193.2.4.4 ob 17:43, 3 februar 2009

2009-02-03T17:43:40Z

← Starejša redakcija		Redakcija: 17:43, 3 februar 2009
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	== Queuing system ==		== Queuing system ==

-	As an example let us write a program which calculates a product and a quotient of two numbers. We first create a directory ''test'' where the program will be located:	+	The queuing system supports two types of jobs: in a '''batch job''' there is no interaction between the user and the job while the job is running. If such an interaction is needed you should ask the queuing system for an '''interactive job'''.
		+
		+	=== Batch jobs ===
		+
		+	As an example let us write a program which waits for two minutes and then calculates a product and a quotient of two numbers. We first create a directory ''test'' where the program will be located:
	<code><font color=blue>rejec@atos:~> mkdir test</font>		<code><font color=blue>rejec@atos:~> mkdir test</font>
	<font color=blue>rejec@atos:~> cd test</font>		<font color=blue>rejec@atos:~> cd test</font>
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	print "a = $a\n";		print "a = $a\n";
	print "b = $b\n";		print "b = $b\n";
		+	print "Waiting for two minutes ...\n";
		+	sleep 120;
	print "a * b = ", $a * $b, "\n";		print "a * b = ", $a * $b, "\n";
	print "a / b = ", $a / $b, "\n";</code>		print "a / b = ", $a / $b, "\n";</code>
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	a = 2		a = 2
	b = 0		b = 0
		+	Waiting for two minutes ...
	a * b = 0		a * b = 0
	Illegal division by zero at ./programcek line 6.</code>		Illegal division by zero at ./programcek line 6.</code>
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	<code><font color=blue>rejec@atos:~/test> cat programcek.sh</font>		<code><font color=blue>rejec@atos:~/test> cat programcek.sh</font>
	#!/bin/bash		#!/bin/bash
		+	#PBS -l walltime=00:03:00
	cd test		cd test
	programcek 2 0</code>		programcek 2 0</code>
-	The shell script should first change the directory to the one where the program itself is located (''cd test''). Then it should run the program (''programcek 2 0'').	+	In the second line we inform the system that the job will run at most three minutes (''#PBS -l walltime=00:03:00''). If the job takes longer to complete it will be killed. If this line is missing in the shell script the default value of one minute will be used. The shell script should then change the directory to the one where the program itself is located (''cd test''). Then it should run the program (''programcek 2 0'').

	Now we are ready to put the program in the queue. This we can do with the ''qsub'' command:		Now we are ready to put the program in the queue. This we can do with the ''qsub'' command:
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	JOBNAME USERNAME STATE PROC WCLIMIT QUEUETIME		JOBNAME USERNAME STATE PROC WCLIMIT QUEUETIME

-	<font color=red>1849 rejec Idle 1 INFINITY Wed Apr 2 18:02:20</font>	+	<font color=red>1849 rejec Idle 1 00:03:00 Wed Apr 2 18:02:20</font>

	1 Idle Job		1 Idle Job
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	1826 vilfan Running 6 INFINITY Wed Apr 2 09:37:38		1826 vilfan Running 6 INFINITY Wed Apr 2 09:37:38
	1827 vilfan Running 4 INFINITY Wed Apr 2 13:32:32		1827 vilfan Running 4 INFINITY Wed Apr 2 13:32:32
-	<font color=red>1849 rejec Running 1 INFINITY Wed Apr 2 18:14:18</font>	+	<font color=red>1849 rejec Running 1 00:03:00 Wed Apr 2 18:14:18</font>

	9 Active Jobs 64 of 96 Processors Active (66.67%)		9 Active Jobs 64 of 96 Processors Active (66.67%)
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	Illegal division by zero at ./programcek line 6.</code>		Illegal division by zero at ./programcek line 6.</code>
	The output and the errors of the job were saved in the ''programcek.sh.o1849'' and ''programcek.sh.e1849'' files, respectively.		The output and the errors of the job were saved in the ''programcek.sh.o1849'' and ''programcek.sh.e1849'' files, respectively.
		+
		+	=== Interactive jobs ===
		+
		+	Use the following command to ask the queuing system for a two hour interacting job:
		+
		+	<code><font color=blue>rejec@atos:~/test/> qsub -l walltime=02:00:00 -I</font>
		+	qsub: waiting for job 12813.atos.ijs.si to start
		+	qsub: job 12813.atos.ijs.si ready
		+
		+	<font color=blue>rejec@n19:~/></font></code>
		+
		+	The system found a free processor on the n19 node and opened a shell there. The shell can be used to do whatever you wish for the next two hours.
		+
		+	=== Additional information ===

	You can find additional information in the [[Media:PBSProUG_5_4_0.pdf\|users manual]].		You can find additional information in the [[Media:PBSProUG_5_4_0.pdf\|users manual]].

193.2.4.4: New page: == Queuing system == As an example let us write a program which calculates a product and a quotient of two numbers. We first create a directory ''test'' where the program will be located:...

2008-07-08T12:45:06Z

New page: == Queuing system == As an example let us write a program which calculates a product and a quotient of two numbers. We first create a directory ''test'' where the program will be located:...

Nova stran

== Queuing system ==

As an example let us write a program which calculates a product and a quotient of two numbers. We first create a directory ''test'' where the program will be located:
<code>rejec@atos:~> mkdir test
rejec@atos:~> cd test
rejec@atos:~/test> </code>
Let's call the program ''programcek''. The code in perl is
<code>rejec@atos:~/test> cat programcek
#!/usr/bin/perl
my ($a, $b) = @ARGV;
print "a = $a\n";
print "b = $b\n";
print "a * b = ", $a * $b, "\n";
print "a / b = ", $a / $b, "\n";</code>
An example output:
<code>rejec@atos:~/test> programcek 2 0
a = 2
b = 0
a * b = 0
Illegal division by zero at ./programcek line 6.</code>
Now we'll run the program using the queuing system. First we need to write a shell script. Let's call it ''programcek.sh''.
<code>rejec@atos:~/test> cat programcek.sh
#!/bin/bash
cd test
programcek 2 0</code>
The shell script should first change the directory to the one where the program itself is located (''cd test''). Then it should run the program (''programcek 2 0'').

Now we are ready to put the program in the queue. This we can do with the ''qsub'' command:
<code>rejec@atos:~/test> qsub programcek.sh
1849.atos.ijs.si</code>
Note that an id number ''1849'' was assigned to the job. From this point on, you'll be able to check the status of job, stop it and access its results only through the id number. So don't forget it.

Let's check what is going on in the queue with the ''showq'' command:
<code>rejec@atos:~/test> showq
ACTIVE JOBS--------------------
JOBNAME USERNAME STATE PROC REMAINING STARTTIME

1732 vilfan Running 5 3:20:30:14 Tue Apr 1 10:32:35
1646 vilfan Running 12 INFINITY Thu Mar 27 17:09:44
1716 vilfan Running 6 INFINITY Mon Mar 31 17:52:49
1717 vilfan Running 6 INFINITY Mon Mar 31 18:01:39
1739 vilfan Running 12 INFINITY Tue Apr 1 13:36:11
1740 vilfan Running 12 INFINITY Tue Apr 1 14:14:54
1826 vilfan Running 6 INFINITY Wed Apr 2 09:37:38
1827 vilfan Running 4 INFINITY Wed Apr 2 13:32:32
1835 rejec Running 4 INFINITY Wed Apr 2 18:00:22
1836 rejec Running 10 INFINITY Wed Apr 2 18:00:35
1838 rejec Running 1 INFINITY Wed Apr 2 18:00:51
1839 rejec Running 10 INFINITY Wed Apr 2 18:00:57
1841 rejec Running 4 INFINITY Wed Apr 2 18:01:33
1845 rejec Running 1 INFINITY Wed Apr 2 18:01:54
1846 rejec Running 1 INFINITY Wed Apr 2 18:02:03
1847 rejec Running 1 INFINITY Wed Apr 2 18:02:14
1848 rejec Running 1 INFINITY Wed Apr 2 18:02:17

17 Active Jobs 96 of 96 Processors Active (100.00%)
24 of 24 Nodes Active (100.00%)

IDLE JOBS----------------------
JOBNAME USERNAME STATE PROC WCLIMIT QUEUETIME

1849 rejec Idle 1 INFINITY Wed Apr 2 18:02:20

1 Idle Job

BLOCKED JOBS----------------
JOBNAME USERNAME STATE PROC WCLIMIT QUEUETIME

Total Jobs: 18 Active Jobs: 17 Idle Jobs: 1 Blocked Jobs: 0</code>
We note that our job is listed under the ''IDLE JOBS''. This means that all the processors are currently occupied and our job has to wait until one of them is free before it can be run. Let's check again few hours later:
<code>rejec@atos:~/test> showq
ACTIVE JOBS--------------------
JOBNAME USERNAME STATE PROC REMAINING STARTTIME

1732 vilfan Running 5 3:20:18:17 Tue Apr 1 10:32:35
1646 vilfan Running 12 INFINITY Thu Mar 27 17:09:44
1716 vilfan Running 6 INFINITY Mon Mar 31 17:52:49
1717 vilfan Running 6 INFINITY Mon Mar 31 18:01:39
1739 vilfan Running 12 INFINITY Tue Apr 1 13:36:11
1740 vilfan Running 12 INFINITY Tue Apr 1 14:14:54
1826 vilfan Running 6 INFINITY Wed Apr 2 09:37:38
1827 vilfan Running 4 INFINITY Wed Apr 2 13:32:32
1849 rejec Running 1 INFINITY Wed Apr 2 18:14:18

9 Active Jobs 64 of 96 Processors Active (66.67%)
23 of 24 Nodes Active (95.83%)

IDLE JOBS----------------------
JOBNAME USERNAME STATE PROC WCLIMIT QUEUETIME

0 Idle Jobs

BLOCKED JOBS----------------
JOBNAME USERNAME STATE PROC WCLIMIT QUEUETIME

Total Jobs: 9 Active Jobs: 9 Idle Jobs: 0 Blocked Jobs: 0</code>
Now the program running: it is listed under the ''ACTIVE JOBS''. If in the meantime you've found out that there is a bug in your program, you should stop it to make the resources available to other users. You can do this with the ''qdel'' command:
<code>rejec@atos:~/test> qdel 1849</code>
Let's assume everything was OK with your program, and you'd waited until it stopped running. The results of the calculation are available in the directory where the job was started:
<code>rejec@atos:~/test> ls
programcek programcek.sh programcek.sh.e1849 programcek.sh.o1849

rejec@atos:~/test> cat programcek.sh.o1849
a = 2
b = 0
a * b = 0

rejec@atos:~/test> cat programcek.sh.e1849
Illegal division by zero at ./programcek line 6.</code>
The output and the errors of the job were saved in the ''programcek.sh.o1849'' and ''programcek.sh.e1849'' files, respectively.

You can find additional information in the [[Media:PBSProUG_5_4_0.pdf|users manual]].

Atos - Zgodovina strani

193.2.4.4 ob 17:43, 3 februar 2009

193.2.4.4: New page: == Queuing system == As an example let us write a program which calculates a product and a quotient of two numbers. We first create a directory ''test'' where the program will be located:...