diff --git a/BIO-applications.md b/BIO-applications.md index 6c25119..d9bf63c 100644 --- a/BIO-applications.md +++ b/BIO-applications.md @@ -12,8 +12,27 @@ - If you get OOM errors ( Out of memory error), this can be due to "general" memory and GPU card "memory" issues (the latter usually mentions "cuda" in the error). You can either increase the memory (--mem=XXX) or you can specifically go for the largest GPU card (merlin-g-015, A500 GPU card with 24GB memory) by using the option `--constraint=gpumem_24gb`. - Debugging: In case of errors, go to the folder and check your scripts, the error messages and log files! +## Cryosparc +[Cryosparc official documentation](https://cryosparc.com/docs) + +[Cryosparc PSI BIO hints](https://intranet.psi.ch/en/bio/computing-cryosparc) + + +### Tips & Tricks & Comments + +- follow the installation procedure very **carefully**, as it is unfortunately not available as module (will probably be a different setup on Merlin7) +- It is also possible to create another "user" from a running cryosparc instance, so not everybody needs to do the full installation +- choose the "project" folders wisely - **not** in your `home` or `/data/user/$USER` folders (not enough disk quota) +- the web interface can be run in your local browser if you are on the PSI network (VPN for instance) or with the nomachine browser +- Cryosparc has several **lanes** (kind of the same as the relion scripts) that have preconfigured SLURM parameters - change those if you want and add your personal lanes! (see BIO documentation) +- OOM errors: see relion +- Debugging the cryosparc instance itself: run `cryosparcm status` and check if everything is running properly or check the instance logs in the "Admin Section" + +![image](uploads/56e753e78c226b8cac6850eb6e16df59/image.png) + +- Debugging Jobs: check the Events Log file in the browser or export the Event Log, especially if you want to provide it to Admins: +drawing - **Use case:** ``` @@ -89,27 +108,6 @@ Increase memory as long as it is enough - limits depending on nodes... 2.) ![image](uploads/d6cb7dfe55369b019cef1b6d06f78132/image.png) -## Cryosparc -[Cryosparc official documentation](https://cryosparc.com/docs) - -[Cryosparc PSI BIO hints](https://intranet.psi.ch/en/bio/computing-cryosparc) - -### Tips & Tricks & Comments - -- follow the installation procedure very **carefully**, as it is unfortunately not available as module (will probably be a different setup on Merlin7) -- It is also possible to create another "user" from a running cryosparc instance, so not everybody needs to do the full installation -- choose the "project" folders wisely - **not** in your `home` or `/data/user/$USER` folders (not enough disk quota) -- the web interface can be run in your local browser if you are on the PSI network (VPN for instance) or with the nomachine browser -- Cryosparc has several **lanes** (kind of the same as the relion scripts) that have preconfigured SLURM parameters - change those if you want and add your personal lanes! (see BIO documentation) -- OOM errors: see relion -- Debugging the cryosparc instance itself: run `cryosparcm status` and check if everything is running properly or check the instance logs in the "Admin Section" - -![image](uploads/56e753e78c226b8cac6850eb6e16df59/image.png) - -- Debugging Jobs: check the Events Log file in the browser or export the Event Log, especially if you want to provide it to Admins: -drawing - - ## Alphafold