#!/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 1941 2016-06-14 05:17:11Z suehring $ # # 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;; (b04*) 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;; (cs*) local_address=136.172.44.131; local_host=nech;; (elephanta) local_address=130.75.105.6; local_host=lcmuk;; (flow01) local_address=10.141.255.71; local_host=lcflow;; (flow02) local_address=10.141.255.72; local_host=lcflow;; (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;; (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;; (jaboticaba) local_address=150.163.25.181; local_host=lcbr;; (sno) local_address=130.75.105.113; local_host=lcmuk;; (levanto) local_address=130.75.105.45; local_host=lcmuk;; (login*) local_address=118.128.66.201; local_host=lckiaps;; (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;; (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;; (*) 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: $remote_host" printf "\n ibm, ibmh, ibmkisti, ibmku, ibms, lc...," printf "\n lckiaps, lctit, nech" printf "\n -m memory demand per process in MByte ---" printf "\n -n jobname " printf "\n -O threads per task (for OpenMP usage) 1" printf "\n -P ssh/scp port default port" printf "\n -q job-queue to be used default" printf "\n -t allowed cpu-time in seconds ---" printf "\n -T tasks per node (on parallel hosts) ---" printf "\n -u username on execution host from .netrc" printf "\n -v no prompt for confirmation ---" printf "\n -X # of processors (on parallel hosts) 1" printf "\n " printf "\n The only possible positional parameter is :" printf "\n The complete NQS-job must be provided here." printf "\n =? creates this outline\n\n") | more exit fi # CHECK, IF JOB-FILE HAS BEEN GIVEN AS ARGUMENT AND IF THE FILE ITSELF EXISTS if [[ "$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 $remote_host in (ibm) queue=p690_standard; remote_address=134.76.99.81; submcom=/usr/lpp/LoadL/full/bin/llsubmit;; (ibmh) queue=cluster; remote_address=136.172.40.15; submcom=/usr/lpp/LoadL/full/bin/llsubmit;; (ibmkisti) queue=class.32plus; remote_address=150.183.146.24; submcom=/usr/lpp/LoadL/full/bin/llsubmit;; (ibmku) queue=s4; remote_address=133.5.4.129; submcom=/usr/local/bin/llsubmit;; (ibms) queue=p_normal; remote_address=150.183.5.101; submcom=/usr/lpp/LoadL/full/bin/llsubmit;; (lcbullhh) queue=compute; remote_address=136.172.50.13; submcom=/usr/bin/sbatch;; (lccrayb) queue=mpp1testq; remote_address=130.73.233.1; submcom=/opt/moab/default/bin/msub;; (lccrayh) queue=mpp1testq; remote_address=130.75.4.1; submcom=/opt/moab/default/bin/msub;; (lccrayf) queue=small; remote_address=86.50.166.21; submcom=/opt/slurm/default/bin/sbatch;; (lcflow) remote_address=10.140.1.72; submcom=qsub;; (lckyoto) remote_address=133.3.51.11; submcom=/thin/local/bin/qsub;; (lck) remote_address=165.132.26.61; submcom=/usr/torque/bin/qsub;; (lckiaps) remote_address=118.128.66.201; submcom=/opt/pbs/default/bin/qsub;; (lckordi) remote_address=210.219.61.8; submcom=/usr/torque/bin/qsub;; (lckyuh) remote_address=133.5.4.33; submcom=/usr/bin/pjsub;; (lckyut) remote_address=133.5.4.37; submcom=/usr/bin/pjsub;; (lcocean) remote_address="ocean"; submcom=qsub;; (lcsb) remote_address=147.46.30.151; submcom=/usr/torque/bin/qsub;; (lctit) queue=S; remote_address=10.1.6.165; submcom=/opt/pbs/tools/bin/t2sub;; (lcxe6) remote_address=129.177.20.113; submcom=/opt/torque/default/bin/qsub;; (lcxt5m) remote_address=193.166.211.144; submcom=/opt/pbs/10.1.0.91350/bin/qsub;; (lcyon) remote_address=165.132.26.68; submcom=/usr/torque/bin/qsub;; (nech) qsubmem=memsz_job; qsubtime=cputim_job; remote_address=136.172.44.147; submcom="/usr/local/bin/qsub";; (*) printf "\n +++ hostname \"$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;; (lcbullhh) case $ndq in (compute|shared) 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;; (lcflow) case $ndq in (cfd_lom_long.q|cfd_him_long.q|cfd_lom_serl.q|cfd_lom_shrt.q|cfd_him_shrt.q|cfd_ivy_shrt.q) 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;; (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 if [[ $remote_host = nech ]] then if (( tasks_per_node != 0 )) then (( cputime = cputime * tasks_per_node )) elif [[ $numprocs != 0 ]] then (( cputime = cputime * numprocs )) fi fi (( stunden = cputime / 3600 )) (( resttime = cputime - stunden * 3600 )) (( minuten = resttime / 60 )) (( sekunden = resttime - minuten * 60 )) timestring=${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 = nech ]] then if (( tasks_per_node != 0 )) then (( Memory = memory * tasks_per_node / 1000 )) elif [[ $numprocs != 0 ]] then (( Memory = memory * numprocs / 1000 )) else (( Memory = memory / 1000 )) fi elif [[ $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 != 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 = lcflow ]] then if [[ $numprocs != 0 ]] then pe_set="#$ -pe impi $numprocs" else pe_set="#$ -pe impi 1" fi if [[ $queue = default ]] then queue_set="" else queue_set="#$ -q $queue" fi [[ "$disc_space" = "" ]] && disc_space=50 cat > $job_to_send << %%END%% #!/bin/bash #$ -S /bin/bash #$ -N $job_name #$ -cwd #$ -l h_rt=$timestring #$ -l h_vmem=${memory}M #$ -o $remote_dayfile #$ -j y $pe_set #$ -R y #$ -l h_fsize=${disc_space}G $queue_set %%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 = 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 = nech ]] then if (( nodes > 1 )) then cat > $job_to_send << %%END%% #!/bin/ksh #PBS -l cpunum_prc=$processes_per_node,cputim_job=$cputime #PBS -l ${qsubmem}=${Memory}gb #PBS -b $nodes #PBS -o $remote_dayfile #PBS -N palm #PBS -j o #PBS -T mpisx %%END%% elif [[ $numprocs != 0 ]] then cat > $job_to_send << %%END%% #!/bin/ksh #PBS -l cpunum_prc=$processes_per_node,cputim_job=$cputime #PBS -l ${qsubmem}=${Memory}gb #PBS -o $remote_dayfile #PBS -N palm #PBS -j o %%END%% else cat > $job_to_send << %%END%% #!/bin/ksh #PBS -l ${qsubmem}=${Memory}gb,${qsubtime}=$cputime #PBS -o $remote_dayfile #PBS -j o %%END%% fi 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 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 = lcflow || $remote_host = lckiaps || $remote_host = lckyu* || $remote_host = lcxe6 || $remote_host = lcocean ]] 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 [[ $remote_host = nech ]] then echo "cd /pf/b/${remote_user}/job_queue" >> $job_to_send echo "cat > scpjob.$identifier << %%END%%" >> $job_to_send echo "#PBS -l ${qsubmem}=1GB,${qsubtime}=100" >> $job_to_send echo "#PBS -o last_job_transfer_protocol" >> $job_to_send echo "#PBS -j o" >> $job_to_send echo " " >> $job_to_send echo "set -x" >> $job_to_send echo "cd /pf/b/${remote_user}/job_queue" >> $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 [[ $remote_host = lcbullhh ]] then echo "cat > scpjob.$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 [[ $remote_host = lcflow ]] then echo "cat > scpjob.${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 -l h_rt=01:00:00" >> $job_to_send echo "SGEPREFIX -l h_vmem=500M" >> $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%%" >> $job_to_send else echo "cat > scpjob.$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 -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 = lcflow || $remote_host = lcocean ]] then echo "mv scpjob.$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 if [[ $remote_host = nech ]] then echo "cd -" >> $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 || $remote_host = lcflow ]] 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 [[ $remote_host = nech ]] then job_catalog_save=$job_catalog job_catalog=/hpf/b/${remote_user}/job_queue fi if [[ $remote_host = nech ]] then # FILES CAN ONLY BE TRANSFERED VIA DKRZ'S ARCHIVE-SERVER scp $PORTOPT $job_to_send ${remote_user}@136.172.44.205:${job_catalog}/$job_on_remhost else scp $PORTOPT $job_to_send ${remote_user}@${remote_address}:${job_catalog}/$job_on_remhost fi if [[ $? = 1 ]] then locat=scp; exit fi if [[ $remote_host = ibms ]] then job_catalog=$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 = lcflow ]] then /usr/bin/ssh $SSH_PORTOPT $remote_address -l $remote_user "$init_cmds $module_calls cd $job_catalog; $submcom $job_on_remhost" else ssh $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 ]] then eval $submcom $job_on_remhost elif [[ $local_host = lctit || $localhost = lcxe6 || $localhost = lck || $localhost = lckordi || $localhost = lcyon || $localhost = lcsb || $localhost = lckyu* ]] then chmod u+x $job_on_remhost eval $submcom $job_on_remhost elif [[ $local_host = nech ]] then if [[ $queue = default ]] then eval $submcom $job_on_remhost else eval $submcom -q $queue $job_on_remhost fi elif [[ $local_host = lcbullhh ]] then if [[ $queue = default ]] then eval $submcom $job_on_remhost fi else qsub $job_on_remhost fi # JOBFILE MUST NOT BE DELETED ON lctit/ibmku/lcflow. THIS WILL BE DONE # AT THE END OF THE JOB if [[ $local_host != lctit && $local_host != ibmku && $local_host != lcflow ]] 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"