#!/bin/ksh #************************************************************** # Author: Sébastien Denvil # Contact: Sebastien.Denvil__at__ipsl.jussieu.fr # $Revision:: $ Revision of last commit # $Author:: $ Author of last commit # $Date:: $ Date of last commit # IPSL (2006) # This software is governed by the CeCILL licence see libIGCM/libIGCM_CeCILL.LIC # #************************************************************** #========================================================= # The documentation of this file can be automatically generated # if you use the prefix #D- for comments to be extracted. # Extract with command: cat lib* | grep "^#D-" | cut -c "4-" #========================================================= #D-#================================================== #D-LibIGCM_sys for IITM IBM machine #D-#================================================== #D- #D- This ksh library if a layer under some usefull #D-environment variables and shell commands. #D-All those definitions depend on host particularities. #D-It manages a stack mechanism and test validity of operations. #D-All function described bellow must be prefixed by IGCM_sys. #==================================================== # libIGCM_sys PARAMETERS #==================================================== #==================================================== # set DEBUG_sys to true to output calls of function typeset -r DEBUG_sys=${DEBUG_sys:=true} #==================================================== # Turn in dry run mode ? (sys_Put_Rest, sys_Put_Out, sys_Get) typeset -r DRYRUN=${DRYRUN:=0} # YOU MUST COMPILE YOUR EXE FILES FOR DRYRUN MODE ! # ------------------------------------------------------------------------------------- # | DRYRUN= | Date computations, | sys_Get | Exe | sys_Put_Out; sys_Put_Rest | # | | Cp/Exe/param/files | | | | # | | Chmod Qsub | | | | # ------------------------------------------------------------------------------------- # | 0 | yes | yes | yes | yes | # ------------------------------------------------------------------------------------- # | 1 | yes | yes | yes | no | # ------------------------------------------------------------------------------------- # | 2 | yes | yes | no | no | # ------------------------------------------------------------------------------------- # | 3 | yes | no | no | no | # ------------------------------------------------------------------------------------- #===================================================== # Global Variables : #===================================================== # Language : "fr" or "en" typeset -r MYLANG="fr" #===================================================== # Host and user names # $hostname ou hostname typeset HOST=${HOST:=$( hostname )} # $username ou whoami typeset LOGIN=${LOGIN:=$( whoami )} # $hostname of the MASTER job typeset MASTER=iitm01 # project name typeset PROJECT=NONE # jobWarningDelay in seconds typeset jobWarningDelay=NONE #D- #D-#================================================== #D-Program used in libIGCM #D-#================================================== # Submit command typeset SUBMIT=${SUBMIT:=/usr/lpp/LoadL/full/bin/llsubmit} # rsync with path typeset -r RSYNC=/usr/bin/rsync # RSYNC_opt args to rsync typeset -r RSYNC_opt="-va" # ie storage filesystem typeset -r STOREHOST=iitm01 typeset -r REMOTE_RSYNC=/usr/bin/rsync #==================================================== # Set environment tools (ferret, nco, cdo, rebuild, ...) #==================================================== # Not applicable here. Only rebuild path export export PATH=${PATH}:/gpfs1/home/sebastien/REBUILD/ #==================================================== # Host specific DIRECTORIES #==================================================== #==================================================== #- MirrorlibIGCM for frontend typeset -r MirrorlibIGCM=${MirrorlibIGCM:=false} #==================================================== #- libIGCM_POST for frontend typeset -r libIGCM_POST=${libIGCM} #==================================================== #- R_EXE (==> BIN_DIR = ${MODIPSL}/bin ) typeset -r R_EXE="${MODIPSL}/bin" #==================================================== #- SUBMIT_DIR : submission dir typeset SUBMIT_DIR=${SUBMIT_DIR:=${LOADL_STEP_INITDIR}} #==================================================== #- IN typeset -r R_IN=${R_IN:=/gpfs1/home/sabin} typeset -r R_IN_ECMWF=${R_IN_ECMWF:=/gpfs1/home/sabin} #==================================================== #- RUN_DIR_PATH : Temporary working directory (=> TMP) typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=$( echo ${HOME} | sed -e "s/gpfs1/gpfs3/" )/RUN/${LOADL_STEP_ID}} #==================================================== #- OUTCOMMAND_PATH : tmp place to store command lines standard error and outputs typeset -r OUTCOMMAND_PATH=/tmp #==================================================== #- HOST_MPIRUN_COMMAND typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="/usr/bin/time poe"} #==================================================== #- Max number of arguments passed to nco operator or demigration command UNIX_MAX_LIMIT=360 #==================================================== #- set PackDefault to false on iitm PackDefault=false #==================================================== #- Number of core per node (max number of OpenMP task) NUM_COREPERNODE=2 #==================================================== #- Default number of MPI task for IPSL coupled model #- required for backward compatibility #- DEFAULT_NUM_PROC_OCE=5 DEFAULT_NUM_PROC_CPL=1 (( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL )) #D-#================================================== #D-function IGCM_sys_defineArchives #D-* Purpose: #D-* Define ARCHIVE : Dedicated to large files #D-* Define STORAGE : Dedicated to small/medium files #D-* Define R_OUT : Output tree located on ARCHIVE #D-* Define R_FIG : Output tree located on STORAGE hosting figures (monitoring and atlas, and/or small files) #D-* Define R_BUF : Output tree located on STORAGE hosting files waiting for rebuild or pack processes #D-* if SpaceName=TEST nothing special will hapen #D-* Examples: #D- function IGCM_sys_defineArchives { IGCM_debug_PushStack "IGCM_sys_defineArchives" if [ ! X${config_UserChoices_ARCHIVE} = X ]; then #==================================================== #- ARCHIVE (dedicated to large files) ARCHIVE=${config_UserChoices_ARCHIVE} else #==================================================== #- ARCHIVE (dedicated to large files) ARCHIVE=$( echo ${HOME} | sed -e "s/gpfs1/gpfs3/" ) fi if [ ! X${config_UserChoices_STORAGE} = X ]; then #==================================================== #- STORAGE (dedicated to small/medium files) STORAGE=${config_UserChoices_STORAGE} else #==================================================== #- STORAGE (dedicated to small/medium files) STORAGE=${ARCHIVE} fi # ON OBELIX NO SPECIAL CASE WHEN X${config_UserChoices_SpaceName} = XTEST #==================================================== #- R_OUT R_OUT=${ARCHIVE}/IGCM_OUT #==================================================== #- R_FIG (hosting figures : monitoring and atlas, and/or small files) R_FIG=${WORKDIR}/IGCM_OUT #==================================================== #- R_BUF (ONLY FOR double copy an scratch) R_BUF=${WORKDIR}/IGCM_OUT IGCM_debug_Print 1 "R_OUT has been defined = ${R_OUT}" IGCM_debug_Print 1 "R_BUF has been defined = ${R_BUF}" IGCM_debug_Print 1 "R_FIG has been defined = ${R_FIG}" IGCM_debug_PopStack "IGCM_sys_defineArchives" } #D-#================================================== #D-function IGCM_sys_RshArchive #D-* Purpose: Archive rsh command #D-* Examples: #D- function IGCM_sys_RshArchive { IGCM_debug_PushStack "IGCM_sys_RshArchive" $@ /bin/ksh <<-EOF ${@} EOF status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_RshArchive : command failed error code ${status}" IGCM_debug_Exit "IGCM_sys_RshArchive" fi IGCM_debug_PopStack "IGCM_sys_RshArchive" } #D-#================================================== #D-function IGCM_sys_RshArchive_NoError #D-* Purpose: Archive rsh command, without error #D-* used only in monitoring.job #D-* Examples: #D- function IGCM_sys_RshArchive_NoError { IGCM_debug_PushStack "IGCM_sys_RshArchive_NoError" $@ /bin/ksh <<-EOF ${@} 2> /dev/null EOF IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError" } #D-#================================================== #D-function IGCM_sys_MkdirArchive #D-* Purpose: Mkdir on Archive #D-* Examples: #D- function IGCM_sys_MkdirArchive { IGCM_debug_PushStack "IGCM_sys_MkdirArchive" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_MkdirArchive :" $@ fi #- creation de repertoire sur le serveur fichier if [ ! -d ${1} ]; then \mkdir -p $1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : mkdir failed error code ${status}" IGCM_debug_Exit "IGCM_sys_MkdirArchive" fi fi IGCM_debug_PopStack "IGCM_sys_MkdirArchive" } #D-#================================================== #D-function IGCM_sys_TestDirArchive #D-* Purpose: Test Directory that must exists on Archive #D-* Examples: #D- function IGCM_sys_TestDirArchive { IGCM_debug_PushStack "IGCM_sys_TestDirArchive" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_TestDirArchive :" $@ fi typeset ExistFlag ExistFlag=$( IGCM_sys_RshArchive "[ -d $1 ] && echo 0 || echo 1" ) IGCM_debug_PopStack "IGCM_sys_TestDirArchive" return ${ExistFlag} } #D-#================================================== #D-function IGCM_sys_IsFileArchived #D-* Purpose: Test file that must NOT EXISTS on Archive based on filename only #D-* Examples: #D- function IGCM_sys_IsFileArchived { IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_IsFileArchived :" $@ fi typeset IsArchivedFlag IsArchivedFlag=$( [ "X$( echo $@ | grep \/gpfs3 )" != "X" ] && echo 0 || echo 1 ) IGCM_debug_PopStack "IGCM_sys_IsFileArchived" return ${IsArchivedFlag} } #D-#================================================== #D-function IGCM_sys_TestFileArchive #D-* Purpose: Test file that must NOT EXISTS on Archive #D-* Examples: #D- function IGCM_sys_TestFileArchive { IGCM_debug_PushStack "IGCM_sys_TestFileArchive" $@ typeset ExistFlag ExistFlag=$( IGCM_sys_RshArchive "[ -f $1 ] && echo 0 || echo 1" ) IGCM_debug_PopStack "IGCM_sys_TestFileArchive" return ${ExistFlag} } #D-#================================================== #D-function IGCM_sys_CountFileArchive #D-* Purpose: Count files on Archive filesystem #D-* Examples: #D- function IGCM_sys_CountFileArchive { IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@ #Command depends on targeted file system DEBUG_sys=false IGCM_sys_IsFileArchived $1 if [ $? = 0 ] ; then IGCM_sys_RshArchive "ls ${@} 2>/dev/null | wc -l" status=$? else ls ${@} 2>/dev/null | wc -l status=$? fi if [ ${status} -gt 0 ] ; then echo "IGCM_sys_CountFileArchive : erreur." fi IGCM_debug_PopStack "IGCM_sys_CountFileArchive" } #D-#================================================== #D-function IGCM_sys_Qsub #D-* Purpose: Qsub new job #D-* Examples: #D- function IGCM_sys_Qsub { IGCM_debug_PushStack "IGCM_sys_Qsub" $@ typeset status if ( $DEBUG_sys ) ; then echo "IGCM_sys_Qsub :" $@ fi # We have to change output/error file [ ${#@} = 1 ] && REP_FOR_JOB=${SUBMIT_DIR} [ ${#@} = 2 ] && REP_FOR_JOB=${2} sed -e "s:\# \@ output *= .*:\# \@ output = ${Script_Output}:" \ -e "s:\# \@ error *= .*:\# \@ error = ${Script_Output}:" \ $1 > ${REP_FOR_JOB}/JOB_FOR_IGCM cd $REP_FOR_JOB ; /usr/lpp/LoadL/full/bin/llsubmit JOB_FOR_IGCM > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 ; status=$? ; cd - ; cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_Qsub $1 : error code ${status}" IGCM_debug_Exit "IGCM_sys_Qsub" else JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ | tail -1 | sed -e s/\"//g ) IGCM_sys_Rm ${REP_FOR_JOB}/JOB_FOR_IGCM fi IGCM_debug_PopStack "IGCM_sys_Qsub" } #D-#================================================== #D-function IGCM_sys_QsubPost #D-* Purpose: Qsub new job on scalaire #D-* Examples: #D- function IGCM_sys_QsubPost { IGCM_debug_PushStack "IGCM_sys_QsubPost" $@ typeset status if ( $DEBUG_sys ) ; then echo "IGCM_sys_QsubPost :" $@ fi # We have to change output/error file [ ${#@} = 1 ] && REP_FOR_JOB=${POST_DIR} [ ${#@} = 2 ] && REP_FOR_JOB=${2} sed -e "s:\# \@ output *= .*:\# \@ output = ${Script_Post_Output}.out:" \ -e "s:\# \@ error *= .*:\# \@ error = ${Script_Post_Output}.out:" \ ${libIGCM_POST}/$1.job > ${REP_FOR_JOB}/JOB_FOR_IGCM cd $REP_FOR_JOB ; /usr/lpp/LoadL/full/bin/llsubmit JOB_FOR_IGCM > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 ; status=$? ; cd - ; cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_QsubPost $1 : error code ${status}" IGCM_debug_Exit "IGCM_sys_QsubPost" else JobID=$( gawk {'print $4'} ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ | tail -1 | sed -e s/\"//g ) IGCM_sys_Rm ${REP_FOR_JOB}/JOB_FOR_IGCM fi IGCM_debug_PopStack "IGCM_sys_QsubPost" } #D-************************* #D- File transfer functions #D-************************* #D- #D-#================================================== #D-function IGCM_sys_RmRunDir #D-* Purpose: rm tmpdir (dummy function most of the time batch #D- scheduler will do the job) #D-* Examples: #D- function IGCM_sys_RmRunDir { IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_RmRunDir :" $@ fi typeset status echo rm $@ > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 \rm $@ >> ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 1 "IGCM_sys_RmRunDir : rm error code is ${status}." cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ IGCM_debug_Exit "IGCM_sys_RmRunDir" else \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ fi IGCM_debug_PopStack "IGCM_sys_RmRunDir" } #D-#================================================== #D-function IGCM_sys_Put_Dir #D-* Purpose: Copy a complete directory on $(ARCHIVE) #D-* Examples: #D- function IGCM_sys_Put_Dir { IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Put_Dir :" $@ fi if [ $DRYRUN = 0 ]; then if [ ! -d ${1} ] ; then echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ." IGCM_debug_PopStack "IGCM_sys_Put_Dir" return fi typeset status # Only if we use rsync #IGCM_sys_TestDirArchive $( dirname $2 ) # #USUAL WAY \cp -r $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_Put_Dir : cp failed error code ${status}" cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ IGCM_debug_Exit "IGCM_sys_Put_Dir" else \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ fi fi IGCM_debug_PopStack "IGCM_sys_Put_Dir" } #D-#================================================== #D-function IGCM_sys_Get_Dir #D-* Purpose: Copy a complete directory from ${ARCHIVE} #D-* Examples: #D- function IGCM_sys_Get_Dir { IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Get_Dir :" $@ fi if [ $DRYRUN = 0 ]; then if [ ! -d ${1} ] ; then echo "WARNING : IGCM_sys_Get_Dir ${1} DOES NOT EXIST ." IGCM_debug_PopStack "IGCM_sys_Get_Dir" return fi typeset status #USUAL WAY \cp -ur $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}" cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ IGCM_debug_Exit "IGCM_sys_Get_Dir" else \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ fi fi IGCM_debug_PopStack "IGCM_sys_Get_Dir" } #D-#================================================== #D-function IGCM_sys_Put_Rest #D-* Purpose: Put computied restarts on ${ARCHIVE}. #D- File and target directory must exist. #D-* Examples: #D- function IGCM_sys_Put_Rest { IGCM_debug_PushStack "IGCM_sys_Put_Rest" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Put_Rest :" $@ fi if [ $DRYRUN = 0 ]; then if [ ! -f ${1} ] ; then echo "ERROR : IGCM_sys_Put_Rest ${1} DOES NOT EXIST ." IGCM_debug_Exit "IGCM_sys_Put_Rest" fi typeset status # if [ X${JobType} = XRUN ] ; then IGCM_sys_Chmod 444 ${1} fi # # Only if we use rsync #IGCM_sys_MkdirArchive $( dirname $2 ) # #USUAL WAY \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_Put_Rest : cp failed error code ${status}" cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ IGCM_debug_Exit "IGCM_sys_Put_Rest" else \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ fi fi IGCM_debug_PopStack "IGCM_sys_Put_Rest" } #D-#================================================== #D-function IGCM_sys_Put_Out #D-* Purpose: Copy a file on ${ARCHIVE} after having chmod it in readonly #D-* Examples: #D- function IGCM_sys_Put_Out { IGCM_debug_PushStack "IGCM_sys_Put_Out" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Put_Out :" $@ fi typeset status if [ $DRYRUN = 0 ]; then if [ ! -f ${1} ] ; then echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ." IGCM_debug_PopStack "IGCM_sys_Put_Out" return 1 fi # IGCM_sys_MkdirArchive $( dirname $2 ) # if [ X${JobType} = XRUN ] ; then if [ X${3} = X ] ; then IGCM_sys_Chmod 444 ${1} fi fi # #USUAL WAY \cp $1 $2 > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_Put_Out : cp failed error code ${status}" cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ IGCM_debug_Exit "IGCM_sys_Put_Out" else \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ fi fi IGCM_debug_PopStack "IGCM_sys_Put_Out" return 0 } #D-#================================================== #D-function IGCM_sys_Get #D-* Purpose: Get a file from ${ARCHIVE} #D-* Examples: IGCM_sys_Get myfile /destpath/myfile_with_PREFIX #D- IGCM_sys_Get /l Array_contain_myfiles /destpath/ function IGCM_sys_Get { IGCM_debug_PushStack "IGCM_sys_Get" $@ typeset DEST status dm_liste if ( $DEBUG_sys ) ; then echo "IGCM_sys_Get :" $@ fi if [ $DRYRUN -le 2 ]; then if [ X${1} = X'/l' ] ; then eval set +A dm_liste \${${2}} else dm_liste=${1} fi eval DEST=\${${#}} # test if the (first) file is present in the old computation : DEBUG_sys=false IGCM_sys_IsFileArchived ${dm_liste[0]} if [ $? = 0 ] ; then IGCM_sys_TestFileArchive ${dm_liste[0]} status=$? else IGCM_sys_TestFileBuffer ${dm_liste[0]} status=$? fi if [ ${status} -gt 0 ] ; then echo "IGCM_sys_Get, ERROR : regular file ${dm_liste[0]} DOES NOT EXIST ." IGCM_debug_Exit "IGCM_sys_Get" return fi #USUAL WAY \cp ${dm_liste[*]} ${DEST} > ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_Get : cp failed error code ${status}" cat ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ IGCM_debug_Exit "IGCM_sys_Get" else \rm ${OUTCOMMAND_PATH}/out_command_${LOGIN}.$$ fi fi IGCM_debug_PopStack "IGCM_sys_Get" } #D-#================================================== #D-function IGCM_sys_Dods_Rm #D-* Purpose: DO NOTHING ! Put ${ARCHIVE} files on DODS internet protocole. #D-* Examples: #D- function IGCM_sys_Dods_Rm { if ( $DEBUG_sys ) ; then echo "IGCM_sys_Dods_Rm :" $@ fi return 0 } #D-#================================================== #D-function IGCM_sys_Dods_Cp #D-* Purpose: Copy $(ARCHIVE) files on DODS internet protocole. #D-* Examples: #D- function IGCM_sys_Dods_Cp { if ( $DEBUG_sys ) ; then echo "IGCM_sys_Dods_Cp :" $@ fi return 0 } #D-#================================================== #D-function IGCM_sys_Put_Dods #D-* Purpose: Put ${ARCHIVE} files on DODS internet protocole. Dummy function here #D-* Examples: #D- function IGCM_sys_Put_Dods { IGCM_debug_PushStack "IGCM_sys_Put_Dods" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Put_Dods :" $@ fi IGCM_debug_PopStack "IGCM_sys_Put_Dods" } ############################################################## # REBUILD OPERATOR #D-#================================================== #D-function IGCM_sys_sync #D-* Purpose: flush buffer on disk (dummy function on Ada) #D-* Examples: #D- function IGCM_sys_sync { IGCM_debug_PushStack "IGCM_sys_sync" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_sync :" $@ echo "Dummy call, let the system do that." fi IGCM_debug_PopStack "IGCM_sys_sync" } ############################################################ # Activate Running Environnment Variables #D-#================================================== #D-function IGCM_sys_activ_variables #D-* Purpose: set environement variables prior to execution #D-* Examples: #D- function IGCM_sys_activ_variables { IGCM_debug_PushStack "IGCM_sys_activ_variables" if ( $DEBUG_sys ) ; then echo "IGCM_sys_activ_variables" fi # -------------------------------------------------------------------- #D- MPI specifications # -------------------------------------------------------------------- # -------------------------------------------------------------------- #D- Other specifications # -------------------------------------------------------------------- IGCM_debug_PopStack "IGCM_sys_activ_variables" } ############################################################ # Desactivate Running Environnment Variables #D-#================================================== #D-function IGCM_sys_desactiv_variables #D-* Purpose: unset environement variables after execution #D-* Examples: #D- function IGCM_sys_desactiv_variables { IGCM_debug_PushStack "IGCM_sys_desactiv_variables" if ( $DEBUG_sys ) ; then echo "IGCM_sys_desactiv_variables" fi # -------------------------------------------------------------------- #D- MPI specifications # -------------------------------------------------------------------- # -------------------------------------------------------------------- #D- Other specifications # -------------------------------------------------------------------- IGCM_debug_PopStack "IGCM_sys_desactiv_variables" } ############################################################ # Update job headers to be used by the scheduler #D-#================================================== #D-function IGCM_sys_updateHeaders #D-* Purpose: Update job headers to be used by the scheduler #D-* Examples: IGCM_sys_updateHeaders /path/to/Job_MYEXP #D- function IGCM_sys_updateHeaders { IGCM_debug_PushStack "IGCM_sys_updateHeaders" if ( $DEBUG_sys ) ; then echo "IGCM_sys_updateHeaders" fi typeset file file=$1 if [ ${executionType} -eq 1 ] ; then # MPMD + MPI sed -e "/::openMPthreads::/d" \ -e "s/::JobNumProcTot::/${coreNumber}/" \ ${file} > ${file}.tmp elif [ ${executionType} -eq 2 ] ; then # MPMD + MPI + OMP sed -e "s/::openMPthreads::/${openMPthreads}/" \ -e "s/::JobNumProcTot::/${coreNumber}/" \ ${file} > ${file}.tmp elif [ ${executionType} -eq 3 ] ; then # SPMD + MPI/OMP sed -e "s/::openMPthreads::/${openMPthreads}/" \ -e "s/::JobNumProcTot::/${mpiTasks}/" \ ${file} > ${file}.tmp elif [ ${executionType} -eq 4 ] ; then # SPMD + MPI only sed -e "s/::JobNumProcTot::/${mpiTasks}/" \ -e "/::openMPthreads::/d" \ ${file} > ${file}.tmp elif [ ${executionType} -eq 5 ] ; then # SPMD + OMP only sed -e "s/::openMPthreads::/${openMPthreads}/" \ -e "/::JobNumProcTot::/d" \ ${file} > ${file}.tmp elif [ ${executionType} -eq 6 ] ; then # SEQUENTIAL THEN sed -e "s/::JobNumProcTot::/1/" \ -e "/::openMPthreads::/d" \ ${file} > ${file}.tmp fi IGCM_sys_Mv ${file}.tmp ${file} IGCM_debug_PopStack "IGCM_sys_updateHeaders" } ############################################################ # Build MPI/OMP scripts run file (dummy function) #D-#================================================== #D-function IGCM_sys_build_run_file #D-* Purpose: build run file (deprecated) #D-* Examples: #D- function IGCM_sys_build_run_file { IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file " } ############################################################ # Build MPI/OMP scripts #D-#================================================== #D-function IGCM_sys_build_execution_scripts #D-* Purpose: build execution scripts to be launch by ${HOST_MPIRUN_COMMAND} #D-* Examples: #D- function IGCM_sys_build_execution_scripts { IGCM_debug_PushStack "IGCM_sys_build_execution_scripts" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_build_execution_scripts " $@ fi typeset NbNodes_Job NbProc_Job comp_proc_mpi_loc comp_proc_omp_loc mpi_count if [ ! -f ${SUBMIT_DIR}/Job_${config_UserChoices_JobName} ] ; then IGCM_debug_Exit "IGCM_sys_iitm build_execution_scripts : Job_${config_UserChoices_JobName} don't exist in SUBMIT_DIR : ${SUBMIT_DIR} " fi if ( ${OK_PARA_MPMD} ) ; then if [ -f run_file ] ; then IGCM_sys_Rm -f run_file fi touch run_file if ( ${OK_PARA_OMP} ) ; then # NEW : 2 Noeuds # @ task_geometry={(0)(1,2,3)} # Nombre de processus demandes echo "Job_${config_UserChoices_JobName} includes task_geometry = \c" cat ${SUBMIT_DIR}/Job_${config_UserChoices_JobName} | grep "task_geometry" | sed -e "s/[^(]*([^(]*/(/g" echo "Job_${config_UserChoices_JobName} includes task_geometry with NbNodes = \c" cat ${SUBMIT_DIR}/Job_${config_UserChoices_JobName} | grep "task_geometry" | sed -e "s/[^(]*([^(]*/(/g" | wc -c NbNodes_Job=$(( $( cat ${SUBMIT_DIR}/Job_${config_UserChoices_JobName} | grep "task_geometry" | sed -e "s/[^(]*([^(]*/(/g" | wc -c ) - 1 )) if [ ${NbNodes_Job} -eq 0 ] ; then IGCM_debug_Print 2 "Error in Job_${config_UserChoices_JobName} ressources : no task_geometry defined with OpenMP run." exit 1 fi else # OLD : # @ total_tasks = 3 # @ environment = "BATCH_NUM_PROC_TOT=3" # Pas d OpenMP # @ resources = ConsumableCpus(1) echo "Job_${config_UserChoices_JobName} includes total_tasks = \c" cat ${SUBMIT_DIR}/Job_${config_UserChoices_JobName} | grep "total_tasks" | sed -e "s/.*total_tasks = //" NbProc_Job=$( cat ${SUBMIT_DIR}/Job_${config_UserChoices_JobName} | grep "total_tasks" | sed -e "s/.*total_tasks = //" ) NbProc_Job=${NbProc_Job:=0} if [ ${NbProc_Job} -eq 0 ] ; then IGCM_debug_Print 2 "Error in Job_${config_UserChoices_JobName} ressources : no total_tasks defined with MPI only run." exit 1 fi if ( $( egrep '^# *@ *resources *= *ConsumableCpus\(1\)' ${SUBMIT_DIR}/Job_${config_UserChoices_JobName} >/dev/null 2>&1 ) ) ; then IGCM_debug_Print 2 "ressources = ConsumableCpus(1) line found into Job_${config_UserChoices_JobName}" else IGCM_debug_Print 2 "Error in Job_${config_UserChoices_JobName} ressources = line not found. Job should include resources = ConsumableCpus(1) " exit 1 fi fi # run_file construction # Then first loop on the components for the coupler ie oasis ### the coupler ie oasis must be the first one for comp in ${config_ListOfComponents[*]} ; do eval ExeNameIn=\${config_Executable_${comp}[0]} eval ExeNameOut=\${config_Executable_${comp}[1]} # for CPL component only if [ "X${comp}" = "XCPL" ] ; then eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} eval comp_proc_omp_loc=\${${comp}_PROC_OMP} if ( ${OK_PARA_MPI} ) ; then (( mpi_count = 1 )) until [ ${mpi_count} -gt ${comp_proc_mpi_loc} ] ; do if ( ${OK_PARA_OMP} ) ; then echo "env OMP_NUM_THREADS=${comp_proc_omp_loc} ./${ExeNameOut} " >> run_file else echo "./${ExeNameOut}" >> run_file fi (( mpi_count = mpi_count + 1 )) done else if ( ${OK_PARA_OMP} ) ; then echo "env OMP_NUM_THREADS=${comp_proc_omp_loc} ./${ExeNameOut} " >> run_file else echo "./${ExeNameOut} " >> run_file fi fi fi done # Then second loop on the components for comp in ${config_ListOfComponents[*]} ; do eval ExeNameIn=\${config_Executable_${comp}[0]} eval ExeNameOut=\${config_Executable_${comp}[1]} # Only if we really have an executable for the component and not the coupler ie oasis: if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${comp}" != "XCPL" ] ) ; then eval comp_proc_mpi_loc=\${${comp}_PROC_MPI} eval comp_proc_omp_loc=\${${comp}_PROC_OMP} if ( ${OK_PARA_MPI} ) ; then (( mpi_count = 1 )) until [ ${mpi_count} -gt ${comp_proc_mpi_loc} ] ; do if ( ${OK_PARA_OMP} ) ; then echo "env OMP_NUM_THREADS=${comp_proc_omp_loc} ./${ExeNameOut} " >> run_file else echo "./${ExeNameOut}" >> run_file fi (( mpi_count = mpi_count + 1 )) done else if ( ${OK_PARA_OMP} ) ; then echo "env OMP_NUM_THREADS=${comp_proc_omp_loc} ./${ExeNameOut} " >> run_file else # to be tested : no MPI only OpenMP into MPMD mode echo "./${ExeNameOut} " >> run_file fi fi fi done EXECUTION="${HOST_MPIRUN_COMMAND} -pgmmodel mpmd -cmdfile ./run_file" IGCM_sys_Chmod u+x run_file if ( $DEBUG_sys ) ; then echo "run_file contains : " cat run_file fi # Only one executable (SPMD mode). else for comp in ${config_ListOfComponents[*]} ; do # Only if we really have an executable for the component : eval ExeNameOut=\${config_Executable_${comp}[1]} if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then EXECUTION="${HOST_MPIRUN_COMMAND} ./${ExeNameOut}" fi done fi IGCM_debug_Print 1 "sys iitm : execution command is" IGCM_debug_Print 1 "$EXECUTION" IGCM_debug_PopStack "IGCM_sys_build_execution_scripts" } #D-#================================================== #D-function IGCM_sys_check_path #D-* Purpose: check that RUN_DIR_PATH that will be removed on some machine #D-* do not point to an important use directory. Stop immediately in that case. #D-* Examples: #D- function IGCM_sys_check_path { IGCM_debug_PushStack "IGCM_sys_check_path" if ( $DEBUG_sys ) ; then echo "IGCM_sys_check_path" fi if ( [ X${RUN_DIR_PATH} = X${HOME} ] || [ X${RUN_DIR_PATH} = X${WORKDIR} ] || [ X${RUN_DIR_PATH} = X${ARCHIVE} ] ) ; then IGCM_debug_Print 1 "Variable RUN_DIR_PATH is pointing to an important directory : ${RUN_DIR_PATH}" IGCM_debug_Print 1 "Please check the RUN_DIR_PATH definition in your Job : Job_${config_UserChoices_JobName}" IGCM_debug_Exit "This will stop the job" fi IGCM_debug_PopStack "IGCM_sys_check_path" } #D-#================================================== #D-function IGCM_sys_check_quota. Dummy call here #D-* Purpose: check user quota. Stop the simulation if quota above 90% #D-* Examples: #D- function IGCM_sys_check_quota { IGCM_debug_PushStack "IGCM_sys_check_quota" if ( $DEBUG_sys ) ; then echo "IGCM_sys_check_quota" fi IGCM_debug_PopStack "IGCM_sys_check_quota" } #D-#================================================== #D-function IGCM_sys_CountJobInQueue #D-* Purpose: Count number of users job #D-* Examples: IGCM_sys_CountJobInQueue ${JobName} NbRun #D- function IGCM_sys_CountJobInQueue { IGCM_debug_PushStack "IGCM_sys_CountJobInQueue" if ( $DEBUG_sys ) ; then echo "IGCM_sys_CountJobInQueue" fi # Print only the full (-W) JobName (%jn) NbRun=$( llq -W -f %jn | grep -c "$1" ) eval ${2}=${NbRun} IGCM_debug_PopStack "IGCM_sys_CountJobInQueue" }