source: trunk/libIGCM/libIGCM_sys/libIGCM_sys_jeanzay.ksh @ 1493

Last change on this file since 1493 was 1493, checked in by jgipsl, 5 years ago

Adapted executaionType=1 and 2 for jean-zay but only tested for 2 executables for now (lmdz+xios).
  • Property licence set to
    The following licence information concerns ONLY the libIGCM tools
    ==================================================================

    Copyright © Centre National de la Recherche Scientifique CNRS
    Commissariat à l'Énergie Atomique CEA

    libIGCM : Library for Portable Models Computation of IGCM Group.

    IGCM Group is the french IPSL Global Climate Model Group.

    This library is a set of shell scripts and functions whose purpose is
    the management of the initialization, the launch, the transfer of
    output files, the post-processing and the monitoring of datas produce
    by any numerical program on any plateforme.

    This software is governed by the CeCILL license under French law and
    abiding by the rules of distribution of free software. You can use,
    modify and/ or redistribute the software under the terms of the CeCILL
    license as circulated by CEA, CNRS and INRIA at the following URL
    "http://www.cecill.info".

    As a counterpart to the access to the source code and rights to copy,
    modify and redistribute granted by the license, users are provided only
    with a limited warranty and the software's author, the holder of the
    economic rights, and the successive licensors have only limited
    liability.

    In this respect, the user's attention is drawn to the risks associated
    with loading, using, modifying and/or developing or reproducing the
    software by the user in light of its specific status of free software,
    that may mean that it is complicated to manipulate, and that also
    therefore means that it is reserved for developers and experienced
    professionals having in-depth computer knowledge. Users are therefore
    encouraged to load and test the software's suitability as regards their
    requirements in conditions enabling the security of their systems and/or
    data to be ensured and, more generally, to use and operate it in the
    same conditions as regards security.

    The fact that you are presently reading this means that you have had
    knowledge of the CeCILL license and that you accept its terms.
  • Property svn:keywords set to Revision Author Date
File size: 54.6 KB
Line 
1#!/bin/ksh
2
3#**************************************************************
4# Author: Sebastien Denvil, Martial Mancip, Arnaud Caubel
5# Contact: Arnaud.Caubel__at__lsce.ipsl.fr
6# $Revision::                                          $ Revision of last commit
7# $Author::                                            $ Author of last commit
8# $Date::                                              $ 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 Jean-Zay
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 user names project maxCpuTime
65# $hostname ou hostname
66typeset HOST=${HOST:=$( hostname )}
67# $username ou whoami
68typeset LOGIN=${LOGIN:=$( whoami )}
69# $hostname of the MASTER job
70typeset MASTER=jeanzay
71# add default project set by ins_job
72typeset PROJECT=$( echo ${SLURM_JOB_ACCOUNT:=::default_project::} | cut -c "1-3" ) 
73### jobWarningDelay in seconds
74##typeset jobWarningDelay=${BRIDGE_MSUB_MAXTIME}
75 
76#D-
77#D-#==================================================
78#D-Program used in libIGCM
79#D-#==================================================
80
81# Submit command
82typeset SUBMIT=${SUBMIT:=sbatch}
83# rsync with path
84typeset -r RSYNC=/usr/bin/rsync
85# RSYNC_opt args to rsync
86typeset -r RSYNC_opt="-va"
87# ie storage filesystem
88typeset -r STOREHOST=${MASTER}
89typeset -r REMOTE_RSYNC=/usr/bin/rsync
90
91#====================================================
92# Access to module command
93#====================================================
94. /usr/share/Modules/init/ksh
95
96#====================================================
97# Set environment tools (ferret, nco, cdo, rebuild, ...)
98#====================================================
99if [ X${TaskType} = Xcomputing ] ; then
100  IGCM_debug_Print 1 "Modules will be loaded later in IGCM_sys_activ_variables."
101else
102  module purge > /dev/null 2>&1
103  . /gpfswork/rech/psl/commun/MachineEnvironment/jeanzay/env_jeanzay > /dev/null 2>&1
104#currently no atlas
105#  . /gpfswork/rech/psl/commun/MachineEnvironment/jeanzay/env_atlas_jeanzay > /dev/null 2>&1
106
107#  export PCMDI_MP=/ccc/work/cont003/igcmg/igcmg/PCMDI-MP
108  export UVCDAT_ANONYMOUS_LOG=FALSE
109fi
110
111# FYI
112[ ! X${TaskType} = Xchecking ] && IGCM_debug_Print 1 "List of loaded modules:"
113[ ! X${TaskType} = Xchecking ] && module list
114
115# For AddNoise and AddPertu3DOCE
116##export PATH=${PATH}:/ccc/cont003/home/igcmg/igcmg/Tools/curie/bin
117#jg no addnoise
118#export PATH=${PATH}:$(ccc_home -u igcmg)/Tools/irene/bin
119
120# For rebuild
121##export PATH=${PATH}:/ccc/cont003/home/igcmg/igcmg/Tools/irene/rebuild/modipsl_IOIPSL_PLUS_v2_2_4/bin
122#jg no yet any rebuild
123#export PATH=${PATH}:$(ccc_home -u igcmg)/Tools/irene/rebuild/modipsl_IOIPSL_PLUS_v2_2_4/bin
124
125#====================================================
126# Host specific DIRECTORIES
127#====================================================
128
129#====================================================
130#- MirrorlibIGCM for frontend
131typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false}
132
133#====================================================
134#- libIGCM_POST for frontend
135typeset -r libIGCM_POST=${libIGCM}
136
137#====================================================
138#- R_EXE   (==> BIN_DIR = ${MODIPSL}/bin )
139typeset -r R_EXE="${MODIPSL}/bin"
140
141#====================================================
142#- SUBMIT_DIR : submission dir
143typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${SLURM_SUBMIT_DIR}}
144
145#====================================================
146#- IN
147typeset -r R_IN=${R_IN:=/gpfswork/rech/psl/commun/IGCM}
148
149#====================================================
150#- RUN_DIR_PATH : Temporary working directory (=> TMP)
151typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=${SCRATCH}/RUN_DIR/${SLURM_JOBID}_${$}}
152
153#====================================================
154#- OUTCOMMAND_PATH : tmp place to store command lines standard error and outputs
155typeset -r OUTCOMMAND_PATH=/tmp
156
157#====================================================
158#- HOST_MPIRUN_COMMAND
159typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="/usr/bin/time srun "}
160
161#====================================================
162#- Max number of arguments passed to nco operator or demigration command
163UNIX_MAX_LIMIT=360
164
165#====================================================
166#- set PackDefault to true
167PackDefault=true
168
169#====================================================
170#- Default number of MPI task for IPSL coupled model
171#- required for backward compatibility
172#-
173DEFAULT_NUM_PROC_OCE=5
174DEFAULT_NUM_PROC_CPL=1
175(( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL ))
176
177#====================================================
178#- Number of computing cores per node
179#-
180NB_CORE_PER_NODE=40
181
182#D-#==================================================
183#D-function IGCM_sys_defineArchives
184#D-* Purpose:
185#D-* Load dfldatadir module : According to project used for submission (default) or set in config.card (optional)
186#D-* Define ARCHIVE : Dedicated to large files
187#D-* Define STORAGE : Dedicated to small/medium files
188#D-* Define R_OUT   : Output tree located on ARCHIVE
189#D-* Define R_FIG   : Output tree located on STORAGE hosting figures (monsitoring and atlas, and/or small files)
190#D-* Define R_BUF   : Output tree located on SCRATCH hosting files waiting for rebuild or pack processes
191#D-* if SpaceName=TEST everything is stored on SCRATCH
192#D-* Examples:
193#D-
194function IGCM_sys_defineArchives {
195  IGCM_debug_PushStack "IGCM_sys_defineArchives"
196
197  # Load dfldatadir depending on the project used for submission (default) or set in config.card (optional)
198  if [ X${config_UserChoices_DataProject} = X ] || [ X${config_UserChoices_DataProject} = DEFAULT ]; then
199    # The variable DataProject is not set in in section UserChoices in config.card or it is set to DEFAULT
200    # Default option: Change IDRPROJ according to the project used for submission
201
202    # jg following line does not work in a submitted job:
203    eval $(idrenv -d ${PROJECT})
204  else
205    # Use the project set by the variable DataProject in section UserChoices in config.card
206    eval $(idrenv -d ${config_UserChoices_DataProject})
207    IGCM_debug_Print 1 "Change DataProject red in config.card : ${config_UserChoices_DataProject}"
208  fi
209  IGCM_debug_Print 1 "Data project for output to be used: ${IDRPROJ}"
210
211  #====================================================
212  #- RUN_DIR_PATH : Temporary working directory (=> TMP)
213  typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=${SCRATCH}/RUN_DIR/${SLURM_JOBID}_${$}}
214
215  if [ ! X${config_UserChoices_ARCHIVE} = X ]; then
216    #====================================================
217    #- ARCHIVE (dedicated to large files)
218    ARCHIVE=${config_UserChoices_ARCHIVE}
219  else
220    #====================================================
221    #- ARCHIVE (dedicated to large files)
222    ARCHIVE=${STORE}
223  fi
224
225  if [ ! X${config_UserChoices_STORAGE} = X ]; then
226    #====================================================
227    #- STORAGE (dedicated to small/medium files)
228    STORAGE=${config_UserChoices_STORAGE}
229  else
230    #====================================================
231    #- STORAGE (dedicated to small/medium files)
232    STORAGE=${WORK}
233  fi
234
235  if [ X${config_UserChoices_SpaceName} = XTEST ]; then
236    #====================================================
237    #- R_OUT
238    R_OUT=${SCRATCH}/IGCM_OUT
239
240    #====================================================
241    #- R_FIG (hosting figures : monitoring and atlas, and/or small files)
242    R_FIG=${SCRATCH}/IGCM_OUT
243
244    IGCM_debug_Print 1 "SpaceName=TEST ==> OVERRULE destination path directories"
245
246  else
247    #====================================================
248    #- R_OUT
249    R_OUT=${ARCHIVE}/IGCM_OUT
250
251    #====================================================
252    #- R_FIG (hosting figures : monitoring and atlas, and/or small files)
253    R_FIG=${STORAGE}/IGCM_OUT
254  fi
255
256  #====================================================
257  #- CMIP6 (hosting CMIP6 files produced by XIOS2 and configured by dr2xml)
258  CMIP6_BUF=${STORAGE}/IGCM_OUT
259
260  #====================================================
261  #- R_BUF (ONLY FOR double copy an scratch)
262  R_BUF=${SCRATCH}/IGCM_OUT
263
264  IGCM_debug_Print 1 "R_OUT has been defined = ${R_OUT}"
265  IGCM_debug_Print 1 "R_BUF has been defined = ${R_BUF}"
266  IGCM_debug_Print 1 "R_FIG has been defined = ${R_FIG}"
267
268  IGCM_debug_PopStack "IGCM_sys_defineArchives"
269}
270
271#D-#==================================================
272#D-function IGCM_sys_RshArchive
273#D-* Purpose: Archive rsh command
274#D-* Examples:
275#D-
276function IGCM_sys_RshArchive {
277  IGCM_debug_PushStack "IGCM_sys_RshArchive" $@
278  /bin/ksh <<-EOF
279    ${@}
280EOF
281  status=$?
282  if [ ${status} -gt 0 ] ; then
283    IGCM_debug_Print 2 "IGCM_sys_RshArchive : command failed error code ${status}"
284    IGCM_debug_Exit "IGCM_sys_RshArchive"
285  fi
286  IGCM_debug_PopStack "IGCM_sys_RshArchive"
287}
288
289#D-#==================================================
290#D-function IGCM_sys_RshArchive_NoError
291#D-* Purpose: Archive rsh command, without error
292#D-*          used only in monitoring.job
293#D-* Examples:
294#D-
295function IGCM_sys_RshArchive_NoError {
296  IGCM_debug_PushStack "IGCM_sys_RshArchive_NoError" $@
297  /bin/ksh <<-EOF
298    ${@} 2> /dev/null
299EOF
300  IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError"
301}
302
303#D-#==================================================
304#D-function IGCM_sys_MkdirArchive
305#D-* Purpose: Mkdir on Archive
306#D-* Examples:
307#D-
308function IGCM_sys_MkdirArchive {
309  IGCM_debug_PushStack "IGCM_sys_MkdirArchive" $@
310  if ( $DEBUG_sys ) ; then
311    echo "IGCM_sys_MkdirArchive :" $@
312  fi
313  #- creation de repertoire sur le serveur fichier
314  if [ ! -d ${1} ]; then
315    \mkdir -p $1
316    status=$?
317
318    if [ ${status} -gt 0 ] ; then
319      IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : mkdir failed error code ${status}"
320      IGCM_debug_Exit "IGCM_sys_MkdirArchive"
321    fi
322  fi
323  IGCM_debug_PopStack "IGCM_sys_MkdirArchive"
324}
325
326#D-#==================================================
327#D-function IGCM_sys_TestDirArchive
328#D-* Purpose: Test Directory that must exists on Archive
329#D-* Examples:
330#D-
331function IGCM_sys_TestDirArchive {
332  IGCM_debug_PushStack "IGCM_sys_TestDirArchive" $@
333  if ( $DEBUG_sys ) ; then
334    echo "IGCM_sys_TestDirArchive :" $@
335  fi
336  typeset ExistFlag
337  ExistFlag=$( [ -d $1 ] && echo 0 || echo 1 )
338  IGCM_debug_PopStack "IGCM_sys_TestDirArchive"
339  return ${ExistFlag}
340}
341
342#D-#==================================================
343#D-function IGCM_sys_IsFileArchived
344#D-* Purpose: Test file that must NOT EXISTS on Archive based on filename only
345#D-* Examples:
346#D-
347function IGCM_sys_IsFileArchived {
348  IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@
349  if ( $DEBUG_sys ) ; then
350    echo "IGCM_sys_IsFileArchived :" $@
351  fi
352  typeset IsArchivedFlag
353  IsArchivedFlag=$( [ X$( echo $@ | grep ^\/ccc\/store ) != X ] && echo 0 || echo 1 )
354  IGCM_debug_PopStack "IGCM_sys_IsFileArchived"
355
356  return ${IsArchivedFlag}
357}
358
359#D-#==================================================
360#D-function IGCM_sys_TestFileArchive
361#D-* Purpose: Test file that must NOT EXISTS on Archive
362#D-* Examples:
363#D-
364function IGCM_sys_TestFileArchive {
365  IGCM_debug_PushStack "IGCM_sys_TestFileArchive" $@
366  typeset ExistFlag
367  ExistFlag=$( [ -f $1 ] && echo 0 || echo 1 )
368  IGCM_debug_PopStack "IGCM_sys_TestFileArchive"
369
370  return ${ExistFlag}
371}
372
373#D-#==================================================
374#D-function IGCM_sys_CountFileArchive
375#D-* Purpose: Count files on Archive filesystem
376#D-* Examples:
377#D-
378function IGCM_sys_CountFileArchive {
379  IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@
380  ls ${@} 2>/dev/null | wc -l
381  if [ $? -gt 0 ] ; then
382    echo "IGCM_sys_CountFileArchive : erreur."
383  fi
384  IGCM_debug_PopStack "IGCM_sys_CountFileArchive"
385}
386
387#D-#==================================================
388#D-function IGCM_sys_Tree
389#D-* Purpose: Tree directories with files on ${ARCHIVE}
390#D-* Examples: IGCM_sys_Tree ${R_IN} ${R_OUT}
391#D-
392function IGCM_sys_Tree {
393  IGCM_debug_PushStack "IGCM_sys_Tree" $@
394  if ( $DEBUG_sys ) ; then
395    echo "IGCM_sys_Tree :" $@
396  fi
397
398  \ls -lR ${@}
399
400  IGCM_debug_PopStack "IGCM_sys_Tree"
401}
402
403#D-#==================================================
404#D-function IGCM_sys_Qsub
405#D-* Purpose: Qsub new job
406#D-* Examples:
407#D-
408function IGCM_sys_Qsub {
409  IGCM_debug_PushStack "IGCM_sys_Qsub" $@
410  if ( $DEBUG_sys ) ; then
411    echo "IGCM_sys_Qsub :" $@
412  fi
413  typeset options status
414  options="-o ${SUBMIT_DIR}/${Script_Output} -e ${SUBMIT_DIR}/${Script_Output}"
415
416  /usr/bin/time sbatch ${options} $1 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
417  status=$?
418
419  cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
420  if [ ${status} -gt 0 ] ; then
421    IGCM_debug_Print 2 "IGCM_sys_Qsub ${options} $1 : error code ${status}"
422    IGCM_debug_Exit "IGCM_sys_Qsub"
423  else
424    JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ )
425  fi
426  IGCM_debug_PopStack "IGCM_sys_Qsub"
427}
428
429#D-#==================================================
430#D-function IGCM_sys_QsubPost
431#D-* Purpose: Qsub new job on scalaire
432#D-* Examples:
433#D-
434function IGCM_sys_QsubPost {
435  IGCM_debug_PushStack "IGCM_sys_QsubPost" $@
436  if ( $DEBUG_sys ) ; then
437    echo "IGCM_sys_QsubPost :" $@
438  fi
439  typeset options status
440  options="-o ${POST_DIR}/${Script_Post_Output}.out -e ${POST_DIR}/${Script_Post_Output}.out"
441
442  sbatch ${options} ${libIGCM_POST}/$1.job > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
443  status=$?
444
445  cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
446  if [ ${status} -gt 0 ] ; then
447    IGCM_debug_Print 2 "IGCM_sys_QsubPost ${options} ${libIGCM_POST}/$1.job : error code ${status}"
448    IGCM_debug_Exit "IGCM_sys_QsubPost"
449  else
450    JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ )
451  fi
452  IGCM_debug_PopStack "IGCM_sys_QsubPost"
453}
454
455#D-*************************
456#D- File transfer functions
457#D-*************************
458#D-
459
460#D-#==================================================
461#D-function IGCM_sys_RmRunDir
462#D-* Purpose: rm tmpdir (dummy function most of the time batch
463#D-                      scheduler will do the job)
464#D-* Examples:
465#D-
466function IGCM_sys_RmRunDir {
467  IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@
468  if ( $DEBUG_sys ) ; then
469    echo "IGCM_sys_RmRunDir :" $@
470  fi
471
472  typeset status
473
474  echo rm $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
475  \rm $@ >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
476  status=$?
477
478  if [ ${status} -gt 0 ] ; then
479    IGCM_debug_Print 1 "IGCM_sys_RmRunDir : rm error code is ${status}."
480    cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
481    IGCM_debug_Exit "IGCM_sys_RmRunDir"
482  else
483    \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
484  fi
485  IGCM_debug_PopStack "IGCM_sys_RmRunDir"
486}
487
488#D-#==================================================
489#D-function IGCM_sys_Put_Dir
490#D-* Purpose: Copy a complete directory on $(ARCHIVE)
491#D-* Examples:
492#D-
493function IGCM_sys_Put_Dir {
494  IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@
495  if ( $DEBUG_sys ) ; then
496    echo "IGCM_sys_Put_Dir :" $@
497  fi
498  if [ $DRYRUN = 0 ]; then
499    if [ ! -d ${1} ] ; then
500      echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ."
501      IGCM_debug_PopStack "IGCM_sys_Put_Dir"
502      return
503    fi
504
505    typeset status
506
507    # Only if we use rsync
508    #IGCM_sys_TestDirArchive $( dirname $2 )
509    #
510    #USUAL WAY
511    \cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
512    status=$?
513
514    if [ ${status} -gt 0 ] ; then
515      IGCM_debug_Print 2 "IGCM_sys_Put_Dir : cp failed error code ${status}"
516      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
517      IGCM_debug_Exit "IGCM_sys_Put_Dir"
518    else
519      \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
520    fi
521  fi
522  IGCM_debug_PopStack "IGCM_sys_Put_Dir"
523}
524
525#D-#==================================================
526#D-function IGCM_sys_Get_Dir
527#D-* Purpose: Copy a complete directory from ${ARCHIVE}
528#D-* Examples:
529#D-
530function IGCM_sys_Get_Dir {
531  IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@
532  if ( $DEBUG_sys ) ; then
533    echo "IGCM_sys_Get_Dir :" $@
534  fi
535  if [ $DRYRUN = 0 ]; then
536    typeset NB_ESSAI DELAI status i
537    # number of tentative
538    NB_ESSAI=3
539    # time delay between tentative
540    DELAI=2
541
542    #
543    # USUAL WAY
544    # add 'ccc_hsm get' (to demigrate all offline files) to reduce time of this command :
545    ccc_hsm get -r $1
546
547    i=0
548    while [ $i -lt $NB_ESSAI ] ; do
549      \cp -ur $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
550      status=$?
551      if [ ${status} -gt 0 ] ; then
552        IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status} ${i}/${NB_ESSAI}"
553        IGCM_debug_Print 2 "IGCM_sys_Get_Dir : sleep ${DELAI} seconds and try again."
554        sleep $DELAI
555      else
556        break
557      fi
558      (( i = i + 1 ))
559    done
560
561    if [ ${status} -gt 0 ] ; then
562      IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}"
563      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
564      IGCM_debug_Exit "IGCM_sys_Get_Dir"
565    else
566      \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
567    fi
568  fi
569  IGCM_debug_PopStack "IGCM_sys_Get_Dir"
570}
571
572#D-#==================================================
573#D-function IGCM_sys_Put_Rest
574#D-* Purpose: Put computied restarts on ${ARCHIVE}.
575#D-           File and target directory must exist.
576#D-* Examples:
577#D-
578function IGCM_sys_Put_Rest {
579  IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@
580  if ( $DEBUG_sys ) ; then
581    echo "IGCM_sys_Put_Rest :" $@
582  fi
583  if [ $DRYRUN = 0 ]; then
584    if [ ! -f ${1} ] ; then
585      echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ."
586      IGCM_debug_Exit "IGCM_sys_Put_Rest"
587    fi
588
589    typeset status
590    #
591    # USUAL WAY
592    \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
593    status=$?
594
595#       #RSYNC WITH NETWORK SSH CALL
596#       echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
597#       ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
598
599#       #RSYNC WITH NFS USE
600#       echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
601#       ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
602
603#       status=$?
604#       IGCM_sys_Rsync_out $status
605
606#       ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
607#       (( status=status+$? ))
608
609    if [ ${status} -gt 0 ] ; then
610      IGCM_debug_Print 2 "IGCM_sys_Put_Rest : cp failed error code ${status}"
611      [ -f ${1} ] && ls -l ${1}
612      [ -f ${2} ] && ls -l ${2}
613      [ -f ${2}/${1} ] && ls -l ${2}/${1}
614      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
615      IGCM_debug_Exit "IGCM_sys_Put_Rest"
616    else
617
618      if [ X${JobType} = XRUN ] ; then
619        [ -f ${2} ] && IGCM_sys_Chmod 444 ${2}
620        [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1}
621      fi
622
623      \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
624    fi
625  fi
626  IGCM_debug_PopStack "IGCM_sys_Put_Rest"
627}
628
629#D-#==================================================
630#D-function IGCM_sys_Put_Out
631#D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly
632#D-* Examples:
633#D-
634function IGCM_sys_Put_Out {
635  IGCM_debug_PushStack "IGCM_sys_Put_Out" $@
636  if ( $DEBUG_sys ) ; then
637    echo "IGCM_sys_Put_Out :" $@
638  fi
639
640  typeset NB_ESSAI DELAI status i exist skip
641  typeset fileDeviceNumberInHex directoryDeviceNumberInHex
642
643  # number of tentative
644  NB_ESSAI=3
645  # time delay between tentative
646  DELAI=2
647
648  if [ $DRYRUN = 0 ]; then
649    if [ ! -f ${1} ] ; then
650      echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ."
651      IGCM_debug_PopStack "IGCM_sys_Put_Out"
652      return 1
653    fi
654    #
655    IGCM_sys_MkdirArchive $( dirname $2 )
656    #
657    exist=false
658    skip=false
659    if [ -f $2 ] ; then
660      IGCM_debug_Print 1 "$2 already exist"
661      ccc_hsm get $2
662      exist=true
663      if [ "X$( diff $1 $2 )" = X ] ; then
664        IGCM_debug_Print 2 "$1 and $2 are the same file, we skip the copy"
665        skip=true
666      else
667        IGCM_debug_Print 2 "$1 and $2 are not the same file, we force the copy"
668        skip=false
669      fi
670    fi
671    #
672    if ( [ X${exist} = Xtrue ] && [ X${skip} = Xfalse ] ) ; then
673      IGCM_sys_Chmod u+w $2
674    fi
675
676    if [ X${skip} = Xfalse ] ; then
677      i=0
678      while [ $i -lt $NB_ESSAI ] ; do
679        # Identify file system
680        fileDeviceNumberInHex=$( stat -c %d $1 )
681        status=$?
682        if [ ${status} -gt 0 ] ; then
683          IGCM_debug_Exit "IGCM_sys_Put_Out"
684        fi
685        # Identify file system
686        directoryDeviceNumberInHex=$( stat -c %d $( dirname $2 ) )
687        status=$?
688        if [ ${status} -gt 0 ] ; then
689          IGCM_debug_Exit "IGCM_sys_Put_Out"
690        fi
691
692        if ( [ ${fileDeviceNumberInHex} -ne ${directoryDeviceNumberInHex} ] || [ X$3 = XNOMOVE ] ) ; then
693          # They are not on the same device. USUAL WAY
694          \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
695          status=$?
696        else
697          # They are on the same device. NOT SO USUAL WAY
698          \mv $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
699          status=$?
700        fi
701        if [ ${status} -gt 0 ]; then
702          IGCM_debug_Print 2 "IGCM_sys_Put_Out : cp failed error code ${status} ${i}/${NB_ESSAI}"
703          IGCM_debug_Print 2 "IGCM_sys_Put_Out : sleep ${DELAI} seconds and try again."
704          [ -f ${1} ] && ls -l ${1}
705          [ -f ${2} ] && ls -l ${2}
706          [ -f ${2}/${1} ] && ls -l ${2}/${1}
707          sleep $DELAI
708        else
709          break
710        fi
711        (( i = i + 1 ))
712      done
713    fi
714
715#       #RSYNC WITH NETWORK SSH CALL
716#       echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
717#       ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
718
719#       #RSYNC WITH NFS USE
720#       echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
721#       ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
722
723#       status=$?
724#       IGCM_sys_Rsync_out $status
725
726#       ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
727#       (( status=status+$? ))
728
729    if [ ${status} -gt 0 ] ; then
730      IGCM_debug_Print 2 "IGCM_sys_Put_Out : cp failed error code ${status}"
731      [ -f ${1} ] && ls -l ${1}
732      [ -f ${2} ] && ls -l ${2}
733      [ -f ${2}/${1} ] && ls -l ${2}/${1}
734      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
735      IGCM_debug_Exit "IGCM_sys_Put_Out"
736    else
737
738      if [ X${JobType} = XRUN ] ; then
739        if [ X${3} = X ] ; then
740          [ -f ${2} ] && IGCM_sys_Chmod 444 ${2}
741          [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1}
742        fi
743      fi
744
745      \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
746    fi
747  fi
748  IGCM_debug_PopStack "IGCM_sys_Put_Out"
749  return 0
750}
751
752#D-#==================================================
753#D-function IGCM_sys_Get
754#D-* Purpose: Get a file from ${ARCHIVE}
755#D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX
756#D-            IGCM_sys_Get /l Array_contain_myfiles /destpath/
757function IGCM_sys_Get {
758  IGCM_debug_PushStack "IGCM_sys_Get" $@
759
760  typeset DEST dm_liste target file_work
761  typeset NB_ESSAI DELAI status i
762
763  if ( $DEBUG_sys ) ; then
764    echo "IGCM_sys_Get :" $@
765  fi
766
767  # number of tentative
768  NB_ESSAI=3
769  # time delay between tentative
770  DELAI=2
771
772  if [ $DRYRUN -le 2 ]; then
773    if [ X${1} = X'/l' ] ; then
774      eval set +A dm_liste \${${2}}
775    else
776      eval set +A dm_liste ${1}
777    fi
778    eval DEST=\${${#}}
779    ccc_hsm get ${dm_liste[*]} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
780    status=$?
781    if [ ${status} -gt 0 ] ; then
782      echo "WARNING IGCM_sys_Get : error code ${status}"
783      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
784      echo "WARNING IGCM_sys_Get : will stop later if the cp fails."
785    fi
786
787    #if [ ${status} -gt 0 ] ; then
788    #  if [ ! "X$( grep "Lost dmusrcmd connection" ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ )" = "X" ] ; then
789    #    cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
790    #    echo "WARNING IGCM_sys_Get : Lost dmusrcmd connection : "
791    #    sleep 30
792    #    echo "We try another time"
793    ##    dmget ${dm_liste[*]} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
794    #    ccc_hsm get ${dm_liste[*]} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
795    #    status=$?
796    #    if [ ${status} -gt 0 ] ; then
797    #      echo "ERROR IGCM_sys_Get : again demigration error :"
798    #      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
799    #      IGCM_debug_Exit "IGCM_sys_Get"
800    #    fi
801    #  else
802    #    echo "ERROR IGCM_sys_Get : demigration error :"
803    #    cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
804    #    IGCM_debug_Exit "IGCM_sys_Get"
805    #  fi
806    #fi
807
808    #   #RSYNC WITH NETWORK SSH CALL
809    #   echo ${RSYNC} ${RSYNC_opt} -e ssh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
810    #   ${RSYNC} ${RSYNC_opt} -e ssh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
811
812    #   #RSYNC WITH NFS USE
813    #   echo ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
814    #   ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
815
816    #   status=$?
817    #   IGCM_sys_Rsync_out $status
818
819    #   ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
820    #   (( status=status+$? ))
821
822    #USUAL WAY
823    if [ X${1} = X'/l' ] ; then
824      for target in ${dm_liste[*]} ; do
825        local_file=$( basename ${target} )
826        # test if the target file is present before the loop
827        IGCM_sys_TestFileArchive ${target}
828        status=$?
829        if [ ${status} -gt 0 ] ; then
830          echo "IGCM_sys_Get, ERROR : regular file ${target} DOES NOT EXIST ."
831          IGCM_debug_Exit "IGCM_sys_Get"
832        else
833          i=0
834          while [ $i -lt $NB_ESSAI ] ; do
835            #if [ X${DoLink} = Xtrue ] ; then
836            #  \ln -s ${target} ${DEST}/${local_file} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
837            #  status=$?
838            #  else
839            #  \cp ${target} ${DEST}/${local_file} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
840            #  status=$?
841            #fi
842            \ln -s ${target} ${DEST}/${local_file} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
843            status=$?
844            if [ ${status} -gt 0 ]; then
845              IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status} ${i}/${NB_ESSAI}"
846              IGCM_debug_Print 2 "IGCM_sys_Get : sleep ${DELAI} seconds and try again."
847              sleep $DELAI
848            else
849              break
850            fi
851            (( i = i + 1 ))
852          done
853          if [ ${status} -gt 0 ] ; then
854            echo "IGCM_sys_Get : error"
855            cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
856            \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
857            IGCM_debug_Exit "IGCM_sys_Get"
858          else
859            \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
860          fi
861        fi
862      done
863    else
864      i=0
865      while [ $i -lt $NB_ESSAI ] ; do
866        \cp ${dm_liste} ${DEST} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
867        status=$?
868        if [ ${status} -gt 0 ]; then
869          IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status} ${i}/${NB_ESSAI}"
870          IGCM_debug_Print 2 "IGCM_sys_Get : sleep ${DELAI} seconds and try again."
871          sleep $DELAI
872        else
873          break
874        fi
875        (( i = i + 1 ))
876      done
877      if [ ${status} -gt 0 ] ; then
878        echo "IGCM_sys_Get : error"
879        cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
880        \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
881        IGCM_debug_Exit "IGCM_sys_Get"
882      else
883        \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
884      fi
885    fi
886  fi
887  IGCM_debug_PopStack "IGCM_sys_Get"
888}
889
890#D-#==================================================
891#D-function IGCM_sys_GetDate_Monitoring
892#D-* Purpose: get the last year for which the monitoring has been computed
893#D-* Examples:
894#D-
895function IGCM_sys_GetDate_Monitoring {
896  IGCM_debug_PushStack "IGCM_sys_GetDate_Monitoring" $@
897  if ( $DEBUG_sys ) ; then
898    echo "IGCM_sys_GetDate_Monitoring :" $@
899  fi
900
901  eval ${2}=$( cdo showyear ${1} 2> /dev/null | gawk '{ print $NF }' )
902
903  IGCM_debug_PopStack "IGCM_sys_GetDate_Monitoring"
904}
905
906#D-#==================================================
907#D-function IGCM_sys_Dods_Rm
908#D-* Purpose: DO NOTHING ! Put ${ARCHIVE} files on DODS internet protocole.
909#D-* Examples:
910#D-
911function IGCM_sys_Dods_Rm {
912  if ( $DEBUG_sys ) ; then
913    echo "IGCM_sys_Dods_Rm :" $@
914  fi
915  typeset status
916  if [ $DRYRUN = 0 ]; then
917
918#    if [ ! -d /dmnfs/cont003/dods/public/${LOGIN}/${R_DODS}/${1} ] ; then
919#      echo "WARNING : IGCM_sys_Dods_Rm /dmnfs/cont003/dods/public/${LOGIN}/${R_DODS}/${1} DOES NOT EXIST ."
920#      echo "Nothing has been done."
921#      return
922#    fi
923
924    if [ "$#" -eq 1 ]; then
925      ## /ccc/cont003/home/igcmg/igcmg/Tools/irene/thredds_rm public/${LOGIN}/${R_DODS}/${1} # > out_dods_rm 2>&1
926      $(ccc_home -u igcmg)/Tools/irene/thredds_rm public/${LOGIN}/${R_DODS}/${1} # > out_dods_rm 2>&1
927      status=$?
928    else
929      ## /ccc/cont003/home/igcmg/igcmg/Tools/irene/thredds_rm public/${LOGIN}/${R_DODS} # > out_dods_rm 2>&1
930      $(ccc_home -u igcmg)/Tools/irene/thredds_rm public/${LOGIN}/${R_DODS} # > out_dods_rm 2>&1
931      status=$?
932    fi
933
934#    if [ ${status} -gt 0 ] ; then
935#      echo "IGCM_sys_Dods_Rm : error."
936#      cat out_dods_rm
937#      IGCM_debug_Exit "IGCM_sys_Dods_Rm"
938#    else
939#      rm out_dods_rm
940#    fi
941
942  fi
943  return $status
944}
945
946#D-#==================================================
947#D-function IGCM_sys_Dods_Cp
948#D-* Purpose: Copy $(ARCHIVE) files on DODS internet protocole.
949#D-* Examples:
950#D-
951function IGCM_sys_Dods_Cp {
952  if ( $DEBUG_sys ) ; then
953    echo "IGCM_sys_Dods_Cp :" $@
954  fi
955  typeset status
956  if [ $DRYRUN = 0 ]; then
957
958#    if [ ! -d ${R_SAVE}/${1} ] ; then
959#      echo "WARNING : IGCM_sys_Dods_Cp ${R_SAVE}/${1} DOES NOT EXIST ."
960#      echo "Nothing has been done."
961#      return
962#    fi
963
964    ## /ccc/cont003/home/igcmg/igcmg/Tools/irene/bin/thredds_cp ${1} public/${LOGIN}/${R_DODS} # > out_dods_cp 2>&1
965    $(ccc_home -u igcmg)/Tools/irene/thredds_cp ${1} public/${LOGIN}/${R_DODS} # > out_dods_cp 2>&1
966    status=$?
967
968#       if [ ${status} -gt 0 ] ; then
969#           echo "IGCM_sys_Dods_Cp : error."
970#           cat out_dods_cp
971#           IGCM_debug_Exit "IGCM_sys_Dods_Cp"
972#       else
973#           rm out_dods_cp
974#       fi
975
976  fi
977  return $status
978}
979
980#D-#==================================================
981#D-function IGCM_sys_Put_Dods
982#D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole.
983#D-* Examples:
984#D-
985function IGCM_sys_Put_Dods {
986  IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@
987  if ( $DEBUG_sys ) ; then
988    echo "IGCM_sys_Put_Dods :" $@
989  fi
990  typeset status
991  if [ $DRYRUN = 0 ]; then
992    if ( [ ! -d ${R_SAVE}/${1} ] && [ ! -d ${R_FIGR}/${1} ] ) ; then
993      echo "WARNING IGCM_sys_Put_Dods : None of the following directories exist. Exactly one should."
994      echo "WARNING IGCM_sys_Put_Dods : ${R_SAVE}/${1} DOES NOT EXIST."
995      echo "WARNING IGCM_sys_Put_Dods : ${R_FIGR}/${1} DOES NOT EXIST."
996      IGCM_debug_PopStack "IGCM_sys_Put_Dods"
997      return
998    fi
999
1000    if ( [ -d ${R_SAVE}/${1} ] && [ -d ${R_FIGR}/${1} ] ) ; then
1001      echo "WARNING IGCM_sys_Put_Dods : Both of the following directories exist. Exactly one should."
1002      echo "WARNING IGCM_sys_Put_Dods : ${R_SAVE}/${1} EXISTS."
1003      echo "WARNING IGCM_sys_Put_Dods : ${R_FIGR}/${1} EXISTS."
1004      IGCM_debug_PopStack "IGCM_sys_Put_Dods"
1005      return
1006    fi
1007    #
1008    if [ -d ${R_SAVE}/${1} ] ; then
1009      cd ${R_SAVE}
1010    elif [ -d ${R_FIGR}/${1} ] ; then
1011      cd ${R_FIGR}
1012    fi
1013
1014    IGCM_sys_Dods_Rm ${1}
1015    IGCM_sys_Dods_Cp ${1}
1016    status=0
1017
1018    if [ ${status} -gt 0 ] ; then
1019      echo "IGCM_sys_Put_Dods : error."
1020      IGCM_debug_Exit "IGCM_sys_Put_Dods"
1021    fi
1022  fi
1023  IGCM_debug_PopStack "IGCM_sys_Put_Dods"
1024}
1025
1026##############################################################
1027# REBUILD OPERATOR
1028
1029#D-#==================================================
1030#D-function IGCM_sys_sync
1031#D-* Purpose: flush buffer on disk
1032#D-* Examples:
1033#D-
1034function IGCM_sys_sync {
1035  IGCM_debug_PushStack "IGCM_sys_sync" $@
1036  if ( $DEBUG_sys ) ; then
1037    echo "IGCM_sys_sync :" $@
1038  fi
1039
1040  /bin/sync
1041
1042  IGCM_debug_PopStack "IGCM_sys_sync"
1043}
1044
1045############################################################
1046# Activate Running Environnment Variables
1047
1048#D-#==================================================
1049#D-function IGCM_sys_activ_variables
1050#D-* Purpose: set environement variables prior to execution
1051#D-* Examples:
1052#D-
1053function IGCM_sys_activ_variables {
1054  IGCM_debug_PushStack "IGCM_sys_activ_variables"
1055  if ( $DEBUG_sys ) ; then
1056    echo "IGCM_sys_activ_variables"
1057  fi
1058
1059# --------------------------------------------------------------------
1060#D- MODULE specifications
1061# --------------------------------------------------------------------
1062  # Source the file EnvFile containing all module load needed to run the model.
1063  # EnvFile can be specified in config.card. If this is the case and if the file exists,
1064  # it will be used. Otherwise a default file will be used.
1065  if [ ! X${config_UserChoices_EnvFile} = X ] && [ -f ${config_UserChoices_EnvFile} ] ; then
1066      # EnvFile is set in config.card and the file exists
1067      IGCM_debug_Print 1 "EnvFile set in config.card will be used"
1068      EnvFile=${config_UserChoices_EnvFile}
1069  else
1070      IGCM_debug_Print 1 "IGCM_sys_active_variables : Default modules will be used"
1071      module purge > /dev/null 2>&1
1072      EnvFile=/gpfswork/rech/psl/commun/MachineEnvironment/jeanzay/env_jeanzay
1073  fi
1074  IGCM_debug_Print 1 "IGCM_sys_active_variables : Following EnvFile will be used :" 
1075  IGCM_debug_Print 1 ${EnvFile}
1076  . ${EnvFile}
1077
1078  IGCM_debug_Print 1 "IGCM_sys_active_variables : Now loaded modules for Jean-Zay. "
1079  module list
1080
1081# --------------------------------------------------------------------
1082#D- MPI specifications
1083# --------------------------------------------------------------------
1084
1085# --------------------------------------------------------------------
1086#D- Other specifications
1087# --------------------------------------------------------------------
1088
1089  ulimit -s unlimited
1090
1091  IGCM_debug_PopStack "IGCM_sys_activ_variables"
1092}
1093
1094############################################################
1095# Desactivate Running Environnment Variables
1096
1097#D-#==================================================
1098#D-function IGCM_sys_desactiv_variables
1099#D-* Purpose: unset environement variables after execution
1100#D-* Examples:
1101#D-
1102function IGCM_sys_desactiv_variables {
1103  IGCM_debug_PushStack "IGCM_sys_desactiv_variables"
1104  if ( $DEBUG_sys ) ; then
1105    echo "IGCM_sys_desactiv_variables"
1106  fi
1107# --------------------------------------------------------------------
1108#D- MPI specifications
1109# --------------------------------------------------------------------
1110
1111# --------------------------------------------------------------------
1112#D- Other specifications
1113# --------------------------------------------------------------------
1114
1115  IGCM_debug_PopStack "IGCM_sys_desactiv_variables"
1116}
1117
1118############################################################
1119# Update job headers to be used by the scheduler
1120
1121#D-#==================================================
1122#D-function IGCM_sys_updateHeaders
1123#D-* Purpose: Update job headers to be used by the scheduler
1124#D-* Examples: IGCM_sys_updateHeaders /path/to/Job_MYEXP
1125#D-
1126function IGCM_sys_updateHeaders {
1127  IGCM_debug_PushStack "IGCM_sys_updateHeaders"
1128  if ( $DEBUG_sys ) ; then
1129    echo "IGCM_sys_updateHeaders"
1130  fi
1131  typeset file
1132  file=$1
1133
1134  if [ ${executionType} -eq 1 ] ; then
1135    # MPMD + MPI
1136    sed -e "/::openMPthreads::/d"                  \
1137        -e "s/::JobNumProcTot::/${coreNumber}/"    \
1138      ${file} > ${file}.tmp
1139
1140  elif [ ${executionType} -eq 2 ] ; then
1141    # MPMD + MPI + OMP
1142      sed -e "s/::openMPthreads::/${openMPthreads}/" \
1143          -e "s/::JobNumProcTot::/${mpiTasks}/"    \
1144          ${file} > ${file}.tmp
1145
1146  elif [ ${executionType} -eq 3 ] ; then
1147    # SPMD + MPI/OMP
1148    sed -e "s/::openMPthreads::/${openMPthreads}/" \
1149        -e "s/::JobNumProcTot::/${mpiTasks}/"      \
1150      ${file} > ${file}.tmp
1151
1152  elif [ ${executionType} -eq 4 ] ; then
1153    # SPMD + MPI only
1154    sed -e "s/::JobNumProcTot::/${mpiTasks}/"      \
1155        -e "/::openMPthreads::/d"                  \
1156      ${file} > ${file}.tmp
1157
1158  elif [ ${executionType} -eq 5 ] ; then
1159    # SPMD + OMP only
1160    sed -e "s/::openMPthreads::/${openMPthreads}/" \
1161        -e "/::JobNumProcTot::/d"                  \
1162      ${file} > ${file}.tmp
1163
1164  elif [ ${executionType} -eq 6 ] ; then
1165    # SEQUENTIAL THEN
1166    sed -e "s/::JobNumProcTot::/1/"                \
1167        -e "/::openMPthreads::/d"                  \
1168      ${file} > ${file}.tmp
1169
1170  fi
1171
1172  IGCM_sys_Mv ${file}.tmp ${file}
1173
1174  IGCM_debug_PopStack "IGCM_sys_updateHeaders"
1175}
1176
1177############################################################
1178# Build MPI/OMP scripts run file (dummy function)
1179
1180#D-#==================================================
1181#D-function IGCM_sys_build_run_file
1182#D-* Purpose: build run file (deprecated)
1183#D-* Examples:
1184#D-
1185function IGCM_sys_build_run_file {
1186  IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file "
1187}
1188
1189############################################################
1190# Build MPI/OMP scripts
1191
1192#D-#==================================================
1193#D-function IGCM_sys_build_execution_scripts
1194#D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND}
1195#D-* Examples:
1196#D-
1197function IGCM_sys_build_execution_scripts
1198{
1199  IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@
1200  if ( $DEBUG_sys ) ; then
1201    echo "IGCM_sys_build_execution_scripts " $@
1202  fi
1203  IGCM_debug_Print 1 "executionType= ${executionType}"
1204  EXECUTION=${HOST_MPIRUN_COMMAND}
1205
1206  if ( ${OK_PARA_MPMD} ) ; then
1207
1208    # MPMD mode
1209    # 1 MPI only : executionType=1
1210    # 2 MPI/OpenMP : executionType=2
1211
1212    if [ -f run_file ] ; then
1213      IGCM_sys_Rm -f run_file
1214    fi
1215    touch run_file
1216
1217    # case 1 : Only MPI (MPMD)
1218    if  ( ! ${OK_PARA_OMP} ) ; then
1219      # Build run_file
1220      current_core=0
1221      # First loop on the components for the coupler ie oasis (only if oasis3)
1222      # the coupler ie oasis3 must be the first one
1223      for comp in ${config_ListOfComponents[*]} ; do
1224
1225        eval ExeNameIn=\${config_Executable_${comp}[0]}
1226        eval ExeNameOut=\${config_Executable_${comp}[1]}
1227
1228        # Only if the component has an executable
1229        if ( [ "X${ExeNameOut}" != X\"\" ] ) ; then
1230
1231          eval comp_proc_mpi_loc=\${${comp}_PROC_MPI}
1232          (( end_core = ${current_core} + ${comp_proc_mpi_loc} - 1 ))
1233          echo "${current_core}-${end_core} ./${ExeNameOut}" >> run_file
1234          (( current_core = ${end_core} + 1 ))
1235        fi
1236      done
1237
1238      EXECUTION="${HOST_MPIRUN_COMMAND} --multi-prog ./run_file"
1239
1240      IGCM_sys_Chmod u+x run_file
1241      if ( $DEBUG_sys ) ; then
1242        echo "run_file contains : "
1243        cat run_file
1244      fi
1245
1246    else 
1247
1248    # 2 MPI/OpenMP : executionType=2
1249
1250    # MPI-OpenMP (MPMD)
1251    # example of run_file
1252    # 0-70   env OMP_NUM_THREADS=8 ./script_lmdz.x.ksh
1253    # 71-71  env OMP_NUM_THREADS=1 ./script_xios.x.ksh
1254
1255      # Loop on the components to build run_file and script_exec files
1256      current_core=0
1257      for comp in ${config_ListOfComponents[*]} ; do
1258
1259        eval ExeNameIn=\${config_Executable_${comp}[0]}
1260        eval ExeNameOut=\${config_Executable_${comp}[1]}
1261
1262        # Not possible if oasis has an executable (i.e old version of oasis3)
1263        if ( [ "X${ExeNameOut}" != X\"\" ] &&  [ "X${comp}" = "XCPL" ] ) ; then
1264          IGCM_debug_Exit "ERROR MPMD with hybrid MPI-OpenMP is not available with oasis3 version"
1265          IGCM_debug_Print 2 "Only available with oasis3-MCT version coupler"
1266          IGCM_debug_Verif_Exit
1267        fi
1268
1269        # Only if we really have an executable for the component :
1270        if [ "X${ExeNameOut}" != X\"\" ] ; then
1271
1272          eval comp_proc_mpi_loc=\${${comp}_PROC_MPI}
1273          eval comp_proc_omp_loc=\${${comp}_PROC_OMP}
1274
1275          # Build script files
1276
1277          echo "#!/bin/ksh" > script_${ExeNameOut}.ksh
1278          echo ""  >> script_${ExeNameOut}.ksh
1279          if [ ${comp_proc_omp_loc} -gt 1 ] ; then
1280            echo "export OMP_STACKSIZE=3g"  >> script_${ExeNameOut}.ksh
1281            echo "export OMP_PLACES=cores"  >> script_${ExeNameOut}.ksh
1282          fi
1283
1284          # to have out/err per process on different files
1285          echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${SLURM_PROCID} 2>out_${ExeNameOut}.err.\${SLURM_PROCID}" >> script_${ExeNameOut}.ksh
1286
1287          IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh
1288
1289          # Complete run_file
1290          eval comp_proc_mpi_loc=\${${comp}_PROC_MPI}
1291          (( end_core = ${current_core} + ${comp_proc_mpi_loc} - 1 ))
1292          echo "${current_core}-${end_core}  env OMP_NUM_THREADS=${comp_proc_omp_loc} ./script_${ExeNameOut}.ksh " >> run_file
1293          (( current_core = ${end_core} + 1 ))
1294
1295        fi
1296      done
1297
1298      ## variable added to stop after 60s instead of 600s by default.
1299      ## This is used when no error comes from executables and when something stopped an executable without notice.
1300      export SLURM_WAIT=60
1301
1302      EXECUTION="${HOST_MPIRUN_COMMAND} --multi-prog ./run_file"
1303
1304      IGCM_sys_Chmod u+x run_file
1305      if ( $DEBUG_sys ) ; then
1306        echo "run_file contains : "
1307        cat run_file
1308      fi
1309
1310    fi # if ${OK_PARA_MPMD}
1311
1312  else
1313  # Only one executable (SPMD mode):  executionType=3, 4, 5 and 6
1314
1315    for comp in ${config_ListOfComponents[*]} ; do
1316
1317      # Only if we really have an executable for the component :
1318      eval ExeNameOut=\${config_Executable_${comp}[1]}
1319      if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then
1320
1321        # Build script files
1322
1323        echo "#!/bin/ksh" > script_${ExeNameOut}.ksh
1324        echo ""  >> script_${ExeNameOut}.ksh
1325        IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh
1326
1327        if ( ${OK_PARA_OMP} ) ; then
1328          eval comp_proc_omp_loc=\${${comp}_PROC_OMP}
1329          echo ""  >> script_${ExeNameOut}.ksh
1330          echo "export OMP_STACKSIZE=3g"  >> script_${ExeNameOut}.ksh
1331          echo "export OMP_PLACES=cores"  >> script_${ExeNameOut}.ksh
1332          echo "OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh
1333        fi
1334
1335        eval comp_proc_mpi_loc=\${${comp}_PROC_MPI}
1336       
1337        # To have out/err per process on different files
1338        echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${SLURM_PROCID} 2>out_${ExeNameOut}.err.\${SLURM_PROCID}"  >> script_${ExeNameOut}.ksh
1339        EXECUTION="${HOST_MPIRUN_COMMAND} ./script_${ExeNameOut}.ksh"
1340
1341        IGCM_debug_Print 1 "sys Irene : script_${ExeNameOut}.ksh contains"
1342        cat script_${ExeNameOut}.ksh
1343
1344      fi
1345
1346    done
1347
1348  fi # ${OK_PARA_MPMD}
1349
1350  IGCM_debug_Print 1 "sys Irene : execution command is "
1351  IGCM_debug_Print 1 "$EXECUTION"
1352
1353  IGCM_debug_PopStack "IGCM_sys_build_execution_scripts"
1354}
1355
1356#D-#==================================================
1357#D-function IGCM_sys_check_path
1358#D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine
1359#D-* do not point to an important use directory. Stop immediately in that case.
1360#D-* Examples:
1361#D-
1362function IGCM_sys_check_path {
1363  IGCM_debug_PushStack "IGCM_sys_check_path"
1364  if ( $DEBUG_sys ) ; then
1365    echo "IGCM_sys_check_path"
1366  fi
1367
1368  if ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X${WORK} ] || [ X${RUN_DIR_PATH} = X${SCRATCH} ] || [ X${RUN_DIR_PATH} = X${STORE} ] ) ; then
1369    IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}"
1370    IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}"
1371    IGCM_debug_Exit "This will stop the job"
1372  fi
1373  IGCM_debug_PopStack "IGCM_sys_check_path"
1374}
1375
1376#D-#==================================================
1377#D-function IGCM_sys_check_quota
1378#D-* Purpose: check user quota. Stop the simulation if quota above 90%
1379#D-* Examples:
1380#D-
1381function IGCM_sys_check_quota {
1382  IGCM_debug_PushStack "IGCM_sys_check_quota"
1383  if ( $DEBUG_sys ) ; then
1384    echo "IGCM_sys_check_quota"
1385  fi
1386  # Limit of quota (in %)
1387  limit_quota=90
1388
1389  # Check of the volume
1390  volume_quota=$(ccc_quota | grep ' scratch' | gawk '{print $2}')
1391  volume_avail=$(ccc_quota | grep ' scratch' | gawk '{print $3}')
1392
1393  if ( [ ! X${volume_quota} = X ] && [ ! ${volume_quota} = "-" ] ) ; then
1394
1395    unit_avail=${volume_avail: -1}
1396    unit_quota=${volume_quota: -1}
1397
1398    if [ "${unit_quota}" = "*" ] ; then
1399      IGCM_debug_Print 1 "Please, check your quota of volume on scratch"
1400      IGCM_debug_Print 1 "More than 100% of your quota is used"
1401      IGCM_debug_Print 1 "Use the ccc_quota command to check"
1402      IGCM_debug_Print 1 "You must have more than 10% available to run"
1403      IGCM_debug_Exit "Not enough space to run ! STOP HERE"
1404      IGCM_debug_Verif_Exit
1405    fi
1406
1407    temp_avail=${volume_avail%%${volume_avail: -1}*}
1408    temp_quota=${volume_quota%%${volume_quota: -1}*}
1409
1410    if [ ! ${unit_avail} = ${unit_quota} ] ; then
1411
1412    # Convertion
1413      if [ ${volume_avail: -1} = "T" ] ; then
1414        (( temp_avail = temp_avail * 1000000000000 ))
1415      elif [ ${volume_avail: -1} = "G" ] ; then
1416        (( temp_avail = temp_avail * 1000000000 ))
1417      elif [ ${volume_avail: -1} = "M" ] ; then
1418        (( temp_avail = temp_avail * 1000000 ))
1419      elif [ ${volume_avail: -1} = "k" ] ; then
1420        (( temp_avail = temp_avail * 1000 ))
1421      else
1422        (( temp_avail = volume_avail ))
1423      fi
1424      if [ ${volume_quota: -1} = "T" ] ; then
1425        (( temp_quota = temp_quota * 1000000000000 ))
1426      elif [ ${volume_quota: -1} = "G" ] ; then
1427        (( temp_quota = temp_quota * 1000000000 ))
1428      elif [ ${volume_quota: -1} = "M" ] ; then
1429        (( temp_quota = temp_quota * 1000000 ))
1430      elif [ ${volume_quota: -1} = "k" ] ; then
1431        (( temp_quota = temp_quota * 1000 ))
1432      else
1433        (( temp_quota = volume_quota ))
1434      fi
1435    fi
1436
1437    quota_volume=$(echo "scale=2 ; $temp_quota/$temp_avail*100" | bc)
1438#    echo "volume ratio is " $quota_volume
1439
1440    if [ ${quota_volume} -ge ${limit_quota} ] ; then
1441      IGCM_debug_Print 1 "Please, check your quota of volume on scratch"
1442      IGCM_debug_Print 1 "${quota_volume}% of your quota is used"
1443      IGCM_debug_Print 1 "Use the ccc_quota command to check"
1444      IGCM_debug_Print 1 "You must have more than 10% available to run"
1445      IGCM_debug_Exit "Not enough space to run ! STOP HERE"
1446      IGCM_debug_Verif_Exit
1447    fi
1448
1449  fi
1450
1451# Check of the number of inodes
1452
1453  inode_quota=$(ccc_quota | grep ' scratch' | gawk '{print $6}')
1454  inode_avail=$(ccc_quota | grep ' scratch' | gawk '{print $7}')
1455
1456  if ( [ ! X${inode_quota} = X ] && [ ! ${inode_quota} = "-" ] ) ; then
1457
1458    unit_avail=${inode_avail: -1}
1459    unit_quota=${inode_quota: -1}
1460
1461    if [ "${unit_quota}" = "*" ] ; then
1462      IGCM_debug_Print 1 "Please, check your quota of inode on scratch"
1463      IGCM_debug_Print 1 "More than 100% of your quota is used"
1464      IGCM_debug_Print 1 "Use the ccc_quota command to check"
1465      IGCM_debug_Print 1 "You must have more than 10% available to run"
1466      IGCM_debug_Exit "Not enough space to run ! STOP HERE"
1467      IGCM_debug_Verif_Exit
1468    fi
1469
1470    temp_avail=${inode_avail%%${inode_avail: -1}*}
1471    temp_quota=${inode_quota%%${inode_quota: -1}*}
1472
1473    if [ ! ${unit_avail} = ${unit_quota} ] ; then
1474
1475    # Convertion
1476      if [ ${inode_avail: -1} = "T" ] ; then
1477        (( temp_avail = temp_avail * 1000000000000 ))
1478      elif [ ${inode_avail: -1} = "G" ] ; then
1479        (( temp_avail = temp_avail * 1000000000 ))
1480      elif [ ${inode_avail: -1} = "M" ] ; then
1481        (( temp_avail = temp_avail * 1000000 ))
1482      elif [ ${inode_avail: -1} = "k" ] ; then
1483        (( temp_avail = temp_avail * 1000 ))
1484      else
1485        (( temp_avail = inode_avail ))
1486      fi
1487
1488      if [ ${inode_quota: -1} = "T" ] ; then
1489        (( temp_quota = temp_quota * 1000000000000 ))
1490      elif [ ${inode_quota: -1} = "G" ] ; then
1491        (( temp_quota = temp_quota * 1000000000 ))
1492      elif [ ${inode_quota: -1} = "M" ] ; then
1493        (( temp_quota = temp_quota * 1000000 ))
1494      elif [ ${inode_quota: -1} = "k" ] ; then
1495        (( temp_quota = temp_quota * 1000 ))
1496      else
1497        (( temp_quota = inode_quota ))
1498      fi
1499    fi
1500    quota_inode=$(echo "scale=2 ; $temp_quota/$temp_avail*100" | bc)
1501#    echo "inode ratio is " $quota_inode
1502
1503    if [ ${quota_inode} -ge ${limit_quota} ] ; then
1504      IGCM_debug_Print 1 "Please, check your quota of inode on scratch"
1505      IGCM_debug_Print 1 "${quota_inode}% of your quota is used"
1506      IGCM_debug_Print 1 "Use the ccc_quota command to check"
1507      IGCM_debug_Print 1 "You must have more than 10% available to run"
1508      IGCM_debug_Exit "Not enough space to run ! STOP HERE"
1509      IGCM_debug_Verif_Exit
1510    fi
1511  fi
1512  IGCM_debug_PopStack "IGCM_sys_check_quota"
1513}
1514
1515#D-#==================================================
1516#D-function IGCM_sys_projectAccounting
1517#D-* Purpose: store project accounting information in a file
1518#D-* Examples:
1519#D-
1520function IGCM_sys_projectAccounting {
1521  IGCM_debug_PushStack "IGCM_sys_projectAccounting"
1522  if ( $DEBUG_sys ) ; then
1523    echo "IGCM_sys_check_quota"
1524  fi
1525
1526  ssh irene191 /usr/bin/ccc_myproject > $1
1527
1528  IGCM_debug_PopStack "IGCM_sys_projectAccounting"
1529}
1530
1531#D-#==================================================
1532#D-function IGCM_sys_getJobSchedulerID
1533#D-* Purpose: Get the job ID during execution
1534#D-* Examples: IGCM_sys_getJobSchedulerID jobSchedulerID
1535#D-
1536function IGCM_sys_getJobSchedulerID {
1537  IGCM_debug_PushStack "IGCM_sys_getJobSchedulerID"
1538  if ( $DEBUG_sys ) ; then
1539    echo "IGCM_sys_getJobSchedulerID"
1540  fi
1541
1542  eval ${1}=${BRIDGE_MSUB_JOBID}
1543
1544  IGCM_debug_PopStack "IGCM_sys_getJobSchedulerID"
1545}
1546
1547#D-#==================================================
1548#D-function IGCM_sys_GetJobID
1549#D-* Purpose: Get the job ID from the JobName
1550#D-* Examples: IGCM_sys_GetJobID ${JobName} ${TargetUsr} JobID
1551#D-
1552function IGCM_sys_GetJobID {
1553  IGCM_debug_PushStack "IGCM_sys_GetJobID"
1554  if ( $DEBUG_sys ) ; then
1555    echo "IGCM_sys_GetJobID"
1556  fi
1557
1558  # With -f option, the full job name is given in the last column
1559  ID=$( ccc_mstat -f -u $2 | \
1560        gawk -v JobName=$1 '( $NF ~ JobName ) { print $1 }' )
1561
1562  eval ${3}=${ID}
1563  IGCM_debug_PopStack "IGCM_sys_GetJobID"
1564}
1565
1566#D-#==================================================
1567#D-function IGCM_sys_CountJobInQueue
1568#D-* Purpose: Count number of users job
1569#D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun
1570#D-
1571function IGCM_sys_CountJobInQueue {
1572  IGCM_debug_PushStack "IGCM_sys_CountJobInQueue"
1573  if ( $DEBUG_sys ) ; then
1574    echo "IGCM_sys_CountJobInQueue"
1575  fi
1576
1577  # With -f option, the full job name is given in the last column
1578  NbRun=$( ccc_mstat -f | gawk -v JobName=$1 'BEGIN { x=0 } ( $NF ~ JobName ) { x=x+1 } END { print x }' )
1579
1580  eval ${2}=${NbRun}
1581
1582  IGCM_debug_PopStack "IGCM_sys_CountJobInQueue"
1583}
1584
1585#D-#==================================================
1586#D-function IGCM_sys_ListJobInQueue
1587#D-* Purpose: Produce a list of users computing jobs (excluding post-processing)
1588#D-* Examples: IGCM_sys_ListJobInQueue ${User} JobNameList
1589#D-
1590function IGCM_sys_ListJobInQueue {
1591  IGCM_debug_PushStack "IGCM_sys_ListJobInQueue"
1592  if ( $DEBUG_sys ) ; then
1593    echo "IGCM_sys_ListJobInQueue"
1594  fi
1595
1596  # With -f option, the full job name is given in the last column
1597  set -A JobList $( ccc_mstat -f | gawk -v User=$1             \
1598                                        '( $2  == User      && \
1599                                           $NF != /TS/      && \
1600                                           $NF !~ /PACK/    && \
1601                                           $NF !~ /REBUILD/ && \
1602                                           $NF !~ /pack/ )     \
1603                                         { print $NF }' | sed -e "s/\(.*\)\.[0-9]*/\1/" )
1604
1605  eval set -A ${2} ${JobList[*]}
1606
1607  IGCM_debug_PopStack "IGCM_sys_ListJobInQueue"
1608}
1609
1610#D-#==================================================
1611#D-function IGCM_sys_atlas
1612#D-* Purpose: encapsulate atlas call so as to manage error code and curie specificity
1613#D-* Examples:
1614#D-
1615function IGCM_sys_atlas {
1616  IGCM_debug_PushStack "IGCM_sys_atlas" $@
1617  if ( $DEBUG_sys ) ; then
1618    echo "IGCM_sys_atlas :" $@
1619  fi
1620
1621  typeset status
1622
1623  \ccc_mprun atlas $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
1624  status=$?
1625  if [ ${status} -gt 0 ] ; then
1626    echo "IGCM_sys_atlas : error code ${status}"
1627    cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
1628    \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
1629    IGCM_debug_PopStack "IGCM_sys_atlas"
1630    return 1
1631  else
1632    IGCM_debug_PopStack "IGCM_sys_atlas"
1633    return 0
1634  fi
1635
1636  IGCM_debug_PopStack "IGCM_sys_atlas"
1637}
1638
1639#D-#==================================================
1640#D-function IGCM_sys_rebuild_nemo
1641#D-* Purpose: rebuild nemo parallel files with nemo specific rebuild on curie
1642#D-* Examples:
1643#D-
1644
1645function IGCM_sys_rebuild_nemo {
1646  IGCM_debug_PushStack "IGCM_sys_rebuild_nemo" $@
1647  if ( $DEBUG_sys ) ; then
1648    echo "IGCM_sys_rebuild_nemo :" $@
1649  fi
1650
1651  $( ccc_home -u igcmg)/Tools/irene/bin/rebuild_nemo ${1} ${2}
1652
1653  IGCM_debug_PopStack "IGCM_sys_rebuild_nemo"
1654}
1655
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