SZIP not found with CMake on MacOSX

[gitporst]

I compile with CMake on MacOSX with the most recent HDF5 lib.
However, the szip library is not found.

If I replace line 733 in CMakeLists.txt:

CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5Z_SZIP "" USE_SZIP)

by

SET(USE_SZIP ON)

all the following build steps run fine, the szip libs are found. Is the H5Z_SZIP function missing in the most recent HDF5 release?

My system specs:

cmake -DCMAKE_INSTALL_PREFIX=/usr/local/netcdf-c_4_8_0_gcc_8_1_0 -DENABLE_NETCDF_4=ON -DENABLE_DAP=ON -DENABLE_TESTS=ON ..
-- Found HDF5 libraries version 1.12.0
-- Using HDF5 include dir: /usr/local/hdf5_1_12_0_gcc_8_1_0/HDF_Group/HDF5/1.12.0/include
-- HDF5 has szip.
-- Found Math library: /usr/lib/libm.dylib
-- Enabling use of fill value when NC_ERANGE
-- Enabling a more relaxed check for NC_EINVALCOORDS
-- Found m4: /usr/bin/m4
-- Found bash: /bin/bash
-- CMAKE_SOURCE_DIR=/Users/ottor/nc/Home/local_libs/others/netcdf-c
-- CMAKE_BINARY_DIR=/Users/ottor/nc/Home/local_libs/others/netcdf-c/build_gcc
-- CMAKE_CURRENT_SOURCE_DIR=/Users/ottor/nc/Home/local_libs/others/netcdf-c/nc_test
-- CMAKE_CURRENT_BINARY_DIR=/Users/ottor/nc/Home/local_libs/others/netcdf-c/build_gcc/nc_test


Configuration Summary:

-- Building Shared Libraries:     ON
-- Building netCDF-4:             ON
-- Building DAP2 Support:         ON
-- Building DAP4 Support:         ON
-- Building Byte-range Support:   OFF
-- Building Utilities:            ON

Tests Enabled:              ON
-- DAP Remote Tests:  ON
-- Extra Tests:       OFF
-- Coverage Tests:    OFF
-- Parallel Tests:    OFF
-- Large File Tests:  OFF
-- Extreme Numbers:   ON
-- Unit Tests:        ON

Compiler:

-- Build Type:           DEBUG
-- CMAKE_C_COMPILER:     /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- CMAKE_C_FLAGS:         -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64
-- CMAKE_C_FLAGS_DEBUG:  -g -Wall -Wshorten-64-to-32 -Wconversion
-- Linking against:      hdf5::hdf5_hl-shared;hdf5::hdf5-shared;/usr/lib/libm.dylib;/usr/local/lib/libsz.dylib;/usr/lib/libcurl.dylib

# NetCDF C Configuration Summary
==============================

# General
-------
NetCDF Version:		4.8.0-development
Dispatch Version:       1
Configured On:		Tue Apr 28 15:39:33 CEST 2020
Host System:		x86_64-Darwin-19.4.0
Build Directory: 	/Users/ottor/nc/Home/local_libs/others/netcdf-c/build_gcc
Install Prefix:         /usr/local/netcdf-c_4_8_0_gcc_8_1_0

# Compiling Options
-----------------
C Compiler:		/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
CFLAGS:			 -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wall -Wshorten-64-to-32 -Wconversion
CPPFLAGS:
LDFLAGS:
AM_CFLAGS:
AM_CPPFLAGS:
AM_LDFLAGS:
Shared Library:		yes
Static Library:		no
Extra libraries:	-lhdf5_hl -lhdf5 -lm -lsz -lcurl

# Features
--------
NetCDF-2 API:		yes
HDF4 Support:		no
HDF5 Support:		yes
NetCDF-4 API:		yes
NC-4 Parallel Support:	no
PnetCDF Support:	no
DAP2 Support:		yes
DAP4 Support:		yes
Byte-Range Support:	no
Diskless Support:	yes
MMap Support:		yes
JNA Support:		no
CDF5 Support:		yes
ERANGE Fill Support:	yes
Relaxed Boundary Check:	yes
SZIP Support:           yes
SZIP Write Support:     yes
Parallel Filters:       no

-- Configuring done
-- Generating done
-- Build files have been written to: /Users/ottor/nc/Home/local_libs/others/netcdf-c/build_gcc

[WardF]

It appears you are using the libhdf5 1.12.x branch; we are not offering official support for this branch, so ymmv (most of our users still seem to be on the 1.8.x branch). I'll investigate the apparent lack of H5Z_SZIP in the 1.12.x branch as we move towards supporting this release officially. Thanks!

[gsjaardema]

This might be fixed by #1918. My MacOSX system will find the SZIP library with netCDF-4.8.0-development (has #1918), but not netCDF-4.7.0

[edwardhartnett]

@WardF I test with HDF5 1.12.0 and 1.12.1 routinely and they work great. I've never found an issue...

[DennisHeimbigner]

It turns out that H5Z_SZIP is a memory array rather than a function.
This may be the source of the problem on a Mac, though why it fails
only with 1.12.x, I do not know. If you can do an nm command
(or Mac equivalent) on libhdf5.a and libhdf5_hl.a, you might see what
it says about the visibility of H5Z_SZIP.
While you are at it, see if there are any exported functions for szip that we
could use instead of H5Z_SZIP.

[DennisHeimbigner]

Ideally, the symbol H5Pset_szip is what we should be searching for, but
it looks like it is always defined, and just returns an error if szip is not available.

[WardF]

It works on my MacOSX system as well, I will investigate @gsjaardema's comment that #1918 has fixed this. If I can hopefully confirm that, I'll close this out. Finally out from under proposal/committee workloads, time to start prepping the 4.8.0 release. Thanks all!

[WardF]

This appears to be corrected; we can reopen if need be, but closing it for now.