netcdf 4.3.3-1.2: HDF5 library version mismatched error
Alexander Barth
barth.alexander@gmail.com
Wed Feb 17 08:37:00 GMT 2016
Hi,
When I run the command:
ncdump.exe -h test_hgroups.nc
with the example NetCDF4 file from
https://www.unidata.ucar.edu/software/netcdf/examples/test_hgroups.nc,
I get the following HDF5 error message below, in particular:
Headers are 1.8.15, library is 1.8.16
Is it possible to recompile netcdf with the current version of HDF5?
This also affects octave-netcdf and possibly all programs which use netcdf.
Thank you for your fine work to maintain cygwin over all these years!
Regards,
Alexander Barth
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 1.8.15, library is 1.8.16
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.16
Configured on: Fri Nov 13 18:23:58 CET 2015
Configured by: marco@GE-MATZERI-EU
Configure mode: production
Host system: x86_64-unknown-cygwin
Uname information: CYGWIN_NT-6.1 GE-MATZERI-EU
2.3.0(0.291/5/3) 20
15-11-09 10:24 x86_64
Cygwin
Byte sex: little-endian
Libraries: shared
Installation point: /usr
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/gcc
CFLAGS: -ggdb -O2 -pipe
-Wimplicit-function-declaration
-fdebug-prefix-map=/pub/devel/hdf5/hdf5-1.8.16-1.x86_64/build=/usr/src/debug/hd
f5-1.8.16-1
-fdebug-prefix-map=/pub/devel/hdf5/hdf5-1.8.16-1.x86_64/src/hdf5-1.8
.16=/usr/src/debug/hdf5-1.8.16-1
H5_CFLAGS:
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS:
Shared C Library: yes
Static C Library: no
Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS: -no-undefined
AM_LDFLAGS:
Extra libraries: -lz -ldl -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: no
C++: yes
C++ Compiler: /usr/bin/g++
C++ Flags: -ggdb -O2 -pipe
-fdebug-prefix-map=/pub/devel/h
df5/hdf5-1.8.16-1.x86_64/build=/usr/src/debug/hdf5-1.8.16-1
-fdebug-prefix-map=/
pub/devel/hdf5/hdf5-1.8.16-1.x86_64/src/hdf5-1.8.16=/usr/src/debug/hdf5-1.8.16-1
H5 C++ Flags:
AM C++ Flags:
Shared C++ Library: yes
Static C++ Library: no
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
Strict File Format Checks: no
Optimization Instrumentation: no
Bye...
Aborted (core dumped)
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