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Update README.md with compute resources
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verku authored Nov 26, 2024
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20 changes: 8 additions & 12 deletions config/slurm/README.md
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Expand Up @@ -47,18 +47,14 @@ you start the pipeline on the command line with `--profile slurm`
`config.yaml` therein. Please make sure to add your slurm compute
project ID in line 13 of `slurm/config.yaml` (`slurm_account`).

> If any rule or group job fails due to too little memory or
run time, their compute resources can be updated in `slurm/config.yaml`.
Note that memory requirements are specified three times in the
configuration file: 1) under `set-threads` (used by Snakemake
to specify threads in rules), 2) under `set-resources` and therein
under `mem_mb`, specifying the memory in Megabytes (multiplying
the number of threads with the available memory per thread),
and 3) under `set-resources` and therein under `cpus-per-task`
(the same number as specified under `set-threads`, required for
correct memory assignment on Dardel). Any rule or group job that
is not listed under `set-threads` or `set-resources` uses the
resources specified under`default-resources`.
> If a rule or group job fails due to too little memory or run time,
their compute resources can be updated in `slurm/config.yaml`.
Rule or group jobs are using `default-resources` unless more threads
(corresponding to cpus-per-task) or longer run times are required,
which are specified per rule or group job under `set-threads` or
`set-resources`, respectively. Memory in MB is automatically calculated
from the number of threads specified under `default-resources` or
`set-threads`, respectively.

5) Start GenErode the following:

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