[Beowulf] scratch File system for small cluster

Joe Landman 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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