[MINC-development] me, I'm stumped

[Jason Lerch]

Ok, this is even more messed up than I first expected:

this works:

rawtominc -byte -clobber -input /dev/null /tmp/junk.mnc 470 2400 2800

this does not:

rawtominc -byte -clobber -input /dev/null /data/rome/temp/jason/test.mnc
470 2400 2800

So ... on a local filesystem everything appears to be OK (I have not yet
waited long enough to check whether the file actually holds sensible
values when I do this with real data - it is running now, but will take
a while), but over NFS it fails at 2GB. I'm running the commands on
yorick.

So I've cc-ed this to the trinity (are any of you on this list) - any
ideas why?

Jason

On Thu, 2003-05-01 at 10:03, Jason Lerch wrote:
> Hello again,
> 
> there is no documentation that I could find about IRIX and large files,
> so I tried John's solution. Turns out you also have to add the NDEBUG
> symbol. Nevertheless, it still crashes at the same place with the same
> error, so no luck here. 
> 
> I guess it is time to start searching for bugs in the minc library
> source code ...
> 
> Jason
> 
> On Wed, 2003-04-30 at 17:37, John G. Sled wrote:
> > Hi Jason,
> > 
> > Under 32-bit linux I was able to get commands such as the following to 
> > work 
> > 
> > rawtominc -short /tmp/junk.mnc 2048 1024 1024 < /dev/zero
> > 
> > Under linux I had to build minc and netcdf with the options
> > 
> >  -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
> > 
> > Is there something similar for IRIX?
> > 
> > John
> > 
> > On Wed, Apr 30, 2003 at 04:23:05PM -0400, Jason Lerch wrote:
> > > Hi all,
> > > 
> > > OK, I'm officially stumped:
> > > 
> > > I'm trying to create a large minc file with the following dimensions:
> > > 470*2800*2400
> > > 
> > > The source is 470 images, each with the dimensions of 2800*2400. So,
> > > naturally, I'm using a 64-bit compiled version of rawtominc. This is the
> > > call:
> > > 
> > > cat *.raw |
> > > /home/bic/jason/seconddir/minc64/src/minc/progs/rawtominc/rawtominc
> > > -clobber -yzx -xstep -0.01 -ystep 0.1 -zstep -0.01 test.mnc 470 2400
> > > 2800
> > > 
> > > This, however, crashes with the following message:
> > > 
> > > ncendef: ncid 3: Invalid argument
> > > 
> > > At the time of the crash, the file has the following size:
> > > 
> > > 2147450880
> > > 
> > > If I resize the input files so that the final output is less than that
> > > magical 2GB limit (and adjust the size options for rawtominc
> > > accordingly), it works just fine. So this appears to be something to do
> > > with files over the 2GB limit. The point of the crash in rawtominc is
> > > here:
> > > 
> > >    (void) miattputstr(cdfid, imgid, MIsigntype, osign);
> > >    if (ovrange_set) 
> > >       (void) miset_valid_range(cdfid, imgid, ovalid_range);
> > > 
> > >    /* End definition mode */
> > >    (void) ncendef(cdfid);
> > > 
> > > It gets to the ncendef call, but does not progress past it.
> > > 
> > > I've spent a good part of today trying to figure out why this would be
> > > the case, but have come up with nothing obvious (and certainly no fix).
> > > So any help/suggestions would be greatly appreciated!
> > > 
> > > Jason
> > > 
> > > P.S. I also tried the 64-bit version of rawtominc that John sent to the
> > > geeks list a few months ago, but with the same results.
> > > 
> > > P.P.S If anybody wants the input files to play with, look here:
> > > 
> > > /data/rome/temp/jason/histo
> > > 
> > > the files there are in raw byte format, as generated by convert file.png
> > > GRAY:file.raw
> > > 
> > > _______________________________________________
> > > MINC-development mailing list
> > > MINC-development@bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
> > > 
> > _______________________________________________
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> > MINC-development@bic.mni.mcgill.ca
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> 
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