Application name is a ... short description taken from project website.
Appname is available as a module on Apocrita. Optionally add some lines about modules if there are special use cases, e.g MPI
Optional section to cover MPI / OpenJDK vs Oracle versions. Not to be used to cover 2.7 -> 2.3 differences, except for things like python 2 / python 3 where major changes have been made and they are effectively separate.
Open JDK is a free and open source implementation of the Java Platform.
Oracle JDK is a free, closed source implementation of the Java Platform.
Using OpenMPI is supported but it is recommended to use IntelMPI.
IntelMPI is better apparently.
Useful and or essential parameters and settings for the application. To run the
latest installed version of appname, simply load the
module load appname
- If the usage page looks neat, add the appname -h output
- If it's ugly, but possible to provide a cleaned up version in < 5 lines, add the appname -h output
- If it's long, tell the user how to find the help documentation (man page, -h , --help) and maybe a typical example or syntax
then run one of the appname commands such as:
appname -wibble -i input.txt
Issues and bugs should be listed here in the usage section unless they affect an optional version e.g. OpenMPI, then they should be listed under that section, be careful to avoid any time sensitive text e.g. 'Will be fixed soon'. See examples:
Known Issue jobRunner
Failure to set
-jobRunner will result in a failed job that does not
request resources correctly.
Appname 2.7 Handling of bob
A bug affecting the handling of values of bob in version 2.7 means bobby drop no work. Further information is available in the bug report.
This issue is fixed in version 2.8 available as a module
module load bob/2.8
$SV_DIR is set by the modulefile allowing Genome STRiP to function correctly.
Here is an example job running on 4 cores:
#!/bin/bash #$ -cwd #$ -j y #$ -pe smp 4 #$ -l h_rt=4:0:0 #$ -l h_vmem=2G module load appname export VARS appname params
#!/bin/bash #$ -cwd #$ -j y #$ -pe parallel 64 #$ -l h_rt=4:0:0 #$ -l infiniband=nxv module load appname export VARS appname params
#!/bin/bash #$ -cwd #$ -j y #$ -pe smp 16 #$ -l h_rt=4:0:0 #$ -l h_vmem=7G #$ -l gpu=1 module load appname export VARS appname params
Installing packages / plugins / addons¶
Optional section on installing packages / plugins e.g. rubygems python venvs
Python modules can be managed via virtualenv...
module load python virtualenv bob source bob/bin/activate pip install requests
List of websites for project page, manuals, tutorials etc.
Template notes / usage¶
Remove this section
- Remove sections that are not required, no blank sections with N/As
- Check any images fit the page and don't distort the layout on desktop or mobile
- Don't just replicate the manual
- Explain how to use the tool on the cluster not the tool itself
- Check that all qsub scripts / commands ACTUALLY work
- Update the main apps page via the script
- If bash code is present, change no-highlight to bash in code blocks
- Change the examples to fit app.
- Follow the examples, don't add sge options that are not required.
- Use the full name of sge options not shortcuts e.g.
- Make sure to keep requests on at a usable size but not excessive as values may be copy pasted by users.
- Ensure that the job actually works.