[MINC-users] HDF5 errors

[Alex Zijdenbos]

Hello all,

I just stumbled across a bunch of HDF5 runtime errors (see below). As
best I can tell these are due to a bogged-down NFS server; the files
the process needs are definitely there, but may take a while to get.
If I restart the exact same process, chances are high it completes
without error. I have so far only come across these only in xfmconcat
(with nonlinear deformations) and minc_displacement.

The main problem is that the errors are not caught; the process exits
gracefully and leaves a seemingly good output MINC file behind;
however upon inspection, the file is only partially written. The only
way to actually find the error is to catch it during some explicit
verification, or by grepping for 'HDF5' in the log files.

Does anybody have any thoughts about this or has seen this before? I
would say the the MINC library (miicv_get?) should catch this somehow
and throw an error causing the process to fail, but clearly that is
currently not happening.

These are locally-built executables based on MINC 2.1, HDF5 1.8.5.

-- Alex

HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
  #000: H5Dio.c line 174 in H5Dread(): can't read data
    major: Dataset
    minor: Read failed
  #001: H5Dio.c line 404 in H5D_read(): can't read data
    major: Dataset
    minor: Read failed
  #002: H5Dchunk.c line 1724 in H5D_chunk_read(): unable to read raw data chunk
    major: Low-level I/O
    minor: Read failed
  #003: H5Dchunk.c line 2737 in H5D_chunk_lock(): data pipeline read failed
    major: Data filters
    minor: Filter operation failed
  #004: H5Z.c line 1116 in H5Z_pipeline(): filter returned failure during read
    major: Data filters
    minor: Read failed
  #005: H5Zdeflate.c line 122 in H5Z_filter_deflate(): inflate() failed
    major: Data filters
    minor: Unable to initialize object
(from miicv_get): Can't read dataset /minc-2.0/image/0/image