`cdo` (Climate Data Operators) in the 'Science' repository is not being linked
consistently to the HDF5 library.
Just to be sure, I'm using the latest release of `cdo` from Science:
# rpm -qi cdo
Name : cdo
Version : 1.8.2
Release : 2.1
Architecture: x86_64
Install Date: Friday 18 August 2017 11 h 48 min 19 s CEST
Group : Productivity/Scientific/Other
Size : 7869837
License : GPL-2.0
Signature : DSA/SHA1, Thursday 10 August 2017 15 h 24 min 03 s CEST, Key ID
01db7302943d8bb8
Source RPM : cdo-1.8.2-2.1.src.rpm
Build Date : Thursday 10 August 2017 15 h 23 min 54 s CEST
Build Host : lamb01
Relocations : (not relocatable)
Vendor : obs://build.opensuse.org/science
URL : https://code.zmaw.de/projects/cdo
Summary : A program for manipulating GRIB/NetCDF/SERVICE/EXTRA/IEG files
Description :
CDO (Climate Data Operators) is a collection of command line Operators
to manipulate and analyse Climate and NWP model Data.
Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG.
There are more than 600 operators available.
Distribution: science / openSUSE_Leap_42.2
It is linked, at the same time, to libnetcdf.so.11 and libhdf5.so.100 (the 1.10
series of HDF5):
# readelf -d /usr/bin/cdo
Dynamic section at offset 0x465cc8 contains 38 entries:
Tag Type Name/Value
0x0000000000000001 (NEEDED) Shared library: [libxml2.so.2]
0x0000000000000001 (NEEDED) Shared library: [libMagPlus.so]
0x0000000000000001 (NEEDED) Shared library: [libcurl.so.4]
0x0000000000000001 (NEEDED) Shared library: [libproj.so.9]
0x0000000000000001 (NEEDED) Shared library: [libeccodes.so]
0x0000000000000001 (NEEDED) Shared library: [libudunits2.so.0]
0x0000000000000001 (NEEDED) Shared library: [libnetcdf.so.11]
0x0000000000000001 (NEEDED) Shared library: [libhdf5_hl.so.100]
0x0000000000000001 (NEEDED) Shared library: [libhdf5.so.100]
0x0000000000000001 (NEEDED) Shared library: [libsz.so.2]
0x0000000000000001 (NEEDED) Shared library: [libm.so.6]
0x0000000000000001 (NEEDED) Shared library: [libgomp.so.1]
0x0000000000000001 (NEEDED) Shared library: [libpthread.so.0]
0x0000000000000001 (NEEDED) Shared library: [libc.so.6]
[irrelevant entries stripped]
Again, I am using the proper version of libnetcdf.so.11 from Science:
# rpm -qi libnetcdf11
Name : libnetcdf11
Version : 4.4.1
Release : 30.4
Architecture: x86_64
Install Date: Tuesday 13 June 2017 09 h 35 min 50 s CEST
Group : System/Libraries
Size : 1768648
License : NetCDF
Signature : DSA/SHA1, Saturday 10 June 2017 11 h 36 min 15 s CEST, Key ID
01db7302943d8bb8
Source RPM : netcdf-4.4.1-30.4.src.rpm
Build Date : Saturday 10 June 2017 11 h 35 min 51 s CEST
Build Host : lamb22
Relocations : (not relocatable)
Vendor : obs://build.opensuse.org/science
URL : http://www.unidata.ucar.edu/software/netcdf/
Summary : Shared libraries for the NetCDF scientific data format
[rest of the output stripped]
However, libnetcdf.so.11 is linked against libhdf5.so.10 (the 1.8 series of
HDF5):
# readelf -d /usr/lib64/libnetcdf.so.11
Dynamic section at offset 0x186b30 contains 31 entries:
Tag Type Name/Value
0x0000000000000001 (NEEDED) Shared library: [libmfhdf.so.4.2.11]
0x0000000000000001 (NEEDED) Shared library: [libhdf5_hl.so.10]
0x0000000000000001 (NEEDED) Shared library: [libhdf5.so.10]
0x0000000000000001 (NEEDED) Shared library: [libm.so.6]
0x0000000000000001 (NEEDED) Shared library: [libcurl.so.4]
0x0000000000000001 (NEEDED) Shared library: [libc.so.6]
0x000000000000000e (SONAME) Library soname: [libnetcdf.so.11]
[irrelevant entries stripped]
This leads to the dreaded HDF5 version mismatch error: (obviously for the
following command you'd need an input file, but any netCDF file will do, I
believe)
# cdo invertlat gmt10.nc tmp.nc
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 1.8.17, library is 1.10.0
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.10.0-patch1
Host system: x86_64-suse-linux-gnu
Byte sex: little-endian
Installation point: /usr
[rest of the output stripped]
Also, when looking at symbol resolution, lots of dubious resolutions are
happening between the HDF5 libraries (.so.10 and .so.100):
# LD_DEBUG=bindings cdo invertlat gmt10.nc tmp.nc
[lots and lots of output stripped]
25643: binding file /usr/lib64/libhdf5.so.10 [0] to
/usr/lib64/libhdf5.so.10 [0]: normal symbol `H5D__chunk_init'
[...]
25643: binding file /usr/lib64/libhdf5.so.10 [0] to
/usr/lib64/libhdf5.so.100 [0]: normal symbol `H5P_LST_FILE_ACCESS_ID_g'
25643: binding file /usr/lib64/libhdf5.so.10 [0] to
/usr/lib64/libhdf5.so.10 [0]: normal symbol `H5P_facc_close'
25643: binding file /usr/lib64/libhdf5.so.10 [0] to
/usr/lib64/libhdf5.so.100 [0]: normal symbol `H5P_CLS_GROUP_CREATE_g'
[...]
25643: binding file /usr/lib64/libhdf5.so.10 [0] to
/usr/lib64/libhdf5.so.100 [0]: normal symbol `H5T_NATIVE_UINT_FAST16_ALIGN_g'
25643: binding file /usr/lib64/libhdf5.so.10 [0] to
/usr/lib64/libhdf5.so.100 [0]: normal symbol `H5E_SYSTEM_g'
25643: binding file /usr/lib64/libhdf5.so.10 [0] to
/usr/lib64/libhdf5.so.100 [0]: normal symbol `H5T__conv_llong_schar'
25643: binding file /usr/lib64/libhdf5.so.10 [0] to
/usr/lib64/libhdf5.so.100 [0]: normal symbol `H5HF_sect_single_free'
25643: binding file /usr/lib64/libhdf5.so.10 [0] to
/usr/lib64/libhdf5.so.100 [0]: normal symbol `H5MF_sect_simple_can_shrink'
[...]
25643: binding file /usr/lib64/libhdf5.so.100 [0] to
/usr/lib64/libhdf5.so.100 [0]: normal symbol `H5A_close'
25643: binding file /usr/lib64/libhdf5.so.100 [0] to
/usr/lib64/libhdf5.so.100 [0]: normal symbol `H5B2_TEST'
25643: binding file /usr/lib64/libhdf5.so.100 [0] to
/usr/lib64/libhdf5.so.100 [0]: normal symbol `H5HF_HUGE_BT2_INDIR'
25643: binding file /usr/lib64/libhdf5.so.100 [0] to
/usr/lib64/libhdf5.so.100 [0]: normal symbol `H5HF_HUGE_BT2_INDIR'
Best regards
Edward