I benchmarked MrBayes 3.1.2 program on my cluster for two cases:

1. use local /tmp for temporary files
2. use the network shared /home/galaxy/galaxy-dist/database/tmp

MrBayes is about 10 times slower for case 2 than for case 1.  What I did was
to set the network shared folder as the default but in the MrBayes wrapper,
I changed the environment variable TEMP to be a local folder.

Luobin

On Tue, Jul 26, 2011 at 10:39 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> On Tue, Jul 26, 2011 at 5:16 PM, Duddy, John <jdu...@illumina.com> wrote:
> > I can give you a very good example - if you are doing alignment and for
> some
> > reason need to convert the input file before operating on them, such that
> you
> > need a complete copy, /tmp may not have enough room. I have had this
> happen
> > to me running lots of instances of an aligner, temporarily using 100G+ of
> temp space.
> >
> > I don't see the need to have a "shared" temp space, but I do see the need
> to
> >  be able to tell the tools where you want them to put temp files.
>
> So in your setup, the cluster nodes are not likely to have 100G+ on /tmp
> (i.e.
> the local hard drive of the node), so you want them to use a temp folder on
> the
> cluster shared storage?
>
> I think needs will differ between tools - in some cases you really want
> a fast local drive for temp files, and putting them on a network drive
> will just kill performance. Using /tmp seems a safe default.
>
> Is there any guidance for tool authors on where to put temp files, and
> how to access any related Galaxy settings? There is nothing currently
> listed here: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
>
> Peter
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