#!/bin/bash
# subjob - script for automatic generation and submission of batch-job files
# for various batch queuing systems
#--------------------------------------------------------------------------------#
# 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 1997-2014 Leibniz Universitaet Hannover
#--------------------------------------------------------------------------------#
#
# Current revisions:
# ------------------
#
#
# Former revisions:
# -----------------
# $Id: subjob 2365 2017-08-21 14:59:59Z raasch $
# Added lckea & lckeam. KIT/IMK-IFU Garmisch cluster. LRZ (SadiqHuq)
#
# 2295 2017-06-27 14:25:52Z raasch
# adjustments for using lcgeohu (cirrus @ HUB)
#
# 2266 2017-06-09 09:27:21Z raasch
# nech related parts removed
#
# 2257 2017-06-07 14:07:05Z witha
# adjustments for lceddy, removed lcflow-specific code
#
# 2188 2017-03-21 06:42:42Z raasch
#
# 2187 2017-03-21 06:41:25Z raasch
# adjustment of compute node names for lckyuh
#
# 2184 2017-03-21 04:31:22Z raasch
# bugfix: localhost renamed local_host
#
# 2148 2017-02-09 16:56:42Z scharf
# added kuma and gharbi to the list of known hosts
#
# 2134 2017-02-02 07:33:46Z raasch
# option -E added to msub commands on HLRN-III machines to allow output of more
# job informations in the job protocol files
#
# 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
#
# 1701 2015-11-02 07:43:04Z maronga
# Bugfix: added missing init_cmds for lccrayh/lccrayb
#
# 1621 2015-07-17 11:39:33Z heinze
# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
#
# 1575 2015-03-27 09:56:27Z raasch
# mpp2-queues added to lccrayh
#
# 1547 2015-01-29 15:09:12Z witha
# adjustments for ForWind computing cluster (lcflow)
#
# 1545 2015-01-29 06:52:23Z heinze
# local host name for blizzard further specified
#
# 1480 2014-10-17 14:41:49Z raasch
# adjustments for 2nd stage of HLRNIII
#
# 1468 2014-09-24 14:06:57Z maronga
# Typo removed (addres->address)
# Adjustments for lcxe6
#
# 1452 2014-08-22 09:41:06Z heinze
# local hosts for blizzard added
#
# 1450 2014-08-21 07:31:51Z heinze
# HLRN-III (lccrayb): testq queue adjusted to mpp1testq
#
# 1442 2014-07-28 07:09:10Z raasch
# HLRN-III (lccrayb/lccrayh) queues adjusted
#
# 1378 2014-04-28 06:04:58Z raasch
# -et option added for lctit
#
# 1350 2014-04-04 13:01:30Z maronga
# location of qsub updated for lcxe6
#
# 1289 2014-03-04 07:12:34Z raasch
# German comments translated to English
# fimm-, necriam-, scirocco-, ibmy-, and sgi-specific code removed
#
# 1279 2014-01-28 12:10:14Z raasch
# node calculation modified due to changes in mrun (tasks_per_node must not be
# an integral divisor of numprocs any more)
#
# 1274 2014-01-09 13:14:54Z heinze
# adjustments for lccrayh
#
# 1266 2013-12-11 12:07:34Z heinze
# further adjustments for lccrayb (use msub instead of qsub)
#
# 1264 2013-12-09 12:46:09Z fricke
# Bugfix: Using number of nodes instead of number of processors (lccrayb)
#
# 1262 2013-12-09 10:57:20Z fricke
# further adjustments for lccrayb
#
# 1260 2013-12-04 12:48:04Z raasch
# jaboticaba admitted
#
# 1255 2013-11-07 14:43:35Z raasch
# further adjustments for lccrayb
#
# 1224 2013-09-16 07:27:23Z raasch
# first adjustments for lccrayb
#
# 1202 2013-07-10 16:22:07Z witha
# adjustments for Forwind cluster (lcflow)
#
# 1199 2013-07-05 14:52:22Z raasch
# adjustments for CSC Helsinki (lccrayf)
#
# use of cluster/express queue enabled (ibmh)
# vinessa added (imuk)
#
# 1103 2013-02-20 02:15:53Z raasch
# bash compatibility adjustments (usage of OPTIND, output formatting with printf
# instead typeset -L/R),
# further adjustments for lckyuh
#
# 2013-02-10 01:47:43Z raasch
# adjustments for Kyushu-Univeristy computing center (lckyuh - hayaka)
# and for Forwind cluster (lcflow)
#
# 1094 2013-02-03 01:52:12Z raasch
# new option -P for explicit setting of ssh/scp port,
# decalpha parts (yonsei) removed
#
# 2013-02-02 07:06:13Z raasch
# adjustments for Kyushu-University computing center (lckyut - tatara)
# old changelog messages removed
#
# 1046 2012-11-09 14:38:45Z maronga
# code put under GPL (PALM 3.9)
#
# 08/07/94 - Siggi - first version finished
# 29/06/94 - Siggi - script development started
#--------------------------------------------------------------------------------#
# subjob - script for automatic generation and submission of batch-job files
# for various batch queuing systems
#--------------------------------------------------------------------------------#
# VARIABLE-DECLARATIONS AND DEFAULT VALUES
delete_dayfile=false
email_notification=none
group_number=none
locat=normal
no_default_queue=none
no_submit=false
job_catalog="~/job_queue"
job_name=none
local_user=$LOGNAME
node_usage=shared
numprocs=0
punkte="..........................................................."
submcom=qsub
queue=default
remote_host=none
remote_user=""
verify=true
typeset -i cputime=0 memory=0 Memory=0 minuten resttime sekunden stunden
typeset -i numprocs mpi_tasks=0 nodes=0 processes_per_node=0 tasks_per_node=0 threads_per_task=1
# ERROR HANDLING
# IN CASE OF EXIT:
trap 'if [[ $locat != normal ]]
then
case $locat in
(option) printf "\n --> available optios can be displayed"
printf " by typing:"
printf "\n \"subjob ?\" \n";;
(ftpcopy|parameter|scp|verify) printf "\n";;
(*) printf "\n +++ unknown error"
printf "\n please inform S. Raasch!\n"
esac
[[ -f $job_to_send ]] && rm $job_to_send
printf "\n\n+++ SUBJOB killed \n\n"
fi' exit
# IN CASE OF TERMINAL-BREAK:
trap '[[ -f $job_to_send ]] && rm $job_to_send
printf "\n\n+++ SUBJOB killed \n\n"
exit
' 2
# DETERMINE NAME OF LOCAL HOST
local_host=$(hostname)
# SET HOST-SPECIFIC VARIABLES VEREINBAREN (CHECK, IF LOCAL HOST
# IS ADMITTED AT ALL)
# NOTE: ONE OF THE ENTRIES FOR "lck" OR "lckordi" ALWAYS HAS TO BE
# COMMENT OUT, BECAUSE THE HOSTNAME (node*) IS SAME FOR BOTH MACHINES
case $local_host in
(ambiel-lx) local_address=134.106.74.48; local_host=lcfor;;
(atmos) local_address=172.20.25.35; local_host=lcide;;
(austru) local_address=130.75.105.128; local_host=lcmuk;;
(autan) local_address=130.75.105.57; local_host=lcmuk;;
(bora) local_address=130.75.105.103; local_host=lcmuk;;
(a0*|b0*) local_address=133.5.4.33; local_host=lckyuh;;
(blizzard1|p0*|p1*|p2*|p3*|p4*|p5*|p6*|p7*|p8*|p9*) local_address=136.172.40.15; local_host=ibmh;;
(blizzard2|p0*|p1*|p2*|p3*|p4*|p5*|p6*|p7*|p8*|p9*) local_address=136.172.40.16; local_host=ibmh;;
(blogin*|bxc*) local_address=130.73.233.1; local_host=lccrayb;;
(hlogin*|hxc*) local_address=130.75.4.1; local_host=lccrayh;;
(breva) local_address=130.75.105.98; local_host=lcmuk;;
(buran) local_address=130.75.105.58; local_host=lcmuk;;
(caurus) local_address=130.75.105.19; local_host=lcmuk;;
(climate*) local_address=165.132.26.68; local_host=lcyon;;
(clogin*) local_address=86.50.166.21; local_host=lccrayf;;
(elephanta) local_address=130.75.105.6; local_host=lcmuk;;
(hpcl*) local_address=eddy.hpc.uni-oldenburg.de; local_host=lceddy;;
(cfd*) local_address=eddy.hpc.uni-oldenburg.de; local_host=lceddy;;
(node*) local_address=165.132.26.61 local_host=lck;;
# (node*) local_address=210.219.61.8 local_host=lckordi;;
(gaia*) local_address=150.183.146.24; local_host=ibmkisti;;
(gharbi) local_address=130.75.105.47; local_host=lcmuk;;
(gallego) local_address=130.75.105.10; local_host=lcmuk;;
(gregale) local_address=130.75.105.109; local_host=lcmuk;;
(hababai) local_address=130.75.105.108; local_host=lcmuk;;
(hayaka*) local_address=133.5.4.33; local_host=lckyuh;;
(hexagon.bccs.uib.no) local_address=129.177.20.113; local_host=lcxe6;;
(hx*) local_address=133.3.51.11; local_host=lckyoto;;
(inferno) local_address=130.75.105.5; local_host=lcmuk;;
(irifi) local_address=130.75.105.104; local_host=lcmuk;;
# (i*) local_address=129.187.11.197; local_host=ibmmuc;;
(jaboticaba) local_address=150.163.25.181; local_host=lcbr;;
(kea*) local_address=172.27.80.109; local_host=lckeal;;
(sno) local_address=130.75.105.113; local_host=lcmuk;;
(kuma) local_address=130.75.105.115; local_host=lcmuk;;
(levanto) local_address=130.75.105.45; local_host=lcmuk;;
(login*) local_address=118.128.66.201; local_host=lckiaps;;
# (login*) local_address=129.187.11.197; local_host=ibmmuc;;
(lm*) local_address=129.187.11.197; local_host=ibmmuc;;
(lx*) local_address=129.187.20.240; local_host=lclrz;;
(mpp2*) local_address=129.187.20.105; local_host=lclrz;;
(maestro) local_address=130.75.105.2; local_host=lcmuk;;
(meller) local_address=134.106.74.155; local_host=lcfor;;
(meteo-login*) local_address=193.166.211.144;local_host=lcxt5m;;
(mlogin1*|m1*) local_address=136.172.50.13; local_host=lcbullhh;;
(hexagon*) local_address=129.177.20.113; local_host=lcxe6;;
(nobel*) local_address=150.183.5.101; local_host=ibms;;
(ocean) local_address="ocean"; local_host=lcocean;;
(orkan) local_address=130.75.105.3; local_host=lcmuk;;
(ostria) local_address=130.75.105.106; local_host=lcmuk;;
(paesano) local_address=130.75.105.46; local_host=lcmuk;;
(pcj*) local_address=172.31.120.1; local_host=lckyut;;
(pingui) local_address=134.106.74.118; local_host=lcfor;;
(quanero) local_address=130.75.105.107; local_host=lcmuk;;
(rte*) local_address=133.5.185.60; local_host=lcrte;;
(schultzl-Latitude-E6540) local_address="schultzl-Latitude-E6540"; local_host=lcsch;;
(shiokaze-lx) local_address=134.106.74.123; local_host=lcfor;;
(sisu-login*) local_address=86.50.166.21; local_host=lccrayf;;
(solano) local_address=130.75.105.110; local_host=lcmuk;;
(sugoka*) local_address=172.31.120.1; local_host=lckyut;;
(tc*) local_address="ocean"; local_host=lcocean;;
(t2a*) local_address=10.1.6.165; local_host=lctit;;
(uc1n*) local_address=129.13.82.89; local_host=lcbwuni;;
(urban*) local_address=147.46.30.151 local_host=lcsb;;
(vinessa) local_address=130.75.105.112; local_host=lcmuk;;
(vorias) local_address=172.20.25.43; local_host=lcmuk;;
(*.cc.kyushu-u.ac.jp) local_address=133.5.4.129; local_host=ibmku;;
(*.cluster) local_address=192.168.1.254; local_host=lcgeohu;;
(*) printf "\n +++ \"$local_host\" unknown";
printf "\n please contact the PALM group at IMUK";
locat=parameter; exit;;
esac
# BY DEFAULT, THE REMOTE HOST IS THE LOCAL HOST
remote_host=$local_host
# READ THE SHELLSCRIPT-OPTIONS
while getopts :c:dDe:g:h:m:n:N:O:P:q:t:T:u:vX: option
do
case $option in
(c) job_catalog=$OPTARG;;
(d) delete_dayfile=true;;
(D) no_submit=true;;
(e) email_notification=$OPTARG;;
(g) group_number=$OPTARG;;
(h) remote_host=$OPTARG;;
(m) memory=$OPTARG;;
(n) job_name=$OPTARG;;
(N) node_usage=$OPTARG;;
(O) threads_per_task=$OPTARG;;
(P) scp_port=$OPTARG;;
(q) no_default_queue=$OPTARG;;
(t) cputime=$OPTARG;;
(T) tasks_per_node=$OPTARG;;
(u) remote_user=$OPTARG;;
(v) verify=false;;
(X) numprocs=$OPTARG;;
(\?) printf "\n +++ Option $OPTARG unknown \n";
locat=option; exit;;
esac
done
# GET THE NAME OF THE JOBFILE AS NEXT ARGUMENT
(( to_shift = $OPTIND - 1 ))
shift $to_shift; file_to_send=$1
# OUTPUT OF SHORT DESCRIPTION OF SCRIPT-OPTIONS
if [ "$1" = "?" ]
then
(printf "\n *** subjob can be called as follows:\n"
printf "\n subjob -c.. -d -D -h.. -m.. -q.. -t.. -u.. -v \n"
printf "\n Description of available options:\n"
printf "\n Option Description Default-Value"
printf "\n -c job-input- and output-catalog ~/job_queue"
printf "\n -d no job-protocol will be created ---"
printf "\n -D only the job-file will be created ---"
printf "\n -h execution host, available hosts: $remote_host"
printf "\n ibm, ibmh, ibmkisti, ibmku, ibms, lc...,"
printf "\n lckiaps, lctit"
printf "\n -m memory demand per process in MByte ---"
printf "\n -n jobname "
printf "\n -O threads per task (for OpenMP usage) 1"
printf "\n -P ssh/scp port default port"
printf "\n -q job-queue to be used default"
printf "\n -t allowed cpu-time in seconds ---"
printf "\n -T tasks per node (on parallel hosts) ---"
printf "\n -u username on execution host from .netrc"
printf "\n -v no prompt for confirmation ---"
printf "\n -X # of processors (on parallel hosts) 1"
printf "\n "
printf "\n The only possible positional parameter is :"
printf "\n The complete NQS-job must be provided here."
printf "\n =? creates this outline\n\n") | more
exit
fi
# CHECK, IF JOB-FILE HAS BEEN GIVEN AS ARGUMENT AND IF THE FILE ITSELF EXISTS
if [[ "$file_to_send" = "" ]]
then
printf "\n +++ job-file missing"
locat=parameter; exit
else
if [[ -f $file_to_send ]]
then
true
else
printf "\n +++ job-file: "
printf "\n $file_to_send"
printf "\n does not exist"
locat=parameter; exit
fi
fi
# IF NO JOBNAME HAS BEEN GIVEN, JOBNAME IS SET TO THE NAME OF THE JOB-FILE,
# PROVIDED THAT THE JOB-FILE NAME DOES NOT CONTAIN ANY PATH
if [[ $job_name = none ]]
then
job_name=$file_to_send
fi
if [[ $(echo $job_name | grep -c "/") != 0 ]]
then
printf "\n +++ job-file name: "
printf "\n $job_name"
printf "\n must not contain \"/\"-characters"
locat=parameter; exit
fi
# SET HOST-SPECIFIC QUANTITIES, OR TERMINATE IN CASE OF UNKNOWN HOST,
# OR IF NO HOST HAS BEEN GIVEN
if [[ $remote_host = none ]]
then
printf "\n +++ host missing"
locat=option; exit
else
case $remote_host in
(ibm) queue=p690_standard; remote_address=134.76.99.81; submcom=/usr/lpp/LoadL/full/bin/llsubmit;;
(ibmh) queue=cluster; remote_address=136.172.40.15; submcom=/usr/lpp/LoadL/full/bin/llsubmit;;
(ibmkisti) queue=class.32plus; remote_address=150.183.146.24; submcom=/usr/lpp/LoadL/full/bin/llsubmit;;
(ibmku) queue=s4; remote_address=133.5.4.129; submcom=/usr/local/bin/llsubmit;;
(ibms) queue=p_normal; remote_address=150.183.5.101; submcom=/usr/lpp/LoadL/full/bin/llsubmit;;
(ibmmuc) remote_address=129.187.11.197; submcom=/usr/bin/llsubmit;;
(lcbwuni) queue=develop; remote_address=129.13.82.89; submcom=/opt/moab/bin/msub;;
(lcbullhh) queue=compute; remote_address=136.172.50.13; submcom=/usr/bin/sbatch;;
(lccrayb) queue=mpp1testq; remote_address=130.73.233.1; submcom="/opt/moab/default/bin/msub -E";;
(lccrayh) queue=mpp1testq; remote_address=130.75.4.1; submcom="/opt/moab/default/bin/msub -E";;
(lccrayf) queue=small; remote_address=86.50.166.21; submcom=/opt/slurm/default/bin/sbatch;;
(lceddy) remote_address=eddy.hpc.uni-oldenburg.de; submcom=sbatch;;
(lcgeohu) remote_address=cirrus.geo.hu-berlin.de; submcom=sbatch;;
(lckyoto) remote_address=133.3.51.11; submcom=/thin/local/bin/qsub;;
(lck) remote_address=165.132.26.61; submcom=/usr/torque/bin/qsub;;
(lckeal) queue=ivy; remote_address=172.27.80.109; submcom=/usr/bin/sbatch;;
(lckiaps) remote_address=118.128.66.201; submcom=/opt/pbs/default/bin/qsub;;
(lckordi) remote_address=210.219.61.8; submcom=/usr/torque/bin/qsub;;
(lckyuh) remote_address=133.5.4.33; submcom=/usr/bin/pjsub;;
(lckyut) remote_address=133.5.4.37; submcom=/usr/bin/pjsub;;
(lclrz) remote_address=129.187.20.240; submcom=/usr/bin/sbatch;;
(lcocean) remote_address="ocean"; submcom=qsub;;
(lcsb) remote_address=147.46.30.151; submcom=/usr/torque/bin/qsub;;
(lctit) queue=S; remote_address=10.1.6.165; submcom=/opt/pbs/tools/bin/t2sub;;
(lcxe6) remote_address=129.177.20.113; submcom=/opt/torque/default/bin/qsub;;
(lcxt5m) remote_address=193.166.211.144; submcom=/opt/pbs/10.1.0.91350/bin/qsub;;
(lcyon) remote_address=165.132.26.68; submcom=/usr/torque/bin/qsub;;
(*) printf "\n +++ hostname \"$remote_host\" not allowed";
locat=parameter; exit;;
esac
fi
# CHECK, IF A VALID QUEUE HAS BEEN GIVEN
if [[ $no_default_queue != none ]]
then
error=false
ndq=$no_default_queue
case $remote_host in
(ibm) case $ndq in
(p690_express|p690_standard|p690_long) error=false;;
(*) error=true;;
esac;;
(ibmh) case $ndq in
(cluster|express) error=false;;
(*) error=true;;
esac;;
(ibmkisti) case $ndq in
(class.32plus|class.1-2|class.2-32) error=false;;
(*) error=true;;
esac;;
(ibmku) case $ndq in
(sdbg1|sdbg2|sdbg4|s4|s16|s32|s32-s) error=false;;
(*) error=true;;
esac;;
(ibms) case $ndq in
(express|normal|p_express|p_normal|p_normal_1.3|p_normal_1.7|grand) error=false;;
(*) error=true;;
esac;;
(ibmmuc*) case $ndq in
(test|micro|general|large|fat|fattest|special|tmp1|tmp2) error=false;;
(*) error=true;;
esac;;
(lcbullhh) case $ndq in
(compute|compute2|shared) error=false;;
(*) error=true;;
esac;;
(lcbwuni) case $ndq in
(develop|singlenode|multinode|verylong|fat) error=false;;
(*) error=true;;
esac;;
(lccrayb) case $ndq in
(dataq|mpp1q|mpp1testq|mpp2q|mpp2testq|smp1q|smp1testq|specialm1q) error=false;;
(*) error=true;;
esac;;
(lccrayh) case $ndq in
(dataq|mpp1q|mpp1testq|mpp2q|mpp2testq|smp1q|smp1testq|specialm1q) error=false;;
(*) error=true;;
esac;;
(lccrayf) case $ndq in
(usup|test*|small|large) error=false;;
(*) error=true;;
esac;;
(lceddy) case $ndq in
(eddy.p|cfdh.p|cfdl.p|carl.p|mpcs.p|mpcl.p|mpcb.p|all_nodes.p) error=false;;
(*) error=true;;
esac;;
(lckiaps) case $ndq in
(express|normal|normal20|quickq) error=false;;
(*) error=true;;
esac;;
(lckyoto) case $ndq in
(eh|ph) error=false;;
(*) error=true;;
esac;;
(lckyuh) case $ndq in
(fx-dbg|fx-single|fx-small|fx-middle|fx-large) error=false;;
(*) error=true;;
esac;;
(lckyut) case $ndq in
(cx-dbg|cx-single|cx-small|cx-middle|cx-large) error=false;;
(*) error=true;;
esac;;
(lclrz) case $ndq in
(mpp1|mpp2|iuv2|myri) error=false;;
(*) error=true;;
esac;;
(lctit) case $ndq in
(G|L128|L256|L512H|S|S96|V) error=false;;
(*) error=true;;
esac;;
(t3eb) case $ndq in
(berte|p50|p100|p392|forfree|p25himem) error=false;;
(*) error=true;;
esac;;
(t3eh) case $ndq in
(para_t3e|em|k|l|lm|comp_t3e|c|p|ht) error=false;;
(*) error=true;;
esac;;
(t3ej2|t3ej5) case $ndq in
(low|normal|high) error=false;;
(*) error=true;;
esac;;
(t3es) case $ndq in
(batch|serial-4|pe4|p48|pe16|pe32|pe64|pe128) error=false;;
(*) error=true;;
esac;;
esac
if [[ $error = true ]]
then
printf "\n +++ queue \"$no_default_queue\" on host \"$remote_host\" not allowed"
locat=parameter; exit
else
queue=$no_default_queue
fi
fi
# CHECK THE CPU-TIME
# SPLIT TIME INTO HOURS, MINUTES, AND SECONDS
done=false
while [[ $done = false ]]
do
if (( $cputime <= 0 ))
then
printf "\n +++ wrong cpu-time or cpu-time missing"
printf "\n >>> Please type cpu-time in seconds as INTEGER:"
printf "\n >>> "
read cputime 1>/dev/null 2>&1
else
done=true
fi
done
(( stunden = cputime / 3600 ))
(( resttime = cputime - stunden * 3600 ))
(( minuten = resttime / 60 ))
(( sekunden = resttime - minuten * 60 ))
timestring=${stunden}:${minuten}:${sekunden}
# CHECK THE MEMORY DEMAND
done=false
while [[ $done = false ]]
do
if (( memory <= 0 ))
then
printf "\n +++ wrong memory demand or memory demand missing"
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
if [[ $remote_host = lctit ]]
then
(( Memory = memory * tasks_per_node / 1000 ))
fi
# MEMORY DEMAND IN CASE OF OPENMP-USAGE ON IBM-SYSTEMS
if [[ $(echo $remote_host | cut -c1-3) = ibm ]]
then
(( memory = memory * threads_per_task ))
fi
# CALCULATE NUMBER OF REQUIRED NODES
if (( tasks_per_node != 0 ))
then
(( nodes = ( numprocs - 1 ) / ( tasks_per_node * threads_per_task ) + 1 ))
fi
# CALCULATE NUMBER OF PROCESSES PER NODE
(( processes_per_node = tasks_per_node * threads_per_task ))
# CALCULATE NUMBER OF MPI TASKS
(( mpi_tasks = numprocs / threads_per_task ))
# SET PORT NUMBER OPTION FOR CALLS OF ssh/scp, subjob AND batch_scp SCRIPTS
if [[ "$scp_port" != "" ]]
then
PORTOPT="-P $scp_port"
SSH_PORTOPT="-p $scp_port"
fi
# HEADER-OUTPUT
if [[ $verify = true ]]
then
printf "\n\n"
printf "#--------------------------------------------------------------# \n"
spalte1=SUBJOB;spalte2=$(date)
printf "| %-20s%40s | \n" "$spalte1" "$spalte2"
printf "| | \n"
printf "| values of parameters/options: | \n"
spalte1=$(echo local_host$punkte | cut -c-20)
spalte2=$punkte$local_host
printf "| %-20s%40s | \n" "$spalte1" "${spalte2: -40}"
spalte1=$(echo remote_host$punkte | cut -c-20)
spalte2=$punkte$remote_host
printf "| %-20s%40s | \n" "$spalte1" "${spalte2: -40}"
spalte1=$(echo queue$punkte | cut -c-20)
spalte2=$punkte$queue
printf "| %-20s%40s | \n" "$spalte1" "${spalte2: -40}"
spalte1=$(echo memory$punkte | cut -c-20)
spalte2="$punkte$memory mb"
printf "| %-20s%40s | \n" "$spalte1" "${spalte2: -40}"
spalte1=$(echo cputime$punkte | cut -c-20)
spalte2="$punkte$cputime sec"
printf "| %-20s%40s | \n" "$spalte1" "${spalte2: -40}"
spalte1=$(echo job_name$punkte | cut -c-20)
spalte2="$punkte$job_name"
printf "| %-20s%40s | \n" "$spalte1" "${spalte2: -40}"
printf "#--------------------------------------------------------------# \n\n"
# QUERY CHECK
antwort="dummy"
while [[ $antwort != y && $antwort != Y && $antwort != n && $antwort != N ]]
do
read antwort?" >>> continue (y/n) ? "
done
if [[ $antwort = n || $antwort = N ]]
then
locat=verify; exit
fi
printf "\n"
fi
# GENERATE RANDOM IDENTIFIER, AND DETERMINE THE JOBNAME ON THE TARGET HOST
identifier=$RANDOM
job_on_remhost=${job_name}_${identifier}_$local_host
job_to_send=job_to_send_$identifier
if [[ $delete_dayfile = false ]]
then
remote_dayfile=${local_host}_${job_name}_result_$identifier
local_dayfile=${remote_host}_${job_name}
else
remote_dayfile=/dev/null
fi
# GENERATE THE BATCH-JOB SCRIPTS (FOR QUEUEING-SYSTEMS qsub/msub/LoadLeveler)
if [[ $(echo $remote_host | cut -c1-3) = ibm && $numprocs != 0 ]]
then
# GENERAL LOADLEVELER SETTINGS
execute_in_shell="#!/bin/ksh"
use_shell="# @ shell = /bin/ksh"
consumable_memory="ConsumableMemory($memory mb)"
class="# @ class = $queue"
environment="# @ environment = OMP_NUM_THREADS=$threads_per_task; MP_SHARED_MEMORY=yes"
network_to_use="# @ network.mpi = sn_all,shared,us"
data_limit="# @ data_limit = 1.76gb"
image_size="# @ image_size = 50"
wall_clock_limit="# @ wall_clock_limit = ${timestring},$timestring"
if [[ $email_notification = none ]]
then
notify_user=""
else
notify_user="# @ notify_user = $email_notification"
if [[ $delete_dayfile = true ]]
then
notification='# @ notification = never'
fi
fi
if [[ $remote_host = ibmh ]]
then
data_limit=""
network_to_use=""
class="# @ class = $queue"
environment=""
rset="# @ rset = RSET_MCM_AFFINITY"
task_affinity="# @ task_affinity = core(1)"
elif [[ $remote_host = ibmkisti ]]
then
network_to_use="# @ network.MPI = sn_all,shared,US"
wall_clock_limit="# @ wall_clock_limit = $timestring"
if [[ $threads_per_task = 1 ]]
then
rset="# @ rset = RSET_MCM_AFFINITY"
mcm_affinity_options="# @ mcm_affinity_options = mcm_mem_pref mcm_sni_none mcm_distribute"
fi
environment=""
use_shell=""
data_limit=""
image_size=""
elif [[ $remote_host = ibmku ]]
then
execute_in_shell="#!/usr/bin/ksh"
use_shell="# @ shell = /usr/bin/ksh"
consumable_memory=""
environment=""
network_to_use="# @ network.mpi = sn_all,shared,us"
data_limit=""
image_size=""
elif [[ $remote_host = ibms ]]
then
network_to_use="# @ network.mpi = csss,shared,us"
fi
cat > $job_to_send << %%END%%
$execute_in_shell
$use_shell
# @ job_type = parallel
# @ job_name = $job_name
# @ resources = ConsumableCpus($threads_per_task) $consumable_memory
# @ output = $remote_dayfile
# @ error = $remote_dayfile
$wall_clock_limit
$image_size
$class
$environment
$network_to_use
$data_limit
$rset
$mcm_affinity_options
$task_affinity
$notification
$notify_user
%%END%%
if (( nodes > 0 ))
then
if [[ $remote_host == ibmmuc* ]]
then
cat > $job_to_send << %%END%%
#!/bin/bash
# @ job_type = parallel
# @ job_name = $job_name
# @ output = $remote_dayfile
# @ error = $remote_dayfile
# @ wall_clock_limit = $timestring
$class
$mcm_affinity_options
$task_affinity
$notify_user
# @ network.MPI = sn_all,not_shared,us
# @ notification = always
# @ energy_policy_tag = table_kit_ifu
# @ minimize_time_to_solution = yes
# @ node = $nodes
# @ total_tasks = $numprocs
# @ node_topology = island
# @ island_count = 1,2
# @ environment = LD_LIBRARY_PATH=/lrz/sys/libraries/netcdf/4.2.1.1_impi4/lib:/lrz/sys/libraries/hdf5/1.8.15/ibmmpi/lib:/lrz/sys/libraries/fftw/3.3.3/avx/lib/
# @ queue
%%END%%
elif [[ $remote_host != ibmkisti ]]
then
cat >> $job_to_send << %%END%%
# @ node = $nodes
# @ tasks_per_node = $processes_per_node
# @ node_usage = $node_usage
# @ queue
%%END%%
else
cat >> $job_to_send << %%END%%
# @ total_tasks = $mpi_tasks
# @ blocking = unlimited
# @ queue
%%END%%
fi
else
cat >> $job_to_send << %%END%%
# @ blocking = unlimited
# @ total_tasks = $numprocs
# @ node_usage = $node_usage
# @ queue
%%END%%
fi
# WORKAROUND BECAUSE OF SILLY JOB FILTER ON ibmkisti
if [[ $remote_host = ibmkisti && $threads_per_task != 1 ]]
then
echo "export OMP_NUM_THREADS=$threads_per_task" >> $job_to_send
fi
elif [[ $(echo $remote_host | cut -c1-3) = ibm && $numprocs = 0 ]]
then
cat > $job_to_send << %%END%%
#!/bin/ksh
# @ job_type = serial
# @ node_usage = $node_usage
# @ job_name = palm
# @ wall_clock_limit = ${timestring},$timestring
# @ resources = ConsumableCpus(1) ConsumableMemory(1 gb)
# @ output = $remote_dayfile
# @ error = $remote_dayfile
$class
$notification
# @ queue
%%END%%
elif [[ $remote_host = lcbullhh ]]
then
if [[ $numprocs != 0 ]]
then
cat > $job_to_send << %%END%%
#!/bin/bash -l
#SBATCH -J $job_name
#SBATCH -t $timestring
#SBATCH -N $nodes
#SBATCH --ntasks-per-node=$processes_per_node
#SBATCH -p $queue
#SBATCH -o $remote_dayfile
#SBATCH -e $remote_dayfile
#SBATCH -A $project_account
$init_cmds
$module_calls
%%END%%
else
cat > $job_to_send << %%END%%
#!/bin/bash -l
#SBATCH -J $job_name
#SBATCH -t $timestring
#SBATCH -l ncpus=1
#SBATCH -l pmem=${memory}mb
#SBATCH -m abe
#SBATCH -o $remote_dayfile
#SBATCH -e $remote_dayfile
#SBATCH -A $project_account
$init_cmds
$module_calls
%%END%%
fi
elif [[ $remote_host = lccrayb || $remote_host = lccrayh ]]
then
if [[ "$feature" != "" ]]
then
featuredir="#PBS -l feature=$feature"
fi
if [[ $numprocs != 0 ]]
then
cat > $job_to_send << %%END%%
#!/bin/bash
#PBS -N $job_name
#PBS -l walltime=$timestring
#PBS -l nodes=$nodes:ppn=$processes_per_node
#PBS -o $remote_dayfile
#PBS -j oe
#PBS -q $queue
$featuredir
$init_cmds
$module_calls
%%END%%
else
continue
fi
elif [[ $remote_host = lccrayf ]]
then
if [[ $numprocs != 0 ]]
then
cat > $job_to_send << %%END%%
#!/bin/bash -l
#SBATCH -J $job_name
#SBATCH -t $timestring
#SBATCH -N $nodes
#SBATCH --ntasks-per-node=$processes_per_node
#SBATCH -p $queue
#SBATCH -o $remote_dayfile
#SBATCH -e $remote_dayfile
$init_cmds
$module_calls
%%END%%
else
cat > $job_to_send << %%END%%
#!/bin/bash -l
#SBATCH -J $job_name
#SBATCH -t $timestring
#SBATCH -l ncpus=1
#SBATCH -l pmem=${memory}mb
#SBATCH -m abe
#SBATCH -o $remote_dayfile
#SBATCH -e $remote_dayfile
$init_cmds
$module_calls
%%END%%
fi
elif [[ $remote_host = lceddy ]]
then
cat > $job_to_send << %%END%%
#!/bin/bash
#SBATCH -J $job_name
#SBATCH -t $timestring
#SBATCH -n $numprocs
#SBATCH -N $nodes
#SBATCH --cpus-per-task 1
#SBATCH -p $queue
#SBATCH -o $remote_dayfile
#SBATCH -e $remote_dayfile
#SBATCH --mem-per-cpu $memory
#SBATCH --exclusive
module load PALMDependencies/.gcc
$init_cmds
$module_calls
%%END%%
elif [[ $remote_host = lck || $remote_host = lckordi || $remote_host = lcsb ]]
then
if [[ $numprocs != 0 ]]
then
cat > $job_to_send << %%END%%
#!/bin/ksh
#PBS -N $job_name
#PBS -l walltime=$timestring
#PBS -l ncpus=$numprocs
#PBS -l pmem=${memory}mb
#PBS -o $remote_dayfile
#PBS -l nodes=$nodes:ppn=${processes_per_node}
#PBS -j oe
mpd &
%%END%%
else
cat > $job_to_send << %%END%%
#!/bin/ksh
#PBS -N $job_name
#PBS -l walltime=$timestring
#PBS -l ncpus=1
#PBS -l pmem=${memory}mb
#PBS -o $remote_dayfile
#PBS -j oe
%%END%%
fi
elif [[ $remote_host = lcgeohu ]]
then
if [[ $email_notification = none ]]
then
notify_user=""
else
notify_user="#SBATCH --mail-type=ALL"
fi
if [[ $numprocs != 0 ]]
then
cat > $job_to_send << %%END%%
#!/bin/bash
#SBATCH --job-name=$job_name
#SBATCH --ntasks=$processes_per_node
#SBATCH --time=$timestring
#SBATCH --output=$remote_dayfile
#SBATCH --error=$remote_dayfile
#SBATCH --qos=short
$notify_user
$init_cmds
$module_calls
%%END%%
else
cat > $job_to_send << %%END%%
#!/bin/bash
#SBATCH --job-name=$job_name
#SBATCH --ntasks=$processes_per_node
#SBATCH --output=$remote_dayfile
#SBATCH --error=$remote_dayfile
#SBATCH -l ncpus=1
$init_cmds
$module_calls
%%END%%
fi
elif [[ $remote_host = lckiaps ]]
then
if [[ $numprocs != 0 ]]
then
cat > $job_to_send << %%END%%
#!/bin/bash
#PBS -N $job_name
#PBS -l walltime=$timestring
#PBS -l select=1:ncpus=$numprocs
#PBS -l pmem=${memory}mb
#PBS -q $queue
#PBS -o $remote_dayfile
#PBS -j oe
#PBS -V
%%END%%
else
cat > $job_to_send << %%END%%
#!/bin/bash
#PBS -N $job_name
#PBS -l walltime=$timestring
#PBS -l ncpus=1
#PBS -l pmem=${memory}mb
#PBS -o $remote_dayfile
#PBS -j oe
%%END%%
fi
elif [[ $remote_host = lcyon ]]
then
if [[ $numprocs != 0 ]]
then
cat > $job_to_send << %%END%%
#!/bin/ksh
#PBS -N $job_name
#PBS -l walltime=$timestring
#PBS -l ncpus=$numprocs
#PBS -l pmem=${memory}mb
#PBS -o $remote_dayfile
#PBS -j oe
%%END%%
else
cat > $job_to_send << %%END%%
#!/bin/ksh
#PBS -N $job_name
#PBS -l walltime=$timestring
#PBS -l ncpus=1
#PBS -l pmem=${memory}mb
#PBS -o $remote_dayfile
#PBS -j oe
%%END%%
fi
elif [[ $remote_host = lcxe6 ]]
then
if [[ $numprocs != 0 ]]
then
cat > $job_to_send << %%END%%
#!/bin/ksh
#PBS -S /bin/ksh
#PBS -N $job_name
#PBS -A $project_account
#PBS -j oe
#PBS -l walltime=$timestring
#PBS -l mppwidth=${numprocs}
#PBS -l mppnppn=${processes_per_node}
#PBS -m abe
#PBS -o $remote_dayfile
$email_directive
$init_cmds
$module_calls
%%END%%
else
cat > $job_to_send << %%END%%
#!/bin/ksh
#PBS -S /bin/ksh
#PBS -N $job_name
#PBS -A $project_account
#PBS -j oe
#PBS -l walltime=$timestring
#PBS -l ncpus=1
#PBS -l pmem=${memory}mb
#PBS -m abe
$email_directive
#PBS -o $remote_dayfile
$init_cmds
$module_calls
%%END%%
fi
elif [[ $remote_host = lckyoto ]]
then
cat > $job_to_send << %%END%%
#!/bin/ksh
# @\$-o $remote_dayfile
# @\$-eo -oi
# @\$-lP 16
# @\$-lp 1
# @\$-lm 28gb -llm unlimited -ls unlimited
# @\$-q $queue
# @\$-Pvn abs_pack
##for intel? @\$-Pvn abs_unpack -Pvs unpack -Pvc unpack
#. /thin/local/etc/setprofile/intel-11.0.sh
#. /thin/local/etc/setprofile/mvapich2-1.4+intel-11.0.sh
. ~/.myprofile
#. /home2/t/t51254/palm/current_version/myprofile
#. /thin/apps/pgi/mpi.sh
#
env
#
set -x
%%END%%
elif [[ $remote_host = lcxt5m ]]
then
if [[ $numprocs != 0 ]]
then
cat > $job_to_send << %%END%%
#!/bin/ksh
#PBS -S /bin/ksh
#PBS -N $job_name
#PBS -j oe
#PBS -l walltime=$timestring
#PBS -l mppwidth=${numprocs}
#PBS -l mppnppn=${processes_per_node}
#PBS -m abe
#PBS -o $remote_dayfile
$init_cmds
$module_calls
%%END%%
else
cat > $job_to_send << %%END%%
#!/bin/ksh
#PBS -S /bin/ksh
#PBS -N $job_name
#PBS -j oe
#PBS -l walltime=$timestring
#PBS -l ncpus=1
#PBS -l pmem=${memory}mb
#PBS -m abe
#PBS -o $remote_dayfile
$init_cmds
$module_calls
%%END%%
fi
elif [[ $remote_host = lckyuh ]]
then
cat > $job_to_send << %%END%%
#!/bin/bash
#PJM -L "rscgrp=$queue"
#PJM -L "node=$nodes"
#PJM --mpi "proc=$numprocs"
#PJM -L "elapse=$timestring"
#PJM -o $remote_dayfile
#PJM -j
#PJM -X
#PJM --no-stging
export LANG=en_US.UTF-8
%%END%%
elif [[ $remote_host = lckyut ]]
then
cat > $job_to_send << %%END%%
#!/bin/bash
#PJM -L "rscgrp=$queue"
#PJM -L "vnode=$numprocs"
#PJM -L "vnode-core=1"
#PJM -L "elapse=$timestring"
#PJM --mpi proc=$numprocs
#PJM -o $remote_dayfile
#PJM -j
#PJM -X
#PJM --no-stging
export LANG=en_US.UTF-8
%%END%%
elif [[ $remote_host = lcocean ]]
then
cat > $job_to_send << %%END%%
#!/bin/bash
#$ -cwd
#$ -V
#$ -N $job_name
#$ -pe orte $numprocs
#$ -o $remote_dayfile
#$ -j y
#$ -R y
$init_cmds
$module_calls
%%END%%
elif [[ $remote_host = lctit ]]
then
cat > $job_to_send << %%END%%
#!/bin/ksh
$init_cmds
$module_calls
%%END%%
# SET OPTIONS FOR SUBMIT-COMMAND
if [[ $tasks_per_node != $processes_per_node ]]
then
submcom="$submcom -W group_list=$group_number -N $job_name -l walltime=$timestring -l select=$nodes:ncpus=$processes_per_node:mpiprocs=$tasks_per_node:mem=${Memory}gb -o $remote_dayfile -j oe -et 1 -q $queue "
else
submcom="$submcom -W group_list=$group_number -N $job_name -l walltime=$timestring -l select=$nodes:ncpus=$processes_per_node:mpiprocs=$tasks_per_node:mem=${Memory}gb -l place=scatter -o $remote_dayfile -j oe -et 1 -q $queue "
fi
elif [[ $remote_host = lclrz ]]
then
cat > $job_to_send << %%END%%
#!/bin/bash
#SBATCH -J $job_name
#SBATCH -t $timestring
#SBATCH -N $nodes
#SBATCH --ntasks-per-node=$processes_per_node
#SBATCH --get-user-env
#SBATCH -o $remote_dayfile
#SBATCH -e $remote_dayfile
#SBATCH --mail-user=${email_notification}
#SBATCH --clusters=$queue
$init_cmds
$module_calls
%%END%%
elif [[ $remote_host = lckea* ]]
then
keal_tasks_per_core=1
if [[ $queue = haswell || $queue = ivy* ]]
then
if (( tasks_per_node > 20 ))
then
keal_tasks_per_core=2
fi
fi
cat > $job_to_send << %%END%%
#!/bin/bash
#SBATCH -J $job_name
#SBATCH -t $timestring
#SBATCH -N $nodes
#SBATCH --ntasks-per-node=$processes_per_node
#SBATCH --ntasks-per-core=$keal_tasks_per_core
#SBATCH --mem-per-cpu=${memory}mb
#SBATCH --get-user-env
#SBATCH -o $remote_dayfile
#SBATCH -e $remote_dayfile
#SBATCH --mail-user=${email_notification}
#SBATCH --mail-type=ALL
#SBATCH --partition=$queue
export MV2_ENABLE_AFFINITY=0
$init_cmds
$module_calls
%%END%%
elif [[ $remote_host=lcbwuni ]]
then
if [[ $email_notification = none ]]
then
email_directive=""
else
email_directive="#PBS -M $email_notification"
fi
cat > $job_to_send << %%END%%
#!/bin/ksh
#PBS -N $job_name
#PBS -l walltime=$timestring
#PBS -l nodes=${nodes}:ppn=$processes_per_node
#PBS -l pmem=${memory}mb
#PBS -m abe
#PBS -o $remote_dayfile
#PBS -j oe
#PBS -q $queue
$email_directive
%%END%%
else
cat > $job_to_send << %%END%%
# @\$-q ${queue}
# @\$-l${qsubtime} $timestring
# @\$-l${qsubmem} ${memory}mb
# @\$-o $remote_dayfile
# @\$-eo
%%END%%
fi
# IN CASE OF JOBS EXECUTING ON REMOTE-HOSTS, THE TRANSFER OF THE DAYFILES
# TO THE LOCAL HOSTS WILL BE INITIATED BY TRAP ON EXIT
# NO TRANSFER POSSIBLE ON IBM IN SEOUL
if [[ $delete_dayfile = false && $remote_host != $local_host ]]
then
echo "set +vx" >> $job_to_send
echo "trap '" >> $job_to_send
echo "set +vx" >> $job_to_send
if [[ $(echo $remote_host | cut -c1-3) = ibm || $remote_host = lcbullhh || $remote_host = lccrayb || $remote_host = lccrayh || $(echo $remote_host | cut -c1-3) = nec || $remote_host = lckiaps || $remote_host = lckyu* || $remote_host = lcxe6 || $remote_host = lcocean || $remote_host = lcgeohu ]]
then
if [[ $remote_host = ibmh ]]
then
return_queue=c1
elif [[ $remote_host = ibmkisti ]]
then
return_queue=class.1-2
elif [[ $remote_host = ibmku ]]
then
return_queue=sdbg2
elif [[ $remote_host = ibms ]]
then
return_queue=p_normal
elif [[ $remote_host = lcbullhh ]]
then
return_queue=shared
elif [[ $remote_host = lccrayb || $remote_host = lccrayh ]]
then
return_queue=dataq
elif [[ $remote_host = lcxe6 ]]
then
return_queue=debug
elif [[ $remote_host = lckiaps ]]
then
return_queue=express
elif [[ $remote_host = lckyuh ]]
then
return_queue=cx-single
elif [[ $remote_host = lckyut ]]
then
return_queue=cx-single
else
return_queue=unknown
fi
if [[ $(echo $remote_host | cut -c1-3) = ibm ]]
then
if [[ $remote_host = ibmku ]]
then
echo "echo \"#!/usr/bin/ksh\" >> scpjob.$identifier" >> $job_to_send
echo "echo \"# @ shell = /usr/bin/ksh\" >> scpjob.$identifier" >> $job_to_send
else
echo "echo \"#!/bin/ksh\" >> scpjob.$identifier" >> $job_to_send
fi
echo "echo \"# @ job_type = serial\" >> scpjob.$identifier" >> $job_to_send
echo "echo \"# @ job_name = transfer\" >> scpjob.$identifier" >> $job_to_send
echo "echo \"# @ resources = ConsumableCpus(1) ConsumableMemory(1 gb)\" >> scpjob.$identifier" >> $job_to_send
echo "echo \"# @ wall_clock_limit = 00:10:00,00:10:00\" >> scpjob.$identifier " >> $job_to_send
echo "echo \"# @ output = job_queue/last_job_transfer_protocol\" >> scpjob.$identifier" >> $job_to_send
echo "echo \"# @ error = job_queue/last_job_transfer_protocol\" >> scpjob.$identifier" >> $job_to_send
if [[ $host != "ibmh" ]]
then
echo "echo \"# @ class = $return_queue\" >> scpjob.$identifier" >> $job_to_send
fi
echo "echo \"# @ image_size = 10\" >> scpjob.$identifier" >> $job_to_send
echo "echo \"# @ notification = never\" >> scpjob.$identifier" >> $job_to_send
echo "echo \"# @ queue\" >> scpjob.$identifier" >> $job_to_send
echo "echo \" \" >> scpjob.$identifier" >> $job_to_send
echo "echo \"set -x\" >> scpjob.$identifier" >> $job_to_send
echo "echo \"batch_scp $PORTOPT -d -w 10 -u $local_user $local_address ${job_catalog}/$remote_dayfile \\\"$job_catalog\\\" $local_dayfile\" >> scpjob.$identifier" >> $job_to_send
if [[ $remote_host = ibmku ]]
then
echo "echo \"rm scpjob.$identifier\" >> scpjob.$identifier" >> $job_to_send
fi
echo "echo \"exit\" >> scpjob.$identifier" >> $job_to_send
elif [[ $remote_host = lcbullhh ]]
then
echo "cat > scpjob.$identifier << %%END%%" >> $job_to_send
echo "#!/bin/bash" >> $job_to_send
echo "#SBATCH --job-name=job_protocol_transfer" >> $job_to_send
echo "#SBATCH -t 00:20:00" >> $job_to_send
echo "#SBATCH -N 1" >> $job_to_send
echo "#SBATCH -n 1" >> $job_to_send
echo "#SBATCH -o \$HOME/job_queue/last_job_transfer_protocol" >> $job_to_send
echo "#SBATCH -o $remote_dayfile" >> $job_to_send
echo "#SBATCH -e $remote_dayfile" >> $job_to_send
echo "#SBATCH -A $project_account" >> $job_to_send
echo "#SBATCH -p $return_queue" >> $job_to_send
echo " " >> $job_to_send
echo "set -x" >> $job_to_send
echo "batch_scp $PORTOPT -d -w 10 -u $local_user $local_address ${job_catalog}/$remote_dayfile \"$job_catalog\" $local_dayfile" >> $job_to_send
echo "[[ \"\$for_subjob_to_do\" != \"\" ]] && eval \$for_subjob_to_do" >> $job_to_send
echo "%%END%%" >> $job_to_send
elif [[ $remote_host = lckyuh ]]
then
echo "cat > scpjob.$identifier << %%END%%" >> $job_to_send
echo "#!/bin/bash" >> $job_to_send
echo "#PJM -L \"node=1\"" >> $job_to_send
echo "#PJM -L \"rscgrp=$return_queue\"" >> $job_to_send
echo "#PJM --no-stging" >> $job_to_send
echo "#PJM -L \"elapse=30:00\"" >> $job_to_send
echo "#PJM -o \$HOME/job_queue/last_job_transfer_protocol" >> $job_to_send
echo "#PJM -j" >> $job_to_send
echo " " >> $job_to_send
echo "export LANG=en_US.UTF-8" >> $job_to_send
echo "set -x" >> $job_to_send
echo "batch_scp $PORTOPT -d -w 10 -u $local_user $local_address $remote_dayfile \"$job_catalog\" $local_dayfile" >> $job_to_send
echo "[[ \"\$for_subjob_to_do\" != \"\" ]] && eval \$for_subjob_to_do" >> $job_to_send
echo "%%END%%" >> $job_to_send
elif [[ $remote_host = lckyut ]]
then
echo "cat > scpjob.$identifier << %%END%%" >> $job_to_send
echo "#!/bin/bash" >> $job_to_send
echo "#PJM -L \"vnode=1\"" >> $job_to_send
echo "#PJM -L \"rscgrp=$return_queue\"" >> $job_to_send
echo "#PJM --no-stging" >> $job_to_send
echo "#PJM -L \"elapse=30:00\"" >> $job_to_send
echo "#PJM -o \$HOME/job_queue/last_job_transfer_protocol" >> $job_to_send
echo "#PJM -j" >> $job_to_send
echo " " >> $job_to_send
echo "export LANG=en_US.UTF-8" >> $job_to_send
echo "set -x" >> $job_to_send
echo "batch_scp $PORTOPT -d -w 10 -u $local_user $local_address $remote_dayfile \"$job_catalog\" $local_dayfile" >> $job_to_send
echo "[[ \"\$for_subjob_to_do\" != \"\" ]] && eval \$for_subjob_to_do" >> $job_to_send
echo "%%END%%" >> $job_to_send
elif [[ $remote_host = lccrayb || $remote_host = lccrayh ]]
then
echo "cat > scpjob.$identifier << %%END%%" >> $job_to_send
echo "#!/bin/bash" >> $job_to_send
echo "#PBS -N job_protocol_transfer" >> $job_to_send
echo "#PBS -l walltime=00:30:00" >> $job_to_send
echo "#PBS -l nodes=1:ppn=1" >> $job_to_send
echo "#PBS -o \$HOME/job_queue/last_job_transfer_protocol" >> $job_to_send
echo "#PBS -j oe" >> $job_to_send
echo " " >> $job_to_send
echo "set -x" >> $job_to_send
echo "batch_scp $PORTOPT -d -w 10 -u $local_user $local_address ${job_catalog}/$remote_dayfile \"$job_catalog\" $local_dayfile" >> $job_to_send
echo "[[ \"\$for_subjob_to_do\" != \"\" ]] && eval \$for_subjob_to_do" >> $job_to_send
echo "%%END%%" >> $job_to_send
elif [[ $remote_host = lcocean ]]
then
echo "cat > scpjob.${identifier}.tmp << %%END%%" >> $job_to_send
echo "#!/bin/bash" >> $job_to_send
echo "SGEPREFIX -S /bin/bash" >> $job_to_send
echo "SGEPREFIX -N transfer_$job_name" >> $job_to_send
echo "SGEPREFIX -cwd" >> $job_to_send
echo "SGEPREFIX -j y" >> $job_to_send
echo "SGEPREFIX -o ${local_host}_${job_name}_scpjob_$identifier" >> $job_to_send
echo " " >> $job_to_send
echo "set -x" >> $job_to_send
echo "export PALM_BIN=$PALM_BIN" | sed -e 's:'$HOME':$HOME:' >> $job_to_send
echo "export PATH=\$PATH:\$PALM_BIN" >> $job_to_send
echo "" >> $job_to_send
echo "batch_scp $PORTOPT -d -w 10 -u $local_user $local_address ${job_catalog}/$remote_dayfile \"$job_catalog\" $local_dayfile" >> $job_to_send
echo "[[ \"\$for_subjob_to_do\" != \"\" ]] && eval \$for_subjob_to_do" >> $job_to_send
echo "rm -f scpjob.${identifier}" >> $job_to_send
echo "%%END%%" >> $job_to_send
echo "sed -e 's/SGEPREFIX/#$/g' scpjob.${identifier}.tmp > scpjob.${identifier}" >> $job_to_send
echo "rm -f scpjob.${identifier}.tmp" >> $job_to_send
elif [[ $remote_host = lcxe6 ]]
then
echo "cat > scpjob.${identifier} << %%END%%" >> $job_to_send
echo "#!/bin/ksh" >> $job_to_send
echo "#PBS -N job_protocol_transfer" >> $job_to_send
echo "#PBS -l walltime=00:30:00" >> $job_to_send
echo "#PBS -A $project_account" >> $job_to_send
echo "#PBS -l mppwidth=1" >> $job_to_send
echo "#PBS -l mppnppn=1" >> $job_to_send
echo "#PBS -o \$HOME/job_queue/last_job_transfer_protocol" >> $job_to_send
echo "#PBS -j oe" >> $job_to_send
echo " " >> $job_to_send
echo "set -x" >> $job_to_send
echo "batch_scp $PORTOPT -d -w 10 -u $local_user $local_address ${job_catalog}/$remote_dayfile \"$job_catalog\" $local_dayfile" >> $job_to_send
echo "[[ \"\$for_subjob_to_do\" != \"\" ]] && eval \$for_subjob_to_do" >> $job_to_send
echo "%%END%%" >> $job_to_send
elif [[ $remote_host = lcgeohu ]]
then
echo "cat > scpjob.$identifier << %%END%%" >> $job_to_send
echo "#!/bin/bash" >> $job_to_send
echo "#SBATCH --job-name=job_protocol_transfer" >> $job_to_send
echo "#SBATCH -t 00:20:00" >> $job_to_send
echo "#SBATCH -N 1" >> $job_to_send
echo "#SBATCH -n 1" >> $job_to_send
echo "#SBATCH -o \$HOME/job_queue/last_job_transfer_protocol" >> $job_to_send
echo "#SBATCH -o $remote_dayfile" >> $job_to_send
echo "#SBATCH -e $remote_dayfile" >> $job_to_send
echo " " >> $job_to_send
echo "set -x" >> $job_to_send
echo "sbatch scpjob.$identifier" >> $job_to_send
echo "%%END%%" >> $job_to_send
else
echo "cat > scpjob.$identifier << %%END%%" >> $job_to_send
echo "# @\\\$-q $return_queue" >> $job_to_send
echo "# @\\\$-l${qsubtime} 10" >> $job_to_send
echo "# @\\\$-l${qsubmem} 10mb" >> $job_to_send
if [[ $remote_host = t3ej2 || $remote_host = t3ej5 || $remote_host = t3es ]]
then
echo "# @\$-l mpp_p=0" >> $job_to_send
fi
echo '# @\$-lF 10mb' >> $job_to_send
echo '# @\$-o job_queue/last_job_transfer_protocol' >> $job_to_send
echo '# @\\\$-eo' >> $job_to_send
echo " " >> $job_to_send
if [[ $remote_host = t3ej2 || $remote_host = t3ej5 ]]
then
echo "set +vx" >> $job_to_send
echo ". .profile" >> $job_to_send
fi
echo "set -x" >> $job_to_send
echo "batch_scp $PORTOPT -d -w 10 -u $local_user $local_address ${job_catalog}/$remote_dayfile \"$job_catalog\" $local_dayfile > /dev/null" >> $job_to_send
echo "[[ \"\$for_subjob_to_do\" != \"\" ]] && eval \$for_subjob_to_do" >> $job_to_send
echo "%%END%%" >> $job_to_send
fi
if [[ $(echo $remote_host | cut -c1-3) = ibm ]]
then
echo "llsubmit scpjob.$identifier" >> $job_to_send
elif [[ $remote_host = lcbullhh ]]
then
echo "sbatch scpjob.$identifier" >> $job_to_send
elif [[ $remote_host = lccrayb || $remote_host = lccrayh ]]
then
echo "msub -E -q $return_queue scpjob.$identifier" >> $job_to_send
elif [[ $remote_host = t3eb || $remote_host = t3eh || $remote_host = t3ej2 || $remote_host = t3ej5 ]]
then
echo "qsub -J n scpjob.$identifier" >> $job_to_send
elif [[ $remote_host = t3es ]]
then
echo "qsub -J n -s /bin/ksh scpjob.$identifier" >> $job_to_send
elif [[ $remote_host = lckiaps ]]
then
echo "mv scpjob.$identifier $job_catalog" >> $job_to_send
echo "ssh $SSH_PORTOPT ${remote_username}@${remote_address} \"$submcom ${job_catalog}/scpjob.$identifier\" " >> $job_to_send
echo "rm ${job_catalog}/scpjob.$identifier" >> $job_to_send
elif [[ $remote_host = lckyu* ]]
then
echo "scp $PORTOPT scpjob.$identifier ${remote_username}@${remote_address}:job_queue" >> $job_to_send
echo "ssh $SSH_PORTOPT ${remote_username}@${remote_address} \"cd job_queue; $submcom scpjob.$identifier; rm scpjob.$identifier\" " >> $job_to_send
elif [[ $remote_host = lcocean ]]
then
echo "mv scpjob.$identifier $job_catalog" >> $job_to_send
echo "/usr/bin/ssh ${remote_username}@${remote_address} \"$init_cmds $module_calls cd $job_catalog; $submcom scpjob.$identifier\" " >> $job_to_send
else
echo "$submcom scpjob.$identifier" >> $job_to_send
fi
if [[ $remote_host != ibmku && $remote_host != lckiaps ]]
then
echo "rm scpjob.$identifier" >> $job_to_send
fi
else
# echo "ftpcopy -d $local_address ${job_catalog}/$remote_dayfile \"$job_catalog\" $local_dayfile" >> $job_to_send
# ??? funktioniert das überhaupt noch ???
echo "nohup ftpcopy -d -w 15 $local_address ${job_catalog}/$remote_dayfile \"$job_catalog\" $local_dayfile > /dev/null &" >> $job_to_send
fi
echo "set -x" >> $job_to_send
echo " ' exit" >> $job_to_send
echo "set -x" >> $job_to_send
fi
# APPEND THE JOB-FILE (CREATE BY mrun) TO THE JOB-DIRECTIVES GENERATED ABOVE
cat $file_to_send >> $job_to_send
if [[ $remote_host = ibm ]]
then
echo " " >> $job_to_send
echo "exit" >> $job_to_send
fi
# REMOVE JOB-FILE
if [[ $remote_host = lctit || $remote_host = ibmku ]]
then
echo " " >> $job_to_send
echo "rm ~/job_queue/$job_on_remhost" >> $job_to_send
fi
# TRANSFER JOB TO THE TARGET HOST (JOB-DIRECTORY)
if [[ $no_submit = false ]]
then
if [[ $remote_host != $local_host ]]
then
[[ $verify = true ]] && printf "\n >>> transfering job to \"$remote_host\"..."
if [[ $remote_host = ibms ]] # ssh on ibms cannot handle "~/"
then
job_catalog_save=$job_catalog
job_catalog=job_queue
elif [[ $remote_host = lcgeohu ]]
then
job_catalog_save=$job_catalog
job_catalog=/home/${remote_user}/job_queue
fi
scp $ssh_key $PORTOPT $job_to_send ${remote_user}@${remote_address}:${job_catalog}/$job_on_remhost
if [[ $? = 1 ]]
then
locat=scp; exit
fi
if [[ $remote_host = ibms || $remote_host = lcgeohu ]]
then
job_catalog=$job_catalog_save
fi
[[ $verify = true ]] && printf "\n >>> finished\n"
else
eval job_catalog=$job_catalog
cp $job_to_send ${job_catalog}/$job_on_remhost
fi
# START NQS- / LOADLEVELER-JOB
if [[ $remote_host != $local_host ]]
then
[[ $verify = true ]] && printf "\n >>> submitting job using \"qsub\"...\n"
if [[ $remote_host = ibmku ]]
then
ssh $SSH_PORTOPT $remote_address -l $remote_user "cd $job_catalog; $submcom $job_on_remhost"
elif [[ $remote_host = lcgeohu ]]
then
ssh $ssh_key $SSH_PORTOPT $remote_address -l $remote_user "cd $job_catalog; $submcom $job_on_remhost"
else
ssh $ssh_key $SSH_PORTOPT $remote_address -l $remote_user "cd $job_catalog; $submcom $job_on_remhost; rm $job_on_remhost"
fi
[[ $verify = true ]] && printf " >>> o.k.\n"
else
cd $job_catalog
if [[ $(echo $local_host | cut -c1-3) = ibm || $(echo $local_host | cut -c1-6) = lccray || $local_host = lceddy || $local_host = lcgeohu ]]
then
eval $submcom $job_on_remhost
elif [[ $local_host = lctit || $local_host = lcxe6 || $local_host = lck || $local_host = lckordi || $local_host = lcyon || $local_host = lcsb || $local_host = lckyu* ]]
then
chmod u+x $job_on_remhost
eval $submcom $job_on_remhost
elif [[ $local_host = lcbullhh ]]
then
if [[ $queue = default ]]
then
eval $submcom $job_on_remhost
fi
elif [[ $local_host = lclrz || $local_host = lckea* ]]
then
eval $submcom $job_on_remhost
elif [[ $local_host = lcbwuni ]]
then
msub -q $queue $job_on_remhost
else
qsub $job_on_remhost
fi
# JOBFILE MUST NOT BE DELETED ON lctit/ibmku. THIS WILL BE DONE
# AT THE END OF THE JOB
if [[ $local_host != lctit && $local_host != ibmku && $local_host != lcgeohu ]]
then
rm $job_on_remhost
fi
cd - > /dev/null
fi
fi
# FINAL ACTIONS
if [[ $no_submit = false ]]
then
rm -f $job_to_send
fi
[[ $verify = true ]] && printf "\n\n *** SUBJOB finished \n\n"