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source: trunk/libIGCM/libIGCM_sys/libIGCM_sys_default.ksh @ 1188

Last change on this file since 1188 was 1186, checked in by sdipsl, 9 years ago
Ada bugfix. House keeping side effect when calling scipt interactively (clean_month, TimeSeriesChecker?, ...)
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: 33.9 KB

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1	#!/bin/ksh
2
3	#**************************************************************
4	# Author: Sebastien Denvil, Martial Mancip
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 Default host
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
36	typeset -r DEBUG_sys=${DEBUG_sys:=true}
37
38	#====================================================
39	# Turn in dry run mode ? (sys_Put_Rest, sys_Put_Out, sys_Get)
40	typeset -r DRYRUN=${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"
61	typeset -r MYLANG="fr"
62
63	#=====================================================
64	# Host and user names
65	# $hostname ou hostname
66	typeset HOST=${HOST:=$( hostname )}
67	# $username ou whoami
68	typeset LOGIN=${LOGIN:=$( whoami )}
69	# $hostname of the MASTER job
70	typeset MASTER=${MASTER:=$( hostname )}
71
72	#D-
73	#D-#==================================================
74	#D-Program used in libIGCM
75	#D-#==================================================
76
77	# Submit command
78	typeset SUBMIT=${SUBMIT:=qsub}
79	# rsync with path
80	typeset -r RSYNC=/usr/bin/rsync
81	# RSYNC_opt args to rsync
82	typeset -r RSYNC_opt="-va"
83	# ie storage filesystem
84	typeset -r STOREHOST=${MASTER}
85
86	#====================================================
87	# Set environment tools (ferret, nco, cdo, rebuild, ...)
88	#====================================================
89	#. /home/${LOGIN}/.atlas_env_${HOST}_ksh
90	#export PATH=${PATH}:/home/${LOGIN}/rebuild/bin/
91
92	#====================================================
93	# Host specific DIRECTORIES
94	#====================================================
95
96	#====================================================
97	#- MirrorlibIGCM for frontend
98	typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false}
99
100	#====================================================
101	#- libIGCM_POST for frontend
102	typeset -r libIGCM_POST=${libIGCM}
103
104	#====================================================
105	#- R_EXE (==> BIN_DIR = ${MODIPSL}/bin )
106	typeset -r R_EXE="${MODIPSL}/bin"
107
108	#====================================================
109	#- SUBMIT_DIR : submission dir
110	typeset -x SUBMIT_DIR=${SUBMIT_DIR:=${PWD}}
111
112	#====================================================
113	#- IN
114	typeset -r R_IN=${R_IN:=/home/${LOGIN}/IGCM}
115	typeset -r R_IN_ECMWF=${R_IN_ECMWF:=/home/${LOGIN}/IGCM}
116
117	#====================================================
118	#- RUN_DIR_PATH : Temporary working directory (=> TMP)
119	typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=/home/${LOGIN}/RUN_DIR/tmp$$}
120
121	#====================================================
122	#- OUTCOMMAND_PATH : tmp place to store command lines standard error and outputs
123	typeset -r OUTCOMMAND_PATH=/tmp
124
125	#====================================================
126	#- HOST_MPIRUN_COMMAND
127	typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="time mpirun"}
128
129	#====================================================
130	#- Max number of arguments passed to nco operator or demigration command
131	UNIX_MAX_LIMIT=360
132
133	#====================================================
134	#- set PackDefault to false on obelix
135	PackDefault=false
136
137	#====================================================
138	#- Number of core per node (max number of OpenMP task)
139	NUM_COREPERNODE=1
140
141	#====================================================
142	#- Default number of MPI task for IPSL coupled model
143	#- required for backward compatibility
144	#-
145	DEFAULT_NUM_PROC_OCE=1
146	DEFAULT_NUM_PROC_CPL=1
147	(( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL ))
148	DEFAULT_NUM_PROC_TOTAL=${BATCH_NUM_PROC_TOT}
149
150	#D-#==================================================
151	#D-function IGCM_sys_defineArchives
152	#D-* Purpose:
153	#D-* Define ARCHIVE : Dedicated to large files
154	#D-* Define STORAGE : Dedicated to small/medium files
155	#D-* Define R_OUT : Output tree located on ARCHIVE
156	#D-* Define R_FIG : Output tree located on STORAGE hosting figures (monitoring and atlas, and/or small files)
157	#D-* Define R_BUF : Output tree located on STORAGE hosting files waiting for rebuild or pack processes
158	#D-* if SpaceName=TEST nothing special will hapen
159	#D-* Examples:
160	#D-
161	function IGCM_sys_defineArchives {
162	IGCM_debug_PushStack "IGCM_sys_defineArchives"
163
164	if [ ! X${config_UserChoices_ARCHIVE} = X ]; then
165	#====================================================
166	#- ARCHIVE (dedicated to large files)
167	ARCHIVE=${config_UserChoices_ARCHIVE}
168	else
169	#====================================================
170	#- ARCHIVE (dedicated to large files)
171	ARCHIVE=${ARCHIVE:=/home/${LOGIN}}
172	fi
173
174	if [ ! X${config_UserChoices_STORAGE} = X ]; then
175	#====================================================
176	#- STORAGE (dedicated to small/medium files)
177	STORAGE=${config_UserChoices_STORAGE}
178	else
179	#====================================================
180	#- STORAGE (dedicated to small/medium files)
181	STORAGE=${ARCHIVE}
182	fi
183
184	# ON DEFAULT MACHINE NO SPECIAL CASE WHEN X${config_UserChoices_SpaceName} = XTEST
185
186	#====================================================
187	#- R_OUT
188	R_OUT=${ARCHIVE}/IGCM_OUT
189
190	#====================================================
191	#- R_FIG (hosting figures : monitoring and atlas, and/or small files)
192	R_FIG=${STORAGE}/IGCM_OUT
193
194	#====================================================
195	#- R_BUF (ONLY FOR double copy an scratch)
196	R_BUF=${STORAGE}/IGCM_OUT
197
198	IGCM_debug_Print 1 "R_OUT has been defined = ${R_OUT}"
199	IGCM_debug_Print 1 "R_BUF has been defined = ${R_BUF}"
200	IGCM_debug_Print 1 "R_FIG has been defined = ${R_FIG}"
201
202	IGCM_debug_PopStack "IGCM_sys_defineArchives"
203	}
204
205	#D-#==================================================
206	#D-function IGCM_sys_RshArchive
207	#D-* Purpose: Archive rsh command
208	#D-* Examples:
209	#D-
210	function IGCM_sys_RshArchive {
211	IGCM_debug_PushStack "IGCM_sys_RshArchive" $@
212	/bin/ksh <<-EOF
213	${@}
214	EOF
215	status=$?
216	if [ ${status} -gt 0 ] ; then
217	IGCM_debug_Print 2 "IGCM_sys_RshArchive : command failed error code ${status}"
218	IGCM_debug_Exit "IGCM_sys_RshArchive"
219	fi
220	IGCM_debug_PopStack "IGCM_sys_RshArchive"
221	}
222
223	#D-#==================================================
224	#D-function IGCM_sys_RshArchive_NoError
225	#D-* Purpose: Archive rsh command, without error
226	#D-* used only in monitoring.job
227	#D-* Examples:
228	#D-
229	function IGCM_sys_RshArchive_NoError {
230	IGCM_debug_PushStack "IGCM_sys_RshArchive_NoError" $@
231	/bin/ksh <<-EOF
232	${@} 2> /dev/null
233	EOF
234	IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError"
235	}
236
237	#D-#==================================================
238	#D-function IGCM_sys_MkdirArchive
239	#D-* Purpose: Mkdir on Archive
240	#D-* Examples:
241	#D-
242	function IGCM_sys_MkdirArchive {
243	IGCM_debug_PushStack "IGCM_sys_MkdirArchive" $@
244	if ( $DEBUG_sys ) ; then
245	echo "IGCM_sys_MkdirArchive :" $@
246	fi
247	#- creation de repertoire sur le serveur fichier
248	if [ ! -d ${1} ]; then
249	\mkdir -p $1
250	status=$?
251
252	if [ ${status} -gt 0 ] ; then
253	IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : mkdir failed error code ${status}"
254	IGCM_debug_Exit "IGCM_sys_MkdirArchive"
255	fi
256	fi
257	IGCM_debug_PopStack "IGCM_sys_MkdirArchive"
258	}
259
260	#D-#==================================================
261	#D-function IGCM_sys_TestDirArchive
262	#D-* Purpose: Test Directory that must exists on Archive
263	#D-* Examples:
264	#D-
265	function IGCM_sys_TestDirArchive {
266	IGCM_debug_PushStack "IGCM_sys_TestDirArchive" $@
267	if ( $DEBUG_sys ) ; then
268	echo "IGCM_sys_TestDirArchive :" $@
269	fi
270	typeset ExistFlag
271	ExistFlag=$( [ -d $1 ] && echo 0 \|\| echo 1 )
272	IGCM_debug_PopStack "IGCM_sys_TestDirArchive"
273	return ${ExistFlag}
274	}
275
276	#D-#==================================================
277	#D-function IGCM_sys_IsFileArchived
278	#D-* Purpose: Test file that must NOT EXISTS on Archive based on filename only
279	#D-* Examples:
280	#D-
281	function IGCM_sys_IsFileArchived {
282	IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@
283	if ( $DEBUG_sys ) ; then
284	echo "IGCM_sys_IsFileArchived :" $@
285	fi
286	typeset IsArchivedFlag
287	# Never archived for this system
288	IsArchivedFlag=1
289	IGCM_debug_PopStack "IGCM_sys_IsFileArchived"
290
291	return ${IsArchivedFlag}
292	}
293
294	#D-#==================================================
295	#D-function IGCM_sys_TestFileArchive
296	#D-* Purpose: Test file that must NOT EXISTS on Archive
297	#D-* Examples:
298	#D-
299	function IGCM_sys_TestFileArchive {
300	IGCM_debug_PushStack "IGCM_sys_TestFileArchive" $@
301	typeset ExistFlag
302	ExistFlag=$( [ -f $1 ] && echo 0 \|\| echo 1 )
303	IGCM_debug_PopStack "IGCM_sys_TestFileArchive"
304
305	return ${ExistFlag}
306	}
307
308	#D-#==================================================
309	#D-function IGCM_sys_CountFileArchive
310	#D-* Purpose: Count files on Archive filesystem
311	#D-* Examples:
312	#D-
313	function IGCM_sys_CountFileArchive {
314	IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@
315	ls ${@} 2>/dev/null \| wc -l
316	if [ $? -gt 0 ] ; then
317	echo "IGCM_sys_CountFileArchive : erreur."
318	fi
319	IGCM_debug_PopStack "IGCM_sys_CountFileArchive"
320	}
321
322	#D-#==================================================
323	#D-function IGCM_sys_Tree
324	#D-* Purpose: Tree directories with files on ${ARCHIVE}
325	#D-* Examples: IGCM_sys_Tree ${R_IN} ${R_OUT}
326	#D-
327	function IGCM_sys_Tree {
328	IGCM_debug_PushStack "IGCM_sys_Tree" $@
329	if ( $DEBUG_sys ) ; then
330	echo "IGCM_sys_Tree :" $@
331	fi
332
333	\tree -f $@
334
335	IGCM_debug_PopStack "IGCM_sys_Tree"
336	}
337
338	#D-#==================================================
339	#D-function IGCM_sys_Qsub
340	#D-* Purpose: Qsub new job
341	#D-* Examples:
342	#D-
343	function IGCM_sys_Qsub {
344	IGCM_debug_PushStack "IGCM_sys_Qsub" $@
345	if ( $DEBUG_sys ) ; then
346	echo "IGCM_sys_Qsub :" $@
347	fi
348	echo "${@} > ${SUBMIT_DIR}/${Script_Output} 2>&1 &"
349	${@} > ${SUBMIT_DIR}/${Script_Output} 2>&1 &
350	if [ $? -gt 0 ] ; then
351	echo "IGCM_sys_Qsub : erreur ${options} $1"
352	IGCM_debug_Exit "IGCM_sys_Qsub"
353	fi
354	IGCM_debug_PopStack "IGCM_sys_Qsub"
355	}
356
357	#D-#==================================================
358	#D-function IGCM_sys_QsubPost
359	#D-* Purpose: Qsub new job on scalaire
360	#D-* Examples:
361	#D-
362	function IGCM_sys_QsubPost {
363	IGCM_debug_PushStack "IGCM_sys_QsubPost" $@
364	if ( $DEBUG_sys ) ; then
365	echo "IGCM_sys_QsubPost :" $@
366	fi
367	echo "${libIGCM_POST}/$1.job > ${POST_DIR}/$1.${PeriodDateEnd}.out 2>&1 &"
368	${libIGCM_POST}/$1.job > ${POST_DIR}/${Script_Post_Output}.out 2>&1 &
369	if [ $? -gt 0 ] ; then
370	echo "IGCM_sys_QsubPost : erreur " $@
371	IGCM_debug_Exit "IGCM_sys_QsubPost"
372	fi
373	IGCM_debug_PopStack "IGCM_sys_QsubPost"
374	}
375
376	#D-*************************
377	#D- File transfer functions
378	#D-*************************
379	#D-
380
381	#D-#==================================================
382	#D-function IGCM_sys_RmRunDir
383	#D-* Purpose: rm tmpdir (dummy function most of the time batch
384	#D- scheduler will do the job)
385	#D-* Examples:
386	#D-
387	function IGCM_sys_RmRunDir {
388	IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@
389	if ( $DEBUG_sys ) ; then
390	echo "IGCM_sys_RmRunDir :" $@
391	IGCM_debug_Print 1 "Dummy call, let the user do that."
392	# IGCM_sys_Rm -rf ${RUN_DIR}
393	fi
394	IGCM_debug_PopStack "IGCM_sys_RmRunDir"
395	}
396
397	#D-#==================================================
398	#D-function IGCM_sys_Put_Dir
399	#D-* Purpose: Copy a complete directory on $(ARCHIVE)
400	#D-* Examples:
401	#D-
402	function IGCM_sys_Put_Dir {
403	IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@
404	if ( $DEBUG_sys ) ; then
405	echo "IGCM_sys_Put_Dir :" $@
406	fi
407	if [ $DRYRUN = 0 ]; then
408	if [ ! -d ${1} ] ; then
409	echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ."
410	IGCM_debug_PopStack "IGCM_sys_Put_Dir"
411	return
412	fi
413
414	typeset status
415
416	# Only if we use rsync
417	#IGCM_sys_TestDirArchive $( dirname $2 )
418	#
419	#USUAL WAY
420	\cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
421	status=$?
422
423	if [ ${status} -gt 0 ] ; then
424	IGCM_debug_Print 2 "IGCM_sys_Put_Dir : cp failed error code ${status}"
425	cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
426	IGCM_debug_Exit "IGCM_sys_Put_Dir"
427	else
428	\rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
429	fi
430	fi
431	IGCM_debug_PopStack "IGCM_sys_Put_Dir"
432	}
433
434	#D-#==================================================
435	#D-function IGCM_sys_Get_Dir
436	#D-* Purpose: Copy a complete directory from ${ARCHIVE}
437	#D-* Examples:
438	#D-
439	function IGCM_sys_Get_Dir {
440	IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@
441	if ( $DEBUG_sys ) ; then
442	echo "IGCM_sys_Get_Dir :" $@
443	fi
444	if [ $DRYRUN = 0 ]; then
445	typeset NB_ESSAI DELAI status i
446	# number of tentative
447	NB_ESSAI=3
448	# time delay between tentative
449	DELAI=2
450
451	#
452	# USUAL WAY
453	i=0
454	while [ $i -lt $NB_ESSAI ] ; do
455	\cp -ur $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
456	status=$?
457	if [ ${status} -gt 0 ] ; then
458	IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status} ${i}/${NB_ESSAI}"
459	IGCM_debug_Print 2 "IGCM_sys_Get_Dir : sleep ${DELAI} seconds and try again."
460	sleep $DELAI
461	else
462	break
463	fi
464	(( i = i + 1 ))
465	done
466
467	if [ ${status} -gt 0 ] ; then
468	IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}"
469	cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
470	IGCM_debug_Exit "IGCM_sys_Get_Dir"
471	else
472	\rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
473	fi
474	fi
475	IGCM_debug_PopStack "IGCM_sys_Get_Dir"
476	}
477
478	#D-#==================================================
479	#D-function IGCM_sys_Put_Rest
480	#D-* Purpose: Put computied restarts on ${ARCHIVE}.
481	#D- File and target directory must exist.
482	#D-* Examples:
483	#D-
484	function IGCM_sys_Put_Rest {
485	IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@
486	if ( $DEBUG_sys ) ; then
487	echo "IGCM_sys_Put_Rest :" $@
488	fi
489	if [ $DRYRUN = 0 ]; then
490	if [ ! -f ${1} ] ; then
491	echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ."
492	IGCM_debug_Exit "IGCM_sys_Put_Rest"
493	fi
494
495	typeset status
496	#
497	# USUAL WAY
498	\cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
499	status=$?
500
501	# #RSYNC WITH NETWORK SSH CALL
502	# echo ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
503	# ${RSYNC} ${RSYNC_opt} -e ssh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
504
505	# #RSYNC WITH NFS USE
506	# echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
507	# ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
508
509	# status=$?
510	# IGCM_sys_Rsync_out $status
511
512	# ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
513	# (( status=status+$? ))
514
515	if [ ${status} -gt 0 ] ; then
516	IGCM_debug_Print 2 "IGCM_sys_Put_Rest : cp failed error code ${status}"
517	[ -f ${1} ] && ls -l ${1}
518	[ -f ${2} ] && ls -l ${2}
519	[ -f ${2}/${1} ] && ls -l ${2}/${1}
520	cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
521	IGCM_debug_Exit "IGCM_sys_Put_Rest"
522	else
523
524	if [ X${JobType} = XRUN ] ; then
525	[ -f ${2} ] && IGCM_sys_Chmod 444 ${2}
526	[ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1}
527	fi
528
529	\rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
530	fi
531	fi
532	IGCM_debug_PopStack "IGCM_sys_Put_Rest"
533	}
534
535	#D-#==================================================
536	#D-function IGCM_sys_Put_Out
537	#D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly
538	#D-* Examples:
539	#D-
540	function IGCM_sys_Put_Out {
541	IGCM_debug_PushStack "IGCM_sys_Put_Out" $@
542	if ( $DEBUG_sys ) ; then
543	echo "IGCM_sys_Put_Out :" $@
544	fi
545
546	typeset status
547
548	if [ $DRYRUN = 0 ]; then
549	if [ ! -f ${1} ] ; then
550	echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ."
551	IGCM_debug_PopStack "IGCM_sys_Put_Out"
552	return 1
553	fi
554	#
555	IGCM_sys_MkdirArchive $( dirname $2 )
556	#
557	if [ X${JobType} = XRUN ] ; then
558	if [ X${3} = X ] ; then
559	IGCM_sys_Chmod 444 ${1}
560	fi
561	fi
562	#
563
564	echo ${RSYNC} ${RSYNC_opt} $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
565	${RSYNC} ${RSYNC_opt} $1 $2 >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
566	status=$?
567	IGCM_sys_Rsync_out $status
568
569	${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
570	(( status=status+$? ))
571
572	if [ ${status} -gt 0 ] ; then
573	IGCM_debug_Print 2 "IGCM_sys_Put_Out : rsync failed error code ${status}"
574	cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
575	IGCM_debug_Exit "IGCM_sys_Put_Out"
576	else
577	\rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
578	fi
579	fi
580	IGCM_debug_PopStack "IGCM_sys_Put_Out"
581	return 0
582	}
583
584	#D-#==================================================
585	#D-function IGCM_sys_Get
586	#D-* Purpose: Get a file from ${ARCHIVE}
587	#D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX
588	#D- IGCM_sys_Get /l Array_contain_myfiles /destpath/
589	function IGCM_sys_Get {
590	IGCM_debug_PushStack "IGCM_sys_Get" $@
591
592	typeset DEST status dm_liste
593
594	if ( $DEBUG_sys ) ; then
595	echo "IGCM_sys_Get :" $@
596	fi
597	if [ $DRYRUN -le 2 ]; then
598	if [ X${1} = X'/l' ] ; then
599	eval set +A dm_liste \${${2}}
600	else
601	dm_liste=${1}
602	fi
603	eval DEST=\${${#}}
604
605	# test if the (first) file is present in the old computation :
606	IGCM_sys_TestFileArchive ${dm_liste[0]}
607	status=$?
608	if [ ${status} -gt 0 ] ; then
609	echo "IGCM_sys_Get, ERROR : regular file ${dm_liste[0]} DOES NOT EXIST ."
610	IGCM_debug_Exit "IGCM_sys_Get"
611	return
612	fi
613
614	#USUAL WAY
615	\cp ${dm_liste[*]} ${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1
616	status=$?
617
618	if [ ${status} -gt 0 ] ; then
619	IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status}"
620	cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
621	IGCM_debug_Exit "IGCM_sys_Get"
622	else
623	\rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$
624	fi
625	fi
626	IGCM_debug_PopStack "IGCM_sys_Get"
627	}
628
629	#D-#==================================================
630	#D-function IGCM_sys_GetDate_Monitoring
631	#D-* Purpose: get the last year for which the monitoring has been computed
632	#D-* Examples:
633	#D-
634	function IGCM_sys_GetDate_Monitoring {
635	IGCM_debug_PushStack "IGCM_sys_GetDate_Monitoring" $@
636	if ( $DEBUG_sys ) ; then
637	echo "IGCM_sys_GetDate_Monitoring :" $@
638	fi
639
640	eval ${2}=$( cdo showyear ${1} 2> /dev/null \| gawk '{ print $NF }' )
641
642	IGCM_debug_PopStack "IGCM_sys_GetDate_Monitoring"
643	}
644
645	#D-#==================================================
646	#D-function IGCM_sys_Dods_Rm
647	#D-* Purpose: DO NOTHING ! Put ${ARCHIVE} files on DODS internet protocole.
648	#D-* Examples:
649	#D-
650	function IGCM_sys_Dods_Rm {
651	if ( $DEBUG_sys ) ; then
652	echo "IGCM_sys_Dods_Rm :" $@
653	fi
654	return 0
655	}
656
657	#D-#==================================================
658	#D-function IGCM_sys_Dods_Cp
659	#D-* Purpose: Copy $(ARCHIVE) files on DODS internet protocole.
660	#D-* Examples:
661	#D-
662	function IGCM_sys_Dods_Cp {
663	if ( $DEBUG_sys ) ; then
664	echo "IGCM_sys_Dods_Cp :" $@
665	fi
666	return 0
667	}
668
669	#D-#==================================================
670	#D-function IGCM_sys_Put_Dods
671	#D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole. Dummy function here
672	#D-* Examples:
673	#D-
674	function IGCM_sys_Put_Dods {
675	IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@
676	if ( $DEBUG_sys ) ; then
677	echo "IGCM_sys_Put_Dods :" $@
678	fi
679	IGCM_debug_PopStack "IGCM_sys_Put_Dods"
680	}
681
682	##############################################################
683	# REBUILD OPERATOR
684
685	#D-#==================================================
686	#D-function IGCM_sys_sync
687	#D-* Purpose: flush buffer on disk (dummy function on Ada)
688	#D-* Examples:
689	#D-
690	function IGCM_sys_sync {
691	IGCM_debug_PushStack "IGCM_sys_sync" $@
692	if ( $DEBUG_sys ) ; then
693	echo "IGCM_sys_sync :" $@
694	echo "Dummy call, let the system do that."
695	fi
696	IGCM_debug_PopStack "IGCM_sys_sync"
697	}
698
699	############################################################
700	# Activate Running Environnment Variables
701
702	#D-#==================================================
703	#D-function IGCM_sys_desactiv_variables
704	#D-* Purpose: set environement variables prior to execution
705	#D-* Examples:
706	#D-
707	function IGCM_sys_activ_variables {
708	IGCM_debug_PushStack "IGCM_sys_activ_variables"
709	if ( $DEBUG_sys ) ; then
710	echo "IGCM_sys_activ_variables"
711	fi
712
713	# --------------------------------------------------------------------
714	#D- MPI specifications
715	# --------------------------------------------------------------------
716
717	# --------------------------------------------------------------------
718	#D- Other specifications
719	# --------------------------------------------------------------------
720
721	IGCM_debug_PopStack "IGCM_sys_activ_variables"
722	}
723
724	############################################################
725	# Desactivate Running Environnment Variables
726
727	#D-#==================================================
728	#D-function IGCM_sys_desactiv_variables
729	#D-* Purpose: unset environement variables after execution
730	#D-* Examples:
731	#D-
732	function IGCM_sys_desactiv_variables {
733	IGCM_debug_PushStack "IGCM_sys_desactiv_variables"
734	if ( $DEBUG_sys ) ; then
735	echo "IGCM_sys_desactiv_variables"
736	fi
737	# --------------------------------------------------------------------
738	#D- MPI specifications
739	# --------------------------------------------------------------------
740
741	# --------------------------------------------------------------------
742	#D- Other specifications
743	# --------------------------------------------------------------------
744
745	IGCM_debug_PopStack "IGCM_sys_desactiv_variables"
746	}
747
748	############################################################
749	# Build MPI/OMP scripts run file (dummy function)
750
751	#D-#==================================================
752	#D-function IGCM_sys_build_run_file
753	#D-* Purpose: build run file (deprecated)
754	#D-* Examples:
755	#D-
756	function IGCM_sys_build_run_file {
757
758	IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file "
759
760	}
761
762	############################################################
763	# Build MPI/OMP scripts
764
765	#D-#==================================================
766	#D-function IGCM_sys_build_execution_scripts
767	#D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND}
768	#D-* Examples:
769	#D-
770	function IGCM_sys_build_execution_scripts
771	{
772	IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@
773	if ( $DEBUG_sys ) ; then
774	echo "IGCM_sys_build_execution_scripts " $@
775	fi
776
777	typeset nodes listnodes init_node start_num init_exec comp ExeNameIn ExeNameOut
778	typeset node_num_current node_current comp_proc_mpi_loc comp_proc_omp_loc
779	typeset num_corempi nombre_restant_node nombre_restant_comp
780
781	if ( ${OK_PARA_MPMD} ) ; then
782
783	if [ -f run_file ] ; then
784	IGCM_sys_Rm -f run_file
785	fi
786	touch run_file
787
788	if ( ${OK_PARA_OMP} ) ; then
789
790	# Hosts treatment
791
792	${HOST_MPIRUN_COMMAND} hostname \| sort \| uniq > hosts.tmp
793
794	i=0
795	rm -f hosts
796	IGCM_debug_Print 1 "sys $( hostname ), Hosts avaible :"
797	for nodes in `cat hosts.tmp` ; do
798	host[$i]=$nodes
799	echo "${host[$i]} slots=1 max_slots=1" >> hosts
800	IGCM_debug_Print 1 ${host[$i]}
801	i=$((i+1))
802	done
803	rm -f hosts.tmp
804
805	listnodes=${host[*]}
806
807	EXECUTION="${HOST_MPIRUN_COMMAND} -hostfile hosts"
808
809	# Initialisation
810
811	init_node=y
812	node_num_current=0
813	start_num=0
814	init_exec=n
815
816	# Build run_file
817
818	# First loop on the components for the coupler ie oasis (only if oasis3)
819	# the coupler ie oasis3 must be the first one
820	for comp in ${config_ListOfComponents[*]} ; do
821
822	if [ "X${comp}" = "XCPL" ] ; then
823
824	eval ExeNameIn=\${config_Executable_${comp}[0]}
825	eval ExeNameOut=\${config_Executable_${comp}[1]}
826
827	echo "#!/bin/ksh" > script_${ExeNameOut}.ksh
828	echo "" >> script_${ExeNameOut}.ksh
829	#echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh
830	#echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh
831	#echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh
832	echo "./${ExeNameOut} > out_${ExeNameOut}.out 2>out_${ExeNameOut}.err" >> script_${ExeNameOut}.ksh
833	IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh
834
835	init_node=n
836
837	(( nombre_restant_node = NUM_COREPERNODE - 1 ))
838	node_num_current=0
839	node_current=${host[${node_num_current}]}
840
841	EXECUTION="${EXECUTION} -H ${node_current} -np 1 ./script_${ExeNameOut}.ksh"
842
843	init_exec=y
844	start_num=1
845
846	fi
847
848	done
849
850	# Then loop on the components (except for oasis)
851
852	for comp in ${config_ListOfComponents[*]} ; do
853
854	eval ExeNameIn=\${config_Executable_${comp}[0]}
855	eval ExeNameOut=\${config_Executable_${comp}[1]}
856
857	# Only if we really have an executable for the component :
858	if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then
859
860	eval comp_proc_mpi_loc=\${${comp}_PROC_MPI}
861	eval comp_proc_omp_loc=\${${comp}_PROC_OMP}
862
863	echo "#!/bin/ksh" > script_${ExeNameOut}.ksh
864	# echo "set -vx" >> script_${ExeNameOut}.ksh
865	echo "" >> script_${ExeNameOut}.ksh
866	#echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh
867	#echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh
868	#echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh
869	echo "OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh
870	echo "(( MYMPIRANK = OMPI_COMM_WORLD_RANK - ${start_num})) " >> script_${ExeNameOut}.ksh
871	echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${MYMPIRANK} 2>out_${ExeNameOut}.err.\${MYMPIRANK}" >> script_${ExeNameOut}.ksh
872	IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh
873
874	node_num=0
875
876	# We define the number of MPI process to be assigned for the component
877
878	nombre_restant_comp=${comp_proc_mpi_loc}
879
880	# Loop on the allocated nodes
881
882	for node in ${listnodes} ; do
883
884	# We go to the current node
885	if [ ${node_num} = ${node_num_current} ] ; then
886
887	node_current=${host[${node_num_current}]}
888
889	# If first time on the node : initialisation
890
891	if [ ${init_node} = y ] ; then
892	nombre_restant_node=${NUM_COREPERNODE}
893	fi
894
895	# Test on the number of OMP threads
896
897	if [ ${comp_proc_omp_loc} -gt ${nombre_restant_node} ] ; then
898	(( node_num = node_num + 1 ))
899	node_num_current=${node_num}
900	init_node=y
901	continue
902	fi
903
904	# Number of MPI process to assign
905
906	(( num_corempi = nombre_restant_node / comp_proc_omp_loc ))
907
908	if [ ${num_corempi} -gt ${nombre_restant_comp} ] ; then
909	num_corempi=${nombre_restant_comp}
910	fi
911
912	(( nombre_restant_node = nombre_restant_node - num_corempi * comp_proc_omp_loc ))
913	(( nombre_restant_comp = nombre_restant_comp - num_corempi ))
914
915	if [ ${init_exec} = y ] ; then
916	EXECUTION="${EXECUTION} : -H ${node_current} -np ${num_corempi} ./script_${ExeNameOut}.ksh"
917	else
918	EXECUTION="${EXECUTION} -H ${node_current} -np ${num_corempi} ./script_${ExeNameOut}.ksh"
919	init_exec=y
920	fi
921
922	(( start_num = num_corempi + start_num ))
923
924	else
925
926	(( node_num = node_num + 1 ))
927	continue
928	fi
929
930	# Test on the number of core/process remaining on the node/component
931
932	if [ ${nombre_restant_node} = 0 ] ; then
933	(( node_num = node_num + 1 ))
934	node_num_current=${node_num}
935	init_node=y
936
937	if [ ${nombre_restant_comp} = 0 ] ; then
938	break 1
939	fi
940	else
941
942	node_num_current=${node_num}
943	init_node=n
944
945	if [ ${nombre_restant_comp} = 0 ] ; then
946	break 1
947	fi
948	fi
949	done
950	fi
951	done
952
953	else
954
955	# Then first loop on the components for the coupler ie oasis
956
957	## the coupler ie oasis must be the first one
958	for comp in ${config_ListOfComponents[*]} ; do
959
960	eval ExeNameOut=\${config_Executable_${comp}[1]}
961
962	# for CPL component only
963	if [ "X${comp}" = "XCPL" ] ; then
964	eval comp_proc_mpi_loc=\${${comp}_PROC_MPI}
965	echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut} " >> run_file
966	fi
967	done
968
969	# Then second loop on the components
970
971	for comp in ${config_ListOfComponents[*]} ; do
972
973	eval ExeNameOut=\${config_Executable_${comp}[1]}
974
975	# Only if we really have an executable for the component and not the coupler ie oasis:
976	if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then
977	eval comp_proc_mpi_loc=\${${comp}_PROC_MPI}
978	echo "-np ${comp_proc_mpi_loc} ./${ExeNameOut}" >> run_file
979	fi
980	done
981	IGCM_sys_Chmod u+x run_file
982
983	EXECUTION="${HOST_MPIRUN_COMMAND} --app ./run_file"
984
985	fi
986
987	else # Only one executable. launch it.
988
989	for comp in ${config_ListOfComponents[*]} ; do
990
991	# Only if we really have an executable for the component :
992	eval ExeNameOut=\${config_Executable_${comp}[1]}
993	if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then
994
995	echo "#!/bin/ksh" > script_${ExeNameOut}.ksh
996	echo "" >> script_${ExeNameOut}.ksh
997	if ( ${OK_PARA_OMP} ) ; then
998	eval comp_proc_omp_loc=\${${comp}_PROC_OMP}
999	echo "OMP_NUM_THREADS=${comp_proc_omp_loc}" >> script_${ExeNameOut}.ksh
1000	fi
1001	if ( ${OK_PARA_MPI} ) ; then
1002	# Default : mpirun used if nb_proc gt 1
1003	# pour sortie out/err par process
1004	# echo "./${ExeNameOut} > out_${ExeNameOut}.out.\${OMPI_COMM_WORLD_RANK} 2>out_${ExeNameOut}.err.\${OMPI_COMM_WORLD_RANK}" >> script_${ExeNameOut}.ksh
1005	echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh
1006	IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh
1007	EXECUTION="${HOST_MPIRUN_COMMAND} ./script_${ExeNameOut}.ksh"
1008	else
1009	# Default : mpirun is NOT used if nb_proc eq 1
1010	# pour sortie out/err par process
1011	# echo "./${ExeNameOut} > out_${ExeNameOut}.out 2>out_${ExeNameOut}.err" >> script_${ExeNameOut}.ksh
1012	echo "./${ExeNameOut}" >> script_${ExeNameOut}.ksh
1013	IGCM_sys_Chmod u+x script_${ExeNameOut}.ksh
1014	EXECUTION="time ./script_${ExeNameOut}.ksh"
1015	fi
1016
1017	IGCM_debug_Print 1 "sys $( hostname ) : script_${ExeNameOut}.ksh contains"
1018	cat script_${ExeNameOut}.ksh
1019
1020	fi
1021
1022	done
1023
1024	fi
1025
1026	IGCM_debug_Print 1 "sys $( hostname ) : execution command is"
1027	IGCM_debug_Print 1 "$EXECUTION"
1028
1029	IGCM_debug_PopStack "IGCM_sys_build_execution_scripts"
1030	}
1031
1032	#D-#==================================================
1033	#D-function IGCM_sys_check_path
1034	#D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine
1035	#D-* do not point to an important use directory. Stop immediately in that case.
1036	#D-* Examples:
1037	#D-
1038	function IGCM_sys_check_path {
1039	IGCM_debug_PushStack "IGCM_sys_check_path"
1040	if ( $DEBUG_sys ) ; then
1041	echo "IGCM_sys_check_path"
1042	fi
1043
1044	if ( [ X${RUN_DIR_PATH} = X${HOME} ] \|\| [ X${RUN_DIR_PATH} = X${ARCHIVE} ] ) ; then
1045	IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}"
1046	IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}"
1047	IGCM_debug_Exit "This will stop the job"
1048	fi
1049	IGCM_debug_PopStack "IGCM_sys_check_path"
1050	}
1051
1052	#D-#==================================================
1053	#D-function IGCM_sys_check_quota. Dummy call here
1054	#D-* Purpose: check user quota. Stop the simulation if quota above 90%
1055	#D-* Examples:
1056	#D-
1057	function IGCM_sys_check_quota {
1058	IGCM_debug_PushStack "IGCM_sys_check_quota"
1059	if ( $DEBUG_sys ) ; then
1060	echo "IGCM_sys_check_quota"
1061	fi
1062	IGCM_debug_PopStack "IGCM_sys_check_quota"
1063	}
1064
1065	#D-#==================================================
1066	#D-function IGCM_sys_CountJobInQueue
1067	#D-* Purpose: Check if job_name is currently
1068	#D- running or in queue
1069	#D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun
1070	#D-
1071	function IGCM_sys_CountJobInQueue {
1072	IGCM_debug_PushStack "IGCM_sys_CountJobInQueue"
1073	if ( $DEBUG_sys ) ; then
1074	echo "IGCM_sys_CountJobInQueue"
1075	fi
1076	IGCM_debug_PopStack "IGCM_sys_CountJobInQueue"
1077	}

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