Re: ncl_convert2nc and HDF5 library version mismatch

From: Mary Haley <haley_at_nyahnyahspammersnyahnyah>
Date: Fri Oct 14 2011 - 10:51:04 MDT

The mismatch is due to our RedHat binaries being built with conflicting HDF5 versions.

I provided Jennifer with a new RedHat binary offline which worked.

If you are having the same problem, you can try one of the Debian binaries, or email me.


On Oct 13, 2011, at 6:51 PM, Jennifer Adams wrote:

> 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
> --
> Jennifer Miletta Adams
> 4041 Powder Mill Road
> Calverton, MD 20705
> _______________________________________________
> ncl-talk mailing list
> List instructions, subscriber options, unsubscribe:

ncl-talk mailing list
List instructions, subscriber options, unsubscribe:
Received on Fri Oct 14 10:51:12 2011

This archive was generated by hypermail 2.1.8 : Tue Oct 18 2011 - 09:42:15 MDT