#!/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 Vargas #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 -r MASTER=vargas #D- #D-#================================================== #D-Program used in libIGCM #D-#================================================== # rsync with path typeset -r RSYNC=/usr/local/bin/rsync # RSYNC_opt args to rsync typeset -r RSYNC_opt="-va" # ie storage filesystem typeset -r STOREHOST=gaya.idris.fr typeset -r REMOTE_RSYNC=/u/rech/ces/rces452/RSYNC/bin/rsync #==================================================== # Host specific DIRECTORIES #==================================================== #==================================================== #- R_EXE (==> BIN_DIR = ${MODIPSL}/bin ) typeset -r R_EXE="${MODIPSL}/bin" #==================================================== #- SUBMIT_DIR : submission dir typeset SUBMIT_DIR=${SUBMIT_DIR:=${LOADL_STEP_INITDIR}} #==================================================== #- ARCHIVE typeset -r ARCHIVE=$( echo ${HOME} | sed -e "s/homegpfs/u/" ) #==================================================== #- Mirror libIGCM from vargas to ulam typeset -r MirrorlibIGCM=${MirrorlibIGCM:=true} #==================================================== #- libIGCM_POST PATHlibIGCM=$( echo ${libIGCM} | gawk -F"${LOGIN}/" '{print $2}' | sed -e "s&/libIGCM&&" ) typeset -r HOME_POST=$( echo ${HOME} | sed -e "s/homegpfs/home/" ) typeset -r libIGCM_POST=${HOME_POST}/MIRROR/${PATHlibIGCM}/libIGCM #==================================================== #- IN typeset -r R_IN=${R_IN:=/u/rech/psl/rpsl035/IGCM} typeset -r R_IN_ECMWF=${R_IN_ECMWF:=/u/rech/psl/rpsl376} #==================================================== #- OUT typeset -r R_OUT=${ARCHIVE}/IGCM_OUT #==================================================== #- R_BUF Buffer to pack files typeset -r R_BUF=${WORKDIR}/IGCM_OUT #==================================================== #- OUT_POST typeset -r R_OUT_POST=$( echo ${HOME} | sed -e "s/homegpfs/workdir/" )/IGCM_OUT #==================================================== #- RUN_DIR_PATH : Temporary working directory (=> TMP) typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=${TMPDIR}} #==================================================== #- BIG_DIR : BIG_DIR to store files waiting for rebuild typeset -r BIG_DIR=${BIG_DIR:=${WORKDIR}/REBUILD} #==================================================== #- HOST_MPIRUN_COMMAND typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="time poe"} #==================================================== #- Max number of arguments passed to nco operator or demigration command UNIX_MAX_LIMIT=120 #==================================================== #- Default number of MPI task for IPSL coupled model #- required for backward compatibility #- DEFAULT_NUM_PROC_OCE=5 DEFAULT_NUM_PROC_CPL=1 [ X${BATCH_NUM_PROC_TOT} = X ] || (( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL )) DEFAULT_NUM_PROC_TOTAL=${BATCH_NUM_PROC_TOT} #D-#================================================== #D-function IGCM_sys_RshMaster #D-* Purpose: Connection to frontend machine. #D-* Examples: #D- (( RshMNum = 0 )) function IGCM_sys_RshMaster { IGCM_debug_PushStack "IGCM_sys_RshMaster" $@ typeset THEFILE OUTFILE ERR RshDIR=${WORKDIR}/RUN_DIR/${config_UserChoices_TagName}/${config_UserChoices_JobName}.${$} if [ ! -d ${RshDIR} ] ; then IGCM_sys_Mkdir ${RshDIR} fi THEFILE=${RshDIR}/file_sys_RshMaster_$$_${RshMNum} echo '#!/bin/ksh' > ${THEFILE} echo "export libIGCM=${libIGCM} > /dev/null 2>&1" >> ${THEFILE} echo "export DEBUG_debug=${DEBUG_debug} > /dev/null 2>&1" >> ${THEFILE} echo ". ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh > /dev/null 2>&1" >> ${THEFILE} echo ". ${libIGCM}/libIGCM_card/libIGCM_card.ksh > /dev/null 2>&1" >> ${THEFILE} echo "${@} " >> ${THEFILE} # No frontend queue on brodie : just rsh the job on the frontend with submission. sed -e "s@IGCM_sys_Qsub\(.*\)@\1@" ${THEFILE} > ${THEFILE}_ chmod u+x ${THEFILE}_ OUTFILE=${RshDIR}/out_RshMaster.$$.${RshMNum} (( RshMNum = RshMNum + 1 )) rsh ${MASTER} 'bash -c "nohup '${THEFILE}'_ > '${OUTFILE}' 2>&1 &"' if [ $? -gt 0 ] ; then echo "IGCM_sys_RshMaster : erreur." IGCM_debug_Exit "IGCM_sys_RshMaster" fi IGCM_debug_PopStack "IGCM_sys_RshMaster" } #D-#================================================== #D-function IGCM_sys_RshArchive #D-* Purpose: Archive rsh command #D-* Examples: #D- function IGCM_sys_RshArchive { IGCM_debug_PushStack "IGCM_sys_RshArchive" $@ rsh ${STOREHOST} exec /bin/ksh <<-EOF ${@} EOF if [ $? -gt 0 ] ; then echo "IGCM_sys_RshArchive : erreur." IGCM_debug_Exit "IGCM_sys_RshArchive" fi IGCM_debug_PopStack "IGCM_sys_RshArchive" } #D-#================================================== #D-function IGCM_sys_RshPost #D-* Purpose: Post-process rsh command #D-* Examples: #D- function IGCM_sys_RshPost { IGCM_debug_PushStack "IGCM_sys_RshPost" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_RshPost :" $@ fi # keep standard input to keep it for postpone if ulam don't answer cat >/tmp/tmp_IGCM_sys_RshPost_$$_${LOGNAME} ## Add submission for old postponed files only if command is a Qsub ## ISITQSUB=0 grep Qsub /tmp/tmp_IGCM_sys_RshPost_$$_${LOGNAME} >/dev/null 2>&1 && ISITQSUB=1 if ( [ ${ISITQSUB} -gt 0 ] ) ; then if [ -d ${SUBMIT_DIR}/POSTPONE ] ; then for postponed_file in ${SUBMIT_DIR}/POSTPONE/* ; do if [ -f ${postponed_file} ] ; then IGCM_debug_Print 2 " submit postponed file : " ${postponed_file} rsh ulam exec /bin/ksh <${postponed_file} if [ $? -eq 0 ] ; then IGCM_sys_Rm ${postponed_file} else IGCM_debug_Print 2 "keep postponed file for an other submission :" ${postponed_file} fi fi done fi fi RETURN=0 # rsh ulam command rsh ulam exec /bin/ksh job_end.mail Dear ${LOGIN}, Simulation ${config_UserChoices_JobName} is ${status} on supercomputer `hostname`. Job started : ${DateBegin} Job ended : ${DateEnd} Output files are available in ${R_SAVE} Script files, Script Outputs and Debug files (if necessary) are available in ${SUBMIT_DIR} END_MAIL if [ ! -z ${config_UserChoices_MailName} ] ; then mailx -s "${config_UserChoices_JobName} ${status}" ${config_UserChoices_MailName} < job_end.mail elif [ -f ~/.forward ] ; then mailx -s "${config_UserChoices_JobName} ${status}" $( cat ~/.forward ) < job_end.mail else mailx -s "${config_UserChoices_JobName} ${status}" ${USER} < job_end.mail fi if [ $? -gt 0 ] ; then echo "IGCM_sys_SendMail : erreur." IGCM_debug_Exit "IGCM_sys_SendMail" fi IGCM_debug_PopStack "IGCM_sys_SendMail" } #D-#================================================== #D-function IGCM_sys_Mkdir #D-* Purpose: Master locale mkdir command #D-* Examples: #D- function IGCM_sys_Mkdir { IGCM_debug_PushStack "IGCM_sys_Mkdir" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Mkdir :" $@ fi if [ ! -d ${1} ]; then \mkdir -p $1 if [ $? -gt 0 ] ; then echo "IGCM_sys_Mkdir : erreur." IGCM_debug_Exit "IGCM_sys_Mkdir" fi fi # vérification : if [ ! -d ${1} ] ; then echo "IGCM_sys_Mkdir : erreur." IGCM_debug_Exit "IGCM_sys_Mkdir" fi IGCM_debug_PopStack "IGCM_sys_Mkdir" } #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 rsh ${STOREHOST} -n mkdir -p $1 if [ $? -gt 0 ] ; then echo "IGCM_sys_MkdirArchive : erreur." IGCM_debug_Exit "IGCM_sys_MkdirArchive" fi IGCM_debug_PopStack "IGCM_sys_MkdirArchive" } #D-#================================================== #D-function IGCM_sys_MkdirWork #D-* Purpose: Mkdir on Work #D-* Examples: #D- function IGCM_sys_MkdirWork { IGCM_debug_PushStack "IGCM_sys_MkdirWork" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_MkdirWork :" $@ fi #- creation de repertoire sur le serveur fichier if [ ! -d ${1} ]; then \mkdir -p $1 if [ $? -gt 0 ] ; then echo "IGCM_sys_MkdirWork : erreur." IGCM_debug_Exit "IGCM_sys_MkdirWork" fi fi IGCM_debug_PopStack "IGCM_sys_MkdirWork" } #D-#================================================== #D-function IGCM_sys_Cd #D-* Purpose: master cd command #D-* Examples: #D- function IGCM_sys_Cd { IGCM_debug_PushStack "IGCM_sys_Cd" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Cd :" $@ fi \cd $1 if [ $? -gt 0 ] ; then echo "IGCM_sys_Cd : erreur." IGCM_debug_Exit "IGCM_sys_Cd" fi IGCM_debug_PopStack "IGCM_sys_Cd" } #D-#================================================== #D-function IGCM_sys_Chmod #D-* Purpose: Chmod #D-* Examples: #D- function IGCM_sys_Chmod { IGCM_debug_PushStack "IGCM_sys_Chmod" -- $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Chmod :" $@ fi if [ $DRYRUN -le 1 ]; then \chmod $@ if [ $? -gt 0 ] ; then echo "IGCM_sys_Chmod : erreur." IGCM_debug_Exit "IGCM_sys_Chmod" fi else ( ${DEBUG_debug} ) && echo "DRYRUN mode = " $DRYRUN >> stack fi IGCM_debug_PopStack "IGCM_sys_Chmod" } #D-#================================================== #D-function IGCM_sys_FileSize #D-* Purpose: Filesize #D-* Examples: #D- function IGCM_sys_FileSize { IGCM_debug_PushStack "IGCM_sys_FileSize" $@ typeset sizeF set +A sizeF -- $( ls -la ${1} ) if [ $? -gt 0 ] ; then IGCM_debug_Exit "IGCM_sys_FileSize" fi eval ${2}=${sizeF[4]} IGCM_debug_PopStack "IGCM_sys_FileSize" } #D-#================================================== #D-function IGCM_sys_TestDir #D-* Purpose: Test Directory that must exists #D-* Examples: #D- function IGCM_sys_TestDir { IGCM_debug_PushStack "IGCM_sys_TestDir" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_TestDir :" $@ fi typeset ExistFlag ExistFlag=$( [ -d $1 ] && echo 0 || echo 1 ) IGCM_debug_PopStack "IGCM_sys_TestDir" return ${ExistFlag} } #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 #D-* always true on vargas. #D-* Examples: #D- function IGCM_sys_IsFileArchived { IGCM_debug_PushStack "IGCM_sys_IsFileArchived" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_IsFileArchived :" $@ fi typeset IsArchivedFlag IsArchivedFlag=$( echo 0 ) 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_TestFileBuffer #D-* Purpose: Test file that must NOT EXISTS on Buffer #D-* Examples: #D- function IGCM_sys_TestFileBuffer { IGCM_debug_PushStack "IGCM_sys_TestFileBuffer" $@ typeset ExistFlag ExistFlag=$( [ -f $1 ] && echo 0 || echo 1 ) IGCM_debug_PopStack "IGCM_sys_TestFileBuffer" 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" $@ IGCM_sys_RshArchive "ls ${@} 2>/dev/null | wc -l" if [ $? -gt 0 ] ; then echo "IGCM_sys_CountFileArchive : erreur." fi IGCM_debug_PopStack "IGCM_sys_CountFileArchive" } #D-#================================================== #D-function IGCM_sys_CountFileBuffer #D-* Purpose: Count files on Scratch filesystem #D-* Examples: #D- function IGCM_sys_CountFileBuffer { IGCM_debug_PushStack "IGCM_sys_CountFileBuffer" $@ ls ${@} 2>/dev/null | wc -l if [ $? -gt 0 ] ; then echo "IGCM_sys_CountFileBuffer : erreur." fi IGCM_debug_PopStack "IGCM_sys_CountFileBuffer" } #D-#================================================== #D-function IGCM_sys_Tree #D-* Purpose: Tree directories with files on ${ARCHIVE} #D-* Examples: IGCM_sys_Tree ${R_IN} ${R_OUT} #D- function IGCM_sys_Tree { IGCM_debug_PushStack "IGCM_sys_Tree" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Tree :" $@ fi \mfls -r $@ IGCM_debug_PopStack "IGCM_sys_Tree" } #D-#================================================== #D-function IGCM_sys_Tar #D-* Purpose: master un-tar command #D-* Examples: #D- function IGCM_sys_Tar { IGCM_debug_PushStack "IGCM_sys_Tar" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Tar :" $@ fi \tar cf $@ if [ $? -gt 0 ] ; then echo "IGCM_sys_Tar : erreur." IGCM_debug_Exit "IGCM_sys_Tar" fi IGCM_debug_PopStack "IGCM_sys_Tar" } #D-#================================================== #D-function IGCM_sys_UnTar #D-* Purpose: master un-tar command #D-* Examples: #D- function IGCM_sys_UnTar { IGCM_debug_PushStack "IGCM_sys_UnTar" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_UnTar :" $@ fi \tar xvf $1 if [ $? -gt 0 ] ; then echo "IGCM_sys_UnTar : erreur." IGCM_debug_Exit "IGCM_sys_UnTar" fi IGCM_debug_PopStack "IGCM_sys_UnTar" } #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 ERROR ERROR=0 if ( $DEBUG_sys ) ; then echo "IGCM_sys_Qsub :" $@ fi # We have to change output/error file [ ${#@} = 1 ] && REP_FOR_JOB=$LOADL_STEP_INITDIR [ ${#@} = 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 { [ ${#@} = 1 ] && ( cd $LOADL_STEP_INITDIR ; /usr/local/bin/llsubmit JOB_FOR_IGCM ; ERROR=$? ; cd - ; ) [ ${#@} = 2 ] && ( cd $2 ; /usr/local/bin/llsubmit JOB_FOR_IGCM ; ERROR=$? ; cd - ; ) } if [ ${ERROR} -gt 0 ] ; then echo "IGCM_sys_Qsub : erreur $@." IGCM_debug_Exit "IGCM_sys_Qsub" fi IGCM_sys_Rm ${REP_FOR_JOB}/JOB_FOR_IGCM 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" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_QsubPost :" $@ fi cd ${POST_DIR} /opt/ibmll/LoadL/full/bin/llsubmit ${libIGCM_POST}/$1.job cd - if [ $? -gt 0 ] ; then echo "IGCM_sys_QsubPost : erreur " $@ IGCM_debug_Exit "IGCM_sys_QsubPost" fi IGCM_debug_PopStack "IGCM_sys_QsubPost" } #D-************************* #D- File transfer functions #D-************************* #D- #D-#================================================== #D-function IGCM_sys_Rsync_out #D-* Purpose: treat return val of rsync #D-* Examples: IGCM_sys_Rsync_out out_RET_rsync #D- Error values and explanations can depend on your system version. function IGCM_sys_Rsync_out { RET=$1 if [ ! $RET ] ; then echo "rsync error !" fi if [ $MYLANG = "fr" ]; then case $RET in 0) return ;; 1) echo "Erreur de rsync ; RERR_SYNTAX : " echo "Erreur de syntaxe ou d'utilisation." return;; 2) echo "Erreur de rsync ; RERR_PROTOCOL : " echo "Incompatibilité de protocole." return;; 3) echo "Erreur de rsync ; RERR_FILESELECT 3" echo "Erreurs lors de la sélection des fichiers d'entrée sortie et" echo "répertoires" return;; 4) echo "Erreur de rsync ; RERR_UNSUPPORTED" echo "Action demandée non supportée : une tentative de manipulation de" echo "fichiers 64-bits sur une plate-forme qui ne les supporte pas a" echo "été faite ; ou une option qui est supportée par le client mais" echo "pas par le serveur a été spécifiée." return;; 10) echo "Erreur de rsync ; RERR_SOCKETIO" echo "Erreur dans le socket d'entrée sortie" return;; 11) echo "Erreur de rsync ; RERR_FILEIO" echo "Erreur d'entrée sortie fichier" return;; 12) echo "Erreur de rsync ; RERR_STREAMIO" echo "Erreur dans flux de donnée du protocole rsync" return;; 13) echo "Erreur de rsync ; RERR_MESSAGEIO" echo "Erreur avec les diagnostics du programme" return;; 14) echo "Erreur de rsync ; RERR_IPC" echo "Erreur dans le code IPC" return;; 20) echo "Erreur de rsync ; RERR_SIGNAL" echo "SIGUSR1 ou SIGINT reçu" return;; 21) echo "Erreur de rsync ; RERR_WAITCHILD" echo "Une erreur retournée par waitpid()" return;; 22) echo "Erreur de rsync ; RERR_MALLOC" echo "Erreur lors de l'allocation des tampons de mémoire de coeur" return;; 23) echo "" echo "Erreur fichier inexistant" return;; 30) echo "Erreur de rsync ; RERR_TIMEOUT" echo "Temps d'attente écoulé dans l'envoi/réception de données" return;; *) echo "Erreur de rsync : code de retour de rsync inconnu :" $RET return;; esac elif [ $MYLANG = "en" ] ; then case $RET in 0) return;; 1) echo "rsync error : Syntax or usage error " return;; 2) echo "rsync error : Protocol incompatibility " return;; 3) echo "rsync error : Errors selecting input/output files, dirs" return;; 4) echo "rsync error : Requested action not supported: an attempt" echo "was made to manipulate 64-bit files on a platform that cannot support" echo "them; or an option was specified that is supported by the client and" echo "not by the server." return;; 5) echo "rsync error : Error starting client-server protocol" return;; 10) echo "rsync error : Error in socket I/O " return;; 11) echo "rsync error : Error in file I/O " return;; 12) echo "rsync error : Error in rsync protocol data stream " return;; 13) echo "rsync error : Errors with program diagnostics " return;; 14) echo "rsync error : Error in IPC code " return;; 20) echo "rsync error : Received SIGUSR1 or SIGINT " return;; 21) echo "rsync error : Some error returned by waitpid() " return;; 22) echo "rsync error : Error allocating core memory buffers " return;; 23) echo "rsync error : Partial transfer due to error" return;; 24) echo "rsync error : Partial transfer due to vanished source files" return;; 30) echo "rsync error : Timeout in data send/receive " return;; *) echo "rsync error : return code of rsync unknown :" $RET return;; esac else echo "unknown language $MYLANG." return fi } #D-#================================================== #D-function IGCM_sys_Miror_libIGCM #D-* Purpose: Mirror libIGCM PATH and lib to ulam #D-* Examples: #D- function IGCM_sys_Mirror_libIGCM { IGCM_debug_PushStack "IGCM_sys_Mirror_libIGCM" if ( $DEBUG_sys ) ; then echo "IGCM_sys_Mirror_libIGCM" fi typeset RET IGCM_sys_RshPost <<-EOF mkdir -p ${HOME_POST}/MIRROR/${PATHlibIGCM} EOF rsh ulam -n hostname > /dev/null 2>&1 RET=$? if [ $RET -eq 0 ] ; then echo ${RSYNC} ${RSYNC_opt} -e "rsh " ${libIGCM} ulam:${HOME_POST}/MIRROR/${PATHlibIGCM} > out_rsync 2>&1 ${RSYNC} ${RSYNC_opt} -e "rsh " ${libIGCM} ulam:${HOME_POST}/MIRROR/${PATHlibIGCM} >> out_rsync 2>&1 RET=$? if [ ${RET} -gt 0 ] ; then echo "IGCM_sys_Mirror_libIGCM Warning : no libIGCM on ulam." cat out_rsync fi IGCM_sys_Rm out_rsync else echo "No POST-TREATMENT avaible because ulam is down." fi IGCM_debug_PopStack "IGCM_sys_Mirror_libIGCM" } #D-#================================================== #D-function IGCM_sys_Cp #D-* Purpose: generic cp #D-* Examples: #D- function IGCM_sys_Cp { IGCM_debug_PushStack "IGCM_sys_Cp" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Cp :" $@ fi typeset RET echo cp $@ > out_rsync 2>&1 \cp $@ >> out_rsync 2>&1 RET=$? if [ ${RET} -gt 0 ] ; then echo "IGCM_sys_Cp : error." cat out_rsync IGCM_debug_Exit "IGCM_sys_Cp" else \rm out_rsync fi IGCM_debug_PopStack "IGCM_sys_Cp" } #D-#================================================== #D-function IGCM_sys_Rm #D-* Purpose: generic rm #D-* Examples: #D- function IGCM_sys_Rm { IGCM_debug_PushStack "IGCM_sys_Rm" -- $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Rm :" $@ fi typeset RET echo rm $@ > out_rsync 2>&1 \rm $@ >> out_rsync 2>&1 RET=$? if [ ${RET} -gt 0 ] ; then echo "IGCM_sys_Rm : error." cat out_rsync IGCM_debug_Exit "IGCM_sys_Rm" else \rm out_rsync fi IGCM_debug_PopStack "IGCM_sys_Rm" } #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 :" $@ echo "Dummy call, let the scheduler do that." fi IGCM_debug_PopStack "IGCM_sys_RmRunDir" } #D-#================================================== #D-function IGCM_sys_Mv #D-* Purpose: generic move #D-* Examples: #D- function IGCM_sys_Mv { IGCM_debug_PushStack "IGCM_sys_Mv" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Mv :" $@ fi if [ $DRYRUN = 0 ]; then typeset RET echo mv $@ > out_rsync 2>&1 \mv $@ >> out_rsync 2>&1 RET=$? if [ ${RET} -gt 0 ] ; then echo "IGCM_sys_Mv : error in mv." cat out_rsync IGCM_debug_Exit "IGCM_sys_Mv" else \rm out_rsync fi else ( ${DEBUG_debug} ) && echo "DRYRUN mode = " $DRYRUN >> stack fi IGCM_debug_PopStack "IGCM_sys_Mv" } #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 RET # Only if we use rsync #IGCM_sys_TestDirArchive $( dirname $2 ) # #USUAL WAY rcp -r $1 ${STOREHOST}:$2 > out_rsync 2>&1 RET=$? if [ ${RET} -gt 0 ] ; then echo "IGCM_sys_Put_Dir : error." cat out_rsync IGCM_debug_Exit "IGCM_sys_Put_Dir" else \rm out_rsync fi else ( ${DEBUG_debug} ) && echo "DRYRUN mode = " $DRYRUN >> stack 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 RET #USUAL WAY rcp -rp ${STOREHOST}:$1 $2 > out_rsync 2>&1 RET=$? if [ ${RET} -gt 0 ] ; then echo "IGCM_sys_Get_Dir : error." cat out_rsync IGCM_debug_Exit "IGCM_sys_Get_Dir" fi else ( ${DEBUG_debug} ) && echo "DRYRUN mode = " $DRYRUN >> stack fi IGCM_debug_PopStack "IGCM_sys_Get_Dir" } #==================================================== #- Call IGCM_sys_Mirror_libIGCM now ! if ( $MirrorlibIGCM ) ; then IGCM_sys_Mirror_libIGCM fi #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 ${1} DOES NOT EXIST ." IGCM_debug_Exit "IGCM_sys_Put_Rest" fi typeset RET # if [ X${JobType} = XRUN ] ; then IGCM_sys_Chmod 444 ${1} fi # # Only if we use rsync #IGCM_sys_MkdirArchive $( dirname $2 ) # #USUAL WAY mfput $1 $2 > out_rsync 2>&1 RET=$? # #RSYNC WITH NETWORK RSH CALL # echo ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${RUN_DIR}/$1 ${STOREHOST}:${2} > out_rsync 2>&1 # ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> out_rsync 2>&1 # #RSYNC WITH NFS USE # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > out_rsync 2>&1 # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> out_rsync 2>&1 # RET=$? # IGCM_sys_Rsync_out $RET # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk out_rsync # (( RET=RET+$? )) if [ ${RET} -gt 0 ] ; then echo "IGCM_sys_Put_Rest : error." cat out_rsync IGCM_debug_Exit "IGCM_sys_Put_Rest" else \rm out_rsync fi else ( ${DEBUG_debug} ) && echo "DRYRUN mode = " $DRYRUN >> stack fi IGCM_debug_PopStack "IGCM_sys_Put_Rest" } #D-#================================================== #D-function IGCM_sys_PutBuffer_Rest #D-* Purpose: Put computied restarts on ${SCRATCHDIR}. #D- File and target directory must exist. #D-* Examples: #D- function IGCM_sys_PutBuffer_Rest { IGCM_debug_PushStack "IGCM_sys_PutBuffer_Rest" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_PutBuffer_Rest :" $@ fi if [ $DRYRUN = 0 ]; then if [ ! -f ${1} ] ; then echo "ERROR : IGCM_sys_PutBuffer_Rest ${1} DOES NOT EXIST ." IGCM_debug_Exit "IGCM_sys_PutBuffer_Rest" fi typeset RET # if [ X${JobType} = XRUN ] ; then IGCM_sys_Chmod 444 ${1} fi # # USUAL WAY \cp $1 $2 > out_rsync 2>&1 RET=$? if [ ${RET} -gt 0 ] ; then echo "IGCM_sys_PutBuffer_Rest : error." cat out_rsync IGCM_debug_Exit "IGCM_sys_PutBuffer_Rest" else \rm out_rsync fi else ( ${DEBUG_debug} ) && echo "DRYRUN mode = " $DRYRUN >> stack fi IGCM_debug_PopStack "IGCM_sys_PutBuffer_Rest" } #D-#================================================== #D-function IGCM_sys_Put_Out #D-* Purpose: Copy a file on $(ARCHIVE) after have 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 if [ $DRYRUN = 0 ]; then if [ ! -f ${1} ] ; then echo "WARNING : IGCM_sys_Put_Out ${1} DOES NOT EXIST ." IGCM_debug_PopStack "IGCM_sys_Put_Out" return 1 fi typeset RET # if [ X${JobType} = XRUN ] ; then if [ X${3} = X ] ; then IGCM_sys_Chmod 444 ${1} fi fi # # Only if we use rsync #IGCM_sys_MkdirArchive $( dirname $2 ) # #USUAL WAY mfput $1 $2 > out_rsync 2>&1 RET=$? # #RSYNC WITH NETWORK RSH CALL # echo ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${RUN_DIR}/$1 ${STOREHOST}:${2} > out_rsync 2>&1 # ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> out_rsync 2>&1 # #RSYNC WITH NFS USE # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > out_rsync 2>&1 # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> out_rsync 2>&1 # RET=$? # IGCM_sys_Rsync_out $RET # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk out_rsync # (( RET=RET+$? )) if [ ${RET} -gt 0 ] ; then echo "IGCM_sys_Put_Out : error." cat out_rsync IGCM_debug_Exit "IGCM_sys_Put_Out" else \rm out_rsync fi IGCM_sys_Rm out_rsync else ( ${DEBUG_debug} ) && echo "DRYRUN mode = " $DRYRUN >> stack fi IGCM_debug_PopStack "IGCM_sys_Put_Out" return 0 } #D-#================================================== #D-function IGCM_sys_PutBuffer_Out #D-* Purpose: Copy a file on ${SCRATCHDIR} after having chmod it in readonly #D-* Examples: #D- function IGCM_sys_PutBuffer_Out { IGCM_debug_PushStack "IGCM_sys_PutBuffer_Out" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_PutBuffer_Out :" $@ fi if [ $DRYRUN = 0 ]; then if [ ! -f ${1} ] ; then echo "WARNING : IGCM_sys_PutBuffer_Out ${1} DOES NOT EXIST ." IGCM_debug_PopStack "IGCM_sys_PutBuffer_Out" return 1 fi # IGCM_sys_Mkdir $( dirname $2 ) # typeset RET if [ X${JobType} = XRUN ] ; then if [ X${3} = X ] ; then IGCM_sys_Chmod 444 ${1} fi fi # # USUAL WAY \cp $1 $2 > out_rsync 2>&1 RET=$? if [ ${RET} -gt 0 ] ; then echo "IGCM_sys_PutBuffer_Out : error." cat out_rsync IGCM_debug_Exit "IGCM_sys_PutBuffer_Out" else \rm out_rsync fi else ( ${DEBUG_debug} ) && echo "DRYRUN mode = " $DRYRUN >> stack fi IGCM_debug_PopStack "IGCM_sys_PutBuffer_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 RET dm_liste ifile target if ( $DEBUG_sys ) ; then echo "IGCM_sys_Get :" $@ fi if [ $DRYRUN -le 2 ]; then if [ X${1} = X'/l' ] ; then # test if the first file is present in the old computation : eval set +A dm_liste \${${2}} else dm_liste=${1} fi eval DEST=\${${#}} # test if the (first) file is present in the old computation : IGCM_sys_TestFileArchive ${dm_liste[0]} RET=$? if [ ${RET} -gt 0 ] ; then echo "IGCM_sys_Get, ERROR : regular file ${dm_liste[0]} DOES NOT EXIST ." IGCM_debug_Exit "IGCM_sys_Get" return fi # SD : dm_liste is not suited for computing job # because we change filename during transfert # dm_liste is better suited for post-treatment #dm_liste=" " #(( ifile=1 )) #while [ $ifile -lt $# ] ; do # dm_liste=$( eval echo ${dm_liste} " "\${${ifile}} ) # (( ifile = ifile + 1 )) #done #DEST=$( eval echo \${${#}} ) #USUAL WAY mfget ${dm_liste[*]} ${DEST} > out_rsync 2>&1 RET=$? # #RSYNC WITH NETWORK RSH CALL # echo ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} > out_rsync 2>&1 # ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} >> out_rsync 2>&1 # #RSYNC WITH NFS USE # echo ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} > out_rsync 2>&1 # ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} >> out_rsync 2>&1 # RET=$? # IGCM_sys_Rsync_out $RET # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk out_rsync # (( RET=RET+$? )) if [ ${RET} -gt 0 ] ; then echo "IGCM_sys_Get : copy error." cat out_rsync IGCM_debug_Exit "IGCM_sys_Get" else \rm out_rsync fi else ( ${DEBUG_debug} ) && echo "DRYRUN mode = " $DRYRUN >> stack fi IGCM_debug_PopStack "IGCM_sys_Get" } #D-#================================================== #D-function IGCM_sys_GetBuffer #D-* Purpose: Get a file from ${SCRATCHDIR} #D-* Examples: IGCM_sys_GetBuffer myfile /destpath/myfile_with_PREFIX #D- IGCM_sys_GetBuffer /l Array_contain_myfiles /destpath/ function IGCM_sys_GetBuffer { IGCM_debug_PushStack "IGCM_sys_GetBuffer" $@ typeset DEST RET buf_liste ifile target file_work if ( $DEBUG_sys ) ; then echo "IGCM_sys_GetBuffer :" $@ fi if [ $DRYRUN -le 2 ]; then if [ X${1} = X'/l' ] ; then # test if the first file is present in the old computation : eval set +A buf_liste \${${2}} else eval set +A buf_liste ${1} fi eval DEST=\${${#}} #USUAL WAY if [ X${1} = X'/l' ] ; then (( RET=0 )) for target in ${buf_liste[*]} ; do local_file=$( basename ${target} ) \cp ${target} ${DEST}/${local_file} >> out_rsync 2>&1 (( RET = RET + $? )) done else \cp ${buf_liste} ${DEST} >> out_rsync 2>&1 RET=$? fi if [ ${RET} -gt 0 ] ; then echo "IGCM_sys_GetBuffer : copy error." cat out_rsync IGCM_debug_Exit "IGCM_sys_GetBuffer" else \rm out_rsync fi else ( ${DEBUG_debug} ) && echo "DRYRUN mode = " $DRYRUN >> stack fi IGCM_debug_PopStack "IGCM_sys_GetBuffer" } ############################################################## A FINIR !! #D-#================================================== #D-function IGCM_sys_GetDate_FichWork #D-* Purpose: donne la date filesys d'un fichier sur le filesystem WORK #D-* Examples: #D- function IGCM_sys_GetDate_FichWork { IGCM_debug_PushStack "IGCM_sys_FichWork" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_GetDate_FichWork :" $@ fi typeset dateF set +A dateF -- $( rsh ${MASTER} -n /opt/freeware/bin/ls -l --full-time --time-style='+%Y%m%d%H%M%S' ${1} ) eval ${2}=${dateF[5]} # donne la date filesys d'un fichier sur la machine work IGCM_debug_PopStack "IGCM_sys_FichWork" } #D-#================================================== #D-function IGCM_sys_GetDate_FichArchive #D-* Purpose: donne la date filesys d'un fichier sur le filesystem ARCHIVE #D-* Examples: #D- function IGCM_sys_GetDate_FichArchive { IGCM_debug_PushStack "IGCM_sys_FichArchive" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_GetDate_FichArchive :" $@ fi typeset dateF set +A dateF -- $( rsh ${STOREHOST} -n ls -l --full-time --time-style='+%Y%m%d%H%M%S' ${1} ) eval ${2}=${dateF[5]} IGCM_debug_PopStack "IGCM_sys_FichArchive" } ############################################################## # REBUILD OPERATOR function IGCM_sys_rebuild { IGCM_debug_PushStack "IGCM_sys_rebuild" -- $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_rebuild :" $@ fi /homegpfs/rech/psl/rpsl035/bin/rebuild -f -o $@ if [ $? -gt 0 ] ; then echo "IGCM_sys_rebuild : erreur ${@}." IGCM_debug_Exit "rebuild" fi IGCM_debug_PopStack "IGCM_sys_rebuild" } function IGCM_sys_rebuild_station { IGCM_debug_PushStack "IGCM_sys_rebuild_station" -- $@ typeset i list_opt file_in file_out prefix_invert list_invert if ( $DEBUG_sys ) ; then echo "IGCM_sys_rebuild_station :" $@ fi list_opt=$@ # Invert Axis : t,x -> x,t # t,pres,x -> x,t,pres # So that we can concatenate along x i=0 for file_in in ${list_opt} ; do (( i = i + 1)) [ ${i} = 1 ] && file_out=${file_in} && continue prefix_invert=$( basename ${file_in} .nc ) IGCM_sys_ncpdq -a x,time_counter -a x,time_counter,presnivs ${file_in} ${prefix_invert}_xt.nc list_invert[${#list_invert[*]}]=${prefix_invert}_xt.nc done # Concatenate IGCM_sys_ncrcat ${list_invert[*]} histstn_xt.nc # Re-ivert file IGCM_sys_ncpdq -a time_counter,x -a time_counter,presnivs,x histstn_xt.nc ${file_out} # Station re-ordering is too expansive to be run within libICGM # This is due to (ncpdq - nrcat - ncpdq) I/O sequence. # This re-ordering must be done "in memory" by the cmorization process # Anyway this is the best sequence using (ncpdq - nrcat - ncpdq) # BEGIN reordering # Only LMDZ text output contains the exact ordering of the station. # We isolate this in the code below: # 0 38 -157.5000000000000 70.98591549295774 # 0 54 27.49999999999999 67.18309859154928 # 0 56 -62.50000000000001 82.39436619718309 # 0 79 12.49999999999999 78.59154929577466 # 0 116 -165.0000000000000 76.05633802816901 # 0 117 130.0000000000000 70.98591549295774 # 0 118 110.0000000000000 87.46478873239437 # 1 40 4.999999999999995 51.97183098591550 # typeset iStation iProc list_opt file_in file_out prefix_invert # typeset -Z4 j4 # typeset -Z3 j3 # unset list_opt # set +A list_opt $@ # Filename after rebuild # file_out=${list_opt[0]} # Prefix of output files # prefix_invert=$( basename ${file_out} .nc ) # Number of procs # num_proc=$( grep -i mpi_size ${PREFIX}_${Exe_Output} | wc -l ) # iProc=0 # while [ ${iProc} -lt ${num_proc} ] ; do # Array containing Station as a number # unset proc_stn # set +A proc_stn $( grep "iophy_mpi rank ip lon lat $iProc" ${PREFIX}_${Exe_Output} | sed -e "s/iophy_mpi rank ip lon lat //g" | awk ' {print $2}' ) # Number of stations produced by processor proc # stationLast=${#proc_stn[*]} # Proc number on 4 digits # j4=${iProc} # Init # iStation=0 # while [ ${iStation} -lt ${stationLast} ] ; do # Station number on 3 digits # j3=${proc_stn[${iStation}]} # Extract station # Invert Axis : t,x -> x,t # t,pres,x -> x,t,pres # So that we can concatenate along x # IGCM_sys_ncpdq -a x,time_counter -a x,time_counter,presnivs -d x,$iStation,$iStation ${prefix_invert}_${j4}.nc ${prefix_invert}_stn_${j3}.nc # (( iStation = iStation + 1 )) # done # (( iProc = iProc + 1 )) # done # Concatenate all station along x # IGCM_sys_ncrcat ${prefix_invert}_stn_???.nc ${prefix_invert}_xt.nc # Re-invert file # IGCM_sys_ncpdq -a time_counter,x -a time_counter,presnivs,x ${prefix_invert}_xt.nc ${file_out} # END reordering IGCM_debug_PopStack "IGCM_sys_rebuild_station" } ############################################################ # Activate Running Environnment Variables function IGCM_sys_activ_variables { IGCM_debug_PushStack "IGCM_sys_activ_variables" if ( $DEBUG_sys ) ; then echo "IGCM_sys_activ_variables " fi # -------------------------------------------------------------------- #D- OpenMP thread memory specifications : only one time # -------------------------------------------------------------------- echo $XLSMPOPTS | grep stack=524288000 1>/dev/null 2>&1 || export XLSMPOPTS=$XLSMPOPTS:stack=524288000 # -------------------------------------------------------------------- #D- Other specifications # -------------------------------------------------------------------- IGCM_debug_PopStack "IGCM_sys_activ_variables" } ############################################################ # Desactivate Running Environnment Variables 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" } ############################################################ # Build MPI/OMP scripts 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_vargas 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 else # Only one executable. launch it. for comp in ${config_ListOfComponents[*]} ; do eval ExeNameIn=\${config_Executable_${comp}[0]} eval ExeNameOut=\${config_Executable_${comp}[1]} if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then EXECUTION="time ./${ExeNameOut}" fi done fi IGCM_debug_Print 1 "sys vargas : execution command is " IGCM_debug_Print 1 "$EXECUTION" IGCM_debug_PopStack "IGCM_sys_build_execution_scripts" } function IGCM_sys_build_run_file { IGCM_debug_Print 3 " dummy function : IGCM_sys_build_run_file " } ############################################################ # Check of space available on temporary filesytems function IGCM_sys_check_quota { IGCM_debug_PushStack "IGCM_sys_check_quota" if ( $DEBUG_sys ) ; then echo "IGCM_sys_check_quota " fi # Limit of quota (in %) limit_quota=90 # Check of the volume volume_quota=$(quota_u -w | grep 'Quota soft' | awk '{print $5}') if [ ! X${volume_quota} = X ] ; then quota_volume=${volume_quota%%\%} # echo $quota_volume if [ ${quota_volume} -ge ${limit_quota} ] ; then IGCM_debug_Print 1 "Please, check your quota of volume on workgpfs" IGCM_debug_Print 1 "${quota_volume}% of your quota is used" IGCM_debug_Print 1 "Use the quota_u -w command to check" IGCM_debug_Print 1 "You must have more than 10% available to run" IGCM_debug_Exit "Not enough space to run ! STOP HERE" IGCM_debug_Verif_Exit fi fi IGCM_debug_PopStack "IGCM_sys_check_quota" }