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prepare_job.sh @ 8517

Last change on this file since 8517 was 8468, checked in by flavoni, 7 years ago
#1936: add in sette_rpt.sh difference of SAS restart_ice files
Property svn:executable set to ``*
File size: 13.5 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"
[7698]	71	usage=" example : ./prepare_job.sh input_ORCA2_LIM_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
[3520]	96
	97	# export EXE_DIR. This directory is used to execute model
	98	#
	99	#
	100	#
	101	echo "date: `date`" >> ${SETTE_DIR}/output.sette
	102	echo "" >> ${SETTE_DIR}/output.sette
	103	echo "running config: ${NEW_CONF}" >> ${SETTE_DIR}/output.sette
	104	echo "" >> ${SETTE_DIR}/output.sette
	105	echo "list of cpp_keys: " >> ${SETTE_DIR}/output.sette
[7715]	106	echo "`more ${CONFIG_DIR}/${NEW_CONF}/cpp_${NEW_CONF}.fcm`" >> ${SETTE_DIR}/output.sette
[3520]	107	echo "" >> ${SETTE_DIR}/output.sette
	108	echo "compiling with: ${CMP_NAM}" >> ${SETTE_DIR}/output.sette
	109	echo "" >> ${SETTE_DIR}/output.sette
	110	echo "executing script : \"fcm_job $@\" " >> ${SETTE_DIR}/output.sette
	111	echo " " >> ${SETTE_DIR}/output.sette
	112
	113	################################################################
[4147]	114	# SET INPUT
[3520]	115	# get the input tarfile if needed
[4147]	116	if [ "$(cat ${SETTE_DIR}/$INPUTARFILE \| wc -w)" -ne 0 ] ; then
	117	echo "looking for input files in ${SETTE_DIR}/$INPUTARFILE " >> ${SETTE_DIR}/output.sette
	118	# number of tarfiles: NBTAR
	119	NBTAR=`cat ${SETTE_DIR}/$INPUTARFILE \|wc -l`
	120	echo "NB of tarfiles ${NBTAR} " >> ${SETTE_DIR}/output.sette
	121	# loop on tarfiles
	122	# read file name and directory
	123	while read tar_file dir_conf_forc
	124	do
	125	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
	126	if [ -f ${FORCING_DIR}/${tar_file} ] && [ -d ${FORCING_DIR}/${dir_conf_forc} ] ; then
	127	# Tarfile and input dir ar there, only check the links
	128	echo "Tarfile and input dir ar there, only check the links" >> ${SETTE_DIR}/output.sette
	129	# extract tarfile
	130	else
[3520]	131
[4147]	132	if [ ! -f ${FORCING_DIR}/${tar_file} ] ; then
	133	echo "tarfile ${FORCING_DIR}/${tar_file} cannot be found we stop " ; exit 2 ; fi
[3520]	134
[4147]	135	echo "mkdir ${FORCING_DIR}/${dir_conf_forc}" >> ${SETTE_DIR}/output.sette
	136	mkdir ${FORCING_DIR}/${dir_conf_forc}
	137	cd ${FORCING_DIR}/${dir_conf_forc}
	138	echo " extract from tarfile ${FORCING_DIR}/${tar_file} in ${FORCING_DIR}/${dir_conf_forc}" >> ${SETTE_DIR}/output.sette
	139	tar xvof ${FORCING_DIR}/${tar_file} ; gunzip -f `find . -name "*.gz"`
	140	fi
	141	# Tarfile and input dir ar there, only check the links
	142	cd ${FORCING_DIR}/${dir_conf_forc}
	143	for fida in *
	144	do
	145	[ -f ${EXE_DIR}/${fida} ] \|\| ln -s ${FORCING_DIR}/${dir_conf_forc}/${fida} ${EXE_DIR}/${fida}
	146	done
	147	done < ${SETTE_DIR}/$INPUTARFILE
[3520]	148
[4147]	149	else
	150	echo "no input file to be searched "
[3520]	151	fi
	152	################################################################
	153
	154	################################################################
	155	# RUN OPA
	156	cd ${EXE_DIR}
	157	if [ ! -r ${EXE_DIR}/opa ]
	158	then
	159	echo "executable opa does not exist"
	160	echo "executable opa does not exist, exit" >> ${SETTE_DIR}/output.sette
	161	exit 1
	162	fi
	163
[4687]	164	# example for NOCS ClusterVision system using SLURM batch submission (requires ${SETTE_DIR}/sette_batch_template file)
[3520]	165	#
[3661]	166	# if [ ${MPI_FLAG} == "no" ] ; then
[3520]	167	case ${COMPILER} in
[4687]	168	X64_MOBILIS)
	169	NB_REM=$( echo $NB_PROC $NXIO_PROC \| awk '{print ( $1 + $2 ) % 16}')
[3520]	170	if [ ${NB_REM} == 0 ] ; then
[4687]	171	# number of processes required is an integer multiple of 16
[3520]	172	#
[4687]	173	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{print ($1 + $2 ) / 16}')
[3520]	174	else
	175	#
[4687]	176	# number of processes required is not an integer multiple of 16
[3520]	177	# round up the number of nodes required.
	178	#
[4687]	179	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{printf("%d",($1 + $2 ) / 16 + 1 )}')
[3520]	180	fi
	181	;;
[4814]	182	XC_ARCHER_INTEL)
	183	# ocean cores are packed 24 to a node
	184	NB_REM=$( echo $NB_PROC \| awk '{print ( $1 % 24 ) }')
	185	if [ ${NB_REM} == 0 ] ; then
	186	# number of processes required is an integer multiple of 24
	187	#
	188	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{print ($1) / 24}')
	189	else
	190	#
	191	# number of processes required is not an integer multiple of 24
	192	# round up the number of nodes required.
	193	#
	194	NB_NODES=$( echo $NB_PROC \| awk '{printf("%d",($1) / 24 + 1 )}')
	195	fi
	196	# xios cores are sparsely packed at 4 to a node
	197	# but can not share nodes with the ocean cores
	198	NB_REM=$( echo $NXIO_PROC \| awk '{print ( $2 % 4 ) }')
	199	if [ ${NB_REM} == 0 ] ; then
	200	# number of processes required is an integer multiple of 4
	201	#
	202	NB_NODES=$( echo $NB_NODES $NXIO_PROC \| awk '{print ($1 + ( $2 / 4 ))}')
	203	else
	204	#
	205	# number of processes required is not an integer multiple of 4
	206	# round up the number of nodes required.
	207	#
[5480]	208	NB_NODES=$( echo $NB_NODES $NXIO_PROC \| awk '{print ($1 + ( $2 / 4 ) + 1)}')
[4814]	209	fi
	210	;;
[5480]	211	XC40_METO*) #Setup for Met Office XC40 with any compiler
	212	# ocean cores are packed 32 to a node
	213	# If we need more than one node then have to use parallel queue and XIOS must have a node to itself
	214	NB_REM=$( echo $NB_PROC \| awk '{print ( $1 % 32 ) }')
	215	if [ ${NB_REM} == 0 ] ; then
	216	# number of processes required is an integer multiple of 32
	217	#
	218	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{print ($1) / 32}')
	219	else
	220	#
	221	# number of processes required is not an integer multiple of 32
	222	# round up the number of nodes required.
	223	#
	224	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{printf("%d",($1) / 32 + 1 )}')
	225	fi
	226	# xios cores are sparsely packed at 4 to a node
	227	if [ $NXIO_PROC == 0 ] ; then
	228	NB_XNODES=0
	229	else
	230	NB_REM=$( echo $NXIO_PROC \| awk '{print ( $1 % 4 ) }')
	231	if [ ${NB_REM} == 0 ] ; then
	232	# number of processes required is an integer multiple of 4
	233	#
	234	NB_XNODES=$( echo $NXIO_PROC \| awk '{print (( $1 / 4 ) + 1)}')
	235	else
	236	#
	237	# number of processes required is not an integer multiple of 4
	238	# round up the number of nodes required.
	239	#
	240	NB_XNODES=$( echo $NXIO_PROC \| awk '{printf("%d",($1) / 4 + 1) }')
	241	fi
	242	fi
	243	if [ ${NB_XNODES} -ge 1 ] ; then
	244	NB_NODES=$((NB_NODES+NB_XNODES))
	245	fi
	246	echo NB_XNODES=${NB_XNODES}
	247	echo Total NB_NODES=${NB_NODES}
[6140]	248	QUEUE=normal
	249	SELECT="select=$NB_NODES"
	250	module unload cray-snplauncher #Make sure snplauncher module is not loaded
[5480]	251	;;
[5559]	252	openmpi_NAVITI_MERCATOR)
[3651]	253	echo NB_PROCS ${NB_PROC}
	254	echo NB_NODES ${NB_NODES}
[3661]	255	echo NB_PROC ${NB_PROC}
[3651]	256	if [ ${NB_PROC} -eq 1 ] ; then
	257	NB_NODES=1
	258	QUEUE=monoproc
[3661]	259	NB_PROC_NODE=${NB_PROC}
[3651]	260	else
[5559]	261	if [ ${NB_PROC} -le 16 ] ; then
[3651]	262	NB_NODES=1
	263	QUEUE=mono
[3661]	264	NB_PROC_NODE=${NB_PROC}
[3651]	265	else
[5559]	266	NB_NODES=$( echo $NB_PROC \| awk '{print $1 - $1 % 16}' \| awk '{print $1 / 16 }')
[3651]	267	QUEUE=multi
[5559]	268	NB_PROC_NODE=16
[3661]	269	fi
	270	fi
[3651]	271	echo NB_PROCS ${NB_PROC}
	272	echo NB_NODES ${NB_NODES}
[3661]	273	echo NB_PROC_NODE ${NB_PROC_NODE}
	274	;;
[3520]	275	*)
	276	NB_NODES=${NB_PROC}
	277	;;
	278
	279	esac
	280	#
	281	# Pass settings into job file by using sed to edit predefined strings
	282	#
[4373]	283	TOTAL_NPROCS=$(( $NB_PROC + $NXIO_PROC ))
[4245]	284	cat ${SETTE_DIR}/job_batch_template \| sed -e"s/NODES/${NB_NODES}/" \
[4373]	285	-e"s/TOTAL_NPROCS/${TOTAL_NPROCS}/" \
[4245]	286	-e"s/NPROCS/${NB_PROC}/" \
	287	-e"s/NXIOPROCS/${NXIO_PROC}/" \
[3520]	288	-e"s:DEF_SETTE_DIR:${SETTE_DIR}:" -e"s:DEF_INPUT_DIR:${INPUT_DIR}:" \
	289	-e"s:DEF_EXE_DIR:${EXE_DIR}:" \
	290	-e"s:DEF_CONFIG_DIR:${CONFIG_DIR}:" \
[8468]	291	-e"s:DEF_TOOLS_DIR:${TOOLS_DIR}:" \
[3520]	292	-e"s:MPI_FLAG:${MPI_FLAG}:" \
	293	-e"s:DEF_NEMO_VALIDATION:${NEMO_VALIDATION_DIR}:" -e"s:DEF_NEW_CONF:${NEW_CONF}:" \
	294	-e"s:DEF_CMP_NAM:${CMP_NAM}:" -e"s:DEF_TEST_NAME:${TEST_NAME}:" > run_sette_test.job
[3661]	295
[3665]	296	case ${COMPILER} in
[5559]	297	openmpi_NAVITI_MERCATOR)
[3665]	298	cat run_sette_test.job \| sed -e"s/NPROC_NODE/${NB_PROC_NODE}/" \
	299	-e"s:QUEUE:${QUEUE}:" > run_sette_test1.job
	300	mv run_sette_test1.job run_sette_test.job
	301	;;
[5480]	302	XC40_METO*)
[6140]	303	cat run_sette_test.job \| sed -e"s/SELECT/${SELECT}/" > run_sette_test1.job
[5480]	304	mv run_sette_test1.job run_sette_test.job
	305	;;
[3665]	306	esac
[3520]	307	#
	308	# create the unique submission job script
	309	#
	310	if [ ! -f $JOB_FILE ] ; then
	311	mv run_sette_test.job $JOB_FILE
	312	else
	313	e=`grep -n "# END_BODY" ${JOB_FILE} \| cut -d : -f 1`
	314	e=$(($e - 1))
	315	head -$e $JOB_FILE > ${JOB_FILE}_new
	316	mv ${JOB_FILE}_new ${JOB_FILE}
	317	l=`wc -l run_sette_test.job \| sed -e "s:run_sette_test.job::"`
	318	b=`grep -n "# BODY" run_sette_test.job \| cut -d : -f 1`
	319	t=$(($l - $b))
	320	tail -$t run_sette_test.job >> $JOB_FILE
	321	fi
	322
[3661]	323	chmod a+x $JOB_FILE ; echo "$JOB_FILE is ready"
[3520]	324
	325	#fi

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