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prepare_job.sh in trunk/NEMOGCM/SETTE – NEMO

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source: trunk/NEMOGCM/SETTE/prepare_job.sh @ 5480

Last change on this file since 5480 was 5480, checked in by timgraham, 9 years ago
Added arch and batch files for running SETTE on new Met Office HPC. Also modified prepare_job.sh but all contained within a case statement so no impact to other users.
Property svn:executable set to ``*
File size: 15.3 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
[4245]	70	usage=" Usage : ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_FLAG JOB_FILE NUM_XIO_SERVERS"
	71	usage=" example : ./prepare_job.sh input_ORCA2_LIM_PISCES.cfg 8 SHORT no/yes $JOB_FILE 0"
[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
	106	echo "`more ${SETTE_DIR}/../CONFIG/${NEW_CONF}/cpp_${NEW_CONF}.fcm`" >> ${SETTE_DIR}/output.sette
	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
[3680]	154	##########################################################################
	155	# COPY RESTART FILES (if needed; i.e. only for SHORT job in RESTART TESTS)
	156	# get the input tarfile if needed
	157	# SF : not ok for the moment because at this point is needed cn_exp variable,
	158	# SF : here it it not known.
	159	#\cd ${EXE_DIR}
	160	#if [ "$(echo ${TEST_NAME} \| grep -c "SHORT" )" -ne 0 ] ; then
	161	# for (( i=1; i<=${NB_PROC}; ${NB_PROC}++)) ; do
	162	# L_NPROC=`printf "%04d\n" $i`
	163	# ln -sf ../LONG/${NEW_CONF}_00000060_restart_${L_NPROC-1}.nc .
	164	# done
	165	#fi
	166	## SF : other way
	167	## for file in ../LONG/${NEW_CONF}_restart_0.nc ; do
	168	## ncpu=`echo $file \| awk -F '_' '{print $NF}' \| cut -f 1 -d '.'`
	169	## ln -sf ${file} .
	170	## done
	171	##fi
	172	##########################################################################
	173
[3520]	174	################################################################
	175	# RUN OPA
	176	cd ${EXE_DIR}
	177	if [ ! -r ${EXE_DIR}/opa ]
	178	then
	179	echo "executable opa does not exist"
	180	echo "executable opa does not exist, exit" >> ${SETTE_DIR}/output.sette
	181	exit 1
	182	fi
	183
[4687]	184	# example for NOCS ClusterVision system using SLURM batch submission (requires ${SETTE_DIR}/sette_batch_template file)
[3520]	185	#
[3661]	186	# if [ ${MPI_FLAG} == "no" ] ; then
[3520]	187	case ${COMPILER} in
[4687]	188	X64_MOBILIS)
	189	NB_REM=$( echo $NB_PROC $NXIO_PROC \| awk '{print ( $1 + $2 ) % 16}')
[3520]	190	if [ ${NB_REM} == 0 ] ; then
[4687]	191	# number of processes required is an integer multiple of 16
[3520]	192	#
[4687]	193	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{print ($1 + $2 ) / 16}')
[3520]	194	else
	195	#
[4687]	196	# number of processes required is not an integer multiple of 16
[3520]	197	# round up the number of nodes required.
	198	#
[4687]	199	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{printf("%d",($1 + $2 ) / 16 + 1 )}')
[3520]	200	fi
	201	;;
[4814]	202	XC_ARCHER_INTEL)
	203	# ocean cores are packed 24 to a node
	204	NB_REM=$( echo $NB_PROC \| awk '{print ( $1 % 24 ) }')
	205	if [ ${NB_REM} == 0 ] ; then
	206	# number of processes required is an integer multiple of 24
	207	#
	208	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{print ($1) / 24}')
	209	else
	210	#
	211	# number of processes required is not an integer multiple of 24
	212	# round up the number of nodes required.
	213	#
	214	NB_NODES=$( echo $NB_PROC \| awk '{printf("%d",($1) / 24 + 1 )}')
	215	fi
	216	# xios cores are sparsely packed at 4 to a node
	217	# but can not share nodes with the ocean cores
	218	NB_REM=$( echo $NXIO_PROC \| awk '{print ( $2 % 4 ) }')
	219	if [ ${NB_REM} == 0 ] ; then
	220	# number of processes required is an integer multiple of 4
	221	#
	222	NB_NODES=$( echo $NB_NODES $NXIO_PROC \| awk '{print ($1 + ( $2 / 4 ))}')
	223	else
	224	#
	225	# number of processes required is not an integer multiple of 4
	226	# round up the number of nodes required.
	227	#
[5480]	228	NB_NODES=$( echo $NB_NODES $NXIO_PROC \| awk '{print ($1 + ( $2 / 4 ) + 1)}')
[4814]	229	fi
	230	;;
[5480]	231	XC40_METO*) #Setup for Met Office XC40 with any compiler
	232	# ocean cores are packed 32 to a node
	233	# If we need more than one node then have to use parallel queue and XIOS must have a node to itself
	234	NB_REM=$( echo $NB_PROC \| awk '{print ( $1 % 32 ) }')
	235	if [ ${NB_REM} == 0 ] ; then
	236	# number of processes required is an integer multiple of 32
	237	#
	238	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{print ($1) / 32}')
	239	else
	240	#
	241	# number of processes required is not an integer multiple of 32
	242	# round up the number of nodes required.
	243	#
	244	NB_NODES=$( echo $NB_PROC $NXIO_PROC \| awk '{printf("%d",($1) / 32 + 1 )}')
	245	fi
	246	# xios cores are sparsely packed at 4 to a node
	247	if [ $NXIO_PROC == 0 ] ; then
	248	NB_XNODES=0
	249	else
	250	NB_REM=$( echo $NXIO_PROC \| awk '{print ( $1 % 4 ) }')
	251	if [ ${NB_REM} == 0 ] ; then
	252	# number of processes required is an integer multiple of 4
	253	#
	254	NB_XNODES=$( echo $NXIO_PROC \| awk '{print (( $1 / 4 ) + 1)}')
	255	else
	256	#
	257	# number of processes required is not an integer multiple of 4
	258	# round up the number of nodes required.
	259	#
	260	NB_XNODES=$( echo $NXIO_PROC \| awk '{printf("%d",($1) / 4 + 1) }')
	261	fi
	262	fi
	263	if [ ${NB_XNODES} -ge 1 ] ; then
	264	NB_NODES=$((NB_NODES+NB_XNODES))
	265	fi
	266	echo NB_XNODES=${NB_XNODES}
	267	echo Total NB_NODES=${NB_NODES}
	268	if [ ${NB_NODES} -eq 1 ] ; then
	269	QUEUE=shared
	270	#Not using XIOS in detatched mode and using less than one node so should be ok on shared node
	271	#Load snplauncher module to allow use of mpiexec
	272	SELECT="select=1:ncpus=$((NXIO_PROC + NB_PROC))":mem=15GB
	273	module load cray-snplauncher
	274	echo 'Shared Queue'
	275	else
	276	QUEUE=normal
	277	SELECT="select=$NB_NODES"
	278	module unload cray-snplauncher #Make sure snplauncher module is not loaded
	279	echo 'Normal Queue'
	280	fi
	281	;;
[3651]	282	ifort_MERCATOR_CLUSTER)
	283	echo NB_PROCS ${NB_PROC}
	284	echo NB_NODES ${NB_NODES}
[3661]	285	echo NB_PROC ${NB_PROC}
[3651]	286	if [ ${NB_PROC} -eq 1 ] ; then
	287	NB_NODES=1
	288	QUEUE=monoproc
[3661]	289	NB_PROC_NODE=${NB_PROC}
[3651]	290	else
[3661]	291	if [ ${NB_PROC} -le 8 ] ; then
[3651]	292	NB_NODES=1
	293	QUEUE=mono
[3661]	294	NB_PROC_NODE=${NB_PROC}
[3651]	295	else
	296	NB_NODES=$( echo $NB_PROC \| awk '{print $1 - $1 % 8}' \| awk '{print $1 / 8 }')
	297	QUEUE=multi
	298	NB_PROC_NODE=8
[3661]	299	fi
	300	fi
[3651]	301	echo NB_PROCS ${NB_PROC}
	302	echo NB_NODES ${NB_NODES}
[3661]	303	echo NB_PROC_NODE ${NB_PROC_NODE}
	304	;;
[3520]	305	*)
	306	NB_NODES=${NB_PROC}
	307	;;
	308
	309	esac
	310	#
	311	# Pass settings into job file by using sed to edit predefined strings
	312	#
[4373]	313	TOTAL_NPROCS=$(( $NB_PROC + $NXIO_PROC ))
[4245]	314	cat ${SETTE_DIR}/job_batch_template \| sed -e"s/NODES/${NB_NODES}/" \
[4373]	315	-e"s/TOTAL_NPROCS/${TOTAL_NPROCS}/" \
[4245]	316	-e"s/NPROCS/${NB_PROC}/" \
	317	-e"s/NXIOPROCS/${NXIO_PROC}/" \
[3520]	318	-e"s:DEF_SETTE_DIR:${SETTE_DIR}:" -e"s:DEF_INPUT_DIR:${INPUT_DIR}:" \
	319	-e"s:DEF_EXE_DIR:${EXE_DIR}:" \
	320	-e"s:DEF_CONFIG_DIR:${CONFIG_DIR}:" \
	321	-e"s:MPI_FLAG:${MPI_FLAG}:" \
	322	-e"s:DEF_NEMO_VALIDATION:${NEMO_VALIDATION_DIR}:" -e"s:DEF_NEW_CONF:${NEW_CONF}:" \
	323	-e"s:DEF_CMP_NAM:${CMP_NAM}:" -e"s:DEF_TEST_NAME:${TEST_NAME}:" > run_sette_test.job
[3661]	324
[3665]	325	case ${COMPILER} in
	326	ifort_MERCATOR_CLUSTER)
	327	#cat run_sette_test.job \| sed -e"s:QUEUE:${QUEUE}:" > run_sette_test1.job
	328	#cat run_sette_test.job \| sed -e"s/NPROC_NODE/${NB_PROC_NODE}/" > run_sette_test1.job
	329	#-e"s/NPROC_NODE/${NB_PROC_NODE}/" > run_sette_test1.job
	330	cat run_sette_test.job \| sed -e"s/NPROC_NODE/${NB_PROC_NODE}/" \
	331	-e"s:QUEUE:${QUEUE}:" > run_sette_test1.job
	332	mv run_sette_test1.job run_sette_test.job
	333	;;
[5480]	334	XC40_METO*)
	335	cat run_sette_test.job \| sed -e"s/QUEUE/${QUEUE}/" \
	336	-e"s/SELECT/${SELECT}/" > run_sette_test1.job
	337	mv run_sette_test1.job run_sette_test.job
	338	;;
[3665]	339	esac
[3520]	340	#
	341	# create the unique submission job script
	342	#
	343	if [ ! -f $JOB_FILE ] ; then
	344	mv run_sette_test.job $JOB_FILE
	345	else
	346	e=`grep -n "# END_BODY" ${JOB_FILE} \| cut -d : -f 1`
	347	e=$(($e - 1))
	348	head -$e $JOB_FILE > ${JOB_FILE}_new
	349	mv ${JOB_FILE}_new ${JOB_FILE}
	350	l=`wc -l run_sette_test.job \| sed -e "s:run_sette_test.job::"`
	351	b=`grep -n "# BODY" run_sette_test.job \| cut -d : -f 1`
	352	t=$(($l - $b))
	353	tail -$t run_sette_test.job >> $JOB_FILE
	354	fi
	355
[3661]	356	chmod a+x $JOB_FILE ; echo "$JOB_FILE is ready"
[3520]	357
	358	#fi

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