Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Help submitting jobs to cluster
Top Forums Shell Programming and Scripting Help submitting jobs to cluster Post 302565074 by theawknewbie on Sunday 16th of October 2011 10:18:59 PM
Old 10-16-2011
Help submitting jobs to cluster
Hi

I am new to submitting jobs. I am trying to submit my perl file to the cluster.

This is what my shell file looks like (shell1.sh):

Code:
#!/bin/sh
#$ -S /bin/sh

cd data/projects/mydir/abbc
perl autocorro.pl

followed by qsub shell1.sh

It takes the qsub, but does nothing. I check qstat and see that I have a job running, but it's not doing anything. But: perl autocorro.pl works at the command line. just not in 'batch' form. Thanks

---------- Post updated at 10:06 PM ---------- Previous update was at 09:39 PM ----------

I've tried making shell script:
Code:
#
perl autocorro.pl

qstat just keeps running and running, even though using the command line 'perl autocorro.pl' takes 5 seconds.

---------- Post updated at 10:18 PM ---------- Previous update was at 10:06 PM ----------

Oh.

Argh, I was qeued. Shows what I get for rushing.
 

10 More Discussions You Might Find Interesting

1. Solaris

cron jobs on cluster?

I have Veritas N+1 cluster on Solaris 9 can I move my cron jobs on cluster? (2 Replies)
Discussion started by: sandeep_pan
2 Replies

2. UNIX for Advanced & Expert Users

Submitting jobs remotely...Experts help reqd

Is there any way I can submit a job to a remote machine and return immediately without withing for the job to finish? What I mean is this...using rsh I can submit a job to a remote machine like this: rsh remotemac1 job.sh But this doesn't return untill the job has finished and as a... (3 Replies)
Discussion started by: arijit
3 Replies

3. Shell Programming and Scripting

background jobs exit status and limit the number of jobs to run

i need to execute 5 jobs at a time in background and need to get the exit status of all the jobs i wrote small script below , i'm not sure this is right way to do it.any ideas please help. $cat run_job.ksh #!/usr/bin/ksh #################################### typeset -u SCHEMA_NAME=$1 ... (1 Reply)
Discussion started by: GrepMe
1 Replies

4. Shell Programming and Scripting

submitting data during a program run

I'm new to this and didn't know what my problem is called but here it is: A program called "prepdata" is run which asks the user to enter in a <input> file for the data to be taken from. However, it won't accept that input filename as an argument: $ prepdata <input> will NOT work ... (2 Replies)
Discussion started by: Rob W
2 Replies

5. HP-UX

Sendmail not submitting Email on '.'

I have several HP/UX nodes running Sendmail 8.13 ...some work fine, some don't. When an Email is coming in, the 'DATA' command never ends. The other side of the connection gets to the point where it enters the '.' on a line by itself, but sendmail doesn't accept it...if fact it keeps on holding... (8 Replies)
Discussion started by: john_exonets
8 Replies

6. Shell Programming and Scripting

waiting on jobs in bash, allowing limited parallel jobs at one time, and then for all to finish

Hello, I am running GNU bash, version 3.2.39(1)-release (x86_64-pc-linux-gnu). I have a specific question pertaining to waiting on jobs run in sub-shells, based on the max number of parallel processes I want to allow, and then wait... (1 Reply)
Discussion started by: srao
1 Replies

7. UNIX for Dummies Questions & Answers

problem submitting job to queue

Hi, I am trying to submit a job to a queue on a cluster. When I run the job ( python script) from the command line it runs without putting python at the start. The script imports everything from another congifuration file (.config) but when I submit to the queue it tells me there is no module... (0 Replies)
Discussion started by: i-dont-know
0 Replies

8. UNIX for Dummies Questions & Answers

Submitting awk script into cluster short.q

Hello, I want to submit my awk script into cluster queue as my job takes about forty minutes to finish so I can not run it on the main node. My awk script is like the following and I have three files. so, I write : qsub -q short.q Myscript.awk file1 file2 file3 It submits the work into... (1 Reply)
Discussion started by: Homa
1 Replies

9. UNIX for Advanced & Expert Users

Submitting multiple qsub jobs

Hi all, Today, I want to ask how to submit multiple qsub jobs. I want to submit 100 .sh files for the simulations. The name of files is run_001.sh, run_002.sh, run_003.sh, ..... ..... run_100.sh Submitting each file manually are time-consuming, hence, I want to make another .sh file... (11 Replies)
Discussion started by: syg3434
11 Replies

10. Shell Programming and Scripting

Shell script to run multiple jobs and it's dependent jobs

I have multiple jobs and each job dependent on other job. Each Job generates a log and If job completed successfully log file end's with JOB ENDED SUCCESSFULLY message and if it failed then it will end with JOB ENDED with FAILURE. I need an help how to start. Attaching the JOB dependency... (3 Replies)
Discussion started by: santoshkumarkal
3 Replies

LEARN ABOUT DEBIAN

condor_continue

condor_continue(1)					      General Commands Manual						condor_continue(1)

Name
       condor_continue continue - suspended jobs from the Condor queue

Synopsis
       condor_continue [-help -version]

       condor_continue[-debug]	[-pool	centralmanagerhostname[:portnumber]-name  scheddname][-addr "<a.b.c.d:port>"] cluster cluster.process user
       -constraint expression-all

Description
       condor_continuecontinues one or more suspended jobs from the Condor job queue. If the -nameoption is specified, the  named  condor_scheddis
       targeted for processing. Otherwise, the local condor_scheddis targeted. The job(s) to be continued are identified by one of the job identi-
       fiers, as described below. For any given job, only the owner of the job or one of the queue super users (defined by the	 QUEUE_SUPER_USERS
       macro) can continue the job.

Options
       -help

	  Display usage information

       -version

	  Display version information

       -pool centralmanagerhostname[:portnumber]

	  Specify a pool by giving the central manager's host name and an optional port number

       -name scheddname

	  Send the command to a machine identified by scheddname

       -addr <a.b.c.d:port>

	  Send the command to a machine located at "<a.b.c.d:port>"

       -debug

	  Causes debugging information to be sent to  stderr , based on the value of the configuration variable  TOOL_DEBUG

       cluster

	  Continue all jobs in the specified cluster

       cluster.process

	  Continue the specific job in the cluster

       user

	  Continue jobs belonging to specified user

       -constraint expression

	  Continue all jobs which match the job ClassAd expression constraint

       -all

	  Continue all the jobs in the queue

Exit Status
       condor_continuewill exit with a status value of 0 (zero) upon success, and it will exit with the value 1 (one) upon failure.

Examples
       To continue all jobs except for a specific user:

       % condor_continue  -constraint 'Owner =!= "foo"'

Author
       Condor Team, University of Wisconsin-Madison

Copyright
       Copyright  (C)  1990-2012  Condor  Team,  Computer  Sciences Department, University of Wisconsin-Madison, Madison, WI. All Rights Reserved.
       Licensed under the Apache License, Version 2.0.

       See the Condor Version 7.8.2 Manualor http://www.condorproject.org/licensefor additional notices. condor-admin@cs.wisc.edu

								  September 2012						condor_continue(1)
All times are GMT -4. The time now is 03:40 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy