Please clarify H5Free

[VictorEijkhout]

-- Plugin support requires libhdf5 with H5Free support. Your libhdf5 install does not provide H5Free.  Please install a newer version of libhdf5 if you require plugin compression support.

1. I'm not requesting plugin compression support:

cmake -D CMAKE_INSTALL_PREFIX=/work2/00434/eijkhout/netcdf/installation-netcdf-4.9.2-stampede3-intel24                     
-D CMAKE_COLOR_DIAGNOSTICS=OFF                     
-D CMAKE_VERBOSE_MAKEFILE=ON                     
-D BUILD_SHARED_LIBS=ON                     
-DNCDIR=/work2/00434/eijkhout/netcdf/installation-netcdf-4.9.2-stampede3-intel24 
-DnetCDF_LIBRARIES=/work2/00434/eijkhout/netcdf/installation-netcdf-4.9.2-stampede3-intel24/lib64/libnetcdf.so 
-DnetCDF_INCLUDE_DIR=/work2/00434/eijkhout/netcdf/installation-netcdf-4.9.2-stampede3-intel24/include                       
/work2/00434/eijkhout/netcdfx/netcdfx-4.3.1/

2. What option for netcdf-c do I need?

Victor.

[WardF]

You should be able to pass -DENABLE_PLUGINS=OFF to turn this off.

[VictorEijkhout]

That option applied to? 1. hdf5 2. netcdf-c 3. netcdf-cxx?

[VictorEijkhout]

Actually, that error was caused by:

CMake Error at CMakeLists.txt:405 (CHECK_LIBRARY_EXISTS):
  CHECK_LIBRARY_EXISTS Macro invoked with incorrect arguments for macro
  named: CHECK_LIBRARY_EXISTS

which comes from:

CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5free_memory "" HAVE_H5FREE_MEMORY)

so apparently that variable is null. Ok, that's a bizarre looking variable, so I define it by hand:

    -D HDF5_C_LIBRARY_hdf5=${TACC_HDF5_LIB}/libhdf5.so 

Why do I have to do this? hdf5 has both .pc and .cmake files but this does not look like a normal naming convention.

Now all that remains is finding the hdf5 include files.

[VictorEijkhout]

And the solution seems to be:

    -D netCDF_INCLUDE_DIR='${TACC_NETCDF_INC};${TACC_HDF5_INC}'

[truenicfel]

I had the same issue today trying to build on my windows machine. I was not able to get it to work in the end. It build but it did not run. My feeling is that especially the MSVC cmake configuration of netcdf-cxx4 is quite broken.

First thing I found was here:

IF(MSVC)
SET(SEARCH_PACKAGE_NAME ${HDF5_PACKAGE_NAME})
FIND_PACKAGE(HDF5 NAMES ${SEARCH_PACKAGE_NAME} COMPONENTS C HL NO_MODULES REQUIRED ${NC_HDF5_LINK_TYPE})
ELSE(MSVC)
FIND_PACKAGE(HDF5 COMPONENTS C HL REQUIRED)
ENDIF(MSVC)

The MSVC section of the if does not work since HDF5_PACKAGE_NAME is empty. CMake therefore tries to search for hdf using an empty name, cant find it and then the CHECK_LIBARARY_EXISTS macro fails a few lines later. Simply using FIND_PACKAGE(HDF5 COMPONENTS C HL REQUIRED) did the trick for me and I was able to progress. This also removed the H5Free problem described in the original issue. I believe that the error was simply the result of it not being able to find the package at all.

When trying to build the examples. I got a strange error that zlib is required but the file C:/share/VS15/x64/lib/zlib.lib does not exist. This did not look right to me as this path does not exist on my system. So I tracked down the problem and found that the netcdf 4.9.2 installation comes with this error built in. In line 58

INTERFACE_LINK_LIBRARIES "hdf5-shared;hdf5_hl-shared;C:/share/VS15/x64/lib/zlib.lib;C:/share/VS15/x64/lib/libcurl_imp.lib"

someone managed to ship their personal system paths into the config file that is supposed to help with including netcdf in your cmake project. So I changed that to:

INTERFACE_LINK_LIBRARIES "hdf5-shared;hdf5_hl-shared;C:/share/VS15/x64/lib/zlib.lib;C:/share/VS15/x64/lib/libcurl_imp.lib"

and I was a step further. But the next error was already waiting to emerge. Now the tests were not able to link netcdf-cxx's own library. I tried removing the BUILD_SHARED_LIBS which worked for compiling but I feel like it caused issues when running the tests as all my tests failed. because apparently my netcdf installation does not support these features which I highly doubt as not even the simple surface pressure example in this repo is running.

I am not sure why all of these things are not an issue on my linux system but I assume that is because zlib, hdf5 and other dependencies are not bundled there but instead installed separately via package managers.