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Update fub_curta.config and fub_curta.md #753

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merged 5 commits into from
Sep 25, 2024
Merged

Update fub_curta.config and fub_curta.md #753

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a58a045
Update fub_curta.config
wassimsalam01 Sep 23, 2024
5459528
Update fub_curta.config
wassimsalam01 Sep 23, 2024
c7e0409
Update fub_curta.md
wassimsalam01 Sep 23, 2024
e2017cd
Merge branch 'master' into master
jfy133 Sep 23, 2024
1f8785b
Update fub_curta.md
wassimsalam01 Sep 23, 2024
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20 changes: 10 additions & 10 deletions conf/fub_curta.config
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Original file line number Diff line number Diff line change
@@ -1,29 +1,29 @@
// Config profile metadata
params {
config_profile_contact = 'Wassim Salam (@wassimsalam01)'
config_profile_contact = 'Wassim Salam (@wassimsalam01)'
config_profile_contact_github = '@wassimsalam01'
config_profile_contact_email = 'TODO'
config_profile_name = 'FUB Curta'
config_profile_description = 'Freie Universität Berlin HPC (Curta) profile'
config_profile_url = 'https://www.fu-berlin.de/en/sites/high-performance-computing/index.html'
config_profile_contact_email = 'wassimsalam49@gmail.com'
config_profile_name = 'FUB Curta'
config_profile_description = 'Freie Universität Berlin HPC (Curta) profile'
config_profile_url = 'https://www.fu-berlin.de/en/sites/high-performance-computing/index.html'

max_cpus = 32
max_cpus = 32
max_memory = 772.GB
max_time = 14.d
max_time = 14.d
}

def membership = ['/bin/bash', '-c', 'groups'].execute().text.trim()

// Slurm configuration parameters
process {
executor = 'slurm'
maxRetries = 3
executor = 'slurm'
maxRetries = 3
clusterOptions = { (membership.startsWith("b") ? '--partition=begendiv,main ' : '--partition=main ') << ( task.time <= 3.h ? '--qos=hiprio' : ( task.time <= 3.d ? '--qos=prio' : '--qos=standard' ) ) }
}

// Singularity parameters
singularity {
enabled = true
enabled = true
autoMounts = true
}

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2 changes: 1 addition & 1 deletion docs/fub_curta.md
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Expand Up @@ -26,7 +26,7 @@ In addition, job submissions are assigned the appropriate quality of service (QO

Institute-specific pipeline profiles exists for:

- [methylseq](pipeline/methylseq/fub_curta.md)
- [methylseq](https://github.com/wassimsalam01/configs/blob/master/docs/pipeline/methylseq/fub_curta.md)
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This should point to the main repo, not your fork - is there any reason why you're keeping the docs on your fork?

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Hi James, sorry about that. Fixing this right away

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Done!


## debug profile

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