#!/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 Ada #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 )} # $hostname of the MASTER job typeset MASTER=ada #D- #D-#================================================== #D-Program used in libIGCM #D-#================================================== # Submit command typeset SUBMIT=${SUBMIT:=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=gaya typeset -r STOREHOST=ergon typeset -r REMOTE_RSYNC=/u/rech/ces/rces452/RSYNC/bin/rsync #==================================================== # Source default environment #==================================================== ##. /etc/profile #==================================================== # Set environment tools (ferret, nco, cdo) #==================================================== source /smplocal/pub/Modules/default/init/ksh . /smphome/rech/psl/rpsl035/.atlas_env_ada_bash > /dev/null 2>&1 export PATH=${PATH}:/smphome/rech/psl/rpsl035/AddNoise/src_X64_ADA/bin export PATH=${PATH}:/smphome/rech/psl/rpsl035/AddPerturbation/src_X64_ADA/bin #==================================================== # 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 -x SUBMIT_DIR=${SUBMIT_DIR:=${LOADL_STEP_INITDIR}} #==================================================== #- IN typeset -r R_IN=${R_IN:=/workgpfs/rech/psl/rpsl035/IGCM} typeset -r R_IN_ECMWF=${R_IN_ECMWF:=/u/rech/psl/rpsl376} #==================================================== #- RUN_DIR_PATH : Temporary working directory (=> TMP) typeset -r RUN_DIR_PATH=${RUN_DIR_PATH:=${TMPDIR}} #==================================================== #- HOST_MPIRUN_COMMAND typeset -r HOST_MPIRUN_COMMAND=${HOST_MPIRUN_COMMAND:="/usr/bin/time poe"} #==================================================== #- Max number of arguments passed to nco operator or demigration command UNIX_MAX_LIMIT=360 #==================================================== #- set PackDefault true on ada PackDefault=true #==================================================== #- Number of core per node (max number of OpenMP task) NUM_COREPERNODE=8 #==================================================== #- Default number of MPI task for IPSL coupled model #- required for backward compatibility #- DEFAULT_NUM_PROC_OCE=5 DEFAULT_NUM_PROC_CPL=1 (( DEFAULT_NUM_PROC_ATM = BATCH_NUM_PROC_TOT - DEFAULT_NUM_PROC_OCE - DEFAULT_NUM_PROC_CPL )) DEFAULT_NUM_PROC_TOTAL=${BATCH_NUM_PROC_TOT} #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 SCRATCHDIR hosting files waiting for rebuild or pack processes #D-* if SpaceName=TEST everything is stored on WORKDIR #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 ${HOME} | sed -e "s,/.*home/,/arch/home/,") fi if [ ! X${config_UserChoices_STORAGE} = X ]; then #==================================================== #- STORAGE (dedicated to small/medium files) STORAGE=${config_UserChoices_STORAGE} else #==================================================== #- STORAGE (dedicated to small/medium files) STORAGE=${WORKDIR} fi if [ X${config_UserChoices_SpaceName} = XTEST ]; then #==================================================== #- R_OUT R_OUT=${WORKDIR}/IGCM_OUT #==================================================== #- R_FIG (hosting figures : monitoring and atlas, and/or small files) R_FIG=${WORKDIR}/IGCM_OUT IGCM_debug_Print 1 "SpaceName=TEST ==> OVERRULE destination path directories" else #==================================================== #- R_OUT R_OUT=${ARCHIVE}/IGCM_OUT #==================================================== #- R_FIG (hosting figures : monitoring and atlas, and/or small files) R_FIG=${ARCHIVE}/IGCM_OUT fi #==================================================== #- R_BUF (ONLY FOR double copy an scratch) R_BUF=${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_RshMaster #D-* Purpose: Connection to frontend machine. #D-* Examples: #D- function IGCM_sys_RshMaster { IGCM_debug_PushStack "IGCM_sys_RshMaster" $@ /bin/ksh <<-EOF export libIGCM=${libIGCM} export DEBUG_debug=${DEBUG_debug} . ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh . ${libIGCM}/libIGCM_card/libIGCM_card.ksh ${@} EOF 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" $@ typeset ergonCount gayaCount DEBUG_sys=false IGCM_sys_IsFileArchived "$@" if [ $? = 0 ] ; then status=0 #special case for the find command. Only used together with RshArchive to find tared restart if [ "X$( echo $@ | grep ^find | grep RESTART )" != "X" ] ; then # Ergon first rsh ${STOREHOST} exec /bin/ksh <<-EOF > ergonList.txt ${@} EOF (( status=status + $? )) # Gaya turn rsh gaya exec /bin/ksh <<-EOF > gayaList.txt ${@} EOF (( status=status + $? )) # the more the better ergonCount=$( cat ergonList.txt | wc -l ) gayaCount=$( cat gayaList.txt | wc -l ) [ ${ergonCount} -ge ${gayaCount} ] && cat ergonList.txt || cat gayaList.txt rm -f ergonList.txt gayaList.txt else rsh ${STOREHOST} exec /bin/ksh <<-EOF ${@} EOF status=$? fi else /bin/ksh <<-EOF ${@} EOF status=$? fi if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_RshArchive : rsh or 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" $@ DEBUG_sys=false IGCM_sys_IsFileArchived "$@" if [ $? = 0 ] ; then rsh ${STOREHOST} exec /bin/ksh <<-EOF ${@} 2> /dev/null EOF else /bin/ksh <<-EOF ${@} 2> /dev/null EOF fi IGCM_debug_PopStack "IGCM_sys_RshArchive_NoError" } #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 (stdin) for the loop onto temporary file cat >/tmp/tmp_IGCM_sys_RshPost_$$_${LOGNAME} /bin/ksh > mail.txt ; done < ${libIGCM}/libIGCM_sys/${mailText} if [ ! -z ${config_UserChoices_MailName} ] ; then mail -s "${config_UserChoices_JobName} ${status}" ${config_UserChoices_MailName} < mail.txt elif [ -f ~/.forward ] ; then mail -s "${config_UserChoices_JobName} ${status}" $( cat ~/.forward ) < mail.txt else mail -s "${config_UserChoices_JobName} ${status}" ${USER} < mail.txt fi sleep 10 rm -f mail.txt 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 DEBUG_sys=false IGCM_sys_IsFileArchived $1 if [ $? = 0 ] ; then rsh ${STOREHOST} -n mkdir -p $1 status=$? else mkdir -p $1 status=$? fi if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_MkdirArchive : rsh or mkdir failed error code ${status}" 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 \chmod $@ if [ $? -gt 0 ] ; then echo "IGCM_sys_Chmod : erreur." IGCM_debug_Exit "IGCM_sys_Chmod" 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 #Command depends on targeted file system DEBUG_sys=false IGCM_sys_IsFileArchived $1 if [ $? = 0 ] ; then ExistFlag=$( IGCM_sys_RshArchive "[ -d $1 ] && echo 0 || echo 1" ) else ExistFlag=$( [ -d $1 ] && echo 0 || echo 1 ) fi 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 ^\/u\/ )" != "X" ] || [ "X$( echo $@ | grep ^\/\arch\/home )" != "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 TempCommandFile # TempCommandFile="[ -f $1 ] && echo 0 || echo 1" # #Command depends on targeted file system # #We want it quiet # DEBUG_sys=false IGCM_sys_IsFileArchived $1 # if [ $? = 0 ] ; then # ExistFlag=$( IGCM_sys_RshArchive ${TempCommandFile} ) # else # ExistFlag=$( ${TempCommandFile} ) # fi # IGCM_debug_PopStack "IGCM_sys_TestFileArchive" # # return ${ExistFlag} #} #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 finalPosition DEBUG_sys=false IGCM_sys_IsFileArchived $1 if [ $? = 0 ] ; then finalPosition=$( mfls $1 2>/dev/null | wc -l ) [ ${finalPosition} -eq 4 ] && ExistFlag=1 || ExistFlag=0 else ExistFlag=$( [ -f $1 ] && echo 0 || echo 1 ) fi 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" $@ # #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_CountFileArchive #D-* Purpose: Count files on Archive filesystem #D-* Examples: #D- function IGCM_sys_CountFileArchive { IGCM_debug_PushStack "IGCM_sys_CountFileArchive" $@ typeset status gayaPosition ergonPosition finalPosition gayaCount ergonCount #Command depends on targeted file system DEBUG_sys=false IGCM_sys_IsFileArchived $1 if [ $? = 0 ] ; then status=0 gayaPosition=$( mfls ${@} 2>/dev/null | grep -n "++ Gaya" | awk -F\: {'print $1'} ) (( status=status + $? )) ergonPosition=$( mfls ${@} 2>/dev/null | grep -n "++ Ergon" | awk -F\: {'print $1'} ) (( status=status + $? )) finalPosition=$( mfls ${@} 2>/dev/null | wc -l ) (( status=status + $? )) (( gayaCount = ergonPosition - gayaPosition - 2 )) (( ergonCount = finalPosition - ergonPosition )) # return number of files found. greater the better [ ${ergonCount} -ge ${gayaCount} ] && echo ${ergonCount} || echo ${gayaCount} # "Ergon only" case #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_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 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 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/bin/llsubmit JOB_FOR_IGCM > /tmp/out_command.$$ 2>&1 ; status=$? ; cd - ; cat /tmp/out_command.$$ if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_Qsub $1 : error code ${status}" IGCM_debug_Exit "IGCM_sys_Qsub" else JobID=$( gawk {'print $4'} /tmp/out_command.$$ | 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_$$ cd $REP_FOR_JOB ; /usr/bin/llsubmit JOB_FOR_IGCM_$$ > /tmp/out_command.$$ 2>&1 ; status=$? ; cd - ; cat /tmp/out_command.$$ 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'} /tmp/out_command.$$ | tail -1 | sed -e s/\"//g ) IGCM_sys_Rm ${REP_FOR_JOB}/JOB_FOR_IGCM_$$ fi IGCM_debug_PopStack "IGCM_sys_QsubPost" } #D-************************* #D- File transfer functions #D-************************* #D- #D-#================================================== #D-function IGCM_sys_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 { status=$1 if [ ! $status ] ; then echo "rsync error !" fi if [ $MYLANG = "fr" ]; then case $status 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 :" $status return;; esac elif [ $MYLANG = "en" ] ; then case $status 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 :" $status return;; esac else echo "unknown language $MYLANG." return fi } #D-#================================================== #D-function IGCM_sys_Miror_libIGCM #D-* Purpose: Mirror libIGCM PATH and lib to frontend #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 status mkdir -p ${HOME}/MIRROR/${PATHlibIGCM} echo ${RSYNC} ${RSYNC_opt} ${libIGCM} ${HOME}/MIRROR/${PATHlibIGCM} > /tmp/out_command.$$ 2>&1 ${RSYNC} ${RSYNC_opt} ${libIGCM} ${HOME}/MIRROR/${PATHlibIGCM} >> /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then echo "IGCM_sys_Mirror_libIGCM Warning : no libIGCM on frontend." cat /tmp/out_command.$$ fi IGCM_debug_PopStack "IGCM_sys_Mirror_libIGCM" } #D-#================================================== #D-function IGCM_sys_Cp #D-* Purpose: generic cp #D-* Examples: #D- function IGCM_sys_Cp { IGCM_debug_PushStack "IGCM_sys_Cp" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Cp :" $@ fi typeset status echo cp $@ > /tmp/out_command.$$ 2>&1 \cp $@ >> /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then echo "IGCM_sys_Cp : error code ${status}" cat /tmp/out_command.$$ IGCM_debug_Exit "IGCM_sys_Cp" else \rm /tmp/out_command.$$ fi IGCM_debug_PopStack "IGCM_sys_Cp" } #D-#================================================== #D-function IGCM_sys_Rm #D-* Purpose: generic rm #D-* Examples: #D- function IGCM_sys_Rm { IGCM_debug_PushStack "IGCM_sys_Rm" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Rm :" $@ fi typeset status echo rm $@ > /tmp/out_command.$$ 2>&1 \rm $@ >> /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then echo "IGCM_sys_Rm : error code ${status}" cat /tmp/out_command.$$ IGCM_debug_Exit "IGCM_sys_Rm" else \rm /tmp/out_command.$$ fi IGCM_debug_PopStack "IGCM_sys_Rm" } #D-#================================================== #D-function IGCM_sys_RmRunDir #D-* Purpose: rm tmpdir (dummy function most of the time batch #D- scheduler will do the job) #D-* Examples: #D- function IGCM_sys_RmRunDir { IGCM_debug_PushStack "IGCM_sys_RmRunDir" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_RmRunDir :" $@ echo "Dummy call, let the scheduler do that." fi IGCM_debug_PopStack "IGCM_sys_RmRunDir" } #D-#================================================== #D-function IGCM_sys_Mv #D-* Purpose: generic move #D-* Examples: #D- function IGCM_sys_Mv { IGCM_debug_PushStack "IGCM_sys_Mv" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Mv :" $@ fi if [ $DRYRUN = 0 ]; then typeset status echo mv $@ > /tmp/out_command.$$ 2>&1 \mv $@ >> /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then echo "IGCM_sys_Mv : error code ${status}" cat /tmp/out_command.$$ IGCM_debug_Exit "IGCM_sys_Mv" else \rm /tmp/out_command.$$ fi fi IGCM_debug_PopStack "IGCM_sys_Mv" } #D-#================================================== #D-function IGCM_sys_Put_Dir #D-* Purpose: Copy a complete directory on $(ARCHIVE) #D-* Examples: #D- function IGCM_sys_Put_Dir { IGCM_debug_PushStack "IGCM_sys_Put_Dir" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Put_Dir :" $@ fi if [ $DRYRUN = 0 ]; then if [ ! -d ${1} ] ; then echo "WARNING : IGCM_sys_Put_Dir ${1} DOES NOT EXIST ." IGCM_debug_PopStack "IGCM_sys_Put_Dir" return fi typeset status # Only if we use rsync #IGCM_sys_TestDirArchive $( dirname $2 ) # #Command depends on targeted file system DEBUG_sys=false IGCM_sys_IsFileArchived $2 if [ $? = 0 ] ; then \rcp -r $1 ${STOREHOST}:$2 > /tmp/out_command.$$ 2>&1 status=$? else \cp -r $1 $2 > /tmp/out_command.$$ 2>&1 status=$? fi if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_Put_Dir : rcp or cp failed error code ${status}" cat /tmp/out_command.$$ IGCM_debug_Exit "IGCM_sys_Put_Dir" else \rm /tmp/out_command.$$ fi fi IGCM_debug_PopStack "IGCM_sys_Put_Dir" } #D-#================================================== #D-function IGCM_sys_Get_Dir #D-* Purpose: Copy a complete directory from ${ARCHIVE} #D-* Examples: #D- function IGCM_sys_Get_Dir { IGCM_debug_PushStack "IGCM_sys_Get_Dir" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Get_Dir :" $@ fi if [ $DRYRUN = 0 ]; then # if [ ! -d ${1} ] ; then # echo "WARNING : IGCM_sys_Get_Dir ${1} DOES NOT EXIST ." # IGCM_debug_PopStack "IGCM_sys_Get_Dir" # return # fi typeset NB_ESSAI DELAI status i # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 # Only if we use rsync #IGCM_sys_TestDirArchive $( dirname $2 ) # # Command depends on targeted filesystem DEBUG_sys=false IGCM_sys_IsFileArchived $1 if [ $? = 0 ] ; then # add dmget (to demigrate all offline files) to reduce time of this command : #IGCM_sys_RshArchive "dmfind $1 -state MIG -o -state OFL -o -state PAR | dmget -q -n" i=0 while [ $i -lt $NB_ESSAI ] ; do \rcp -rp ${STOREHOST}:$1 $2 > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ]; then IGCM_debug_Print 2 "IGCM_sys_Get_Dir : rcp failed error code ${status} ${i}/${NB_ESSAI}" IGCM_debug_Print 2 "IGCM_sys_Get_Dir : sleep ${DELAI} seconds and try again." sleep $DELAI else break fi (( i = i + 1 )) done else \cp -rp $1 $2 > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_Get_Dir : cp failed error code ${status}" cat /tmp/out_command.$$ IGCM_debug_Exit "IGCM_sys_Get_Dir" else \rm /tmp/out_command.$$ fi fi if [ ${status} -gt 0 ] ; then echo "IGCM_sys_Get_Dir : error." cat /tmp/out_command.$$ IGCM_debug_Exit "IGCM_sys_Get_Dir" else \rm /tmp/out_command.$$ fi fi IGCM_debug_PopStack "IGCM_sys_Get_Dir" } #D-#================================================== #D-function IGCM_sys_Get_Master #D-* Purpose: Copy a complete directory from MASTER filesystem #D-* Examples: #D- function IGCM_sys_Get_Master { IGCM_debug_PushStack "IGCM_sys_Get_Master" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_Get_Master :" $@ fi if [ $DRYRUN = 0 ]; then if ( [ ! -d ${1} ] && [ ! -f ${1} ] ) ; then echo "WARNING : IGCM_sys_Get_Master ${1} DOES NOT EXIST ." IGCM_debug_PopStack "IGCM_sys_Get_Master" return fi typeset NB_ESSAI DELAI status i # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 i=0 while [ $i -lt $NB_ESSAI ] ; do \cp -urL $1 $2 > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ]; then IGCM_debug_Print 2 "IGCM_sys_Get_Master : cp failed error code ${status} ${i}/${NB_ESSAI}" IGCM_debug_Print 2 "IGCM_sys_Get_Master : sleep ${DELAI} seconds and try again." sleep $DELAI else break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_Get_Master : error." cat /tmp/out_command.$$ IGCM_debug_Exit "IGCM_sys_Get_Master" else \rm /tmp/out_command.$$ fi fi IGCM_debug_PopStack "IGCM_sys_Get_Master" } #==================================================== #- 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 ${1} DOES NOT EXIST ." IGCM_debug_Exit "IGCM_sys_Put_Rest" fi typeset status # if [ X${JobType} = XRUN ] ; then IGCM_sys_Chmod 444 ${1} fi # # #Command depends on targeted file system DEBUG_sys=false IGCM_sys_IsFileArchived $2 if [ $? = 0 ] ; then mfput $1 $2 > /tmp/out_command.$$ 2>&1 status=$? else IGCM_sys_MkdirArchive $( dirname $2 ) \cp $1 $2 > /tmp/out_command.$$ 2>&1 status=$? fi # #RSYNC WITH NETWORK RSH CALL # IGCM_sys_MkdirArchive $( dirname $2 ) # echo ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${RUN_DIR}/$1 ${STOREHOST}:${2} > /tmp/out_command.$$ 2>&1 # ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> /tmp/out_command.$$ 2>&1 # #RSYNC WITH NFS USE # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > /tmp/out_command.$$ 2>&1 # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> /tmp/out_command.$$ 2>&1 # status=$? # IGCM_sys_Rsync_out $status # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk /tmp/out_command.$$ # (( status=status+$? )) if [ ${status} -gt 0 ] ; then echo "IGCM_sys_Put_Rest : mfput or cp failed error code ${status}" cat /tmp/out_command.$$ IGCM_debug_Exit "IGCM_sys_Put_Rest" else \rm /tmp/out_command.$$ fi fi IGCM_debug_PopStack "IGCM_sys_Put_Rest" } #D-#================================================== #D-function IGCM_sys_PutBuffer_Rest #D-* Purpose: Put computied restarts on ${SCRATCHDIR}. #D- File and target directory must exist. #D-* Examples: #D- function IGCM_sys_PutBuffer_Rest { IGCM_debug_PushStack "IGCM_sys_PutBuffer_Rest" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_PutBuffer_Rest :" $@ fi if [ $DRYRUN = 0 ]; then if [ ! -f ${1} ] ; then echo "ERROR : IGCM_sys_PutBuffer_Rest ${1} DOES NOT EXIST ." IGCM_debug_Exit "IGCM_sys_PutBuffer_Rest" fi typeset status # if [ X${JobType} = XRUN ] ; then IGCM_sys_Chmod 444 ${1} fi # # USUAL WAY \cp $1 $2 > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then echo "IGCM_sys_PutBuffer_Rest : error code ${status}" [ -f ${2} ] && ls -l ${2} [ -f ${2}/${1} ] && ls -l ${2}/${1} cat /tmp/out_command.$$ IGCM_debug_Exit "IGCM_sys_PutBuffer_Rest" else \rm /tmp/out_command.$$ fi fi IGCM_debug_PopStack "IGCM_sys_PutBuffer_Rest" } #D-#================================================== #D-function IGCM_sys_PrepareTaredRestart #D-* Purpose: Prepare tared restart to be access by computing job. #D-* Examples: #D- function IGCM_sys_PrepareTaredRestart { IGCM_debug_PushStack "IGCM_sys_PrepareTaredRestart" $@ if [ $DRYRUN = 0 ]; then [ ! -f $( basename $1 ) ] && IGCM_sys_Get $1 . fi IGCM_debug_PopStack "IGCM_sys_PrepareTaredRestart" } #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 ${1} DOES NOT EXIST ." IGCM_debug_PopStack "IGCM_sys_Put_Out" return 1 fi # if [ X${JobType} = XRUN ] ; then if [ X${3} = X ] ; then IGCM_sys_Chmod 444 ${1} fi fi # # #Command depends on targeted file system DEBUG_sys=false IGCM_sys_IsFileArchived $2 if [ $? = 0 ] ; then mfput $1 $2 > /tmp/out_command.$$ 2>&1 status=$? else IGCM_sys_MkdirArchive $( dirname $2 ) \cp $1 $2 > /tmp/out_command.$$ 2>&1 status=$? fi # #RSYNC WITH NETWORK RSH CALL # IGCM_sys_MkdirArchive $( dirname $2 ) # echo ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${RUN_DIR}/$1 ${STOREHOST}:${2} > /tmp/out_command.$$ 2>&1 # ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${RUN_DIR}/$1 ${STOREHOST}:${2} >> /tmp/out_command.$$ 2>&1 # #RSYNC WITH NFS USE # echo ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} > /tmp/out_command.$$ 2>&1 # ${RSYNC} ${RSYNC_opt} ${RUN_DIR}/$1 ${2} >> /tmp/out_command.$$ 2>&1 # status=$? # IGCM_sys_Rsync_out $status # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk /tmp/out_command.$$ # (( status=status+$? )) if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_Put_Out : mfput or cp failed error code ${status}" cat /tmp/out_command.$$ IGCM_debug_Exit "IGCM_sys_Put_Out" else \rm /tmp/out_command.$$ fi fi IGCM_debug_PopStack "IGCM_sys_Put_Out" return 0 } #D-#================================================== #D-function IGCM_sys_PutBuffer_Out #D-* Purpose: Copy a file on ${WORKDIR} after having chmod it in readonly #D-* Examples: #D- function IGCM_sys_PutBuffer_Out { IGCM_debug_PushStack "IGCM_sys_PutBuffer_Out" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_PutBuffer_Out :" $@ fi typeset NB_ESSAI DELAI status i exist skip # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 if [ $DRYRUN = 0 ]; then if [ ! -f ${1} ] ; then echo "WARNING : IGCM_sys_PutBuffer_Out ${1} DOES NOT EXIST ." IGCM_debug_PopStack "IGCM_sys_PutBuffer_Out" return 1 fi # IGCM_sys_Mkdir $( dirname $2 ) # exist=false skip=false if [ -f $2 ] ; then IGCM_debug_Print 1 "$2 already exist" exist=true if [ "X$( diff $1 $2 )" = X ] ; then IGCM_debug_Print 2 "$1 and $2 are the same file, we skip the copy" status=0 skip=true else IGCM_debug_Print 2 "$1 and $2 are not the same file, we force the copy" skip=false fi fi # if ( [ X${exist} = Xtrue ] && [ X${skip} = Xfalse ] ) ; then IGCM_sys_Chmod u+w $2 fi if [ X${skip} = Xfalse ] ; then i=0 while [ $i -lt $NB_ESSAI ] ; do # USUAL WAY \cp $1 $2 > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ]; then IGCM_debug_Print 2 "IGCM_sys_PutBuffer_Out : cp failed error code ${status} ${i}/${NB_ESSAI}" IGCM_debug_Print 2 "IGCM_sys_PutBuffer_Out : sleep ${DELAI} seconds and try again." [ -f ${2} ] && ls -l ${2} [ -f ${2}/${1} ] && ls -l ${2}/${1} sleep $DELAI else break fi (( i = i + 1 )) done fi if [ ${status} -gt 0 ] ; then echo "IGCM_sys_PutBuffer_Out : error." [ -f ${2} ] && ls -l ${2} [ -f ${2}/${1} ] && ls -l ${2}/${1} cat /tmp/out_command.$$ IGCM_debug_Exit "IGCM_sys_PutBuffer_Out" else if [ X${JobType} = XRUN ] ; then if [ X${3} = X ] ; then [ -f ${2} ] && IGCM_sys_Chmod 444 ${2} [ -f ${2}/${1} ] && IGCM_sys_Chmod 444 ${2}/${1} fi fi \rm /tmp/out_command.$$ fi 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 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 #Command depends on targeted file system DEBUG_sys=false IGCM_sys_IsFileArchived ${dm_liste[0]} if [ $? = 0 ] ; then mfget ${dm_liste[*]} ${DEST} > /tmp/out_command.$$ 2>&1 status=$? else \cp ${dm_liste[*]} ${DEST} > /tmp/out_command.$$ 2>&1 status=$? fi # #RSYNC WITH NETWORK RSH CALL # echo ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} > /tmp/out_command.$$ 2>&1 # ${RSYNC} ${RSYNC_opt} --rsync-path=${REMOTE_RSYNC} -e rsh ${STOREHOST}:"${dm_liste}" ${STOREHOST}:${RUN_DIR}/${DEST} >> /tmp/out_command.$$ 2>&1 # #RSYNC WITH NFS USE # echo ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} > /tmp/out_command.$$ 2>&1 # ${RSYNC} ${RSYNC_opt} ${dm_liste} ${RUN_DIR}/${DEST} >> /tmp/out_command.$$ 2>&1 # status=$? # IGCM_sys_Rsync_out $status # ${libIGCM}/libIGCM_sys/IGCM_analyse_rsync_out.awk /tmp/out_command.$$ # (( status=status+$? )) if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_Get : mfget or cp failed error code ${status}" cat /tmp/out_command.$$ IGCM_debug_Exit "IGCM_sys_Get" else \rm /tmp/out_command.$$ fi fi IGCM_debug_PopStack "IGCM_sys_Get" } #D-#================================================== #D-function IGCM_sys_GetBuffer #D-* Purpose: Get a file from ${SCRATCHDIR} #D-* Examples: IGCM_sys_GetBuffer myfile /destpath/myfile_with_PREFIX #D- IGCM_sys_GetBuffer /l Array_contain_myfiles /destpath/ function IGCM_sys_GetBuffer { IGCM_debug_PushStack "IGCM_sys_GetBuffer" $@ typeset DEST buf_liste target file_work typeset NB_ESSAI DELAI status i if ( $DEBUG_sys ) ; then echo "IGCM_sys_GetBuffer :" $@ fi # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 if [ $DRYRUN -le 2 ]; then if [ X${1} = X'/l' ] ; then eval set +A buf_liste \${${2}} else eval set +A buf_liste ${1} fi eval DEST=\${${#}} #USUAL WAY if [ X${1} = X'/l' ] ; then for target in ${buf_liste[*]} ; do local_file=$( basename ${target} ) i=0 while [ $i -lt $NB_ESSAI ] ; do \cp ${target} ${DEST}/${local_file} >> /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ]; then IGCM_debug_Print 2 "IGCM_sys_GetBuffer : cp failed error code ${status} ${i}/${NB_ESSAI}" IGCM_debug_Print 2 "IGCM_sys_GetBuffer : sleep ${DELAI} seconds and try again." sleep $DELAI else break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_Get : error" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Exit "IGCM_sys_GetBuffer" else \rm /tmp/out_command.$$ fi done else i=0 while [ $i -lt $NB_ESSAI ] ; do \cp ${buf_liste} ${DEST} >> /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ]; then IGCM_debug_Print 2 "IGCM_sys_GetBuffer : cp failed error code ${status} ${i}/${NB_ESSAI}" IGCM_debug_Print 2 "IGCM_sys_GetBuffer : sleep ${DELAI} seconds and try again." sleep $DELAI else break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_Get : error" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Exit "IGCM_sys_GetBuffer" else \rm /tmp/out_command.$$ fi fi fi IGCM_debug_PopStack "IGCM_sys_GetBuffer" } #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 if [ $# -ge 3 ] ; then mode=$3 TimeStyle=$4 else mode="default" TimeStyle="%Y%m%d%H%M%S" fi typeset dateF set +A dateF -- $( ls -l --full-time --time-style=+"${TimeStyle}" ${1} ) case $mode in "default") eval ${2}=${dateF[5]} ;; "SplitFields") eval ${2}="${dateF[5]}\ ${dateF[6]}" ;; esac # 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" } #D-#================================================== #D-function IGCM_sys_GetDate_Monitoring #D-* Purpose: get the last year for which the monitoring has been computed #D-* Examples: #D- function IGCM_sys_GetDate_Monitoring { IGCM_debug_PushStack "IGCM_sys_GetDate_Monitoring" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_GetDate_Monitoring :" $@ fi IGCM_sys_Cd /tmp IGCM_sys_Get ${1} . eval ${2}=$( cdo showyear $( basename ${1} ) 2> /dev/null | gawk '{ print $NF }' ) IGCM_sys_Cd - IGCM_debug_PopStack "IGCM_sys_GetDate_Monitoring" } #D-#================================================== #D-function IGCM_sys_Put_Dods #D-* Purpose: Put $(ARCHIVE) files on DODS internet protocole. #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 if [ $DRYRUN = 0 ]; then # We take our time on that sleep 10 IGCM_sys_TestDirArchive ${R_SAVE}/${1} if [ $? != 0 ] ; then echo "WARNING : IGCM_sys_Put_Dods ${R_SAVE}/${1} DOES NOT EXIST ." IGCM_debug_PopStack "IGCM_sys_Put_Dods" return fi typeset status # rsh ${STOREHOST} exec /bin/ksh < /dev/null 2>&1 /bin/chmod -R u+w ${R_SAVE}/${1} /arch/local/bin/dods_cp ${1} DODS/pub/${LOGIN}/${R_DODS} > /dev/null 2>&1 /bin/chmod -R +rX ${R_SAVE}/${1} /bin/chmod -R u+w ${R_SAVE}/${1} EOF status=$? if [ ${status} -gt 0 ] ; then echo "IGCM_sys_Put_Dods : error." IGCM_debug_Exit "IGCM_sys_Put_Dods" fi fi IGCM_debug_PopStack "IGCM_sys_Put_Dods" } ############################################################## # REBUILD OPERATOR #D-#================================================== #D-function IGCM_sys_rebuild #D-* Purpose: rebuild parallel files #D-* Examples: #D- function IGCM_sys_rebuild { IGCM_debug_PushStack "IGCM_sys_rebuild" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_rebuild :" $@ fi typeset NB_ESSAI DELAI status i firstArg # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 i=0 while [ $i -lt $NB_ESSAI ] ; do /smphome/rech/psl/rpsl035/bin/rebuild -f -o $@ > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_rebuild : error code ${status}" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Print 2 "IGCM_sys_rebuild : ${i}/${NB_ESSAI} sleep ${DELAI} seconds and try again." firstArg=${1} \rm ${firstArg} sleep $DELAI else \rm /tmp/out_command.$$ break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_rebuild : rebuild error code is ${status}" IGCM_debug_Exit "rebuild" fi IGCM_debug_PopStack "IGCM_sys_rebuild" } #D-#================================================== #D-function IGCM_sys_rebuild_station #D-* Purpose: rebuild parallel files describing station #D-* Examples: #D- 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 # detect time counter and do the job only if present var_unlim=$(ncdump -h ${file_in} | grep UNLIMITED | cut -d ' ' -f 1) if [ X${var_unlim} = Xtime_counter ] ; then 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 fi 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 libIGCM # 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" | gawk ' {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 #D-#================================================== #D-function IGCM_sys_desactiv_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 ( $DEBUG_sys ) ; then echo "IGCM_sys_activ_variables" fi # -------------------------------------------------------------------- #D- MPI specifications # -------------------------------------------------------------------- # -------------------------------------------------------------------- #D- Other specifications # -------------------------------------------------------------------- ulimit -s unlimited ## to be done only one time ## export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/smplocal/pub/NetCDF/4.1.3/lib:/smplocal/pub/HDF5/1.8.9/seq/lib ## echo ${LD_LIBRARY_PATH} | grep -i netcdf >/dev/null 2>&1 || export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/smplocal/pub/NetCDF/4.1.3/lib:/smplocal/pub/HDF5/1.8.9/seq/lib IGCM_debug_Print 1 "set LD_LIBRARY_PATH=${LD_LIBRARY_PATH}" export MP_STDOUTMODE=combined IGCM_debug_Print 1 "set MP_STDOUTMODE=${MP_STDOUTMODE}" ## fix to reduce memory usage. Required since 2014/22/04. On ada IDRIS. export MP_EUILIBPATH=/smplocal/lib/ibmhpc/pe12012/ppe.pami/gnu/lib64/pami64 IGCM_debug_Print 1 "set MP_EUILIBPATH=${MP_EUILIBPATH}" 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" } ############################################################ # 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 " $@ fi EXECUTION=${HOST_MPIRUN_COMMAND} if ( ${OK_PARA_MPMD} ) ; then if [ -f run_file ] ; then IGCM_sys_Rm -f run_file fi touch run_file # 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 ${comp_proc_mpi_loc} ] ; do echo "./${ExeNameOut}" >> run_file (( mpi_count = mpi_count + 1 )) done else echo "./${ExeNameOut} " >> run_file 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 ${comp_proc_mpi_loc} ] ; do echo "./${ExeNameOut}" >> run_file (( mpi_count = mpi_count + 1 )) done else echo "./${ExeNameOut} " >> run_file fi fi done EXECUTION="${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 ${config_ListOfComponents[*]} ; do # Only if we really have an executable for the component : eval ExeNameOut=\${config_Executable_${comp}[1]} if ( [ "X${ExeNameOut}" != X\"\" ] && [ "X${ExeNameOut}" != "Xinca.dat" ] ) ; then if ( ${OK_PARA_OMP} ) ; then eval comp_proc_omp_loc=\${${comp}_PROC_OMP} export KMP_STACKSIZE=200m #export KMP_LIBRARY=turnaround #echo "export KMP_STACKSIZE=3g" >> script_${ExeNameOut}.ksh #echo "export KMP_LIBRARY=turnaround" >> script_${ExeNameOut}.ksh #echo "export MKL_SERIAL=YES" >> script_${ExeNameOut}.ksh fi EXECUTION="${HOST_MPIRUN_COMMAND} ./${ExeNameOut}" fi done fi IGCM_debug_Print 1 "sys ada : execution command is " IGCM_debug_Print 1 "$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 #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 ( $DEBUG_sys ) ; then echo "IGCM_sys_check_quota" fi # Limit of quota (in %) limit_quota=90 # Check of the volume volume_quota=$(quota_u -w 2>/dev/null| grep 'Quota soft' | gawk '{print $5}') if [ ! X${volume_quota} = X ] ; then quota_volume=${volume_quota%%\%} # echo $quota_volume if [ $(echo "${quota_volume} > ${limit_quota}" | bc) -eq 1 ] ; then IGCM_debug_Print 1 "Please, check your quota of volume on workgpfs" IGCM_debug_Print 1 "${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" } #D-#================================================== #D-function IGCM_sys_GetJobID #D-* Purpose: Check if job_name is currently #D- running or in queue #D-* Examples: IGCM_sys_GetJobID ${JobName} NbRun #D- function IGCM_sys_GetJobID { IGCM_debug_PushStack "IGCM_sys_GetJobID" if ( $DEBUG_sys ) ; then echo "IGCM_sys_GetJobID" fi # Print only the full (-W) JobID (%id) and JobName (%jn) ID=$( llq -u $2 -W -f %id %jn | \ gawk -v JobName=$1 '( $NF ~ JobName ) { print $1 }' ) eval ${3}=${ID} IGCM_debug_PopStack "IGCM_sys_GetJobID" } #D-#================================================== #D-function IGCM_sys_CountJobInQueue #D-* Purpose: Check if job_name is currently #D- running or in queue #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" } #D-#================================================== #D-function IGCM_sys_ListJobInQueue #D-* Purpose: Check if job_name is currently #D- running or in queue #D-* Examples: IGCM_sys_ListJobInQueue ${User} JobNameList #D- function IGCM_sys_ListJobInQueue { IGCM_debug_PushStack "IGCM_sys_ListJobInQueue" if ( $DEBUG_sys ) ; then echo "IGCM_sys_ListJobInQueue" fi # With -W option, column width is as large as necessary set -A JobList $( llq -u $1 -W -f %jn | head -n -2 | tail -n +3 | \ gawk '( $1 != /TS/ && \ $1 !~ /PACK/ && \ $1 !~ /REBUILD/ && \ $1 !~ /pack/ ) \ { print $1 }' | sed -e "s/\(.*\)\.[0-9]*/\1/" ) eval set -A ${2} ${JobList[*]} IGCM_debug_PopStack "IGCM_sys_ListJobInQueue" } ############################################################## # NCO OPERATOR #D-#================================================== #D-function IGCM_sys_ncap2 #D-* Purpose: encapsulate ncap2 call so as to manage error code and retry #D-* Examples: #D- function IGCM_sys_ncap2 { IGCM_debug_PushStack "IGCM_sys_ncap2" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_ncap2 :" $@ fi typeset NB_ESSAI DELAI status i # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 i=0 while [ $i -lt $NB_ESSAI ] ; do ncap2 "$@" > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_ncap2 : error code ${status}" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Print 2 "IGCM_sys_ncap2 : ${i}/${NB_ESSAI} sleep ${DELAI} seconds and try again." sleep $DELAI else \rm /tmp/out_command.$$ break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_ncap2 : ncap2 error" IGCM_debug_Exit "ncap2" fi IGCM_debug_PopStack "IGCM_sys_ncap2" } #D-#================================================== #D-function IGCM_sys_ncatted #D-* Purpose: encapsulate ncatted call so as to manage error code and retry #D-* Examples: #D- function IGCM_sys_ncatted { IGCM_debug_PushStack "IGCM_sys_ncatted" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_ncatted :" $@ fi typeset NB_ESSAI DELAI status i # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 i=0 while [ $i -lt $NB_ESSAI ] ; do ncatted "$@" > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_ncatted : error code ${status}" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Print 2 "IGCM_sys_ncatted : ${i}/${NB_ESSAI} sleep ${DELAI} seconds and try again." sleep $DELAI else \rm /tmp/out_command.$$ break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_ncatted : ncatted error" IGCM_debug_Exit "ncatted" fi IGCM_debug_PopStack "IGCM_sys_ncatted" } #D-#================================================== #D-function IGCM_sys_ncbo #D-* Purpose: encapsulate ncbo call so as to manage error code and retry #D-* Examples: #D- function IGCM_sys_ncbo { IGCM_debug_PushStack "IGCM_sys_ncbo" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_ncbo :" $@ fi typeset NB_ESSAI DELAI status i # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 i=0 while [ $i -lt $NB_ESSAI ] ; do ncbo $@ > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_ncbo : error code ${status}" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Print 2 "IGCM_sys_ncbo : ${i}/${NB_ESSAI} sleep ${DELAI} seconds and try again." sleep $DELAI else \rm /tmp/out_command.$$ break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_ncbo : ncbo error" IGCM_debug_Exit "ncbo" fi IGCM_debug_PopStack "IGCM_sys_ncbo" } #D-#================================================== #D-function IGCM_sys_ncdif #D-* Purpose: encapsulate ncdiff call so as to manage error code and retry #D-* Examples: #D- function IGCM_sys_ncdiff { IGCM_debug_PushStack "IGCM_sys_ncdiff" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_ncdiff :" $@ fi typeset NB_ESSAI DELAI status i # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 i=0 while [ $i -lt $NB_ESSAI ] ; do ncdiff $@ > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_ncdiff : error code ${status}" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Print 2 "IGCM_sys_ncdiff : ${i}/${NB_ESSAI} sleep ${DELAI} seconds and try again." sleep $DELAI else \rm /tmp/out_command.$$ break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_ncdiff : ncdiff error" IGCM_debug_Exit "ncdiff" fi IGCM_debug_PopStack "IGCM_sys_ncdiff" } #D-#================================================== #D-function IGCM_sys_ncea #D-* Purpose: encapsulate ncea call so as to manage error code and retry #D-* Examples: #D- function IGCM_sys_ncea { IGCM_debug_PushStack "IGCM_sys_ncea" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_ncea :" $@ fi typeset NB_ESSAI DELAI status i # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 i=0 while [ $i -lt $NB_ESSAI ] ; do ncea $@ > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_ncea : error code ${status}" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Print 2 "IGCM_sys_ncea : ${i}/${NB_ESSAI} sleep ${DELAI} seconds and try again." sleep $DELAI else \rm /tmp/out_command.$$ break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_ncea : ncea error" IGCM_debug_Exit "ncea" fi IGCM_debug_PopStack "IGCM_sys_ncea" } #D-#================================================== #D-function IGCM_sys_ncecat #D-* Purpose: encapsulate ncecat call so as to manage error code and retry #D-* Examples: #D- function IGCM_sys_ncecat { IGCM_debug_PushStack "IGCM_sys_ncecat" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_ncecat :" $@ fi typeset NB_ESSAI DELAI status i # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 i=0 while [ $i -lt $NB_ESSAI ] ; do ncecat $@ > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_ncecat : error code ${status}" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Print 2 "IGCM_sys_ncecat : ${i}/${NB_ESSAI} sleep ${DELAI} seconds and try again." sleep $DELAI else \rm /tmp/out_command.$$ break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_ncecat : ncecat error" IGCM_debug_Exit "ncecat" fi IGCM_debug_PopStack "IGCM_sys_ncecat" } #D-#================================================== #D-function IGCM_sys_ncflint #D-* Purpose: encapsulate ncflint call so as to manage error code and retry #D-* Examples: #D- function IGCM_sys_ncflint { IGCM_debug_PushStack "IGCM_sys_ncflint" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_ncflint :" $@ fi typeset NB_ESSAI DELAI status i # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 i=0 while [ $i -lt $NB_ESSAI ] ; do ncflint $@ > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_ncflint : error code ${status}" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Print 2 "IGCM_sys_ncflint : ${i}/${NB_ESSAI} sleep ${DELAI} seconds and try again." sleep $DELAI else \rm /tmp/out_command.$$ break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_ncflint : ncflint error" IGCM_debug_Exit "ncflint" fi IGCM_debug_PopStack "IGCM_sys_ncflint" } #D-#================================================== #D-function IGCM_sys_ncks #D-* Purpose: encapsulate ncks call so as to manage error code and retry #D-* Examples: #D- function IGCM_sys_ncks { IGCM_debug_PushStack "IGCM_sys_ncks" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_ncks :" $@ fi typeset NB_ESSAI DELAI status i # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 i=0 while [ $i -lt $NB_ESSAI ] ; do ncks $@ > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_ncks : error code ${status}" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Print 2 "IGCM_sys_ncks : ${i}/${NB_ESSAI} sleep ${DELAI} seconds and try again." sleep $DELAI else \rm /tmp/out_command.$$ break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_ncks : ncks error" IGCM_debug_Exit "ncks" fi IGCM_debug_PopStack "IGCM_sys_ncks" } #D-#================================================== #D-function IGCM_sys_ncpdq #D-* Purpose: encapsulate ncpdq call so as to manage error code and retry #D-* Examples: #D- function IGCM_sys_ncpdq { IGCM_debug_PushStack "IGCM_sys_ncpdq" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_ncpdq :" $@ fi typeset NB_ESSAI DELAI status i # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 i=0 while [ $i -lt $NB_ESSAI ] ; do ncpdq $@ > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_ncpdq : error code ${status}" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Print 2 "IGCM_sys_ncpdq : ${i}/${NB_ESSAI} sleep ${DELAI} seconds and try again." sleep $DELAI else \rm /tmp/out_command.$$ break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_ncpdq : ncpdq error" IGCM_debug_Exit "ncpdq" fi IGCM_debug_PopStack "IGCM_sys_ncpdq" } #D-#================================================== #D-function IGCM_sys_ncra #D-* Purpose: encapsulate ncra call so as to manage error code and retry #D-* Examples: #D- function IGCM_sys_ncra { IGCM_debug_PushStack "IGCM_sys_ncra" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_ncra :" $@ fi typeset NB_ESSAI DELAI status i # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 i=0 while [ $i -lt $NB_ESSAI ] ; do ncra $@ > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_ncra : error code ${status}" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Print 2 "IGCM_sys_ncra : ${i}/${NB_ESSAI} sleep ${DELAI} seconds and try again." sleep $DELAI else \rm /tmp/out_command.$$ break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_ncra : ncra error" IGCM_debug_Exit "ncra" fi IGCM_debug_PopStack "IGCM_sys_ncra" } #D-#================================================== #D-function IGCM_sys_ncrcat #D-* Purpose: encapsulate ncrcat call so as to manage error code and retry #D-* Examples: #D- function IGCM_sys_ncrcat { IGCM_debug_PushStack "IGCM_sys_ncrcat" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_ncrcat :" $@ fi typeset NB_ESSAI DELAI status i lastArg # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 i=0 while [ $i -lt $NB_ESSAI ] ; do ncrcat $@ > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_ncrcat : error code ${status}" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Print 2 "IGCM_sys_ncrcat : ${i}/${NB_ESSAI} sleep ${DELAI} seconds and try again." sleep $DELAI elif [ ! "X$( grep "WARNING Intra-file non-monotonicity" /tmp/out_command.$$ )" = "X" ] ; then IGCM_debug_Print 2 "IGCM_sys_ncrcat : WARNING Intra-file non-monotonicity" cat /tmp/out_command.$$ # remove files having corrupted time axis eval lastArg=\${$#} IGCM_debug_Print 2 "IGCM_sys_ncrcat : Delete ${lastArg}" \rm ${lastArg} \rm /tmp/out_command.$$ IGCM_debug_Print 2 "IGCM_sys_ncrcat : ${i}/${NB_ESSAI} sleep ${DELAI} seconds and try again." sleep $DELAI else \rm /tmp/out_command.$$ break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_ncrcat : ncrcat error" #IGCM_debug_Exit "ncrcat" fi IGCM_debug_PopStack "IGCM_sys_ncrcat" } #D-#================================================== #D-function IGCM_sys_ncrename #D-* Purpose: encapsulate ncrename call so as to manage error code and retry #D-* Examples: #D- function IGCM_sys_ncrename { IGCM_debug_PushStack "IGCM_sys_ncrename" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_ncrename :" $@ fi typeset NB_ESSAI DELAI status i # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 i=0 while [ $i -lt $NB_ESSAI ] ; do ncrename $@ > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_ncrename : error code ${status}" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Print 2 "IGCM_sys_ncrename : ${i}/${NB_ESSAI} sleep ${DELAI} seconds and try again." sleep $DELAI else \rm /tmp/out_command.$$ break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_ncrename : ncrename error" IGCM_debug_Exit "ncrename" fi IGCM_debug_PopStack "IGCM_sys_ncrename" } #D-#================================================== #D-function IGCM_sys_ncwa #D-* Purpose: encapsulate ncwa call so as to manage error code and retry #D-* Examples: #D- function IGCM_sys_ncwa { IGCM_debug_PushStack "IGCM_sys_ncwa" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_ncwa :" $@ fi typeset NB_ESSAI DELAI status i # number of tentative NB_ESSAI=3 # time delay between tentative DELAI=2 i=0 while [ $i -lt $NB_ESSAI ] ; do ncwa $@ > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then IGCM_debug_Print 2 "IGCM_sys_ncwa : error code ${status}" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_Print 2 "IGCM_sys_ncwa : ${i}/${NB_ESSAI} sleep ${DELAI} seconds and try again." sleep $DELAI else \rm /tmp/out_command.$$ break fi (( i = i + 1 )) done if [ ${status} -gt 0 ] ; then echo "IGCM_sys_ncwa : ncwa error" IGCM_debug_Exit "ncwa" fi IGCM_debug_PopStack "IGCM_sys_ncwa" } ############################################################## # CDO OPERATOR #D-#================================================== #D-function IGCM_sys_cdo #D-* Purpose: encapsulate cdo call so as to manage error code and retry #D-* Examples: #D- function IGCM_sys_cdo { IGCM_debug_PushStack "IGCM_sys_cdo" $@ if ( $DEBUG_sys ) ; then echo "IGCM_sys_cdo :" $@ fi typeset status \cdo $@ > /tmp/out_command.$$ 2>&1 status=$? if [ ${status} -gt 0 ] ; then echo "IGCM_sys_cdo : error code ${status}" cat /tmp/out_command.$$ \rm /tmp/out_command.$$ IGCM_debug_PopStack "IGCM_sys_cdo" return 1 else IGCM_debug_PopStack "IGCM_sys_cdo" return 0 fi IGCM_debug_PopStack "IGCM_sys_cdo" }