  typeset status
420
421  echo rm $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
422  \rm $@ >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
423  status=$?
424
425  if [ ${status} -gt 0 ] ; then
426    IGCM_debug_Print 1 "IGCM_sys_RmRunDir : rm error code is ${status}."
427    cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
428    IGCM_debug_Exit "IGCM_sys_RmRunDir"
429  else
430    \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
431  fi
432  IGCM_debug_PopStack "IGCM_sys_RmRunDir"
433}
434
435#D-#==================================================
436#D-function IGCM_sys_Put_Dir
437#D-* Purpose: Copy a complete directory on $(ARCHIVE)
438#D-* Examples:
439#D-
440function IGCM_sys_Put_Dir {
441  IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@
442  if ( $DEBUG_sys ) ; then
443    echo "IGCM_sys_Put_Dir :" $@
444  fi
445  if [ $DRYRUN = 0 ]; then
446    if [ ! -d ${1} ] ; then
447      echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ."
448      IGCM_debug_PopStack "IGCM_sys_Put_Dir"
449      return
450    fi
451
452    typeset status
453
454    # Only if we use rsync
455    #IGCM_sys_TestDirArchive $( dirname $2 )
456    #
457    #USUAL WAY
458    \cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
459    status=$?
460
461    if [ ${status} -gt 0 ] ; then
462      IGCM_debug_Print 2 "IGCM_sys_Put_Dir : cp failed error code ${status}"
463      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
464      IGCM_debug_Exit "IGCM_sys_Put_Dir"
465    else
466      \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
467    fi
468  fi
469  IGCM_debug_PopStack "IGCM_sys_Put_Dir"
470}
471
472#D-#==================================================
473#D-function IGCM_sys_Get_Dir
474#D-* Purpose: Copy a complete directory from ${ARCHIVE}
475#D-* Examples:
476#D-
477function IGCM_sys_Get_Dir {
478  IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@
479  if ( $DEBUG_sys ) ; then
480    echo "IGCM_sys_Get_Dir :" $@
481  fi
482  if [ $DRYRUN = 0 ]; then
483    if [ ! -d ${1} ] ; then
484      echo "WARNING : IGCM_sys_Get_Dir ${1} DOES NOT EXIST ."
485      IGCM_debug_PopStack "IGCM_sys_Get_Dir"
486      return
487    fi
488
489    typeset status
490
491    #USUAL WAY
492    \cp -ur $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
493    status=$?
494
495    if [ ${status} -gt 0 ] ; then
496      IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}"
497      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
498      IGCM_debug_Exit "IGCM_sys_Get_Dir"
499    else
500      \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
501    fi
502  fi
503  IGCM_debug_PopStack "IGCM_sys_Get_Dir"
504}
505
506#D-#==================================================
507#D-function IGCM_sys_Put_Rest
508#D-* Purpose: Put computied restarts on ${ARCHIVE}.
509#D-           File and target directory must exist.
510#D-* Examples:
511#D-
512function IGCM_sys_Put_Rest {
513  IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@
514  if ( $DEBUG_sys ) ; then
515    echo "IGCM_sys_Put_Rest :" $@
516  fi
517  if [ $DRYRUN = 0 ]; then
518    if [ ! -f ${1} ] ; then
519      echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ."
520      IGCM_debug_Exit "IGCM_sys_Put_Rest"
521    fi
522
523    typeset status
524    #
525    if [ X${JobType} = XRUN ] ; then
526      IGCM_sys_Chmod 444 ${1}
527    fi
528    #
529    # Only if we use rsync
530    #IGCM_sys_MkdirArchive $( dirname $2 )
531    #
532    #USUAL WAY
533    \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
534    status=$?
535
536    if [ ${status} -gt 0 ] ; then
537      IGCM_debug_Print 2 "IGCM_sys_Put_Rest : cp failed error code ${status}"
538      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
539      IGCM_debug_Exit "IGCM_sys_Put_Rest"
540    else
541      \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
542    fi
543  fi
544  IGCM_debug_PopStack "IGCM_sys_Put_Rest"
545}
546
547#D-#==================================================
548#D-function IGCM_sys_Put_Out
549#D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly
550#D-* Examples:
551#D-
552function IGCM_sys_Put_Out {
553  IGCM_debug_PushStack "IGCM_sys_Put_Out" $@
554  if ( $DEBUG_sys ) ; then
555    echo "IGCM_sys_Put_Out :" $@
556  fi
557
558  typeset status
559
560  if [ $DRYRUN = 0 ]; then
561    if [ ! -f ${1} ] ; then
562      echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ."
563      IGCM_debug_PopStack "IGCM_sys_Put_Out"
564      return 1
565    fi
566    #
567    IGCM_sys_MkdirArchive $( dirname $2 )
568    #
569    if [ X${JobType} = XRUN ] ; then
570      if [ X${3} = X ] ; then
571        IGCM_sys_Chmod 444 ${1}
572      fi
573    fi
574    #
575    #USUAL WAY
576    \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
577    status=$?
578
579    if [ ${status} -gt 0 ] ; then
580      IGCM_debug_Print 2 "IGCM_sys_Put_Out : cp failed error code ${status}"
581      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
582      IGCM_debug_Exit "IGCM_sys_Put_Out"
583    else
584      \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
585    fi
586  fi
587  IGCM_debug_PopStack "IGCM_sys_Put_Out"
588  return 0
589}
590
591#D-#==================================================
592#D-function IGCM_sys_Get
593#D-* Purpose: Get a file from ${ARCHIVE}
594#D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX
595#D-            IGCM_sys_Get /l Array_contain_myfiles /destpath/
596function IGCM_sys_Get {
597  IGCM_debug_PushStack "IGCM_sys_Get" $@
598
599  typeset DEST status dm_liste
600
601  if ( $DEBUG_sys ) ; then
602    echo "IGCM_sys_Get :" $@
603  fi
604  if [ $DRYRUN -le 2 ]; then
605    if [ X${1} = X'/l' ] ; then
606      eval set +A dm_liste \${${2}}
607    else
608      dm_liste=${1}
609    fi
610    eval DEST=\${${#}}
611
612    # test if the (first) file is present in the old computation :
613    DEBUG_sys=false IGCM_sys_IsFileArchived ${dm_liste[0]}
614    if [ $? = 0 ] ; then
615      IGCM_sys_TestFileArchive ${dm_liste[0]}
616      status=$?
617    else
618      IGCM_sys_TestFileBuffer ${dm_liste[0]}
619      status=$?
620    fi
621
622    if [ ${status} -gt 0 ] ; then
623      echo "IGCM_sys_Get, ERROR : regular file ${dm_liste[0]} DOES NOT EXIST ."
624      IGCM_debug_Exit "IGCM_sys_Get"
625      return
626    fi
627
628    #USUAL WAY
629    \cp ${dm_liste[*]} ${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
630    status=$?
631
632    if [ ${status} -gt 0 ] ; then
633      IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status}"
634      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
635      IGCM_debug_Exit "IGCM_sys_Get"
636    else
637      \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
638    fi
639  fi
640  IGCM_debug_PopStack "IGCM_sys_Get"
641}
642
643#D-#==================================================
644#D-function IGCM_sys_Dods_Rm
645#D-* Purpose: DO NOTHING ! Put ${ARCHIVE} files on DODS internet protocole.
646#D-* Examples:
647#D-
648function IGCM_sys_Dods_Rm {
649  if ( $DEBUG_sys ) ; then
650    echo "IGCM_sys_Dods_Rm :" $@
651  fi
652  return 0
653}
654
655#D-#==================================================
656#D-function IGCM_sys_Dods_Cp
657#D-* Purpose: Copy $(ARCHIVE) files on DODS internet protocole.
658#D-* Examples:
659#D-
660function IGCM_sys_Dods_Cp {
661  if ( $DEBUG_sys ) ; then
662    echo "IGCM_sys_Dods_Cp :" $@
663  fi
664  return 0
665}
666
667#D-#==================================================
668#D-function IGCM_sys_Put_Dods
669#D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole. Dummy function here
670#D-* Examples:
671#D-
672function IGCM_sys_Put_Dods {
673  IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@
674  if ( $DEBUG_sys ) ; then
675    echo "IGCM_sys_Put_Dods :" $@
676  fi
677  IGCM_debug_PopStack "IGCM_sys_Put_Dods"
678}
679
680##############################################################
681# REBUILD OPERATOR
682
683#D-#==================================================
684#D-function IGCM_sys_sync
685#D-* Purpose: flush buffer on disk (dummy function on Ada)
686#D-* Examples:
687#D-
688function IGCM_sys_sync {
689  IGCM_debug_PushStack "IGCM_sys_sync" $@
690  if ( $DEBUG_sys ) ; then
691    echo "IGCM_sys_sync :" $@
692    echo "Dummy call, let the system do that."
693  fi
694  IGCM_debug_PopStack "IGCM_sys_sync"
695}
696
697############################################################
698# Activate Running Environnment Variables
699
700#D-#==================================================
701#D-function IGCM_sys_activ_variables
702#D-* Purpose: set environement variables prior to execution
703#D-* Examples:
704#D-
705function IGCM_sys_activ_variables {
706  IGCM_debug_PushStack "IGCM_sys_activ_variables"
707  if ( $DEBUG_sys ) ; then
708    echo "IGCM_sys_activ_variables"
709  fi
710
711# --------------------------------------------------------------------
712#D- MPI specifications
713# --------------------------------------------------------------------
714
715# --------------------------------------------------------------------
716#D- Other specifications
717# --------------------------------------------------------------------
718
719  IGCM_debug_PopStack "IGCM_sys_activ_variables"
720}
721
722############################################################
723# Desactivate Running Environnment Variables
724
725#D-#==================================================
726#D-function IGCM_sys_desactiv_variables
727#D-* Purpose: unset environement variables after execution
728#D-* Examples:
729#D-
730function IGCM_sys_desactiv_variables {
731  IGCM_debug_PushStack "IGCM_sys_desactiv_variables"
732  if ( $DEBUG_sys ) ; then
733    echo "IGCM_sys_desactiv_variables"
734  fi
735# --------------------------------------------------------------------
736#D- MPI specifications
737# --------------------------------------------------------------------
738
739# --------------------------------------------------------------------
740#D- Other specifications
741# --------------------------------------------------------------------
742
743  IGCM_debug_PopStack "IGCM_sys_desactiv_variables"
744}
745
746############################################################
747# Update job headers to be used by the scheduler
748
749#D-#==================================================
750#D-function IGCM_sys_updateHeaders
751#D-* Purpose: Update job headers to be used by the scheduler
752#D-* Examples: IGCM_sys_updateHeaders /path/to/Job_MYEXP
753#D-
754function IGCM_sys_updateHeaders {
755  IGCM_debug_PushStack "IGCM_sys_updateHeaders"
756  if ( $DEBUG_sys ) ; then
757    echo "IGCM_sys_updateHeaders"
758  fi
759  typeset file
760  file=$1
761
762  if [ ${executionType} -eq 1 ] ; then
763    # MPMD + MPI
764    sed -e "/::openMPthreads::/d"                  \
765        -e "s/::JobNumProcTot::/${coreNumber}/"    \
766      ${file} > ${file}.tmp
767
768  elif [ ${executionType} -eq 2 ] ; then
769    # MPMD + MPI + OMP
770    sed -e "s/::openMPthreads::/${openMPthreads}/" \
771        -e "s/::JobNumProcTot::/${coreNumber}/"    \
772      ${file} > ${file}.tmp
773
774  elif [ ${executionType} -eq 3 ] ; then
775    # SPMD + MPI/OMP
776    sed -e "s/::openMPthreads::/${openMPthreads}/" \
777        -e "s/::JobNumProcTot::/${mpiTasks}/"      \
778      ${file} > ${file}.tmp
779
780  elif [ ${executionType} -eq 4 ] ; then
781    # SPMD + MPI only
782    sed -e "s/::JobNumProcTot::/${mpiTasks}/"      \
783        -e "/::openMPthreads::/d"                  \
784      ${file} > ${file}.tmp
785
786  elif [ ${executionType} -eq 5 ] ; then
787    # SPMD + OMP only
788    sed -e "s/::openMPthreads::/${openMPthreads}/" \
789        -e "/::JobNumProcTot::/d"                  \
790      ${file} > ${file}.tmp
791
792  elif [ ${executionType} -eq 6 ] ; then
793    # SEQUENTIAL THEN
794    sed -e "s/::JobNumProcTot::/1/"                \
795        -e "/::openMPthreads::/d"                  \
796      ${file} > ${file}.tmp
797
798  fi
799
800  IGCM_sys_Mv ${file}.tmp ${file}
801
802  IGCM_debug_PopStack "IGCM_sys_updateHeaders"
803}
804
805############################################################
806# Build MPI/OMP scripts run file (dummy function)
807
808#D-#==================================================
809#D-function IGCM_sys_build_run_file
810#D-* Purpose: build run file (deprecated)
811#D-* Examples:
812#D-
813function IGCM_sys_build_run_file {
814
815  IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file "
816
817}
818
819############################################################
820# Build MPI/OMP scripts
821
822#D-#==================================================
823#D-function IGCM_sys_build_execution_scripts
824#D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND}
825#D-* Examples:
826#D-
827function IGCM_sys_build_execution_scripts
828{
829  IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@
830  if ( $DEBUG_sys ) ; then
831    echo "IGCM_sys_build_execution_scripts " $@
832  fi
833
834  typeset NbNodes_Job NbProc_Job comp_proc_mpi_loc comp_proc_omp_loc mpi_count
835
836  if [ ! -f ${SUBMIT_DIR}/Job_${config_UserChoices_JobName} ]  ; then
837    IGCM_debug_Exit "IGCM_sys_iitm build_execution_scripts : Job_${config_UserChoices_JobName} don't exist in SUBMIT_DIR : ${SUBMIT_DIR} "
838  fi
839
840  if ( ${OK_PARA_MPMD} ) ; then
841
842    if [ -f run_file ] ; then
843      IGCM_sys_Rm -f run_file
844    fi
845    touch run_file
846
847    if ( ${OK_PARA_OMP} ) ; then
848# NEW : 2 Noeuds
849# @ task_geometry={(0)(1,2,3)}
850# Nombre de processus demandes
851      echo "Job_${config_UserChoices_JobName} includes task_geometry = \c"
852      cat ${SUBMIT_DIR}/Job_${config_UserChoices_JobName} | grep "task_geometry" | sed -e "s/[^(]*([^(]*/(/g"
853      echo "Job_${config_UserChoices_JobName} includes task_geometry  with NbNodes = \c"
854      cat ${SUBMIT_DIR}/Job_${config_UserChoices_JobName} | grep "task_geometry" | sed -e "s/[^(]*([^(]*/(/g" | wc -c
855      NbNodes_Job=$(( $( cat ${SUBMIT_DIR}/Job_${config_UserChoices_JobName} | grep "task_geometry" | sed -e "s/[^(]*([^(]*/(/g" | wc -c ) - 1 ))
856
857      if [ ${NbNodes_Job} -eq 0 ] ; then
858        IGCM_debug_Print 2 "Error in Job_${config_UserChoices_JobName} ressources : no task_geometry defined with OpenMP run."
859        exit 1
860      fi
861    else
862
863# OLD :
864# @ total_tasks = 3
865# @ environment = "BATCH_NUM_PROC_TOT=3"
866# Pas d OpenMP
867# @ resources = ConsumableCpus(1)
868
869      echo "Job_${config_UserChoices_JobName} includes total_tasks = \c"
870      cat ${SUBMIT_DIR}/Job_${config_UserChoices_JobName} | grep "total_tasks" | sed -e "s/.*total_tasks = //"
871      NbProc_Job=$( cat ${SUBMIT_DIR}/Job_${config_UserChoices_JobName} | grep "total_tasks" | sed -e "s/.*total_tasks = //" )
872      NbProc_Job=${NbProc_Job:=0}
873      if [ ${NbProc_Job} -eq 0 ] ; then
874        IGCM_debug_Print 2 "Error in Job_${config_UserChoices_JobName} ressources : no total_tasks defined with MPI only run."
875        exit 1
876      fi
877      if ( $( egrep '^# *@ *resources *= *ConsumableCpus\(1\)' ${SUBMIT_DIR}/Job_${config_UserChoices_JobName} >/dev/null 2>&1 ) ) ; then
878        IGCM_debug_Print 2 "ressources =  ConsumableCpus(1) line found into Job_${config_UserChoices_JobName}"
879      else
880        IGCM_debug_Print 2 "Error in Job_${config_UserChoices_JobName} ressources = line not found. Job should include resources = ConsumableCpus(1) "
881        exit 1
882      fi
883    fi
884
885# run_file construction
886
887# Then first loop on the components for the coupler ie oasis
888
889### the coupler ie oasis must be the first one
890    for comp in ${config_ListOfComponents[*]} ; do
891
892      eval ExeNameIn=\${config_Executable_${comp}[0]}
893      eval ExeNameOut=\${config_Executable_${comp}[1]}
894
895      # for CPL component only
896      if [ "X${comp}" = "XCPL" ] ; then
897
898        eval comp_proc_mpi_loc=\${${comp}_PROC_MPI}
899        eval comp_proc_omp_loc=\${${comp}_PROC_OMP}
900
901        if ( ${OK_PARA_MPI} ) ; then
902          (( mpi_count = 1 ))
903          until [ ${mpi_count} -gt ${comp_proc_mpi_loc} ] ; do
904            if ( ${OK_PARA_OMP} ) ; then
905              echo "env OMP_NUM_THREADS=${comp_proc_omp_loc} ./${ExeNameOut} " >> run_file
906            else
907              echo "./${ExeNameOut}" >> run_file
908            fi
909            (( mpi_count = mpi_count + 1 ))
910          done
911        else
912          if ( ${OK_PARA_OMP} ) ; then
913            echo "env OMP_NUM_THREADS=${comp_proc_omp_loc} ./${ExeNameOut} " >> run_file
914          else
915            echo "./${ExeNameOut} " >> run_file
916          fi
917        fi
918      fi
919    done
920
921# Then second loop on the components
922
923    for comp in ${config_ListOfComponents[*]} ; do
924
925      eval ExeNameIn=\${config_Executable_${comp}[0]}
926      eval ExeNameOut=\${config_Executable_${comp}[1]}
927
928      # Only if we really have an executable for the component and not the coupler ie oasis:
929      if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then
930
931        eval comp_proc_mpi_loc=\${${comp}_PROC_MPI}
932        eval comp_proc_omp_loc=\${${comp}_PROC_OMP}
933
934        if ( ${OK_PARA_MPI} ) ; then
935          (( mpi_count = 1 ))
936          until [ ${mpi_count} -gt ${comp_proc_mpi_loc} ] ; do
937            if ( ${OK_PARA_OMP} ) ; then
938              echo "env OMP_NUM_THREADS=${comp_proc_omp_loc} ./${ExeNameOut} " >> run_file
939            else
940              echo "./${ExeNameOut}" >> run_file
941            fi
942            (( mpi_count = mpi_count + 1 ))
943          done
944        else
945          if ( ${OK_PARA_OMP} ) ; then
946            echo "env OMP_NUM_THREADS=${comp_proc_omp_loc} ./${ExeNameOut} " >> run_file
947          else
948                    # to be tested : no MPI only OpenMP into MPMD mode
949            echo "./${ExeNameOut} " >> run_file
950          fi
951        fi
952      fi
953    done
954
955    EXECUTION="${HOST_MPIRUN_COMMAND} -pgmmodel mpmd -cmdfile ./run_file"
956
957    IGCM_sys_Chmod u+x run_file
958    if ( $DEBUG_sys ) ; then
959      echo "run_file contains : "
960      cat run_file
961    fi
962
963  # Only one executable (SPMD mode).
964  else
965
966    for comp in ${config_ListOfComponents[*]} ; do
967
968      # Only if we really have an executable for the component :
969      eval ExeNameOut=\${config_Executable_${comp}[1]}
970      if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then
971        EXECUTION="${HOST_MPIRUN_COMMAND} ./${ExeNameOut}"
972      fi
973
974    done
975
976  fi
977
978  IGCM_debug_Print 1 "sys iitm : execution command is"
979  IGCM_debug_Print 1 "$EXECUTION"
980
981  IGCM_debug_PopStack "IGCM_sys_build_execution_scripts"
982}
983
984#D-#==================================================
985#D-function IGCM_sys_check_path
986#D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine
987#D-* do not point to an important use directory. Stop immediately in that case.
988#D-* Examples:
989#D-
990function IGCM_sys_check_path {
991  IGCM_debug_PushStack "IGCM_sys_check_path"
992  if ( $DEBUG_sys ) ; then
993    echo "IGCM_sys_check_path"
994  fi
995
996  if ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X${WORKDIR} ] || [ X${RUN_DIR_PATH} = X${ARCHIVE} ] ) ; then
997    IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}"
998    IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}"
999    IGCM_debug_Exit "This will stop the job"
1000  fi
1001  IGCM_debug_PopStack "IGCM_sys_check_path"
1002}
1003
1004#D-#==================================================
1005#D-function IGCM_sys_check_quota. Dummy call here
1006#D-* Purpose: check user quota. Stop the simulation if quota above 90%
1007#D-* Examples:
1008#D-
1009function IGCM_sys_check_quota {
1010  IGCM_debug_PushStack "IGCM_sys_check_quota"
1011  if ( $DEBUG_sys ) ; then
1012    echo "IGCM_sys_check_quota"
1013  fi
1014  IGCM_debug_PopStack "IGCM_sys_check_quota"
1015}
1016
1017#D-#==================================================
1018#D-function IGCM_sys_CountJobInQueue
1019#D-* Purpose: Count number of users job
1020#D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun
1021#D-
1022function IGCM_sys_CountJobInQueue {
1023  IGCM_debug_PushStack "IGCM_sys_CountJobInQueue"
1024  if ( $DEBUG_sys ) ; then
1025    echo "IGCM_sys_CountJobInQueue"
1026  fi
1027
1028  # Print only the full (-W) JobName (%jn)
1029  NbRun=$( llq -W -f %jn | grep -c "$1" )
1030
1031  eval ${2}=${NbRun}
1032
1033  IGCM_debug_PopStack "IGCM_sys_CountJobInQueue"
1034}
1035
1036#D-#==================================================
1037#D-function IGCM_sys_rebuild_nemo
1038#D-* Purpose: rebuild nemo parallel files with general rebuild
1039#D-* Examples:
1040#D-
1041
1042function IGCM_sys_rebuild_nemo {
1043  IGCM_debug_PushStack "IGCM_sys_rebuild_nemo" $@
1044  if ( $DEBUG_sys ) ; then
1045    echo "IGCM_sys_rebuild_nemo :" $@
1046  fi
1047
1048  nemo_generic_restart_file_name_out=${1}
1049  nemo_extension_out=${3}
1050  shift ; shift ; shift
1051
1052  IGCM_sys_rebuild -o ${nemo_generic_restart_file_name_out}.${nemo_extension_out} $@
1053
1054  IGCM_debug_PopStack "IGCM_sys_rebuild_nemo"
1055}
1056
1057
Note: See TracBrowser for help on using the repository browser.