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prepare_job.sh in utils/CI/sette – NEMO

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source: utils/CI/sette/prepare_job.sh @ 13292

Last change on this file since 13292 was 13292, checked in by smasson, 4 years ago
update sette with sette/r12931_sette_ticket2366
Property svn:executable set to ``*
File size: 13.8 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
[13292]	124	while read tar_file dir_conf_forc
	125	do
	126	echo looking for tarfile ${tar_file} and directory ${FORCING_DIR}/${dir_conf_forc}
	127	echo looking for tarfile ${tar_file} and directory ${FORCING_DIR}/${dir_conf_forc} >> ${SETTE_DIR}/output.sette
	128	if [ -d ${FORCING_DIR}/${dir_conf_forc} ] ; then
	129	# input dir ar there, only check the links
	130	echo "input dir ar there, only check the links" >> ${SETTE_DIR}/output.sette
	131	# extract tarfile
	132	else
	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
[13292]	136	echo " extract from tarfile ${FORCING_DIR}/${tar_file} in ${FORCING_DIR}/${dir_conf_forc}" >> ${SETTE_DIR}/output.sette
[3520]	137
[13292]	138	istgz=$( echo ${FORCING_DIR}/${tar_file} \| grep -c "gz$" )
	139	if [ $istgz -eq 1 ]
	140	then
	141	withdir=$( tar tfz ${FORCING_DIR}/${tar_file} \| head -n 1 \| grep -c "${dir_conf_forc}/$" )
	142	else
	143	withdir=$( tar tf ${FORCING_DIR}/${tar_file} \| head -n 1 \| grep -c "${dir_conf_forc}/$" )
	144	fi
	145	if [ $withdir -eq 0 ]
	146	then
	147	mkdir ${FORCING_DIR}/${dir_conf_forc}
	148	cd ${FORCING_DIR}/${dir_conf_forc}
	149	else
	150	cd ${FORCING_DIR}
	151	fi
	152	if [ $istgz -eq 1 ]
	153	then
	154	tar xvfz ${FORCING_DIR}/${tar_file}
	155	else
	156	tar xvf ${FORCING_DIR}/${tar_file}
	157	[ $( ls -1 gz 2>/dev/null \| wc -l ) -gt 0 ] && gunzip -f gz
	158	fi
	159	fi
	160	# Tarfile and input dir ar there, only check the links
	161	cd ${FORCING_DIR}/${dir_conf_forc}
	162	for fida in *
	163	do
[4147]	164	[ -f ${EXE_DIR}/${fida} ] \|\| ln -s ${FORCING_DIR}/${dir_conf_forc}/${fida} ${EXE_DIR}/${fida}
[13292]	165	done
	166	done < ${SETTE_DIR}/$INPUTARFILE
	167
[4147]	168	else
[13292]	169	echo "no input file to be searched "
[3520]	170	fi
	171	################################################################
	172
	173	################################################################
	174	# RUN OPA
	175	cd ${EXE_DIR}
[9576]	176	if [ ! -r ${EXE_DIR}/nemo ]
[3520]	177	then
[9576]	178	echo "executable nemo does not exist"
	179	echo "executable nemo does not exist, exit" >> ${SETTE_DIR}/output.sette
[3520]	180	exit 1
	181	fi
	182
[4687]	183	# example for NOCS ClusterVision system using SLURM batch submission (requires ${SETTE_DIR}/sette_batch_template file)
[3520]	184	#
[3661]	185	# if [ ${MPI_FLAG} == "no" ] ; then
[3520]	186	case ${COMPILER} in
[4687]	187	X64_MOBILIS)
	188	NB_REM=$( echo $NB_PROC $NXIO_PROC \| awk '{print ( $1 + $2 ) % 16}')
[3520]	189	if [ ${NB_REM} == 0 ] ; then
[4687]	190	# number of processes required is an integer multiple of 16
[3520]	191	#
[4687]	192	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{print ($1 + $2 ) / 16}')
[3520]	193	else
	194	#
[4687]	195	# number of processes required is not an integer multiple of 16
[3520]	196	# round up the number of nodes required.
	197	#
[4687]	198	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{printf("%d",($1 + $2 ) / 16 + 1 )}')
[3520]	199	fi
	200	;;
[4814]	201	XC_ARCHER_INTEL)
	202	# ocean cores are packed 24 to a node
	203	NB_REM=$( echo $NB_PROC \| awk '{print ( $1 % 24 ) }')
	204	if [ ${NB_REM} == 0 ] ; then
	205	# number of processes required is an integer multiple of 24
	206	#
	207	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{print ($1) / 24}')
	208	else
	209	#
	210	# number of processes required is not an integer multiple of 24
	211	# round up the number of nodes required.
	212	#
	213	NB_NODES=$( echo $NB_PROC \| awk '{printf("%d",($1) / 24 + 1 )}')
	214	fi
	215	# xios cores are sparsely packed at 4 to a node
	216	# but can not share nodes with the ocean cores
	217	NB_REM=$( echo $NXIO_PROC \| awk '{print ( $2 % 4 ) }')
	218	if [ ${NB_REM} == 0 ] ; then
	219	# number of processes required is an integer multiple of 4
	220	#
	221	NB_NODES=$( echo $NB_NODES $NXIO_PROC \| awk '{print ($1 + ( $2 / 4 ))}')
	222	else
	223	#
	224	# number of processes required is not an integer multiple of 4
	225	# round up the number of nodes required.
	226	#
[5480]	227	NB_NODES=$( echo $NB_NODES $NXIO_PROC \| awk '{print ($1 + ( $2 / 4 ) + 1)}')
[4814]	228	fi
	229	;;
[5480]	230	XC40_METO*) #Setup for Met Office XC40 with any compiler
	231	# ocean cores are packed 32 to a node
	232	# If we need more than one node then have to use parallel queue and XIOS must have a node to itself
	233	NB_REM=$( echo $NB_PROC \| awk '{print ( $1 % 32 ) }')
	234	if [ ${NB_REM} == 0 ] ; then
	235	# number of processes required is an integer multiple of 32
	236	#
	237	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{print ($1) / 32}')
	238	else
	239	#
	240	# number of processes required is not an integer multiple of 32
	241	# round up the number of nodes required.
	242	#
	243	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{printf("%d",($1) / 32 + 1 )}')
	244	fi
	245	# xios cores are sparsely packed at 4 to a node
	246	if [ $NXIO_PROC == 0 ] ; then
	247	NB_XNODES=0
	248	else
	249	NB_REM=$( echo $NXIO_PROC \| awk '{print ( $1 % 4 ) }')
	250	if [ ${NB_REM} == 0 ] ; then
	251	# number of processes required is an integer multiple of 4
	252	#
	253	NB_XNODES=$( echo $NXIO_PROC \| awk '{print (( $1 / 4 ) + 1)}')
	254	else
	255	#
	256	# number of processes required is not an integer multiple of 4
	257	# round up the number of nodes required.
	258	#
	259	NB_XNODES=$( echo $NXIO_PROC \| awk '{printf("%d",($1) / 4 + 1) }')
	260	fi
	261	fi
	262	if [ ${NB_XNODES} -ge 1 ] ; then
	263	NB_NODES=$((NB_NODES+NB_XNODES))
	264	fi
	265	echo NB_XNODES=${NB_XNODES}
	266	echo Total NB_NODES=${NB_NODES}
[6140]	267	QUEUE=normal
	268	SELECT="select=$NB_NODES"
	269	module unload cray-snplauncher #Make sure snplauncher module is not loaded
[5480]	270	;;
[11645]	271	X64_JEANZAY*) #Setup for Jean-Zay
	272	export GROUP_IDRIS=`echo ${USER} \|cut -c 2-4`
	273	;;
[12798]	274	openmpi_KARA_MERCATOR*)
[11805]	275	NB_PROC_NODE=32
[12798]	276	NB_NODES=$( echo $NB_PROC \| awk '{print $1 - $1 % $NB_PROC_NODE }' \| awk '{print $1 / $NB_PROC_NODE }' )
[9480]	277	if [ ${NB_PROC} -le 128 ] ; then
	278	QUEUE=multi
	279	fi
	280	;;
[12798]	281	ifort_beaufix_sette*)
	282	NB_PROC_NODE=40
	283	NB_NODES=$( echo $NB_PROC \| awk '{print $1 - $1 % $NB_PROC_NODE }' \| awk '{print $1 / $NB_PROC_NODE }' )
	284	;;
[3520]	285	*)
	286	NB_NODES=${NB_PROC}
	287	;;
	288	esac
	289	#
	290	# Pass settings into job file by using sed to edit predefined strings
	291	#
[4373]	292	TOTAL_NPROCS=$(( $NB_PROC + $NXIO_PROC ))
[12798]	293	cat ${SETTE_DIR}/job_batch_template \| sed -e"s/\(=\\| \)NODES/\1${NB_NODES}/" \
[4373]	294	-e"s/TOTAL_NPROCS/${TOTAL_NPROCS}/" \
[4245]	295	-e"s/NPROCS/${NB_PROC}/" \
	296	-e"s/NXIOPROCS/${NXIO_PROC}/" \
[3520]	297	-e"s:DEF_SETTE_DIR:${SETTE_DIR}:" -e"s:DEF_INPUT_DIR:${INPUT_DIR}:" \
	298	-e"s:DEF_EXE_DIR:${EXE_DIR}:" \
	299	-e"s:DEF_CONFIG_DIR:${CONFIG_DIR}:" \
[8468]	300	-e"s:DEF_TOOLS_DIR:${TOOLS_DIR}:" \
[3520]	301	-e"s:MPI_FLAG:${MPI_FLAG}:" \
[11161]	302	-e"s:DEF_NEMO_VALIDATION:${NEMO_VALID}:" -e"s:DEF_NEW_CONF:${NEW_CONF}:" \
[3520]	303	-e"s:DEF_CMP_NAM:${CMP_NAM}:" -e"s:DEF_TEST_NAME:${TEST_NAME}:" > run_sette_test.job
[3661]	304
[3665]	305	case ${COMPILER} in
[9480]	306	openmpi_KARA_MERCATOR_XIOS )
	307	cat run_sette_test.job \| sed -e"s/NPROC_NODE/${NB_PROC_NODE}/" \
	308	-e"s:QUEUE:${QUEUE}:" > run_sette_test1.job
	309	mv run_sette_test1.job run_sette_test.job
	310	;;
[5480]	311	XC40_METO*)
[6140]	312	cat run_sette_test.job \| sed -e"s/SELECT/${SELECT}/" > run_sette_test1.job
[5480]	313	mv run_sette_test1.job run_sette_test.job
	314	;;
[11645]	315	X64_JEANZAY*)
	316	cat run_sette_test.job \| sed -e"s/GROUP_IDRIS/${GROUP_IDRIS}/" > run_sette_test1.job
	317	mv run_sette_test1.job run_sette_test.job
	318	;;
[3665]	319	esac
[3520]	320	#
	321	# create the unique submission job script
	322	#
	323	if [ ! -f $JOB_FILE ] ; then
	324	mv run_sette_test.job $JOB_FILE
	325	else
	326	e=`grep -n "# END_BODY" ${JOB_FILE} \| cut -d : -f 1`
	327	e=$(($e - 1))
	328	head -$e $JOB_FILE > ${JOB_FILE}_new
	329	mv ${JOB_FILE}_new ${JOB_FILE}
	330	l=`wc -l run_sette_test.job \| sed -e "s:run_sette_test.job::"`
	331	b=`grep -n "# BODY" run_sette_test.job \| cut -d : -f 1`
	332	t=$(($l - $b))
	333	tail -$t run_sette_test.job >> $JOB_FILE
	334	fi
	335
[3661]	336	chmod a+x $JOB_FILE ; echo "$JOB_FILE is ready"
[3520]	337
	338	#fi

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