[Bioclusters] recompiling redhat source rpms from .spec files to add large file support?

Joe Landman bioclusters@bioinformatics.org
08 May 2002 16:05:38 -0400

Hi Chris:

  Large file support comes from a variety of switches, and your memory
is almost correct...


  Also, I have found significant (negative) issues in dealing with large
files on non-XFS file systems.  On ext2/3 or reiserfs, these utilities
(even properly compiled) would fail with a File Too Large error (as seen
in strace).  Identical binaries work fine under XFS on the same machine.



ps: we opened up biodevelopers list (cc:ed for good measure) just for
these discussions :)


On Wed, 2002-05-08 at 15:43, Chris Dagdigian wrote:
> Hey folks,
> Hopefully this is a trivial question for someone on this list..
> Support for large files has been in modern kernels and filesystems for a 
> while now. What I constantly run into though are programs that bomb out 
> when faced with large files. Particularly when I'm trying to build large 
> blast databases :)
> I'm seeing this right now with RedHat 7.2 -- the /bin/zcat program will 
> dump core if you try to get it to process the latest nonredundant 'nt.Z' 
> database from the NCBI. 'uncompress' and '/bin/cat' work just fine.
> The easy solution is just to recompile the programs as you discover them 
> to enable large file support. I did this all the time back at the prior 
> job.
> My problem is that despite a quick google search and trawl through my 
> own notes I can't remember the specific compiler arguments that you need 
> to pass through make to enable largefile support on RH linux systems. It 
> was something really simple like "-D64_BIT_OFFSET -DENABLE_LARGE_FILES"
> Can anyone help jog my memory? I want to start collecting .spec files 
> for the various problematic utilities so I can roll my own RPMs whenever 
> I need them on a project.
> Thanks!
> -Chris
> -- 
> Chris Dagdigian, <dag@sonsorol.org>
> Independent life science IT & research computing consulting
> Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193
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Joseph Landman, Ph.D.
Senior Scientist,
MSC Software High Performance Computing
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