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subjob @ 131

Last change on this file since 131 was 129, checked in by letzel, 17 years ago

prognostic_equations include the respective wall_*flux in the parameter list of
calls of diffusion_s. Same as before, only the values of wall_heatflux(0:4)
can be assigned. At present, wall_humidityflux, wall_qflux, wall_salinityflux,
wall_scalarflux are kept zero. diffusion_s uses the respective wall_*flux
instead of wall_heatflux. This update serves two purposes:

it avoids errors in calculations with humidity/scalar/salinity and prescribed

non-zero wall_heatflux,

it prepares PALM for a possible assignment of wall fluxes of

humidity/scalar/salinity in a future release.

Bugfix: assignment of fluxes at walls

Updates to documentation:
chapter_4.2.html#mode_dvrp
chapter_3.5.4.html#time_series

Default for mrun options -q and -n is "sla3" for lctit. Queues bes1 and bes2
removed. DOC/misc/Tsubame.html updated.

Modified default paths (/work/...) for lctit in .mrun.config.default

Property svn:keywords set to Rev

File size: 37.0 KB

Line
1	#!/bin/ksh
2	# subjob - Plot-Shellskript Version: @(#)SUBJOB 1.0
3	# $Id: subjob 54 2007-03-08 00:00:02Z raasch $
4
5	# Prozedur zum automatischen Generieren von Batch-Jobs, die unter NQS
6	# laufen sollen und deren Ergebnis (Dayfile) zum Job-generierenden
7	# Host zurueckgeschickt werden sollen
8
9
10	# letzte Aenderung:
11	# 29/06/94 - Siggi - Beginn mit Erstellung der Originalversion
12	# 08/07/94 - Siggi - Originalversion abgeschlossen (Version 1.0)
13	# 06/02/98 - Siggi - berte validiert
14	# 27/01/01 - Siggi - ground.yonsei.ac.kr validiert, Jobs zur T3E in Korea
15	# moeglich
16	# 08/02/01 - Siggi - alle subjob-Meldungen ins englische uebersetzt
17	# 25/05/02 - Siggi - Unterstuetzung des LoadLeveler
18	# 30/05/02 - Siggi - Validierung fuer ibm-Rechner in Seoul (nobel) sowie
19	# allgemeine Anpassungen fuer ibm-Rechner
20	# 15/10/02 - Siggi - Neue Default-Jobklasse (p_normal) fuer IBM in Seoul
21	# Ruecktransfer des Jobprotokolls fuer diese
22	# Maschine abgeschaltet
23	# 31/10/02 - Siggi - berni validiert
24	# 06/11/02 - Siggi - Neue Jobklassen auf ibmb und ibmh
25	# 08/11/02 - Siggi - quanero validiert
26	# 11/12/02 - Siggi - Notification fuer Transfer-Jobs abgeschaltet
27	# 23/01/03 - Siggi - hostname nobel changed to nobela
28	# 06/02/03 - Siggi - gregale validated
29	# 12/02/03 - Siggi - orkan and maestro validated
30	# 21/02/03 - Siggi - all nobel nodes in Seoul validated
31	# 12/03/03 - Siggi - nec at DKRZ validated
32	# 13/03/03 - Siggi - new nqs resource variable Memory
33	# 07/04/03 - Siggi - processor request option -c on nech needs tasks per
34	# node
35	# 11/04/03 - Siggi - network on ibms has attribute "shared"
36	# 31/07/03 - Siggi - nqs2 on nech implemented (provisional: -h nech2)
37	# cxxl added to ibmh
38	# 29/08/03 - Siggi - changes in job queues and communication system on
39	# ibms
40	# 24/10/03 - Siggi - using alternate hanni address 130.75.4.2
41	# 30/10/03 - Siggi - nech is not supported any more
42	# 10/11/03 - Siggi - nech2 renamed to nech
43	# 20/11/03 - Siggi - submit command on nech changed from qsub.test to qsub
44	# 29/03/04 - Siggi - ground not supported any more, gfdl3 validated
45	# 31/03/04 - Siggi - new option -N for node usage
46	# 12/04/04 - Siggi - scp2 instead of scp used for transfer from decalpha
47	# due to error in ssh installation (otherwise a prompt
48	# for the password appears)
49	# 23/07/04 - Siggi - changes due to the new berni configuration
50	# (federation switch)
51	# 01/09/04 - Gerald new job-classes on hanni
52	# 08/09/04 - Siggi - hanni IP address changed to 130.75.4.10
53	# 23/11/04 - Siggi - new job class cdata on hanni and berni
54	# 03/12/04 - Siggi - notification on ibm switched of in case of
55	# delete_dayfile = true, node usage in cdev set to
56	# shared
57	# 16/02/05 - Gerald hababai validated
58	# 29/03/05 - Micha - new job class channi on hanni
59	# 11/05/05 - Siggi - ConsumableMemory is now required as resource keyword
60	# on ibms
61	# 24/05/05 - Siggi - Default queue on ibms changed from p_normal_1.3 to
62	# p_normal
63	# 30/06/05 - Siggi - network changed for queue cdev from "us" to "ip"
64	# 12/07/05 - Siggi - in network.mpi on ibmh/ibmb "csss" changed to
65	# "sn_all", new job class cexp
66	# 08/09/05 - Siggi - IP-address of gfdl3 changed
67	# 31/10/05 - Siggi - new job class pp on hurricane, serial jobs on
68	# hurricane (with -X0)
69	# 01/11/05 - Siggi - missing queue for jobs submitted on nech (for nech)
70	# added
71	# 30/12/05 - Siggi - change of IP adresses in subnet 130.75.105
72	# 09/02/06 - Siggi - ibmy admitted
73	# 10/02/06 - Siggi - scp2 changed to /bin/scp on decalpha
74	# 13/04/06 - Siggi - ostria admitted
75	# 18/04/06 - Siggi - new option -O for OpenMP usage
76	# 24/05/06 - Siggi - lctit admitted, ftpjob renamed scpjob
77	# 25/07/06 - Siggi - gfdl5 (ibmy) admitted for submitting jobs
78	# 27/09/06 - Siggi - breg/hreg extended with berni/hanni
79	# 25/10/06 - Siggi - data_limit set to 1.76 GByte on hanni and berni
80	# 28/11/06 - Siggi - levanto admitted
81	# 13/02/07 - Siggi - hpmuk releated code removed
82	# 01/03/07 - Siggi - adjustments for RIAM machines gate and NEC-SX8 (n-sx)
83	# 12/04/07 - Siggi - option -f (filetransfer protocol) removed, scp only
84	# 27/07/07 - Siggi - autan admitted
85	# 03/08/07 - Marcus- lcfimm admitted
86	# 08/10/07 - Siggi - further job classes added for hanni (csoloh...)
87	# 15/10/07 - Siggi - preliminary adjustments for lctit based on Jin's
88	# suggestions
89	# 19/10/07 - Marcus- add new optional argument -g group_number
90	# 19/10/07 - Siggi - a ";" was missing in the last change done by Marcus
91	# 30/10/07 - Marcus- further adjustments for queues on lctit
92
93
94	# VARIABLENVEREINBARUNGEN + DEFAULTWERTE
95	delete_dayfile=false
96	group_number=none
97	locat=normal
98	no_default_queue=none
99	no_submit=false
100	job_catalog="~/job_queue"
101	job_name=none
102	local_user=$LOGNAME
103	node_usage=shared
104	numprocs=1
105	punkte="..........................................................."
106	submcom=qsub
107	queue=default
108	remote_host=none
109	remote_user=""
110	verify=true
111
112	typeset -i cputime=0 memory=0 Memory=0 minuten resttime sekunden stunden
113	typeset -i inumprocs nodes=0 tasks_per_node=0 threads_per_task=1
114	typeset -L20 spalte1
115	typeset -R40 spalte2
116	typeset -L60 spalte3
117
118
119
120	# FEHLERBEHANDLUNG
121	# BEI EXIT:
122	trap 'if [[ $locat != normal ]]
123	then
124	case $locat in
125	(option) printf "\n --> available optios can be displayed"
126	printf " by typing:"
127	printf "\n \"subjob ?\" \n";;
128	(ftpcopy\|parameter\|scp\|verify) printf "\n";;
129	(*) printf "\n +++ unknown error"
130	printf "\n please inform S. Raasch!\n"
131	esac
132	[[ -f $job_to_send ]] && rm $job_to_send
133	printf "\n\n+++ SUBJOB killed \n\n"
134	fi' exit
135
136
137	# BEI TERMINAL-BREAK:
138	trap '[[ -f $job_to_send ]] && rm $job_to_send
139	printf "\n\n+++ SUBJOB killed \n\n"
140	exit
141	' 2
142
143
144
145
146	# LOKALEN HOSTNAMEN FESTSTELLEN
147	local_host=$(hostname)
148
149
150
151	# HOSTSPEZIFISCHE VARIABLEN VEREINBAREN BZW. PRUEFEN, OB LOKALER HOST
152	# UEBERHAUPT ZULAESSIG IST
153	case $local_host in
154	(atmos) local_addres=172.20.25.35; local_host=lcide;;
155	(autan) local_addres=130.75.105.57; local_host=lcmuk;;
156	(bora) local_addres=130.75.105.103; local_host=lcmuk;;
157	(breg-en0\|berni-en0) local_addres=130.73.230.10; local_host=ibmb;;
158	(breva) local_addres=130.75.105.98; local_host=lcmuk;;
159	(compute-*.local) local_addres=172.20.4.2; local_host=lcfimm;;
160	(cs*) local_addres=136.172.44.131; local_host=nech;;
161	(elephanta) local_addres=130.75.105.6; local_host=lcmuk;;
162	(fimm.bccs.uib.no) local_addres=172.20.4.2; local_host=lcfimm;;
163	(gallego) local_addres=130.75.105.10; local_host=lcmuk;;
164	(gate\|n-sx) local_addres=133.5.178.11; local_host=neck;;
165	(gfdl5) local_addres=165.132.26.58; local_host=ibmy;;
166	(gfdl3.yonsei.ac.kr) local_addres=165.132.26.56; local_host=decalpha;;
167	(gregale) local_addres=130.75.105.109; local_host=lcmuk;;
168	(hababai) local_addres=130.75.105.108; local_host=lcmuk;;
169	(hreg-en0\|hanni-en0) local_addres=130.75.4.10; local_host=ibmh;;
170	(irifi) local_addres=130.75.105.104; local_host=lcmuk;;
171	(levanto) local_addres=130.75.105.45; local_host=lcmuk;;
172	(maestro) local_addres=130.75.105.2; local_host=lcmuk;;
173	(nobel*) local_addres=150.183.5.101; local_host=ibms;;
174	(orkan) local_addres=130.75.105.3; local_host=lcmuk;;
175	(ostria) local_addres=130.75.105.106; local_host=lcmuk;;
176	(quanero) local_addres=130.75.105.107; local_host=lcmuk;;
177	(scirocco) local_addres=172.20.25.41; local_host=lcmuk;;
178	(sun1\|sun2) local_addres=130.75.6.1; local_host=unics;;
179	(tgg*) local_addres=172.17.75.161; local_host=lctit;;
180	(vorias) local_addres=172.20.25.43; local_host=lcmuk;;
181	(*) printf "\n +++ \"$local_host\" unknown";
182	printf "\n please inform S. Raasch!";
183	locat=parameter; exit;;
184	esac
185
186
187
188	# REMOTE HOST DEFAULTMAESSIG = LOCAL HOST SETZEN
189	remote_host=$local_host
190
191
192
193
194	# PROZEDUROPTIONEN EINLESEN
195	while getopts :c:dDg:h:m:n:N:O:q:t:T:u:vX: option
196	do
197	case $option in
198	(c) job_catalog=$OPTARG;;
199	(d) delete_dayfile=true;;
200	(D) no_submit=true;;
201	(g) group_number=$OPTARG;;
202	(h) remote_host=$OPTARG;;
203	(m) memory=$OPTARG;;
204	(n) job_name=$OPTARG;;
205	(N) node_usage=$OPTARG;;
206	(O) threads_per_task=$OPTARG;;
207	(q) no_default_queue=$OPTARG;;
208	(t) cputime=$OPTARG;;
209	(T) tasks_per_node=$OPTARG;;
210	(u) remote_user=$OPTARG;;
211	(v) verify=false;;
212	(X) numprocs=$OPTARG;;
213	(\?) printf "\n +++ Option $OPTARG unknown \n";
214	locat=option; exit;;
215	esac
216	done
217
218
219	# JOBDATEINAMEN ALS NAECHSTES ARGUMENT HOLEN
220	shift OPTIND-1; file_to_send=$1
221
222
223	# KURZE AUFRUFBESCHREIBUNG WIRD HIER AUSGEGEBEN
224	if [ "$1" = "?" ]
225	then
226	(printf "\n *** subjob can be called as follows:\n"
227	printf "\n subjob -c.. -d -D -h.. -m.. -q.. -t.. -u.. -v <jobfile>\n"
228	printf "\n Description of available options:\n"
229	printf "\n Option Description Default-Value"
230	printf "\n -c job-input- and output-catalog ~/job_queue"
231	printf "\n -d no job-protocol will be created ---"
232	printf "\n -D only the job-file will be created ---"
233	printf "\n -h execution host, available hosts: $remote_host"
234	printf "\n ibm, ibmb, ibmh, ibms, ibmy, lcmuk,"
235	printf "\n lctit, nech, neck, unics"
236	printf "\n -m memory demand per process in MByte ---"
237	printf "\n -n jobname <jobdatei>"
238	printf "\n -O threads per task (for OpenMP usage) 1"
239	printf "\n -q job-queue to be used default"
240	printf "\n -t allowed cpu-time in seconds ---"
241	printf "\n -T tasks per node (on parallel hosts) ---"
242	printf "\n -u username on execution host from .netrc"
243	printf "\n -v no prompt for confirmation ---"
244	printf "\n -X # of processors (on parallel hosts) 1"
245	printf "\n "
246	printf "\n The only possible positional parameter is <jobfile>:"
247	printf "\n The complete NQS-job must be provided here."
248	printf "\n <jobfile>=? creates this outline\n\n") \| more
249	exit
250	fi
251
252
253
254	# PRUEFEN, OB JOBDATEI ANGEGEBEN WURDE UND OB SIE AUCH EXISTIERT
255	if [[ "$file_to_send" = "" ]]
256	then
257	printf "\n +++ job-file missing"
258	locat=parameter; exit
259	else
260	if [[ -f $file_to_send ]]
261	then
262	true
263	else
264	printf "\n +++ job-file: "
265	printf "\n $file_to_send"
266	printf "\n does not exist"
267	locat=parameter; exit
268	fi
269	fi
270
271
272
273	# FALLS KEIN JOBNAME ANGEGEBEN WURDE, WIRD JOBNAME = JOBDATEINAME
274	# GESETZT. VORAUSSETZUNG: JOBDATEINAME BEINHALTET KEINE PFADE
275	if [[ $job_name = none ]]
276	then
277	job_name=$file_to_send
278	fi
279	if [[ $(echo $job_name \| grep -c "/") != 0 ]]
280	then
281	printf "\n +++ job-file name: "
282	printf "\n $job_name"
283	printf "\n must not contain \"/\"-characters"
284	locat=parameter; exit
285	fi
286
287
288
289
290	# HOSTSPEZIFISCHE GROESSEN VEREINBAREN BZW. ABBRUCH BEI UNZULAESSIGEM HOST
291	# ODER WENN HOST NICHT ANGEGEBEN WURDE
292	if [[ $remote_host = none ]]
293	then
294	printf "\n +++ host missing"
295	locat=option; exit
296	else
297	case $remote_host in
298	(ibm) queue=p690_standard; remote_addres=134.76.99.81; submcom=/usr/lpp/LoadL/full/bin/llsubmit;;
299	(ibmb) queue=cpar; remote_addres=130.73.230.10; submcom=/usr/lpp/LoadL/full/bin/llsubmit;;
300	(ibmh) queue=cpar; remote_addres=130.75.4.10; submcom=/usr/lpp/LoadL/full/bin/llsubmit;;
301	(ibms) queue=p_normal; remote_addres=150.183.5.101; submcom=/usr/lpp/LoadL/full/bin/llsubmit;;
302	(ibmy) queue=parallel; remote_addres=165.132.26.58; submcom=/usr/lpp/LoadL/full/bin/llsubmit;;
303	(lcfimm) remote_addres=172.20.4.2; submcom=/opt/torque/bin/qsub;;
304	(lctit) queue=lctit; remote_addres=172.17.75.161; submcom=/n1ge/TITECH_GRID/tools/bin/n1ge;;
305	(nech) qsubmem=memsz_job; qsubtime=cputim_job; remote_addres=136.172.44.147; submcom="/usr/local/bin/qsub";;
306	(neck) qsubmem=memsz_job; qsubtime=cputim_job; remote_addres=133.5.178.11; submcom="/usr/bin/nqsII/qsub";;
307	(vpp) qsubmem=m; qsubtime=t; queue=vpp; remote_addres=130.75.4.130;;
308	(unics) qsubmem=d; qsubtime=t; queue=unics; remote_addres=130.75.6.1;;
309	(*) printf "\n +++ hostname \"$remote_host\" not allowed";
310	locat=parameter; exit;;
311	esac
312	fi
313
314
315	# EVTL. PRUEFEN, OB ANGEGEBENE QUEUE ZULAESSIG IST
316	if [[ $no_default_queue != none ]]
317	then
318	error=false
319	ndq=$no_default_queue
320	case $remote_host in
321	(ibm) case $ndq in
322	(p690_express\|p690_standard\|p690_long) error=false;;
323	(*) error=true;;
324	esac;;
325	(ibmb) case $ndq in
326	(cdata\|cdev\|cexp\|c1\|cshare\|csolo\|cspec) error=false;;
327	(*) error=true;;
328	esac;;
329	(ibmh) case $ndq in
330	(cdata\|cdev\|cexp\|channi\|cxxl\|c1\|cshare\|csolo\|csoloh3h\|csoloh6h\|csoloh12h\|csoloh1d\|csoloh2d\|cspec) error=false;;
331	(*) error=true;;
332	esac;;
333	(ibms) case $ndq in
334	(express\|normal\|p_express\|p_normal\|p_normal_1.3\|p_normal_1.7\|grand) error=false;;
335	(*) error=true;;
336	esac;;
337	(ibmy) case $ndq in
338	(parallel) error=false;;
339	(*) error=true;;
340	esac;;
341	(lctit) case $ndq in
342	(novice\|sla1\|sla2\|sla3\|RAM64GB\|RAM128GB) error=false;;
343	(*) error=true;;
344	esac;;
345	(t3eb) case $ndq in
346	(berte\|p50\|p100\|p392\|forfree\|p25himem) error=false;;
347	(*) error=true;;
348	esac;;
349	(t3eh) case $ndq in
350	(para_t3e\|em\|k\|l\|lm\|comp_t3e\|c\|p\|ht) error=false;;
351	(*) error=true;;
352	esac;;
353	(t3ej2\|t3ej5) case $ndq in
354	(low\|normal\|high) error=false;;
355	(*) error=true;;
356	esac;;
357	(t3es) case $ndq in
358	(batch\|serial-4\|pe4\|p48\|pe16\|pe32\|pe64\|pe128) error=false;;
359	(*) error=true;;
360	esac;;
361	(unics) case $ndq in
362	(unics\|ht) error=false;;
363	(*) error=true;;
364	esac;;
365	esac
366	if [[ $error = true ]]
367	then
368	printf "\n +++ queue \"$no_default_queue\" on host \"$remote_host\" not allowed"
369	locat=parameter; exit
370	else
371	queue=$no_default_queue
372	fi
373	fi
374
375
376
377	# KNOTENNUTZUNG IN ENTWICKLERQUEUE MUSS SHARED SEIN
378	if [[ $node_usage != shared && $queue = cdev ]]
379	then
380	node_usage=shared
381	fi
382
383
384
385	# PRUEFEN DER CPU-ZEIT, ZEIT NACH STUNDEN, MINUTEN UND SEKUNDEN
386	# AUFTEILEN
387	done=false
388	while [[ $done = false ]]
389	do
390	if (( $cputime <= 0 ))
391	then
392	printf "\n +++ wrong cpu-time or cpu-time missing"
393	printf "\n >>> Please type cpu-time in seconds as INTEGER:"
394	printf "\n >>> "
395	read cputime 1>/dev/null 2>&1
396	else
397	done=true
398	fi
399	done
400	if [[ $remote_host = nech ]]
401	then
402	if (( tasks_per_node != 0 ))
403	then
404	(( cputime = cputime * tasks_per_node ))
405	elif [[ $numprocs != 0 ]]
406	then
407	(( cputime = cputime * numprocs ))
408	fi
409	fi
410	(( stunden = cputime / 3600 ))
411	(( resttime = cputime - stunden * 3600 ))
412	(( minuten = resttime / 60 ))
413	(( sekunden = resttime - minuten * 60 ))
414	timestring=${stunden}:${minuten}:${sekunden}
415
416
417
418	# PRUEFEN DER KERNSPEICHERANFORDERUNG
419	done=false
420	while [[ $done = false ]]
421	do
422	if (( memory <= 0 ))
423	then
424	printf "\n +++ wrong memory demand or memory demand missing"
425	printf "\n >>> Please type memory in MByte per process as INTEGER:"
426	printf "\n >>> "
427	read memory 1>/dev/null 2>&1
428	else
429	done=true
430	fi
431	done
432
433	if [[ $remote_host = nech \|\| $remote_host = neck ]]
434	then
435	if (( tasks_per_node != 0 ))
436	then
437	(( Memory = memory * tasks_per_node / 1000 ))
438	elif [[ $numprocs != 0 ]]
439	then
440	(( Memory = memory * numprocs / 1000 ))
441	else
442	(( Memory = memory / 1000 ))
443	fi
444	fi
445
446
447	# SPEICHERBERECHNUNG BEI OPENMP-NUTZUNG
448	if [[ $(echo $remote_host \| cut -c1-3) = ibm ]]
449	then
450	(( memory = memory * threads_per_task ))
451	fi
452
453
454	# BERECHNUNG DER ANZAHL DER ZU VERWENDENDEN KNOTEN
455	if (( tasks_per_node != 0 ))
456	then
457	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
458	fi
459
460
461
462	# HEADER-AUSGABE
463	if [[ $verify = true ]]
464	then
465	printf "\n\n"
466	printf "#--------------------------------------------------------------# \n"
467	spalte1=SUBJOB;spalte2=$(date)
468	printf "\| $spalte1$spalte2 \| \n"
469	printf "\| \| \n"
470	printf "\| values of parameters/options: \| \n"
471	spalte1=local_host$punkte; spalte2=$punkte$local_host
472	printf "\| $spalte1$spalte2 \| \n"
473	spalte1=remote_host$punkte; spalte2=$punkte$remote_host
474	printf "\| $spalte1$spalte2 \| \n"
475	spalte1=queue$punkte; spalte2=$punkte$queue
476	printf "\| $spalte1$spalte2 \| \n"
477	spalte1=memory$punkte; spalte2="$punkte$memory mb"
478	printf "\| $spalte1$spalte2 \| \n"
479	spalte1=cputime$punkte; spalte2="$punkte$cputime sec"
480	printf "\| $spalte1$spalte2 \| \n"
481	spalte1=job_name$punkte; spalte2="$punkte$job_name"
482	printf "\| $spalte1$spalte2 \| \n"
483	printf "#--------------------------------------------------------------# \n\n"
484
485
486	# KONTROLLABFRAGE, OB ALLES O.K.
487	antwort="dummy"
488	while [[ $antwort != y && $antwort != Y && $antwort != n && $antwort != N ]]
489	do
490	read antwort?" >>> continue (y/n) ? "
491	done
492	if [[ $antwort = n \|\| $antwort = N ]]
493	then
494	locat=verify; exit
495	fi
496	printf "\n"
497	fi
498
499
500
501	# ZUFALLSKENNUNG GENERIEREN UND JOBNAMEN AUF ZIELRECHNER BESTIMMEN
502	kennung=$RANDOM
503	job_on_remhost=${job_name}_${kennung}_$local_host
504	job_to_send=job_to_send_$kennung
505	if [[ $delete_dayfile = false ]]
506	then
507	remote_dayfile=${local_host}_${job_name}_result_$kennung
508	local_dayfile=${remote_host}_${job_name}
509	else
510	remote_dayfile=/dev/null
511	if [[ $(echo $remote_host \| cut -c1-3) = ibm ]]
512	then
513	notification='# @ notification = never'
514	fi
515	fi
516
517
518
519	# QSUB- ODER LL-KOMMANDOS BZW. SKRIPTE GENERIEREN
520	if [[ $(echo $remote_host \| cut -c1-3) = ibm && $numprocs != 0 ]]
521	then
522
523	if [[ $remote_host = ibmy ]]
524	then
525	consumable_memory=""
526	else
527	consumable_memory="ConsumableMemory($memory mb)"
528	fi
529	if [[ $queue = cdev ]]
530	then
531	data_limit="# @ data_limit = 1.76gb"
532	network_to_use="# @ network.mpi = sn_all,shared,ip"
533	else
534	if [[ $remote_host = ibms ]]
535	then
536	network_to_use="# @ network.mpi = csss,shared,us"
537	elif [[ $remote_host = ibmy ]]
538	then
539	network_to_use=""
540	else
541	network_to_use="# @ network.mpi = sn_all,shared,us"
542	data_limit="# @ data_limit = 1.76gb"
543	fi
544	fi
545
546	cat > $job_to_send << %%END%%
547	#!/bin/ksh
548
549	# @ job_type = parallel
550	# @ job_name = palm
551	# @ wall_clock_limit = ${timestring},$timestring
552	# @ resources = ConsumableCpus($threads_per_task) $consumable_memory
553	# @ output = $remote_dayfile
554	# @ error = $remote_dayfile
555	# @ image_size = 50
556	# @ class = $queue
557	# @ environment = OMP_NUM_THREADS=$threads_per_task; MP_SHARED_MEMORY=yes
558	$network_to_use
559	$data_limit
560	$notification
561
562	%%END%%
563
564	if (( nodes > 0 ))
565	then
566
567	cat >> $job_to_send << %%END%%
568	# @ node = $nodes
569	# @ tasks_per_node = $tasks_per_node
570	# @ node_usage = $node_usage
571	# @ queue
572
573	%%END%%
574
575	else
576
577	if [[ $remote_host != ibmy ]]
578	then
579
580	cat >> $job_to_send << %%END%%
581	# @ blocking = unlimited
582	# @ total_tasks = $numprocs
583	# @ node_usage = $node_usage
584	# @ queue
585
586	%%END%%
587
588	else
589
590	cat >> $job_to_send << %%END%%
591	# @ node = 1
592	# @ total_tasks = $numprocs
593	# @ queue
594
595	%%END%%
596
597	fi
598
599	fi
600
601	elif [[ $(echo $remote_host \| cut -c1-3) = ibm && $numprocs = 0 ]]
602	then
603
604	cat > $job_to_send << %%END%%
605	#!/bin/ksh
606
607	# @ job_type = serial
608	# @ node_usage = $node_usage
609	# @ job_name = palm
610	# @ wall_clock_limit = ${timestring},$timestring
611	# @ resources = ConsumableCpus(1) ConsumableMemory(1 gb)
612	# @ output = $remote_dayfile
613	# @ error = $remote_dayfile
614	# @ class = $queue
615	$notification
616
617	# @ queue
618
619	%%END%%
620
621	elif [[ $remote_host = lcfimm ]]
622	then
623
624	if [[ $numprocs != 0 ]]
625	then
626	cat > $job_to_send << %%END%%
627	#!/bin/ksh
628	#PBS -N $job_name
629	#PBS -A nersc
630	#PBS -l walltime=$timestring
631	#PBS -l nodes=${nodes}:ppn=$tasks_per_node
632	#PBS -l pmem=${memory}mb
633	#PBS -m abe
634	#PBS -M igore@nersc.no
635	#PBS -o $remote_dayfile
636	#PBS -j oe
637	mpd &
638
639	%%END%%
640
641	else
642	cat > $job_to_send << %%END%%
643	#!/bin/ksh
644	#PBS -N $job_name
645	#PBS -A nersc
646	#PBS -l walltime=$timestring
647	#PBS -l ncpus=1
648	#PBS -l pmem=${memory}mb
649	#PBS -m abe
650	#PBS -M igore@nersc.no
651	#PBS -o $remote_dayfile
652	#PBS -j oe
653
654	%%END%%
655
656	fi
657
658	elif [[ $remote_host = nech ]]
659	then
660
661	if (( nodes > 1 ))
662	then
663	cat > $job_to_send << %%END%%
664	#!/bin/ksh
665	#PBS -l cpunum_prc=$tasks_per_node,cputim_job=$cputime
666	#PBS -l ${qsubmem}=${Memory}gb
667	#PBS -b $nodes
668	#PBS -o $remote_dayfile
669	#PBS -N palm
670	#PBS -j o
671	#PBS -T mpisx
672
673	%%END%%
674
675	elif [[ $numprocs != 0 ]]
676	then
677	cat > $job_to_send << %%END%%
678	#!/bin/ksh
679	#PBS -l cpunum_prc=$tasks_per_node,cputim_job=$cputime
680	#PBS -l ${qsubmem}=${Memory}gb
681	#PBS -o $remote_dayfile
682	#PBS -N palm
683	#PBS -j o
684
685	%%END%%
686
687	else
688	cat > $job_to_send << %%END%%
689	#!/bin/ksh
690	#PBS -l ${qsubmem}=${Memory}gb,${qsubtime}=$cputime
691	#PBS -o $remote_dayfile
692	#PBS -j o
693
694	%%END%%
695
696	fi
697
698	elif [[ $remote_host = neck ]]
699	then
700
701	if (( nodes > 1 ))
702	then
703	cat > $job_to_send << %%END%%
704	#!/bin/ksh
705	#PBS -l cpunum_prc=$tasks_per_node,cputim_job=$cputime
706	#PBS -l ${qsubmem}=${Memory}gb
707	#PBS -b $nodes
708	#PBS -o $remote_dayfile
709	#PBS -N palm
710	#PBS -j o
711	#PBS -T mpisx
712
713	%%END%%
714
715	elif [[ $numprocs != 0 ]]
716	then
717	cat > $job_to_send << %%END%%
718	#!/bin/ksh
719	#PBS -q ${queue}
720	#PBS -l cpunum_prc=$tasks_per_node,cputim_job=$cputime
721	#PBS -l ${qsubmem}=${Memory}gb
722	#PBS -o $remote_dayfile
723	#PBS -N palm
724	#PBS -j o
725	#PBS -T mpisx
726
727	%%END%%
728
729	else
730	cat > $job_to_send << %%END%%
731	#!/bin/ksh
732	#PBS -l ${qsubmem}=${Memory}gb,${qsubtime}=$cputime
733	#PBS -o $remote_dayfile
734	#PBS -j o
735
736	%%END%%
737
738	fi
739
740	elif [[ $remote_host = lctit ]]
741	then
742	cat > $job_to_send << %%END%%
743	#!/bin/bash
744	#$ -S /bin/bash
745	cd $job_catalog
746	export PATH=$PALM_BIN:\$PATH
747	echo \$PATH
748
749	%%END%%
750
751	# OPTIONEN FUER SUBMIT-KOMMANDO ZUSAMMENSTELLEN
752	# submcom="$submcom -N $job_name -sgeout $remote_dayfile -q default"
753	submcom="$submcom -g $group_number -N $job_name -rt 4320 -sgeout $remote_dayfile -q $node_usage "
754
755	else
756
757	cat > $job_to_send << %%END%%
758	# @\$-q ${queue}
759	# @\$-l${qsubtime} $timestring
760	# @\$-l${qsubmem} ${memory}mb
761	# @\$-o $remote_dayfile
762	# @\$-eo
763
764	%%END%%
765
766	fi
767
768
769	# BEI RECHNUNG AUF REMOTE-MASCHINEN RUECKTRANSFER DES DAYFILES PER TRAP
770	# BEI EXIT VERANLASSEN
771	# VEKTORRECHNER MUSS EIGENEN JOB STARTEN, DA DORT NOHUP NICHT FUNKTIONIERT
772	# AUF IBM IN SEOUL IST RUECKTRANSFER ZUR ZEIT GENERELL NICHT MOEGLICH
773	if [[ $delete_dayfile = false && $remote_host != $local_host ]]
774	then
775	echo "set +vx" >> $job_to_send
776	echo "trap '" >> $job_to_send
777	echo "set +vx" >> $job_to_send
778	if [[ $(echo $remote_host \| cut -c1-3) = ibm \|\| $(echo $remote_host \| cut -c1-3) = nec \|\| $remote_host = lctit ]]
779	then
780	if [[ $remote_host = ibmb \|\| $remote_host = ibmh ]]
781	then
782	return_queue=c1
783	elif [[ $remote_host = ibms ]]
784	then
785	return_queue=p_normal
786	elif [[ $remote_host = ibmy ]]
787	then
788	return_queue=serial
789	elif [[ $remote_host = lctit ]]
790	then
791	return_queue=sla3
792	elif [[ $remote_host = neck ]]
793	then
794	return_queue=S
795	else
796	return_queue=unknown
797	fi
798
799	if [[ $(echo $remote_host \| cut -c1-3) = ibm ]]
800	then
801
802	echo "echo \"#!/bin/ksh\" >> scpjob.$kennung" >> $job_to_send
803	echo "echo \"# @ job_type = serial\" >> scpjob.$kennung" >> $job_to_send
804	echo "echo \"# @ job_name = transfer\" >> scpjob.$kennung" >> $job_to_send
805	echo "echo \"# @ resources = ConsumableCpus(1) ConsumableMemory(1 gb)\" >> scpjob.$kennung" >> $job_to_send
806	echo "echo \"# @ wall_clock_limit = 00:10:00,00:10:00\" >> scpjob.$kennung " >> $job_to_send
807	echo "echo \"# @ output = job_queue/last_job_transfer_protocol\" >> scpjob.$kennung" >> $job_to_send
808	echo "echo \"# @ error = job_queue/last_job_transfer_protocol\" >> scpjob.$kennung" >> $job_to_send
809	echo "echo \"# @ class = $return_queue\" >> scpjob.$kennung" >> $job_to_send
810	echo "echo \"# @ image_size = 10\" >> scpjob.$kennung" >> $job_to_send
811	echo "echo \"# @ notification = never\" >> scpjob.$kennung" >> $job_to_send
812
813	echo "echo \"# @ queue\" >> scpjob.$kennung" >> $job_to_send
814	echo "echo \" \" >> scpjob.$kennung" >> $job_to_send
815
816	echo "echo \"set -x\" >> scpjob.$kennung" >> $job_to_send
817	echo "echo \"batch_scp -d -w 10 -u $local_user $local_addres ${job_catalog}/$remote_dayfile \\\"$job_catalog\\\" $local_dayfile\" >> scpjob.$kennung" >> $job_to_send
818	echo "echo \"exit\" >> scpjob.$kennung" >> $job_to_send
819
820	elif [[ $remote_host = nech ]]
821	then
822	echo "cd /pf/b/${remote_user}/job_queue" >> $job_to_send
823	echo "cat > scpjob.$kennung << %%END%%" >> $job_to_send
824	echo "#PBS -l ${qsubmem}=1GB,${qsubtime}=100" >> $job_to_send
825	echo "#PBS -o last_job_transfer_protocol" >> $job_to_send
826	echo "#PBS -j o" >> $job_to_send
827	echo " " >> $job_to_send
828	echo "set -x" >> $job_to_send
829	echo "cd /pf/b/${remote_user}/job_queue" >> $job_to_send
830	echo "batch_scp -d -w 10 -u $local_user $local_addres $remote_dayfile \"$job_catalog\" $local_dayfile" >> $job_to_send
831	echo "[[ \"\$for_subjob_to_do\" != \"\" ]] && eval \$for_subjob_to_do" >> $job_to_send
832	echo "%%END%%" >> $job_to_send
833
834	elif [[ $remote_host = neck ]]
835	then
836	echo "cat > scpjob.$kennung << %%END%%" >> $job_to_send
837	echo "#PBS -q $return_queue" >> $job_to_send
838	echo "#PBS -l ${qsubmem}=1GB,${qsubtime}=100" >> $job_to_send
839	echo "#PBS -o last_job_transfer_protocol" >> $job_to_send
840	echo "#PBS -j o" >> $job_to_send
841	echo " " >> $job_to_send
842	echo "set -x" >> $job_to_send
843	echo "batch_scp -d -w 10 -u $local_user $local_addres $remote_dayfile \"$job_catalog\" $local_dayfile" >> $job_to_send
844	echo "[[ \"\$for_subjob_to_do\" != \"\" ]] && eval \$for_subjob_to_do" >> $job_to_send
845	echo "%%END%%" >> $job_to_send
846
847	elif [[ $remote_host = lctit ]]
848	then
849	echo "cat > scpjob.$kennung << %%END%%" >> $job_to_send
850	echo "set -x" >> $job_to_send
851	echo "PATH=\$PATH:$job_catalog/../pub" >> $job_to_send
852	echo "cd $job_catalog" >> $job_to_send
853	echo "batch_scp -d -w 10 -u $local_user $local_addres $remote_dayfile \"$job_catalog\" $local_dayfile" >> $job_to_send
854	echo "[[ \"\$for_subjob_to_do\" != \"\" ]] && eval \$for_subjob_to_do" >> $job_to_send
855	echo "%%END%%" >> $job_to_send
856
857	else
858
859	echo "cat > scpjob.$kennung << %%END%%" >> $job_to_send
860	echo "# @\\\$-q $return_queue" >> $job_to_send
861	echo "# @\\\$-l${qsubtime} 10" >> $job_to_send
862	echo "# @\\\$-l${qsubmem} 10mb" >> $job_to_send
863	if [[ $remote_host = t3ej2 \|\| $remote_host = t3ej5 \|\| $remote_host = t3es ]]
864	then
865	echo "# @\$-l mpp_p=0" >> $job_to_send
866	fi
867	echo '# @\$-lF 10mb' >> $job_to_send
868	# echo '# @\$-o /dev/null' >> $job_to_send
869	echo '# @\$-o job_queue/last_job_transfer_protocol' >> $job_to_send
870	echo '# @\\\$-eo' >> $job_to_send
871	echo " " >> $job_to_send
872	if [[ $remote_host = t3ej2 \|\| $remote_host = t3ej5 ]]
873	then
874	echo "set +vx" >> $job_to_send
875	echo ". .profile" >> $job_to_send
876	fi
877	echo "set -x" >> $job_to_send
878	echo "batch_scp -d -w 10 -u $local_user $local_addres ${job_catalog}/$remote_dayfile \"$job_catalog\" $local_dayfile > /dev/null" >> $job_to_send
879	echo "[[ \"\$for_subjob_to_do\" != \"\" ]] && eval \$for_subjob_to_do" >> $job_to_send
880	echo "%%END%%" >> $job_to_send
881	fi
882
883	if [[ $(echo $remote_host \| cut -c1-3) = ibm ]]
884	then
885	echo "llsubmit scpjob.$kennung" >> $job_to_send
886	elif [[ $remote_host = lctit ]]
887	then
888	echo "chmod u+x scpjob.$kennung" >> $job_to_send
889	echo "rm -rf ${job_catalog}/last_job_transfer_protocol" >> $job_to_send
890	echo "n1ge -N jobtransfer -q $return_queue -sgeout ${job_catalog}/last_job_transfer_protocol scpjob.$kennung" >> $job_to_send
891	echo "sleep 10" >> $job_to_send
892	elif [[ $remote_host = t3eb \|\| $remote_host = t3eh \|\| $remote_host = t3ej2 \|\| $remote_host = t3ej5 ]]
893	then
894	echo "qsub -J n scpjob.$kennung" >> $job_to_send
895	elif [[ $remote_host = t3es ]]
896	then
897	echo "qsub -J n -s /bin/ksh scpjob.$kennung" >> $job_to_send
898	else
899	echo "qsub scpjob.$kennung" >> $job_to_send
900	fi
901	echo "rm scpjob.$kennung" >> $job_to_send
902	if [[ $remote_host = nech ]]
903	then
904	echo "cd -" >> $job_to_send
905	fi
906	else
907	# echo "ftpcopy -d $local_addres ${job_catalog}/$remote_dayfile \"$job_catalog\" $local_dayfile" >> $job_to_send
908	echo "nohup ftpcopy -d -w 15 $local_addres ${job_catalog}/$remote_dayfile \"$job_catalog\" $local_dayfile > /dev/null &" >> $job_to_send
909	fi
910	echo "set -x" >> $job_to_send
911	echo " ' exit" >> $job_to_send
912	echo "set -x" >> $job_to_send
913	fi
914
915
916
917	# EIGENTLICHE JOB-DATEI AN QSUB-KOMMANDOS ANHAENGEN
918	cat $file_to_send >> $job_to_send
919
920	if [[ $remote_host = ibm ]]
921	then
922	echo " " >> $job_to_send
923	echo "exit" >> $job_to_send
924	fi
925	if [[ $remote_host = lctit ]]
926	then
927	echo " " >> $job_to_send
928	echo "rm ~/job_queue/$job_on_remhost" >> $job_to_send
929	fi
930
931
932
933	# USER-NAME AUF ZIELRECHNER AUS .NETRC-DATEI ERMITTELN
934	if [[ -z $remote_user ]]
935	then
936	if [[ $remote_host = t3eb \|\| $remote_host = t3eh \|\| $remote_host = t3ej2 \|\| $remote_host = t3ej5 \|\| $remote_host = t3es \|\| $remote_host = vpp ]]
937	then
938	grep $remote_addres ~/.netrc \| read dum dum dum remote_user dum dum
939	fi
940	fi
941
942
943
944	# JOB AUF ZIELRECHNER TRANSFERIEREN BZW. INS JOBVERZEICHNIS KOPIEREN
945	if [[ $no_submit = false ]]
946	then
947	if [[ $remote_host != $local_host ]]
948	then
949	[[ $verify = true ]] && printf "\n >>> transfering job to \"$remote_host\"..."
950	if [[ $remote_host = ibms \|\| $remote_host = ibmy ]] # ssh on ibms cannot handle "~/"
951	then
952	job_catalog_save=$job_catalog
953	job_catalog=job_queue
954	elif [[ $remote_host = nech ]]
955	then
956	job_catalog_save=$job_catalog
957	job_catalog=/hpf/b/${remote_user}/job_queue
958	fi
959	if [[ $local_host = decalpha ]]
960	then
961	# VERWENDUNG VON SCP AUF DECALPHA FRAGT FEHLERHAFTERWEISE
962	# PASSWORT AB
963	/bin/scp $job_to_send ${remote_user}@${remote_addres}:${job_catalog}/$job_on_remhost
964	elif [[ $remote_host = nech ]]
965	then
966	# DATEIEN KOENNEN NUR UEBER DEN ARCHIVE-SERVER DES DKRZ
967	# TRANSFERIERT WERDEN
968	scp $job_to_send ${remote_user}@136.172.44.205:${job_catalog}/$job_on_remhost
969	else
970	scp $job_to_send ${remote_user}@${remote_addres}:${job_catalog}/$job_on_remhost
971	fi
972	if [[ $? = 1 ]]
973	then
974	locat=scp; exit
975	fi
976	if [[ $remote_host = ibms ]]
977	then
978	job_catalog=$job_catalog_save
979	fi
980	[[ $verify = true ]] && printf "\n >>> finished\n"
981	else
982	eval job_catalog=$job_catalog
983	cp $job_to_send ${job_catalog}/$job_on_remhost
984	fi
985
986
987
988	# NQS- BZW. LOADLEVELER-JOB STARTEN
989	if [[ $remote_host != $local_host ]]
990	then
991	[[ $verify = true ]] && printf "\n >>> submitting job using \"qsub\"...\n"
992	if [[ $remote_host != lctit ]]
993	then
994	ssh $remote_addres -l $remote_user "cd $job_catalog; $submcom $job_on_remhost; rm $job_on_remhost"
995	else
996	# TIT ERLAUBT NUR DIE AUSFÜHRUNG GANZ BESTIMMTER KOMMANDOS
997	# MIT SSH, DESHALB AUFRUF PER PIPE
998	# UEBERGANGSWEISE CHECK, OB N1GE ENVIRONMENT WIRKLICH VERFUEGBAR
999	print "cd $job_catalog; chmod u+x $job_on_remhost" \| ssh $remote_addres -l $remote_user > /dev/null 2>&1
1000	echo "first try" > send_protocol
1001	while [[ $(cat send_protocol \| grep -c "Forwarding to N1GE") = 0 ]]
1002	do
1003	if [[ $(cat send_protocol \| grep -c "first try") = 1 ]]
1004	then
1005	printf "\n trying to submit job to TIT cluster..."
1006	else
1007	printf "\n +++ failed ... trying to submit again ..."
1008	fi
1009	print "cd $job_catalog; $submcom $job_on_remhost" \| ssh $remote_addres -l $remote_user > send_protocol 2>&1
1010	cat send_protocol
1011	done
1012	sleep 10
1013	print "cd $job_catalog; rm $job_on_remhost" \| ssh $remote_addres -l $remote_user > /dev/null 2>&1
1014	echo "$submcom $job_on_remhost"
1015	rm send_protocol
1016	fi
1017
1018	[[ $verify = true ]] && printf " >>> o.k.\n"
1019	else
1020	cd $job_catalog
1021	if [[ $(echo $local_host \| cut -c1-3) = ibm ]]
1022	then
1023	eval $submcom $job_on_remhost
1024	elif [[ $local_host = lcfimm ]]
1025	then
1026	eval $submcom $job_on_remhost
1027	echo "$submcom $job_on_remhost"
1028	chmod u+x $job_on_remhost
1029	elif [[ $local_host = lctit ]]
1030	then
1031	eval $submcom $job_on_remhost
1032	echo "$submcom $job_on_remhost"
1033	chmod u+x $job_on_remhost
1034	elif [[ $local_host = nech ]]
1035	then
1036	if [[ $queue = default ]]
1037	then
1038	eval $submcom $job_on_remhost
1039	else
1040	eval $submcom -q $queue $job_on_remhost
1041	fi
1042	else
1043	qsub $job_on_remhost
1044	fi
1045	# JOBFILE DARF AUF LCTIT NICHT GELOESCHT WERDEN!! GESCHIEHT ERST AM JOBENDE
1046	[[ $local_host != lctit ]] && rm $job_on_remhost
1047	cd - > /dev/null
1048	fi
1049	fi
1050
1051
1052
1053	# ABSCHLUSSARBEITEN
1054
1055	if [[ $no_submit = false ]]
1056	then
1057	rm $job_to_send
1058	fi
1059	[[ $verify = true ]] && printf "\n\n *** SUBJOB finished \n\n"

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source: palm/trunk/SCRIPTS/subjob @ 131

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