11-01-2015
Quote:
Originally Posted by
syg3434
I have tried the code that you suggest, but it also has the same problem.
However, when I am trying to run a single simulation, "qsub" works well.
If I want to run the "runAll.sh" file, I use a command which is "qsub runAll.sh".
I think if I utilize appropriate options for qsub command, it can help to solve the issue.
But, it is hard to guess which option is appropriate for the simulation.
Could you suggest any qsub options for submitting this sh file?
Thanks a lot!
It appears that you completely ignored:
Quote:
After you set and exported PATH to include the directory in which you have installed qsub, ...
in my last response. I can't suggest anything on how to use
qsub other than to try the code that you said is already working. I don't have
qsub installed on my machine, and the
qsub man page I found doesn't have the
-d directory option that you're using. But, there is clearly no way that adding options to
qsub is going to make any difference if
qsub can't be found in your
$PATH and you don't specify an absolute pathname to where you have installed
qsub on your system. All I can do is help you with the
bash shell syntax.
10 More Discussions You Might Find Interesting
1. UNIX for Dummies Questions & Answers
I have an ftp user, which has been setup to run ftp jobs to a specific machine (different jobs). for the first job i created .netrc in the ftp users home directory and added the appropriate commands
machine FTPBOX01 login user1 password xxx
macdef init
etc
etc
get file
bye
I use the... (3 Replies)
Discussion started by: hcclnoodles
3 Replies
2. UNIX for Advanced & Expert Users
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
I have a list of jobs. their expected start time and their expected duration.
my needs are
monitor multiple jobs (starting at different time and their execution time also differs)
Need to mail if any of the job running longer than its expected duration.
Whats the efficient way to scripting... (1 Reply)
Discussion started by: vikram3.r
1 Replies
4. Shell Programming and Scripting
Hello,
I would like to write a perl script which executes several jobs. The key thing is I only want 4 jobs to be executed at one time (that's because my machine as 4 cpu, and I want one job per cpu). Is there any way that I can get perl to co-operate with me in this?
Thanks! (1 Reply)
Discussion started by: amcrisan
1 Replies
5. UNIX for Advanced & Expert Users
Hello,
I have a perl script that takes in one file of input and outputs to a file. I would like to run this script on several input files, and I would like to run it with qsub, something like this:
Input files:
FileListDssp.txt.numaa
FileListDssp.txt.numab
FileListDssp.txt.numac
etc..
... (1 Reply)
Discussion started by: InfoSeeker
1 Replies
6. Shell Programming and Scripting
I have a sequence of tasks that I routinely run and I'm trying to parallelize certain portions of the sequence. Specifically, there are 3 tasks which all read from the same file, each performing different operations and writing to their own seperate file. I was wondering if I could execute these... (3 Replies)
Discussion started by: erichpowell
3 Replies
7. Shell Programming and Scripting
Hi,
I ran two crontab commands
using:
crontab program1
crontab program2
However when I type crontab -l only the second cron job shows up, how do I see all cron jobs running and how do I edit all at the same time
Thanks in Advance
S:D (10 Replies)
Discussion started by: walforum
10 Replies
8. Shell Programming and Scripting
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):
#!/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... (1 Reply)
Discussion started by: theawknewbie
1 Replies
9. Shell Programming and Scripting
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
10. UNIX for Beginners Questions & Answers
I have two scripts which I'm tying to run one after the other- this is what I've tried:
00 14 * * * /path/one.sh && /path/two.sh
I've also tried putting each script on a different line:
00 14 * * * /path/one.sh
00 14 * * * /path/two.sh
Can this be done? (1 Reply)
Discussion started by: $shell_Learner
1 Replies
LEARN ABOUT DEBIAN
qorder
qorder(1B) PBS qorder(1B)
NAME
qorder - exchange order of two pbs batch jobs in a queue.
SYNOPSIS
qorder job_identifier job_identifier
DESCRIPTION
To order two jobs is to exchange the jobs positions in the queue or queues in which the jobs resides. The two jobs must be located at the
same server. No attribute of the job, such as priority is changed. The impact of interchanging the order with the queue(s) is dependent
on local job scheduled policy, contact your systems administrator.
A job in the running state cannot be reordered.
OPERANDS
Both operands are job_identifiers which specify the jobs to be exchanged. The qorder command accepts two job_identifier operands of the
form:
sequence_number[.server_name][@server]
The server specification for the two jobs must agree as to the current location of the two job IDs.
STANDARD ERROR
The qorder command will write diagnostic messages to standard error for each error occurrence.
EXIT STATUS
Upon successful processing of all the operands presented to the qorder command, the exit status will be a value of zero.
If the qorder command fails to process any operand, the command exits with a value greater than zero.
SEE ALSO
qsub(1B), qmove(1B), pbs_orderjob(3B), pbs_movejob(3B)
Local qorder(1B)