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Feature/slurm #6

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merged 13 commits into from Jul 30, 2013

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vals commented Jul 18, 2013

Here are the SLURM (<=2.5) launchers I worked on at the Codefest 2013.

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roryk Jul 19, 2013

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Great! This is awesome, I'm so glad you guys jumped on this grenade.

Sorry to rehash what we already talked about, but I am a slow thinker: I was wondering if you thought it might be possible to be able to be able to still use the num_jobs and cores_per_job fields rather than specifying the number of machines. For example I am thinking of a situation like this: you have a cluster of two nodes with 64 cores each and you want to run an IPython cluster with 4 engines and each engine be dedicated 12 cores because you are calling out to subprocess with a command that runs as a threaded application, and you want to give each call out 12 cores to work with. -N tells it to dedicate it on 2 separate nodes, which isn't exactly what we want since now we need to know about the machines in our cluster. Ideally, in our 2x64 core cluster above, if one node is empty it should run all 4 engines, each with 12 cores dedicated to it, on one node and fill it up. If each node is half full, it should run 2 engines on one node and 2 on the other. If one node is completely full and the other is half full it should stay pending.

Is there a way we can have SLURM handle that and figure out how many machines to put the job on? Ideally we shouldn't care about anything other than for each engine, it has 12 cores dedicated on the same node, that is all and not how many different nodes they are on. Does srun -n 4 --cpus-per-task=12 do that?

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roryk commented Jul 19, 2013

Great! This is awesome, I'm so glad you guys jumped on this grenade.

Sorry to rehash what we already talked about, but I am a slow thinker: I was wondering if you thought it might be possible to be able to be able to still use the num_jobs and cores_per_job fields rather than specifying the number of machines. For example I am thinking of a situation like this: you have a cluster of two nodes with 64 cores each and you want to run an IPython cluster with 4 engines and each engine be dedicated 12 cores because you are calling out to subprocess with a command that runs as a threaded application, and you want to give each call out 12 cores to work with. -N tells it to dedicate it on 2 separate nodes, which isn't exactly what we want since now we need to know about the machines in our cluster. Ideally, in our 2x64 core cluster above, if one node is empty it should run all 4 engines, each with 12 cores dedicated to it, on one node and fill it up. If each node is half full, it should run 2 engines on one node and 2 on the other. If one node is completely full and the other is half full it should stay pending.

Is there a way we can have SLURM handle that and figure out how many machines to put the job on? Ideally we shouldn't care about anything other than for each engine, it has 12 cores dedicated on the same node, that is all and not how many different nodes they are on. Does srun -n 4 --cpus-per-task=12 do that?

Merge pull request #1 from brainstorm/feature/SLURM
Integration with bcbio-nextgen pipeline parameter passing
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brainstorm Jul 25, 2013

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Hopefully we'll get an upgrade @UPPMAX to allow for jobarrays, that could get us closer to the requirements that @roryk points out without having to implement a jobarrays-like hack in ipython-cluster-helper ourselves.

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brainstorm commented Jul 25, 2013

Hopefully we'll get an upgrade @UPPMAX to allow for jobarrays, that could get us closer to the requirements that @roryk points out without having to implement a jobarrays-like hack in ipython-cluster-helper ourselves.

Roman Valls Guimera and others added some commits Jul 25, 2013

Merge pull request #2 from brainstorm/feature/SLURM
Fixup the example to work with resources (batch system native specs) and...

chapmanb added a commit that referenced this pull request Jul 30, 2013

@chapmanb chapmanb merged commit ed7a6f7 into roryk:master Jul 30, 2013

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chapmanb Jul 30, 2013

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@vals and @brainstorm -- thanks for all the work on this. Merged in and will be included with the next release of bcbio-nextgen coming soon. We'll also be testing slurm here locally soon so this is really appreciated.

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chapmanb commented Jul 30, 2013

@vals and @brainstorm -- thanks for all the work on this. Merged in and will be included with the next release of bcbio-nextgen coming soon. We'll also be testing slurm here locally soon so this is really appreciated.

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