Migrate a few more entries from EU #103
Conversation
| toolshed.g2.bx.psu.edu/repos/ecology/srs_preprocess_s2/srs_preprocess_s2/.*: | ||
| mem: 16 | ||
| toolshed.g2.bx.psu.edu/repos/ecology/wildlife_megadetector_huggingface/wildlife_megadetector_huggingface/.*: | ||
| gpus: 1 |
There was a problem hiding this comment.
Is it ok to specify here GPUs?
There was a problem hiding this comment.
If it doesn't work without I would say yes
| mem: 12 | ||
| mem: 24 | ||
| env: | ||
| EGGNOG_DBMEM: --dbmem |
There was a problem hiding this comment.
I have a related question here. @cat-bro do you know if on AU all those envs are passed into the containers without any extra magic?
| cores: 4 | ||
| mem: 30 | ||
| scheduling: | ||
| require: |
There was a problem hiding this comment.
I can remove that. But what is the preferred way to indicate that this tool can/should run in Singularity?
| - singularity | ||
| rules: | ||
| - if: input_size >= 0.01 | ||
| gpus: 1 |
There was a problem hiding this comment.
flag GPU here, if we don't want this in a shared DB.
| - if: input_size >= 0.01 | ||
| gpus: 1 | ||
| params: | ||
| singularity_run_extra_arguments: ' --nv ' |
There was a problem hiding this comment.
this is enabling Singularity containers to setup the containers for GPU/Nvidia ...
There was a problem hiding this comment.
My initial thought would be: keep this but remove the scheduling tag for singularity and add a comment? But in general running things in singularity is the recommended approach, or not?
| mem: 8 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/.*: | ||
| cores: 2 | ||
| cores: 16 |
There was a problem hiding this comment.
We have way more cores on EU ... but the memory rule here is very sophisticated ... maybe both?
| toolshed.g2.bx.psu.edu/repos/iuc/nanopolishcomp_eventaligncollapse/nanopolishcomp_eventaligncollapse/.*: | ||
| cores: 10 | ||
| mem: 12 | ||
| toolshed.g2.bx.psu.edu/repos/iuc/ncbi_fcs_gx/ncbi_fcs_gx/.*: |
There was a problem hiding this comment.
This is a very expensive and inefficient tool for VGP - TODO look at ORGs rule.
| toolshed.g2.bx.psu.edu/repos/iuc/pureclip/pureclip/.*: | ||
| cores: 2 | ||
| mem: 32 | ||
| # 4GB is enough for most of the runs as it seems |
There was a problem hiding this comment.
I had this in my notes, so idea why we have here so much more memory :(
| cores: 12 | ||
| mem: 92 | ||
| - id: | ||
| if: input_size >= 1 |
There was a problem hiding this comment.
We are bailing out when we see large files and recommend Spades.
No description provided.