#!/bin/ksh # mrun - script for running PALM jobs # $Id: mrun 759 2011-09-15 13:58:31Z maronga $ # Procedure for interactive/batch PALM runs (initial runs and automatic # restart runs) # Last changes: # 03/03/94 - Siggi - Entwicklungsbeginn # 21/03/94 - Siggi - Entwicklungsabschluss (Version 1.0) # 09/12/94 - Siggi - allexport unterbunden; statt dessen werden jetzt ein- # zelne Variable exportiert. Dies ist noetig, weil an- # sonsten irgendein Speicher ueberlaeuft und von mrun # aufgerufene Programme (z.B. stageout) mit Fehlern # abbrechen (too many arguments) # 20/06/95 - Siggi - noclobber muss explizit abgeschaltet, da jetzt # defaultmaessig im RRZN-Profile eingeschaltet # 10/06/97 - Siggi - Zusaetzliche Option -C bei cpp, damit // nicht # wegfallen # 25/04/00 - Siggi - Version 1.5 # remote_addres und remote_user in return_addres bzw. # return_username umbenannt, return_username wird dem # mrun-Aufruf im Job ueber Option -U mitgegeben. # Neue Variable remote_username, die beim interaktiven # mrun-Aufruf zwingend ueber die neue Option -u oder # in der Konfigurationsdatei angegeben werden muss. # 08/02/01 - Siggi - Alle mrun-Meldungen ins englische uebersetzt, # Version 1.7 # 05/05/02 - Siggi - Uebersetzungen mittels make-Mechanismus moeglich # 21/11/02 - Siggi - ENV-Variable XLFRTEOPTS wird vor Ausfuehrung auf # IBM gesetzt, um Record-Laenge der NAMELIST-Dateien, # zu bestimmen; Praeprozessoroptionen haben nun alle # die Form -Dtext=text, weil auf IBM sonst text durch # die leere Zeichenkette ersetzt wird # 01/08/03 - Siggi - Test of implementing dvrp+1PE on ibm # 07/01/04 - Siggi - additional preprocessor directive for ibm included # (-D$OMP=OMP) in order to avoid problems with # OMP_NUM_THREADS # 04/01/05 - Siggi - archiving on hanni and berni is done in separate # tar files, one for each node used # 07/01/04 - Siggi - old code for t3e, vpp and hpcs eliminated # 09/01/05 - Siggi - workaround for getting the IP address on gfdl3 # 17/01/05 - Siggi - job for data transfer to local machine now within # job class c1 (HLRN) # 27/01/05 - Siggi - IP address workaround for gfdl3 removed # 28/01/05 - Siggi - tar-filenames on $PERM (HLRN) now include the # base filename and cycle number # 16/02/05 - Gerald - hababai validated # 14/03/05 - Siggi - abort on NEC after first runtime error (F_ERRCNT) # 29/03/05 - Marcus - berni*-en0 validated # 21/04/05 - Siggi - transfer-job-protocol for avs-data is no more stored # 24/04/05 - Siggi - netcdf support on lcmuk # 25/04/05 - Siggi - netcdf support on gfld3 (decalpha) # 11/05/05 - Siggi - files with non-numeric extensions (.xxx after cycle # number) can now be used within interactive runs # 12/05/05 - Siggi - netcdf support on ibm # 13/05/05 - Siggi - error in tar-filenames on $PERM (HLRN) removed # 18/05/05 - Siggi - netcdf support on nec # 24/05/05 - Siggi - netcdf support on ibms # 14/06/05 - Siggi - sleep interval after submit of restart job increased # to 30 seconds # 28/06/05 - Siggi - bora adjusted to new intel compiler (LD_LIBRARY_ # PATH is temporarily set) # 07/09/05 - Siggi - setting of MP_EAGER_LIMIT switched off because it # caused warnings in the job protocol # 20/10/05 - Siggi - update of netcdf-version on decalpha (gfdl3) # 25/10/05 - Siggi - error in listing files for getting the cycle number # removed # 26/10/05 - Siggi - new paths for dvrp-library, transfer of catalogs # realized by file attribute trpe # 28/10/05 - Siggi - if existing, the file extension is output in case # of missing input file - no job abort in case of # missing input files with file extensions # (preliminary solution) # 31/10/05 - Siggi - data transfer from nech now within seperate job # 04/11/05 - Siggi - netcdf 3.6.0-p1 on ibmh/ibmb # 07/12/05 - Siggi - gallego and elephanta admitted # 30/12/05 - Siggi - gfdl5 (ibmy) admitted # 10/01/06 - Siggi - cpp directive for NetCDF 64bit support # 20/01/06 - Siggi - cpp directive for ibmy # 09/02/06 - Siggi - ibmy admitted for batch mode # 13/04/06 - Siggi - ostria admitted # 18/04/06 - Siggi - usage of OpenMP implemented (additional option -O) # 10/05/06 - Siggi - environment variable XLSMPOPTS set on IBM for # optimization of OpenMP runs (option stacksize is # necessary for large gridpoint numbers because # otherwise a segmentation fault occurs) # 23/05/05 - Siggi - lctit (SUN Fire X4600) admitted # 21/08/06 - Siggi - standard mrun path on scirocco is as on bora # 23/08/06 - Siggi - netcdf support for scirocco (notebook) # 20/09/06 - Marcus - add DVRP library on nech # 24/10/06 - Siggi - Environment variables for PALM steering are written # on local NAMELIST file ENVPAR # 24/11/06 - Siggi - levanto admitted, maestro switched to ifc 9.1 # 28/11/06 - Siggi - call to interpret_config.x_levanto because of SuSe 10 # 06/02/07 - Siggi - add DVRP library on lcmuk # 07/02/07 - Siggi - revision of source code handling, source code is # now expected in directory given by source_path and # not in the current working directory, source code # files provided in add_source_path are allways # compiled, source code to be compiled is allways # sampled in SOURCES_FOR_RUN_$fname which is a # subdirectory of the current working directory, # -s TEST changed to -s WRITE_PERMIT or -s WP, # adapted for RIAM (neck) # bugfix for cycle number of output file (extout) # all hpmuk-related code removed # 14/02/07 - Siggi - dvrp support for neck added # 28/02/07 - Siggi - empty lines in configuration file are accepted # mrun_path replaced by PALM_BIN, # all machines are calling interpret_config.x # 14/03/07 - Siggi - fimm admitted, revision number added to terminal # output # 16/03/07 - Siggi - adjustments for lctit # 29/03/07 - Siggi - global revision transfered to batch job by new # option -G # 30/03/07 - Siggi - compilation "by hand" removed, cpp-directives/options # + netcdf/dvrp-options are read from configuration # file, host identifier (local_host) is read from # config file, code related to ftp filetransfer # removed (incl. option -f) # 19/06/07 - Siggi - time limit for cdata jobs increased # 25/07/07 - Siggi - two sets of executables can be started on lcmuk, # if new option -Y (coupling) is given, # output of executables to aout_output removed, # messages are immediately written to stdout instead # 03/08/07 - Marcus - add XOPT="-X $numprocs" for lcfimm # 09/08/07 - Marcus - workaround on lcfimm to propagate environment # variables out to the nodes in coupled mode -disabled- # 13/08/07 - Marcus - start local restart jobs per ssh on lcfimm # 28/08/07 - Marcus - completely remove workaround on lcfimm to propagate # environment variables out to the nodes in coupled mode # 15/10/07 - Siggi - Preliminary adjustments for lctit, based on Jin's # suggestions # 19/10/07 - Marcus - further adjustments for lctit: add new optional # argument -g group_number, admit all sla* node_usage # queues # 30/10/07 - Marcus - further adjustments for queues on lctit # 14/02/08 - Bjoern - link of restart files with long file name possible # 28/02/08 - Marcus - If environment variable link_local_output is set to # true, mrun tries "ln -f" on local output and resorts # to "cp" or "cp -r" on error # 15/04/08 - Siggi - argument -c introduced to most of the subjob calls, # which allows the user to choose his own job catalog # by setting job_catalog in the configuration file # (default is ~/job_queue), # workaround for mpiexec with -env option, # adjustments for lcxt4 (Bergen Center for Computational # Science) # 22/05/08 - Marcus - If environment variable link_local_input is set to # true, mrun tries "ln -f" on local input and resorts # to "cp" or "cp -r" on error # 27/05/08 - Siggi - PATH is set to PALM_BIN everywhere (missing so far) # 14/07/08 - Siggi - adjustments for lcsgih # 08/08/08 - Marcus - typo removed in lcxt4 branch # 17/09/08 - Siggi - restart mechanism adjusted for lcsgi # 02/10/08 - BjornM - argument "-Y" modified, adjustments for coupled runs # 21/10/08 - Siggi - bugfix for the case that -K has more than one # argument # 08/11/08 - Siggi - bugfix for depository path settings in configuration # file # 11/11/08 - Siggi - rules for using user code files changed: user # code splitted into one file per subroutine, # user can provide his/her own makefile, only # default source-code filenames are allowed # 14/11/08 - Siggi - cond1 and cond2 are part of the depository name # 08/01/09 - Siggi - mpi module on sgi machines to be used can be set # with environment variable mpilib # 13/01/09 - Siggi - totalview on hice/bice can be used in debug mode # using environment variable totalview # 25/02/09 - Siggi - cputime-option (-t) is allowed to be omitted for # interactive runs # 05/03/09 - Siggi - adjustments for new NEC-SX9 at RIAM (necriam) # 16/03/09 - Siggi - dvrp_lib, dvrp_inc replaced by dvr_lib, dvr_inc, # dvr streaming server is automatically started using # new variable dvr_server and a configuration file # .dvrserver.config, # processing of dvr output files using new script # process_dvr_output implemented, in order to make # dvr application more user friendly # 20/03/09 - Marcus - update of n1ge command for lctit # 16/04/09 - Siggi - new option -y for precursor (uncoupled) ocean runs # to be followed by a coupled atmosphere-ocean run # 21/04/09 - Siggi - adjustments for new IBM at DKRZ, which is now ibmh # 24/06/09 - BjornM - adjustments for coupled/precursor runs on ibmy # 08/07/09 - Siggi - default value for email_notification is none, # option -e added to subjob # 19/08/09 - Marcus - MPI debug option # 21/08/09 - Marcus - totalview on hice/bice also available for mvapich2 # 25/08/09 - BjornM - adpated for lck # 26/08/09 - Siggi - additional environment variables for mpt on ice2 # 26/08/09 - Marcus - adjustment for ice2 on lcsgib # 29/09/09 - Siggi - default value for archiving is false, option "-A" # switches on archiving, archiving on SGI-ICE enabled # 16/10/09 - Carolin- adjustments for archiving on SGI-ICE of binary files; # adjustment for special1q # 18/12/09 - Carolin- modification of archiving (permq) # 01/02/10 - Siggi - adapted for lcxt5m and lckyoto (Fujitsu HX600) # 03/02/10 - Siggi - make options (mopts) to be set by configuration file # implemented # 08/02/10 - Siggi - loading of modules now controlled via configuration # file (modules) # 02/03/10 - Siggi - for each block in the configuration file, separate # utility programs are used, combine_plot_fields is # directly called and must not be given by an output # command in the configuration file any more # 15/06/10 - Rieke - ssh from compute nodes to login nodes on hosts # lcsgih/lcsgib is done using the names # hicegate0/bicegate0 instead of the IP addresses # 17/08/10 - BjornM - adjustments for interactive runs on lcxt4 # 07/09/10 - Siggi - bugfix for wrong netcdf/3.6.3 module on lcsgi # 08/12/10 - Siggi - new handling of openmp/hybrid runs, option -O # has now argument threads_per_task # adjustments for Kyushu Univ. (lcrte, ibmku) # 14/12/10 - Siggi - adjustments for new Tsubame system at Tokyo # institute of technology (lctit) # 23/12/10 - Micha - different number of processors in ocean and # atmosphere is now allowed # 02/02/10 - Siggi - further adjustments on Tsubame and concerning openMP # usage # 09/03/10 - Siggi - adjustments for ibmkisti, mpt bugfix for netCDF4 # usage, totalview usage extended # 17/03/11 - Siggi - adjustments for openmp usage on ibmkisti # 03/04/11 - Micha - added lckordi # 06/04/11 - BjornM - bugfix for runs with mpt on lcsgi # 17/08/11 - Siggi - extensions for impi library # 18/08/11 - Siggi - bugfix for local append of output files with suffix # (.nc) # 18/08/11 - Marcus - support for Linux OS with German locale # - properly report hosts on general Linux clusters # 29/08/11 - BjornW - adapted for lcflow (ForWind cluster in Oldenburg) # 29/08/11 - Carolin- initiating restart-run: adjustment of the path at # IMUK # 15/09/11 - Siggi - new option -w tp set the maximum number of parallel # io streams, option -T is obligatory from now on # VARIABLENVEREINBARUNGEN + DEFAULTWERTE set +o allexport # SICHERHEITSHALBER UNTERBINDEN, DA SONST EVTL. STAGEOUT # NICHT LAUEFT (TOO MANY ARGUMENTS - PROBLEM) set +o noclobber # EXISTIERENDE DATEIEN DUERFEN UEBERSCHRIEBEN WERDEN AddFilenames="" additional_conditions="" add_source_path="" afname="" archive_save=true archive_system=none compiler_name="" cond1="" cond2="" config_file=.mrun.config coupled_dist="" coupled_mode="mpi1" cpp_opts="" cpp_options="" cpumax=0 cpurest=0 delete_temporary_catalog=true do_batch=false do_compile=true do_remote=false do_stagein=true do_stageout=true do_trace=false email_notification="none" exclude="" executable="" execution_error=false fimm=false fname=test fromhost="" global_revision="" group_number=none host="" host_file="" hp="" ignore_archive_error=false input_list="" interpreted_config_file="" job_catalog="~/job_queue" job_on_file="" keep_data_from_previous_run=false link_local_input=false link_local_output=false localhost_realname=$(hostname) local_compile=false local_dvrserver_running=.FALSE. locat=normal mainprog="" makefile="" max_par_io_str="" mc=$0 while [[ $(echo $mc | grep -c "/") != 0 ]] do mc=`echo $mc | cut -f2- -d"/"` done module_calls="" mrun_script_name=$mc netcdf_inc="" netcdf_lib="" netcdf_support=false node_usage=default numprocs="" numprocs_atmos=0 numprocs_ocean=0 OOPT="" openmp=false output_list="" package_list="" punkte="..........................................................." queue=none read_from_config="" restart_run=false if [[ `hostname` = rte10 ]] then return_addres=133.5.185.60 echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!" elif [[ `hostname` = climate0 ]] then return_addres=165.132.26.68 echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!" else return_addres=$(nslookup `hostname` 2>&1 | grep "Address:" | tail -1 | awk '{print $2}') fi return_password="" return_username=$LOGNAME remotecall=false remote_username="" run_coupled_model=false run_mode="" scirocco=false store_on_archive_system=false striche=" ----------------------------------------------------------------------------" silent=false source_list="" source_path=SOURCE tasks_per_node="" threads_per_task=1 tmpcreate=false tmp_data_catalog="" transfer_problems=false usern=$LOGNAME use_openmp=false working_directory=`pwd` TOPT="" XOPT="" zeit=$( date | cut -c 12-19 ) typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 memory=0 stagein_anz=0 stageout_anz=0 typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek maxcycle minuten nodes pes sekunden tp1 typeset -R30 calltime typeset -L20 spalte1 typeset -L40 spalte2 typeset -L60 spalte3 typeset -L35 string1=`date` typeset -L12 string2=$usern typeset -L12 string3=$localhost_realname typeset -L12 string4 typeset -L12 string5 typeset -L30 version="MRUN 2.0 Rev$Rev: 759 $" # EINZELNE VARIABLE FUER HAUPTPROGRAMM EXPORTIEREN export cpurest fname host localhost return_addres return_username remotecall tasks_per_node # FOLGENDE VARIABLEN MUESSEN FUER DIE INTERPRETATION DER KONFIGURATIONSDATEI # EXPORTIERT WERDEN export afname config_file cpp_opts cpumax do_batch do_trace fname fromhost export group_number input_list memory numprocs output_list queue run_mode # FEHLERBEHANDLUNG # BEI EXIT: trap 'rm -rf $working_directory/tmp_mrun if [[ $locat != localhost ]] then # if [[ ! -f ${mrun_path}/statistik/mrun_statistik ]] # then # cat > ${mrun_path}/statistik/mrun_statistik << %STATEND% #MRUN-calls on $localhost # #date and time user localhost remotehost termination mrun-command #-------------------------------------------------------------------------------------------------------------------- #%STATEND% # chmod 666 ${mrun_path}/statistik/mrun_statistik # fi # # # EINTRAG IN DIE STATISTIK-DATEI # string4=$host # string5=$locat # if [[ "$job_on_file" = "" && $locat != control_c && $locat != user_abort ]] # then # if [[ $do_batch = true ]] # then # printf "$string1$string2$string3$string4$string5$mrun_com \n" >> ${mrun_path}/statistik/mrun_statistik # else # printf "$string1$string2$string3$string4$string5$mc \n" >> ${mrun_path}/statistik/mrun_statistik # fi # fi echo " " > /dev/null fi if [[ $locat != normal && $locat != control_c && $locat != local_compile ]] then # EVENTUELLE ERROR-KOMMANDOS ABARBEITEN (( i = 0 )) while (( i < iec )) do (( i = i + 1 )) printf "\n *** Execution of ERROR-command:\n" printf " >>> ${err_command[$i]}\n" eval ${err_command[$i]} done if [[ -n $interpreted_config_file ]] then rm -rf $interpreted_config_file fi if [[ -n .mrun_environment ]] then rm -rf .mrun_environment fi if [[ $tmpcreate = true ]] then printf "\n *** Contents of \"$TEMPDIR\":\n" ls -al; cd [[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR fi if [[ "$dvrserver_id" != "" ]] then echo "+++ killing dvrserver_id=$dvrserver_id" kill $dvrserver_id fi if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]] then rm -rf ~/job_queue/JOBINFO.$QSUB_REQID fi printf "\n\n+++ MRUN killed \n\n" elif [[ $locat != control_c ]] then printf "\n\n --> all actions finished\n\n" printf " Bye, bye $usern !!\n\n" fi' exit # BEI TERMINAL-BREAK: trap 'rm -rf $working_directory/tmp_mrun [[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR) if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]] then rm -rf ~/job_queue/JOBINFO.$QSUB_REQID fi if [[ "$dvrserver_id" != "" ]] then echo "+++ killing dvrserver_id=$dvrserver_id" kill $dvrserver_id fi printf "\n+++ MRUN killed by \"^C\" \n\n" locat=control_c exit ' 2 # CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS # BEEN SET if [[ "$PALM_BIN" = "" ]] then printf "\n +++ environment variable PALM_BIN has not been set" printf "\n please set it to the directory where the PALM scripts are located" locat=palm_bin; exit fi export PATH=$PALM_BIN:$PATH # SHELLSCRIPT-OPTIONEN EINLESEN UND KOMMANDO NEU ZUSAMMENSETZEN, FALLS ES # FUER FOLGEJOBS BENOETIGT WIRD while getopts :a:AbBc:Cd:D:Fg:G:h:H:i:IkK:m:M:n:o:O:p:P:q:r:R:s:St:T:u:U:vw:xX:yY: option do case $option in (a) afname=$OPTARG;; (A) store_on_archive_system=true; mc="$mc -A";; (b) do_batch=true; mc="$mc -b";; (B) delete_temporary_catalog=false; mc="$mc -B";; (c) config_file=$OPTARG; mc="$mc -c$OPTARG";; (C) restart_run=true; mc="$mc -C";; (d) fname=$OPTARG; mc="$mc -d$OPTARG";; (D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";; (F) job_on_file="-D"; mc="$mc -F";; (g) group_number=$OPTARG; mc="$mc -g$OPTARG";; (G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";; (h) host=$OPTARG; mc="$mc -h$OPTARG";; (H) fromhost=$OPTARG; mc="$mc -H$OPTARG";; (i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";; (I) ignore_archive_error=true; mc="$mc -I";; (k) keep_data_from_previous_run=true; mc="$mc -k";; (K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";; (m) memory=$OPTARG; mc="$mc -m$OPTARG";; (M) makefile=$OPTARG; mc="$mc -M$OPTARG";; (n) node_usage=$OPTARG; mc="$mc -n$OPTARG";; (o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";; (O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";; (p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";; (P) return_password=$OPTARG; mc="$mc -P$OPTARG";; (q) queue=$OPTARG; mc="$mc -q$OPTARG";; (r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";; (R) remotecall=true;return_addres=$OPTARG; mc="$mc -R$OPTARG";; (s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";; (S) read_from_config=false; mc="$mc -S";; (t) cpumax=$OPTARG; mc="$mc -t$OPTARG";; (T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";; (u) remote_username=$OPTARG; mc="$mc -u$OPTARG";; (U) return_username=$OPTARG; mc="$mc -U$OPTARG";; (v) silent=true; mc="$mc -v";; (w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";; (x) do_trace=true;set -x; mc="$mc -x";; (X) numprocs=$OPTARG; mc="$mc -X$OPTARG";; (y) ocean_file_appendix=true; mc="$mc -y";; (Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";; (\?) printf "\n +++ unknown option $OPTARG \n" printf "\n --> type \"$0 ?\" for available options \n" locat=parameter;exit;; esac done # EVTL. POSITIONSPARAMETER EINLESEN # ZUR ZEIT GIBT ES NUR DEN PARAMETER ? (=KURZINFO) shift OPTIND-1 # KURZE AUFRUFBESCHREIBUNG WIRD HIER AUSGEGEBEN if [[ "$1" = "?" ]] then (printf "\n *** mrun can be called as follows:\n" printf "\n $mrun_script_name -b -c.. -d.. -D.. -f.. -F -h.. -i.. -I -K.. -m.. -o.. -p.. -r.. -R -s.. -t.. -T.. -v -x -X.. -y -Y.. \n" printf "\n Description of available options:\n" printf "\n Option Description Default-Value" printf "\n -a base name of input files equiv. -d" printf "\n -A archiving when using file-attribute fl" printf "\n -b batch-job on local machine ---" printf "\n -B do not delete temporary directory at end ---" printf "\n -c configuration file .mrun.config" printf "\n -d base name of files attached to program test" printf "\n -D preprocessor(cpp)-directives \"\" " printf "\n -F create remote job file only ---" printf "\n -h execution host $localhost_realname" printf "\n -i INPUT control list \"\" " printf "\n -I archiving errors of previous batch-jobs" printf "\n will be ignored" printf "\n -k keep data from previous run" printf "\n -K additional conditions for controling" printf "\n usage of conditional code and" printf "\n env-variables in configuration file \"\" " printf "\n -m memory demand in MB (batch-jobs) 0 MB" printf "\n -M Makefile name Makefile" printf "\n -n node usage (shared/not_shared) depending on -h" printf "\n -o OUTPUT control list \"\" " printf "\n -O use OpenMP ---" printf "\n -p software package list \"\" " printf "\n -q queue \"$queue\" " printf "\n -r run control list (combines -i -o) \"\" " printf "\n -s filenames of routines to be compiled \"\" " printf "\n must end with .f, .f90, .F, or .c !" printf "\n use \"..\" for more than one file and wildcards" printf "\n -s TEST compiles all files with w-permit" printf "\n -S config file interpreted by shellscript ---" printf "\n -t allowed cpu-time in seconds (batch) 0" printf "\n -T tasks per node depending on -h" printf "\n -u username on remote machine \"\" " printf "\n -v no prompt for confirmation ---" printf "\n -w maximum parallel io streams as given by -X" printf "\n -x tracing of mrun for debug purposes ---" printf "\n -X # of processors (on parallel machines) 1" printf "\n -y add appendix \"_O\" to all local output" printf "\n files (ocean precursor runs followed by" printf "\n coupled atmosphere-ocean runs) ---" printf "\n -Y run coupled model, \"#1 #2\" with" printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X" printf "\n " printf "\n Possible values of positional parameter :" printf "\n \"?\" - this outline \n\n") | more exit elif [[ "$1" != "" ]] then printf "\n +++ positional parameter $1 unknown \n" locat=parameter; exit fi # KURZE STARTMELDUNG printf "\n*** $version " printf "\n will be executed. Please wait ..." # PRUEFEN, OB KONFIGURATIONS-DATEI VORHANDEN if [[ ! -f $config_file ]] then printf "\n\n +++ configuration file: " printf "\n $config_file" printf "\n does not exist" locat=connect; exit fi # HOST-IDENTIFIER (local_host) AUS KONFIGURATIONSDATEI BESTIMMEN line="" grep "%host_identifier" $config_file > tmp_mrun while read line do if [[ "$line" != "" && $(echo $line | cut -c1) != "#" ]] then HOSTNAME=`echo $line | cut -d" " -s -f2` host_identifier=`echo $line | cut -d" " -s -f3` if [[ $localhost_realname = $HOSTNAME ]] then localhost=$host_identifier break fi fi done < tmp_mrun if [[ "$localhost" = "" ]] then printf "\n\n +++ no host identifier found in configuration file \"$config_file\"" printf "\n for local host \"$localhost_realname\"." printf "\n Please add line" printf "\n \"\%host_identifier $localhost_realname \"" printf "\n to the configuration file." locat=localhost; exit fi # HOSTSPEZIFISCHE VARIABLEN SETZEN case $localhost_realname in (r1*|r2*|h01*|b01*) archive_system=tivoli;; (cs*) archive_system=ut;; (fimm.bccs.uib.no) fimm=true;; (gate|n-sx) PATH=$PALM_BIN:$PATH:/usr/bin/nqsII;; (scirocco) scirocco=true;; esac # BASISNAME DER INPUT-DATEIEN GLEICH ALLGEMEINEM BASISNAMEN SETZEN, # WENN NICHT VOM BENUTZER ANDERS BESTIMMT [[ "$afname" = "" ]] && afname=$fname # EVTL. RUN-MODUS DEN I/O-LISTEN HINZUFUEGEN if [[ "$run_mode" != "" ]] then input_list="$input_list $run_mode" output_list="$output_list $run_mode" fi # RECHNERNAMEN ABSPEICHERN, VON DEM AUS JOB GESTARTET WIRD, # ALLERDINGS NUR DANN, WENN NICHT PER OPTION -H BEREITS EIN WERT # ZUGEWIESEN WURDE (MRUN MACHT DIES IMMER, WENN ES SELBST BATCH-JOBS # STARTET) if [[ "$fromhost" = "" ]] then fromhost=$localhost fi # PRUEFEN, OB MRUN NUR TESTWEISE AUF DER LOKALEN MASCHINE KOMPILIEREN SOLL if [[ "$source_list" = LOCAL_COMPILE_TEST ]] then source_list=TEST local_compile=true host=$localhost fi # PRUEFEN, OB AUF REMOTE-MASCHINE GERECHNET WERDEN SOLL # WERT VON do_remote WIRD FUER DATEIVERBINDUNGEN BENOETIGT. # WENN AUF REMOTE-MASCHINE GERECHNET WIRD, IST GLEICHZEITIG KLAR, # DASS EIN BATCH-JOB GESTARTET WERDEN MUSS if [[ -n $host && "$host" != $localhost ]] then do_batch=true do_remote=true case $host in (ibm|ibmh|ibmkisti|ibmku|ibms|ibmy|nech|necriam|lckyoto|lcsgib|lcsgih|unics|lcxt4|lcxt5m|lck|lckordi) true;; (*) printf "\n" printf "\n +++ sorry: execution of batch jobs on remote host \"$host\"" printf "\n is not available" locat=nqs; (( iec = 0 )); exit;; esac else host=$localhost fi # ZUSATZBEDINGUNGEN (OPTION -K) AUSWERTEN if [[ -n $additional_conditions ]] then # echo $additional_conditions | cut -d" " -f1-3 | read cond1 cond2 dummy cond1=`echo $additional_conditions | cut -d" " -f1` cond2=`echo $additional_conditions | cut -d" " -s -f2` dummy=`echo $additional_conditions | cut -d" " -s -f3` if [[ -n $dummy ]] then printf "\n +++ more than 2 additional conditions given for Option \"-K\"" locat=options; exit fi block=_$cond1 [[ -n $cond2 ]] && block=${block}_$cond2 fi # KOPPLUNGSEIGENSCHAFTEN (-Y) AUSWERTEN UND coupled_mode BESTIMMEN if [[ $run_coupled_model = true ]] then if [[ -n $coupled_dist ]] then numprocs_atmos=`echo $coupled_dist | cut -d" " -s -f1` numprocs_ocean=`echo $coupled_dist | cut -d" " -s -f2` if (( $numprocs_ocean + $numprocs_atmos != $numprocs )) then printf "\n +++ number of processors does not fit to specification by \"-Y\"." printf "\n PEs (total) : $numprocs" printf "\n PEs (atmosphere): $numprocs_atmos" printf "\n PEs (ocean) : $numprocs_ocean" locat=coupling; exit fi else (( numprocs_ocean = $numprocs / 2 )) (( numprocs_atmos = $numprocs / 2 )) fi coupled_dist=`echo "$numprocs_atmos $numprocs_ocean"` # GET coupled_mode FROM THE CONFIG FILE line="" grep "%cpp_options.*-D__mpi2.*$host" $config_file > tmp_mrun while read line do if [[ "$line" != "" && $(echo $line | cut -c1) != "#" && ( $(echo $line | cut -d" " -s -f4) = $cond1 || $(echo $line | cut -d" " -s -f4) = $cond2 ) ]] then coupled_mode="mpi2" fi done < tmp_mrun fi # PRUEFEN, OB EVTL. BEI VORHERGEHENDEM LAUF (KETTENJOB) EINE # ARCHIVIERUNG FEHLGESCHLAGEN IST if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]] then if [[ $ignore_archive_error = false ]] then printf "\n +++ data archiving of previous run failed" printf "\n see directory \~/job_queue on remote machine" locat=archive; exit else printf "\n +++ warning: data archiving in a previous run failed" printf "\n MRUN continues, trying to get backup copy" fi fi # LESEN UND INTERPRETIEREN DER KONFIGURATIONS-DATEI VOM SHELLSCRIPT AUS # VORUEBERGEHEND ZWINGEND AUF LINUX-RECHNERN if [[ "$read_from_config" = false ]] then [[ $silent = false ]] && printf "\n Reading the configuration file... " while read zeile do [[ $silent = false ]] && printf "." # ZUERST EVENTUELL VORKOMMENDE ENVIRONMENT-VARIABLEN DURCH IHRE WERTE # ERSETZEN eval zeile=\"$zeile\" # INTERPRETATION DER ZEILE if [[ "$(echo $zeile)" = "" ]] then # LEERZEILE, KEINE AKTION continue elif [[ "$(echo $zeile | cut -c1)" = "#" ]] then # ZEILE IST KOMMENTARZEILE true elif [[ "$(echo $zeile | cut -c1)" = "%" ]] then # ZEILE DEFINIERT ENVIRONMENT-VARIABLE zeile=$(echo $zeile | cut -c2-) # echo $zeile | cut -d" " -f1-5 | read var value for_host for_cond1 for_cond2 var=`echo $zeile | cut -d" " -f1` value=`echo $zeile | cut -d" " -s -f2` for_host=`echo $zeile | cut -d" " -s -f3` for_cond1=`echo $zeile | cut -d" " -s -f4` for_cond2=`echo $zeile | cut -d" " -s -f5` if [[ "$for_host" = "" || ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) || $(echo "$input_list$output_list"|grep -c "$for_host") != 0 ]] then # BEI COMPILER- CPP- ODER LINKEROPTIONEN EVTL ":" DURCH " " # ERSETZEN. "::" WIRD DURCH ":" ERSETZT. value=`echo $value | sed 's/::/%DUM%/g' | sed 's/:/ /g' | sed 's/%DUM%/:/g'` # ENVIRONMENT-VARIABLE WIRD WERT AUS KONFIGURATIONSDATEI # ZUGEWIESEN, WENN SIE SELBST NOCH KEINEN WERT UEBER DIE # ENTSPRECHENDE SCRIPT-OPTION ERHALTEN HAT. SOLCHE # VARIABLEN HAETTEN DANN DEN WERT "" ODER IM INTEGER-FALL DEN # WERT 0. ALLGEMEINE REGEL ALSO: SCRIPT-OPTION GEHT UEBER # KONFIGURATIONSDATEI if [[ "$(eval echo \$$var)" = "" || "$(eval echo \$$var)" = "0" ]] then eval $var=\$value # EVTL. BILDSCHIRMAUSGABEN DER ENVIRONMENT-VARIABLEN if [[ $do_trace = true ]] then printf "\n*** ENVIRONMENT-VARIABLE $var = $value" fi fi # WENN ENVIRONMENT-VARIABLE HOST VEREINBART, DANN SOFORT AUSWERTEN # WERT VON do-remote WIRD BEI DATEIVERBINDUNGEN BENOETIGT # WENN AUF REMOTE-MASCHINE GERECHNET WIRD, IST GLEICHZEITIG KLAR, # DASS EIN BATCH-JOB GESTARTET WERDEN MUSS if [[ $var = host ]] then if [[ -n $host && "$host" != $localhost ]] then do_batch=true do_remote=true case $host in (ibm|ibmh|ibmkisti|ibmku|ibms|ibmy|lckyoto|lcsgib|lcsgih|nech|necriam|unics|lcxt4|lcxt5m|lck|lckordi) true;; (*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\"" printf "\n is not available" locat=nqs; exit;; esac else host=$localhost fi fi # VOM BENUTZER DEFINIERTE ENVIRONMENT VARIABLEN MUESSEN PRINZIPIELL # EXPORTIERT WERDEN, DA SIE VIELLEICHT IN WEITER UNTEN AUFZURUFEN- # DEN PROGRAMMEN BENOETIGT WERDEN export $var fi elif [[ "$(echo $zeile | cut -c1-3)" = "EC:" ]] then # ZEILE DEFINIERT ERROR-KOMMANDO (( iec = iec + 1 )) zeile=$(echo $zeile | cut -c4-) err_command[$iec]="$zeile" elif [[ "$(echo $zeile | cut -c1-3)" = "IC:" ]] then # ZEILE DEFINIERT INPUT-KOMMANDO (( iic = iic + 1 )) zeile=$(echo $zeile | cut -c4-) in_command[$iic]="$zeile" elif [[ "$(echo $zeile | cut -c1-3)" = "OC:" ]] then # ZEILE DEFINIERT OUTPUT-KOMMANDO (( ioc = ioc + 1 )) zeile=$(echo $zeile | cut -c4-) out_command[$ioc]="$zeile" else # ZEILE DEFINIERT DATEIVERBINDUNG. EINLESEN DER DATEIEIGENSCHAFTEN # s2a: in/out - Feld # s2b: loc - Feld (optional) # s2c: tr/ar - Feld (optional) # echo $zeile | cut -d" " -f1-2 | read s1 s2 s1=`echo $zeile | cut -d" " -f1` s2=`echo $zeile | cut -d" " -s -f2` s2a=$(echo $s2 | cut -d":" -f1) if [[ $(echo $s2 | grep -c ":") = 0 ]] then s2b="" s2c="" else # echo $s2 | cut -d":" -f2-3 | sed 's/:/ /g' | read s2b s2c s2b=`echo $s2 | cut -d":" -f2 | sed 's/:/ /g'` s2c=`echo $s2 | cut -d":" -s -f3 | sed 's/:/ /g'` fi # echo $zeile | cut -d" " -f3-6 | read s3 s4 s5 s6 s3=`echo $zeile | cut -d" " -f3` s4=`echo $zeile | cut -d" " -s -f4` s5=`echo $zeile | cut -d" " -s -f5` s6=`echo $zeile | cut -d" " -s -f6` # ABSPEICHERN DER DATEIVERBINDUNG, FALLS IN INPUT- ODER OUTPUT-LIST # VERMERKT. VARIABLE S3 KANN AUCH LISTE ENTHALTEN (FELDTRENNER ":") # DATEIVERBINDUNG WIRD DANN NICHT ABGESPEICHERT UND GEPRUEFT, WENN # PROGRAMMLAUF AUF REMOTE-MASCHINE ERFOLGT UND DATEI NUR LOKAL VOR- # HANDEN SEIN MUSS (D.H. s2b = loc) IFSALT="$IFS"; IFS="$IFS:" if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc || "$s2b" = locopt ) ) ]] then found=false for actual in $input_list do for formal in $s3 do [[ $actual = $formal || "$formal" = "-" ]] && found=true done done if [[ $found = true ]] then (( iin = iin + 1 )) localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c; typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5; extin[$iin]=$s6 fi elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]] then found=false for actual in $output_list do for formal in $s3 do [[ $actual = $formal || "$formal" = "-" ]] && found=true done done if [[ $found = true ]] then (( iout = iout + 1 )) localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3; pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6 fi elif [[ "$s2a" != in && "$s2a" != out ]] then printf "\n +++ I/O-attribute in configuration file $config_file has the invalid" printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!" locat=connect; exit fi IFS="$IFSALT" fi done < $config_file else # INTERPRETATION DER KONFIGURATIONSDATEI MITTELS FORTRAN 90 - PROGRAMM [[ $silent = false ]] && printf "..." export cond1 cond2 config_file do_remote do_trace input_list localhost output_list export interpreted_config_file=.icf.$RANDOM # ENVIRONMENT-VARIABLEN FUER INTERPRET_CONFIG UEBER NAMELIST_DATEI ZUR # VERFUEGUNG STELLEN cat > .mrun_environment << %%END%% &mrun_environment cond1 = '$cond1', cond2 = '$cond2', config_file = '$config_file', do_remote = '$do_remote', do_trace = '$do_trace', host = '$host', input_list = '$input_list', icf = '$interpreted_config_file', localhost = '$localhost', output_list = '$output_list' / %%END%% # WERTE VON MRUN-OPTIONEN SICHERN UND DAMIT GEGEBENENFALLS SPAETER DIE # IN DER KONFIGURAIONSDATEI ANGEGEBENEN WERTE UEBERSTEUERN mrun_memory=$memory mrun_group_number=$group_number mrun_cpumax=$cpumax mrun_numprocs=$numprocs if [[ $localhost_realname = "sx-fep" ]] then /home/COAR/NC/raasch/pub/interpret_config_necriam.x else if [[ "$host" != $localhost ]] then # REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null` if [[ $? != 0 ]] then printf "\n\n +++ no interpret_config found" printf "\n run \"mbuild -u -h ...\" to generate utilities for this host" locat=interpret_config; exit fi interpret_config_executable=`echo $interpret_config_executable | cut -d" " -f1` $interpret_config_executable else # CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]] then printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\"" printf "\n run \"mbuild -u -h ...\" to generate utilities for this block" locat=interpret_config; exit else interpret_config${block}.x fi fi fi rm .mrun_environment # AUSFUEHRUNG DER GENERIERTEN SHELL-KOMMANDOS IN DIESER SHELL chmod u+x $interpreted_config_file export PATH=$PATH:. . $interpreted_config_file rm $interpreted_config_file # OPTIONSWERTE UEBERSTEUERN KONFIGURATIONSDATEI [[ $mrun_memory != 0 ]] && memory=$mrun_memory [[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number [[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax [[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs [[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str [[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node fi # QUELLTEXTVERZEICHNIS AUF LOKALER MASCHINE AUS KONFIGURATIONSDATEI # BESTIMMEN (WUERDE SONST EVTL. DAS VERZEICHNIS DES JEWEILS UNTER -h # ANGEGEBENEN REMOTE-RECHNERS SEIN) # BEI BATCH-JOBS SIND DIE ZU UEBERSETZENDEN PROGRAMMTEILE SCHON KOMPLETT if [[ "$SOURCES_COMPLETE" = "" ]] then # ZUERST PRUEFEN, OB EIN GLOBALER QUELLTEXTPFAD FUER ALLE RECHNER # VEREINBART WURDE source_path="" line="" grep "%source_path" $config_file > tmp_mrun while read line do if [[ "$line" != "" && $(echo $line | cut -c1) != "#" ]] then if [[ "$(echo $line | cut -d" " -f3)" = "" ]] then global_source_path=`echo $line | cut -d" " -f2` fi fi done < tmp_mrun line="" found=false grep " $localhost" $config_file | grep "%source_path" > tmp_mrun while read line do if [[ "$line" != "" && $(echo $line | cut -c1) != "#" ]] then if [[ $found = true ]] then printf "\n\n +++ more than one source path found in configuration file" printf "\n for local host \"$localhost\" " locat=source_path; exit fi source_path=`echo $line | cut -d" " -f2` found=true fi done < tmp_mrun rm tmp_mrun if [[ "$source_path" = "" ]] then if [[ "$global_source_path" != "" ]] then source_path=$global_source_path else printf "\n\n +++ no source path found in configuration file" printf "\n for local host \"$localhost\" " locat=source_path; exit fi fi eval source_path=$source_path if [[ ! -d $source_path ]] then printf "\n\n +++ source path \"$source_path\" on local host" printf "\n \"$localhost\" does not exist" locat=source_path; exit fi fi # GLOBALE REVISIONSNUMMER ERMITTELN (FORTSETZUNGSLAEUFEN WIRD DIESE # DURCH OPTION -G MITGETEILT) if [[ "$global_revision" = "" && $host != "ibmkisti" ]] then global_revision=`svnversion $source_path 2>/dev/null` global_revision="Rev: $global_revision" fi # NOCHMAL PRUEFEN, OB AUF REMOTE-MASCHINE GERECHNET WERDEN SOLL # (HOST KANN IN KONFIGURATIONSDATEI ANDERS FESTGELEGT WORDEN SEIN) # WERT VON do_remote WIRD FUER DATEIVERBINDUNGEN BENOETIGT. # WENN AUF REMOTE-MASCHINE GERECHNET WIRD, IST GLEICHZEITIG KLAR, # DASS EIN BATCH-JOB GESTARTET WERDEN MUSS if [[ -n $host && "$host" != $localhost ]] then do_batch=true do_remote=true case $host in (ibm|ibmh|ibmkisti|ibmku|ibms|ibmy|lckyoto|lcsgib|lcsgih|nech|necriam|unics|lcxt4|lcxt5m|lck|lckordi) true;; (*) printf "\n" printf "\n +++ sorry: execution of batch jobs on remote host \"$host\"" printf "\n is not available" locat=nqs; (( iec = 0 )); exit;; esac else host=$localhost fi # PRUEFUNG EINIGER PROZESSORZAHLANGABEN BEI RECHNUNGEN AUF PARALLELRECHNERN if [[ "$cond1" = parallel || "$cond2" = parallel ]] then # PRUEFEN, OB DIE ANZAHL DER ZU VERWENDENDEN PES ANGEGEBEN WURDE if [[ ! -n $numprocs ]] then printf "\n" printf "\n +++ option \"-K parallel\" requires additional specification" printf "\n of the number of processors to be used by" printf "\n mrun-option \"-X\" or by environment-variable" printf "\n \"numprocs\" in the configuration file" locat=numprocs; (( iec = 0 )); exit fi # PRUEFEN, OB DIE PROZESSORANZAHL PRO KNOTEN ANGEGEBEN WURDE (GGF. # DEFAULT-WERT SETZEN) UND OB SIE EIN GANZZAHLIGER TEILER DER # GESAMTPROZESSORANZAHL IST if [[ "$tasks_per_node" = "" ]] then printf "\n" printf "\n +++ option \"-T\" (tasks per node) is missing" printf "\n set -T option or define tasks_per_node in the config file" locat=tasks_per_node; (( iec = 0 )); exit fi (( ival = $tasks_per_node )) (( pes = numprocs )) # if [[ $(echo $package_list | grep -c dvrp_graphics+1PE) = 1 ]] # then # (( pes = pes - 1 )) # fi (( ii = pes / ival )) if (( pes - ii * ival > 0 )) then printf "\n" printf "\n +++ tasks per node (option \"-T\") must be an integral" printf "\n divisor of the total number of processors (option \"-X\")" printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\"" locat=tasks_per_node; (( iec = 0 )); exit fi # IBMY HAT NUR EINEN KNOTEN if [[ $host = ibmy ]] then if [[ "$tasks_per_node" != "" && "$tasks_per_node" != "$numprocs" ]] then printf "\n" printf "\n +++ on ibmy, tasks per node (option \"-T\") must be equal to the" printf "\n total number of processors (option \"-X\")" printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\"" locat=tasks_per_node; (( iec = 0 )); exit fi fi # SETTINGS FOR SUBJOB-COMMAND TOPT="-T $tasks_per_node" OOPT="-O $threads_per_task" # GESAMTZAHL DER KNOTEN BESTIMMEN if [[ "$tasks_per_node" != "" ]] then (( nodes = numprocs / ( tasks_per_node * threads_per_task ) )) fi # PRUEFEN, OB NODE USAGE EINEN ERLAUBTEN WERT HAT BZW. DEN DEFAULT # SETZEN if [[ $node_usage = default ]] then if [[ $host = ibms ]] then node_usage=shared elif [[ $(echo $host | cut -c1-5) = lcsgi ]] then node_usage=singlejob else node_usage=not_shared fi fi if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage | cut -c1-3)" != "sla" ]] then printf "\n" printf "\n +++ node usage (option \"-n\") is only allowed to be set" printf "\n \"shared\" or \"not_shared\"" locat=tasks_per_node; (( iec = 0 )); exit fi fi # PRUEFEN, OB HOSTFILE EXISTIERT if [[ -n $hostfile ]] then if [[ ! -f $hostfile ]] then printf "\n" printf "\n +++ hostfile \"$hostfile\" does not exist" locat=hostfile; exit fi fi # PRUEFEN, OB RHOSTS DATEI EXISTIERT. GEGEBENENFALLS ANLEGEN BZW. ERWEITERN if [[ $host = ibmy && $do_remote = false ]] then if [[ ! -f $HOME/.rhosts ]] then echo "gfdl5.yonsei.ac.kr" > $HOME/.rhosts printf "\n\n *** file:" printf "\n $HOME/.rhosts" printf "\n was created\n" fi if [[ $(grep -c gfdl5.yonsei.ac.kr $HOME/.rhosts) = 0 ]] then echo "gfdl5.yonsei.ac.kr" >> $HOME/.rhosts printf "\n\n *** file:" printf "\n $HOME/.rhosts" printf "\n was extended by the name of the current host\n" fi fi # Set default value for the maximum number of parallel io streams if [[ "$maximum_parallel_io_streams" = "" ]] then maximum_parallel_io_streams=$numprocs fi # FALLS NICHT VORGEGEBEN, DEFAULT-QUEUE AUF DER ZIELMASCHINE FESTLEGEN if [[ $queue = none ]] then case $host in (ibmh) queue=no_class;; (ibmkisti) queue=class.32plus;; (ibmy) queue=parallel;; (lckyoto) queue=ph;; (lcsgib) queue=bigq;; (lcsgih) queue=bigq;; (lctit) queue=S;; (nech) queue=none;; (necriam) queue=SP;; (unics) queue=unics;; esac fi # VOLLSTAENDIGE DATEINAMEN DER INPUT-FILES BILDEN, # INPUT-DATEIEN AUF VORHANDENSEIN PRUEFEN UND EVTL. HOECHSTE ZYKLUSNUMMER # ERMITTELN (( i = 0 )) while (( i < iin )) do (( i = i + 1 )) (( maxcycle = 0 )) # NAMENSBILDUNG (EVTL. IST FESTER DATEINAME VORGEGEBEN) if [[ "${actionin[$i]}" = di ]] then remotepathin[$i]=${pathin[$i]}/${endin[$i]} # REMOTE-PFAD ERST AUF # REM-MASCHINE AUSWERTEN eval filename=${pathin[$i]}/${endin[$i]} else remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # REMOTE-PFAD ERST AUF # REM-MASCHINE AUSWERTEN eval filename=${pathin[$i]}/${afname}${endin[$i]} fi # PRUEFEN AUF VORHANDENSEIN if [[ $(ls $filename* 2>&1 | grep -c "not found") = 1 || \ $(ls $filename* 2>&1 | grep -c "nicht gefunden") = 1 || \ $(ls $filename* 2>&1 | grep -c "No such file") = 1 || \ $(ls $filename* 2>&1 | grep -c "does not exist") = 1 ]] then # DATEIEN MIT EXTENSION (Z.B. NC) MUESSEN NICHT ZWINGEND VORHANDEN # SEIN, DESHALB IN SOLCHEN FAELLEN KEIN ABBRUCH. DIES IST NUR EINE # VORUEBERGEHENDE LOESUNG (OKT 05). NICHT ZWINGEND BENOETIGTE # EINGABEDATEIEN SOLLTEN EINE SPEZIELLE OPTION IN DER DATEI- # VERBINDUNGSANWEISUNG BEKOMMEN (Z.B. inopt?) if [[ "${transin[$i]}" != "locopt" ]] then printf "\n\n +++ INPUT-file: " if [[ "${extin[$i]}" = "" ]] then printf "\n $filename" else printf "\n $filename.${extin[$i]}" fi printf "\n does not exist\n" locat=input; exit else transin[$i]="unavailable" fi else # ZYKLUSNUMMER FESTSTELLEN ls -1 -d $filename > filelist 2>/dev/null ls -1 -d $filename.* >> filelist 2>/dev/null while read zeile do cycle=$(print $zeile | cut -f2 -d".") if [[ "$cycle" = "$zeile" ]] then (( icycle = 0 )) elif [[ "$cycle" = "${extin[$i]}" ]] then (( icycle = 0 )) else (( icycle = $cycle )) fi if (( icycle > maxcycle )) then (( maxcycle = icycle )) file_to_be_used=$zeile fi done 0 )) then if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]] then filename=${filename}.$maxcycle.${extin[$i]} else filename=${filename}.$maxcycle fi else if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]] then filename=${filename}.${extin[$i]} fi fi # DATEINAMEN OHNE PFAD ABER MIT ZYKLUSNUMMER ABSPEICHERN, # DA SPAETER BEI RUECKSPEICHERN VOM ARCHIVSYSTEM EVTL. BENOETIGT absnamein[$i]=$filename if (( maxcycle > 0 )) then if [[ "${actionin[$i]}" = di ]] then frelin[$i]=${endin[$i]}.$maxcycle else frelin[$i]=${afname}${endin[$i]}.$maxcycle fi else if [[ "${actionin[$i]}" = di ]] then frelin[$i]=${endin[$i]} else frelin[$i]=${afname}${endin[$i]} fi fi fi done # VOLLSTAENDIGE DATEINAMEN (OHNE $ ODER ~) DER OUTPUT-FILES BILDEN, # OUTPUT-DATEIEN AUF VORHANDENSEIN PRUEFEN UND EVTL. HOECHSTE ZYKLUSNUMMER # ERMITTELN ODER, FALLS NICHT VORHANDEN, PRUEFEN, OB SIE SICH ANLEGEN LASSEN # DIESE AKTIONEN FINDEN NICHT STATT, WENN PROGRAMM AUF REMOTE-MASCHINE # RECHNET UND DATEI ANSCHLIESSEND TRANSFERIERT WERDEN SOLL! (( i = 0 )) while (( i < iout )) do (( i = i + 1 )) if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]] then if [[ "${actionout[$i]}" = tr ]] then actionout[$i]="" elif [[ "${actionout[$i]}" = trpe ]] then actionout[$i]=pe elif [[ "${actionout[$i]}" = tra ]] then actionout[$i]=a fi (( maxcycle = 0 )) eval filename=${pathout[$i]}/${fname}${endout[$i]} eval catalogname=${pathout[$i]} if [[ $(ls $filename* 2>&1 | grep -c "not found") = 1 || \ $(ls $filename* 2>&1 | grep -c "nicht gefunden") = 1 || \ $(ls $filename* 2>&1 | grep -c "No such file") = 1 || \ $(ls $filename* 2>&1 | grep -c "does not exist") = 1 ]] then # OUTPUT-DATEI NICHT VORHANDEN. PRUEFEN, OB ANLEGEN MOEGLICH. if cat /dev/null > $filename then rm $filename else # PRUEFEN, OB KATALOG VORHANDEN UND EVTL. DIESEN ANLEGEN if [[ ! -d $catalogname ]] then if mkdir -p $catalogname then printf "\n\n *** directory:" printf "\n $catalogname" printf "\n was created\n" else printf "\n\n +++ OUTPUT-file:" printf "\n $filename" printf "\n cannot be created, because directory does not exist" printf "\n and cannot be created either" printf "\n" locat=output ; exit fi 2>/dev/null else printf "\n\n +++ OUTPUT-file:" printf "\n $filename" printf "\n cannot be created, although directory exists" printf "\n" locat=output ; exit fi fi 2>/dev/null else # ZYKLUSNUMMER FESTSTELLEN ls -1 -d $filename > filelist 2>/dev/null ls -1 -d $filename.* >> filelist 2>/dev/null while read zeile do cycle=$(print $zeile | cut -f2 -d".") if [[ "$cycle" = "$zeile" || "$cycle" = ${extout[$i]} ]] then (( icycle = 1 )) else (( icycle = $cycle + 1 )) fi if (( icycle > maxcycle )) then (( maxcycle = icycle )) fi done 0 )) then filename=${filename}.$maxcycle if cat /dev/null > $filename then rm $filename else printf "\n +++ OUTPUT-file:" printf "\n $filename" printf "\n cannot be created" locat=output ; exit fi fi else (( maxcycle = maxcycle - 1 )) if (( maxcycle > 0 )) then filename=${filename}.$maxcycle fi fi # DATEINAMEN OHNE PFAD ABER MIT ZYKLUSNUMMER ABSPEICHERN, # DA SPAETER BEI ABLAGE AUF ARCHIVSYSTEM BZW. FUER # DATEI OUTPUT_FILE_CONNECTIONS EVTL. BENOETIGT pathout[$i]=$filename if (( maxcycle > 0 )) then frelout[$i]=${fname}${endout[$i]}.$maxcycle else frelout[$i]=${fname}${endout[$i]} fi fi done # DAS DVR-PAKET ERFORDERT EINE ENTSPRECHENDE BIBLIOTHEK if [[ $(echo $package_list | grep -c dvrp_graphics) != 0 ]] then if [[ "$dvr_inc" = "" ]] then printf "\n\n +++ no value for \"dvr_inc\" given in configuration file" printf "\n This is required for the dvrp_graphics package.\n" locat=dvr; exit fi if [[ "$dvr_lib" = "" ]] then printf "\n\n +++ no value for \"dvr_lib\" given in configuration file" printf "\n This is required for the dvrp_graphics package.\n" locat=dvr; exit fi fi # PRUEFEN, OB ENTWEDER HAUPTPROGRAMM ODER NUR EIN AUSFUEHRBARES # PROGRAMM VEREINBART WURDE (IN DIESEM FALL BRAUCHT IM WEITEREN NICHT # UEBERSETZT ZU WERDEN) if [[ "$mainprog" = "" && "$executable" = "" ]] then printf "\n +++ neither main program nor executable defined" locat=source; exit elif [[ "$mainprog" != "" && "$executable" != "" ]] then printf "\n +++ main program as well as executable defined" locat=source; exit elif [[ "$mainprog" = "" && "$executable" != "" ]] then do_compile=false fi # SOURCE-VERZEICHNIS ZUM AUFSAMMELN DER ZU UEBERSETZENDEN PROGRAMMTEILE # ERZEUGEN. HIERHIN WERDEN SPAETER IM FALL VON BATCH-JOBS AUCH DAS MRUN- # SCRIPTS SOWIE DIE KONFIGURATIONSDATEI KOPIERT if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]] then rm -rf SOURCES_FOR_RUN_$fname mkdir SOURCES_FOR_RUN_$fname fi # ALLE ZU UEBERSETZENDEN PROGRAMMTEILE ZUSAMMENSAMMELN # BEI BATCH-JOBS IST DIES NICHT NOETIG, WEIL DIE PROGRAMMTEILE BEREITS DURCH # DEN MRUN-AUFRUF ERMITTELT SIND, DER DEN BATCH-JOB GENERIERT HAT, UND # IM VERZEICHNIS SOURCES_FOR_RUN_... ABGELEGT SIND if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]] then [[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED [[ "$source_list" = WP ]] && source_list=WRITE_PERMIT # EVTL. ZU UEBERSETZENDE PROGRAMMTEILE DADURCH BESTIMMEN, DASS GEPRUEFT # WIRD, WELCHE DATEIEN WRITE-PERMIT BESITZEN (DATEIEN SOLLTEN DESHALB # UNTER RCS-KONTROLLE STEHEN). MIT DER VARIABLEN EXCLUDE KOENNEN # BESTIMMTE DATEIEN GRUNDSAETZLICH VON DER UEBERSETZUNG AUSGESCHLOSSEN # WERDEN. DIES IST NUR BEI MANUELLEM START VON MRUN DURCH DEN BENUTZER # MOEGLICH, DA BEI AUTOMATISCHEN RESTARTS TEST DURCH DIE TATSAECHLICH # ZU UBERSETZENDEN DATEIEN ERSETZT IST. # ALLE ERMITTELTEN DATEIEN WERDEN IM VERZEICHNIS SOURCES_FOR_RUN_... # GESAMMELT if [[ "$source_list" = WRITE_PERMIT ]] then source_list="" cd $source_path # ALLE MOEGLICHEN QUELLCODEDATEIEN AUFLISTEN Names=$(ls -1 *.f90 2>&1) [[ $(echo $Names | grep -c '*.f90') = 0 ]] && Filenames="$Names" Names=$(ls -1 *.F90 2>&1) [[ $(echo $Names | grep -c '*.F90') = 0 ]] && Filenames="$Filenames $Names" Names=$(ls -1 *.F 2>&1) [[ $(echo $Names | grep -c '*.F') = 0 ]] && Filenames="$Filenames $Names" Names=$(ls -1 *.f 2>&1) [[ $(echo $Names | grep -c '*.f') = 0 ]] && Filenames="$Filenames $Names" Names=$(ls -1 *.c 2>&1) [[ $(echo $Names | grep -c '*.c') = 0 ]] && Filenames="$Filenames $Names" # DATEIEN MIT WRITE-PERMIT NACH SOURCES_FOR_RUN_... KOPIEREN for dateiname in $Filenames do if [[ -w $dateiname ]] then if [[ "$exclude" = "" || $(echo $exclude | grep -c $dateiname) = 0 ]] then cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname source_list=$source_list"$dateiname " fi fi done cd - > /dev/null elif [[ "$source_list" = LOCALLY_MODIFIED ]] then # MODIFIZIERTE DATEIEN DER SVN-ARBEITSKOPIE BESTIMMEN source_list="" cd $source_path # PRUEFEN, OB VERZEICHNIS UEBERHAUPT UNTER SVN-KONTROLLE STEHT if [[ ! -d .svn ]] then printf "\n\n +++ source directory" printf "\n \"$source_path\" " printf "\n is not under control of \"subversion\"." printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n" fi # ALLE MODIFIZIERTEN QUELLCODEDATEIEN AUFLISTEN Filenames="" svn status > tmp_mrun while read line do firstc=`echo $line | cut -c1` if [[ $firstc = M || $firstc = "?" ]] then Name=`echo "$line" | cut -c8-` extension=`echo $Name | cut -d. -f2` if [[ "$extension" = f90 || "$extension" = F90 || "$extension" = f || "$extension" = F || "$extension" = c ]] then Filenames="$Filenames "$Name fi fi done < tmp_mrun # DATEIEN NACH SOURCES_FOR_RUN_... KOPIEREN for dateiname in $Filenames do cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname source_list=$source_list"$dateiname " done cd - > /dev/null # MITTELS OPTION -s ANGEGEBENE DATEIEN NACH SOURCES_FOR_RUN_... KOPIEREN # BEI AUTOMATISCHEN FORTSETZUNGSLAEUFEN SIND DORT SCHON ALLE DATEIEN # VORHANDEN elif [[ "$source_list" != "" && $restart_run != true ]] then cd $source_path for filename in $source_list do # QUELLTEXT-DATEI DARF KEINE PFADE BEINHALTEN if [[ $(print $filename | grep -c "/") != 0 ]] then printf "\n +++ source code file: $filename" printf "\n must not contain (\"/\") " locat=source; exit fi if [[ ! -f $filename ]] then printf "\n +++ source code file: $filename" printf "\n does not exist" locat=source; exit else cp $filename $working_directory/SOURCES_FOR_RUN_$fname fi done cd - > /dev/null fi # PRUEFEN, OB ENTWEDER HAUPTPROGRAMM VORHANDEN UND ES EVTL. IN DER # LISTE DER ZU UEBERSETZENDEN PROGRAMMTEILE MIT ENTHALTEN IST (WENN # NICHT, WIRD ES DIESER LISTE HINZUGEFUEGT) if [[ $restart_run != true ]] then if [[ ! -f "$source_path/$mainprog" ]] then printf "\n\n +++ main program: $mainprog" printf "\n does not exist in source directory" printf "\n \"$source_path\"\n" locat=source; exit else if [[ $(echo $source_list | grep -c $mainprog) = 0 ]] then cp $source_path/$mainprog SOURCES_FOR_RUN_$fname source_list=${mainprog}" $source_list" fi fi fi # MAKEFILE AUF VORHANDENSEIN PRUEFEN UND KOPIEREN # BEI RESTART-LAEUFEN LIEGT ES SCHON IM VERZEICHNIS SOURCES_FOR_RUN... if [[ "$restart_run" != true ]] then [[ "$makefile" = "" ]] && makefile=$source_path/Makefile if [[ ! -f $makefile ]] then printf "\n +++ file \"$makefile\" does not exist" locat=make; exit else cp $makefile SOURCES_FOR_RUN_$fname/Makefile fi fi # DATEIEN AUS ZUSAETZLICHEM QUELLVERZEICHNIS HINZUFUEGEN if [[ $restart_run != true && "$add_source_path" != "" ]] then # GIBT ES DAS VERZEICHNIS UEBERHAUPT? if [[ ! -d $add_source_path ]] then printf "\n\n +++ WARNING: additional source code directory" printf "\n \"$add_source_path\" " printf "\n does not exist or is not a directory." printf "\n No source code will be used from this directory!\n" add_source_path="" sleep 3 else cd $add_source_path found=false Names=$(ls -1 *.f90 2>&1) [[ $(echo $Names | grep -c '*.f90') = 0 ]] && AddFilenames="$Names" Names=$(ls -1 *.F90 2>&1) [[ $(echo $Names | grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names" Names=$(ls -1 *.F 2>&1) [[ $(echo $Names | grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names" Names=$(ls -1 *.f 2>&1) [[ $(echo $Names | grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names" Names=$(ls -1 *.c 2>&1) [[ $(echo $Names | grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names" cd - > /dev/null cd SOURCES_FOR_RUN_$fname # COPY MAKEFILE IF EXISTING if [[ -f $add_source_path/Makefile ]] then printf "\n\n *** user Makefile from directory" printf "\n \"$add_source_path\" is used \n" sleep 1 cp $add_source_path/Makefile . fi for dateiname in $AddFilenames do if [[ -f $dateiname ]] then printf "\n +++ source code file \"$dateiname\" found in additional" printf "\n source code directory \"$add_source_path\" " printf "\n but was also given with option \"-s\" which means that it should be taken" printf "\n from directory \"$source_path\"." locat=source; exit fi cp $add_source_path/$dateiname . source_list="$source_list $dateiname" # CHECK IF FILE IS CONTAINED IN MAKEFILE if [[ $(grep -c $dateiname Makefile) = 0 ]] then printf "\n\n +++ user file \"$dateiname\" " printf "\n is not listed in Makefile \n" locat=source; exit else # Default User-Interface von der Liste entfernen, falls Datei # ein User-Interface enthaelt # if [[ $( cat $dateiname | grep -c "END SUBROUTINE user_parin" ) != 0 ]] # then # if [[ $dateiname != user_interface.f90 && -f user_interface.f90 ]] # then # rm -rf user_interface.f90 # source_list=`echo $source_list | sed -e 's/user_interface.f90//'` # printf "\n\n *** default \"user_interface.f90\" removed from the files to be translated" # printf "\n since a user-interface is found in file" # printf "\n \"$add_source_path/$dateiname\" \n" # sleep 3 # else if [[ $found = false ]] then found=true printf "\n\n *** following user file(s) added to the" printf " files to be translated:\n " fi printf "$dateiname " sleep 0.5 fi done [[ $found = true ]] && printf "\n" cd - > /dev/null fi fi # ALLE UNTERPROGRAMME, DIE ZU VEREINBARTEN SOFTWAREPAKETEN GEHOEREN, # DER LISTE DER ZU UEBERSETZENDEN DATEIEN HINZUFUEGEN if [[ $restart_run != true && -n $package_list ]] then cd $source_path for package in $package_list do [[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics # ERMITTELE ALLE DATEIEN, DIE ZUM PAKET GEHOEREN # FEHLERMELDUNGEN WERDEN ABGEFANGEN, DA * AUCH VERZEICHNISSNAMEN # LIEFERT package_source_list=`grep "defined( __$package " * 2>/dev/null | cut -f1 -d:` # FUEGE DIESE DATEIEN DER LISTE DER ZU UEBERSETZENDEN DATEIEN # HINZU, FALLS SIE NOCH NICHT DAZUGEHOEREN for source_list_name in $package_source_list do if [[ $(echo $source_list | grep -c $source_list_name) = 0 ]] then # NUR DATEIEN MIT GUELTIGEN ENDUNGEN VERWENDEN ending=`echo $source_list_name | cut -f2 -d.` if [[ "$ending" = f90 || "$ending" = F90 || "$ending" = f || "$ending" = F || "$ending" = c ]] then cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname source_list="$source_list $source_list_name" fi fi done done cd - > /dev/null fi # MAKEFILE AUF VORHANDENSEIN PRUEFEN UND KOPIEREN # BEI RESTART-LAEUFEN LIEGT ES SCHON IM VERZEICHNIS SOURCES_FOR_RUN... # if [[ "$restart_run" != true ]] # then # [[ "$makefile" = "" ]] && makefile=$source_path/Makefile # if [[ ! -f $makefile ]] # then # printf "\n +++ file \"$makefile\" does not exist" # locat=make; exit # else # cp $makefile SOURCES_FOR_RUN_$fname/Makefile # fi # fi fi # do_compile=true # FALLS PROGRAMMTEILE UEBERSETZT WERDEN SOLLEN, FOLGEN JETZT EINIGE # UEBERPRUEFUNGEN UND DAS SETZEN DER PRAEPROZESSOR-DIREKTIVEN if [[ $do_compile = true ]] then # PRAEPROZESSOR-DIREKTIVEN ZUM SELEKTIVEN AUSWAEHLEN VON CODETEILEN # ZUSAMMENSETZEN # DIREKTIVEN ZUM AKTIVIEREN VON RECHNERSPEZIFISCHEM CODE if [[ $(echo $localhost | cut -c1-3) = ibm ]] then cpp_options="${cpp_options},-D__ibm=__ibm" elif [[ $(echo $localhost | cut -c1-3) = nec ]] then cpp_options="$cpp_options -D__nec" elif [[ $(echo $localhost | cut -c1-2) = lc ]] then cpp_options="$cpp_options -D__lc" else cpp_options="$cpp_options -D__$localhost" fi # DIREKTIVEN DIE DURCH OPTION -K BESTIMMT WERDEN (Z.B. PARALLEL) if [[ $(echo $localhost | cut -c1-3) = ibm ]] then [[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1" [[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2" else [[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1" [[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2" fi # DIREKTIVEN DIE SOFTWAREPAKETE AKTIVIEREN (OPTION -p) if [[ -n $package_list ]] then for package in $package_list do if [[ $(echo $localhost | cut -c1-3) = ibm ]] then if [[ $package != "dvrp_graphics+1PE" ]] then cpp_options="${cpp_options},-D__$package=__$package" else cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics" export use_seperate_pe_for_dvrp_output=true fi else if [[ $package != "dvrp_graphics+1PE" ]] then cpp_options="$cpp_options -D__$package" else cpp_options="$cpp_options -D__dvrp_graphics" export use_seperate_pe_for_dvrp_output=true fi fi done fi # DIREKTIVEN DIE DURCH OPTION -D FESTGELEGT SIND if [[ -n $cpp_opts ]] then for popts in $cpp_opts do if [[ $(echo $localhost | cut -c1-3) = ibm ]] then cpp_options="${cpp_options},-D__$popts=__$popts" else cpp_options="$cpp_options -D__$popts" fi done fi else # BEI LOKALEN RECHNUNGEN PRUEFEN, OB EXECUTABLE VORHANDEN if [[ $do_remote = false ]] then if [[ ! -f $executable ]] then printf "\n +++ executable file: $executable" printf "\n does not exist" locat=executable; exit fi fi fi # JOBMODUS FESTSTELLEN if [[ "$ENVIRONMENT" = BATCH ]] then jobmo=BATCH else jobmo=INTERACTIVE fi # no interactive runs on lctit if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]] then printf "\n +++ no interactive runs allowed on host \"$host\" " printf "\n please submit batch job using mrun option \"-b\" \n" locat=normal; exit fi # HOSTSPEZIFISCHE DEFAULT-COMPILER SETZEN, FALLS NICHT BEREITS # DURCH BENUTZER ANDERWEITIG VEREINBART if [[ "$compiler_name" = "" ]] then printf "\n +++ no compiler specified for \"$host $cond1 $cond2\"" locat=compiler_name; exit fi # COMPILER AUF RIAMS NEC UEBERSCHREIBEN [[ $localhost = necriam ]] && compiler_name=mpif90 # TEMPORAEREN KATALOGNAMEN BESTIMMEN kennung=$RANDOM if [[ "$tmp_user_catalog" = "" ]] then if [[ $localhost = ibmh ]] then tmp_user_catalog=$SCRATCH elif [[ $localhost = nech ]] then tmp_user_catalog=$WRKSHR else tmp_user_catalog=/tmp fi fi TEMPDIR=$tmp_user_catalog/${usern}.$kennung # KATALOGNAMEN FUER ZWISCHENSPEICHERUNG VON FORTSETZUNGSLAUFDATEIEN # BESTIMMEN if [[ "$tmp_data_catalog" = "" ]] then if [[ $localhost = nech ]] then tmp_data_catalog=$WRKSHR/mrun_restart_data else tmp_data_catalog=/tmp/mrun_restart_data fi fi # EVENTUELL BEI LOKALEN RECHNUNGEN $-ZEICHEN IN ENVIRONMENT-VARIABLEN # ERSETZEN if [[ $do_remote = false && $do_compile = true ]] then eval fopts=\"$fopts\" eval lopts=\"$lopts\" fi # COMPILE- UND LINK-OPTIONEN BESTIMMEN fopts="$fopts $netcdf_inc $dvr_inc" lopts="$lopts $netcdf_lib $dvr_lib" ROPTS="$ropts" if [[ ( $(echo $host | cut -c1-3) = nec || $(echo $host | cut -c1-3) = ibm || $host = lckyoto || $host = lcsgih || $host = lcsgib || $host = lctit || $host = lcfimm || $host = lcxt4 || $host = lcxt5m || $host = lck || $host = lckordi) && -n $numprocs ]] then XOPT="-X $numprocs" fi # PRUEFEN DER CPU-ZEIT. (CPUMAX WIRD ALS ENV-VARIABLE VOM HAUTPRO- # GRAMM BENOETIGT done=false while [[ $done = false ]] do cputime=$cpumax if (( $cputime == 0 )) then if [[ $do_batch = true ]] then printf "\n +++ cpu-time is undefined" printf "\n >>> Please type CPU-time in seconds as INTEGER:" printf "\n >>> " read cputime 1>/dev/null 2>&1 else cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS fi else done=true fi cpumax=$cputime done (( minuten = cputime / 60 )) (( sekunden = cputime - minuten * 60 )) # PRUEFEN DER KERNSPEICHERANFORDERUNG if [[ $do_batch = true ]] then done=false while [[ $done = false ]] do if (( memory == 0 )) then printf "\n +++ memory demand is undefined" printf "\n >>> Please type memory in MByte per process as INTEGER:" printf "\n >>> " read memory 1>/dev/null 2>&1 else done=true fi done fi # PRUEFEN, OB FUER REMOTE-RECHNUNGEN EIN BENUTZERNAME ANGEGEBEN WURDE if [[ $do_remote = true && -z $remote_username ]] then while [[ -z $remote_username ]] do printf "\n +++ username on remote host \"$host\" is undefined" printf "\n >>> Please type username:" printf "\n >>> " read remote_username done mc="$mc -u$remote_username" fi # set module load command and export for subjob if [[ "$modules" != "" ]] then if [[ $host = lctit ]] then export module_calls=". $modules" else export module_calls="module load ${modules};" fi fi # bugfix for wrong netcdf module and for netCDF4 usage in case of mpt if [[ $host = lcsgib || $host = lcsgih ]] then if [[ $(echo $module_calls | grep -c netcdf/3.6.3-intel) != 0 ]] then export module_calls="$module_calls export LD_LIBRARY_PATH=/sw/dataformats/netcdf/3.6.3-intel/lib:\$LD_LIBRARY_PATH;" fi # if [[ $(echo $module_calls | grep -c mpt) != 0 ]] # then # export module_calls="$module_calls export LD_LIBRARY_PATH=/sw/sgi/mpt/2011-02-07/lib:\$LD_LIBRARY_PATH;" # echo "*** module_calls = $module_calls" # fi fi # SET DEFAULT VALUE FOR MPI MODULE TO BE USED ON SGI-ALTIX if [[ $host = lcsgib || $host = lcsgih ]] then if [[ $(echo $modules | grep -c mpt ) != 0 ]] then mpilib=mpt elif [[ $(echo $modules | grep -c mvapich ) != 0 ]] then mpilib=mvapich elif [[ $(echo $modules | grep -c impi ) != 0 ]] then mpilib=impi fi fi ########################################################################### # HEADER-AUSGABE ########################################################################### calltime=$(date) printf "\n" # [[ $silent = false ]] && clear printf "#--------------------------------------------------------------# \n" printf "| $version$calltime | \n" printf "| | \n" spalte1="called on:"; spalte2=$localhost_realname printf "| $spalte1$spalte2 | \n" if [[ $local_compile = false ]] then if [[ $do_remote = true ]] then spalte1="execution on:"; spalte2="$host (username: $remote_username)" else spalte1="execution on:"; spalte2="$host ($localhost_realname)" fi else spalte1="compiling test only!"; spalte2="" fi printf "| $spalte1$spalte2 | \n" if [[ -n $numprocs ]] then spalte1="number of PEs:"; spalte2=$numprocs printf "| $spalte1$spalte2 | \n" fi if [[ -n $tasks_per_node ]] then spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)" printf "| $spalte1$spalte2 | \n" fi if [[ $maximum_parallel_io_streams != $numprocs ]] then spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams" printf "| $spalte1$spalte2 | \n" fi if [[ $use_openmp = true ]] then spalte1="threads per task:"; spalte2="$threads_per_task" printf "| $spalte1$spalte2 | \n" fi printf "| | \n" if [[ $do_compile = true ]] then if [[ "$mopts" != "" ]] then spalte1="make options:"; spalte2=$mopts printf "| $spalte1$spalte2 | \n" zeile=$(echo "$mopts" | cut -c41-) while [[ "$zeile" != "" ]] do spalte1="" spalte2=$zeile printf "| $spalte1$spalte2 | \n" zeile=$(echo "$zeile" | cut -c41-) done fi spalte1="cpp directives:"; spalte2=$cpp_options printf "| $spalte1$spalte2 | \n" zeile=$(echo "$cpp_options" | cut -c41-) while [[ "$zeile" != "" ]] do spalte1="" spalte2=$zeile printf "| $spalte1$spalte2 | \n" zeile=$(echo "$zeile" | cut -c41-) done spalte1="compiler options:"; spalte2="$fopts" printf "| $spalte1$spalte2 | \n" zeile=$(echo "$fopts" | cut -c41-) while [[ "$zeile" != "" ]] do spalte1="" spalte2=$zeile printf "| $spalte1$spalte2 | \n" zeile=$(echo "$zeile" | cut -c41-) done spalte1="linker options:"; spalte2=$lopts printf "| $spalte1$spalte2 | \n" zeile=$(echo "$lopts" | cut -c41-) while [[ "$zeile" != "" ]] do spalte1="" spalte2=$zeile printf "| $spalte1$spalte2 | \n" zeile=$(echo "$zeile" | cut -c41-) done spalte1="modules to be load:"; spalte2=$modules printf "| $spalte1$spalte2 | \n" zeile=$(echo "$modules" | cut -c41-) while [[ "$zeile" != "" ]] do spalte1="" spalte2=$zeile printf "| $spalte1$spalte2 | \n" zeile=$(echo "$zeile" | cut -c41-) done spalte1="main program":; spalte2=$mainprog printf "| $spalte1$spalte2 | \n" else spalte1=executable:; spalte2=$executable printf "| $spalte1$spalte2 | \n" fi printf "| | \n" spalte1="base name of files":; spalte2=$fname printf "| $spalte1$spalte2 | \n" if [[ $fname != $afname ]] then spalte1="base name of input files":; spalte2=$afname printf "| $spalte1$spalte2 | \n" fi spalte1="INPUT control list":; spalte2=$input_list printf "| $spalte1$spalte2 | \n" spalte1="OUTPUT control list":; spalte2=$output_list printf "| $spalte1$spalte2 | \n" if [[ $do_batch = true || "$LOADLBATCH" = yes ]] then spalte1="memory demand / PE":; spalte2="$memory MB" printf "| $spalte1$spalte2 | \n" spalte1=CPU-time:; spalte2="$minuten:$sekunden" printf "| $spalte1$spalte2 | \n" fi if [[ $do_compile = true ]] then printf "| | \n" printf "| Files to be compiled: | \n" zeile=$source_list while [[ "$zeile" != "" ]] do spalte3=$zeile printf "| $spalte3 | \n" zeile=$(echo "$zeile" | cut -c61-) done fi printf "#--------------------------------------------------------------#" # BEDINGTE AUSGABE DER DATEIVERBINDUNGEN if [[ $do_trace = true ]] then (( i = 0 )) while (( i < iin )) do (( i = i + 1 )) if (( i == 1 )) then printf "\n\n >>> INPUT-file assignments:\n" fi printf "\n ${localin[$i]} : ${absnamein[$i]}" done (( i = 0 )) while (( i < iout )) do (( i = i + 1 )) if (( i == 1 )) then printf "\n\n >>> OUTPUT-file assignments:\n" fi printf "\n ${localout[$i]} : ${pathout[$i]}" done (( i = 0 )) while (( i < iic )) do (( i = i + 1 )) if (( i == 1 )) then printf "\n\n >>> INPUT-commands:\n" fi printf "\n ${in_command[$i]}" done (( i = 0 )) while (( i < ioc )) do (( i = i + 1 )) if (( i == 1 )) then printf "\n\n >>> OUTPUT-commands:\n" fi printf "\n ${out_command[$i]}" done fi # ABFRAGEN BEI AUFRUF AUF LOKALER MASCHINE if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]] then antwort=dummy printf "\n\n" while [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]] do printf " >>> everything o.k. (y/n) ? " read antwort done if [[ $antwort = n || $antwort = N ]] then locat=user_abort; (( iec = 0 )); exit fi if [[ $do_batch = true ]] then printf " >>> batch-job will be created and submitted" else if [[ $local_compile = false ]] then printf " >>> MRUN will now continue to execute on this machine" else printf " >>> a test compilation will now be carried out on this machine" fi fi fi # FALLS AUF DIESER MASCHINE GERECHNET WERDEN SOLL, WERDEN JETZT ENTSPRE- # CHENDE AKTIONEN DURCHGEFUEHRT if [[ $do_batch = false ]] then # TEMPORAEREN KATALOG ERZEUGEN mkdir -p $TEMPDIR chmod go+rx $TEMPDIR tmpcreate=true # set striping on lustre file system # if [[ $localhost = lcsgih ]] # then # lfs setstripe -s 8192k -c 16 $TEMPDIR # lfs getstripe $TEMPDIR # fi # SAEMTLICHE QUELLTEXT-DATEIEN BZW. AUSFUEHRBARES PROGRAMM IN # TEMPORAERES VERZEICHNIS KOPIEREN if [[ $do_compile = true ]] then # ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING # CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS) if [[ $localhost = nech ]] then TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung if mkdir -p $TEMPDIR_COMPILE then printf "\n *** \"$TEMPDIR_COMPILE\" " printf "\n is generated as temporary directory for cross compiling\n" else printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" " printf "\n needed for cross compilation failed" locat=compile exit fi else TEMPDIR_COMPILE=$TEMPDIR fi # PFADNAMEN FUER DAS MAKE-DEPOSITORY ERMITTELN line="" grep "%depository_path" $config_file > tmp_mrun while read line do if [[ "$line" != "" && $(echo $line | cut -c1) != "#" ]] then if [[ "$(echo $line | cut -d" " -s -f3)" = "" ]] then global_depository_path=`echo $line | cut -d" " -s -f2` fi fi done < tmp_mrun line="" grep " $localhost" $config_file | grep "%depository_path" > tmp_mrun while read line do if [[ "$line" != "" && $(echo $line | cut -c1) != "#" ]] then if [[ "$(echo $line | cut -d" " -s -f4)" = "$cond1" && "$(echo $line | cut -d" " -s -f5)" = "$cond2" ]] then local_depository_path=`echo $line | cut -d" " -s -f2` fi fi done < tmp_mrun if [[ "$local_depository_path" = "" ]] then if [[ "$global_depository_path" != "" ]] then local_depository_path=$global_depository_path else printf "\n\n +++ no depository path found in configuration file" printf "\n for local host \"$localhost\" " printf "\n please set \"\%depository_path\" in configuration file\n" locat=config_file; exit fi fi eval local_depository_path=$local_depository_path [[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1 [[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2 basename=`print $mainprog | cut -f1 -d"."` eval make_depository=${local_depository_path}/${basename}_current_version.tar if [[ ! -f $make_depository ]] then printf "\n" printf "\n *** WARNING: make depository \"$make_depository\" not found" printf "\n \"make\" will fail, if the Makefile or other source files are missing\n" else cp $make_depository $TEMPDIR_COMPILE cd $TEMPDIR_COMPILE tar -xf $make_depository > /dev/null 2>&1 cd - > /dev/null fi cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE else cp $executable ${TEMPDIR}/a.out fi # WECHSEL IN TEMPORAEREN KATALOG cd $TEMPDIR printf "\n *** changed to temporary directory: $TEMPDIR" # OUTPUT-DATEI-VERBINDUNGEN AUF TEMPORAERER DATEI ABLEGEN # DIESE DATEI KANN VON SPAETER AUFZURUFENDEN BENUTZERPROZEDUREN GELESEN # WERDEN, UM ZU LOKALEN DATEINAMEN GEHOERENDE PERMANENTE NAMEN ZU # ERMITTELN (( i = 0 )) while (( i < iout )) do (( i = i + 1 )) if [[ "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ]] then printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS else printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS fi done # EVTL. UEBERSETZUNGSAKTIONEN STARTEN if [[ $do_compile = true ]] then # COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS) printf "\n\n\n *** compilation starts \n$striche\n" printf " *** compilation with make using following options:\n" printf " make depository: $make_depository" if [[ "$mopts" != "" ]] then printf " make options: $mopts\n" fi printf " compilername: $compiler_name\n" printf " compiler options: $fopts\n" printf " preprocessor directives: $cpp_options \n" printf " linker options: $lopts \n" if [[ "$modules" != "" ]] then printf " modules to be load: $modules \n" fi printf " source code files: $source_list \n" if [[ $localhost = nech ]] then ssh 136.172.44.192 -l $usern ". /SX/opt/etc/initsx.sh; $module_calls cd \$HOME/work/${usern}.$kennung; sxmake $mopts -f Makefile PROG=a.out F90=$compiler_name COPT=\"$cpp_options\" F90FLAGS=\"$fopts\" LDFLAGS=\"$lopts\" " cp $TEMPDIR_COMPILE/a.out . [[ $? != 0 ]] && compile_error=true rm -rf $TEMPDIR_COMPILE elif [[ $localhost = ibmh ]] then printf " compiler is called via ssh on \"plogin1\" \n" ssh plogin1 -l $usern "export PATH=/sw/ibm/xlf/12.1.0.3/usr/bin:$PATH; $module_calls cd $TEMPDIR; make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT=\"$cpp_options\" F90FLAGS=\"$fopts\" LDFLAGS=\"$lopts\" " [[ ! -f a.out ]] && compile_error=true continue # ANDERENFALLS IST STATUS=1, FALLS A.OUT VORHANDEN elif [[ $localhost = lcsgib ]] then printf " compiler is called via ssh on \"bicegate0\" \n" ssh bicegate0 -l $usern ". /usr/share/modules/init/bash; $module_calls cd $TEMPDIR; make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT=\"$cpp_options\" F90FLAGS=\"$fopts\" LDFLAGS=\"$lopts\" " [[ ! -f a.out ]] && compile_error=true continue # ANDERENFALLS IST STATUS=1, FALLS A.OUT VORHANDEN elif [[ $localhost = lcsgih ]] then printf " compiler is called via ssh on \"hicegate0\" \n" ssh hicegate0 -l $usern ". /usr/share/modules/init/bash; $module_calls cd $TEMPDIR; make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT=\"$cpp_options\" F90FLAGS=\"$fopts\" LDFLAGS=\"$lopts\" 2>&1 " [[ ! -f a.out ]] && compile_error=true continue # ANDERENFALLS IST STATUS=1, FALLS A.OUT VORHANDEN elif [[ $localhost = lcflow ]] then printf " compiler is called via ssh on \"flow\" \n" ssh flow02.hpc.uni-oldenburg.de -l $usern ". /cm/local/apps/environment-modules/3.2.6/Modules/3.2.6/init/bash; echo $MODULEPATH; echo $MODULESHOME; MODULEPATH=/cm/shared/modulefiles/; module load netcdf/intel/64/4.1.3 intel/ics/64/2011.0.013 intel/impi/64/4.0.1.007 hdf5/intel/64/1.8.7; cd $TEMPDIR; make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT=\"$cpp_options\" F90FLAGS=\"$fopts\" LDFLAGS=\"$lopts\" " [[ ! -f a.out ]] && compile_error=true continue # ANDERENFALLS IST STATUS=1, FALLS A.OUT VORHANDEN else [[ $localhost = lcxt4 ]] && . /opt/modules/default/init/ksh [[ "$module_calls" != "" ]] && eval $module_calls make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts" fi if [[ $? != 0 || "$compile_error" = true || "$module_compile_error" = true ]] then printf "\n +++ error occured while compiling or linking" locat=compile # WORKAROUND: REMOVE IF CONSTRUCT LATER, BUT KEEP THE EXIT! # if [[ $localhost != lcsgib && $localhost != lcsgih ]] # then exit # else # locat=normal # fi else printf "$striche\n *** compilation finished \n" fi fi # FALLS NUR TESTWEISE KOMPILIERT WERDEN SOLLTE, IST MRUN JETZT FERTIG if [[ $local_compile = true ]] then cd $HOME rm -rf $TEMPDIR locat=local_compile; exit fi # BEREITSTELLEN DER INPUT-DATEIEN # SCHLEIFE UEBER ALLE VOM BENUTZER ANGEGEBENEN DATEIEN (( i = 0 )) while (( i < iin )) do (( i = i + 1 )) if (( i == 1 )) then printf "\n\n *** providing INPUT-files:\n$striche" fi # OPTIONALE DATEIEN BEI NICHTVORHANDENSEIN UEBERGEHEN if [[ "${transin[$i]}" = unavailable ]] then if [[ "${extin[$i]}" = "" || "${extin[$i]}" = " " ]] then printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" " printf "\n is not available!" else printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" " printf "\n is not available!" fi continue fi # PRUEFEN, OB EINZELDATEI ODER DATEI PRO PROZESSOR files_for_pes=false; datentyp=file if [[ "${actionin[$i]}" = pe && -n $numprocs ]] then files_for_pes=true; datentyp=directory actionin[$i]="" elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]] then actionin[$i]="" elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]] then files_for_pes=true; datentyp=directory actionin[$i]="ar" elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]] then actionin[$i]="ar" elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]] then files_for_pes=true; datentyp=directory actionin[$i]="fl" elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]] then actionin[$i]="fl" fi if [[ $files_for_pes = true ]] then printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}" else printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}" fi # INPUT-DATEI FUER EINEN FORTSETZUNGSLAUF. ES WIRD GEPRUEFT, # OB DIESE DATEI NOCH AUF DEM TEMPORAEREN DATENKATALOG VORHANDEN # IST. FALLS NICHT, WIRD VERSUCHT, SIE ANSCHLIESSEND VOM ARCHIV- # SERVER ZU HOLEN if [[ "${actionin[$i]}" = fl ]] then printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !" if [[ $files_for_pes = false ]] then if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]] then ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]} got_tmp[$i]=true elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]] then printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !" printf "\n *** trying to use backup copy in \"$WORK\" " cp $WORK/${frelin[$i]} ${localin[$i]} else printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" " printf "\n or \"$tmp_data_catalog\" does not exist!" printf "\n *** trying to get copy from archive" actionin[$i]=ar fi else if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]] then mkdir ${localin[$i]} cd $tmp_data_catalog/${frelin[$i]} for file in $(ls *) do ln $file $TEMPDIR/${localin[$i]} done cd $TEMPDIR got_tmp[$i]=true elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]] then printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !" printf "\n *** trying to use backup copy in \"$WORK\" " cp -r $WORK/${frelin[$i]} ${localin[$i]} else printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" " printf "\n or \"$tmp_data_catalog\" does not exist!" printf "\n *** trying to get copy from archive" actionin[$i]=ar fi fi fi # DATEI LIEGT AUF ARCHIV-SERVER if [[ "${actionin[$i]}" = ar ]] then if [[ $files_for_pes = false ]] then printf "\n file will be restored from archive-system ($archive_system)!" else printf "\n directory will be restored from archive-system ($archive_system)!" fi file_restored=false if [[ $archive_system = asterix ]] then do_stagein=true (( stagein_anz = 0 )) while [[ $do_stagein = true ]] do if [[ $files_for_pes = false ]] then stagein -O ${frelin[$i]} > STAGEIN_OUTPUT else stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT fi cat STAGEIN_OUTPUT if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]] then file_restored=true do_stagein=false else (( stagein_anz = stagein_anz + 1 )) if (( stagein_anz == 10 )) then printf "\n +++ stagein stoped after 10 tries" locat=stage exit fi printf "\n +++ restoring from archive failed, trying again:" sleep 900 fi done elif [[ $archive_system = DMF ]] then if [[ $files_for_pes = false ]] then printf "\n +++ restoring of single files impossible with $archive_system !\n" locat=DMF exit else find $ARCHIVE/${frelin[$i]} -type m -print | dmget cp -r $ARCHIVE/${frelin[$i]} $PWD file_restored=true fi elif [[ $archive_system = tivoli ]] then if [[ $files_for_pes = false ]] then if [[ $localhost = lcsgih ]] then ssh $usern@hicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD" else ssh $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD" fi else (( inode = 0 )) while (( inode < nodes )) do if [[ $localhost = lcsgih ]] then ssh $usern@hicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar" else ssh $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar" fi (( inode = inode + 1 )) done fi file_restored=true elif [[ $archive_system = ut ]] then if [[ $files_for_pes = false ]] then cp $UT/${frelin[$i]} . else (( inode = 0 )) while (( inode < nodes )) do tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar (( inode = inode + 1 )) done fi file_restored=true else printf "\n +++ archive_system=\"$archive_system\" restore impossible!" locat=rearchive exit fi if [[ $file_restored = true ]] then # DATEI AUCH AUF TEMPORAERES DATENVERZEICHNIS LEGEN, DAMIT # SIE BEI WEITEREN ZUGRIFFEN NOCH VORHANDEN IST [[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog if [[ $files_for_pes = false ]] then ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]} else mkdir $tmp_data_catalog/${frelin[$i]} ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]} fi got_tmp[$i]=true # DATEI UNTER LOKALEM NAMEN ZUR VERFUEGUNG STELLEN mv ${frelin[$i]} ${localin[$i]} fi fi # DATEI LIEGT IM VOM BENUTZER ANGEGEBENEN VERZEICHNIS if [[ "${actionin[$i]}" = "" || "${actionin[$i]}" = "di" || "${actionin[$i]}" = "npe" ]] then if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]] then # DATEI WIRD FUER DIE PROZESSOREN EINES PARALLERECHNERS BEREITGESTELLT printf "\n file will be provided for $numprocs processors" mkdir ${localin[$i]} ival=$numprocs (( ii = 0 )) while (( ii <= ival-1 )) do if (( ii < 10 )) then cp ${absnamein[$i]} ${localin[$i]}/_000$ii elif (( ii < 100 )) then cp ${absnamein[$i]} ${localin[$i]}/_00$ii elif (( ii < 1000 )) then cp ${absnamein[$i]} ${localin[$i]}/_0$ii else cp ${absnamein[$i]} ${localin[$i]}/_$ii fi (( ii = ii + 1 )) done else if [[ $files_for_pes = true ]] then # DIE DEN PROZESSOREN EINES PARALLELRECHNERS ZUGEHOERIGEN # DATEIEN WERDEN BEREITGESTELLT, INDEM ZUERST DER GESAMTE # KATALOGINHALT KOPIERT UND DANN DIE EINZELNEN DATEIEN # PER MOVE UMBENANNT WERDEN printf "\n providing $numprocs files for the respective processors" mkdir ${localin[$i]} if [[ $link_local_input = true ]] then printf " using ln -f\n" cd ${absnamein[$i]} for file in $(ls *) do ln -f $file ${localin[$i]} done cd $TEMPDIR fi # If "ln -f" fails of if "$link_local_input = false" do a normal "cp -r" if [[ ! -f "${localin[$i]}/_0000" ]] then if [[ $link_local_input = true ]] then printf " ln failed for .../_0000, using cp...\n" fi cp -r ${absnamein[$i]}/* ${localin[$i]} fi else # BEREITSTELLUNG AUF EINPROZESSORRECHNERN if [[ $link_local_input = true ]] then printf " using ln -f\n" ln -f ${absnamein[$i]} ${localin[$i]} fi # If "ln -f" fails of if "$link_local_input = false" do a normal "cp" if [[ ! -f "${localin[$i]}" ]] then if [[ $link_local_input = true ]] then printf " ln failed, using cp...\n" fi cp ${absnamein[$i]} ${localin[$i]} fi fi fi fi done if (( i != 0 )) then printf "\n$striche\n *** all INPUT-files provided \n" fi # EVENTUELLE INPUT-KOMMANDOS ABARBEITEN (( i = 0 )) while (( i < iic )) do (( i = i + 1 )) if (( i == 1 )) then printf "\n\n *** execution of INPUT-commands:\n$striche" fi printf "\n >>> ${in_command[$i]}" eval ${in_command[$i]} if (( i == iic )) then printf "\n$striche\n" fi done # VERBLEIBENDE CPU-ZEIT BERECHNEN cpurest=${cpumax}. # START DVR STREAMING SERVER if [[ $(echo $package_list | grep -c dvrp_graphics) != 0 ]] then if [[ "$dvr_server" != "" ]] then printf "\n\n *** preparing the dvr streaming server configuration file" # Check, if a dvr server is already running running_dvrserver_id=`echo $(ps -edaf | grep .dvrserver.config | grep -v grep) | cut -d" " -f2` if [[ "$running_dvrserver_id" != "" ]] then printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!" printf "\n This server is used instead starting a new one!" printf "\n If required, script \"process_dvr_output\" has to be run manually." else # COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE if [[ -f ${PALM_BIN}/.dvrserver.config ]] then cp ${PALM_BIN}/.dvrserver.config . # Entering the BASEDIR, UID and GID into this file user_id=`id -u` group_id=`id -g` # & is needed as seperator, because TEMPDIR contains / sed "s&&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1 sed "s//$user_id/g" .dvrserver.1 > .dvrserver.2 sed "s//$group_id/g" .dvrserver.2 > .dvrserver.3 mv .dvrserver.3 .dvrserver.config rm .dvrserver.1 .dvrserver.2 # Start dvr server in background, get his id and print on terminal $dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 & dvrserver_id=`echo $(ps -edaf | grep .dvrserver.config) | cut -d" " -f2` printf "\n *** streaming server with id=$dvrserver_id is started in background" local_dvrserver_running=.TRUE. else printf "\n +++ missing file \".dvrserver.config\" in directory:" printf "\n \"$PALM_BIN\" " locat=dvr exit fi fi else printf "\n\n --- INFORMATIVE: no dvr streaming server will be started" fi fi # NAMELIST-DATEI MIT WERTEN VON ENVIRONMENT-VARIABLEN ERZEUGEN (ZU # LESEN VON PALM) cat > ENVPAR << %%END%% &envpar run_identifier = '$fname', host = '$localhost', write_binary = '$write_binary', tasks_per_node = $tasks_per_node, maximum_parallel_io_streams = $maximum_parallel_io_streams, maximum_cpu_time_allowed = ${cpumax}., revision = '$global_revision', local_dvrserver_running = $local_dvrserver_running / %%END%% # PROGRAMMSTART printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$striche\n" PATH=$PATH:$TEMPDIR # MPI debug option (argument checking, slows down execution due to increased latency) if [[ "$mpi_debug" = true ]] then export MPI_CHECK_ARGS=1 printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS" fi if [[ "$totalview" = true ]] then printf "\n *** totalview debugger will be used" tv_opt="-tv" else tv_opt="" fi if [[ "$cond1" = debug || "$cond2" = debug ]] then if [[ "$ENVIRONMENT" = BATCH ]] then if [[ $(echo $localhost | cut -c1-5) != lcsgi ]] then printf "\n +++ debug is allowed in interactive mode only" locat=debug exit fi fi if [[ $localhost = decalpha ]] then dxladebug a.out elif [[ $localhost = ibmh ]] then # SETUP THE IBM MPI ENVIRONMENT export MP_SHARED_MEMORY=yes export AIXTHREADS_SCOPE=S export OMP_NUM_THREADS=$threads_per_task export AUTHSTATE=files export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT # FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW export MP_ADAPTER_USE=shared export MP_CPU_USE=multiple export MP_TIMEOUT=1200 unset MP_TASK_AFFINITY # SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION #(( ii = 1 )) #while (( ii <= $numprocs )) #do # echo $localhost_realname >> hostfile # (( ii = ii + 1 )) #done #export MP_HOSTFILE=hostfile if [[ "$LOADLBATCH" = yes ]] then totalview poe a.out $ROPTS else echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS export TVDSVRLAUNCHCMD=ssh totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS fi elif [[ $(echo $localhost | cut -c1-5) = lcsgi ]] then # CURRENTLY NO DEBUGGER ON LCSGI if [[ $run_coupled_model = true ]] then printf "\n +++ no debug in coupled mode available on \"$localhost\" " locat=debug exit else echo "no_coupling" > runfile_atmos fi (( ii = $numprocs / $threads_per_task )) export OMP_NUM_THREADS=$threads_per_task echo "OMP_NUM_THREADS=$OMP_NUM_THREADS" if [[ $threads_per_task != 1 ]] then printf "\n threads per task: $threads_per_task" fi printf "\n\n" if [[ $( echo $mpilib | cut -c1-3 ) = mpt ]] then # export MPI_LAUNCH_TIMEOUT=360 if [[ "$totalview" = true ]] then printf "\n running totalview debugger" mpiexec_mpt $tv_opt -n $ii ./a.out $ROPTS < runfile_atmos else mpiexec_mpt -np $ii ./a.out $ROPTS < runfile_atmos fi elif [[ $( echo $mpilib | cut -c1-3 ) = mva ]] then # ulimit -s 300000 # A too large stack size causes problems # export MV2_NUM_PORTS=2 # export MV2_CPU_MAPPING=0:1:2:3 if [[ "$totalview" = true ]] then printf "\n running totalview debugger" mpiexec $tv_opt ./a.out $ROPTS < runfile_atmos else mpiexec ./a.out $ROPTS < runfile_atmos fi fi else printf "\n +++ no debug available on \"$localhost\" " printf "\n or not implemented in mrun so far" locat=debug exit fi # end debug mode else # normal execution if [[ -n $numprocs ]] then # RUNNING THE PROGRAM ON PARALLEL MACHINES if [[ $(echo $host | cut -c1-3) = ibm ]] then # SETUP THE IBM MPI ENVIRONMENT if [[ $host != ibmh && $host != ibmkisti ]] then export MP_SHARED_MEMORY=yes export AIXTHREAD_SCOPE=S export OMP_NUM_THREADS=$threads_per_task export XLSMPOPTS="spins=0:yields=0:stack=20000000" export AUTHSTATE=files export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT # export MP_PRINTENV=yes # TUNING-VARIABLEN ZUR VERBESSERUNG DER KOMMUNIKATION # ZEIGEN ABER DERZEIT (SEP 04, FEDERATION) KAUM WIRKUNG export MP_WAIT_MODE=poll [[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes fi if [[ $host = ibmkisti ]] then export LANG=en_US export MP_SHARED_MEMORY=yes if [[ $threads_per_task = 1 ]] then export MP_SINGLE_THREAD=yes export MEMORY_AFFINITY=MCM else export OMP_NUM_THREADS=$threads_per_task fi fi if [[ "$LOADLBATCH" = yes ]] then printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n" if [[ "$cond1" = hpmcount || "$cond2" = hpmcount ]] then /opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS else if [[ $run_coupled_model = false ]] then if [[ "$ocean_file_appendix" = true ]] then echo "precursor_ocean" > runfile_atmos else echo "precursor_atmos" > runfile_atmos fi else (( iia = $numprocs_atmos / $threads_per_task )) (( iio = $numprocs_ocean / $threads_per_task )) printf "\n coupled run ($iia atmosphere, $iio ocean)" printf "\n using $coupled_mode coupling" printf "\n\n" echo "coupled_run $iia $iio" > runfile_atmos fi poe ./a.out $ROPTS < runfile_atmos fi else if [[ $localhost = ibmh || $localhost = ibms ]] then poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS elif [[ $localhost = ibmkisti || $localhost = ibmku || $localhost = ibmy ]] then if [[ -f $hostfile ]] then cp $hostfile hostfile else (( ii = 1 )) while (( ii <= $numprocs )) do echo $localhost_realname >> hostfile (( ii = ii + 1 )) done fi export MP_HOSTFILE=hostfile if [[ $run_coupled_model = false ]] then if [[ "$ocean_file_appendix" = true ]] then echo "precursor_ocean" > runfile_atmos else echo "precursor_atmos" > runfile_atmos fi else (( iia = $numprocs_atmos / $threads_per_task )) (( iio = $numprocs_ocean / $threads_per_task )) printf "\n coupled run ($iia atmosphere, $iio ocean)" printf "\n using $coupled_mode coupling" printf "\n\n" echo "coupled_run $iia $iio" > runfile_atmos fi if [[ $localhost = ibmy ]] then ./a.out -procs $tasks_per_node $ROPTS < runfile_atmos else poe ./a.out -procs $numprocs $ROPTS < runfile_atmos fi else if [[ "$host_file" = "" ]] then printf "\n +++ no hostfile given in configuration file" locat=config_file exit else eval host_file=$host_file fi export MP_HOSTFILE=$host_file poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS fi fi elif [[ $host = nech || $host = necriam ]] then (( ii = nodes )) if [[ $ii = 1 ]] then export F_ERRCNT=0 # acceptable number of errors before program is stopped export MPIPROGINF=YES # export F_TRACE=YES|FMT1|FMT2 # output of ftrace informations to job protocol echo "*** execution on single node with mpirun" mpirun -np $numprocs ./a.out $ROPTS else (( i = 0 )) while (( i < ii )) do echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config (( i = i + 1 )) done echo "#!/bin/sh" > mpi_exec_shell echo " " >> mpi_exec_shell echo "set -u" >> mpi_exec_shell echo "F_ERRCNT=0" >> mpi_exec_shell echo "MPIPROGINV=YES" >> mpi_exec_shell echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell echo "cpurest=$cpurest" >> mpi_exec_shell echo "fname=$fname" >> mpi_exec_shell echo "localhost=$localhost" >> mpi_exec_shell echo "return_addres=$return_addres" >> mpi_exec_shell echo "return_username=$return_username" >> mpi_exec_shell echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell echo "write_binary=$write_binary" >> mpi_exec_shell echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell echo " " >> mpi_exec_shell echo "export F_ERRCNT" >> mpi_exec_shell echo "export MPIPROGINV" >> mpi_exec_shell echo "export OMP_NUM_THREADS" >> mpi_exec_shell echo "export cpurest" >> mpi_exec_shell echo "export fname" >> mpi_exec_shell echo "export localhost" >> mpi_exec_shell echo "export return_addres" >> mpi_exec_shell echo "export return_username" >> mpi_exec_shell echo "export tasks_per_node" >> mpi_exec_shell echo "export write_binary" >> mpi_exec_shell echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell echo " " >> mpi_exec_shell echo "exec ./a.out" >> mpi_exec_shell chmod u+x mpi_exec_shell export MPIPROGINF=YES mpirun -f multinode_config & wait fi elif [[ $(echo $host | cut -c1-2) = lc && $host != lckyoto && $host != lctit ]] then # COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT # DOES NOT EXIST if [[ $host != lcsgih && $host != lcsgib ]] then if [[ -f $hostfile ]] then cp $hostfile hostfile (( ii = $numprocs / $threads_per_task )) else (( ii = 1 )) while (( ii <= $numprocs / $threads_per_task )) do echo $localhost_realname >> hostfile (( ii = ii + 1 )) done fi eval zeile=\"`head -n $ii hostfile`\" printf "\n *** running on: $zeile" fi (( ii = $numprocs / $threads_per_task )) export OMP_NUM_THREADS=$threads_per_task # echo "*** OMP_NUM_THREADS=$OMP_NUM_THREADS" if [[ $threads_per_task != 1 ]] then # increase stack size to unlimited, because large runs # may abort otherwise ulimit -Ss unlimited printf "\n threads per task: $threads_per_task stacksize: unlimited" fi if [[ $run_coupled_model = false ]] then if [[ "$ocean_file_appendix" = true ]] then echo "precursor_ocean" > runfile_atmos else echo "precursor_atmos" > runfile_atmos fi printf "\n\n" if [[ $host = lcsgih || $host = lcsgib ]] then if [[ $( echo $mpilib | cut -c1-3 ) = mpt ]] then # MPI_DSM_DISTRIBUTE not necessary when MPI_DSM_CPULIST is set # export MPI_DSM_DISTRIBUTE=1 # MPI_DSM_CPULIST: pin MPI processes to cores if [[ $use_openmp = false ]] then if [[ "$sgi_feature" = ice2 ]] then export MPI_DSM_CPULIST="0,4,1,5,2,6,3,7:allhosts" else export MPI_DSM_CPULIST="0,1,4,5,2,3,6,7:allhosts" fi else unset MPI_DSM_CPULIST fi # MPI_IB_RAILS: use both IB rails on ICE2 export MPI_BUFS_PER_HOST=512 export MPI_IB_RAILS=2 # NECESSARY, IF MORE THAN 4096 PEs ARE USED export MPI_CONNECTIONS_THRESHOLD=8192 # echo "*** MPI_DSM_CPULIST=$MPI_DSM_CPULIST" export MPI_TYPE_DEPTH=20 # echo "*** MPI_TYPE_DEPTH=$MPI_TYPE_DEPTH" export MPI_GROUP_MAX=64 # echo "*** MPI_GROUP_MAX=$MPI_GROUP_MAX" if [[ $use_openmp = true ]] then echo " mpiexec -npernode $tasks_per_node ./a.out $ROPTS < runfile_atmos" mpiexec -npernode $tasks_per_node $tv_opt ./a.out $ROPTS < runfile_atmos else mpiexec_mpt -np $ii $tv_opt ./a.out $ROPTS < runfile_atmos fi # next is test for openmp usage # echo "mpiexec -npernode $tasks_per_node ./a.out $ROPTS < runfile_atmos" # mpiexec -npernode $tasks_per_node ./a.out $ROPTS < runfile_atmos elif [[ $( echo $mpilib | cut -c1-3 ) = mva ]] then export MV2_NUM_PORTS=2 # The default setting of MV2_CPU_MAPPING gives best results # export MV2_ENABLE_AFFINITY=1 # export MV2_CPU_MAPPING=0,1,4,5,2,3,6,7 # if [[ "$sgi_feature" = ice2 ]] # then # export MV2_CPU_MAPPING=0,4,1,5,2,6,3,7 # else # export MV2_CPU_MAPPING=0,1,4,5,2,3,6,7 # fi if [[ $use_openmp = true ]] then unset MV2_CPU_MAPPING export MV2_ENABLE_AFFINITY=0 fi echo "*** MV2_CPU_MAPPING=$MV2_CPU_MAPPING" echo "*** MV2_ENABLE_AFFINITY=$MV2_ENABLE_AFFINITY" if [[ $use_openmp = true ]] then echo " mpiexec -npernode $tasks_per_node ./a.out $ROPTS < runfile_atmos" mpiexec -npernode $tasks_per_node $tv_opt ./a.out $ROPTS < runfile_atmos else mpiexec -np $ii $tv_opt ./a.out $ROPTS < runfile_atmos fi elif [[ "$mpilib" = impi ]] then echo "mpirun -np $tasks_per_node inspxe-cl -r result -collect mi3 -- ./a.out < runfile_atmos" mpirun -np $tasks_per_node inspxe-cl -r result -collect mi3 -- ./a.out < runfile_atmos fi elif [[ $host = lcxt4 || $host = lcxt5m ]] then aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos elif [[ $host = lcflow ]] then mpiexec -machinefile $TMPDIR/machines -n $ii -env I_MPI_FABRICS shm:ofa a.out < runfile_atmos $ROPTS else mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS fi else # currently there is no full MPI-2 support on ICE and XT4 (( iia = $numprocs_atmos / $threads_per_task )) (( iio = $numprocs_ocean / $threads_per_task )) printf "\n coupled run ($iia atmosphere, $iio ocean)" printf "\n using $coupled_mode coupling" printf "\n\n" if [[ $coupled_mode = "mpi2" ]] then echo "atmosphere_to_ocean $iia $iio" > runfile_atmos echo "ocean_to_atmosphere $iia $iio" > runfile_ocean if [[ $host = lcsgih || $host = lcsgib ]] then if [[ $( echo $mpilib | cut -c1-3 ) = mpt ]] then # export MPI_LAUNCH_TIMEOUT=360 mpiexec_mpt -np $iia ./a.out $ROPTS < runfile_atmos & mpiexec_mpt -np $iio ./a.out $ROPTS < runfile_ocean & elif [[ $( echo $mpilib | cut -c1-3 ) = mva ]] then # ulimit -s 300000 # A too large stack size causes problems # export MV2_NUM_PORTS=2 # export MV2_CPU_MAPPING=0:1:2:3 mpiexec -n $iia ./a.out $ROPTS < runfile_atmos & mpiexec -n $iio ./a.out $ROPTS < runfile_ocean & fi elif [[ $host = lcxt4 || $host = lcxt5m ]] then aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS & aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS & else # WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos & mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean & # mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS & # mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS & fi wait else echo "coupled_run $iia $iio" > runfile_atmos if [[ $host = lcsgih || $host = lcsgib ]] then if [[ $( echo $mpilib | cut -c1-3 ) = mpt ]] then # export MPI_LAUNCH_TIMEOUT=360 mpiexec_mpt -np $ii ./a.out $ROPTS < runfile_atmos elif [[ $( echo $mpilib | cut -c1-3 ) = mva ]] then # ulimit -s 300000 # A too large stack size causes problems # export MV2_NUM_PORTS=2 # export MV2_CPU_MAPPING=0:1:2:3 mpiexec ./a.out $ROPTS < runfile_atmos fi elif [[ $host = lcxt4 || $host = lcxt5m ]] then aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS elif [[ $host = lck || $host = lckordi ]] then mpiexec -n $ii ./a.out $ROPTS < runfile_atmos & fi wait fi fi elif [[ $host = decalpha ]] then dmpirun -np $numprocs a.out $ROPTS elif [[ $host = lckyoto ]] then set -xv export P4_RSHCOMMAND=plesh echo " P4_RSHCOMMAND = $P4_RSHCOMMAND" if [[ "$ENVIRONMENT" = BATCH ]] then if [[ "$cond2" = fujitsu ]] then mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler elif [[ "cond2" = pgi ]] then mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS else mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} || /bin/true fi else if [[ "$cond2" = "" ]] then mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel else mpirun -np $numprocs ./a.out $ROPTS fi fi set +xv elif [[ $host = lctit ]] then export OMP_NUM_THREADS=$threads_per_task echo "OMP_NUM_THREADS=$OMP_NUM_THREADS" if [[ "$threads_per_task" != 1 ]] then export MV2_ENABLE_AFFINITY=0 fi echo "----- PBS_NODEFILE content:" cat $PBS_NODEFILE echo "-----" (( ii = $numprocs / $threads_per_task )) echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS" mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS else mpprun -n $numprocs a.out $ROPTS fi [[ $? != 0 ]] && execution_error=true # PERFORMANCE-AUSWERTUNG MIT APPRENTICE if [[ "$cond1" = apprentice || "$cond2" = apprentice ]] then apprentice fi else a.out $ROPTS fi fi if [[ $? != 0 || $execution_error = true ]] then # ABBRUCH BEI LAUFZEITFEHLER # [[ ! ( "$cond1" = debug || "$cond2" = debug ) ]] && cat aout_output* printf "\n +++ runtime error occured" locat=execution exit else # [[ ! ( "$cond1" = debug || "$cond2" = debug ) ]] && cat aout_output* printf "\n$striche\n *** execution finished \n" # Stop the dvr streaming server and process the dvr output in order # to create dvrs- and html-files containing all streams if [[ "$dvrserver_id" != "" ]] then kill $dvrserver_id printf "\n *** dvr server with id=$dvrserver_id has been stopped" # If there is a directory, data have been output by the # streaming server. Otherwise, user has chosen dvrp_output=local if [[ -d DATA_DVR ]] then # Add the current dvr configuration file to the dvr output # directory cp .dvrserver.config DATA_DVR # Process the dvr output (option -s for also generating # sequence mode data) process_dvr_output -d DATA_DVR -f $fname -s else # Process the local output process_dvr_output -l -d DATA_DVR -f $fname fi elif [[ $(echo $package_list | grep -c dvrp_graphics) != 0 ]] then # Process dvr output generated in local mode (dvrp_output=local) process_dvr_output -l -d DATA_DVR -f $fname fi fi # Call of combine_plot_fields in order to merge single files written # by each PE into one file. if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]] then printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\"" printf "\n 2d- and/or 3d-data may be incomplete!" printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n" else printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..." combine_plot_fields${block}.x fi # EVENTUELLE OUTPUT-KOMMANDOS ABARBEITEN (( i = 0 )) while (( i < ioc )) do (( i = i + 1 )) if (( i == 1 )) then printf "\n\n *** execution of OUTPUT-commands:\n$striche" fi printf "\n >>> ${out_command[$i]}" eval ${out_command[$i]} if (( i == ioc )) then printf "\n$striche\n" fi done # EVTL. INHALT DES AKTUELLEN VERZEICHNISSES AUSGEBEN if [[ $do_trace = true ]] then printf "\n\n" ls -al fi # OUTPUT-DATEIEN AN IHRE ZIELORTE KOPIEREN (( i = 0 )) while (( i < iout )) do (( i = i + 1 )) if (( i == 1 )) then printf "\n\n *** saving OUTPUT-files:\n$striche" fi # PRUEFEN, OB EINZELDATEI ODER DATEI PRO PROZESSOR files_for_pes=false; filetyp=file if [[ "${actionout[$i]}" = pe && -n $numprocs ]] then files_for_pes=true; filetyp=directory actionout[$i]="" elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]] then actionout[$i]="" elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]] then files_for_pes=true; filetyp=directory actionout[$i]="ar" elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]] then actionout[$i]="ar" elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]] then files_for_pes=true; filetyp=directory actionout[$i]="fl" elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]] then actionout[$i]="fl" elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]] then files_for_pes=true; filetyp=directory actionout[$i]="tr" elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]] then actionout[$i]="tr" fi if [[ ! -f ${localout[$i]} && $files_for_pes = false ]] then printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n" elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]] then printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n" else # KOPIEREN PER FTP/SCP (IMMER IM BINAERMODUS, -M: FALLS ZIELKATALOG # NICHT VORHANDEN, WIRD VERSUCHT, IHN ANZULEGEN), ABER NUR BEI # REMOTE-RECHNUNGEN if [[ "${actionout[$i]}" = tr ]] then if [[ $localhost != $fromhost ]] then if [[ $files_for_pes = false ]] then cps="" cst="" else cps=-c cst="/" fi if [[ $localhost = nech ]] then # TRANSFER IN EIGENSTAENDIGEM JOB # ZUERST KOPIE DER DATEI INS TEMPORAERE DATENVERZEICHNIS [[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung if [[ $files_for_pes = false ]] then ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer else mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer fi echo "set -x" > transfer_${localout[$i]} echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]} printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to" printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst" printf "\n or higher cycle\n" echo "batch_scp $cps -b -m -u $return_username $return_addres $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]} echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]} if [[ $localhost = nech ]] then subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 transfer_${localout[$i]} else if [[ "$LOGNAME" = b323013 ]] then subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog transfer_${localout[$i]} else subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog transfer_${localout[$i]} fi fi else # TRANSFER INNERHALB DIESES JOBS transfer_failed=false printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to" printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n" batch_scp $cps -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]} [[ $? != 0 ]] && transfer_failed=true # BEI FEHLGESCHLAGENEM TRANSFER SICHERUNGSKOPIE AUF # LOKALER MASCHINE ANLEGEN if [[ $transfer_failed = true ]] then printf " +++ transfer failed. Trying to save a copy on the local host under:\n" printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n" # ERSTMAL PRUEFEN, OB VERZEICHNIS EXISTIERT. GEGEBENENFALLS # ANLEGEN. eval local_catalog=${pathout[$i]} if [[ ! -d $local_catalog ]] then printf " *** local directory does not exist. Trying to create:\n" printf " $local_catalog \n" mkdir -p $local_catalog fi eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung transfer_problems=true fi fi else # WERTZUWEISUNG, SO DASS WEITER UNTEN NUR KOPIERT WIRD actionout[$i]="" fi fi # APPEND PER FTP/SCP (IMMER IM BINAERMODUS, -M: FALLS ZIELKATALOG # NICHT VORHANDEN, WIRD VERSUCHT, IHN ANZULEGEN), ABER NUR BEI # REMOTE-RECHNUNGEN if [[ "${actionout[$i]}" = tra ]] then if [[ $localhost != $fromhost ]] then if [[ $localhost = ibmh || $localhost = nech ]] then # TRANSFER IN EIGENSTAENDIGEM JOB # ZUERST KOPIE DER DATEI INS TEMPORAERE DATENVERZEICHNIS [[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer echo "set -x" > transfer_${localout[$i]} echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]} printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to" printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}" printf "\n or higher cycle\n" echo "batch_scp -A -b -m -u $return_username $return_addres $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]} echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]} if [[ $localhost = nech ]] then subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 transfer_${localout[$i]} else if [[ $LOGNAME = b323013 ]] then subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog transfer_${localout[$i]} else subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog transfer_${localout[$i]} fi fi else # TRANSFER INNERHALB DIESES JOBS transfer_failed=false printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to" printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n" batch_scp -A -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]} [[ $? != 0 ]] && transfer_failed=true # BEI FEHLGESCHLAGENEM TRANSFER SICHERUNGSKOPIE AUF # LOKALER MASCHINE ANLEGEN if [[ $transfer_failed = true ]] then printf " +++ transfer failed. Trying to save a copy on the local host under:\n" printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n" # ERSTMAL PRUEFEN, OB VERZEICHNIS EXISTIERT. GEGEBENENFALLS # ANLEGEN eval local_catalog=${pathout[$i]} if [[ ! -d $local_catalog ]] then printf " *** local directory does not exist. Trying to create:\n" printf " $local_catalog \n" mkdir -p $local_catalog fi eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung transfer_problems=true fi fi else # WERTZUWEISUNG, SO DASS WEITER UNTEN NUR APPEND AUF # LOKALER MASCHINE DURCHGEFUEHRT WIRD actionout[$i]=a fi fi # OUTPUT-DATEI FUER EINEN FORTSETZUNGSLAUF. DATEI WIRD PER # LINK AUF DEN TEMPORAEREN DATENKATALOG GELEGT. OPTION -f WIRD # VERWENDET, FALLS DORT NOCH EINE DATEI GLEICHEN NAMENS VORHANDEN # SEIN SOLLTE. ANSCHLIESSEND WIRD SEINE ARCHIVIERUNG ANGESTOSSEN if [[ "${actionout[$i]}" = fl ]] then [[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog chmod g+rx $tmp_data_catalog if [[ $files_for_pes = false ]] then printf "\n >>> OUTPUT: ${localout[$i]} to" printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n" ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]} else printf "\n >>> OUTPUT: ${localout[$i]}/.... to" printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n" mkdir $tmp_data_catalog/${frelout[$i]} cd ${localout[$i]} for file in $(ls *) do ln -f $file $tmp_data_catalog/${frelout[$i]} done cd $TEMPDIR fi # ARCHIVIERUNGSJOB WIRD ERZEUGT UND ABGESCHICKT if [[ $store_on_archive_system = true ]] then if [[ $archive_system = asterix ]] then echo "cd $tmp_data_catalog" >> archive_${frelout[$i]} if [[ $files_for_pes = false ]] then echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]} else echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]} fi echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]} echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]} echo "then" >> archive_${frelout[$i]} echo " do_stageout=false" >> archive_${frelout[$i]} echo "else" >> archive_${frelout[$i]} echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]} echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]} echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]} echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]} if [[ $files_for_pes = false ]] then echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]} else echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]} fi echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]} echo "fi" >> archive_${frelout[$i]} echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]} elif [[ $archive_system = DMF ]] then echo "cd $tmp_data_catalog" >> archive_${frelout[$i]} if [[ $files_for_pes = false ]] then printf "\n +++ archiving of single files impossible with $archive_system !\n" locat=DMF exit else # FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH # EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.) echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]} echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]} fi elif [[ $archive_system = tivoli ]] then echo "cd $tmp_data_catalog" >> archive_${frelout[$i]} if [[ $files_for_pes = false ]] then # EVENTUELL NOCH VORHANDENE DATEI IM ARCHIV LOSCHEN echo "set -x" >> archive_${frelout[$i]} echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]} echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]} else echo "set -x" >> archive_${frelout[$i]} echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]} echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]} cd $tmp_data_catalog all_files=`ls -1 ${frelout[$i]}/*` cd - > /dev/null (( inode = 0 )) (( tp1 = tasks_per_node + 1 )) while (( inode < nodes )) do # echo "*** all_files = \"$all_files\" " files=`echo $all_files | cut -d" " -f1-$tasks_per_node` all_files=`echo $all_files | cut -d" " -f$tp1-` # echo "*** tasks_per_node = \"$tasks_per_node\" " # echo "*** files = \"$files\" " # echo "*** all_files = \"$all_files\" " echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]} ### echo "tar cvf ${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]} ### echo "cp ${frelout[$i]}.node_$inode.tar \$PERM/${frelout[$i]}/" >> archive_${frelout[$i]} ###echo "rm ${frelout[$i]}.node_$inode.tar" >> archive_${frelout[$i]} # echo "dsmc incremental \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar" >> archive_${frelout[$i]} # echo "dsmmigrate \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar" >> archive_${frelout[$i]} (( inode = inode + 1 )) done # echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]} # echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]} fi elif [[ $archive_system = ut ]] then echo "cd $tmp_data_catalog" >> archive_${frelout[$i]} if [[ $files_for_pes = false ]] then # EVENTUELL NOCH VORHANDENE DATEI IM ARCHIV LOSCHEN echo "set -x" >> archive_${frelout[$i]} echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]} echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]} else echo "set -x" >> archive_${frelout[$i]} echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]} echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]} cd $tmp_data_catalog all_files=`ls -1 ${frelout[$i]}/*` cd - > /dev/null (( inode = 0 )) (( tp1 = tasks_per_node + 1 )) while (( inode < nodes )) do files=`echo $all_files | cut -d" " -f1-$tasks_per_node` all_files=`echo $all_files | cut -d" " -f$tp1-` echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]} (( inode = inode + 1 )) done fi elif [[ $archive_system = none ]] then printf " +++ archiving on $localhost not available!\n" fi if [[ $archive_system != none ]] then if [[ $localhost = lcsgih || $localhost = lcsgib ]] then # subjob -d -v -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog archive_${frelout[$i]} subjob -v -q permq -X 1 -T 1 -m 1000 -t 172800 -c $job_catalog archive_${frelout[$i]} elif [[ $localhost = nech ]] then subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 archive_${frelout[$i]} fi printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n" fi else printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n" fi # LEERDATEI IM BENUTZERVERZEICHNIS ANLEGEN, DAMIT BEKANNT IST, # WIE DIE HOECHSTE ZYKLUSNUMMER AUF DEM ARCHIV-SYSTEM LAUTET if [[ $files_for_pes = false ]] then cat /dev/null > ${pathout[$i]} else mkdir -p ${pathout[$i]} fi fi # KOPIEREN AUF LOKALER MASCHINE ZUM ARCHIV-SYSTEM # AUSSERDEM MUSS LEERDATEI ANGELEGT WERDEN, DAMIT BEKANNT IST, # WIE DIE HOECHSTE ZYKLUSNUMMER AUF DEM ARCHIV-SYSTEM LAUTET # FALLS IRGENDEINE (VON MEHREREN) ARCHIVIERUNGEN SCHIEF GEHT, # WIRD FLAG GESETZT UND BLEIBT AUCH BEI WEITEREN ORDNUNGS- # GEMAESSEN ARCHIVIERUNGEN GESETZT if [[ "${actionout[$i]}" = ar ]] then if [[ $files_for_pes = false ]] then printf "\n >>> OUTPUT: ${localout[$i]} to" printf "\n ${pathout[$i]}" printf "\n File will be copied to archive-system ($archive_system) !\n" else printf "\n >>> OUTPUT: ${localout[$i]}/_.... to" printf "\n ${pathout[$i]}" printf "\n Directory will be copied to archive-system ($archive_system) !\n" fi mv ${localout[$i]} ${frelout[$i]} file_saved=false if [[ $archive_system = asterix ]] then do_stageout=true (( stageout_anz = 0 )) while [[ $do_stageout = true ]] do if [[ $files_for_pes = false ]] then stageout ${frelout[$i]} > STAGE_OUTPUT else stageout -t ${frelout[$i]} > STAGE_OUTPUT fi cat STAGE_OUTPUT if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]] then file_saved=true do_stageout=false else if [[ $files_for_pes = false ]] then printf "\n +++ file ${frelout[$i]} could not be saved on archive-system" else printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system" fi (( stageout_anz = stageout_anz + 1 )) if (( stageout_anz == 10 )) then printf "\n +++ stoped after 10 unsuccessful tries!" archive_save=false do_stageout=false else printf "\n *** new try to store on archive after 15 min:" sleep 900 fi fi done elif [[ $archive_system = DMF ]] then if [[ $files_for_pes = false ]] then printf "\n +++ archiving of single files impossible on $archive_system!\n" locat=DMF exit else rm -rf $ARCHIVE/${frelout[$i]} cp -r ${frelout[$i]} $ARCHIVE fi file_saved=true elif [[ $archive_system = tivoli ]] then # ARCHIVIERUNG NUR PER BATCH-JOB MOEGLICH # DATEI MUSS ZWISCHENZEITLICH INS TEMPORAERE DATENVERZEICHNIS # GELEGT WERDEN [[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog chmod g+rx $tmp_data_catalog if [[ $files_for_pes = false ]] then ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]} else mkdir $tmp_data_catalog/${frelout[$i]} ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]} fi # BATCH JOB GENERIEREN UND ABSCHICKEN; DATEI MUSS WIEDER # AUS TEMPORAEREM DATENVERZEICHNIS ENTFERNT WERDEN echo "cd $tmp_data_catalog" > archive_${frelout[$i]} if [[ $files_for_pes = false ]] then # EVENTUELL NOCH VORHANDENE DATEI IM ARCHIV LOSCHEN echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]} echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]} echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]} else echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]} echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]} echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]} fi subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog archive_${frelout[$i]} printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n" file_saved=true elif [[ $archive_system = ut ]] then # ARCHIVIERUNG NUR PER BATCH-JOB MOEGLICH # DATEI MUSS ZWISCHENZEITLICH INS TEMPORAERE DATENVERZEICHNIS # GELEGT WERDEN [[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog chmod g+rx $tmp_data_catalog if [[ $files_for_pes = false ]] then ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]} else mkdir $tmp_data_catalog/${frelout[$i]} ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]} fi # BATCH JOB GENERIEREN UND ABSCHICKEN; DATEI MUSS WIEDER # AUS TEMPORAEREM DATENVERZEICHNIS ENTFERNT WERDEN echo "cd $tmp_data_catalog" > archive_${frelout[$i]} if [[ $files_for_pes = false ]] then # EVENTUELL NOCH VORHANDENE DATEI IM ARCHIV LOSCHEN echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]} echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]} echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]} else echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]} echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]} echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]} fi subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 archive_${frelout[$i]} printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n" file_saved=true else printf "\n +++ archive_system=\"$archive_system\" archiving impossible!" archive_save=false fi if [[ $file_saved = true ]] then if [[ $files_for_pes = false ]] then cat /dev/null > ${pathout[$i]} else mkdir -p ${pathout[$i]} fi fi fi # APPEND AUF LOKALER MASCHINE if [[ "${actionout[$i]}" = "a" ]] then if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]] then printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n" cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]} else printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n" cat ${localout[$i]} >> ${pathout[$i]} fi fi # KOPIEREN AUF LOKALER MASCHINE # ES MUSS KOPIERT WERDEN, DA MOVE NICHT UEBER FILESYSTEM HINAUS MOEGLICH if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]] then # KOPIEREN AUF EINPROZESSORMASCHINE if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]] then printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n" if [[ $link_local_output = true ]] then printf " using ln -f\n" ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]} fi # If "ln -f" fails of if "$link_local_output = false" do a normal "cp" if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]] then if [[ $link_local_output = true ]] then printf " ln failed, using cp...\n" fi cp ${localout[$i]} ${pathout[$i]}.${extout[$i]} fi else printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n" if [[ $link_local_output = true ]] then printf " using ln -f\n" ln -f ${localout[$i]} ${pathout[$i]} fi # If "ln -f" fails of if "$link_local_output = false" do a normal "cp" if [[ ! -f "${pathout[$i]}" ]] then if [[ $link_local_output = true ]] then printf " ln failed, using cp...\n" fi cp ${localout[$i]} ${pathout[$i]} fi fi elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]] then # DIE DEN PROZESSOREN EINES PARALLELRECHNERS ZUGEHOERIGEN # DATEIEN WERDEN ERST IN EINEM KATALOG GESAMMELT UND DIESER # WIRD DANN KOPIERT # PER MOVE UMBENANNT WERDEN printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n" if [[ $link_local_output = true ]] then printf " using ln -f\n" mkdir ${pathout[$i]} cd ${localout[$i]} for file in $(ls *) do ln -f $file ${pathout[$i]} done cd $TEMPDIR fi # If "ln -f" fails of if "$link_local_output = false" do a normal "cp -r" if [[ ! -f "${pathout[$i]}/_0000" ]] then if [[ $link_local_output = true ]] then printf " ln failed for .../_0000, using cp...\n" fi cp -r ${localout[$i]} ${pathout[$i]} fi fi fi done if (( i != 0 )) then if [[ $transfer_problems = true ]] then printf "\n$striche\n *** OUTPUT-files saved" printf "\n +++ WARNING: some data transfers failed! \n" else printf "\n$striche\n *** all OUTPUT-files saved \n" fi fi # EVENTUELL FOLGEJOB STARTEN # DATEI CONTINUE_RUN MUSS VOM BENUTZERPROGRAMM AUS ERZEUGT WERDEN if [[ -f CONTINUE_RUN ]] then if [[ $archive_save = true ]] then # ZUERST IN MRUN-AUFRUF OPTIONEN FUER FORTSETZUNGSLAUF, FUER # STILLES ABARBEITEN (OHNE INTERAKTIVE RUECKFAGEN) UND FUER # BATCH-BETRIEB (NUR WICHTIG, FALLS BATCH AUF LOKALER MASCHINE # DURCHGEFUEHRT WERDEN SOLL) EINFUEGEN, FALLS NICHT BEREITS VOR- # HANDEN [[ $(echo $mc | grep -c "\-C") = 0 ]] && mc="$mc -C" [[ $(echo $mc | grep -c "\-v") = 0 ]] && mc="$mc -v" [[ $(echo $mc | grep -c "\-b") = 0 ]] && mc="$mc -b" if [[ $(echo $mc | grep -c "#") != 0 ]] then mc=`echo $mc | sed 's/#/f/g'` fi # JOB STARTEN printf "\n\n *** initiating restart-run on \"$return_addres\" using command:\n" echo " $mc" printf "\n$striche\n" if [[ $localhost != $fromhost ]] then if [[ $localhost = lcsgih || $localhost = lcsgib || $localhost = nech || $localhost = ibmh || $localhost = ibmkisti || $localhost = ibmku || $localhost = ibms ]] then echo "*** ssh will be used to initiate restart-runs!" echo " return_addres=\"$return_addres\" " echo " return_username=\"$return_username\" " if [[ $(echo $return_addres | grep -c "130.75.105") = 1 ]] then ssh $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export LD_LIBRARY_PATH=\$LD_LIBRARY_PATH:/muksoft/packages/intel/Compiler/11.1/073/lib/intel64/;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc " else if [[ $localhost = ibmkisti ]] then ssh $usern@gaiad "ssh $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" " else ssh $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc " fi fi else printf "\n +++ no restart mechanism available for host \"$localhost\" " locat=restart; exit fi # WARTEN, DAMIT SICH RESTART JOB IN QUEUE EINREIHEN KANN, BEVOR # DER AKTUELLE JOB ENDET if [[ $queue = special1q ]] then sleep 120 else sleep 30 fi else # BEI RECHNUNGEN AUF LOKALER MASCHINE KANN MRUN DIREKT AUFGE- # RUFEN WERDEN, AUSSER AUF lcfimm cd $LOCAL_PWD if [[ $localhost = lcfimm ]] then ssh $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc " else eval $mc # ' MUESSEN AUSGEWERTET WERDEN fi cd - > /dev/null fi printf "\n$striche\n *** restart-run initiated \n" # EVENTUELL INPUT-DATEIEN, DIE VON TEMPORAEREM DATENVERZEICHNIS # GEHOLT WORDEN SIND, LOESCHEN (( i = 0 )) while (( i < iin )) do (( i = i + 1 )) if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]] then rm -r $tmp_data_catalog/${frelin[$i]} fi done else printf "\n +++ no restart-run possible, since errors occured" printf "\n during the archive process" fi fi # EVTL. EMAIL-BENACHRICHTIGUNG UEBER ABGESCHLOSSENEN LAUF if [[ "$email_notification" != "none" ]] then if [[ $localhost != $fromhost ]] then if [[ -f CONTINUE_RUN ]] then echo "PALM restart run necessary" > email_text echo "description header of actual run:" >> email_text cat CONTINUE_RUN >> email_text echo "mrun-command to restart:" >> email_text echo "$mc" >> email_text else echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text fi mail $email_notification < email_text printf "\n *** email notification sent to \"$email_notification\" " fi fi # ALLE ARBEITEN BEENDET. TEMPORAERER KATALOG KANN GELOESCHT WERDEN cd $HOME [[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR else # FALLS AUF REMOTE-MASCHINE GERECHNET WERDEN SOLL, WERDEN JETZT ENTSPRE- # CHENDE AKTIONEN DURCHGEFUEHRT # MRUN-BEFEHL FUER REMOTE-MASCHINE ZUSAMMENSTELLEN mrun_com="$mrun_script_name -a $afname -c $config_file -d $fname -h $host -H $fromhost -m $memory -t $cpumax -q \$queue -R $return_addres -U $return_username -u $remote_username" [[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\"" [[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\"" [[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number" [[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\"" [[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\"" [[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I" [[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k" [[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\"" # [[ "$makefile" != "$source_path/Makefile" ]] && mrun_com=${mrun_com}" -M \"$makefile\"" [[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\"" [[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S" [[ $do_trace = true ]] && mrun_com=${mrun_com}" -x" [[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs" if [[ $use_openmp = true ]] then mrun_com=${mrun_com}" -O $threads_per_task" fi [[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node" [[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A" [[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\"" [[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password" [[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B" [[ $node_usage != default && "$(echo $node_usage | cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage" [[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y" [[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\"" [[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str" if [[ $do_remote = true ]] then printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n" fi # ZUSAMMENSTELLUNG DES JOBSCRIPTS AUF DATEI jobfile jobfile=jobfile.$RANDOM # TEMPORAERES VERZEICHNIS GENERIEREN UND NACH DORT WECHSELN echo "mkdir $TEMPDIR" >> $jobfile echo "cd $TEMPDIR" >> $jobfile # EVENTUELL FEHLERVERFOLGUNG AKTIVIEREN if [[ $do_trace = true ]] then echo "set -x" >> $jobfile else echo "set +vx" >> $jobfile fi # BEREITSTELLUNG VON QUELLTEXTEN, MRUN-SCRIPTS UND KONFIGURATIONS- # DATEI FUER DEN JOB if [[ $( echo $host | cut -c1-5 ) = lcsgi || $host = ibmkisti ]] then # KONFIGURATIONSDATEI UND MRUN_SCRIPT IN DAS SOURCE-VERZEICHNIS # KOPIEREN if [[ $restart_run != true ]] then cp $config_file $working_directory/SOURCES_FOR_RUN_$fname cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname fi # SOURCE-VERZEICHNIS VOM LOKALEN RECHNER PER SCP TRANSFERIEREN # (BEI JOBS AUF LOKALEM RECHNER REICHT CP) echo "set -x" >> $jobfile if [[ $host = $localhost ]] then echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile else if [[ $host != ibmkisti ]] then echo "scp -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile else # on KISTI's IBM firewall is only opened on interactive node echo "localdir=\`pwd\`" >> $jobfile echo "ssh $remote_username@gaiad \"cd \$localdir; scp -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile fi fi echo "export SOURCES_COMPLETE=true" >> $jobfile # QUELLTEXTE, MRUN-SCRIPT UND KONFIGURATIONSDATEI IN DAS AKTUELLE # ARBEITSVERZEICHNIS VERSCHIEBEN echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile echo "execute_mrun=true" >> $jobfile echo " " >> $jobfile else # ABSPEICHERN DER QUELLTEXTE (NUR FALLS UEBERSETZT WERDEN SOLL) # SOWIE GEGEBENENFALLS DES MAKEFILES if [[ $do_compile = true ]] then source_catalog=SOURCES_FOR_RUN_$fname # UNTERVERZEICHNIS FUER QUELLTEXTE UND MAKEFILE ANLEGEN # MRUN WIRD DIESES VRZEICHNIS UEBER ENVIRONMENT VARIABLE # MITGETEILT (UEBERSTEUERT ANGABE IN KONFIGURATIONSDATEI) echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile echo "export SOURCES_COMPLETE=true" >> $jobfile echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile for filename in $source_list do # ABDECKZEICHEN VERHINDERN, DASS ERSETZUNGEN ERFOLGEN echo "cat > $filename << \"%END%\"" >> $jobfile cat $source_catalog/$filename >> $jobfile echo " " >> $jobfile echo "%END%" >> $jobfile echo " " >> $jobfile done # ABDECKZEICHEN VERHINDERN, DASS ERSETZUNGEN ERFOLGEN echo "cat > Makefile << \"%END%\"" >> $jobfile cat $source_catalog/Makefile >> $jobfile echo " " >> $jobfile echo "%END%" >> $jobfile echo " " >> $jobfile echo "cd - > /dev/null" >> $jobfile fi # ABSPEICHERN DER KONFIGURATIONSDATEI # ABDECKZEICHEN VERHINDERN, DASS ERSETZUNGEN ERFOLGEN echo "cat > $config_file << \"%END%\"" >> $jobfile cat $config_file >> $jobfile echo "%END%" >> $jobfile echo " " >> $jobfile # ABSPEICHERN DER AKTUELLEN MRUN-VERSION # ABDECKZEICHEN VERHINDERN, DASS ERSETZUNGEN ERFOLGEN echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile cat ${PALM_BIN}/$mrun_script_name >> $jobfile echo "%END%" >> $jobfile echo "chmod u+x $mrun_script_name" >> $jobfile echo "execute_mrun=true" >> $jobfile echo " " >> $jobfile fi # EVTL. BENOETIGTE INPUT-DATEIEN PER FTP HOLEN ODER DEM JOB DIREKT # MITGEBEN UND AUF DEM REMOTE-RECHNER IM BENUTZERVERZEICHNIS ABLEGEN # FALLS DIESES NICHT EXISTIERT, WIRD VERSUCHT, DAS JEWEILS LETZTE # UNTERVERZEICHNIS DES PFADNAMENS ANZULEGEN if [[ $do_remote = true ]] then (( i = 0 )) while (( i < iin )) do (( i = i + 1 )) echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile if [[ "${transin[$i]}" = job ]] then echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile echo " " >> $jobfile echo "%END%" >> $jobfile else echo "batch_scp -b -o -g -s -u $return_username $return_addres ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile fi # UEBERPRUEFEN, OB DATEI ANGELEGT WERDEN KONNTE echo "if [[ \$? = 1 ]]" >> $jobfile echo "then" >> $jobfile echo " echo \" \" " >> $jobfile echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile echo " echo \" please check, if directory exists on $host!\" " >> $jobfile echo " echo \"+++ MRUN will not be continued\" " >> $jobfile echo " execute_mrun=false" >> $jobfile echo "fi" >> $jobfile done fi # ARBEITSKATALOG AUF DER LOKALEN MASCHINE FUER EVENTUELLE # FORTSETZUNGSLAUEFE PER ENV-VARIABLE UEBERGEBEN echo "LOCAL_PWD=$working_directory" >> $jobfile echo "export LOCAL_PWD" >> $jobfile # EBENSO LOKALEN MRUN-KATALOG UEBERGEBEN echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile echo "export LOCAL_MRUN_PATH" >> $jobfile # WORKAROUND FUER RIAM-NEC-JOBS WEGEN PROFILE-SCHWIERIGKEITEN if [[ $localhost_realname = "gate" || $localhost = lctit ]] then echo "export PALM_BIN=$PALM_BIN" >> $jobfile fi # MRUN AUF ZIELRECHNER AUFRUFEN (queue is workaround for ibmkisti) echo "set -x" >> $jobfile echo "queue=$queue" >> $jobfile echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile echo 'ls -al; echo `pwd`' >> $jobfile echo "cd \$HOME" >> $jobfile echo "rm -rf $TEMPDIR" >> $jobfile # JOB PER SUBJOB STARTEN if [[ $silent = false ]] then printf "\n " else printf "\n\n" fi subjob $job_on_file -h $host -u $remote_username -g $group_number -q $queue -m $memory -N $node_usage -t $cpumax $XOPT $TOPT $OOPT -n $fname -v -c $job_catalog -e $email_notification $jobfile rm -rf $jobfile fi # ENDE REMOTE-TEIL # ENDE DER PROZEDUR