YH-T-Template: Difference between revisions

From Research Computing Center Wiki
Jump to navigation Jump to search
No edit summary
No edit summary
Line 20: Line 20:


=== Running Program ===
=== Running Program ===
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 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 -->


To use this version, please first load the module with
To use this version, please loads the module with
<pre class="gscript">
<pre class="gscript">
ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> [options]
ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END -->
</pre>  
</pre>  


Here is an example of a shell script, sub.sh, to run on at the batch queue:  
Here is an example of a shell script, sub.sh, to run on at the batch queue:  
<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END -->
#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=<!-- NAME BEGIN -->trinity<!-- NAME END -->.%j.out
cd $SLURM_SUBMIT_DIR
ml <!-- TEST_COMMAND BEGIN --><!-- TEST_COMMAND END --> [options] 
</pre>
where [options] need to be replaced by the options (command and arguments) you want to use.  Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the job name need to be modified appropriately as well.


<div class="gscript2">
<div class="gscript2">
Line 66: Line 46:
</div>
</div>
In the real submission script, at least all the above underlined values need to be replaced by the proper values.   
In the real submission script, at least all the above underlined values need 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.


Here is an example of job submission command:
Here is an example of job submission command:

Revision as of 14:42, 7 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 loads the module with 

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

Here is an example of a shell script, sub.sh, to run on at 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

cd $SLURM_SUBMIT_DIR

ml [options]

In the real submission script, at least all the above underlined values need 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

<!-- TEST_COMMAND_HELP BEGIN --><!-- TEST_COMMAND_HELP END -->

Back to Top

Installation

Source code is obtained from Trinity

System

64-bit Linux

Retrieved from "https://wiki.gacrc.uga.edu/index.php?title=YH-T-Template&oldid=12769"