CryoSparc Merlin scripts
This repository collects cryosparc 'lanes' suitable for running jobs at PSI.
Lanes
- merlin6. Default lane. 7 day time limit, uses all resources.
- merlin6-big. Requests exclusive node usage, with full memory. If GPUs are needed, requests 4 GPUs with 11GB of video memory
- merlin6-short. Short requests. 1 hour time limit.
Installing
This repo can be cloned using git on merlin. Typically this is done from your
cryosparc install directory (/data/user/<user>/cryosparc/), although this
isn't required.`
git clone https://git.psi.ch/lsm-hpce/merlin-cryosparc.git config
Next, all cluster_info.json scripts need to be modified to include the correct
worker path by replacing USERNAME. A script is provided to do this
automatically:
dev/install_filters.sh
Finally, connect the newly modified scripts to cryosparc. This should be done on same machine cryosparc runs on. To connect all lanes:
./connect_all.sh
Alternately, you can install individual lanes manually:
cd <lane>
cryosparcm cluster connect
Updating
Scripts are updated regularly with features and bug fixes. To get the newest version, update git:
git pull
Then, connect the lanes to your cryosparc cluster as in installation:
./connect_all.sh
Developers
If you plan on committing changes to this repository, make sure you run
dev/install_filters.sh to install git hooks and filters.
When releasing a new version, dev/mkrelease.sh will update version numbers
consistently.