source: branches/2013/dev_MERGE_2013/NEMOGCM/SETTE/prepare_job.sh @ 4373

Last change on this file since 4373 was 4373, checked in by epico, 7 years ago

new SETTE test for testing XIOS in its 4 modes Attached/Detached?, One/Multiple? with both Low and High resolution.
A modification of BATCH file for each machine is required to enable MPMD jobs. See batch-gfortran_athena_xios as example

  • Property svn:executable set to *
File size: 9.5 KB
Line 
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######################################################
13#set -vx
14set -o posix
15#set -u
16#set -e
17#+
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#
32#  $ ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_FLAG JOB_FILE
33#
34#
35# DESCRIPTION
36# ===========
37#
38# Part of the SETTE package to run tests for NEMO
39#
40# prepare the script $JOB_FILE to run the tests
41#
42# EXAMPLES
43# ========
44#
45# ::
46#
47#  $ ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_FLAG $JOB_FILE
48#
49# prepare the $JOB_FILE for execution
50#
51#
52# TODO
53# ====
54#
55# option debug
56#
57#
58# EVOLUTIONS
59# ==========
60#
61# $Id: prepare_job.sh 3050 2011-11-07 14:11:34Z acc $
62#
63#
64#
65#   * creation
66#
67#-
68#
69
70usage=" Usage : ./prepare_job.sh INPUT_FILE_CONFIG_NAME NUMBER_PROC TEST_NAME MPI_FLAG JOB_FILE NUM_XIO_SERVERS"
71usage=" example : ./prepare_job.sh input_ORCA2_LIM_PISCES.cfg 8 SHORT no/yes $JOB_FILE 0"
72
73
74minargcount=6
75        if [ ${#} -lt ${minargcount} ]
76        then
77                echo "not enough arguments for prepare_job.sh script"
78                echo "control number of argument of prepare_job.sh in sette.sh"
79                echo "${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#
90INPUTARFILE=$1
91NB_PROC=$2
92TEST_NAME=$3
93MPI_FLAG=$4
94JOB_FILE=$5
95NXIO_PROC=$6
96
97# export EXE_DIR. This directory is used to execute model
98#
99#
100#
101echo "date: `date`" >> ${SETTE_DIR}/output.sette
102echo "" >> ${SETTE_DIR}/output.sette
103echo "running config: ${NEW_CONF}" >> ${SETTE_DIR}/output.sette
104echo "" >> ${SETTE_DIR}/output.sette
105echo "list of cpp_keys: " >> ${SETTE_DIR}/output.sette
106echo "`more ${SETTE_DIR}/../CONFIG/${NEW_CONF}/cpp_${NEW_CONF}.fcm`" >> ${SETTE_DIR}/output.sette
107echo "" >> ${SETTE_DIR}/output.sette
108echo "compiling with: ${CMP_NAM}" >> ${SETTE_DIR}/output.sette
109echo "" >> ${SETTE_DIR}/output.sette
110echo "executing script : \"fcm_job $@\" " >> ${SETTE_DIR}/output.sette
111echo "            " >> ${SETTE_DIR}/output.sette
112
113################################################################
114# SET INPUT
115# get the input tarfile if needed
116if [ "$(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
123while read tar_file dir_conf_forc
124do
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
131
132if [ ! -f ${FORCING_DIR}/${tar_file} ] ; then 
133     echo "tarfile  ${FORCING_DIR}/${tar_file} cannot be found we stop " ; exit 2 ; fi
134
135echo "mkdir ${FORCING_DIR}/${dir_conf_forc}" >> ${SETTE_DIR}/output.sette
136         mkdir ${FORCING_DIR}/${dir_conf_forc} 
137         cd    ${FORCING_DIR}/${dir_conf_forc}
138echo " 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
148
149else
150  echo "no input file to be searched "
151fi
152################################################################
153
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
174################################################################
175# RUN OPA
176cd ${EXE_DIR}
177if [ ! -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
182fi
183
184# example for NOCS Altix system using PBS batch submission (requires ${SETTE_DIR}/sette_batch_template file)
185#
186  #  if [ ${MPI_FLAG} == "no" ] ; then
187      case ${COMPILER} in
188         ALTIX_NAUTILUS_MPT)
189                                NB_REM=$( echo $NB_PROC $NXIO_PROC | awk '{print ( $1 + $2 ) % 4}')
190               if [ ${NB_REM} == 0 ] ; then
191               # number of processes required is an integer multiple of 4
192               #
193               NB_NODES=$( echo $NB_PROC $NXIO_PROC | awk '{print ($1 + $2 ) / 4}')
194            else
195               #
196               # number of processes required is not an integer multiple of 4
197               # round up the number of nodes required.
198               #
199               NB_NODES=$( echo $NB_PROC $NXIO_PROC | awk '{printf("%d",($1 + $2 ) / 4 + 1 )}')
200                  fi
201            ;;
202                        ifort_MERCATOR_CLUSTER)
203                                echo NB_PROCS ${NB_PROC}
204                                echo NB_NODES ${NB_NODES}
205                                echo  NB_PROC ${NB_PROC}
206                                if [ ${NB_PROC} -eq 1 ] ; then
207                                   NB_NODES=1
208                                   QUEUE=monoproc
209                                   NB_PROC_NODE=${NB_PROC}
210                                else
211                                   if [ ${NB_PROC} -le 8 ] ; then
212                                      NB_NODES=1
213                                      QUEUE=mono
214                                      NB_PROC_NODE=${NB_PROC}
215                                   else
216                                      NB_NODES=$( echo $NB_PROC | awk '{print $1 - $1 % 8}'  | awk '{print $1 / 8 }')
217                                      QUEUE=multi
218                                      NB_PROC_NODE=8
219                                  fi
220                                fi
221                                echo NB_PROCS     ${NB_PROC}
222                                echo NB_NODES     ${NB_NODES}
223                                echo NB_PROC_NODE ${NB_PROC_NODE}
224                                ;;
225         *)
226            NB_NODES=${NB_PROC}
227            ;;
228
229      esac
230#
231# Pass settings into job file by using sed to edit predefined strings
232#
233        TOTAL_NPROCS=$(( $NB_PROC + $NXIO_PROC ))
234        cat ${SETTE_DIR}/job_batch_template | sed -e"s/NODES/${NB_NODES}/" \
235             -e"s/TOTAL_NPROCS/${TOTAL_NPROCS}/" \
236             -e"s/NPROCS/${NB_PROC}/" \
237             -e"s/NXIOPROCS/${NXIO_PROC}/" \
238             -e"s:DEF_SETTE_DIR:${SETTE_DIR}:" -e"s:DEF_INPUT_DIR:${INPUT_DIR}:" \
239             -e"s:DEF_EXE_DIR:${EXE_DIR}:" \
240             -e"s:DEF_CONFIG_DIR:${CONFIG_DIR}:" \
241             -e"s:MPI_FLAG:${MPI_FLAG}:" \
242             -e"s:DEF_NEMO_VALIDATION:${NEMO_VALIDATION_DIR}:" -e"s:DEF_NEW_CONF:${NEW_CONF}:" \
243             -e"s:DEF_CMP_NAM:${CMP_NAM}:" -e"s:DEF_TEST_NAME:${TEST_NAME}:" > run_sette_test.job
244
245        case ${COMPILER} in
246              ifort_MERCATOR_CLUSTER)
247                    #cat run_sette_test.job | sed -e"s:QUEUE:${QUEUE}:" > run_sette_test1.job
248                    #cat run_sette_test.job | sed -e"s/NPROC_NODE/${NB_PROC_NODE}/" > run_sette_test1.job
249                                                 #-e"s/NPROC_NODE/${NB_PROC_NODE}/" > run_sette_test1.job
250                    cat run_sette_test.job | sed -e"s/NPROC_NODE/${NB_PROC_NODE}/" \
251                                                 -e"s:QUEUE:${QUEUE}:" > run_sette_test1.job
252                    mv run_sette_test1.job run_sette_test.job
253                    ;;
254   esac
255#
256# create the unique submission job script
257#
258   if [ ! -f $JOB_FILE ] ; then
259      mv run_sette_test.job $JOB_FILE
260   else
261       e=`grep -n "# END_BODY" ${JOB_FILE} | cut -d : -f 1`
262            e=$(($e - 1))
263       head -$e $JOB_FILE > ${JOB_FILE}_new
264       mv ${JOB_FILE}_new ${JOB_FILE}
265       l=`wc -l run_sette_test.job | sed -e "s:run_sette_test.job::"`
266       b=`grep -n "# BODY" run_sette_test.job | cut -d : -f 1`
267       t=$(($l - $b))
268       tail -$t run_sette_test.job >> $JOB_FILE
269   fi
270   
271   chmod a+x $JOB_FILE ; echo "$JOB_FILE is ready"
272
273#fi
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