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glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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PBS/Torque support #71

Open xingwu2 opened 7 years ago

xingwu2 commented 7 years ago

Hi,

I am using a PBS/Torque cluster. I wonder do you have a modified release that supports the PBS/Torque or Slurm cluster?

Best

Xing Wu

joelarmstrong commented 7 years ago

Hi,

Sorry for not replying sooner. There isn't any support for Torque by default. There was some work done in getting jobTree (our scheduling abstraction) to support Torque, but I wasn't involved in that and can't say whether it actually worked. I think it been left unfinished, or had bugs, because it never was merged into jobTree.

I notice there is a "torque" branch of jobTree -- https://github.com/benedictpaten/jobTree/tree/torque -- maybe changing to the submodules/jobTree directory and checking out the torque branch will provide (experimental) support? I wouldn't hold out much hope of that working, though.

glennhickey commented 7 years ago

Torque never panned out because it didn't handle the loads of tiny jobs JobTree spawns well enough. It would take hours just to run small examples. We talked about adding some kind of job batching support to get around this but I don't think it got too far.

On Tue, Jan 3, 2017 at 7:56 PM, Joel Armstrong notifications@github.com wrote:

Hi,

Sorry for not replying sooner. There isn't any support for Torque by default. There was some work done in getting jobTree (our scheduling abstraction) to support Torque, but I wasn't involved in that and can't say whether it actually worked. I think it been left unfinished, or had bugs, because it never was merged into jobTree.

I notice there is a "torque" branch of jobTree -- https://github.com/ benedictpaten/jobTree/tree/torque -- maybe changing to the submodules/jobTree directory and checking out the torque branch will provide (experimental) support? I wouldn't hold out much hope of that working, though.

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ljyanesm commented 7 years ago

I've been working on a SLURM option for jobTree based on the torque branch.

You can have a look here: https://github.com/ljyanesm/jobTree

It's WIP also, we need to specify the queue on our systems and there is no configuration for that atm so it's hardcoded.

rlim19 commented 7 years ago

Hi @ljyanesm , I'm interested in using the progressiveCactus on SLURM, I was wondering if you could provide a guidance, please.

Thanks in advance. I look forward to hearing from you.

ljyanesm commented 7 years ago

Hi,

Have a look at the following commit: https://github.com/ljyanesm/jobTree/commit/6aa62436b59ad3759110286995644b613da484c1

There you can find the modifications we had to do in order to use SLURM at EI. You still need to be aware that the configuration files have to express the memory requirement values in MB instead of bytes as the original ones do.

The other bit you should be mindful of is the partition (-p) if your site doesn't have a long enough "default" partition you can set it when submitting the jobs as is done on batchSystems/drmaaSlurm.py