ncl_convert2nc and HDF5 library version mismatch

From: Jennifer Adams <jma_at_nyahnyahspammersnyahnyah>
Date: Thu Oct 13 2011 - 18:51:13 MDT

Dear Experts,
I have just downloaded ncl-6.0.0 (redhat x86_64) in order to use ncl_convert2nc to convert grib2 into compressed netcdf. The grib2 data in question are the CFS v2 reforecast monthly mean data that have erroneous time metadata -- the beginning and ending times of the averaging periods are wrong. This makes it extremely awkward for GrADS to use in its native format. Converting to netcdf seems to be the only legitimate way forward. My first test worked great:

# ncl_convert2nc
Processing file:
 Copyright (C) 1995-2011 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.0.0
 The use of this software is governed by a License Agreement.
 See for more details.
Classic model NetCDF does not support string types, converting initial_time0 to a character array
Dimension 'ncl_strlen_0' will be added

Unfortunately, my output file was 5 times larger than the grib2 file. The I/O for compressed netcdf is much faster anyway, so I added the options "-nc4c -cl 1" , but got a core dump:

# ncl_convert2nc -nc4c -cl 1
Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.8.5, library is 1.8.6
<summary of HDF5 configuration snipped>

I'm pretty sure this is not a problem with my local environment, since ncl_convert2nc is not dynamically linked with anything:

# ldd ~/ncl-6.0.0/bin/ncl_convert2nc
        not a dynamic executable

The data file I'm using is at

Respectfully submitted,

Jennifer Miletta Adams
4041 Powder Mill Road
Calverton, MD 20705

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Received on Thu Oct 13 18:51:19 2011

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