Acceleration Card Optimization

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Acceleration Card Optimization

panza1370
Hello All,

I recently was gifted an ioFusion ioFX acceleration card to help speed
my bioinformatics work along and I am wondering how best to integrate it
into my instance to make Galaxy more efficient. Is it sufficient to
merely ensure that the datasets being operated on are on the flash
storage (I guess by placing the main Galaxy directory there) or are
there other elements that should also move lest they create bottlenecks
elsewhere (tmp directory,  files related to proxy/ftp server, tool shed,
etc.)? Suggestions will be greatly appreciated.

Thanks,
Adam


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Re: Acceleration Card Optimization

Nate Coraor (nate@bx.psu.edu)
Hi Adam,

This is going to depend entirely on the tools you're using. I'd suggest running your typical workload and examining the I/O patterns to determine what makes the most sense. I'd think the temp directory, input dataset, and output dataset filesystems to be the most utilized.

--nate


On Fri, Feb 14, 2014 at 12:31 PM, Panzer, Adam <[hidden email]> wrote:
Hello All,

I recently was gifted an ioFusion ioFX acceleration card to help speed
my bioinformatics work along and I am wondering how best to integrate it
into my instance to make Galaxy more efficient. Is it sufficient to
merely ensure that the datasets being operated on are on the flash
storage (I guess by placing the main Galaxy directory there) or are
there other elements that should also move lest they create bottlenecks
elsewhere (tmp directory,  files related to proxy/ftp server, tool shed,
etc.)? Suggestions will be greatly appreciated.

Thanks,
Adam


The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/