[gmx-users] FAQ: File too big

[David]

On Wed, 2003-05-21 at 22:22, Oliver Beckstein wrote:
> Hi,
> 
> I wondered if anyone has finally found out to how fix the annoying
> 'File too big problem' (the latest post was
> http://www.gromacs.org/pipermail/gmx-users/2003-April/031896.html
> ). David suggests the workaround to access the file through nfs (which
> works for me) but it is not really the thing that I want to do with a
> few times 3+ GB of data.
> 
> Splitting the xtc is not a good solution as I need a continous time
> series (perhaps one could allow the analysis tools to read multiple
> xtc's which they concat internally?).
> 
> For the archive:
> 
> The problem manifests itself as the message 'File not found' when
> any of the analysis tools (including gmxcheck) refeuses to read a file
> which is clearly there (and can be manipulated with standard unix
> tools (cat, cp, split. hexdump, ...).
> 
> In detail:
> 
> ls -l big.xtc:
> -rw-r--r--    1 oliver oliver 2735936052 May 21 17:48 big.xtc
> 
> strace gmxcheck -f big.xtc:
> [...]
> open("big.xtc", O_RDONLY) = -1 EFBIG (File too large)

man open

       O_LARGEFILE
              On  32-bit  systems  that  support the Large Files System,
allow
              files whose sizes cannot be represented in 31 bits to be
opened.
 

Maybe we should try implementing this.
I don't know whether it is portable though.

> 
> 
> Howvere, I was under the impression that my kernel Linux
> 2.4.18-27.8.0smp (RedHat vanilla) has full large file support, and
> configure's output looks promising:
> 
> [...]
> checking for special C compiler options needed for large files... no
> checking for _FILE_OFFSET_BITS value needed for large files... 64
> checking for _LARGE_FILES value needed for large files... no
> checking for _LARGEFILE_SOURCE value needed for large files... 1
> [...]
> 
> Perhaps someone out there knows a simple solution?
> 
> Oli
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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