SJTU-HPC / bc_relion

Open OnDemand app for SJTU Pi

Batch Connect - SJTU Relion

A Batch Connect app designed for OSC OnDemand that launches Relion within an SJTU Pi batch job.

Prerequisites

This Batch Connect app requires the following software be installed on the compute nodes that the batch job is intended to run on (NOT the OnDemand node):

For VNC server support:

• TurboVNC 2.1+
• websockify 0.8.0+

For singularity:

• Singularity 3.5.3+

• An image similar to allupaku/relion

  (Remember to modify the path to the location of image in template/script.sh.erb to your own setting.)

For hardware rendering support:

• X server
• VirtualGL 2.3+

Other software:

• Lmod 6.0.1+ or any other module purge and module load <modules> based CLI used to load appropriate environments within the batch job
• Xfce Desktop 4+

Install

Use git to clone this app and checkout the desired branch/version you want to use:

scl enable git19 -- git clone <repo>
cd <dir>
scl enable git19 -- git checkout <tag/branch>

You will not need to do anything beyond this as all necessary assets are installed. You will also not need to restart this app as it isn't a Passenger app.

To update the app you would:

cd <dir>
scl enable git19 -- git fetch
scl enable git19 -- git checkout <tag/branch>

Again, you do not need to restart the app as it isn't a Passenger app.

Contributing

1. Fork it
2. Create your feature branch (git checkout -b my-new-feature)
3. Commit your changes (git commit -am 'Add some feature')
4. Push to the branch (git push origin my-new-feature)
5. Create a new Pull Request

License

• Code is licensed under MIT (see LICENSE)