On Tue, Jan 24, 2012 at 2:51 PM, mailing list <margeemail@gmail.com> wrote:

Hi guys,

So I'm trying to take a bioinformatics pipeline we currently run on
our own SGE cluster (which seems to have a lot of customizations ! I'm
finding out) and I want to run it on Amazon using CloudMan.

Glad to hear this! Please let me know how it goes in the end.

So I'm trying to figure out what the differences are. Here are my
questions so far:

We seem to have 8 slots per node. Do you guys know if the same is
true on CloudMan? I'm assuming more than one submitted qsub job can
run on one node at one time?

The number of slots per node depends on the type of instance used. CloudMan will configure an SGE instance to have as many slots as there are processing cores. So, for example, a large instance will have 2 slots, an extra large instance will have 4 slots. Each qsub job then gets submitted to one slot.

Also is there a way to reserve a certain amount of memory for a job
submitted via qsub, or alternatively to request that the job have
exclusive access to a node so it keeps all the memory available?

There are no preconfigured provisions for this in the SGE configuration provided by CloudMan. However, this is a vanilla SGE setup so it is entirely possible to manually setup the queues as you'd like and have it do the various resource reservations. SGE is installed under /opt/sge

Thanks,

Greg
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