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assman_g
2024-06-12 15:57:42 +02:00
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BIO-applications.md

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[Relion PSI BIO hints](https://intranet.psi.ch/en/bio/computing-relion)
### Tips & Tricks
- can be loaded with module load relion
- go through the tutorial provided by relion
- default scripts requesting different types of hardware
- on the BIO page, recommendations for different Job Types are given
- make sure to provide "Extra Slurm Arguments" if you want to change parameters from the default scripts: (`--time`) for instance - think about your SLURM priority)
- 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
## Alphafold
[Alphafold repository](https://github.com/google-deepmind/alphafold)