YH-T-Template: Difference between revisions

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=== Running Program ===
=== Running Program ===
Please refer to [[Running Jobs on Teaching]], [[Running_Jobs_on_Teaching#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_Teaching#Running_an_Interactive_Job | Run interactive Jobs]] for generic details about running jobs at Teaching.


The last version of this application is at <!-- APP_PATH BEGIN -->trinity<!-- APP_PATH END -->
The last version of this application is at <!-- APP_PATH BEGIN -->trinity<!-- APP_PATH END -->


Here is an example of a shell script, sub.sh, to run on at the batch queue:
To use this version, please load the module with
<pre class="gscript">
<pre class="gscript">
#PBS -S /bin/bash
ml <!-- TEST_MODULE BEGIN --><!-- TEST_MODULE END -->
#PBS -N j_<!-- NAME BEGIN -->trinity<!-- NAME END -->
</pre>
#PBS -q batch
 
#PBS -l nodes=1:ppn=1:AMD
Here is an example of a shell script, sub.sh, to run on the batch queue:
#PBS -l walltime=480:00:00
 
#PBS -l mem=10gb
<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash<br>
<nowiki>#</nowiki>SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END --><br>  
<nowiki>#</nowiki>SBATCH --partition=batch<br>       
<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>
<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u><br> 
<nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br> 
<nowiki>#</nowiki>SBATCH --mem=<u>10gb</u><br>   
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> 
<nowiki>#</nowiki>SBATCH --output=<!-- NAME BEGIN -->trinity<!-- NAME END -->.%j.out<br>
<nowiki>#</nowiki>SBATCH --error=<!-- NAME BEGIN -->trinity<!-- NAME END -->.%j.err<br>
cd $SLURM_SUBMIT_DIR<br>
ml <!-- TEST_MODULE BEGIN --><!-- TEST_MODULE END --><br>   
<!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> <u>[options]</u><br> 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. 
 
Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.


cd $PBS_O_WORKDIR
<!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> [options] 
</pre>


Here is an example of job submission command:
Here is an example of job submission command:
<pre  class="gcommand">
<pre  class="gcommand">
qsub  ./sub.sh  
sbatch ./sub.sh  
</pre>
</pre>


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<pre  class="gcommand">
<pre  class="gcommand">
<!-- TEST_COMMAND_HELP BEGIN --><!-- TEST_COMMAND_HELP END -->
ml <!-- TEST_MODULE BEGIN --><!-- TEST_MODULE END -->
<!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> <!-- TEST_COMMAND_HELP BEGIN --><!-- TEST_COMMAND_HELP END -->
</pre>
</pre>
[[#top|Back to Top]]
[[#top|Back to Top]]

Latest revision as of 12:59, 10 August 2018

Category

Bioinformatics

Program On

Teaching

Version

2.0.6

Author / Distributor

Trinity

Description

"" More details are at Trinity

Running Program

The last version of this application is at trinity

To use this version, please load the module with 

ml <!-- TEST_MODULE BEGIN --><!-- TEST_MODULE END -->

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_trinity
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=trinity.%j.out
#SBATCH --error=trinity.%j.err

cd $SLURM_SUBMIT_DIR
ml 

[options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.


Here is an example of job submission command: 

sbatch ./sub.sh

Documentation

ml <!-- TEST_MODULE BEGIN --><!-- TEST_MODULE END --> 
<!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> <!-- TEST_COMMAND_HELP BEGIN --><!-- TEST_COMMAND_HELP END -->

Back to Top

Installation

Source code is obtained from Trinity

System

64-bit Linux

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