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docs: improved documentation #8

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Mar 25, 2024
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docs: improved documentation #8

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08a8029
Updated README and further documentation
jannisspeer Mar 21, 2024
dbb5b89
Merge branch 'main' into docs/documentation
jannisspeer Mar 25, 2024
62dee41
Edited Further documentation section
jannisspeer Mar 25, 2024
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1 change: 1 addition & 0 deletions README.md
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# Snakemake executor plugin: HTCondor

A Snakemake executor plugin for submitting jobs with HTCondor.
The documentation can be found in the [Snakemake plugin catalog](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/htcondor.html).
24 changes: 20 additions & 4 deletions docs/further.md
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It is recommended to use the dedicated snakemake profile for HTCondor, which you can find [here](https://github.com/Snakemake-Profiles/htcondor).
This plugin currently only supports job submission with a shared file system.
As executable the jobs use `bin/bash`.
As default the jobs will be executed with the same set of environment variables that the user had at submit time. If you don't want this behavior set the following in resources `getenv: False`.
- It is recommended to use the dedicated snakemake profile for HTCondor, which you can find [here](https://github.com/Snakemake-Profiles/htcondor).
- This plugin currently only supports job submission with a shared file system.
- The jobs use the python binary of the environment that the user had when starting snakemake as the executable.
- Error messages, the output of stdout and log files are written to `htcondor-jobdir` (see in the usage section above).
- The job directive `threads` is used to set `request_cpu` command for HTCondor.
- As default, the jobs will be executed with the same set of environment variables that the user had at submit time.
If you don't want this behavior, set the following in resources `getenv: False`.
- For the job status, this plugin reports the values of the [job ClassAd Attribute](https://htcondor.readthedocs.io/en/latest/classad-attributes/job-classad-attributes.html) `JobStatus`.
- To determine whether a job was successful, this plugin relies on `htcondor.Schedd.history` (see [API reference](https://htcondor.readthedocs.io/en/latest/apis/python-bindings/api/htcondor.html)) and checks the values of the [job ClassAd Attribute](https://htcondor.readthedocs.io/en/latest/classad-attributes/job-classad-attributes.html) `ExitCode`.


The following [submit description file commands](https://htcondor.readthedocs.io/en/latest/man-pages/condor_submit.html) are supported (add them as user-defined resources):
| Basic | Matchmaking | Matchmaking (GPU) | Policy |
| ----------------- | ---------------- | ------------------------- | -------------------------- |
| `getenv` | `rank` | `request_gpus` | `max_retries` |
| `environment` | `request_disk` | `require_gpus` | `allowed_execute_duration` |
| `input` | `request_memory` | `gpus_minimum_capability` | `allowed_job_duration` |
| `max_materialize` | `requirements` | `gpus_minimum_memory` | `retry_until` |
| `max_idle` | | `gpus_minimum_runtime` | |
| | | `cuda_version` | |
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