Difference between revisions of "YH-T-Template"
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=== Running Program === | === Running Program === | ||
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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 load the module with | |
<pre class="gscript"> | <pre class="gscript"> | ||
| − | #!/bin/bash | + | ml <!-- TEST_MODULE BEGIN --><!-- TEST_MODULE END --> |
| − | #SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END --> | + | </pre> |
| − | #SBATCH --partition=< | + | |
| − | + | Here is an example of a shell script, sub.sh, to run on the batch queue: | |
| − | #SBATCH --mail-user=username@uga.edu | + | |
| − | #SBATCH --ntasks=1 | + | <div class="gscript2"> |
| − | #SBATCH --mem=10gb | + | <nowiki>#</nowiki>!/bin/bash<br> |
| − | #SBATCH --time=08:00:00 | + | <nowiki>#</nowiki>SBATCH --job-name=j_<!-- NAME BEGIN -->trinity<!-- NAME END --><br> |
| − | #SBATCH --output=<!-- NAME BEGIN -->trinity<!-- NAME END -->.%j.out | + | <nowiki>#</nowiki>SBATCH --partition=batch<br> |
| − | + | <nowiki>#</nowiki>SBATCH --mail-type=ALL<br> | |
| − | cd $SLURM_SUBMIT_DIR | + | <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. | ||
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Here is an example of job submission command: | Here is an example of job submission command: | ||
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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 13:59, 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 -->
Installation
Source code is obtained from Trinity
System
64-bit Linux