Hi Jeremy, Enis,
That makes sense. I know I can configure how many threads BWA uses in
its wrapper, with bwa -t. But, is there somewhere that I need to tell
Galaxy the corresponding information, ie that this command-line task
will make use of up to 4 cores?
Or, does this imply that there is always exactly one job per node? So
if I have (for instance) a cluster made of 4-core nodes, and a
single-threaded task (e.g. samtools), are the other 3 cores just going
to waste or will the scheduler allocate multiple single-threaded jobs
to one node?
I've cc'd galaxy-dev instead of galaxy-user as I think the
conversation has gone that way!
On Fri, Nov 18, 2011 at 2:36 PM, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:
>> On Fri, Nov 18, 2011 at 12:56 AM, Jeremy Goecks <jeremy.goe...@emory.edu>
>>> Scalability issues are more likely to arise on the back end than the front
>>> end, so you'll want to ensure that you have enough compute nodes. BWA uses
>>> four nodes by default--Enis, does the cloud config change this
>>> parameter?--so you'll want 4x50 or 200 total nodes if you want everyone to
>>> be able to run a BWA job simultaneously.
>> Actually, one other question - this paragraph makes me realise that I
>> don't really understand how Galaxy is distributing jobs. I had thought
>> that each job would only use one node, and in some cases take
>> advantage of multiple cores within that node. I'm taking a "node" to
>> be a set of cores with their own shared memory, so in this case a VM
>> instance, is this right? If some types of jobs can be distributed over
>> multiple nodes, can I configure, in Galaxy, how many nodes they should
> You're right -- my word choices were poor. Replace 'node' with 'core' in my
> paragraph to get an accurate suggestion for resources.
> Galaxy uses a job scheduler--SGE on the cloud--to distribute jobs to
> different cluster nodes. Jobs that require multiple cores typically run on a
> single node. Enis can chime in on whether CloudMan supports job submission
> over multiple nodes; this would require setup of an appropriate parallel
> environment and a tool that can make use of this environment.
> Good luck,
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