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prepare_job.sh in utils/CI/sette – NEMO

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source: utils/CI/sette/prepare_job.sh @ 11655

Last change on this file since 11655 was 11645, checked in by clem, 5 years ago
make sette work for jean-zay machine
Property svn:executable set to ``*
File size: 14.8 KB

Rev	Line
[3520]	1	#####################################################
	2	# Author : Simona Flavoni for NEMO
	3	# Contact : sflod@locean-ipsl.upmc.fr
	4	#
	5	# ----------------------------------------------------------------------
	6	# NEMO/SETTE , NEMO Consortium (2010)
	7	# Software governed by the CeCILL licence (NEMOGCM/NEMO_CeCILL.txt)
	8	# ----------------------------------------------------------------------
	9	#
	10	# Some scripts called by sette.sh
	11	# prepare_job.sh : creates the job script for running job
	12	######################################################
[3661]	13	#set -vx
[3520]	14	set -o posix
	15	#set -u
	16	#set -e
[3661]	17	#+
[3520]	18	#
	19	# ================
	20	# prepare_job.sh
	21	# ================
	22	#
	23	# -------------------------------------------------
	24	# script that creates the job script for NEMO tests
	25	# -------------------------------------------------
	26	#
	27	# SYNOPSIS
	28	# ========
	29	#
	30	# ::
	31	#
[3661]	32	# $ ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_FLAG JOB_FILE
[3520]	33	#
	34	#
	35	# DESCRIPTION
	36	# ===========
	37	#
[3661]	38	# Part of the SETTE package to run tests for NEMO
[3520]	39	#
[3661]	40	# prepare the script $JOB_FILE to run the tests
[3520]	41	#
	42	# EXAMPLES
	43	# ========
	44	#
	45	# ::
	46	#
[3661]	47	# $ ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_FLAG $JOB_FILE
[3520]	48	#
[3661]	49	# prepare the $JOB_FILE for execution
[3520]	50	#
	51	#
	52	# TODO
	53	# ====
	54	#
	55	# option debug
	56	#
	57	#
	58	# EVOLUTIONS
	59	# ==========
	60	#
[3661]	61	# $Id: prepare_job.sh 3050 2011-11-07 14:11:34Z acc $
[3520]	62	#
	63	#
	64	#
	65	# * creation
	66	#
	67	#-
	68	#
	69
[7753]	70	usage=" Usage : ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_FLAG JOB_FILE NUM_XIO_SERVERS"
[9663]	71	usage=" example : ./prepare_job.sh input_ORCA2_ICE_PISCES.cfg 8 SHORT no/yes $JOB_FILE 0 2"
[3520]	72
	73
[4245]	74	minargcount=6
[3520]	75	if [ ${#} -lt ${minargcount} ]
	76	then
[3661]	77	echo "not enough arguments for prepare_job.sh script"
	78	echo "control number of argument of prepare_job.sh in sette.sh"
[3520]	79	echo "${usage}"
	80	exit 1
	81	fi
	82	unset minargcount
	83	if [ ! -f ${SETTE_DIR}/output.sette ] ; then
	84	touch ${SETTE_DIR}/output.sette
	85	fi
	86
	87	#
	88	# set and export TEST_NAME. It will be used within the post_test_tidyup function
	89	#
	90	INPUTARFILE=$1
	91	NB_PROC=$2
	92	TEST_NAME=$3
	93	MPI_FLAG=$4
	94	JOB_FILE=$5
[4245]	95	NXIO_PROC=$6
[11161]	96	NEMO_VALID=$7
[3520]	97
	98	# export EXE_DIR. This directory is used to execute model
	99	#
	100	#
	101	#
	102	echo "date: `date`" >> ${SETTE_DIR}/output.sette
	103	echo "" >> ${SETTE_DIR}/output.sette
	104	echo "running config: ${NEW_CONF}" >> ${SETTE_DIR}/output.sette
	105	echo "" >> ${SETTE_DIR}/output.sette
	106	echo "list of cpp_keys: " >> ${SETTE_DIR}/output.sette
[7715]	107	echo "`more ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm`" >> ${SETTE_DIR}/output.sette
[3520]	108	echo "" >> ${SETTE_DIR}/output.sette
	109	echo "compiling with: ${CMP_NAM}" >> ${SETTE_DIR}/output.sette
	110	echo "" >> ${SETTE_DIR}/output.sette
	111	echo "executing script : \"fcm_job $@\" " >> ${SETTE_DIR}/output.sette
	112	echo " " >> ${SETTE_DIR}/output.sette
	113
	114	################################################################
[4147]	115	# SET INPUT
[3520]	116	# get the input tarfile if needed
[4147]	117	if [ "$(cat ${SETTE_DIR}/$INPUTARFILE \| wc -w)" -ne 0 ] ; then
	118	echo "looking for input files in ${SETTE_DIR}/$INPUTARFILE " >> ${SETTE_DIR}/output.sette
	119	# number of tarfiles: NBTAR
	120	NBTAR=`cat ${SETTE_DIR}/$INPUTARFILE \|wc -l`
	121	echo "NB of tarfiles ${NBTAR} " >> ${SETTE_DIR}/output.sette
	122	# loop on tarfiles
	123	# read file name and directory
	124	while read tar_file dir_conf_forc
	125	do
	126	echo looking for tarfile ${tar_file} and directory ${FORCING_DIR}/${dir_conf_forc} ; echo looking for tarfile ${tar_file} and directory ${FORCING_DIR}/${dir_conf_forc} >> ${SETTE_DIR}/output.sette
	127	if [ -f ${FORCING_DIR}/${tar_file} ] && [ -d ${FORCING_DIR}/${dir_conf_forc} ] ; then
	128	# Tarfile and input dir ar there, only check the links
	129	echo "Tarfile and input dir ar there, only check the links" >> ${SETTE_DIR}/output.sette
	130	# extract tarfile
	131	else
[3520]	132
[4147]	133	if [ ! -f ${FORCING_DIR}/${tar_file} ] ; then
	134	echo "tarfile ${FORCING_DIR}/${tar_file} cannot be found we stop " ; exit 2 ; fi
[3520]	135
[4147]	136	echo "mkdir ${FORCING_DIR}/${dir_conf_forc}" >> ${SETTE_DIR}/output.sette
	137	mkdir ${FORCING_DIR}/${dir_conf_forc}
	138	cd ${FORCING_DIR}/${dir_conf_forc}
	139	echo " extract from tarfile ${FORCING_DIR}/${tar_file} in ${FORCING_DIR}/${dir_conf_forc}" >> ${SETTE_DIR}/output.sette
	140	tar xvof ${FORCING_DIR}/${tar_file} ; gunzip -f `find . -name "*.gz"`
	141	fi
	142	# Tarfile and input dir ar there, only check the links
	143	cd ${FORCING_DIR}/${dir_conf_forc}
	144	for fida in *
	145	do
	146	[ -f ${EXE_DIR}/${fida} ] \|\| ln -s ${FORCING_DIR}/${dir_conf_forc}/${fida} ${EXE_DIR}/${fida}
	147	done
	148	done < ${SETTE_DIR}/$INPUTARFILE
[3520]	149
[4147]	150	else
	151	echo "no input file to be searched "
[3520]	152	fi
	153	################################################################
	154
	155	################################################################
	156	# RUN OPA
	157	cd ${EXE_DIR}
[9576]	158	if [ ! -r ${EXE_DIR}/nemo ]
[3520]	159	then
[9576]	160	echo "executable nemo does not exist"
	161	echo "executable nemo does not exist, exit" >> ${SETTE_DIR}/output.sette
[3520]	162	exit 1
	163	fi
	164
[4687]	165	# example for NOCS ClusterVision system using SLURM batch submission (requires ${SETTE_DIR}/sette_batch_template file)
[3520]	166	#
[3661]	167	# if [ ${MPI_FLAG} == "no" ] ; then
[3520]	168	case ${COMPILER} in
[4687]	169	X64_MOBILIS)
	170	NB_REM=$( echo $NB_PROC $NXIO_PROC \| awk '{print ( $1 + $2 ) % 16}')
[3520]	171	if [ ${NB_REM} == 0 ] ; then
[4687]	172	# number of processes required is an integer multiple of 16
[3520]	173	#
[4687]	174	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{print ($1 + $2 ) / 16}')
[3520]	175	else
	176	#
[4687]	177	# number of processes required is not an integer multiple of 16
[3520]	178	# round up the number of nodes required.
	179	#
[4687]	180	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{printf("%d",($1 + $2 ) / 16 + 1 )}')
[3520]	181	fi
	182	;;
[4814]	183	XC_ARCHER_INTEL)
	184	# ocean cores are packed 24 to a node
	185	NB_REM=$( echo $NB_PROC \| awk '{print ( $1 % 24 ) }')
	186	if [ ${NB_REM} == 0 ] ; then
	187	# number of processes required is an integer multiple of 24
	188	#
	189	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{print ($1) / 24}')
	190	else
	191	#
	192	# number of processes required is not an integer multiple of 24
	193	# round up the number of nodes required.
	194	#
	195	NB_NODES=$( echo $NB_PROC \| awk '{printf("%d",($1) / 24 + 1 )}')
	196	fi
	197	# xios cores are sparsely packed at 4 to a node
	198	# but can not share nodes with the ocean cores
	199	NB_REM=$( echo $NXIO_PROC \| awk '{print ( $2 % 4 ) }')
	200	if [ ${NB_REM} == 0 ] ; then
	201	# number of processes required is an integer multiple of 4
	202	#
	203	NB_NODES=$( echo $NB_NODES $NXIO_PROC \| awk '{print ($1 + ( $2 / 4 ))}')
	204	else
	205	#
	206	# number of processes required is not an integer multiple of 4
	207	# round up the number of nodes required.
	208	#
[5480]	209	NB_NODES=$( echo $NB_NODES $NXIO_PROC \| awk '{print ($1 + ( $2 / 4 ) + 1)}')
[4814]	210	fi
	211	;;
[5480]	212	XC40_METO*) #Setup for Met Office XC40 with any compiler
	213	# ocean cores are packed 32 to a node
	214	# If we need more than one node then have to use parallel queue and XIOS must have a node to itself
	215	NB_REM=$( echo $NB_PROC \| awk '{print ( $1 % 32 ) }')
	216	if [ ${NB_REM} == 0 ] ; then
	217	# number of processes required is an integer multiple of 32
	218	#
	219	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{print ($1) / 32}')
	220	else
	221	#
	222	# number of processes required is not an integer multiple of 32
	223	# round up the number of nodes required.
	224	#
	225	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{printf("%d",($1) / 32 + 1 )}')
	226	fi
	227	# xios cores are sparsely packed at 4 to a node
	228	if [ $NXIO_PROC == 0 ] ; then
	229	NB_XNODES=0
	230	else
	231	NB_REM=$( echo $NXIO_PROC \| awk '{print ( $1 % 4 ) }')
	232	if [ ${NB_REM} == 0 ] ; then
	233	# number of processes required is an integer multiple of 4
	234	#
	235	NB_XNODES=$( echo $NXIO_PROC \| awk '{print (( $1 / 4 ) + 1)}')
	236	else
	237	#
	238	# number of processes required is not an integer multiple of 4
	239	# round up the number of nodes required.
	240	#
	241	NB_XNODES=$( echo $NXIO_PROC \| awk '{printf("%d",($1) / 4 + 1) }')
	242	fi
	243	fi
	244	if [ ${NB_XNODES} -ge 1 ] ; then
	245	NB_NODES=$((NB_NODES+NB_XNODES))
	246	fi
	247	echo NB_XNODES=${NB_XNODES}
	248	echo Total NB_NODES=${NB_NODES}
[6140]	249	QUEUE=normal
	250	SELECT="select=$NB_NODES"
	251	module unload cray-snplauncher #Make sure snplauncher module is not loaded
[5480]	252	;;
[11645]	253	X64_JEANZAY*) #Setup for Jean-Zay
	254	export GROUP_IDRIS=`echo ${USER} \|cut -c 2-4`
	255	;;
[5559]	256	openmpi_NAVITI_MERCATOR)
[3651]	257	echo NB_PROCS ${NB_PROC}
	258	echo NB_NODES ${NB_NODES}
[3661]	259	echo NB_PROC ${NB_PROC}
[3651]	260	if [ ${NB_PROC} -eq 1 ] ; then
	261	NB_NODES=1
	262	QUEUE=monoproc
[3661]	263	NB_PROC_NODE=${NB_PROC}
[3651]	264	else
[5559]	265	if [ ${NB_PROC} -le 16 ] ; then
[3651]	266	NB_NODES=1
	267	QUEUE=mono
[3661]	268	NB_PROC_NODE=${NB_PROC}
[3651]	269	else
[5559]	270	NB_NODES=$( echo $NB_PROC \| awk '{print $1 - $1 % 16}' \| awk '{print $1 / 16 }')
[3651]	271	QUEUE=multi
[5559]	272	NB_PROC_NODE=16
[3661]	273	fi
	274	fi
[3651]	275	echo NB_PROCS ${NB_PROC}
	276	echo NB_NODES ${NB_NODES}
[3661]	277	echo NB_PROC_NODE ${NB_PROC_NODE}
	278	;;
[9480]	279	openmpi_KARA_MERCATOR_XIOS)
	280	NB_NODES=$( echo $NB_PROC \| awk '{print $1 - $1 % 32}' \| awk '{print $1 / 32 }')
	281	NB_PROC_NODE=16
	282
	283	if [ ${NB_PROC} -le 128 ] ; then
	284	QUEUE=multi
	285	NB_PROC_NODE=32
	286	fi
	287	echo NB_PROCS ${NB_PROC}
	288	echo NB_NODES ${NB_NODES}
	289	echo NB_PROC_NODE ${NB_PROC_NODE}
	290	;;
[3520]	291	*)
	292	NB_NODES=${NB_PROC}
	293	;;
	294
	295	esac
	296	#
	297	# Pass settings into job file by using sed to edit predefined strings
	298	#
[4373]	299	TOTAL_NPROCS=$(( $NB_PROC + $NXIO_PROC ))
[4245]	300	cat ${SETTE_DIR}/job_batch_template \| sed -e"s/NODES/${NB_NODES}/" \
[4373]	301	-e"s/TOTAL_NPROCS/${TOTAL_NPROCS}/" \
[4245]	302	-e"s/NPROCS/${NB_PROC}/" \
	303	-e"s/NXIOPROCS/${NXIO_PROC}/" \
[3520]	304	-e"s:DEF_SETTE_DIR:${SETTE_DIR}:" -e"s:DEF_INPUT_DIR:${INPUT_DIR}:" \
	305	-e"s:DEF_EXE_DIR:${EXE_DIR}:" \
	306	-e"s:DEF_CONFIG_DIR:${CONFIG_DIR}:" \
[8468]	307	-e"s:DEF_TOOLS_DIR:${TOOLS_DIR}:" \
[3520]	308	-e"s:MPI_FLAG:${MPI_FLAG}:" \
[11161]	309	-e"s:DEF_NEMO_VALIDATION:${NEMO_VALID}:" -e"s:DEF_NEW_CONF:${NEW_CONF}:" \
[3520]	310	-e"s:DEF_CMP_NAM:${CMP_NAM}:" -e"s:DEF_TEST_NAME:${TEST_NAME}:" > run_sette_test.job
[3661]	311
[3665]	312	case ${COMPILER} in
[9480]	313	openmpi_NAVITI_MERCATOR )
[3665]	314	cat run_sette_test.job \| sed -e"s/NPROC_NODE/${NB_PROC_NODE}/" \
	315	-e"s:QUEUE:${QUEUE}:" > run_sette_test1.job
	316	mv run_sette_test1.job run_sette_test.job
	317	;;
[9480]	318	openmpi_KARA_MERCATOR_XIOS )
	319	cat run_sette_test.job \| sed -e"s/NPROC_NODE/${NB_PROC_NODE}/" \
	320	-e"s:QUEUE:${QUEUE}:" > run_sette_test1.job
	321	mv run_sette_test1.job run_sette_test.job
	322	;;
[5480]	323	XC40_METO*)
[6140]	324	cat run_sette_test.job \| sed -e"s/SELECT/${SELECT}/" > run_sette_test1.job
[5480]	325	mv run_sette_test1.job run_sette_test.job
	326	;;
[11645]	327	X64_JEANZAY*)
	328	cat run_sette_test.job \| sed -e"s/GROUP_IDRIS/${GROUP_IDRIS}/" > run_sette_test1.job
	329	mv run_sette_test1.job run_sette_test.job
	330	;;
[3665]	331	esac
[3520]	332	#
	333	# create the unique submission job script
	334	#
	335	if [ ! -f $JOB_FILE ] ; then
	336	mv run_sette_test.job $JOB_FILE
	337	else
	338	e=`grep -n "# END_BODY" ${JOB_FILE} \| cut -d : -f 1`
	339	e=$(($e - 1))
	340	head -$e $JOB_FILE > ${JOB_FILE}_new
	341	mv ${JOB_FILE}_new ${JOB_FILE}
	342	l=`wc -l run_sette_test.job \| sed -e "s:run_sette_test.job::"`
	343	b=`grep -n "# BODY" run_sette_test.job \| cut -d : -f 1`
	344	t=$(($l - $b))
	345	tail -$t run_sette_test.job >> $JOB_FILE
	346	fi
	347
[3661]	348	chmod a+x $JOB_FILE ; echo "$JOB_FILE is ready"
[3520]	349
	350	#fi

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