#!/bin/bash # palmrun - script for running PALM jobs #--------------------------------------------------------------------------------# # This file is part of the PALM model system. # # PALM is free software: you can redistribute it and/or modify it under the terms # of the GNU General Public License as published by the Free Software Foundation, # either version 3 of the License, or (at your option) any later version. # # PALM is distributed in the hope that it will be useful, but WITHOUT ANY # WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR # A PARTICULAR PURPOSE. See the GNU General Public License for more details. # # You should have received a copy of the GNU General Public License along with # PALM. If not, see . # # Copyright 2017-2018 Leibniz Universitaet Hannover #--------------------------------------------------------------------------------# # # Current revisions: # ------------------ # # # Former revisions: # ----------------- # $Id: palmrun 2718 2018-01-02 08:49:38Z maronga $ # parameters are allowed in output commands (OC:) # # 2718 2018-01-02 08:49:38Z maronga # bugfix: exit if no queue has been given neither with option -q nor in the # configuration file # # 2718 2018-01-02 08:49:38Z maronga # file connection file from trunk/SCRIPTS is taken by default # # 2718 2018-01-02 08:49:38Z maronga # Corrected "Former revisions" section # # 2696 2017-12-14 17:12:51Z kanani # Change in file header (GPL part) # # 2693 2017-12-13 12:33:49Z raasch # replacement of variables given by {{}} in configuration file is now # done in a more general way, variable names are written in small letters # # 2670 2017-12-06 16:32:19Z raasch # test printouts removed # # 2669 2017-12-06 16:03:27Z raasch # file attributes in .palm.iofiles restructured, "loc" attribute completely # removed, # wildcard (*) allowed in .palm.iofiles as file activation string for output # files, # informative messages in case of missing optional input files shortened # bugfix: variable cycle explicitly interpreted with 10 as the number base # # 2638 2017-11-23 12:44:23Z raasch # use of wildcards in file connection statements enabled # # 2605 2017-11-09 15:31:46Z raasch # in case of remote jobs, input files with "job" or "jobopt" (new) attribute # will not be sent with the job file any more, but copied into the # SOURCES_FOR_RUN... folder on the remote host, before the job is submitted # # 2600 2017-11-01 14:11:20Z raasch # cycle numbers are made three digits wide # # 2566 2017-10-20 08:50:47Z raasch # execute command for combine_plot_fields added # "TEMPDIR" renamed "tempdir" # temporary working directory for local batch jobs is created immediately within # the user's palmrun call, due to a requirement of the "grid engine" batch # system, where the working directory is given with batch directive -wd and must # already exist when the job is submitted, # informative messages in non-trace mode reduced and partly reformatted # # 2551 2017-10-18 07:25:11Z raasch # TEMPDIR added as replacement string to be used in batch directives # # 2512 2017-10-04 08:26:59Z raasch # bugfix for determining cycle numbers of NetCDF input files # # 2506 2017-09-29 08:30:37Z raasch # option -V added to check for an existing SOURCES_FOR_RUN_... folder # host configuration added to SOURCES_FOR_RUN_... folder name # host_identifier renamed host_configuration # option -W added to allow for job dependencies # # 2501 2017-09-26 11:41:55Z raasch # default value for number of cores (option -X) set to 1 # bugfix for mechanism which overwrites configuration file settings with values # provided by palmrun options # # 2499 2017-09-22 16:47:58Z kanani # option -h named configuration identifier # # 2480 2017-09-19 06:24:14Z maronga # bugfix for last revision # # 2479 2017-09-19 06:12:16Z raasch # option -A (project account number) added # # 2422 2017-09-08 08:25:41Z raasch # initial revision # #--------------------------------------------------------------------------------# # palmrun - script for running PALM jobs on local and remote hosts #--------------------------------------------------------------------------------# # DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS # LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN # (TOO MANY ARGUMENTS - PROBLEM) set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0 typeset -i nr_of_output_files=0 typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE # SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE # SCRIPT-OPTION ARGUMENTS typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio typeset -i icycle inode ival maxcycle mpi_tasks typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task activation_string_list="" AddFilenames="" combine_plot_fields=true compiler_name="" compiler_name_ser="" compiler_options="" cores=1 cores_atmos=0 cores_ocean=0 coupled_dist="" cpp_options="" cpumax=0 create_batch_job=false create_jobfile_only=false create_remote_batch_job=false dashes=" ----------------------------------------------------------------------------" defaultqueue="" delete_temporary_catalog=true do_compile=true do_trace=false executable="" execute_command="" execution_error=false fileconnection_file=trunk/SCRIPTS/.palm.iofiles fname=test global_revision="" host_configuration="default" hostfile="" hp="" keep_data_from_previous_run=false link_local_input=false link_local_output=false linker_options="" local_jobcatalog="" locat=normal makefile="" max_par_io_str="" prc=$0 while [[ $(echo $prc | grep -c "/") != 0 ]] do prc=`echo $prc | cut -f2- -d"/"` done module_calls="" palmrun_memory="" palmrun_script_name=$prc openmp=false previous_job="" project_account="" queue=none restart_run=false return_address="" remote_jobcatalog="" remote_username="" running_in_batch_mode=false run_coupled_model=false run_id="" silent=false source_list="" source_path="" tasks_per_node=0 threads_per_task=1 transfer_problems=false user_source_path="" use_existing_sources_folder="" use_openmp=false version="palmrun 1.0 Rev$Rev: 2799 $" working_directory=`pwd` write_binary="" TOPT="" # ERROR HANDLING IN CASE OF EXIT trap 'if [[ $locat != normal && $locat != control_c ]] then # CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:) (( 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 [[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir) printf "\n\n+++ palmrun killed \n\n" elif [[ $locat != control_c ]] then printf "\n --> palmrun finished\n\n" fi' exit # ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C): trap 'cd; rm -rf $tempdir printf "\n+++ palmrun killed by \"^C\" \n\n" locat=control_c exit ' 2 # READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc), # WHICH WILL BE USED TO START RESTART-JOBS while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option do case $option in (a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";; (A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";; (b) create_batch_job=true; prc="$prc -b";; (B) delete_temporary_catalog=false; prc="$prc -B";; (C) restart_run=true; prc="$prc -C";; (d) fname=$OPTARG; prc="$prc -d$OPTARG";; (F) create_jobfile_only=true;; (G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";; (h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";; (j) running_in_batch_mode=true;; (k) keep_data_from_previous_run=true; prc="$prc -k";; (m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";; (M) makefile=$OPTARG; prc="$prc -M$OPTARG";; (O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";; (q) queue=$OPTARG; prc="$prc -q$OPTARG";; (r) run_id=$OPTARG;; (R) return_address=$OPTARG;; (s) source_list=$OPTARG;; (t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";; (T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";; (u) remote_username=$OPTARG; prc="$prc -u$OPTARG";; (U) return_username=$OPTARG; prc="$prc -U$OPTARG";; (v) silent=true; prc="$prc -v";; (V) use_existing_sources_folder="-V";; (w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";; (W) previous_job=$OPTARG;; (x) do_trace=true;set -x; prc="$prc -x";; (X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";; (y) ocean_file_appendix=true; prc="$prc -y";; (Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";; (Z) combine_plot_fields=false; prc="$prc -Z";; (\?) printf "\n +++ unknown option $OPTARG \n" printf "\n --> type \"$0 ?\" for available options \n" locat=parameter;exit;; esac done # SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN # CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED (( to_shift = $OPTIND - 1 )) shift $to_shift # PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS if [[ "$1" = "?" ]] then (printf "\n *** Description of available palmrun options:\n" printf "\n Option Description Default-Value" printf "\n -a activation string list \"\" " printf "\n -A project account number ---" printf "\n -b batch-job on local machine ---" printf "\n -B do not delete temporary directory at end ---" printf "\n -d base name of files attached to program test" printf "\n -F create batch job file only ---" printf "\n -h host configuration \"default\" " printf "\n -k keep data from previous run" printf "\n -m memory demand in MB (batch-jobs) 0 MB" printf "\n -M Makefile name Makefile" printf "\n -O threads per openMP task ---" printf "\n -q queue \"$queue\" " 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 LM compiles all locally modified files" printf "\n -t allowed cpu-time in seconds (batch) 0" printf "\n -T tasks per node ---" printf "\n -u username on remote machine \"\" " printf "\n -v no prompt for confirmation ---" printf "\n -V check if SOURCES_FOR_RUN_... exists ---" printf "\n -w maximum parallel io streams as given by -X" printf "\n -W name of job to wait for ---" printf "\n -x tracing of palmrun 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 -Z skip combine_plot_fields at the end of " printf "\n the simulation ---" 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 # SHORT STARTING MESSAGE printf "\n*** $version " printf "\n will be executed. Please wait ..." # BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME config_file=.palm.config.$host_configuration sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname # CHECK, IF CONFIGURATION FILE EXISTS if [[ ! -f $config_file ]] then printf "\n\n +++ configuration file: " printf "\n $config_file" printf "\n does not exist" locat=connect; exit fi # CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE if [[ -f .palm.iofiles ]] then fileconnection_file=.palm.iofiles fi # CHECK, IF FILE CONNECTION FILE EXISTS if [[ ! -f $fileconnection_file ]] then printf "\n\n +++ file connection file: " printf "\n $fileconnection_file" printf "\n does not exist" locat=connect; exit fi # CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN if [[ "$activation_string_list" = "" ]] then printf "\n\n +++ no activation string list given: " printf "\n please set palmrun option \"-a\" " locat=palmrun_option; exit fi # SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS if [[ $(echo $activation_string_list | grep -c "restart") != 0 ]] then write_binary=true else write_binary=false fi # READ AND EVALUATE THE CONFIGURATION-FILE [[ $silent = false ]] && printf "\n\n Reading the configuration file... " # READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE while read line do # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES eval line=\"$line\" # INTERPRET THE LINE if [[ "$(echo $line)" = "" ]] then # EMPTY LINE, NO ACTION continue elif [[ "$(echo $line | cut -c1)" = "#" ]] then # LINE IS A COMMENT LINE continue elif [[ "$(echo $line | cut -c1)" = "%" ]] then # LINE DEFINES AN ENVIRONMENT-VARIABLE var=`echo $line | cut -d" " -s -f1 | cut -c2-` value=`echo $line | cut -d" " -s -f2-` # VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE # ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY # ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS). # NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER). # HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE # CONFIGURATION-FILE. if [[ "$(eval echo \$$var)" = "" || "$(eval echo \$$var)" = "0" ]] then eval export $var="\$value" # TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on if [[ $do_trace = true ]] then printf "\n*** ENVIRONMENT-VARIABLE $var = $value" fi fi elif [[ "$(echo $line | cut -c1-3)" = "BD:" ]] then # LINE DEFINES BATCH-DIRECTIVE (( ibd = ibd + 1 )) line=$(echo $line | cut -c4-) batch_directive[$ibd]="$line" elif [[ "$(echo $line | cut -c1-4)" = "BDT:" ]] then # LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A # REMOTE TO A LOCAL HOST (( ibdt = ibdt + 1 )) line=$(echo $line | cut -c5-) batch_directive_transfer[$ibdt]="$line" elif [[ "$(echo $line | cut -c1-3)" = "EC:" ]] then # LINE DEFINES ERROR-COMMAND (( iec = iec + 1 )) line=$(echo $line | cut -c4-) err_command[$iec]="$line" elif [[ "$(echo $line | cut -c1-3)" = "IC:" ]] then # LINE DEFINES INPUT-COMMAND (( iic = iic + 1 )) line=$(echo $line | cut -c4-) in_command[$iic]="$line" elif [[ "$(echo $line | cut -c1-3)" = "OC:" ]] then # LINE DEFINES OUTPUT-COMMAND (( ioc = ioc + 1 )) line=$(echo $line | cut -c4-) out_command[$ioc]="$line" else # SKIP ALL OTHER LINES continue fi done < $config_file # CHECK SETTING OF REQUIRED PARAMETERS if [[ "$compiler_name" = "" ]] then printf "\n +++ no compiler name found in $config_file" printf "\n Please add line \"compiler_name ...\" to that file." locat=config_file; exit fi if [[ "$compiler_name_ser" = "" ]] then printf "\n +++ no compiler name for non-paralle compilation found in $config_file" printf "\n Please add line \"compiler_name_ser ...\" to that file." locat=config_file; exit fi if [[ "$compiler_options" = "" ]] then printf "\n +++ no compiler options found in $config_file" printf "\n Please add line \"compiler_options ...\" to that file." locat=config_file; exit fi if [[ "$linker_options" = "" ]] then printf "\n +++ no linker options found in $config_file" printf "\n Please add line \"linker_options ...\" to that file." locat=config_file; exit fi if [[ "$execute_command" = "" ]] then printf "\n +++ no execute command found in $config_file" printf "\n Please add line \"execute_command ...\" to that file." locat=config_file; exit fi if [[ "$hostfile" != "" ]] then if [[ $hostfile != auto && ! -f $hostfile ]] then printf "\n +++ no hostfile \"$hostfile\" found" printf "\n Please check line \"hostfile ...\" in $config_file" locat=config_file; exit fi fi # DETERMINE THE CALL STATUS if [[ "$return_address" != "" ]] then # I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN # BATCH MODE AND ... running_on_remote=true else # I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST if [[ "$remote_ip" != "" ]] then # I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST create_remote_batch_job=true fi running_on_remote=false fi # READ AND EVALUATE THE I/O-FILE LIST [[ $silent = false ]] && printf "\n Reading the I/O files... " # READ THE FILE CONNECTION FILE LINE BY LINE while read line do # REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE line=`echo "$line" | sed -e "s/\s\{1,\}/ /g"` # INTERPRET THE LINE if [[ "$(echo $line)" = "" ]] then # EMPTY LINE, NO ACTION continue elif [[ "$(echo $line | cut -c1)" = "#" ]] then # LINE IS A COMMENT LINE true else # LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES. # s2a: in/out - field # s2b: action - field (optional) s1=`echo "$line" | cut -d" " -f1` s2=`echo "$line" | cut -d" " -s -f2` if [[ $(echo $s2 | grep -c ":") = 0 ]] then s2a=$s2 s2b="" else s2a=`echo $s2 | cut -d":" -f1` s2b=`echo $s2 | cut -d":" -f2` fi s3=`echo "$line" | cut -d" " -f3 | sed 's/*/wildcard /g'` s4=`echo "$line" | cut -d" " -s -f4` eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES s5=`echo "$line" | cut -d" " -s -f5` s6=`echo "$line" | cut -d" " -s -f6` # STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM # INPUT- OR OUTPUT-LIST. # VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":"). # IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY # LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION # IS NOT CHECKED AND STORED. IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR if [[ ( "$s2a" = in || "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]] then found=false for actual in $activation_string_list do for formal in $s3 do [[ $actual = $formal || "$formal" = "-" ]] && found=true done done if [[ $found = true ]] then (( iin = iin + 1 )) localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b; pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6 if [[ "$s2a" = inopt ]] then optin_pre[$iin]=yes else optin_pre[$iin]=no fi # FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN # FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST if [[ $running_on_remote = true && "$s2b" = tr ]] then pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog} fi # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE # THE WILDCARD FROM THE ENDING if [[ "${s5: -1}" = "*" ]] then if [[ "$s2b" = "di" ]] then printf "\n +++ wildcards (*) not allowed with \"di\" file attribute." printf "\n see file \"$fileconnection_file\", line" printf "\n$line" locat=iofiles_file; exit fi multin[$iin]=true string=${endin_pre[$iin]} endin_pre[$iin]="${string%?}" else multin[$iin]=false fi fi elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]] then found=false for actual in $activation_string_list do for formal in $s3 do [[ $actual = $formal || $formal = wildcard ]] && found=true done done if [[ $found = true ]] then (( iout = iout + 1 )) localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6 # CHECK IF WILDCARD IS USED AS ACTIVATION STRING # IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST if [[ $formal = wildcard ]] then warnout_pre[$iout]=false else warnout_pre[$iout]=true fi # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE # THE WILDCARD FROM THE LOCAL FILENAME if [[ "${s1: -1}" = "*" ]] then if [[ "$s2b" = "di" ]] then printf "\n +++ wildcards (*) not allowed with \"di\" file attribute." printf "\n see file \"$fileconnection_file\", line" printf "\n$line" locat=iofiles_file; exit fi multout[$iout]=true string=${localout_pre[$iout]} localout_pre[$iout]="${string%?}" else multout[$iout]=false fi fi elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]] then printf "\n +++ I/O-attribute in file $fileconnection_file has invalid" printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!" locat=connect; exit fi IFS="$IFSALT" fi done < $fileconnection_file # VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE [[ $palmrun_memory != "" ]] && memory=$palmrun_memory [[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax [[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores [[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str [[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node # EVALUATE MODEL COUPLING FEATURES (OPTION -Y) if [[ $run_coupled_model = true ]] then cores_atmos=`echo $coupled_dist | cut -d" " -s -f1` cores_ocean=`echo $coupled_dist | cut -d" " -s -f2` if (( $cores_ocean + $cores_atmos != $cores )) then printf "\n +++ number of processors does not fit to specification by \"-Y\"." printf "\n PEs (total) : $cores" printf "\n PEs (atmosphere): $cores_atmos" printf "\n PEs (ocean) : $cores_ocean" locat=coupling; exit fi fi # IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES # HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_... # FOLDER if [[ $running_in_batch_mode = true ]] then if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]] then printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing" printf "\n Please check the output of the palmrun-call" printf "\n that you did on your local host." locat=SOURCES_FOR_RUN; exit fi else # CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN # AUTOMATIC RESTART RUN # AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN if [[ $restart_run = false ]] then # COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON # THE LOCAL HOST if [[ ! -d $source_path ]] then printf "\n\n +++ source path \"$source_path\" on local host" printf "\n \"$(hostname)\" does not exist" locat=source_path; exit fi rm -rf $sources_for_run_catalog mkdir -p $sources_for_run_catalog if [[ "$source_list" = LM ]] then # DETERMINE MODIFIED FILES OF THE SVN WORKING COPY source_list="" cd $source_path # CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL if [[ ! -d ../.svn ]] then printf "\n\n +++ source directory" printf "\n \"$source_path\" " printf "\n is not under control of \"subversion\"." printf "\n Please do not use palmrun-option \"-s LM\"\n" fi # LIST ALL MODIFIED SOURCE CODE FILES Filenames="" svn status > tmp_svnstatus 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_svnstatus rm -rf tmp_svnstatus # COPY FILES TO SOURCES_FOR_RUN_... for filename in $Filenames do cp $filename ${working_directory}/${sources_for_run_catalog} source_list=$source_list"$filename " done cd - > /dev/null # COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_... elif [[ "$source_list" != "" ]] then cd $source_path for filename in $source_list do # SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH if [[ $(echo $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_catalog} fi done cd - > /dev/null fi # CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY [[ "$makefile" = "" ]] && makefile=$source_path/Makefile if [[ ! -f $makefile ]] then printf "\n +++ file \"$makefile\" does not exist" locat=make; exit else cp $makefile ${sources_for_run_catalog}/Makefile fi # COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE if [[ "$user_source_path" != "" ]] then # DOES THE DIRECTORY EXIST? if [[ ! -d $user_source_path ]] then printf "\n\n *** INFORMATIVE: additional source code directory" printf "\n \"$user_source_path\" " printf "\n does not exist or is not a directory." printf "\n No source code will be used from this directory!\n" user_source_path="" if [[ $silent == false ]] then sleep 2 fi else cd $user_source_path found=false Names=$(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_catalog # COPY MAKEFILE IF EXISTING if [[ -f $user_source_path/Makefile ]] then printf "\n\n *** user Makefile from directory" printf "\n \"$user_source_path\" is used \n" if [[ $silent == false ]] then sleep 1 fi cp $user_source_path/Makefile . fi for filename in $AddFilenames do if [[ -f $filename ]] then printf "\n +++ source code file \"$filename\" found in additional" printf "\n source code directory \"$user_source_path\" " printf "\n but was also given with option \"-s\" which means that it should be taken" printf "\n from directory \"$source_path\"." locat=source; exit fi cp $user_source_path/$filename . source_list="$source_list $filename" # CHECK IF FILE IS CONTAINED IN MAKEFILE if [[ $(grep -c $filename Makefile) = 0 ]] then printf "\n\n +++ user file \"$filename\" " printf "\n is not listed in Makefile \n" locat=source; exit else if [[ $found = false ]] then found=true printf "\n\n *** following user file(s) added to the" printf " files to be translated:\n " fi printf "$filename " if [[ $silent == false ]] then sleep 0.5 fi fi done [[ $found = true ]] && printf "\n" cd - > /dev/null fi fi # COPY CONFIGURATION FILES cp $config_file $sources_for_run_catalog cp $fileconnection_file $sources_for_run_catalog # COPY SHELLSCRIPTS cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog fi fi # GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY # (HANDED OVER TO RESTART-RUNS USING OPTION -G) if [[ "$global_revision" = "" ]] then global_revision=`svnversion $source_path 2>/dev/null` global_revision="Rev: $global_revision" fi # IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS if [[ -n $cores ]] then # CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN # INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X if [[ $tasks_per_node = 0 ]] 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 if (( cores < tasks_per_node )) then printf "\n" printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)" printf "\n given values: -T $tasks_per_node -X $cores" locat=tasks_per_node; (( iec = 0 )); exit fi (( nodes = cores / ( tasks_per_node * threads_per_task ) )) (( mpi_tasks = cores / threads_per_task )) [[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 )) (( ii = cores / tasks_per_node )) (( remaining_cores = cores - ii * tasks_per_node )) if (( remaining_cores > 0 )) then printf "\n" printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral" printf "\n divisor of the total number of cores (option \"-X\")" printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\"" printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks" (( nodes = nodes + 1 )) fi # SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW) if [[ "$tasks_per_node" != "" ]] then TOPT="-T $tasks_per_node" fi fi # SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS if [[ "$maximum_parallel_io_streams" = "" ]] then maximum_parallel_io_streams=$cores fi # SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT if [[ "$scp_port" != "" ]] then PORTOPT="-P $scp_port" SSH_PORTOPT="-p $scp_port" fi # DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE # CONFIG-FILE if [[ "$ssh_key" != "" ]] then ssh_key="-i $HOME/.ssh/$ssh_key" fi # SET QUEUE, IF NOT GIVEN if [[ $create_batch_job = true || $create_remote_batch_job = true ]] then if [[ $queue = none && "$defaultqueue" = "" ]] then printf "\n" printf "\n +++ no default queue given in configuration file and no queue" printf "\n given with option -q" locat=queue; exit fi if [[ $queue = none ]] then queue=$defaultqueue fi fi # GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH # CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST) (( i = 0 )) (( nr_of_input_files = 0 )) while (( i < iin )) do (( i = i + 1 )) # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE # FILE IDENTIFIER IS NOT PART OF THE FILENAME)) if [[ "${actionin_pre[$i]}" = di ]] then eval filename=${pathin_pre[$i]}/${endin_pre[$i]} else eval filename=${pathin_pre[$i]}/${fname}${endin_pre[$i]} fi # CHECK IF FILE EXISTS if ! ls $filename* 1>/dev/null 2>&1 then # FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST. if [[ "${optin_pre[$i]}" != "yes" ]] then printf "\n\n +++ INPUT-file: " if [[ "${extin_pre[$i]}" = "" || "${extin_pre[$i]}" = " " ]] then printf "\n $filename" else printf "\n $filename.${extin_pre[$i]}" fi printf "\n does not exist\n" locat=input; exit else (( nr_of_input_files = nr_of_input_files + 1 )) localin[$nr_of_input_files]="${localin_pre[$i]}" optin[$nr_of_input_files]="${optin_pre[$i]}" actionin[$nr_of_input_files]="unavailable" pathin[$nr_of_input_files]="${pathin_pre[$i]}" endin[$nr_of_input_files]="${endin_pre[$i]}" extin[$nr_of_input_files]="${extin_pre[$i]}" fi else # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($fname) AND # CREATE A LIST FOR THE DETECTED BASENAME ENDINGS if [[ "${multin[$i]}" = true ]] then # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES ls -1 -d ${filename} > filelist 2>/dev/null ls -1 -d ${filename}.* >> filelist 2>/dev/null ls -1 -d ${filename}_* >> filelist 2>/dev/null endings="" while read line do # filename without path (i.e. after the last "/") basefilename=$(basename ${line}) # check if there is an extension and remove it ext=${basefilename##*.} if [[ "$ext" = "${extin_pre[$i]}" ]] then basefilename=${basefilename%.*} fi # check for an existing cycle number and remove it cycle=${basefilename##*.} if [[ $cycle =~ ^-?[0-9]+$ ]] then basefilename=${basefilename%.*} fi # remove the fname from the beginning length_fname=${#fname} ending=${basefilename:${length_fname}} # remove the ending given in the .iofiles from the beginning endingstring="${endin_pre[$i]}" length_ending=${#endingstring} ending=${ending:${length_ending}} if [[ "$ending" = "" ]] then # standard ending as given in the .iofiles if [[ $(echo $endings | grep -c DEFAULT) = 0 ]] then endings="$endings DEFAULT" fi else # ending must start with "_", otherwise its a different file if [[ "${ending:0:1}" = "_" ]] then if [[ $(echo $endings | grep -c "$ending") = 0 ]] then endings="$endings $ending" fi fi fi done filelist 2>/dev/null ls -1 -d $filename.* >> filelist 2>/dev/null while read line do # filename without path (i.e. after the last "/") basefilename=$(basename ${line}) # check if there is an extension extension=${basefilename##*.} if [[ "$extension" = "${extin[$nr_of_input_files]}" ]] then basefilename=${basefilename%.*} fi # check for an existing cycle number cycle=${basefilename##*.} if [[ $cycle =~ ^-?[0-9]+$ ]] then # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10 (( icycle = $((10#$cycle)) )) else (( icycle = 0 )) fi if (( icycle > maxcycle )) then (( maxcycle = icycle )) # FOR COMPATIBILITY REASONS WITH OLDER VERSIONS # CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS if [[ $(echo $cycle | cut -c1) = 0 ]] then leading_zero=true else leading_zero=false fi fi done 0 )) then if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]] then filename=${filename}.$cyclestring.${extin[$nr_of_input_files]} else filename=${filename}.$cyclestring fi else if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]] then filename=${filename}.${extin[$nr_of_input_files]} fi fi # STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER, # IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE) absnamein[$nr_of_input_files]=$filename if (( maxcycle > 0 )) then if [[ "${actionin[$nr_of_input_files]}" = di ]] then frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring else frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}.$cyclestring fi else if [[ "${actionin[$nr_of_input_files]}" = di ]] then frelin[$nr_of_input_files]=${endin[$nr_of_input_files]} else frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]} fi fi done fi done # GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~), # CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST), # OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED # THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO # THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE # REMOTE HOST) (( i = 0 )) while (( i < iout )) do (( i = i + 1 )) if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr || "${actionout_pre[$i]}" = tra || "${actionout_pre[$i]}" = trpe ) ) ]] then if [[ "${actionout_pre[$i]}" = tr ]] then actionout_pre[$i]="" elif [[ "${actionout_pre[$i]}" = trpe ]] then actionout_pre[$i]=pe elif [[ "${actionout_pre[$i]}" = tra ]] then actionout_pre[$i]=a fi (( maxcycle = 0 )) eval filename=${pathout_pre[$i]}/${fname}${endout_pre[$i]} eval catalogname=${pathout_pre[$i]} if ! ls $filename* 1>/dev/null 2>&1 then # IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED if cat /dev/null > $filename then rm $filename else # CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS # IF IT DOES NOT EXIST, TRY TO CREATE IT 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 fi fi done # DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY if [[ $running_in_batch_mode = false ]] then run_id=$RANDOM job_id=${fname}.$run_id tempdir=$fast_io_catalog/$job_id fi # CHECK SETTINGS REQUIRED FOR BATCH JOBS if [[ $create_batch_job = true || $create_remote_batch_job = true ]] then # CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE if [[ $ibd = 0 ]] then printf "\n" printf "\n +++ no batch directives found in configuration file" locat=config_file_batch_directives; (( iec = 0 )); exit fi # CHECK IF CPUTIME IS GIVEN FOR JOB done=false cputime=$cpumax while [[ $done = false ]] do if (( cputime == 0 )) then printf "\n +++ cpu-time is undefined" printf "\n >>> Please type CPU-time in seconds as INTEGER:" printf "\n >>> " read cputime 1>/dev/null 2>&1 else done=true fi done cpumax=$cputime # CHECK THE MEMORY DEMAND 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 # IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN if [[ $create_remote_batch_job = true && -z $remote_username ]] then while [[ -z $remote_username ]] do printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined" printf "\n >>> Please type username:" printf "\n >>> " read remote_username done fi else if [[ $running_in_batch_mode = false ]] then cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS cpumax=$cputime else cputime=$cpumax fi fi # CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES (( cpu_hours = cputime / 3600 )) (( resttime = cputime - cpu_hours * 3600 )) (( cpu_minutes = resttime / 60 )) (( cpu_seconds = resttime - cpu_minutes * 60 )) timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds} # OUTPUT OF THE PALMRUN-HEADER calltime=$(date) printf "\n" printf "#------------------------------------------------------------------------# \n" printf "| %-35s%35s | \n" "$version" "$calltime" printf "| | \n" column1="called on:"; column2=$(hostname) printf "| %-25s%-45s | \n" "$column1" "$column2" if [[ $create_remote_batch_job = true ]] then column1="execution on:"; column2="$host_configuration (username: $remote_username)" else if [[ $running_on_remote = true ]] then column1="execution on:"; column2="$host_configuration (IP:$remote_ip)" else column1="execution on:"; column2="$host_configuration (IP:$local_ip)" fi fi printf "| %-25s%-45s | \n" "$column1" "$column2" column1="running in:" if [[ $running_in_batch_mode = true ]] then column2="batch job mode" else if [[ $create_batch_job = true || $create_remote_batch_job = true ]] then column2="job creation mode" else column2="interactive run mode" fi fi printf "| %-25s%-45s | \n" "$column1" "$column2" if [[ $running_in_batch_mode = true || $create_batch_job = true || $create_remote_batch_job = true ]] then if [[ "$project_account" != "" ]] then column1="project account number:" column2="$project_account" printf "| %-25s%-45s | \n" "$column1" "$column2" fi fi if [[ -n $cores ]] then if [[ $run_coupled_model = false ]] then column1="number of cores:"; column2=$cores else column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)" fi printf "| %-25s%-45s | \n" "$column1" "$column2" fi if [[ -n $tasks_per_node ]] then column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)" printf "| %-25s%-45s | \n" "$column1" "$column2" if (( remaining_cores > 0 )) then column1=" "; column2="one of the nodes only filled with $remaining_cores tasks" printf "| %-25s%-45s | \n" "$column1" "$column2" fi fi if [[ $maximum_parallel_io_streams != $cores ]] then column1="max par io streams:"; column2="$maximum_parallel_io_streams" printf "| %-25s%-45s | \n" "$column1" "$column2" fi if [[ $use_openmp = true ]] then column1="threads per task:"; column2="$threads_per_task" printf "| %-25s%-45s | \n" "$column1" "$column2" fi if [[ $create_batch_job = true || $create_remote_batch_job = true || $running_in_batch_mode = true ]] then column1="memory demand / PE":; column2="$memory MB" printf "| %-25s%-45s | \n" "$column1" "$column2" column1="job cpu time (h:m:s):"; column2="$timestring" printf "| %-25s%-45s | \n" "$column1" "$column2" fi printf "| | \n" if [[ "$source_list" != "" ]] then if [[ "$make_options" != "" ]] then column1="make options:"; column2=$(echo "$make_options" | cut -c-45) printf "| %-25s%-45s | \n" "$column1" "$column2" line=$(echo "$make_options" | cut -c46-) while [[ "$line" != "" ]] do column1="" column2=$(echo "$line" | cut -c-45) printf "| %-25s%-45s | \n" "$column1" "$column2" line=$(echo "$line" | cut -c46-) done fi fi column1="cpp directives:"; column2=$(echo "$cpp_options" | cut -c-45) printf "| %-25s%-45s | \n" "$column1" "$column2" line=$(echo "$cpp_options" | cut -c46-) while [[ "$line" != "" ]] do column1="" column2=$(echo "$line" | cut -c-45) printf "| %-25s%-45s | \n" "$column1" "$column2" line=$(echo "$line" | cut -c46-) done column1="compiler options:"; column2=$(echo "$compiler_options" | cut -c-45) printf "| %-25s%-45s | \n" "$column1" "$column2" line=$(echo "$compiler_options" | cut -c46-) while [[ "$line" != "" ]] do column1="" column2=$(echo "$line" | cut -c-45) printf "| %-25s%-45s | \n" "$column1" "$column2" line=$(echo "$line" | cut -c46-) done column1="linker options:"; column2=$(echo "$linker_options" | cut -c-45) printf "| %-25s%-45s | \n" "$column1" "$column2" line=$(echo "$linker_options" | cut -c46-) while [[ "$line" != "" ]] do column1="" column2=$(echo "$line" | cut -c-45) printf "| %-25s%-45s | \n" "$column1" "$column2" line=$(echo "$line" | cut -c46-) done if [[ "$login_init_cmd" != "" ]] then column1="login init commands:"; column2=$(echo "$login_init_cmd" | cut -c-45) printf "| %-25s%-45s | \n" "$column1" "$column2" line=$(echo "$login_init_cmd" | cut -c46-) while [[ "$line" != "" ]] do column1="" column2=$(echo "$line" | cut -c-45) printf "| %-25s%-45s | \n" "$column1" "$column2" line=$(echo "$line" | cut -c46-) done fi if [[ "$module_commands" != "" ]] then column1="module commands:"; column2=$(echo "$module_commands" | cut -c-45) printf "| %-25s%-45s | \n" "$column1" "$column2" line=$(echo "$module_commands" | cut -c46-) while [[ "$line" != "" ]] do column1="" column2=$(echo "$line" | cut -c-45) printf "| %-25s%-45s | \n" "$column1" "$column2" line=$(echo "$line" | cut -c46-) done fi printf "| | \n" column1="base name of files:"; column2=$fname printf "| %-25s%-45s | \n" "$column1" "$column2" column1="activation string list:"; column2=$(echo $activation_string_list) printf "| %-25s%-45s | \n" "$column1" "$column2" if [[ "$ocean_file_appendix" = true ]] then printf "| %-35s%-35s | \n" "suffix \"_O\" is added to local files" " " fi if [[ "$source_list" != "" ]] then printf "| | \n" printf "| Files to be compiled: | \n" line=$source_list while [[ "$line" != "" ]] do linestart=$(echo $line | cut -c-70) printf "| %-70s | \n" "$linestart" line=$(echo "$line" | cut -c71-) done fi printf "#------------------------------------------------------------------------#" # OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK if [[ $do_trace = true ]] then (( i = 0 )) while (( i < nr_of_input_files )) 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 # QUERY FOR CONTINUE if [[ $silent = false && $running_in_batch_mode = false ]] then antwort=dummy printf "\n\n" printf " >>> everything o.k. (y/n) ? " while read antwort do if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]] then printf " >>> everything o.k. (y/n) ? " else break fi done if [[ $antwort = n || $antwort = N ]] then locat=user_abort; (( iec = 0 )); exit fi if [[ $create_batch_job = true || $create_remote_batch_job = true ]] then printf "\n *** batch-job will be created and submitted" else printf "\n *** PALMRUN will now continue to execute on this machine" fi fi # PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE if [[ $restart_run = false && $running_in_batch_mode = false ]] then if [[ $create_batch_job = true || $create_remote_batch_job = true ]] then printf "\n\n *** creating executable and other sources for the remote host\n" else printf "\n\n *** creating executable and other sources for the local host\n" fi # FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF # IT SHALL BE CREATED ask_for_make_depository=false if [[ $create_remote_batch_job = true ]] then line=`grep %base_directory $config_file` make_depository=`echo $line | cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration} echo "[[ ! -d ${make_depository} ]] && echo depository not found" | ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 | tee ${host_configuration}_last_make_protokoll if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]] then printf "\n\n +++ make depository \"${make_depository}\"" printf "\n on remote host not found!" ask_for_make_depository=true fi rm ${host_configuration}_last_make_protokoll else # CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration} if [[ ! -d ${make_depository} ]] then printf "\n\n +++ make depository \"${make_depository}\"" printf "\n on local host not found!" ask_for_make_depository=true fi fi if [[ $ask_for_make_depository = true ]] then antwort=dummy printf "\n\n" printf " >>> Create a new one (y/n) ? " while read antwort do if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]] then printf " >>> Create a new one (y/n) ? " else break fi done if [[ $antwort = n || $antwort = N ]] then locat=user_abort; (( iec = 0 )); exit fi if [[ $do_trace = true ]] then palmbuild -h $host_configuration else palmbuild -v -h $host_configuration fi if [[ $? != 0 ]] then # ABORT IN CASE OF COMPILATION PROBLEMS printf "\n +++ error while compiling for the MAKE_DEPOSITORY" locat=make_depository exit else echo " *** now continue with creating executable and other sources" fi fi # NOW CREATE THE SOURCES_FOR_RUN FOLDER palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname if [[ $? != 0 ]] then # ABORT IN CASE OF COMPILATION PROBLEMS printf "\n +++ error while creating executable and/or other sources" locat=execution rm -rf $sources_for_run_catalog exit else printf " *** executable and other sources created\n" rm -rf $sources_for_run_catalog fi fi # WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT # WILL BE COPIED TO THE REMOTE HOST if [[ $create_remote_batch_job = true ]] then (( i = 0 )) while (( i < nr_of_input_files )) do (( i = i + 1 )) if [[ "${actionin[$i]}" = tr ]] then eval inputfile=${pathin[$i]}/${frelin[$i]} scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]} fi done if (( i > 0 )) then printf " *** input files have been copied to the remote host\n" fi fi # NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE # (COMPILING/LINKING, EXECUTING, COPYING I/O FILES) if [[ $create_batch_job = false && $create_remote_batch_job = false ]] then # CHANGE TO THE TEMPORARY WORKING DIRECTORY if [[ $running_in_batch_mode = false ]] then # CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT # FOLDER mkdir -p $tempdir chmod go+rx $tempdir cd $tempdir cp ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*} $tempdir printf "\n *** changed to temporary directory: $tempdir" else # IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR printf "\n *** running in temporary directory: $tempdir" fi # PROVIDE THE INPUT FILES # LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE) optional_files_missing=false (( i = 0 )) while (( i < nr_of_input_files )) do (( i = i + 1 )) if (( i == 1 )) then printf "\n\n *** providing INPUT-files:\n$dashes" fi # SKIP OPTIONAL FILES, IF THEY DO NOT EXIST if [[ "${actionin[$i]}" = unavailable ]] then optional_files_missing=true continue fi # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION) files_for_cores=false; filetype=file if [[ "${actionin[$i]}" = pe && -n $cores ]] then files_for_cores=true; filetype=files actionin[$i]="" elif [[ "${actionin[$i]}" = pe && ! -n $cores ]] then actionin[$i]="" elif [[ "${actionin[$i]}" = lnpe && -n $cores ]] then files_for_cores=true; filetype=files actionin[$i]="ln" elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]] then actionin[$i]="ln" fi if [[ $files_for_cores = true ]] then printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}" else printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}" fi # INPUT-FILES TO BE LINKED if [[ "${actionin[$i]}" = ln ]] then printf "\n $filetype will be linked" if [[ $files_for_cores = false ]] then if [[ -f "${absnamein[$i]}" ]] then ln ${absnamein[$i]} ${localin[$i]} got_tmp[$i]=true fi else if [[ -d "${absnamein[$i]}" ]] then mkdir -p ${localin[$i]} cd ${absnamein[$i]} for file in $(ls *) do ln $file $tempdir/${localin[$i]} done >|/dev/null 2>&1 cd $tempdir fi # IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r" if [[ ! -f "${localin[$i]}/_000000" ]] then printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)" cp -r ${absnamein[$i]}/* ${localin[$i]} fi got_tmp[$i]=true fi fi # FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE if [[ "${actionin[$i]}" = "" || "${actionin[$i]}" = "di" || "${actionin[$i]}" = "tr" || "${actionin[$i]}" = "npe" ]] then if [[ "${actionin[$i]}" = "npe" && -n $cores ]] then # FILE COPIES ARE PROVIDED FOR ALL CORES # EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER printf "\n file will be provided for $cores processors" mkdir -p ${localin[$i]} ival=$cores (( 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_cores = true ]] then # PROVIDE FILES FOR EACH CORE # FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES # FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE printf "\n providing $cores files for the respective cores" mkdir -p ${localin[$i]} if [[ $link_local_input = true ]] then printf " files will be linked\n" cd ${absnamein[$i]} for file in $(ls *) do ln -f $file ${localin[$i]} done cd $tempdir fi # IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r" if [[ ! -f "${localin[$i]}/_000000" ]] then if [[ $link_local_input = true ]] then printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)" fi cp -r ${absnamein[$i]}/* ${localin[$i]} fi else # PROVIDE FILE FOR RUNS ON A SINGLE CORE if [[ $link_local_input = true ]] then printf " file will be linked\n" ln -f ${absnamein[$i]} ${localin[$i]} fi # If "ln -f" fails or if "$link_local_input = false" do a normal "cp" if [[ ! -f "${localin[$i]}" ]] then if [[ $link_local_input = true ]] then printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)" fi if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]] then mv ${absnamein[$i]} ${localin[$i]} else cp ${absnamein[$i]} ${localin[$i]} fi fi fi fi fi done if (( i != 0 )) then if [[ $optional_files_missing = true ]] then printf "\n *** INFORMATIVE: some optional INPUT-files are not present" fi printf "\n$dashes\n *** all INPUT-files provided \n" fi # EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE (( i = 0 )) while (( i < iic )) do (( i = i + 1 )) if (( i == 1 )) then printf "\n\n *** execution of INPUT-commands:\n$dashes" fi printf "\n >>> ${in_command[$i]}" eval ${in_command[$i]} if (( i == iic )) then printf "\n$dashes\n" fi done # CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM # (FILE ENVPAR WILL BE READ BY PALM) cat > ENVPAR << EOF &envpar run_identifier = '$fname', host = '$host_configuration', write_binary = .${write_binary}., tasks_per_node = $tasks_per_node, maximum_parallel_io_streams = $maximum_parallel_io_streams, maximum_cpu_time_allowed = ${cpumax}., revision = '$global_revision', batch_job = .${running_in_batch_mode}. / EOF # STARTING THE EXECUTABLE printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n" PATH=$PATH:$tempdir # REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES line=`echo "${execute_command}" | sed 's/{{/$/g' | sed 's/}}//g'` line2=`echo "${execute_command}" | sed 's/{{mpi_tasks}}/1/g' | sed 's/{{tasks_per_node}}/1/g' | sed 's/palm/combine_plot_fields.x/g'` eval line=\"$line\" execute_command="$line" # EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS if [[ "$execute_command_for_combine" = "" ]] then eval line2=\"$line2\" execute_command_for_combine="$line2" fi # PROVIDE A HOSTFILE, IF REQUIRED if [[ "$hostfile" != "" ]] then if [[ $hostfile = auto ]] then # CREATE A NEW HOSTFILE (( ii = 1 )) while (( ii <= cores / threads_per_task )) do echo $(hostname) >> hostfile (( ii = ii + 1 )) done if (( cores / threads_per_task == 0 )) then echo $(hostname) >> hostfile fi else cp $hostfile hostfile fi eval line=\"`head -n $ii hostfile`\" printf "\n *** running on: $line" fi # SET THE NUMBER OF OPENMP-THREADS if [[ $use_openmp = true ]] then export OMP_NUM_THREADS=$threads_per_task printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS" else export OMP_NUM_THREADS=1 fi # PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING if [[ $run_coupled_model = false ]] then if [[ "$ocean_file_appendix" = true ]] then echo "precursor_ocean" > coupling_steering else echo "precursor_atmos" > coupling_steering fi else (( iia = $cores_atmos / $threads_per_task )) (( iio = $cores_ocean / $threads_per_task )) printf "\n coupled run ($iia atmosphere, $iio ocean)" printf "\n\n" echo "coupled_run $iia $iio" > coupling_steering fi printf "\n *** execute command:" printf "\n \"$execute_command\" \n\n" $execute_command < coupling_steering if [[ $? != 0 ]] then # ABORT IN CASE OF RUNTIME ERRORS printf "\n +++ runtime error occured" locat=execution exit else printf "\n$dashes\n *** execution finished \n" fi # CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN # BY EACH CORE INTO ONE FILE if [[ ! -f combine_plot_fields.x ]] then printf "\n\n\n +++ WARNING: no combine_plot_fields found" printf "\n 2d- and/or 3d-data may be incomplete!" printf "\n Your previous palmbuild may have failed. Please check.\n" elif [[ "$combine_plot_fields" == true ]] then printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..." $execute_command_for_combine else # TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF # DATA OUTPUT printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..." fi # EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE (( i = 0 )) while (( i < ioc )) do (( i = i + 1 )) if (( i == 1 )) then printf "\n\n *** execution of OUTPUT-commands:\n$dashes" fi # REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES out_command[$i]=`echo "${out_command[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'` printf "\n >>> ${out_command[$i]}" eval ${out_command[$i]} if (( i == ioc )) then printf "\n$dashes\n" fi done # IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF # WILDCARDS (( i = 0 )) (( nr_of_output_files = 0 )) while (( i < iout )) do (( i = i + 1 )) # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND # CREATE A LIST FOR THE DETECTED ENDINGS if [[ "${multout[$i]}" = true ]] then # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null endings="DEFAULT" while read line do # remove the local name from the beginning localnamestring="${localout_pre[$i]}" length_localname=${#localnamestring} ending=${line:${length_localname}} if [[ "$ending" != "" ]] then endings="$endings $ending" fi done filelist 2>/dev/null ls -1 -d $filename.* >> filelist 2>/dev/null while read line do # filename without path (i.e. after the last "/") basefilename=$(basename ${line}) # check if there is an extension extension=${basefilename##*.} if [[ "$extension" = "${extout[$i]}" ]] then basefilename=${basefilename%.*} fi # check for an existing cycle number cycle=${basefilename##*.} if [[ $cycle =~ ^-?[0-9]+$ ]] then # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10 (( icycle = $((10#$cycle)) + 1 )) else (( icycle = 1 )) fi if (( icycle > maxcycle )) then (( maxcycle = icycle )) fi done = cycnum[$i] )) then (( cycnum[$i] = run_number )) else if (( run_number > 0 )) then printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number" fi fi fi if (( cycnum[$i] > 0 )) then cyclestring=`printf "%03d" ${cycnum[$i]}` pathout[$i]=${pathout[$i]}.$cyclestring fi fi # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION) files_for_cores=false; filetype=file link_local_output=false if [[ "${actionout[$i]}" = pe && -n $cores ]] then files_for_cores=true; filetype=directory actionout[$i]="" elif [[ "${actionout[$i]}" = pe && ! -n $cores ]] then actionout[$i]="" elif [[ "${actionout[$i]}" = lnpe && -n $cores ]] then files_for_cores=true; filetype=directory link_local_output=true actionout[$i]="" elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]] then link_local_output actionout[$i]="" elif [[ "${actionout[$i]}" = trpe && -n $cores ]] then files_for_cores=true; filetype=directory actionout[$i]="tr" elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]] then actionout[$i]="tr" fi if [[ ! -f ${localout[$i]} && $files_for_cores = false ]] then if [[ ${warnout[$i]} = true ]] then printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n" fi elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]] then if [[ ${warnout[$i]} = true ]] then printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n" fi else # COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m) # IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT if [[ "${actionout[$i]}" = tr || "${actionout[$i]}" = tra ]] then if [[ $running_on_remote = true ]] then # SET OPTIONS FOR TRANSFER if [[ "${actionout[$i]}" = tr ]] then if [[ $files_for_cores = false ]] then catalog_option="" catalog_string="" else catalog_option="-c" catalog_string="/" fi append_option="" append_string="" else append_option="-A" append_string="append" fi transfer_failed=false printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to" printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n" # TRANSFER VIA SCP if [[ "$remote_loginnode" != "" ]] then echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}" | ssh -q $remote_username@$remote_loginnode else batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]} fi [[ $? != 0 ]] && transfer_failed=true # IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE if [[ $transfer_failed = true ]] then printf " +++ transfer failed. Trying to save a copy on this host under:\n" printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n" # FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY eval local_catalog=${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]}/${host_configuration}_${fname}${endout[$i]}_$run_id transfer_problems=true fi else # UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST # BE COPIED OR APPENDED ON THIS MACHINE if [[ "${actionout[$i]}" = tr ]] then actionout[$i]="" else actionout[$i]="a" fi fi fi # APPEND ON THIS MACHINE if [[ "${actionout[$i]}" = "a" ]] then if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]] then printf "\n >>> OUTPUT: ${localout[$i]} append to" printf "\n ${pathout[$i]}.${extout[$i]}\n" cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]} else printf "\n >>> OUTPUT: ${localout[$i]} append to" printf "\n ${pathout[$i]}\n" cat ${localout[$i]} >> ${pathout[$i]} fi fi # COPY ON THIS MACHINE # COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE # ON DIFFERENT FILE-SYSTEMS if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]] then # COPY IN CASE OF RUNS ON SINGLE CORES if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]] then printf "\n >>> OUTPUT: ${localout[$i]} to" printf "\n ${pathout[$i]}.${extout[$i]}\n" if [[ $link_local_output = true ]] then printf " file will be linked\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 " --- WARNING: ln failed, using cp instead (might be time consuming...)\n" fi cp ${localout[$i]} ${pathout[$i]}.${extout[$i]} else printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n" fi else printf "\n >>> OUTPUT: ${localout[$i]} to" printf "\n ${pathout[$i]}\n" if [[ $link_local_output = true ]] then printf " file will be linked\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 " --- WARNING: ln failed, using cp instead (might be time consuming...)\n" fi cp ${localout[$i]} ${pathout[$i]} else printf "+++ no copy because file ${pathout[$i]} exists\n" fi fi elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]] then # FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY # AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED printf "\n >>> OUTPUT: ${localout[$i]}/_.... to" printf "\n ${pathout[$i]}\n" if [[ $link_local_output = true ]] then printf " files will be linked\n" mkdir -p ${pathout[$i]} cd ${localout[$i]} for file in $(ls *) do ln -f $file ${pathout[$i]} done >|/dev/null 2>&1 cd $tempdir fi # IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r" if [[ ! -f "${pathout[$i]}/_000000" ]] then if [[ $link_local_output = true ]] then printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n" fi cp -r ${localout[$i]}/* ${pathout[$i]} fi fi fi done if (( i != 0 )) then if [[ $transfer_problems = true ]] then printf "\n$dashes\n *** OUTPUT-files saved" printf "\n +++ WARNING: some data transfers failed! \n" else printf "\n$dashes\n *** all OUTPUT-files saved \n" fi fi # IF REQUIRED, START A RESTART-JOB # FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM) if [[ -f CONTINUE_RUN ]] then # ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY): # -C TELLS PALMRUN THAT IT IS A RESTART-RUN # -v SILENT MODE WITHOUT INTERACTIVE QUERIES # -b START A BATCH JOB [[ $(echo $prc | grep -c "\-C") = 0 ]] && prc="$prc -C" [[ $(echo $prc | grep -c "\-v") = 0 ]] && prc="$prc -v" [[ $(echo $prc | grep -c "\-b") = 0 ]] && prc="$prc -b" # REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a) # SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN if [[ $(echo $prc | grep -c "#") != 0 ]] then prc=`echo $prc | sed 's/#/r/g'` fi # START THE RESTART-JOB printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n" echo " $prc" printf "\n$dashes\n" if [[ $running_on_remote = true ]] then echo "*** ssh will be used to initiate restart-runs!" echo " return_address=\"$return_address\" " echo " return_username=\"$local_username\" " if [[ "$remote_loginnode" != "" ]] then echo "echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" | ssh -q $SSH_PORTOPT $local_username@$return_address " | ssh -q $remote_username@$remote_loginnode else echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" | ssh -q $SSH_PORTOPT $local_username@$return_address fi # WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED sleep 30 else # START THE RESTART JOB ON THE LOCAL HOST eval $prc # THE ' MUST BE EVALUATED cd - > /dev/null fi printf "\n$dashes\n *** restart-run initiated \n" # DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA # DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB. # THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES # MAY BE VERY HUGE) (( i = 0 )) while (( i < nr_of_input_files )) do (( i = i + 1 )) if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]] then rm -r ${absnamein[$i]} fi done fi # ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED cd $HOME [[ $delete_temporary_catalog = true ]] && rm -rf $tempdir else # PREPARING ACTIONS, # IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE # BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username" [[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\"" [[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\"" [[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k" [[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x" [[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores" [[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task" [[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node" [[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B" [[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y" [[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\"" [[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z" [[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str" [[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account" if [[ $create_remote_batch_job = true ]] then palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip" if [[ $do_trace = true ]] then printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n" fi elif [[ $create_batch_job = true ]] then palmrun_com=${palmrun_com}" -j" if [[ $do_trace = true ]] then printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n" fi fi # DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND # REMOTE HOST job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id} job_protocol_file=$job_protocol_file_local if [[ $create_remote_batch_job = true ]] then job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id} job_protocol_file=$job_protocol_file_remote job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol scpjob_file=${remote_jobcatalog}/scpjob.$run_id fi # BUILD THE JOB-SCRIPTS ON FILE jobfile jobfile=jobfile.$run_id # FIRST CREATE THE BATCH DIRECTIVES (( i = 0 )) while (( i < ibd )) do (( i = i + 1 )) line=`echo "${batch_directive[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'` eval line=\"$line\" echo "$line" >> $jobfile done echo " " >> $jobfile # FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB # PROTOCOL if [[ $create_remote_batch_job = true ]] then echo "set +vx" >> $jobfile echo "trap '" >> $jobfile echo "set +vx" >> $jobfile echo "cd ${remote_jobcatalog}" >> $jobfile echo "cat > scpjob.$run_id << %%END%%" >> $jobfile # ADD THE BATCH DIRECTIVES (( i = 0 )) while (( i < ibdt )) do (( i = i + 1 )) line=`echo "${batch_directive_transfer[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'` eval line=\"$line\" echo "$line" >> $jobfile done echo " " >> $jobfile echo "set -x" >> $jobfile echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_configuration}_${fname}" >> $jobfile echo "%%END%%" >> $jobfile echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile echo "$submit_command $scpjob_file" >> $jobfile echo "rm $scpjob_file" >> $jobfile echo "rm -rf $job_transfer_protocol_file" >> $jobfile echo "set -x" >> $jobfile echo " ' exit" >> $jobfile fi # ACTIVATE ERROR-TRACEBACK if [[ $do_trace = true ]] then echo "set -x" >> $jobfile else echo "set +vx" >> $jobfile fi # INITIALIZE THE ENVIRONMENT AND LOAD MODULES if [[ "$login_init_cmd" != "" ]] then echo "$login_init_cmd" >> $jobfile fi if [[ "$module_commands" != "" ]] then echo "$module_commands" >> $jobfile fi # CREATE TEMPORARY DIRECTORY AND SWITCH TO IT if [[ $create_remote_batch_job = true ]] then echo "mkdir $tempdir" >> $jobfile echo "chmod go+rx $tempdir" >> $jobfile else # DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A # REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN # BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED) mkdir $tempdir chmod go+rx $tempdir fi echo "cd $tempdir" >> $jobfile echo "export tempdir=$tempdir" >> $jobfile echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*} ." >> $jobfile echo "export PATH=.:\$PATH" >> $jobfile echo "export execute_palmrun=true" >> $jobfile # PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS # STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN # IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED echo "LOCAL_PWD=$working_directory" >> $jobfile echo "export LOCAL_PWD" >> $jobfile # PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile echo "export LOCAL_PALMRUN_PATH" >> $jobfile # CALL PALMRUN WITHIN THE JOB # AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB echo "set -x" >> $jobfile echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile # TRANSFER JOBFILE TO THE TARGET HOST if [[ $create_jobfile_only = false ]] then if [[ $create_remote_batch_job = true ]] then echo " " echo " *** transfer of job to remote host via scp" if [[ $do_trace = true ]] then echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}" fi scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null printf " *** submit the job (output of submit command, e.g. the job-id, may follow)" if [[ $do_trace = true ]] then echo " cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id} | ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1" fi echo "cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id}" | ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1 elif [[ $create_batch_job = true ]] then eval local_jobcatalog=$local_jobcatalog cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id} cd $local_jobcatalog echo " " echo " *** submit the job" if [[ $do_trace = true ]] then echo "$submit_command ${host_configuration}_${job_id}" fi $submit_command ${host_configuration}_${job_id} rm ${host_configuration}_${job_id} cd - > /dev/null fi rm -rf $jobfile else printf "\n *** jobfile created under name \"$jobfile\" " printf "\n no batch-job has been sent!" fi fi # END OF REMOTE-PART