QSUB(1) User Contributed Perl Documentation QSUB(1)NAME
qsub - submit a batch job in a familiar pbs format
SYNOPSIS
qsub [-a date_time]
[-A account_string]
[-b secs]
[-C directive_prefix]
[-e path]
[-I]
[-l resource_list]
[-m mail_options] [-M user_list]
[-N name]
[-o path]
[-p priority]
[-q destination]
[-W additional_attributes]
[-h]
[script]
DESCRIPTION
The qsub command displays information about nodes. It is aimed to be feature-compatible with PBS' qsub.
OPTIONS -a Display information for all nodes. This is the default if no node name is specified.
-I Interactive execution.
-j join
It is not necessary (currently also not possible) since stderr/stdout are always joined.
-v [variable_list]
Exporting single variables via -v is not supported, since the entire login environment is exported by the default.
-V The -V option to export the current environment is not required since it is done by default.
-? | --help
brief help message
--man
full documentation
perl v5.14.2 2012-04-10 QSUB(1)
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QSUB(1) User Contributed Perl Documentation QSUB(1)NAME
qsub - submit a batch job in a familiar pbs format
SYNOPSIS
qsub [-a date_time]
[-A account_string]
[-b secs]
[-C directive_prefix]
[-e path]
[-I]
[-l resource_list]
[-m mail_options] [-M user_list]
[-N name]
[-o path]
[-p priority]
[-q destination]
[-W additional_attributes]
[-h]
[script]
DESCRIPTION
The qsub command displays information about nodes. It is aimed to be feature-compatible with PBS' qsub.
OPTIONS -a Display information for all nodes. This is the default if no node name is specified.
-I Interactive execution.
-j join
It is not necessary (currently also not possible) since stderr/stdout are always joined.
-v [variable_list]
Exporting single variables via -v is not supported, since the entire login environment is exported by the default.
-V The -V option to export the current environment is not required since it is done by default.
-? | --help
brief help message
--man
full documentation
perl v5.14.2 2012-04-10 QSUB(1)
I am trying to run a Matlab function, file.m, with qsub. Here is a portion of my .sge file:
echo Starting to run Matlab
matlab -nojvm -nodesktop -r "file('${inputfile}');exit;"
echo finished running Matlab
The last two lines of the Matlab function are:
disp('finished');
exit
So my... (1 Reply)
So I have been submitting a lot of pbs jobs using the qsub command:
qsub -l nodes=1: ppn=1,walltime=4:00:00 run.csh
and everything works perfect except that I get the following error at the top of each output file:
Warning: no access to tty (Bad file descriptor).
Thus no job control in this... (0 Replies)
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)
Hey all,
I have a binary file, named "exe1" that receives a parameter. (I don't have its source code).
Executing "exe1" results in creating 3 output files.
I have a bash script that runs "exe1".
I want to enter "exe1" to cluster queue (using subq command)
But i want to do it more than... (1 Reply)
Dear All
I am trying to write a script to set the SGE job execution order. I named each job with 'job1', 'job2' and 'job3'. I want my script to do: When 'job1' execution is complete, 'job2' is executed; when both 'job1' and 'job2' are complete, 'job3' is executed.
First, I tried this... (0 Replies)
I was just wondering if it is permissible to qsub from a bash script as follows:
#! /bin/sh
echo "altering .txt in dir $DIR with retokenize.py"
for f in $DIR/txt/*.txt; do
echo $f;
/l2/nlp/i2b2/retokenize.py < $f > ${f//.txt/.tok};
done
echo "altering .tok in dir $DIR with awk... (0 Replies)
Hello,
I have some issue with qsub and the standard output : I launch a script that "echoes" the string "abc" and then executes a C program in which I print informations with the printf function ; the .o file contains "abc" but not the information displayed by printf. I also tried... (0 Replies)
Hello. Hopefully this is the right forum, did a search and found some similar questions here.
I'm trying to find out if there is a way to get the job id while submitting a job using qsub. I want to monitor the list of active jobs using qstat and when my jobid is no longer on the active list, I... (3 Replies)
Hello again,
I am runnning a job on a cluster and I submit a job with the command
qsub script.sh
where script.sh is a script with the command i want o use. When i enter this command the cluster gives a huber like 123456 as the JOB ID.
I want the job to run about 12 hours and when it... (5 Replies)
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)
Hi All,
I was going through some makefiles where I saw occurrences of explib_subdirs and expinc_subdirs, which I could not understand.
Exporting libs to subdirs ? Exporting include files to specified subdirs ? When do we need to do that ?
What I could understand is, for a build, I would... (4 Replies)
Edit - I don't know how to delete posts. The question I asked here ended up not being the question I should have asked as I didn't realise I needed to edit my script to comply with SGE.
Hi,
My script is:
#!/bin/bash
# Perform fastqc on files in a specified directory.
for ((j=1;... (8 Replies)
Linux Server
Hi!
just some help...
I'm using a "Sun Grid Engine" with "qsub"
In one hand I have this code
while read -r H; do echo ${H}; done < list
The number of the lines in the list file is 100.
On the other hand I want to create a job array with the option -t
echo... (3 Replies)
Hello,
I'm working on a SGE cluster and trying to echo the variables passed to the qsub command.
My script is as follows
#!/bin/bash
#$ -V
#$ -cwd
#$ -pe make 10
if ; then
echo "Variable is not set"
else
echo "Variable says: $StatedUserName"
fi
and I run the... (1 Reply)