[MINC-users] mincconvert error

[Audette, Michel]

Hi again, 

turns out that both I and other Minc-users have seen this error before, and it is resolved with a newer version of hdf5 (1.6.7) than I currently have on the machine where I am playing with this tissue data (not my usual machine). 

Please disregard the previous message. 

Best wishes, 

Michel

-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Audette, Michel
Sent: Thu 10/16/2008 4:04 PM
To: MINC users mailing list
Subject: [MINC-users] mincconvert error
 
Hi folks, 

my mincconcat error has now morphed into a mincconvert error (it's apparent that memory consumption was an issue with my minc-1 attempts). 

maudette at icaw164059:/data> mincconvert -2 -clob KoreanVisible/full_gray/0000.mnc KoreanVisible/full_gray/0000_2.mnc
HDF5-DIAG: Error detected in HDF5 library version: 1.6.1 thread 0.  Back trace follows.
  #000: H5F.c line 3191 in H5Fclose(): decrementing file ID failed
    major(07): Atom layer
    minor(16): Unable to close file
  #001: H5F.c line 3119 in H5F_close(): unable to flush cache
    major(08): Meta data cache layer
    minor(36): Unable to flush data from cache
  #002: H5F.c line 2881 in H5F_flush(): low level flush failed
    major(05): Low-level I/O layer
    minor(23): Write failed
  #003: H5FD.c line 3265 in H5FD_flush(): driver flush request failed
    major(22): Virtual File Layer
    minor(27): Unable to initialize object
  #004: H5FDsec2.c line 822 in H5FD_sec2_flush(): unable to extend file properly
    major(05): Low-level I/O layer
    minor(21): Seek failed

Is this an environment variable that I neglected to set in my .bashrc file? 

Best wishes, 

Michel
-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Andrew Janke
Sent: Thu 10/16/2008 11:05 AM
To: MINC users mailing list
Subject: Re: [MINC-users] mincconcat error
 
> I hit a size limit somewhere:
>
> maudette at icaw164059:/data/KoreanVisible> mincconcat -clobber -filetype -filelist files.tmp -concat_dimension zspace -sequential full.mnc
> Processing:.mincconcat: ncx.c:1716: ncx_put_size_t: Assertion `*ulp <= 4294967295U' failed.
> Aborted
>
> I should emphasize that I am working with 64-bit Suse 10 Linux.

Hi Michel,

Claude eluded to this but I dont think asked directly. Are these MINC1
or MINC2 files?  ie: what does:

   $ file fred.mnc

return?  the ncx_....  calls would insinuate to me that these are
netcdf (MINC 1) files. In that case I am not surprised that you are
hitting limits.


-- 
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883
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