[Beowulf] scratch File system for small cluster
landman at scalableinformatics.com
Thu Sep 25 11:08:23 PDT 2008
Greg Lindahl wrote:
> On Thu, Sep 25, 2008 at 10:19:26AM -0400, Joe Landman wrote:
>> BLAST uses mmap'ed IO. This has some interesting ... interactions ...
>> with parallel file systems.
> The PathScale compilers use mmap on their temporary files. This led to
> some interesting bugs being reported... fortunately, we were able to
> pinpoint the parallel filesystems as being the guilty parties without
> too much work.
It looks like people use mmap files to explicitly avoid seeks,
replacing semantics of file IO with memory access semantics. We have a
customer who uses mmap for some large files (multiple GB). Sadly, mmap
on linux uses the paging mechanism which is pretty much stuck at 4kB
pages for most distributions. I think the SiCortex folks and a few
others are working with 64 kB page kernels.
I am sure there are good reasons for using mmap. I just don't know
what they are, and in what contexts. I would rather have
direct/explicit control over the IO if possible.
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web : http://www.scalableinformatics.com
phone: +1 734 786 8423 x121
fax : +1 866 888 3112
cell : +1 734 612 4615
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