#!/bin/bash
# mrun - script for running PALM jobs
#--------------------------------------------------------------------------------#
# This file is part of PALM.
#
# 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 1997-2015 Leibniz Universitaet Hannover
#--------------------------------------------------------------------------------#
#
# Current revisions:
# ------------------
#
#
# Former revisions:
# -----------------
# $Id: mrun 2261 2017-06-08 14:25:57Z raasch $
# unified cycle numbers for output files are used,
# paths and filenames are allowed to contain arbitrary numbers of dots ".",
# creation of file OUTPUT_FILE_CONNECTIONS removed,
# archive feature completely removed from the script,
# nech related parts completely removed
#
# 2257 2017-06-07 14:07:05Z witha
# adjustments for lceddy, removed lcflow-specific code
#
# 2186 2017-03-21 05:36:31Z raasch
#
# 2185 2017-03-21 05:09:29Z raasch
# adjustment for lykyo*-hosts (PJM_ENVIRONMENT defines BATCH)
#
# 2148 2017-02-09 16:56:42Z scharf
# changed allocation of resources for lcbullhh in srun command
#
# 2141 2017-02-06 10:19:32Z gronemeier
# made check for existing files language independent
#
# 1944 2016-06-15 06:29:00Z raasch
# adjustments for using HLRN ssh-keys
#
# 1940 2016-06-14 05:15:20Z raasch $
# adjustments for lckiaps
#
# 1866 2016-04-15 06:50:59Z raasch
# adjusted for lcocean
#
# 1841 2016-04-07 19:14:06Z raasch
# script now running under bash
#
# 1804 2016-04-05 16:30:18Z maronga
# test: implementing an execute mechanism where the execute command is given in the
# configuration file
# ROPTS removed from execution commands
# Warnings about missing optional files or user code changed to informative messages
# Removed parameter file check
#
# 1755 2016-02-22 13:53:39Z maronga
# Minor bugfix to last commit
#
# 1753 2016-02-22 13:49:49Z maronga
# Bugfix: use random job number when PBS job nummer retrieval fails on lccray*
#
# 1622 2015-07-20 06:21:36Z heinze
# bugfix for Mistral (lcbullhh)
#
# 1621 2015-07-17 11:39:33Z heinze
# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
#
# 1609 2015-07-03 15:37:58Z maronga
# Modified the random number of the temporary working directory to match the
# queuing system number on HLRN-III (lccray*).
#
# 1604 2015-06-23 15:48:03Z suehring
# Enable coupled runs for lcmuk
#
# 1598 2015-05-29 06:45:40Z raasch
# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
#
# 1549 2015-01-30 14:26:16Z suehring
# Enable interactive debug sessions with allinea debugger
#
# 1547 2015-01-29 15:09:12Z witha
# adjustments for ForWind computing cluster (lcflow)
#
# 1491 2014-11-12 08:12:57Z heinze
# correct setting of batch_job allowed for ibm-machines
#
# 1468 2014-09-24 14:06:57Z maronga
# Typo removed (addres->address)
# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
# Added support for restart runs (remote) for lcxe6
#
# 1442 2014-07-28 07:09:10Z raasch
# default queues for HLRN-III (lccrayb/lccrayh) defined
#
# 1422 2014-07-02 10:01:25Z kanani
# automatic restarts enabled for lccrayb,
# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
#
# 1420 2014-06-10 06:24:14Z raasch
# -j1 option added to aprung command for lccrayf (CSC)
#
# 1402 2014-05-09 14:25:13Z raasch
# batch_job added to envpar-NAMELIST
#
# 1357 2014-04-11 15:02:03Z witha
# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
# possible)
#
# 1320 2014-03-20 08:40:49Z raasch
# check namelist file set false by default
#
# 1304 2014-03-12 10:29:42Z raasch
# ulimit option changed from -Ss to -s
#
# bugfix: missing "fi" in r1289
#
# 1289 2014-03-04 07:12:34Z raasch
# comments translated to English
# necriam-, fimm-, ibmy-, and sgi-specific code removed
# export of variables for palm and interpret_config removed
#
# 1281 2014-02-01 07:55:49Z raasch
# rsync-copy restricted to Cray machines, since command is unavailable on some
# other systems
#
# 1279 2014-01-28 12:10:14Z raasch
# tasks_per_node must not be an integral divisor of numprocs any more. This was done
# in order to remove annoying restrictions concerning the number of processors which
# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
# restriction, one of the nodes will be filled with less than the given number of
# tasks per node. A respective warning is given.
#
# 1274 2014-01-09 13:14:54Z heinze
# adjustments for lccrayh
#
# 1272 2014-01-08 10:19:32Z witha
# small adjustment for lcflow
#
# 1270 2013-12-16 11:05:01Z fricke
# call of combine_plot_fields adjusted for lccrayb/lccrayh
#
# 1255 2013-11-07 14:43:35Z raasch
# further adjustments for lccrayb remote access
#
# 1241 2013-10-30 11:36:58Z heinze
# Enable use of nudging input and input of large scale forcing from
# external files
#
# 1229 2013-09-20 06:55:19Z raasch
# further adjustments for lccrayb
#
# 1224 2013-09-16 07:27:23Z raasch
# first adjustments for lccrayb
#
# 1210 2013-08-14 10:58:20Z raasch
# fftw support added
#
# 1201 2013-07-10 16:17:59Z witha
# adjustments for Forwind cluster (lcflow)
#
# 1199 2013-07-05 14:52:22Z raasch
# adjustments for CSC Helsinki (lccrayf),
# executables for batch jobs can be created in advance, in order to avoid calling
# the compiler within the batch job (only works if batch jobs are submitted on
# local host)
#
# 1190 2013-06-25 09:39:21Z heinze
# enable use of automatic restarts for ibmh
# use of cluster/express queue enabled (ibmh)
#
# 1124 2013-04-09 15:46:52Z raasch
# variable "memory" is exported via typeset option -x, because otherwise an unknown
# side effect may lead to data loss while getopts is reading the script-option arguments
#
# 1122 2013-04-09 08:37:16Z heinze
# Bugfix: change type of variable last_char
#
# 1119 2013-04-05 15:11:19Z raasch
# Bugfix for setting -T option for subjob
#
# 1108 2013-03-05 07:03:32Z raasch
# bugfix for coupled runs on lckyut/lckyuh
#
# 1106 2013-03-04 05:31:38Z raasch
# --stdin argument for mpiexec on lckyuh
# -y and -Y settings output to header
#
# 1103 2013-02-20 02:15:53Z raasch
# default script runs again under ksh, because of unsolved problems with read
# from stdin: when bash script is called from a ksh, message "read error: 0:
# Resource temporarily unavailable" appears and script does not stop,
# further bash compatibility adjustments,
# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
# on lckyuh, but mrun does not terminate and issues a warning instead
#
# 1101 2013-02-17 10:20:21Z raasch
# script now running under bash instead of ksh, which required small adjustments
# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
# read from stdin),
# cross compilername on lckyuh compute nodes replaced by real compiler name
#
# 1099 2013-02-10 01:47:43Z raasch
# adjustments for Kyushu-University computing center (lckyuh - hayaka)
# and for Forwind cluster (lcflow)
# small further adjustments for lckyut
#
# 1094 2013-02-03 01:52:12Z raasch
# explicit ssh/scp port can be set in config file with environment variable
# scp_port. This port is handled to all ssh/scp/batch_scp calls.
# decalpha parts (yonsei) removed
#
# 2013-02-02 07:06:13Z raasch
# adjustments for Kyushu-University computing center (lckyut - tatara)
#
# 1083 2013-01-04 10:22:09Z maronga
# bugfix in parameter file check (read %cpp_options was missing)
#
# 1069 2012-11-28 16:18:43Z maronga
# bugfix: coupling mode was always set to mpi2, typos removed
#
# 1058 2012-11-21 07:00:35Z raasch
# Intel inspector (inspxe) is given the number of PEs instead of the number of
# nodes
#
# 1046 2012-11-09 14:38:45Z maronga
# code put under GPL (PALM 3.9)
#
# 21/03/94 - Siggi - first version finished
# 03/03/94 - Siggi - script development started
#
#--------------------------------------------------------------------------------#
# mrun - script for running PALM jobs
#--------------------------------------------------------------------------------#
# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
# (TOO MANY ARGUMENTS - PROBLEM)
set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
AddFilenames=""
additional_conditions=""
add_source_path=""
afname=""
check_namelist_files=false
combine_plot_fields=true
compiler_name=""
cond1=""
cond2=""
config_file=.mrun.config
coupled_dist=""
coupled_mode="mpi1"
cpp_opts=""
cpp_options=""
cpumax=0
cpurest=0
create_executable_for_batch=false
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=""
execute_command="none"
execution_error=false
fftw_inc=""
fftw_lib=""
fftw_support=false
fname=test
fromhost=""
global_revision=""
group_number=none
host=""
host_file=""
hp=""
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_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=""
queue=none
read_from_config=""
restart_run=false
if [[ `hostname` = rte10 ]]
then
return_address=133.5.185.60
echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
elif [[ `hostname` = climate0 ]]
then
return_address=165.132.26.68
echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
elif [[ `hostname` = "schultzl-Latitude-E6540" ]]
then
return_address="schultzl-Latitude-E6540"
echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
elif [[ `hostname` = urban00 ]]
then
return_address=147.46.30.151
echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
else
return_address=$(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=""
dashes=" ----------------------------------------------------------------------------"
silent=false
source_list=""
source_path=SOURCE
tasks_per_node=""
threads_per_task=1
tmpcreate=false
tmp_data_catalog=""
transfer_problems=false
usern=$LOGNAME
use_openmp=false
version="MRUN 2.1 Rev$Rev: 2261 $"
working_directory=`pwd`
TOPT=""
XOPT=""
zeit=$( date | cut -c 12-19 )
typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=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 cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes run_number sekunden tp1
# ERROR HANDLING IN CASE OF EXIT
trap 'rm -rf $working_directory/tmp_mrun
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
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
# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
trap 'rm -rf $working_directory/tmp_mrun
rm -rf $working_directory/tmp_check_namelist_files
[[ $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
# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
# WHICH WILL BE USED TO START RESTART-JOBS
while getopts :a:bBc:Cd:D:Fg:G:h:H:i:kK:m:M:n:o:O:p:P:q:r:R:s:St:T:u:U:vw:xX:yY:zZ option
do
case $option in
(a) afname=$OPTARG;;
(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$OPTARG";;
(F) job_on_file="-D"; mc="$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'$OPTARG'";;
(k) keep_data_from_previous_run=true; mc="$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_address=$OPTARG; mc="$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'$OPTARG'";;
(z) check_namelist_files=false; mc="$mc -z";;
(Z) combine_plot_fields=false; mc="$mc -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 MRUN OPTIONS
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.. -Z \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 -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 $localhost_realname"
printf "\n -i INPUT control list \"\" "
printf "\n -k keep data from previous run"
printf "\n -K additional conditions for controling"
printf "\n usage of conditional code and"
printf "\n env-variables in configuration file \"\" "
printf "\n -m memory demand in MB (batch-jobs) 0 MB"
printf "\n -M Makefile name Makefile"
printf "\n -n node usage (shared/not_shared) depending on -h"
printf "\n -o OUTPUT control list \"\" "
printf "\n -O threads per openMP task ---"
printf "\n -p software package list \"\" "
printf "\n -q queue \"$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 LM compiles all locally modified files"
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 -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 ..."
# 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
# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
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 $localhost_realname \""
printf "\n to the configuration file."
locat=localhost; exit
fi
# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
[[ "$afname" = "" ]] && afname=$fname
# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
# STATEMENTS IN THE CONFIGURATION FILE
if [[ "$run_mode" != "" ]]
then
input_list="$input_list $run_mode"
output_list="$output_list $run_mode"
fi
# ??? is this (and the respective option -H) really required ???
# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
if [[ "$fromhost" = "" ]]
then
fromhost=$localhost
fi
# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
# TO BE SUBMITTED (I.E. do_batch=true)
if [[ -n $host && "$host" != $localhost ]]
then
do_batch=true
do_remote=true
case $host in
(ibm|ibmh|ibmkisti|ibmku|ibms|lcbullhh|lccrayb|lccrayh|lccrayf|lceddy|lckyoto|lcocean|unics|lcxe6|lcxt5m|lck|lckiaps|lckordi|lckyuh|lckyut|lcsb) true;;
(*) printf "\n"
printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
printf "\n is not available"
locat=nqs; (( iec = 0 )); exit;;
esac
else
host=$localhost
fi
# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
if [[ -n $additional_conditions ]]
then
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
# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
if [[ $run_coupled_model = true ]]
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) : $numprocs_ocean"
locat=coupling; exit
fi
# GET coupled_mode FROM THE CONFIG FILE
line=""
grep "%cpp_options.*-D__mpi2.*$host" $config_file > tmp_mrun
while read line
do
echo line=\"$line\"
if [[ "$line" != "" && $(echo $line | cut -c1) != "#" && $(echo $line | cut -d" " -s -f4) = $cond1 && $(echo $line | cut -d" " -s -f5) = $cond2 ]]
then
coupled_mode="mpi2"
fi
done < tmp_mrun
fi
# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
mrun_memory=$memory
mrun_group_number=$group_number
mrun_cpumax=$cpumax
mrun_numprocs=$numprocs
# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
if [[ "$read_from_config" = false ]]
then
[[ $silent = false ]] && printf "\n Reading the configuration file... "
# READ THE CONFIGURATION FILE LINE BY LINE
while read zeile
do
[[ $silent = false ]] && printf "."
# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
eval zeile=\"$zeile\"
# INTERPRET THE LINE
if [[ "$(echo $zeile)" = "" ]]
then
# EMPTY LINE, NO ACTION
continue
elif [[ "$(echo $zeile | cut -c1)" = "#" ]]
then
# LINE IS A COMMENT LINE
true
elif [[ "$(echo $zeile | cut -c1)" = "%" ]]
then
# LINE DEFINES AN ENVIRONMENT-VARIABLE
zeile=$(echo $zeile | cut -c2-)
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
# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
# "::" IS REPLACED BY ":".
value=`echo $value | sed 's/::/%DUM%/g' | sed 's/:/ /g' | sed 's/%DUM%/:/g'`
# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
# CONFIGURATION-FILE.
if [[ "$(eval echo \$$var)" = "" || "$(eval echo \$$var)" = "0" ]]
then
eval $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
# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
# MUST HAVE TO BE STARTED
if [[ $var = host ]]
then
if [[ -n $host && "$host" != $localhost ]]
then
do_batch=true
do_remote=true
case $host in
(ibm|ibmh|ibmkisti|ibmku|ibms|lcbullhh|lccrayb|lccrayh|lccrayf|lceddy|lckyoto|lcocean|unics|lcxe6|lcxt5m|lck|lckiaps|lckordi|lckyuh|lckyut|lcsb) true;;
(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
printf "\n is not available"
locat=nqs; exit;;
esac
else
host=$localhost
fi
fi
# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
# BY MRUN (E.G. subjob)
export $var
fi
elif [[ "$(echo $zeile | cut -c1-3)" = "EC:" ]]
then
# LINE DEFINES ERROR-COMMAND
(( iec = iec + 1 ))
zeile=$(echo $zeile | cut -c4-)
err_command[$iec]="$zeile"
elif [[ "$(echo $zeile | cut -c1-3)" = "IC:" ]]
then
# LINE DEFINES INPUT-COMMAND
(( iic = iic + 1 ))
zeile=$(echo $zeile | cut -c4-)
in_command[$iic]="$zeile"
elif [[ "$(echo $zeile | cut -c1-3)" = "OC:" ]]
then
# LINE DEFINES OUTPUT-COMMAND
(( ioc = ioc + 1 ))
zeile=$(echo $zeile | cut -c4-)
out_command[$ioc]="$zeile"
else
# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
# s2a: in/out - field
# s2b: loc - field (optional)
# s2c: tr/ar - field (optional)
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
s2b=`echo $s2 | cut -d":" -f2 | sed 's/:/ /g'`
s2c=`echo $s2 | cut -d":" -s -f3 | sed 's/:/ /g'`
fi
s3=`echo $zeile | cut -d" " -f3`
s4=`echo $zeile | cut -d" " -s -f4`
s5=`echo $zeile | cut -d" " -s -f5`
s6=`echo $zeile | cut -d" " -s -f6`
# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
# INPUT- OR OUTPUT-LIST.
# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
# IS NOT CHECKED AND STORED.
IFSALT="$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
# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
[[ $silent = false ]] && printf "..."
interpreted_config_file=.icf.$RANDOM
# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
cat > .mrun_environment << EOF
&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' /
EOF
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
rm .mrun_environment
# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
chmod u+x $interpreted_config_file
export PATH=$PATH:.
. $interpreted_config_file
rm $interpreted_config_file
fi
# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[[ $mrun_memory != 0 ]] && memory=$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
# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
# FOR SOURCE-FILES TO BE COMPILED.
# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
if [[ "$SOURCES_COMPLETE" = "" ]]
then
# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
# HAS BEEN DEFINED
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 \"$localhost\" does not exist"
locat=source_path; exit
fi
fi
# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
then
global_revision=`svnversion $source_path 2>/dev/null`
global_revision="Rev: $global_revision"
fi
# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
if [[ -n $host && "$host" != $localhost ]]
then
do_batch=true
do_remote=true
case $host in
(ibm|ibmh|ibmkisti|ibmku|ibms|lcbullhh|lccrayb|lccrayh|lccrayf|lceddy|lckyoto|lcocean|unics|lcxe6|lcxt5m|lck|lckiaps|lckordi|lckyuh|lckyut|lcsb) true;;
(*) printf "\n"
printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
printf "\n is not available"
locat=nqs; (( iec = 0 )); exit;;
esac
else
host=$localhost
fi
# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
if [[ "$cond1" = parallel || "$cond2" = parallel ]]
then
# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
if [[ ! -n $numprocs ]]
then
printf "\n"
printf "\n +++ option \"-K parallel\" requires additional specification"
printf "\n of the number of processors to be used by"
printf "\n mrun-option \"-X\" or by environment-variable"
printf "\n \"numprocs\" in the configuration file"
locat=numprocs; (( iec = 0 )); exit
fi
# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
if [[ "$tasks_per_node" = "" && $host != lcxt5m ]]
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 (( numprocs < tasks_per_node ))
then
printf "\n"
printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
printf "\n given values: -T $tasks_per_node -X $numprocs"
locat=tasks_per_node; (( iec = 0 )); exit
fi
if [[ $host != lcxt5m ]]
then
(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
(( ival = $tasks_per_node ))
(( pes = numprocs ))
(( ii = pes / ival ))
(( remaining_pes = pes - ii * ival ))
if (( remaining_pes > 0 ))
then
printf "\n"
printf "\n +++ WARNING: tasks per node (option \"-T\") is not 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\""
printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
(( nodes = nodes + 1 ))
fi
fi
# SETTINGS FOR SUBJOB-COMMAND
OOPT="-O $threads_per_task"
# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
if [[ "$tasks_per_node" != "" ]]
then
TOPT="-T $tasks_per_node"
fi
# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
if [[ $node_usage = default ]]
then
if [[ $host = ibms ]]
then
node_usage=shared
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
# CHECK IF HOSTFILE EXISTS
if [[ -n $hostfile ]]
then
if [[ ! -f $hostfile ]]
then
printf "\n"
printf "\n +++ hostfile \"$hostfile\" does not exist"
locat=hostfile; exit
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
# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
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 DEFAULT-QUEUE, IF NOT GIVEN
if [[ $queue = none ]]
then
case $host in
(ibmh) queue=cluster;;
(ibmkisti) queue=class.32plus;;
(lcbullhh) queue=compute;;
(lccrayb) queue=mpp1q;;
(lccrayh) queue=mpp1q;;
(lckiaps) queue=normal;;
(lckyoto) queue=ph;;
(lckyuh) queue=fx-single;;
(lckyut) queue=cx-single;;
(lctit) queue=S;;
(unics) queue=unics;;
esac
fi
# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
(( i = 0 ))
while (( i < iin ))
do
(( i = i + 1 ))
(( maxcycle = 0 ))
# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
if [[ "${actionin[$i]}" = di ]]
then
remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
# HOST ONLY
eval filename=${pathin[$i]}/${endin[$i]}
else
remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
# HOST ONLY
eval filename=${pathin[$i]}/${afname}${endin[$i]}
fi
eval pathname=${pathin[$i]}
# CHECK IF FILE EXISTS
if ! ls $filename* 1>/dev/null 2>&1
then
# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
if [[ "${transin[$i]}" != "locopt" ]]
then
printf "\n\n +++ INPUT-file: "
if [[ "${extin[$i]}" = "" || "${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
# DETERMINE THE FILE'S CYCLE NUMBER
ls -1 -d $filename > filelist 2>/dev/null
ls -1 -d $filename.* >> filelist 2>/dev/null
while read zeile
do
# filename without path (i.e. after the last "/")
basefilename=$(basename ${zeile})
# check if there is an extension
extension=${basefilename##*.}
if [[ "$extension" = "$extin[$i]" ]]
then
basefilename=${basefilename&.*}
fi
# check for an existing cycle number
cycle=${basefilename##*.}
if [[ $cycle =~ ^-?[0-9]+$ ]]
then
(( icycle = $cycle ))
else
(( icycle = 0 ))
fi
if (( icycle > maxcycle ))
then
(( maxcycle = icycle ))
fi
# cycle=$(echo $zeile | cut -f2 -d".")
# if [[ "$cycle" = "$zeile" ]]
# then
# (( icycle = 0 ))
# elif [[ "$cycle" = "${extin[$i]}" ]]
# then
# (( icycle = 0 ))
# else
# (( icycle = $cycle ))
# fi
# if (( icycle > maxcycle ))
# then
# (( maxcycle = icycle ))
# fi
done 0 ))
then
if [[ "${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
# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
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
# 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 TRASFERRED 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 [[ ! ( $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* 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"
echo "### filename = $filename"
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
# DETERMINE THE CYCLE NUMBER
ls -1 -d $filename > filelist 2>/dev/null
ls -1 -d $filename.* >> filelist 2>/dev/null
while read zeile
do
# filename without path (i.e. after the last "/")
basefilename=$(basename ${zeile})
# check if there is an extension
extension=${basefilename##*.}
if [[ "$extension" = "$extin[$i]" ]]
then
basefilename=${basefilename&.*}
fi
# check for an existing cycle number
cycle=${basefilename##*.}
if [[ $cycle =~ ^-?[0-9]+$ ]]
then
(( icycle = $cycle + 1 ))
else
(( icycle = 1 ))
fi
if (( icycle > maxcycle ))
then
(( maxcycle = icycle ))
fi
# cycle=$(echo $zeile | cut -f2 -d".")
# if [[ "$cycle" = "$zeile" || "$cycle" = ${extout[$i]} ]]
# then
# (( icycle = 1 ))
# else
# (( icycle = $cycle + 1 ))
# fi
# if (( icycle > maxcycle ))
# then
# (( maxcycle = icycle ))
# fi
done 0 ))
then
filename_tmp=${filename}.$maxcycle
if cat /dev/null > $filename_tmp
then
rm $filename_tmp
else
printf "\n +++ OUTPUT-file:"
printf "\n $filename_tmp"
printf "\n cannot be created"
locat=output ; exit
fi
fi
else
(( maxcycle = maxcycle - 1 ))
fi
(( cycnum[$i] = maxcycle ))
pathout[$i]=$filename
fi
done
# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
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 [[ "$dvr_lib" = "" ]]
then
printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
printf "\n This is required for the dvrp_graphics package.\n"
locat=dvr; exit
fi
fi
# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
# EXECUTABLES DO NOT NEED TO BE COMPILED.
if [[ "$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
# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
then
rm -rf SOURCES_FOR_RUN_$fname
mkdir SOURCES_FOR_RUN_$fname
fi
# COLLECT ALL ROUTINES TO BE COMPILED
# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
then
[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
if [[ "$source_list" = LOCALLY_MODIFIED ]]
then
# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
source_list=""
cd $source_path
# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
if [[ ! -d .svn ]]
then
printf "\n\n +++ source directory"
printf "\n \"$source_path\" "
printf "\n is not under control of \"subversion\"."
printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
fi
# LIST ALL MODIFIED SOURCE CODE FILES
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
# COPY FILES TO SOURCES_FOR_RUN_...
for dateiname in $Filenames
do
cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
source_list=$source_list"$dateiname "
done
cd - > /dev/null
# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
elif [[ "$source_list" != "" && $restart_run != true ]]
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 $working_directory/SOURCES_FOR_RUN_$fname
fi
done
cd - > /dev/null
fi
# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
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}" $source_list"
fi
fi
fi
# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
if [[ "$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
# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
if [[ $restart_run != true && "$add_source_path" != "" ]]
then
# DOES THE DIRECTORY EXIST?
if [[ ! -d $add_source_path ]]
then
printf "\n\n *** INFORMATIVE: additional source code directory"
printf "\n \"$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=""
if [[ $silent == false ]]
then
sleep 3
fi
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"
if [[ $silent == false ]]
then
sleep 1
fi
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
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 "
if [[ $silent == false ]]
then
sleep 0.5
fi
fi
done
[[ $found = true ]] && printf "\n"
cd - > /dev/null
fi
fi
# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
# TO THE LIST OF FILES TO BE COMPILED
if [[ $restart_run != true && -n $package_list ]]
then
cd $source_path
for package in $package_list
do
[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
# DETERMINE FILES BELONGING TO THE PACKAGE
# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
# THE NAME OF THE DIRECTORY
package_source_list=`grep "defined( __$package " * 2>/dev/null | cut -f1 -d:`
# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
# IF THEY ARE NOT ALREADY PART OF THE LIST
for source_list_name in $package_source_list
do
if [[ $(echo $source_list | grep -c $source_list_name) = 0 ]]
then
# ONLY TAKE FILES WITH VALID SUFFIX
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
fi # do_compile=true
# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
# AND SET PRE-PROCESSOR DIRECTIVES
if [[ $do_compile = true || $create_executable_for_batch = true ]]
then
# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC 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
# SET DIRECTIVES GIVEN BY OPTION -K (E.G. 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
# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (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
# SET DIRECTIVES GIVEN BY OPTION -D
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
# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
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
# DETERMINE THE JOB MODE
if [[ $(echo $localhost | cut -c1-3) = ibm ]]
then
if [[ "$LOADLBATCH" = yes ]]
then
batch_job=.TRUE.
jobmo=BATCH
else
batch_job=.FALSE.
jobmo=INTERACTIVE
fi
else
if [[ "$ENVIRONMENT" = BATCH || "$PJM_ENVIRONMENT" = BATCH ]]
then
batch_job=.TRUE.
jobmo=BATCH
else
batch_job=.FALSE.
jobmo=INTERACTIVE
fi
fi
# NO INTERACTIVE RUNS ALLOWED 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
# CHECK, IF USER DEFINED A COMPILER
if [[ "$compiler_name" = "" ]]
then
printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
locat=compiler_name; exit
fi
# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
if [[ $do_batch = false && $(echo $host | cut -c1-6) = lccray ]]
then
kennung=$(checkjob $PBS_JOBID | grep Reservation | cut -d" " -s -f2 | cut -d"." -s -f2 | sed "s/['\"]//g")
if [[ "$kennung" = "" ]]
then
kennung=$RANDOM
fi
else
kennung=$RANDOM
fi
if [[ "$tmp_user_catalog" = "" ]]
then
if [[ $localhost = ibmh ]]
then
tmp_user_catalog=$SCRATCH
else
tmp_user_catalog=/tmp
fi
fi
TEMPDIR=$tmp_user_catalog/${usern}.$kennung
# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
if [[ "$tmp_data_catalog" = "" ]]
then
tmp_data_catalog=/tmp/mrun_restart_data
fi
# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
if [[ $do_remote = false && $do_compile = true || $create_executable_for_batch = true ]]
then
eval fopts=\"$fopts\"
eval lopts=\"$lopts\"
fi
# DETERMINE COMPILE- AND LINK-OPTIONS
fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
XOPT="-X $numprocs"
# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
# EXECUTABLE VIA NAMELIST-PARAMETER cputime
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 ))
# CHECK THE MEMORY DEMAND
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
# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
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
# CHECK FOR INITIAL COMMANDS AFTER LOGIN
if [[ "$login_init_cmd" != "" ]]
then
export init_cmds="${login_init_cmd};"
fi
# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
if [[ "$modules" != "" ]]
then
if [[ $host = lctit ]]
then
export module_calls=". $modules"
else
export module_calls="module load ${modules};"
fi
fi
# OUTPUT OF THE MRUN-HEADER
calltime=$(date)
printf "\n"
printf "#------------------------------------------------------------------------# \n"
printf "| %-35s%35s | \n" "$version" "$calltime"
printf "| | \n"
spalte1="called on:"; spalte2=$localhost_realname
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
if [[ $do_remote = true ]]
then
spalte1="execution on:"; spalte2="$host (username: $remote_username)"
else
spalte1="execution on:"; spalte2="$host ($localhost_realname)"
fi
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
if [[ -n $numprocs ]]
then
if [[ $run_coupled_model = false ]]
then
spalte1="number of PEs:"; spalte2=$numprocs
else
spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
fi
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
fi
if [[ -n $tasks_per_node ]]
then
spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
if (( remaining_pes > 0 ))
then
spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
fi
fi
if [[ $maximum_parallel_io_streams != $numprocs ]]
then
spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
fi
if [[ $use_openmp = true ]]
then
spalte1="threads per task:"; spalte2="$threads_per_task"
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
fi
printf "| | \n"
if [[ $do_compile = true ]]
then
if [[ "$mopts" != "" ]]
then
spalte1="make options:"; spalte2=$(echo "$mopts" | cut -c-45)
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
zeile=$(echo "$mopts" | cut -c46-)
while [[ "$zeile" != "" ]]
do
spalte1=""
spalte2=$(echo "$zeile" | cut -c-45)
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
zeile=$(echo "$zeile" | cut -c46-)
done
fi
spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" | cut -c-45)
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
zeile=$(echo "$cpp_options" | cut -c46-)
while [[ "$zeile" != "" ]]
do
spalte1=""
spalte2=$(echo "$zeile" | cut -c-45)
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
zeile=$(echo "$zeile" | cut -c46-)
done
spalte1="compiler options:"; spalte2=$(echo "$fopts" | cut -c-45)
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
zeile=$(echo "$fopts" | cut -c46-)
while [[ "$zeile" != "" ]]
do
spalte1=""
spalte2=$(echo "$zeile" | cut -c-45)
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
zeile=$(echo "$zeile" | cut -c46-)
done
spalte1="linker options:"; spalte2=$(echo "$lopts" | cut -c-45)
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
zeile=$(echo "$lopts" | cut -c46-)
while [[ "$zeile" != "" ]]
do
spalte1=""
spalte2=$(echo "$zeile" | cut -c-45)
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
zeile=$(echo "$zeile" | cut -c46-)
done
spalte1="modules to be load:"; spalte2=$(echo "$modules" | cut -c-45)
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
zeile=$(echo "$modules" | cut -c46-)
while [[ "$zeile" != "" ]]
do
spalte1=""
spalte2=$(echo "$zeile" | cut -c-45)
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
zeile=$(echo "$zeile" | cut -c46-)
done
spalte1="main program:"; spalte2=$mainprog
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
else
spalte1=executable:; spalte2=$executable
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
fi
printf "| | \n"
spalte1="base name of files:"; spalte2=$fname
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
if [[ $fname != $afname ]]
then
spalte1="base name of input files:"; spalte2=$afname
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
fi
spalte1="INPUT control list:"; spalte2=$(echo $input_list)
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
if [[ "$ocean_file_appendix" = true ]]
then
printf "| %-35s%-35s | \n" "suffix \"_O\" is added to local files" " "
fi
if [[ $do_batch = true || "$LOADLBATCH" = yes ]]
then
spalte1="memory demand / PE":; spalte2="$memory MB"
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
spalte1=CPU-time:; spalte2="$minuten:$sekunden"
printf "| %-25s%-45s | \n" "$spalte1" "$spalte2"
fi
if [[ $do_compile = true ]]
then
printf "| | \n"
printf "| Files to be compiled: | \n"
zeile=$source_list
while [[ "$zeile" != "" ]]
do
linestart=$(echo $zeile | cut -c-70)
printf "| %-70s | \n" "$linestart"
zeile=$(echo "$zeile" | cut -c71-)
done
fi
printf "#------------------------------------------------------------------------#"
# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
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
# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
then
antwort=dummy
printf "\n\n"
printf " >>> everything o.k. (y/n) ? "
while read antwort
do
if [[ "$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 [[ $do_batch = true ]]
then
printf " >>> batch-job will be created and submitted"
else
printf " >>> MRUN will now continue to execute on this machine"
fi
fi
# DETERMINE PATH FOR MAKE DEPOSITORY
if [[ $do_batch = false || $create_executable_for_batch = true ]]
then
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=`echo $mainprog | cut -f1 -d"."`
eval make_depository=${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"
fi
fi
# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
if [[ $do_batch = false ]]
then
# CREATE THE TEMPORARY WORKING DIRECTORY
mkdir -p $TEMPDIR
chmod go+rx $TEMPDIR
tmpcreate=true
# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
# INTO THE TEMPORARY WORKING DIRECTORY
if [[ $do_compile = true ]]
then
TEMPDIR_COMPILE=$TEMPDIR
cp $make_depository $TEMPDIR_COMPILE
cd $TEMPDIR_COMPILE
tar -xf $make_depository > /dev/null 2>&1
cd - > /dev/null
# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
if [[ $(echo $host | cut -c1-6) = lccray ]]
then
rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
else
cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
fi
else
cp $executable ${TEMPDIR}/a.out
fi
# CHANGE TO THE TEMPORARY WORKING DIRECTORY
cd $TEMPDIR
printf "\n *** changed to temporary directory: $TEMPDIR"
# IF REQUIRED, START WITH COMPILING
if [[ $do_compile = true ]]
then
if [[ -f a.out ]]
then
# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
printf "\n\n\n *** executable a.out found"
printf "\n no compilation required \n"
else
# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
printf "\n\n\n *** compilation starts \n$dashes\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 = ibmh ]]
then
printf " compiler is called via ssh on \"plogin1\" \n"
ssh $SSH_PORTOPT plogin1 -l $usern "$init_cmds export PATH=/sw/ibm/xlf/13.1.0.8/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 # STATUS=1, IF a.out EXISTS
elif [[ $localhost = lcocean ]]
then
printf " compiler is called via ssh on \"ocean\" \n"
echo $PWD
ssh $SSH_PORTOPT ocean -l $usern "$init_cmds $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 # STATUS=1, IF a.out EXISTS
elif [[ $localhost = lcbullhh || $localhost = lccrayb || $localhost = lccrayf || $localhost = lccrayh ]]
then
make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
elif [[ $localhost = lceddy ]]
then
which mpifc
make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
else
[[ "$init_cmds" != "" ]] && eval $init_cmds
[[ "$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 || "$module_compile_error" = true ]]
then
printf "\n +++ error occured while compiling or linking"
locat=compile
exit
else
printf "$dashes\n *** compilation finished \n"
fi
fi
fi
# PROVIDE THE INPUT FILES
# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
(( i = 0 ))
while (( i < iin ))
do
(( i = i + 1 ))
if (( i == 1 ))
then
printf "\n\n *** providing INPUT-files:\n$dashes"
fi
# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
if [[ "${transin[$i]}" = unavailable ]]
then
if [[ "${extin[$i]}" = "" || "${extin[$i]}" = " " ]]
then
printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
printf "\n is not available!"
else
printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
printf "\n is not available!"
fi
continue
fi
# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
files_for_pes=false; datentyp=file
if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
then
files_for_pes=true; datentyp=files
actionin[$i]=""
elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
then
actionin[$i]=""
elif [[ "${actionin[$i]}" = lnpe && -n $numprocs ]]
then
files_for_pes=true; datentyp=files
actionin[$i]="ln"
elif [[ "${actionin[$i]}" = lnpe && ! -n $numprocs ]]
then
actionin[$i]="ln"
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-FILES TO BE LINKED
if [[ "${actionin[$i]}" = ln ]]
then
printf "\n $datentyp will be linked"
if [[ $files_for_pes = false ]]
then
if [[ -f "${absnamein[$i]}" ]]
then
ln ${absnamein[$i]} ${localin[$i]}
got_tmp[$i]=true
fi
else
if [[ -d "${absnamein[$i]}" ]]
then
mkdir ${localin[$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[$i]}" = "npe" ]]
then
if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
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 $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
# 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 $numprocs files for the respective processors"
mkdir ${localin[$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 of 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
cp ${absnamein[$i]} ${localin[$i]}
fi
fi
fi
fi
done
if (( i != 0 ))
then
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$dashes\n"
fi
done
# SET THE REMAINING CPU-TIME
cpurest=${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 ${PALM_BIN}/.dvrserver.config .
# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
user_id=`id -u`
group_id=`id -g`
# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
sed "s&&${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 \"$PALM_BIN\" "
locat=dvr
exit
fi
fi
else
printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
fi
fi
# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
# (FILE ENVPAR WILL BE READ BY PALM)
cat > ENVPAR << EOF
&envpar run_identifier = '$fname', host = '$localhost',
write_binary = '$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,
batch_job = $batch_job /
EOF
# STARTING THE EXECUTABLE
printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
PATH=$PATH:$TEMPDIR
if [[ $execute_command != "none" ]]
then
printf "\n +++ branch still not realized"
locat=execution
exit
else
# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
if [[ "$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
#Interactive ALLINEA DEBUG seesion
if [[ "$ENVIRONMENT" != BATCH ]]
then
if [[ $host = lccrayb || $host = lccrayh ]]
then
if [[ "$allinea" = true ]]
then
echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
ddt aprun -n $ii -N $tasks_per_node a.out
wait
fi
fi
fi
if [[ $localhost = ibmh ]]
then
# SETUP THE IBM MPI ENVIRONMENT
export MP_SHARED_MEMORY=yes
export AIXTHREADS_SCOPE=S
export OMP_NUM_THREADS=$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
if [[ "$LOADLBATCH" = yes ]]
then
totalview poe a.out
else
echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
export TVDSVRLAUNCHCMD=ssh
totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
fi
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-VARIABLES TO IMPROVE COMMUNICATION SPEED
# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
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
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 < runfile_atmos
fi
else
if [[ $localhost = ibmh || $localhost = ibms ]]
then
poe a.out -procs $numprocs -nodes 1 -rmpool 0
elif [[ $localhost = ibmkisti || $localhost = ibmku ]]
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
poe ./a.out -procs $numprocs < runfile_atmos
else
if [[ "$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
fi
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 != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut && $host != lcocean && $host != lceddy ]]
then
if [[ -f $hostfile ]]
then
cp $hostfile hostfile
(( ii = $numprocs / $threads_per_task ))
[[ $ii = 0 ]] && (( ii = 1 ))
else
(( ii = 1 ))
while (( ii <= $numprocs / $threads_per_task ))
do
echo $localhost_realname >> hostfile
(( ii = ii + 1 ))
done
if (( $numprocs / $threads_per_task == 0 ))
then
echo $localhost_realname >> hostfile
fi
fi
eval zeile=\"`head -n $ii hostfile`\"
printf "\n *** running on: $zeile"
fi
(( ii = $numprocs / $threads_per_task ))
[[ $ii = 0 ]] && (( ii = 1 ))
export OMP_NUM_THREADS=$threads_per_task
if [[ $threads_per_task != 1 ]]
then
# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
# MAY ABORT
ulimit -s 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 = lccrayb || $host = lccrayh ]]
then
echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
elif [[ $host = lcbullhh ]]
then
export OMPI_MCA_pml=cm
export OMPI_MCA_mtl=mxm
export OMPI_MCA_coll=^ghc
export OMPI_MCA_mtl_mxm_np=0
export MXM_RDMA_PORTS=mlx5_0:1
export MXM_LOG_LEVEL=ERROR
export OMP_NUM_THREADS=$threads_per_task
export KMP_AFFINITY=verbose,granularity=core,compact,1
export KMP_STACKSIZE=64m
srun -n $ii --ntasks-per-node=$tasks_per_node ./a.out < runfile_atmos
elif [[ $host = lccrayf ]]
then
aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out < runfile_atmos
elif [[ $host = lcxe6 || $host = lcxt5m ]]
then
aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
elif [[ $host = lceddy ]]
then
echo $ii
echo $tasks_per_node
echo $nodes
mpirun -n $ii a.out < runfile_atmos
elif [[ $host = lcocean ]]
then
mpirun a.out $ROPTS < runfile_atmos
elif [[ $host = lcsb ]]
then
mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE | wc -l` a.out < runfile_atmos
elif [[ $host = lckiaps ]]
then
mpirun -np $ii -machinefile $PBS_NODEFILE ./a.out < runfile_atmos
elif [[ $host = lckyu* ]]
then
mpiexec -n $ii --stdin runfile_atmos ./a.out
else
mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
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 = lccrayf || $host = lcxe6 || $host = lcxt5m ]]
then
aprun -n $iia -N $tasks_per_node a.out < runfile_atmos &
aprun -n $iio -N $tasks_per_node a.out < runfile_ocean &
else
# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
mpiexec -machinefile hostfile -n $iia a.out < runfile_atmos &
mpiexec -machinefile hostfile -n $iio a.out < runfile_ocean &
# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out &
# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out &
fi
wait
else
echo "coupled_run $iia $iio" > runfile_atmos
if [[ $host = lccrayf || $host = lcxe6 || $host = lcxt5m ]]
then
aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
elif [[ $host = lck || $host = lckordi ]]
then
mpiexec -n $ii ./a.out < runfile_atmos &
elif [[ $host = lckyu* ]]
then
mpiexec -n $ii --stdin runfile_atmos ./a.out
elif [[ $host = lcmuk ]]
then
mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
fi
wait
fi
fi
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 # for fujitsu-compiler
elif [[ "cond2" = pgi ]]
then
mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out
else
mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out || /bin/true
fi
else
if [[ "$cond2" = "" ]]
then
mpiruni_rsh -np $numprocs ./a.out # for intel
else
mpirun -np $numprocs ./a.out
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"
mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out
else
mpprun -n $numprocs a.out
fi
else
a.out
fi
fi # end normal (non-debug) execution
fi # end explicit execute_command or host-specific execute actions
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"
# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
# TO CREAT 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 GENERATING
# SEQUENCE MODE DATA TOO)
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 GENERATD 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 CORE 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 $localhost\" to generate utilities for this block.\n"
elif [[ "$combine_plot_fields" == true ]]
then
if [[ $localhost = lccrayh || $localhost = lccrayb ]]
then
printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
aprun -n 1 -N 1 combine_plot_fields${block}.x
else
printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
combine_plot_fields${block}.x
fi
else
# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
# ??? koennen wir das streichen ???
printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
fi
# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
(( i = 0 ))
while (( i < ioc ))
do
(( i = i + 1 ))
if (( i == 1 ))
then
printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
fi
printf "\n >>> ${out_command[$i]}"
eval ${out_command[$i]}
if (( i == ioc ))
then
printf "\n$dashes\n"
fi
done
# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
if [[ $do_trace = true ]]
then
printf "\n\n"
ls -al
fi
# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
(( i = 0 ))
while (( i < iout ))
do
(( i = i + 1 ))
if (( i == 1 ))
then
printf "\n\n *** saving OUTPUT-files:"
# GET RUN NUMBER ASSIGNED BY PALM
if [[ -f RUN_NUMBER ]]
then
read run_number < RUN_NUMBER
printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
usecycle_option="-U $run_number"
else
run_number=0
usecycle_option=""
fi
printf "\n$dashes"
fi
# ADD CYCLE NUMBER TO FILENAME
if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]]
then
# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
if [[ "${actionout[$i]}" != "a" ]]
then
# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
# WITH AN EXISTING CYCLE NUMBER
if (( run_number >= cycnum[$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
pathout[$i]=${pathout[$i]}.${cycnum[$i]}
fi
fi
# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
files_for_pes=false; filetyp=file
link_local_output=false
if [[ "${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]}" = lnpe && -n $numprocs ]]
then
files_for_pes=true; filetyp=directory
link_local_output=true
actionout[$i]=""
elif [[ "${actionout[$i]}" = lnpe && ! -n $numprocs ]]
then
link_local_output
actionout[$i]=""
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
# 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 ]]
then
if [[ $localhost != $fromhost ]]
then
if [[ $files_for_pes = false ]]
then
cps=""
cst=""
else
cps=-c
cst="/"
fi
transfer_failed=false
printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
if [[ $localhost = lccrayb ]]
then
ssh $usern@blogin1 ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
elif [[ $localhost = lccrayh ]]
then
ssh $usern@hlogin1 ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
elif [[ $localhost = lcbullhh ]]
then
ssh $usern@mlogin101 ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
elif [[ $localhost = lcxe6 ]]
then
ssh $usern@hexagon ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
else
batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${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]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
eval local_catalog=${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]}/${localhost}_${fname}${endout[$i]}_$kennung
transfer_problems=true
fi
else
# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
actionout[$i]=""
fi
fi
# APPEND 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]}" = tra ]]
then
if [[ $localhost != $fromhost ]]
then
if [[ $localhost = ibmh ]]
then
# TRANSFER IN SEPERATE JOB
# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
[[ ! -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 $PORTOPT -A -b -m -u $return_username $return_address $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
if [[ $LOGNAME = b323013 ]]
then
subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
else
subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
fi
else
# TRANSFER WITHIN THIS JOB
transfer_failed=false
printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
if [[ $localhost = lccrayb ]]
then
ssh $usern@blogin1 ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
elif [[ $localhost = lccrayh ]]
then
ssh $usern@hlogin1 ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
elif [[ $localhost = lcxe6 ]]
then
ssh $usern@hexagon ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
else
batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${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]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
eval local_catalog=${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]}/${localhost}_${fname}${endout[$i]}_$kennung
transfer_problems=true
fi
fi
else
# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
actionout[$i]=a
fi
fi
# APPEND ON THIS MACHINE
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
# 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]}" = "" && $files_for_pes = false ]]
then
# COPY IN CASE OF RUNS ON SINGLE CORES
if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
then
printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$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 ${pathout[$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_pes = 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 ${pathout[$i]}\n"
if [[ $link_local_output = true ]]
then
printf " files will be linked\n"
mkdir ${pathout[$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 MRUN-CALL (IF THEY ARE NOT USED ALREADY):
# -C TELLS MRUN THAT IT IS A RESTART-RUN
# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
[[ $(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 $mc | sed 's/#/f/g'`
fi
# START THE RESTART-JOB
printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
echo " $mc"
printf "\n$dashes\n"
if [[ $localhost != $fromhost ]]
then
if [[ $localhost = lcbullhh || $localhost = lccrayb || $localhost = lccrayh || $localhost = ibmh || $localhost = ibmkisti || $localhost = ibmku || $localhost = ibms || $localhost = lceddy || $localhost = lckyu* || $localhost = lcxe6 ]]
then
echo "*** ssh will be used to initiate restart-runs!"
echo " return_address=\"$return_address\" "
echo " return_username=\"$return_username\" "
if [[ $(echo $return_address | grep -c "130.75.105") = 1 ]]
if [[ $localhost = lcbullhh || $localhost = lccrayb || $localhost = lccrayh || $localhost = ibmh || $localhost = ibmkisti || $localhost = ibmku || $localhost = ibms || $localhost = lceddy || $localhost = lckyu* || $localhost = lcxe6 ]]
then
if [[ $localhost = ibmh ]]
then
ssh $SSH_PORTOPT $usern@136.172.40.15 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
elif [[ $localhost = lcbullhh ]]
then
ssh $SSH_PORTOPT $usern@mlogin101 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
elif [[ $localhost = lccrayb ]]
then
ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
elif [[ $localhost = lccrayh ]]
then
ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
elif [[ $localhost = lcxe6 ]]
then
ssh $usern@hexagon "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
else
ssh $SSH_PORTOPT $return_address -l $return_username ". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
fi
else
if [[ $localhost = ibmkisti ]]
then
ssh $SSH_PORTOPT $usern@gaiad "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
elif [[ $localhost = lceddy ]]
then
/usr/bin/ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
elif [[ $localhost = lcocean ]]
then
/usr/bin/ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
elif [[ $localhost = lccrayb ]]
then
ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
elif [[ $localhost = lccrayh ]]
then
ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
else
ssh $SSH_PORTOPT $return_address -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
# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
if [[ $queue = special1q ]]
then
sleep 120
else
sleep 30
fi
else
# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
# USING SSH)
cd $LOCAL_PWD
if [[ $localhost = lckyuh ]]
then
printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
printf "\n please restart job manually using command:\n"
printf "\n \"$mc\" "
else
eval $mc # THE ' MUST BE EVALUATED
fi
cd - > /dev/null
fi
if [[ $localhost = lckyuh ]]
then
printf "\n$dashes\n *** restart-run to be initiated manually\n"
else
printf "\n$dashes\n *** restart-run initiated \n"
fi
# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
# MAY BE VERY HUGE)
(( i = 0 ))
while (( i < iin ))
do
(( i = i + 1 ))
if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
then
rm -r ${absnamein[$i]}
fi
done
fi
# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
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
# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
cd $HOME
[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
else
# PREPARING ACTIONS,
# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
mrun_com="$mrun_script_name -a $afname -c $config_file -d $fname -h $host -H $fromhost -m $memory -t $cpumax -q $queue -R $return_address -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\""
[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
[[ "$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"
[[ $package_list != "" ]] && mrun_com=${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 \"$coupled_dist\""
[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
[[ "$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
# CREATE EXECUTABLE FOR BATCH JOB
if [[ $create_executable_for_batch = true && $restart_run != true ]]
then
printf "\n *** creating the executable for batch job\n"
# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
if [[ $host != $localhost ]]
then
printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
printf "\n Please set create_executable_for_batch = false in the config-file.\n"
locat=create_executable; exit
fi
mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
cp $make_depository .
tar -xf $make_depository > /dev/null 2>&1
cp ../* . > /dev/null 2>&1
make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
if [[ $? != 0 || "$compile_error" = true || "$module_compile_error" = true ]]
then
printf "\n +++ error occured while compiling or linking"
locat=compile
exit
fi
mv a.out ..
cd - > /dev/null 2>&1
rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
fi
# BUILD THE JOB-SCRIPTS ON FILE jobfile
jobfile=jobfile.$RANDOM
# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
echo "mkdir $TEMPDIR" >> $jobfile
echo "cd $TEMPDIR" >> $jobfile
# ACTIVATE ERROR-TRACEBACK
if [[ $do_trace = true ]]
then
echo "set -x" >> $jobfile
else
echo "set +vx" >> $jobfile
fi
# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
if [[ "$init_cmds" != "" ]]
then
echo "$init_cmds" >> $jobfile
fi
if [[ "$module_calls" != "" ]]
then
echo "$module_calls" >> $jobfile
fi
# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
# QUEUEING-SYSTEMS
if [[ $host = ibmkisti || $host = lcbullhh || $host = lccrayb || $host = lccrayf || $host = lccrayh || $host = lcocean ]]
then
# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
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
# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
echo "set -x" >> $jobfile
if [[ $host = $localhost ]]
then
# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
if [[ $(echo $host | cut -c1-6) = lccray ]]
then
echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
else
echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
fi
else
if [[ $host = ibmkisti ]]
then
# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
echo "localdir=\`pwd\`" >> $jobfile
echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
elif [[ $host = lcbullhh ]]
then
echo "localdir=\`pwd\`" >> $jobfile
echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
elif [[ $host = lccrayb ]]
then
echo "localdir=\`pwd\`" >> $jobfile
echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
elif [[ $host = lccrayh ]]
then
echo "localdir=\`pwd\`" >> $jobfile
echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
else
echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
fi
fi
echo "export SOURCES_COMPLETE=true" >> $jobfile
# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
# WORKING DIRECTORY OF THE JOB
echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
echo "chmod u+rwx $mrun_script_name" >> $jobfile
echo "execute_mrun=true" >> $jobfile
echo " " >> $jobfile
else
# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
if [[ $do_compile = true ]]
then
source_catalog=SOURCES_FOR_RUN_$fname
# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
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
# BACKSLASH IS USED FOR MASKING
echo "cat > $filename << \"%END%\"" >> $jobfile
cat $source_catalog/$filename >> $jobfile
echo " " >> $jobfile
echo "%END%" >> $jobfile
echo " " >> $jobfile
done
# BACKSLASH IS USED FOR MASKING
echo "cat > Makefile << \"%END%\"" >> $jobfile
cat $source_catalog/Makefile >> $jobfile
echo " " >> $jobfile
echo "%END%" >> $jobfile
echo " " >> $jobfile
echo "cd - > /dev/null" >> $jobfile
fi
# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
# BACKSLASH IS USED FOR MASKING
# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
echo "cat > $config_file << \"%END%\"" >> $jobfile
if [[ $host = lckyuh ]]
then
# NO CROSS-COMPILER ON COMPUTE NODE
sed 's/frtpx/frt/g' $config_file >> $jobfile
else
sed 's/#$.*//g' $config_file >> $jobfile
fi
echo "%END%" >> $jobfile
echo " " >> $jobfile
# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
# BACKSLASH IS USED FOR MASKING
echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
if [[ $host = lckyuh ]]
then
sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
else
cat ${PALM_BIN}/$mrun_script_name >> $jobfile
fi
echo "%END%" >> $jobfile
echo "chmod u+x $mrun_script_name" >> $jobfile
echo "execute_mrun=true" >> $jobfile
echo " " >> $jobfile
fi
# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
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 $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
fi
# CHECK, IF FILE COULD BE CREATED
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" >> $jobfile
done
fi
# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
echo "LOCAL_PWD=$working_directory" >> $jobfile
echo "export LOCAL_PWD" >> $jobfile
# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
echo "export LOCAL_MRUN_PATH" >> $jobfile
# lceddy ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
if [[ $host = lceddy || $localhost = lceddy ]]
then
echo "export PALM_BIN=$PALM_BIN" | sed -e 's:'$HOME':$HOME:' >> $jobfile
echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
fi
# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
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
# START THE JOB USING SUBJOB-COMMAND
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 $PORTOPT $jobfile
rm -rf $jobfile
fi # END OF REMOTE-PART