source: trunk/libIGCM/libIGCM_sys/libIGCM_sys_obelix.ksh @ 1511

Last change on this file since 1511 was 1487, checked in by jgipsl, 5 years ago

Set new version for rebuild tool at obelix due to system changes.
  • 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: 40.4 KB
Line 
1#!/bin/ksh
2
3#**************************************************************
4# Author: Sebastien Denvil, Martial Mancip, Christian Laguerre
5# Contact: Martial.Mancip__at__ipsl.jussieu.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 obelix
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# $hostname of the MASTER job
70typeset MASTER=${MASTER:=$( hostname )}
71# project name
72typeset PROJECT=NONE
73# jobWarningDelay in seconds
74typeset jobWarningDelay=${PBS_WALLTIME}
75
76#D-
77#D-#==================================================
78#D-Program used in libIGCM
79#D-#==================================================
80
81# Submit command
82typeset SUBMIT=${SUBMIT:=qsub}
83# rsync with path
84typeset -r RSYNC=/usr/bin/rsync
85# RSYNC_opt args to rsync
86typeset -r RSYNC_opt="-va"
87# ie storage filesystem
88typeset -r STOREHOST=${MASTER}
89
90#====================================================
91# Access to module command
92#====================================================
93. /usr/share/Modules/init/ksh
94
95#====================================================
96# Set environment tools (ferret, nco, cdo, rebuild, ...)
97#====================================================
98if [ X${TaskType} = Xcomputing ] ; then
99    IGCM_debug_Print 1 "Modules will be loaded later in IGCM_sys_activ_variables."
100else
101    . /home/orchideeshare/igcmg/MachineEnvironment/obelix/env_atlas_obelix
102fi
103
104[ ! X${TaskType} = Xchecking ] && IGCM_debug_Print 1 "List of loaded modules:"
105[ ! X${TaskType} = Xchecking ] && module list
106
107# Load python
108module load python/2.7.5
109
110#====================================================
111# Host specific DIRECTORIES
112#====================================================
113# For rebuild
114export PATH=${PATH}:/home/orchideeshare/igcmg/IOIPSL_PLUS/modipsl.tagv2_2_4.28082019/bin/
115
116#====================================================
117#- MirrorlibIGCM for frontend
118typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false}
119
120#====================================================
121#- libIGCM_POST for frontend
122typeset -r libIGCM_POST=${libIGCM}
123
124#====================================================
125#- R_EXE   (==> BIN_DIR = ${MODIPSL}/bin )
126typeset -r R_EXE="${MODIPSL}/bin"
127
128#====================================================
129#- SUBMIT_DIR : submission dir
130if [ X${PBS_O_WORKDIR} != X ] ; then
131  typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${PBS_O_WORKDIR}}
132else
133  typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${PWD}}
134fi
135
136#====================================================
137#- IN
138typeset -r R_IN=${R_IN:=/home/orchideeshare/igcmg/IGCM}
139
140#====================================================
141#- RUN_DIR_PATH : Temporary working directory (=> TMP)
142if [ X${PBS_JOBID} != X ] ; then
143  typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/scratch/$PBS_O_LOGNAME.$PBS_JOBID}
144else
145  typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/tmp/tmp$$}
146fi
147
148#====================================================
149#- OUTCOMMAND_PATH : tmp place to store command lines standard error and outputs
150typeset -r OUTCOMMAND_PATH=/tmp
151
152#====================================================
153#- HOST_MPIRUN_COMMAND
154typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="time mpirun"}
155
156#====================================================
157#- Max number of arguments passed to nco operator or demigration command
158UNIX_MAX_LIMIT=360
159
160#====================================================
161#- set PackDefault to false on obelix
162PackDefault=false
163
164#====================================================
165#- Default number of MPI task for IPSL coupled model
166#- required for backward compatibility
167#-
168DEFAULT_NUM_PROC_OCE=5
169DEFAULT_NUM_PROC_CPL=1
170(( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL ))
171
172#D-#==================================================
173#D-function IGCM_sys_defineArchives
174#D-* Purpose:
175#D-* Define ARCHIVE : Dedicated to large files
176#D-* Define STORAGE : Dedicated to small/medium files
177#D-* Define R_OUT   : Output tree located on ARCHIVE
178#D-* Define R_FIG   : Output tree located on STORAGE hosting figures (monitoring and atlas, and/or small files)
179#D-* Define R_BUF   : Output tree located on STORAGE hosting files waiting for rebuild or pack processes
180#D-* if SpaceName=TEST nothing special will hapen
181#D-* Examples:
182#D-
183function IGCM_sys_defineArchives {
184  IGCM_debug_PushStack "IGCM_sys_defineArchives"
185
186  if [ ! X${config_UserChoices_ARCHIVE} = X ]; then
187    #====================================================
188    #- ARCHIVE (dedicated to large files)
189    ARCHIVE=${config_UserChoices_ARCHIVE}
190  else
191    #====================================================
192    #- ARCHIVE (dedicated to large files)
193    ARCHIVE=${ARCHIVE:=/home/scratch01/${LOGIN}}
194  fi
195
196  if [ ! X${config_UserChoices_STORAGE} = X ]; then
197    #====================================================
198    #- STORAGE (dedicated to small/medium files)
199    STORAGE=${config_UserChoices_STORAGE}
200  else
201    #====================================================
202    #- STORAGE (dedicated to small/medium files)
203    STORAGE=${ARCHIVE}
204  fi
205
206  # ON OBELIX NO SPECIAL CASE WHEN X${config_UserChoices_SpaceName} = XTEST
207
208  #====================================================
209  #- R_OUT
210  R_OUT=${ARCHIVE}/IGCM_OUT
211
212  #====================================================
213  #- R_FIG (hosting figures : monitoring and atlas, and/or small files)
214  R_FIG=${STORAGE}/IGCM_OUT
215
216  #====================================================
217  #- CMIP6 (hosting CMIP6 files produced by XIOS2 and configured by dr2xml)
218  CMIP6_BUF=${STORAGE}/IGCM_OUT
219
220  #====================================================
221  #- R_BUF (ONLY FOR double copy an scratch)
222  R_BUF=${STORAGE}/IGCM_OUT
223
224  IGCM_debug_Print 1 "R_OUT has been defined = ${R_OUT}"
225  IGCM_debug_Print 1 "R_BUF has been defined = ${R_BUF}"
226  IGCM_debug_Print 1 "R_FIG has been defined = ${R_FIG}"
227
228  IGCM_debug_PopStack "IGCM_sys_defineArchives"
229}
230
231#D-#==================================================
232#D-function IGCM_sys_RshArchive
233#D-* Purpose: Archive rsh command
234#D-* Examples:
235#D-
236function IGCM_sys_RshArchive {
237  IGCM_debug_PushStack "IGCM_sys_RshArchive" $@
238  /bin/ksh <<-EOF
239    ${@}
240EOF
241  status=$?
242  if [ ${status} -gt 0 ] ; then
243    IGCM_debug_Print 2 "IGCM_sys_RshArchive : command failed error code ${status}"
244    IGCM_debug_Exit "IGCM_sys_RshArchive"
245  fi
246  IGCM_debug_PopStack "IGCM_sys_RshArchive"
247}
248
249#D-#==================================================
250#D-function IGCM_sys_RshArchive_NoError
251#D-* Purpose: Archive rsh command, without error
252#D-*          used only in monitoring.job
253#D-* Examples:
254#D-
255function IGCM_sys_RshArchive_NoError {
256  IGCM_debug_PushStack "IGCM_sys_RshArchive_NoError" $@
257  /bin/ksh <<-EOF
258    ${@} 2> /dev/null
259EOF
260  IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError"
261}
262
263#D-#==================================================
264#D-function IGCM_sys_MkdirArchive
265#D-* Purpose: Mkdir on Archive
266#D-* Examples:
267#D-
268function IGCM_sys_MkdirArchive {
269  IGCM_debug_PushStack "IGCM_sys_MkdirArchive" $@
270  if ( $DEBUG_sys ) ; then
271    echo "IGCM_sys_MkdirArchive :" $@
272  fi
273  #- creation de repertoire sur le serveur fichier
274  if [ ! -d ${1} ]; then
275    \mkdir -p $1
276    status=$?
277
278    if [ ${status} -gt 0 ] ; then
279      IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : mkdir failed error code ${status}"
280      IGCM_debug_Exit "IGCM_sys_MkdirArchive"
281    fi
282  fi
283  IGCM_debug_PopStack "IGCM_sys_MkdirArchive"
284}
285
286#D-#==================================================
287#D-function IGCM_sys_TestDirArchive
288#D-* Purpose: Test Directory that must exists on Archive
289#D-* Examples:
290#D-
291function IGCM_sys_TestDirArchive {
292  IGCM_debug_PushStack "IGCM_sys_TestDirArchive" $@
293  if ( $DEBUG_sys ) ; then
294    echo "IGCM_sys_TestDirArchive :" $@
295  fi
296  typeset ExistFlag
297  ExistFlag=$( [ -d $1 ] && echo 0 || echo 1 )
298  IGCM_debug_PopStack "IGCM_sys_TestDirArchive"
299  return ${ExistFlag}
300}
301
302#D-#==================================================
303#D-function IGCM_sys_IsFileArchived
304#D-* Purpose: Test file that must NOT EXISTS on Archive based on filename only
305#D-* Examples:
306#D-
307function IGCM_sys_IsFileArchived {
308  IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@
309  if ( $DEBUG_sys ) ; then
310    echo "IGCM_sys_IsFileArchived :" $@
311  fi
312  typeset IsArchivedFlag
313  # Never archived for this system
314  IsArchivedFlag=1
315  IGCM_debug_PopStack "IGCM_sys_IsFileArchived"
316
317  return ${IsArchivedFlag}
318}
319
320#D-#==================================================
321#D-function IGCM_sys_TestFileArchive
322#D-* Purpose: Test file that must NOT EXISTS on Archive
323#D-* Examples:
324#D-
325function IGCM_sys_TestFileArchive {
326  IGCM_debug_PushStack "IGCM_sys_TestFileArchive" $@
327  typeset ExistFlag
328  ExistFlag=$( [ -f $1 ] && echo 0 || echo 1 )
329  IGCM_debug_PopStack "IGCM_sys_TestFileArchive"
330
331  return ${ExistFlag}
332}
333
334#D-#==================================================
335#D-function IGCM_sys_CountFileArchive
336#D-* Purpose: Count files on Archive filesystem
337#D-* Examples:
338#D-
339function IGCM_sys_CountFileArchive {
340  IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@
341  ls ${@} 2>/dev/null | wc -l
342  if [ $? -gt 0 ] ; then
343    echo "IGCM_sys_CountFileArchive : erreur."
344  fi
345  IGCM_debug_PopStack "IGCM_sys_CountFileArchive"
346}
347
348#D-#==================================================
349#D-function IGCM_sys_Tree
350#D-* Purpose: Tree directories with files on ${ARCHIVE}
351#D-* Examples: IGCM_sys_Tree ${R_IN} ${R_OUT}
352#D-
353function IGCM_sys_Tree {
354  IGCM_debug_PushStack "IGCM_sys_Tree" $@
355  if ( $DEBUG_sys ) ; then
356    echo "IGCM_sys_Tree :" $@
357  fi
358
359  \ls -lR ${@}
360
361  IGCM_debug_PopStack "IGCM_sys_Tree"
362}
363
364#D-#==================================================
365#D-function IGCM_sys_Qsub
366#D-* Purpose: Qsub new job
367#D-* Examples:
368#D-
369function IGCM_sys_Qsub {
370  IGCM_debug_PushStack "IGCM_sys_Qsub" $@
371  if ( $DEBUG_sys ) ; then
372    echo "IGCM_sys_Qsub :" $@
373  fi
374  typeset options status
375  options="-o ${SUBMIT_DIR}/${Script_Output}"
376  /usr/local/bin/qsub ${options} $1 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
377  status=$?
378
379  cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
380  if [ ${status} -gt 0 ] ; then
381    IGCM_debug_Print 2 "IGCM_sys_Qsub ${options} $1 : error code ${status}"
382    IGCM_debug_Exit "IGCM_sys_Qsub"
383  else
384    JobID=$( gawk {'print $1'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ )
385  fi
386  IGCM_debug_PopStack "IGCM_sys_Qsub"
387}
388
389#D-#==================================================
390#D-function IGCM_sys_QsubPost
391#D-* Purpose: Qsub new job on scalaire
392#D-* Examples:
393#D-
394function IGCM_sys_QsubPost {
395  IGCM_debug_PushStack "IGCM_sys_QsubPost" $@
396  if ( $DEBUG_sys ) ; then
397    echo "IGCM_sys_QsubPost :" $@
398  fi
399  typeset options status
400  options="-o ${POST_DIR}/${Script_Post_Output}.out -v ${listVarEnv}"
401  /usr/local/bin/qsub ${options} ${libIGCM_POST}/$1.job > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
402  status=$?
403
404  cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
405  if [ ${status} -gt 0 ] ; then
406    IGCM_debug_Print 2 "IGCM_sys_QsubPost ${options} ${libIGCM_POST}/$1.job : error code ${status}"
407    IGCM_debug_Exit "IGCM_sys_QsubPost"
408  else
409    JobID=$( gawk {'print $1'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ )
410  fi
411  IGCM_debug_PopStack "IGCM_sys_QsubPost"
412}
413
414#D-*************************
415#D- File transfer functions
416#D-*************************
417#D-
418
419#D-#==================================================
420#D-function IGCM_sys_RmRunDir
421#D-* Purpose: rm tmpdir (dummy function most of the time batch
422#D-                      scheduler will do the job)
423#D-* Examples:
424#D-
425function IGCM_sys_RmRunDir {
426  IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@
427  if ( $DEBUG_sys ) ; then
428    echo "IGCM_sys_RmRunDir :" $@
429    echo "Dummy call, let the scheduler do that."
430  fi
431  IGCM_debug_PopStack "IGCM_sys_RmRunDir"
432}
433
434#D-#==================================================
435#D-function IGCM_sys_Put_Dir
436#D-* Purpose: Copy a complete directory on $(ARCHIVE)
437#D-* Examples:
438#D-
439function IGCM_sys_Put_Dir {
440  IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@
441  if ( $DEBUG_sys ) ; then
442    echo "IGCM_sys_Put_Dir :" $@
443  fi
444  if [ $DRYRUN = 0 ]; then
445    if [ ! -d ${1} ] ; then
446      echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ."
447      IGCM_debug_PopStack "IGCM_sys_Put_Dir"
448      return
449    fi
450
451    typeset status
452
453    # Only if we use rsync
454    #IGCM_sys_TestDirArchive $( dirname $2 )
455    #
456    #USUAL WAY
457    \cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
458    status=$?
459
460    if [ ${status} -gt 0 ] ; then
461      IGCM_debug_Print 2 "IGCM_sys_Put_Dir : cp failed error code ${status}"
462      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
463      IGCM_debug_Exit "IGCM_sys_Put_Dir"
464    else
465      \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
466    fi
467  fi
468  IGCM_debug_PopStack "IGCM_sys_Put_Dir"
469}
470
471#D-#==================================================
472#D-function IGCM_sys_Get_Dir
473#D-* Purpose: Copy a complete directory from ${ARCHIVE}
474#D-* Examples:
475#D-
476function IGCM_sys_Get_Dir {
477  IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@
478  if ( $DEBUG_sys ) ; then
479    echo "IGCM_sys_Get_Dir :" $@
480  fi
481  if [ $DRYRUN = 0 ]; then
482    typeset NB_ESSAI DELAI status i
483    # number of tentative
484    NB_ESSAI=3
485    # time delay between tentative
486    DELAI=2
487
488    #
489    # USUAL WAY
490    i=0
491    while [ $i -lt $NB_ESSAI ] ; do
492      \cp -ur $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
493      status=$?
494      if [ ${status} -gt 0 ] ; then
495        IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status} ${i}/${NB_ESSAI}"
496        IGCM_debug_Print 2 "IGCM_sys_Get_Dir : sleep ${DELAI} seconds and try again."
497        sleep $DELAI
498      else
499        break
500      fi
501      (( i = i + 1 ))
502    done
503
504    if [ ${status} -gt 0 ] ; then
505      IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}"
506      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
507      IGCM_debug_Exit "IGCM_sys_Get_Dir"
508    else
509      \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
510    fi
511  fi
512  IGCM_debug_PopStack "IGCM_sys_Get_Dir"
513}
514
515#D-#==================================================
516#D-function IGCM_sys_Put_Rest
517#D-* Purpose: Put computied restarts on ${ARCHIVE}.
518#D-           File and target directory must exist.
519#D-* Examples:
520#D-
521function IGCM_sys_Put_Rest {
522  IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@
523  if ( $DEBUG_sys ) ; then
524    echo "IGCM_sys_Put_Rest :" $@
525  fi
526  if [ $DRYRUN = 0 ]; then
527    if [ ! -f ${1} ] ; then
528      echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ."
529      IGCM_debug_Exit "IGCM_sys_Put_Rest"
530    fi
531
532    typeset status
533    #
534    # USUAL WAY
535    \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
536    status=$?
537
538#       #RSYNC WITH NETWORK SSH CALL
539#       echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
540#       ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
541
542#       #RSYNC WITH NFS USE
543#       echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
544#       ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
545
546#       status=$?
547#       IGCM_sys_Rsync_out $status
548
549#       ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
550#       (( status=status+$? ))
551
552    if [ ${status} -gt 0 ] ; then
553      IGCM_debug_Print 2 "IGCM_sys_Put_Rest : cp failed error code ${status}"
554      [ -f ${1} ] && ls -l ${1}
555      [ -f ${2} ] && ls -l ${2}
556      [ -f ${2}/${1} ] && ls -l ${2}/${1}
557      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
558      IGCM_debug_Exit "IGCM_sys_Put_Rest"
559    else
560
561      if [ X${JobType} = XRUN ] ; then
562        [ -f ${2} ] && IGCM_sys_Chmod 444 ${2}
563        [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1}
564      fi
565
566      \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
567    fi
568  fi
569  IGCM_debug_PopStack "IGCM_sys_Put_Rest"
570}
571
572#D-#==================================================
573#D-function IGCM_sys_Put_Out
574#D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly
575#D-* Examples:
576#D-
577function IGCM_sys_Put_Out {
578  IGCM_debug_PushStack "IGCM_sys_Put_Out" $@
579  if ( $DEBUG_sys ) ; then
580    echo "IGCM_sys_Put_Out :" $@
581  fi
582
583  typeset status
584
585  if [ $DRYRUN = 0 ]; then
586    if [ ! -f ${1} ] ; then
587      echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ."
588      IGCM_debug_PopStack "IGCM_sys_Put_Out"
589      return 1
590    fi
591    #
592    IGCM_sys_MkdirArchive $( dirname $2 )
593    #
594    if [ X${JobType} = XRUN ] ; then
595      if [ X${3} = X ] ; then
596        IGCM_sys_Chmod 444 ${1}
597      fi
598    fi
599    #
600
601    echo ${RSYNC} ${RSYNC_opt} $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
602    ${RSYNC} ${RSYNC_opt} $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
603    status=$?
604    IGCM_sys_Rsync_out $status
605
606    ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
607    (( status=status+$? ))
608
609    if [ ${status} -gt 0 ] ; then
610      IGCM_debug_Print 2 "IGCM_sys_Put_Out : rsync failed error code ${status}"
611      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
612      IGCM_debug_Exit "IGCM_sys_Put_Out"
613    else
614      \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
615    fi
616  fi
617  IGCM_debug_PopStack "IGCM_sys_Put_Out"
618  return 0
619}
620
621#D-#==================================================
622#D-function IGCM_sys_Get
623#D-* Purpose: Get a file from ${ARCHIVE}
624#D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX
625#D-            IGCM_sys_Get /l Array_contain_myfiles /destpath/
626function IGCM_sys_Get {
627  IGCM_debug_PushStack "IGCM_sys_Get" $@
628
629  typeset DEST status dm_liste
630
631  if ( $DEBUG_sys ) ; then
632    echo "IGCM_sys_Get :" $@
633  fi
634  if [ $DRYRUN -le 2 ]; then
635    if [ X${1} = X'/l' ] ; then
636      eval set +A dm_liste \${${2}}
637    else
638      dm_liste=${1}
639    fi
640    eval DEST=\${${#}}
641
642    # test if the (first) file is present in the old computation :
643    IGCM_sys_TestFileArchive ${dm_liste[0]}
644    status=$?
645    if [ ${status} -gt 0 ] ; then
646      echo "IGCM_sys_Get, ERROR : regular file ${dm_liste[0]} DOES NOT EXIST ."
647      IGCM_debug_Exit "IGCM_sys_Get"
648      return
649    fi
650
651    #USUAL WAY
652    \cp ${dm_liste[*]} ${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
653    status=$?
654
655    if [ ${status} -gt 0 ] ; then
656      IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status}"
657      cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
658      IGCM_debug_Exit "IGCM_sys_Get"
659    else
660      \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
661    fi
662  fi
663  IGCM_debug_PopStack "IGCM_sys_Get"
664}
665
666#D-#==================================================
667#D-function IGCM_sys_GetDate_Monitoring
668#D-* Purpose: get the last year for which the monitoring has been computed
669#D-* Examples:
670#D-
671function IGCM_sys_GetDate_Monitoring {
672  IGCM_debug_PushStack "IGCM_sys_GetDate_Monitoring" $@
673  if ( $DEBUG_sys ) ; then
674    echo "IGCM_sys_GetDate_Monitoring :" $@
675  fi
676
677  eval ${2}=$( cdo showyear ${1} 2> /dev/null | gawk '{ print $NF }' )
678
679  IGCM_debug_PopStack "IGCM_sys_GetDate_Monitoring"
680}
681
682#D-#==================================================
683#D-function IGCM_sys_Dods_Rm
684#D-* Purpose: DO NOTHING ! Put ${ARCHIVE} files on DODS internet protocole.
685#D-* Examples:
686#D-
687function IGCM_sys_Dods_Rm {
688  if ( $DEBUG_sys ) ; then
689    echo "IGCM_sys_Dods_Rm :" $@
690  fi
691  return 0
692}
693
694#D-#==================================================
695#D-function IGCM_sys_Dods_Cp
696#D-* Purpose: Copy $(ARCHIVE) files on DODS internet protocole.
697#D-* Examples:
698#D-
699function IGCM_sys_Dods_Cp {
700  if ( $DEBUG_sys ) ; then
701    echo "IGCM_sys_Dods_Cp :" $@
702  fi
703  return 0
704}
705
706#D-#==================================================
707#D-function IGCM_sys_Put_Dods
708#D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole. Dummy function here
709#D-* Examples:
710#D-
711function IGCM_sys_Put_Dods {
712  IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@
713  if ( $DEBUG_sys ) ; then
714    echo "IGCM_sys_Put_Dods :" $@
715  fi
716  IGCM_debug_PopStack "IGCM_sys_Put_Dods"
717}
718
719##############################################################
720# REBUILD OPERATOR
721
722#D-#==================================================
723#D-function IGCM_sys_sync
724#D-* Purpose: flush buffer on disk (dummy function on Obelix)
725#D-* Examples:
726#D-
727function IGCM_sys_sync {
728  IGCM_debug_PushStack "IGCM_sys_sync" $@
729  if ( $DEBUG_sys ) ; then
730    echo "IGCM_sys_sync :" $@
731    echo "Dummy call, let the system do that."
732  fi
733  IGCM_debug_PopStack "IGCM_sys_sync"
734}
735
736############################################################
737# Activate Running Environnment Variables
738
739#D-#==================================================
740#D-function IGCM_sys_activ_variables
741#D-* Purpose: set environement variables prior to execution
742#D-* Examples:
743#D-
744function IGCM_sys_activ_variables {
745  IGCM_debug_PushStack "IGCM_sys_activ_variables"
746  if ( $DEBUG_sys ) ; then
747    echo "IGCM_sys_activ_variables"
748  fi
749
750# --------------------------------------------------------------------
751#D- MODULE specifications
752# --------------------------------------------------------------------
753  # Source the file EnvFile containing all module load needed to run the model.
754  # EnvFile can be specified in config.card. If this is the case and if the file exists,
755  # it will be used. Otherwise a default file will be used.
756  if [ ! X${config_UserChoices_EnvFile} = X ] && [ -f ${config_UserChoices_EnvFile} ] ; then
757      # EnvFile is set in config.card and the file exists
758      IGCM_debug_Print 1 "EnvFile set in config.card will be used"
759      EnvFile=${config_UserChoices_EnvFile}
760  else
761      IGCM_debug_Print 1 "IGCM_sys_active_variables : Default modules will be used"
762      EnvFile=/home/orchideeshare/igcmg/MachineEnvironment/obelix/env_atlas_obelix
763  fi
764  IGCM_debug_Print 1 "IGCM_sys_active_variables : Following EnvFile will be used :" 
765  IGCM_debug_Print 1 ${EnvFile}
766  . ${EnvFile}
767
768  IGCM_debug_Print 1 "IGCM_sys_active_variables : Now loaded modules for obelix. "
769  module list
770
771# --------------------------------------------------------------------
772#D- MPI specifications
773# --------------------------------------------------------------------
774
775# --------------------------------------------------------------------
776#D- Other specifications
777# --------------------------------------------------------------------
778
779  ulimit -s unlimited
780
781  IGCM_debug_PopStack "IGCM_sys_activ_variables"
782}
783
784############################################################
785# Desactivate Running Environnment Variables
786
787#D-#==================================================
788#D-function IGCM_sys_desactiv_variables
789#D-* Purpose: unset environement variables after execution
790#D-* Examples:
791#D-
792function IGCM_sys_desactiv_variables {
793  IGCM_debug_PushStack "IGCM_sys_desactiv_variables"
794  if ( $DEBUG_sys ) ; then
795    echo "IGCM_sys_desactiv_variables"
796  fi
797# --------------------------------------------------------------------
798#D- MPI specifications
799# --------------------------------------------------------------------
800
801# --------------------------------------------------------------------
802#D- Other specifications
803# --------------------------------------------------------------------
804
805  IGCM_debug_PopStack "IGCM_sys_desactiv_variables"
806}
807
808############################################################
809# Update job headers to be used by the scheduler
810
811#D-#==================================================
812#D-function IGCM_sys_updateHeaders
813#D-* Purpose: Update job headers to be used by the scheduler
814#D-* Examples: IGCM_sys_updateHeaders /path/to/Job_MYEXP
815#D-
816function IGCM_sys_updateHeaders {
817  IGCM_debug_PushStack "IGCM_sys_updateHeaders"
818  if ( $DEBUG_sys ) ; then
819    echo "IGCM_sys_updateHeaders"
820  fi
821  typeset file
822  file=$1
823
824  if [ ${executionType} -eq 1 ] ; then
825    # MPMD + MPI
826    sed -e "/::openMPthreads::/d"                  \
827        -e "s/::JobNumProcTot::/${coreNumber}/"    \
828      ${file} > ${file}.tmp
829
830  elif [ ${executionType} -eq 2 ] ; then
831    # MPMD + MPI + OMP
832    sed -e "s/::openMPthreads::/${openMPthreads}/" \
833        -e "s/::JobNumProcTot::/${coreNumber}/"    \
834      ${file} > ${file}.tmp
835
836  elif [ ${executionType} -eq 3 ] ; then
837    # SPMD + MPI/OMP
838    sed -e "s/::openMPthreads::/${openMPthreads}/" \
839        -e "s/::JobNumProcTot::/${mpiTasks}/"      \
840      ${file} > ${file}.tmp
841
842  elif [ ${executionType} -eq 4 ] ; then
843    # SPMD + MPI only
844    sed -e "s/::JobNumProcTot::/${mpiTasks}/"      \
845        -e "/::openMPthreads::/d"                  \
846      ${file} > ${file}.tmp
847
848  elif [ ${executionType} -eq 5 ] ; then
849    # SPMD + OMP only
850    sed -e "s/::openMPthreads::/${openMPthreads}/" \
851        -e "/::JobNumProcTot::/d"                  \
852      ${file} > ${file}.tmp
853
854  elif [ ${executionType} -eq 6 ] ; then
855    # SEQUENTIAL THEN
856    sed -e "s/::JobNumProcTot::/1/"                \
857        -e "/::openMPthreads::/d"                  \
858      ${file} > ${file}.tmp
859
860  fi
861
862  IGCM_sys_Mv ${file}.tmp ${file}
863
864  IGCM_debug_PopStack "IGCM_sys_updateHeaders"
865}
866
867############################################################
868# Build MPI/OMP scripts run file (dummy function)
869
870#D-#==================================================
871#D-function IGCM_sys_build_run_file
872#D-* Purpose: build run file (deprecated)
873#D-* Examples:
874#D-
875function IGCM_sys_build_run_file {
876  IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file "
877}
878
879############################################################
880# Build MPI/OMP scripts
881
882#D-#==================================================
883#D-function IGCM_sys_build_execution_scripts
884#D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND}
885#D-* Examples:
886#D-
887function IGCM_sys_build_execution_scripts
888{
889  IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@
890  if ( $DEBUG_sys ) ; then
891    echo "IGCM_sys_build_execution_scripts " $@
892  fi
893
894  EXECUTION=${HOST_MPIRUN_COMMAND}
895
896  # MPMD mode
897  if ( ${OK_PARA_MPMD} ) ; then
898
899    # Only MPI (MPMD)
900    if  ( ! ${OK_PARA_OMP} ) ; then
901
902      if [ -f run_file ] ; then
903        IGCM_sys_Rm -f run_file
904      fi
905      touch run_file
906
907      # Build run_file
908
909      # First loop on the components for the coupler ie oasis (only if oasis3)
910      # the coupler ie oasis3 must be the first one
911      for comp in ${config_ListOfComponents[*]} ; do
912
913        eval ExeNameIn=\${config_Executable_${comp}[0]}
914        eval ExeNameOut=\${config_Executable_${comp}[1]}
915
916        # for CPL component only
917        if [ "X${comp}" = "XCPL" ]  && [ "X${ExeNameOut}" != X\"\" ] ; then
918          eval comp_proc_mpi_loc=\${${comp}_PROC_MPI}
919          eval comp_proc_omp_loc=\${${comp}_PROC_OMP}
920          echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut} " >> run_file
921        fi
922      done
923
924      # Then second loop on the components
925      for comp in ${config_ListOfComponents[*]} ; do
926
927        eval ExeNameIn=\${config_Executable_${comp}[0]}
928        eval ExeNameOut=\${config_Executable_${comp}[1]}
929
930        # Only if we really have an executable for the component and not the coupler ie oasis:
931        if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then
932
933          eval comp_proc_mpi_loc=\${${comp}_PROC_MPI}
934          eval comp_proc_omp_loc=\${${comp}_PROC_OMP}
935          echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut}" >> run_file
936        fi
937      done
938
939      EXECUTION="${HOST_MPIRUN_COMMAND} --app ./run_file"
940
941      IGCM_sys_Chmod u+x run_file
942      if ( $DEBUG_sys ) ; then
943        echo "run_file contains : "
944        cat run_file
945      fi
946 
947    # MPI-OpenMP (MPMD)
948    else
949
950      #  Hosts treatment
951      ${HOST_MPIRUN_COMMAND} hostname | sort | uniq > hosts.tmp
952
953      i=0
954      rm -f hosts
955      IGCM_debug_Print 1 "sys Obelix, Hosts available :"
956      for nodes in `cat hosts.tmp` ; do
957        host[$i]=$nodes
958        echo "${host[$i]} slots=1 max_slots=1" >> hosts
959        IGCM_debug_Print 1 ${host[$i]}
960        i=$((i+1))
961      done
962      rm -f hosts.tmp
963
964      listnodes=${host[*]}
965
966      EXECUTION="${HOST_MPIRUN_COMMAND} -hostfile hosts"
967
968      # Initialisation
969      rank=0
970      current_core=0
971      core_per_node=6
972      init_exec=n
973
974      # Loop on the components
975      for comp in ${config_ListOfComponents[*]} ; do
976
977        eval ExeNameIn=\${config_Executable_${comp}[0]}
978        eval ExeNameOut=\${config_Executable_${comp}[1]}
979
980        # Not possible if oasis has an executable (i.e old version of oasis3)
981        if ( [ "X${ExeNameOut}" != X\"\" ] &&  [ "X${comp}" = "XCPL" ] ) ; then
982          IGCM_debug_Exit "ERROR MPMD with hybrid MPI-OpenMP is not available with oasis3 version"
983          IGCM_debug_Print 2 "Only available with oasis3-MCT version coupler"
984          IGCM_debug_Verif_Exit
985        fi
986
987        # Only if we really have an executable for the component :
988        if [ "X${ExeNameOut}" != X\"\" ] ; then
989
990          eval comp_proc_mpi_loc=\${${comp}_PROC_MPI}
991          eval comp_proc_omp_loc=\${${comp}_PROC_OMP}
992
993          echo "#!/bin/ksh" > script_${ExeNameOut}.ksh
994          echo ""  >> script_${ExeNameOut}.ksh
995          if [ ${comp_proc_omp_loc} -gt 1 ] ; then
996
997            # Check if the number of threads is correct
998            case ${comp_proc_omp_loc} in
999            2|4|6)
1000              IGCM_debug_Print 1 "You run ${ExeNameOut} on ${comp_proc_omp_loc} OMP threads"
1001              ;;
1002            *)
1003              IGCM_debug_Exit "ERROR with OMP parameters !"
1004              IGCM_debug_Print 2 "${comp_proc_omp_loc} is not possible as number of OMP threads"
1005              IGCM_debug_Print 2 "Only 2,4,6 as number of OMP threads are possible "
1006              IGCM_debug_Verif_Exit
1007              ;;
1008            esac
1009            #echo "export KMP_STACKSIZE=3g"  >> script_${ExeNameOut}.ksh
1010            #echo "export KMP_LIBRARY=turnaround"  >> script_${ExeNameOut}.ksh
1011            #echo "export MKL_SERIAL=YES"  >> script_${ExeNameOut}.ksh
1012            echo "export OMP_STACKSIZE=200M" >> script_${ExeNameOut}.ksh
1013            echo "export OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh
1014          fi
1015
1016          #echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh
1017          echo "(( MYMPIRANK = OMPI_COMM_WORLD_RANK )) " >> script_${ExeNameOut}.ksh
1018          echo "MYMPIRANK=\$(printf '%3.3d\n' \${MYMPIRANK})" >> script_${ExeNameOut}.ksh
1019          echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${MYMPIRANK} 2>out_${ExeNameOut}.err.\${MYMPIRANK}" >> script_${ExeNameOut}.ksh
1020          IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh
1021
1022          if [ ${init_exec} = y ] ; then
1023            EXECUTION="${EXECUTION} : -np ${comp_proc_mpi_loc} ./script_${ExeNameOut}.ksh"
1024          else
1025            EXECUTION="${EXECUTION} -np ${comp_proc_mpi_loc} ./script_${ExeNameOut}.ksh"
1026            init_exec=y
1027          fi
1028
1029          # Build rankfile : method used to assign cores and nodes for the MPI process
1030          # Ex :
1031          #rank 0=curie5296 slot=0,1,2,3
1032          #rank 1=curie5296 slot=4,5,6,7
1033          # Example of final command :
1034          # mpirun -hostfile hosts -rankfile rankfile -np 27 ./script_lmdz.x.ksh : -np 5 ./script_opa.xx.ksh
1035          # with script_lmdz.x.ksh :
1036          # #!/bin/ksh
1037          #export OMP_STACKSIZE=200M
1038          #export OMP_NUM_THREADS=4
1039          #./lmdz.x
1040
1041          for nb_proc_mpi in `seq 0 $(($comp_proc_mpi_loc-1))`; do
1042            (( index_host = current_core / core_per_node ))
1043            host_value=${host[${index_host}]}
1044            (( slot =  current_core % core_per_node ))
1045            virg=","
1046            string_final=""
1047            for index in `seq $slot $(($slot+$comp_proc_omp_loc-1))`; do
1048              string=$index$virg
1049              string_final=$string_final$string
1050            done
1051            string_final=$( echo $string_final | sed "s/.$//" )
1052            echo "rank $rank=$host_value slot=$string_final" >> rankfile
1053            (( rank = rank + 1 ))
1054            (( current_core = current_core + comp_proc_omp_loc ))
1055          done
1056        fi
1057      done
1058    fi
1059
1060  # Only one executable (SPMD mode).
1061  else
1062
1063    for comp in ${config_ListOfComponents[*]} ; do
1064
1065      # Only if we really have an executable for the component :
1066      eval ExeNameOut=\${config_Executable_${comp}[1]}
1067      if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then
1068
1069        echo "#!/bin/ksh" > script_${ExeNameOut}.ksh
1070        echo ""  >> script_${ExeNameOut}.ksh
1071        if ( ${OK_PARA_OMP} ) ; then
1072          eval comp_proc_omp_loc=\${${comp}_PROC_OMP}
1073          echo "export OMP_STACKSIZE=200M" >> script_${ExeNameOut}.ksh
1074          echo "export OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh
1075        fi
1076
1077        if [ ${mpiTasks} -eq 1 ] && [ ${openMPthreads} -eq 1 ] ; then
1078          # Case with only one proc
1079          # mpirun should not be used at obelix for only one proc
1080          # Output text per process
1081          echo "./${ExeNameOut} > out_${ExeNameOut}.out 2>out_${ExeNameOut}.err" >> script_${ExeNameOut}.ksh
1082          IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh
1083          EXECUTION="time ./script_${ExeNameOut}.ksh"
1084        elif  ( ${OK_PARA_MPI} ) ; then
1085          # Default : mpirun used if nb_proc gt 1
1086          # Output text per process
1087          echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${OMPI_COMM_WORLD_RANK} 2>out_${ExeNameOut}.err.\${OMPI_COMM_WORLD_RANK}"  >> script_${ExeNameOut}.ksh
1088          IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh
1089          EXECUTION="${HOST_MPIRUN_COMMAND} ./script_${ExeNameOut}.ksh"
1090        elif [ ${executionType} -eq 6 ] ; then
1091          # Sequentiel case: this is the same as the first case.
1092          echo "./${ExeNameOut} > out_${ExeNameOut}.out 2>out_${ExeNameOut}.err" >> script_${ExeNameOut}.ksh
1093          IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh
1094          EXECUTION="time ./script_${ExeNameOut}.ksh"
1095        else
1096          # Strange case.
1097          IGCM_debug_Exit "ERROR with OK_PARA_MPI"
1098          IGCM_debug_Print 2 "sys Obelix : OK_PARA_MPI=False and mpiTask/openMPthreds different from 1"
1099          IGCM_debug_Verif_Exit
1100        fi
1101
1102        IGCM_debug_Print 1 "sys Obelix : script_${ExeNameOut}.ksh contains"
1103        cat script_${ExeNameOut}.ksh
1104
1105      fi
1106
1107    done
1108
1109  fi
1110
1111  IGCM_debug_Print 1 "sys Obelix : execution command is"
1112  IGCM_debug_Print 1 "$EXECUTION"
1113
1114  IGCM_debug_PopStack "IGCM_sys_build_execution_scripts"
1115}
1116
1117#D-#==================================================
1118#D-function IGCM_sys_check_path
1119#D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine
1120#D-* do not point to an important use directory. Stop immediately in that case.
1121#D-* Examples:
1122#D-
1123function IGCM_sys_check_path {
1124  IGCM_debug_PushStack "IGCM_sys_check_path"
1125  if ( $DEBUG_sys ) ; then
1126    echo "IGCM_sys_check_path"
1127  fi
1128
1129  if ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X${ARCHIVE} ] ) ; then
1130    IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}"
1131    IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}"
1132    IGCM_debug_Exit "This will stop the job"
1133  fi
1134  IGCM_debug_PopStack "IGCM_sys_check_path"
1135}
1136
1137#D-#==================================================
1138#D-function IGCM_sys_check_quota. Dummy call here
1139#D-* Purpose: check user quota. Stop the simulation if quota above 90%
1140#D-* Examples:
1141#D-
1142function IGCM_sys_check_quota {
1143  IGCM_debug_PushStack "IGCM_sys_check_quota"
1144  if ( $DEBUG_sys ) ; then
1145    echo "IGCM_sys_check_quota"
1146  fi
1147
1148  # TO BE IMPLEMENTED
1149
1150  IGCM_debug_PopStack "IGCM_sys_check_quota"
1151}
1152
1153#D-#==================================================
1154#D-function IGCM_sys_projectAccounting
1155#D-* Purpose: store project accounting information in a file
1156#D-* Examples:
1157#D-
1158function IGCM_sys_projectAccounting {
1159  IGCM_debug_PushStack "IGCM_sys_projectAccounting"
1160  if ( $DEBUG_sys ) ; then
1161    echo "IGCM_sys_check_quota"
1162  fi
1163
1164  touch $1
1165
1166  IGCM_debug_PopStack "IGCM_sys_projectAccounting"
1167}
1168
1169#D-#==================================================
1170#D-function IGCM_sys_getJobSchedulerID
1171#D-* Purpose: Get the job ID during execution
1172#D-* Examples: IGCM_sys_getJobSchedulerID jobSchedulerID
1173#D-
1174function IGCM_sys_getJobSchedulerID {
1175  IGCM_debug_PushStack "IGCM_sys_getJobSchedulerID"
1176  if ( $DEBUG_sys ) ; then
1177    echo "IGCM_sys_getJobSchedulerID"
1178  fi
1179
1180  eval ${1}=$( echo ${PBS_JOBID} | awk -F. '{print $1}' )
1181
1182  IGCM_debug_PopStack "IGCM_sys_getJobSchedulerID"
1183}
1184
1185#D-#==================================================
1186#D-function IGCM_sys_GetJobID
1187#D-* Purpose: Get the job ID from the JobName
1188#D-* Examples: IGCM_sys_GetJobID ${JobName} ${TargetUsr} JobID
1189#D-
1190function IGCM_sys_GetJobID {
1191  IGCM_debug_PushStack "IGCM_sys_GetJobID"
1192  if ( $DEBUG_sys ) ; then
1193    echo "IGCM_sys_GetJobID"
1194  fi
1195
1196  # With -f option, the full job name is given in the last column
1197  ID="$( qstat -u $2 | grep -w $1 | gawk '-F ' '{print $10}' )"
1198
1199  eval ${3}=${ID}
1200  IGCM_debug_PopStack "IGCM_sys_GetJobID"
1201}
1202
1203#D-#==================================================
1204#D-function IGCM_sys_CountJobInQueue
1205#D-* Purpose: Count number of users job
1206#D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun
1207#D-
1208function IGCM_sys_CountJobInQueue {
1209  IGCM_debug_PushStack "IGCM_sys_CountJobInQueue"
1210  if ( $DEBUG_sys ) ; then
1211    echo "IGCM_sys_CountJobInQueue"
1212  fi
1213  IGCM_debug_PopStack "IGCM_sys_CountJobInQueue"
1214}
1215
1216#D-#==================================================
1217#D-function IGCM_sys_atlas
1218#D-* Purpose: encapsulate atlas call so as to manage error code and curie specificity
1219#D-* Examples:
1220#D-
1221function IGCM_sys_atlas {
1222  IGCM_debug_PushStack "IGCM_sys_atlas" $@
1223  if ( $DEBUG_sys ) ; then
1224    echo "IGCM_sys_atlas :" $@
1225  fi
1226
1227  typeset status
1228
1229  \atlas $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
1230  status=$?
1231  if [ ${status} -gt 0 ] ; then
1232    echo "IGCM_sys_atlas : error code ${status}"
1233    cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
1234    \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
1235    IGCM_debug_PopStack "IGCM_sys_atlas"
1236    return 1
1237  else
1238    IGCM_debug_PopStack "IGCM_sys_atlas"
1239    return 0
1240  fi
1241
1242  IGCM_debug_PopStack "IGCM_sys_atlas"
1243}
1244
1245
1246#D-#==================================================
1247#D-function IGCM_sys_rebuild_nemo
1248#D-* Purpose: rebuild nemo parallel files with general rebuild
1249#D-* Examples:
1250#D-
1251
1252function IGCM_sys_rebuild_nemo {
1253  IGCM_debug_PushStack "IGCM_sys_rebuild_nemo" $@
1254  if ( $DEBUG_sys ) ; then
1255    echo "IGCM_sys_rebuild_nemo :" $@
1256  fi
1257
1258  nemo_generic_restart_file_name_out=${1}
1259  nemo_extension_out=${3}
1260  shift ; shift ; shift
1261
1262  IGCM_sys_rebuild -o ${nemo_generic_restart_file_name_out}.${nemo_extension_out} $@
1263
1264  IGCM_debug_PopStack "IGCM_sys_rebuild_nemo"
1265}
1266
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