CLS-IT/bio_tutorial_docu
0
0
Wiki

Update BIO applications

assman_g
2024-06-24 08:44:59 +02:00
parent 7404f023f8
commit df0b1c70b1
1 changed files with 20 additions and 22 deletions
Download Patch File Download Diff File Expand all files Collapse all files
BIO-applications.md
+20 -22
@@ -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/$USER` folders (not enough disk quota)
- the web interface can be run in your local browser if you are on the PSI network (VPN for instance) or with the nomachine browser
- Cryosparc has several **lanes** (kind of the same as the relion scripts) that have preconfigured SLURM parameters - change those if you want and add your personal lanes! (see BIO documentation)
- OOM errors: see relion
- Debugging the cryosparc instance itself: run `cryosparcm status` and check if everything is running properly or check the instance logs in the "Admin Section"
![image](uploads/56e753e78c226b8cac6850eb6e16df59/image.png)
- Debugging Jobs: check the Events Log file in the browser or export the Event Log, especially if you want to provide it to Admins:
<img src="uploads/e139c07804105107dd34d92f82028f9f/image.png" alt="drawing" width="300"/>
**Use case:**
```
@@ -89,27 +108,6 @@ Increase memory as long as it is enough - limits depending on nodes...
2.)
![image](uploads/d6cb7dfe55369b019cef1b6d06f78132/image.png)
## Cryosparc
[Cryosparc official documentation](https://cryosparc.com/docs)
[Cryosparc PSI BIO hints](https://intranet.psi.ch/en/bio/computing-cryosparc)
### Tips & Tricks & Comments
- follow the installation procedure very **carefully**, as it is unfortunately not available as module (will probably be a different setup on Merlin7)
- It is also possible to create another "user" from a running cryosparc instance, so not everybody needs to do the full installation
- choose the "project" folders wisely - **not** in your `home` or `/data/user/$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:
<img src="uploads/e139c07804105107dd34d92f82028f9f/image.png" alt="drawing" width="300"/>
## Alphafold