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source: trunk/libIGCM/ins_job @ 1470

Last change on this file since 1470 was 1470, checked in by mafoipsl, 6 years ago

For ins_job :

delete actions done for curie
for irene, set default postprocessing node to xlarge
for irene add the list of cmip6 sous-imputation instead of gencmip6. i (it takes some times. Message added : Wait for the next question ...)

Property svn:executable set to *
Property svn:keywords set to Revision Author Date

File size: 17.4 KB

Line
1	#!/bin/ksh
2
3	#**************************************************************
4	# Author: Jacques Belier
5	# Contact:
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	#- Installation of jobs according to environment
15	#---------------------------------------------------------------------
16	function ins_job_Usage
17	{
18	print - "
19	ins_job installs the jobs in the directories
20	which contain a file config.card
21
22	ins_job must be launched on the host
23	on which the job will be submitted
24
25	Usage :
26	${b_n} [-h] [-v] [-e]
27	or on curie/TGCC :
28	${b_n} [-h] [-v] [-e] [-p project] [-c number of cores]
29	or on irene/TGCC :
30	${b_n} [-h] [-v] [-e] [-p project] [-s post-project] [-q type_of_node] [-c number of cores]
31	or on ada /IDRIS
32	${b_n} [-h] [-v] [-e] [-m MPI environment]
33	Options :
34	-h : help
35	-v : verbose mode
36	-e : turn on ensemble mode (hindcast/forecast or date restart)
37	-f : ins_job is force to create jobs even if they already exist
38	on irene only :
39	-p project : add default project on irene
40	-s post-project : add default project use for post-processing on irene
41	-q type_of_node : add default type of nodes for postprocessing on irene skylake/xlarge
42	-c number of cores : add default number of cores for postprocessing on irene 1-112
43	on ada only :
44	- m MPI environment : add default MPI environment (Intel MPI or IBM MPI)
45	"
46	}
47	function ins_job_Warning
48	{
49	[[ ${x_v} = 'verbose' ]] && print - "\n############### WARNING ###############";
50	[[ ${x_v} = 'verbose' ]] && print - "File ${n_f} already exists\nin directory ${j}";
51	[[ ${x_v} = 'verbose' ]] && print - "You must delete this file to update !";
52	}
53
54	function ins_job_Check_JobName
55	{
56	verif=${JobName##[a-zA-Z]*(?([.\-])[a-zA-Z0-9])}
57
58	if [ ${#verif} -ne 0 ] ; then
59	echo "################ ERROR ################"
60	echo "${JobName} is invalid."
61	echo "- JobName can only contain alphanumeric characters, \".\" and \"-\""
62	echo "- JobName must start with a letter"
63
64	((NbErr=NbErr+1))
65
66	Status=1
67	else
68	Status=0
69	fi
70
71	return ${Status}
72	}
73
74	#-
75	# dirname and basename
76	#-
77	d_n=$(dirname ${0}); b_n=$(basename ${0});
78	#-
79	# Retrieving and validation of the options
80	#-
81	x_v='silencious';
82	x_e=false;
83	x_f=false;
84	x_p=false;
85	x_q=false;
86	x_s=false;
87	x_c=false;
88	x_m=false;
89	while getopts :hvefc:p:m:q:s: V ; do
90	case $V in
91	(h) ins_job_Usage; exit 0;;
92	(v) x_v='verbose';;
93	(e) x_e=true;;
94	(f) x_f=true;;
95	(p) x_p=true
96	ProjectID=${OPTARG} ;;
97	(s) x_s=true
98	PostID=${OPTARG} ;;
99	(q) x_q=true
100	ProjectNode=${OPTARG} ;;
101	(c) x_c=true
102	ProjectCore=${OPTARG} ;;
103	(m) x_m=true
104	MPIEnvironment=${OPTARG} ;;
105	(:) echo ${b_n}" : -"${OPTARG}" option : missing value" 1>&2;
106	exit 2;;
107	(\?) echo ${b_n}" : -"${OPTARG}" option : not supported" 1>&2;
108	exit 2;;
109	esac
110	done
111	[ ${x_v} = 'silencious' ] && export DEBUG_sys=false
112	shift $(($OPTIND-1));
113	#-
114	# Define working files
115	#-
116	F_MOD=$(cd ${d_n}'/..';/bin/pwd;)
117	# [[ ${F_MOD##*/} != 'modipsl' ]] && \
118	# { print - "directory 'modipsl' unreachable"; exit 3; }
119	W_W=${d_n}'/../libIGCM'
120	[[ ! -d ${W_W} ]] && { print - "${W_W} unreachable"; exit 3; }
121	libIGCM=$(cd ${W_W};/bin/pwd;)
122	F_JOB=${libIGCM}'/AA_job';
123	[[ ! -f ${F_JOB} ]] && { print - "${F_JOB} unreachable"; exit 3; }
124	F_RCI=${libIGCM}'/run.card.init';
125	[[ ! -f ${F_RCI} ]] && { print - "${F_RCI} unreachable"; exit 3; }
126	#-
127	# Accessing to functions (without stack)
128	#-
129	# No verbosity (0, 1, 2, 3)
130	Verbosity=0
131	# No de debug
132	DEBUG_debug=false
133	# Dont move libIGCM
134	MirrorlibIGCM=false
135	# Behave like computing job
136	TaskType=computing
137	# Source libIGCM
138	. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
139	. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
140	. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
141	. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
142	. ${libIGCM}/libIGCM_config/libIGCM_config.ksh
143	if [ $x_e = 'true' ] ; then
144	. ${libIGCM}/libIGCM_ensemble/libIGCM_ensemble.ksh
145	fi
146
147	#-
148	[[ ${x_v} = 'verbose' ]] && \
149	{
150	print - "";
151	print - '--- Host : '${SYSTEM};
152	print - '--- modipsl : '${F_MOD};
153	print - '--- libIGCM : '${libIGCM};
154	print - '--- basic job : '${F_JOB};
155	print - '--- basic card : '${F_RCI};
156	}
157	#-
158	[[ ${x_v} = 'verbose' ]] && print - "\nInstallation of jobs for '${SYSTEM}'";
159	#-
160
161	NbErr=0
162
163	#-
164	# Define Project parameters to set up jobs header for Irene (TGCC)
165	# on Irene define ProjectID and ProjectCore : option or answer
166	# on Irene ProjectNode default projectnode set to xlarge since 17/10/2018
167	#-
168
169
170	if [ X"${SYSTEM}" == "Xirene" ] ; then
171
172	#- set ProjectID if required
173	if ( ! ${x_p} ) ; then
174	#- default ProjectID
175	ProjectID=$( ccc_myproject \| grep -i irene \|grep -i skylake \| gawk '{ if ( $3 ~ /^project$/ && $4 !~ /^tgcc/ ) { print $4 } }' \| sort -u \| grep -v gencmip6 \| head -n 1 )
176	ProjectID=${ProjectID:="gch0316"}
177	answer=""
178	print - "Wait for the next question ..."
179	print - "Hit Enter or give project ID (default is ${ProjectID}), possible projects are $( echo $( ccc_myproject \| grep -i irene \| grep -i skylake \| gawk '{ if ( $3 ~ /^project$/ && $4 !~ /^tgcc/ ) { print $4 } }' \| grep -v gencmip6 \| sort -u ) ) or other xxxcmip6 : $(for i in $(groups) ; do echo $i\|grep -v gencmip6\|grep .cmip6 1>/dev/null 2>&1 && echo -n $i " " ; done ; echo ) "
180	read answer
181
182	if [ "X${answer}" != "X" ] ; then
183	ProjectID=${answer}
184	fi
185
186	fi # if ( ! ${x_p} )
187
188	echo ProjectID is ${ProjectID} at Irene
189
190
191	# set ProjectNode if required
192	if ( ! ${x_q} ) ; then
193	#- default ProjectNode
194	ProjectNode="xlarge"
195	answerOK=false
196
197	while ( ! ${answerOK} ) ; do
198	answer=""
199	print - "Hit Enter or give TYPE OF NODE required for post-processing (default is \"${ProjectNode}\"), possible types of nodes are \"skylake\" or \"xlarge\" : "
200	read answer
201	[ "X${answer}" == "X" ] \|\| [ "X${answer}" == "Xskylake" ] \|\| [ "X${answer}" == "Xxlarge" ] && answerOK=true
202	done
203
204	if [ "X${answer}" != "X" ] ; then
205	ProjectNode=${answer}
206	fi
207
208	fi # if ( ! ${x_q} )
209	echo ProjectNode for post-processing is ${ProjectNode} at Irene
210
211	#- ProjectNode is known (option or answer) set ProjectCoreMax
212	[ "${ProjectNode}" = "xlarge" ] && ProjectCoreMax="112" \|\| ProjectCoreMax="48"
213	#- ProjectCoreMax is 48 for standard and 112 for xlarge
214
215	if ( ! ${x_c} ) ; then
216	#- ProjectNode is known (option or answer), set ProjectCore default
217	[ "${ProjectNode}" = "xlarge" ] && ProjectCore="8" \|\| ProjectCore="4"
218
219	# let check minimum/maximum value 1/${ProjectCoreMax}
220
221	answerOK=false
222
223	while ( ! ${answerOK} ) ; do
224	answer=""
225	print - "Hit Enter or give NUMBER OF CORES required for post-processing (default is \"${ProjectCore}\")"
226	print - "possible numbers of cores are \"1\" to \"${ProjectCoreMax}\" for ${ProjectNode} : "
227	read answer
228	[ "X${answer}" == "X" ] \|\| [ ${answer} -ge 1 -a ${answer} -le ${ProjectCoreMax} ] && answerOK=true
229	done
230
231	if [ "X${answer}" != "X" ] ; then
232	ProjectCore=${answer}
233	fi
234
235	fi # if ( ! ${x_c} )
236
237	echo ProjectCore for post-processing is ${ProjectCore}
238	#- ProjectCore is set (option or answer)
239
240	#- ProjetCore is known (option or answer) set PostID : project ID for post-processing
241
242	if ( ! ${x_s} ) ; then
243	#- ProjetCore is known (option or answer) set PostID : project ID for post-processing
244	PostID=$( ccc_myproject \| grep -i irene \| grep -i ${ProjectNode} \| gawk '{ if ( $3 ~ /^project$/ && $4 !~ /^tgcc/ ) { print $4 } }' \| sort -u \| grep -v gencmip6 \| head -n 1 )
245	PostID=${PostID:="${ProjectID}"}
246	answer=""
247	print - "Wait for the next question ..."
248	print - "Hit Enter or give project ID (default is ${PostID}), possible projects are $( echo $( ccc_myproject \| grep -i irene \| grep -i ${ProjectNode} \| gawk '{ if ( $3 ~ /^project$/ && $4 !~ /^tgcc/ ) { print $4 } }' \| grep -v gencmip6 \| sort -u ) ) or other xxxcmip6 : $(for i in $(groups) ; do echo $i\|grep -v gencmip6\|grep .cmip6 1>/dev/null 2>&1 && echo -n $i " " ; done ; echo ) "
249	read answer
250
251	if [ "X${answer}" != "X" ] ; then
252	PostID=${answer}
253	fi
254
255	fi # if ( ! ${x_p} )
256
257	echo PostID is ${PostID} at Irene on ${ProjectNode} for post-processing
258
259	elif [ X"${SYSTEM}" == "Xada" ] ; then
260	if ( ! ${x_m} ) ; then
261	MPIEnvironment=IBM
262	# Intel MPI Environment.
263	answerOK=false
264	while ( ! ${answerOK} ) ; do
265	answer=""
266	print - "Hit Enter or give MPI Environement (default is ${MPIEnvironment}), possible MPI environments are IBM (MPI IBM) and Intel (MPI Intel) :"
267	read answer
268	[ "X${answer}" == "X" ] \|\| [ "X${answer}" == "XIBM" ] \|\| [ "X${answer}" == "XIntel" ] && answerOK=true
269	done
270
271	if [ "X${answer}" != "X" ] ; then
272	MPIEnvironment=${answer}
273	fi
274	fi # if ( ! ${x_pm} )
275	echo MPIEnvironment is ${MPIEnvironment}
276
277	elif [ X"${SYSTEM}" == "Xlxiv8" ] \|\| [ X"${SYSTEM}" == "Xifort_CICLAD" ] ; then
278	# obelix, ciclad, climserv
279	echo ""
280	echo "You need to check and maybe adapt headers in the main job especially the line: "
281	echo " #PBS -l nodes=x:ppn=y "
282	echo "where x is the number of nodes, y the number of cores per node and x*y is the total number of cores for the job. "
283	echo "y must not be bigger than the maximum numer of cores per node on the machine (often 8 or 16)."
284	fi # if [ X"${SYSTEM}" == "Xcurie" ]
285
286	#-
287	# Define the pattern string to substitute
288	#-
289	W_P='#-Q- '; W_W=${W_P}${SYSTEM};
290	#-
291	# Extract list of 'config.card' files
292	# and create jobs with AA_job
293	#-
294	F_CFG='config.card';
295	F_CFG_ENS='ensemble.card';
296	SUBMIT_DIR_ENS=$( pwd )
297	for i in $( pwd )/config.card
298	do
299	if [ ! -f $i ] ; then
300	echo ""
301	echo "################## WARNING ##################"
302	echo "No config.card available in current directory"
303	echo ""
304	continue
305	fi
306
307
308	j=$(cd ${i%/*};/bin/pwd;)
309	n_f=${F_RCI##*/};
310
311	if [ ! X$( echo ${j} \| grep EXPERIMENTS ) = X ] ; then
312	# Do not treat config.card if it is in sub-directory of EXPERIMENTS
313	# Continue to next config.card
314	continue
315	else
316	[[ ${x_v} = 'verbose' ]] && print - "\nWorking with file ${F_CFG}\nin directory ${j}\nfor ${n_f}";
317	fi
318
319	# Find out if new structure and set .resol filename
320	if [ -d ${j}/EXPERIMENTS ] && [ -d ${j}/GENERAL ] ; then
321	# New Structure
322	[[ ${x_v} = 'verbose' ]] && echo "This is new configuration structure"
323	new_struct=yes
324	resolfile=$j/.resol
325	else
326	# Old Structure
327	new_struct=no
328	resolfile=$j/../.resol
329	fi
330
331	# Get all variables declared in section UserChoices in config.card
332	IGCM_card_DefineArrayFromSection ${j}'/'${F_CFG} UserChoices
333	# Set default values
334	config_UserChoices_ExpType=""
335	RESOL_ATM_3D=this_is_a_test_string
336	RESOL=this_is_another_test_string
337	typeset option
338	for option in ${config_UserChoices[*]} ; do
339	IGCM_card_DefineVariableFromOption ${j}'/'${F_CFG} UserChoices ${option}
340	done
341
342	# Find the JobName : JobName might contain the variable RESOL_ATM_3D that will be replaced by what is in .resol file
343	if [ ! X$( echo ${config_UserChoices_JobName} \| grep ${RESOL_ATM_3D} ) = X ] ; then
344	TRUERESOL=$( tail -1 $resolfile \| awk "-F=" '{print $2}' )
345	echo TRUERESOL = $TRUERESOL
346	JobName=$( echo ${config_UserChoices_JobName} \| sed -e "s/${RESOL_ATM_3D}/${TRUERESOL}/" )
347	IGCM_card_WriteOption ${j}'/'${F_CFG} UserChoices JobName ${JobName}
348	elif [ ! X$( echo ${config_UserChoices_JobName} \| grep ${RESOL} ) = X ] ; then
349	TRUERESOL=$( head -1 $resolfile )
350	JobName=$( echo ${config_UserChoices_JobName} \| sed -e "s/${RESOL}/${TRUERESOL}/" )
351	IGCM_card_WriteOption ${j}'/'${F_CFG} UserChoices JobName ${JobName}
352	else
353	JobName=${config_UserChoices_JobName}
354	fi
355
356	# Check JobName validity : only alphanumerical characters, "-" and "." are authorized
357	ins_job_Check_JobName
358	RetCode=$?
359	[[ $RetCode -gt 0 ]] && continue
360
361	[[ ${x_v} = 'verbose' ]] && echo "JobName=${JobName}"
362
363	# Add specific treatment for new type of directory structure
364	if [ ${new_struct} == yes ] ; then
365
366	if [ "X${config_UserChoices_ExpType}" = X ] ; then
367	echo "\nERROR in ${j}/config.card"
368	echo "ins_job stops here"
369	echo "=> The variable ExpType must be added in config.card in section UserChoices"
370	echo "=> ExpType gives the directory for the .card configuration files for the wanted experiement. For exemple ExpType=IPSLCM5/historical"
371	exit 4
372	else
373	[[ ${x_v} = 'verbose' ]] && echo "ExpType= ${config_UserChoices_ExpType}"
374	fi
375
376	if [ -d ${j}/${JobName} ] ; then
377	echo "Directory ${j}/${JobName} exists already. It will not be overwritten."
378	echo "Remove the existing directory or change JobName before relaunching ins_job."
379	continue
380	fi
381	echo "=> Submit directory ${JobName} will be created with cards from EXPERIMENTS/${config_UserChoices_ExpType}"
382	cp -r ${j}/EXPERIMENTS/${config_UserChoices_ExpType} ${j}/${JobName}
383	cp -r ${j}/GENERAL/* ${j}/${JobName}/.
384	cp -f ${j}/${F_CFG} ${j}/${JobName}/.
385	if [ -f ${F_CFG_ENS} ] ; then
386	cp -f ${j}/${F_CFG_ENS} ${j}/${JobName}/.
387	SUBMIT_DIR_ENS=${j}/${JobName}
388	fi
389	rm -f ${j}/${F_CFG}
390	rm -f ${j}/${F_CFG_ENS}
391	rm -f ${j}/${F_CFG}.bak
392	j=${j}/${JobName}
393	[[ ${x_v} = 'verbose' ]] && echo new j=$j
394	fi
395	# end specific treatment for new type directory structure
396
397	[[ -f ${j}'/'${n_f} ]] && { ins_job_Warning; } \|\| \
398	{
399	[[ ${x_v} = 'verbose' ]] && print - "\nCopying file ${F_RCI}\nin directory ${j}";
400	\cp ${F_RCI} ${j};
401	}
402
403	#==================================
404	# Read ListOfComponents section:
405	#echo
406	#IGCM_debug_Print 1 "DefineArrayFromSection : ListOfComponents"
407
408	IGCM_card_DefineArrayFromSection ${j}'/'${F_CFG} ListOfComponents
409	for comp in ${config_ListOfComponents[*]} ; do
410	IGCM_card_DefineArrayFromOption ${j}'/'${F_CFG} ListOfComponents ${comp}
411	done
412	#IGCM_debug_Print 3 ${config_ListOfComponents[*]}
413
414	#==================================
415	# Read Executable section:
416	IGCM_card_DefineArrayFromSection ${j}'/'${F_CFG} Executable
417
418	# Define the execution context (MPMD, SPMD, MPI/OMP ...)
419	IGCM_config_ConfigureExecution ${j}'/'${F_CFG}
420
421	# coreNumber : TOTAL NUMBER OF CORES
422	# mpiTasks : TOTAL NUMBER OF MPI TASKS
423	# openMPthreads : NUMBER OF OpenMP THREADS
424
425	# File name for Job
426	n_f='Job_'${JobName};
427	[[ ${x_f} = 'false' ]] && [[ -f ${j}'/'${n_f} ]] && { ins_job_Warning; continue; }
428	[[ ${x_v} = 'verbose' ]] && print - "\nWorking with file ${F_CFG}\nin directory ${j}\nfor ${n_f}";
429	sed -e "/^${W_W} */ s///" \
430	-e "/^${W_P}/d" \
431	-e "s%::modipsl::%${F_MOD}%" \
432	-e "s/::Jobname::/${JobName}/" \
433	-e "s/::default_project::/${ProjectID}/" \
434	${F_JOB} > ${j}'/'${n_f}
435	chmod u+x ${j}'/'${n_f}
436
437	# update Headers so that ressources description are accurate (MPMD/SPMD/...)
438	IGCM_sys_updateHeaders ${j}'/'${n_f}
439	done
440
441	#-
442	# Extract list of AA_* files in libIGCM
443	# and create jobs (for all except AA_job)
444	#-
445	for i in $(find ${libIGCM} -maxdepth 1 -name "AA_*" -print)
446	do
447	i_f=${i##*/};
448	[[ ${i_f} = 'AA_job' ]] && { continue; }
449	j=${i%/*}; n_f=${i_f#AA_}'.job';
450	[[ ${x_f} = 'false' ]] && [[ -f ${j}'/'${n_f} ]] && { ins_job_Warning; continue; }
451	[[ ${x_v} = 'verbose' ]] && print - "\nIn directory ${j}\n${i_f} -> ${n_f}"
452	sed -e "/^${W_W} */ s///" \
453	-e "s%::modipsl::%${F_MOD}%" \
454	-e "/^${W_P}/d" \
455	-e "s/::default_node::/${ProjectNode}/" \
456	-e "s/::default_core::/${ProjectCore}/" \
457	-e "s/::default_project::/${ProjectID}/" \
458	-e "s/::default_post_project::/${PostID}/" \
459	${i} > ${j}'/'${n_f}
460	chmod u+x ${j}'/'${n_f}
461	done
462	#-
463	# set default_project in libIGCM_sys_curie.ksh too.
464	#-
465	if [ X"${SYSTEM}" == "Xcurie" ] ; then
466	i=${libIGCM}/libIGCM_sys/libIGCM_sys_curie.ksh
467	sed -i -e "s/::default_project::/${ProjectID}/" ${i}
468	fi
469	#-
470	# Limited to hindcast/forecast and date restart Ensemble for the time being
471	if [ ${x_e} = 'true' ] ; then
472	#.. Read input data from ensemble.card ..
473	SUBMIT_DIR=${SUBMIT_DIR_ENS}
474	RUN_DIR="${WORKDIR}/ENSEMBLE_TMP"
475	#
476	# Copy initial things around and define variables (hindcast/forecast case)
477	IGCM_sys_Cd ${SUBMIT_DIR}
478	IGCM_ensemble_Init
479
480	if [[ ${ensemble_Ens_PARAMETRIC_active} = 'y' ]] ; then
481	echo "WARNING: Parametric Ensemble is not implemented yet..."
482	fi
483
484	if [[ ${ensemble_Ens_DATE_active} = 'y' ]] ; then
485	IGCM_sys_Cd ${SUBMIT_DIR}
486	IGCM_ensemble_DateInit
487	# As it says
488	IGCM_sys_Cd ${SUBMIT_DIR}
489	IGCM_ensemble_DatePeriodicStarts
490	# As it says
491	IGCM_sys_Cd ${SUBMIT_DIR}
492	IGCM_ensemble_DateNonPeriodicStarts
493	# Clean
494	IGCM_sys_Rm -rf ${RUN_DIR}
495	fi
496
497	if [[ ${ensemble_Ens_PERTURB_active} = 'y' ]] ; then
498	IGCM_sys_Cd ${SUBMIT_DIR}
499	IGCM_ensemble_CastInit
500	# As it says
501	IGCM_sys_Cd ${SUBMIT_DIR}
502	IGCM_ensemble_CastPeriodicStarts
503	# As it says
504	IGCM_sys_Cd ${SUBMIT_DIR}
505	IGCM_ensemble_CastNonPeriodicStarts
506	# As it says
507	IGCM_sys_Cd ${SUBMIT_DIR}
508	IGCM_ensemble_CastMemberList
509	# Done
510	#IGCM_sys_Cp ${RUN_DIR}/CreatedDir.txt ${SUBMIT_DIR}
511	IGCM_sys_Cd ${SUBMIT_DIR}
512	# Clean
513	IGCM_sys_Rm -rf ${RUN_DIR}
514	fi
515	fi
516	#-
517	[[ ${x_v} = 'verbose' ]] && print - "";
518	#-
519	# That's all folks
520	#-
521
522	if [ ${NbErr} -ne 0 ] ; then
523	echo "################ ERROR ################"
524	echo "${NbErr} invalid JobName(s) found, check the log"
525	fi
526
527
528	exit 0;

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