[netcdfgroup] HDF error, and now what?

• To: netcdfgroup@xxxxxxxxxxxxxxxx
• Subject: [netcdfgroup] HDF error, and now what?
• From: ezaron <ezaron@xxxxxxx>
• Date: Tue, 22 Jul 2014 11:49:00 -0700 (PDT)

Hi All,

I've been trying to understand and/or fix a problem where occasional "HDF
Error" is reported on reads from netcdf files. The errors are sporadic (but
reproducible) and necessitate a lot of "try/catch" type of structures to
deal with the few values that are apparently corrupt. I've got to read
terabytes of many small netcdf files and performance has been a problem in
matlab, so I'm switching to fortran and hoping I can find out what the
problem is and fix the netcdf, if possible.

There is an old thread, referenced in my subject line, which mentions a
function
nf_set_log_level
but this symbol seems to be missing from my netcdf library. Since it is
undocumented, I wonder if anyone here can help.

Netcdf Information: (nc-config --all)
This netCDF 4.3.1.1 has been built with the following features:

  --cc        -> /usr/bin/clang
  --cflags    ->  -I/opt/local/include -I/opt/local/include -DNDEBUG
  --libs      -> -L/opt/local/lib -lnetcdf

  --has-c++   -> no
  --cxx       ->
  --has-c++4  -> no
  --cxx4      ->

  --fc        -> /opt/local/bin/gfortran-mp-4.8
  --fflags    -> -pipe -Os -I/opt/local/include
  --flibs     -> -L/opt/local/lib -lnetcdff -L/opt/local/lib
-Wl,-headerpad_max_install_names -lnetcdf -lnet\
cdf
  --has-f90   -> yes

  --has-dap   -> yes
  --has-nc2   -> yes
  --has-nc4   -> yes
  --has-hdf5  -> yes
  --has-hdf4  -> no
  --has-pnetcdf-> no

  --prefix    -> /opt/local
  --includedir-> /opt/local/include
  --version   -> netCDF 4.3.1.1


NB: The many files I am working with are huge enough that I am utilizing the
netcdf compression feature, which I believe are available only in netcdf 4.
If not for this, I would downgrade to netcdf 3.

-Ed




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• Follow-Ups:
  • Re: [netcdfgroup] HDF error, and now what?
    • From: ezaron
  • Re: [netcdfgroup] HDF error, and now what?
    • From: Rob Latham