sz is missing from the libs

[mwestphal]

To report a non-security related issue, please provide:

• the version of the software with which you are encountering an issue: 4.9.2
• environmental information (i.e. Operating System, compiler info, java version, python version, etc.): MacOS
• a description of the issue with the steps needed to reproduce it

build netcdf on macos with:

   -DCURL_INCLUDE_DIR:STRING=0
   -DCURL_LIBRARY:STRING=0

   -DHAVE_HDF5_ZLIB:BOOL=1
   -DUSE_HDF5_SZIP:BOOL=1

   -DBUILD_SHARED_LIBS:BOOL=OFF
   -DNC_FIND_SHARED_LIBS:BOOL=OFF
   -DBUILD_TESTING:BOOL=OFF
   -DCMAKE_INSTALL_NAME_DIR:PATH=install/lib
   -DENABLE_BYTERANGE:BOOL=OFF
   -DENABLE_DAP_REMOTE_TESTS:BOOL=OFF
   -DENABLE_EXAMPLES:BOOL=OFF
   -DENABLE_FILTER_TESTING:BOOL=OFF
   -DENABLE_NCZARR_FILTERS_TESTING:BOOL=OFF
   -DENABLE_PARALLEL4:BOOL=OFF
   -DENABLE_PARALLEL_TESTS:BOOL=OFF
   -DENABLE_TESTS:BOOL=OFF
   -DTEST_PARALLEL:BOOL=OFF
   -DBUILD_UTILITIES:BOOL=OFF
   -DUSE_SZIP:BOOL=OFF
   -DENABLE_DAP:BOOL=OFF
   -DENABLE_NCZARR:BOOL=OFF
   -DCMAKE_INSTALL_LIBDIR:BOOL=lib

Fails with:

2023-10-28T06:55:28.4134090Z Undefined symbols for architecture x86_64:
2023-10-28T06:55:28.4235720Z   "_SZ_BufftoBuffCompress", referenced from:
2023-10-28T06:55:28.4336290Z       _H5Z__filter_szip in libhdf5.a(H5Zszip.c.o)
2023-10-28T06:55:28.4436960Z   "_SZ_BufftoBuffDecompress", referenced from:
2023-10-28T06:55:28.4537600Z       _H5Z__filter_szip in libhdf5.a(H5Zszip.c.o)
2023-10-28T06:55:28.4638050Z   "_SZ_encoder_enabled", referenced from:
2023-10-28T06:55:28.4738220Z       _H5Z_init in libhdf5.a(H5Z.c.o)
2023-10-28T06:55:28.4838960Z ld: symbol(s) not found for architecture x86_64

It looks like some logic is missing from liblib/CMakeLists.txt to add -lsz when HAVE_SZ is true.

Worked around using NC_EXTRA_DEPS.

[WardF]

Was libhdf5 compiled statically or as a shared library, out of curiosity?

[mwestphal]

static lib, with following args:

    -DBUILD_TESTING:BOOL=OFF
    -DBUILD_SHARED_LIBS:BOOL=OFF
    -DBUILD_STATIC_LIBS:BOOL=ON
    -DDEFAULT_API_VERSION:STRING=v18
    -DHDF5_BUILD_CPP_LIB:BOOL=ON
    -DHDF5_BUILD_TOOLS:BOOL=OFF
    -DHDF5_BUILD_UTILS:BOOL=OFF
    -DHDF5_BUILD_EXAMPLES:BOOL=OFF
    -DHDF5_ENABLE_PARALLEL:BOOL=OFF
    -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=TRUE
    -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=TRUE
    -DHDF5_ENABLE_SZIP_ENCODING:BOOL=TRUE
    -DSZIP_USE_EXTERNAL:BOOL=TRUE
    -DZLIB_USE_EXTERNAL:BOOL=TRUE
    -DHDF5_BUILD_HL_LIB:BOOL=TRUE
    -DHDF5_BUILD_WITH_INSTALL_NAME:BOOL=ON

[mwestphal]

Turns out the needed fix looks like this imo:

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3ee1367..1bad305 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -911,6 +911,7 @@ IF(USE_HDF5)
    int x = 1;}" USE_HDF5_SZIP)
   IF(USE_HDF5_SZIP)
     SET(HAVE_H5Z_SZIP yes)
+    FIND_LIBRARY(SZIP_LIBRARY NAMES sz)
   ENDIF()
 
   ####

SZIP_LIBRARY is already linked in liblib/CMakeLists.txt but we never search for it.

If that sounds like the right fix, I can open a PR.

[mwestphal]

Here is a much better, corrected patch:

--- a/liblib/CMakeLists.txt
+++ b/liblib/CMakeLists.txt
@@ -91,7 +91,7 @@ IF(Bz2_FOUND)
 SET(TLL_LIBS ${TLL_LIBS} ${Bz2_LIBRARIES})
 ENDIF()
 IF(SZIP_FOUND)
-SET(TLL_LIBS ${TLL_LIBS} ${SZIP_LIBRARIES})
+SET(TLL_LIBS ${TLL_LIBS} ${Szip_LIBRARIES})
 ENDIF()
 
 IF(HAVE_LIBDL)
@@ -119,13 +119,13 @@ IF(USE_HDF5)
     # builds:
     # Make sure that HDF5_C_LIBRARY appears *after*
     # HDF5_HL_LIBRARY.
-    SET(TLL_LIBS ${HDF5_HL_LIBRARIES} ${HDF5_C_LIBRARIES} ${HDF5_LIBRARIES} ${TLL_LIBS} ${SZIP_LIBRARY})
+    SET(TLL_LIBS ${HDF5_HL_LIBRARIES} ${HDF5_C_LIBRARIES} ${HDF5_LIBRARIES} ${TLL_LIBS} ${Szip_LIBRARIES})
   ELSE() # Windows CMake defines HDF5_LIBRARIES.
     set(mpi_libs)
     if (HDF5_PARALLEL)
       set(mpi_libs ${MPI_C_LIBRARIES})
     endif ()
-    SET(TLL_LIBS ${HDF5_LIBRARIES} ${mpi_libs} ${TLL_LIBS} ${SZIP_LIBRARY})
+    SET(TLL_LIBS ${HDF5_LIBRARIES} ${mpi_libs} ${TLL_LIBS} ${Szip_LIBRARIES})
   ENDIF()
 ENDIF()
 

[WardF]

Thanks; any chance you could submit this as a PR?

[mathstuf]

I recently ended up having to do a similar thing for netcdf4-python recently: https://gitlab.kitware.com/ben.boeckel/common-superbuild/-/blob/42770907fc2f077a30d7c4be2c50ed342deec4ea/projects/patches/pythonnetcdf4-szip-libname.patch

Once I have it working for our stuff, I'll submit the relevant patches there too.

[mwestphal]

Thanks; any chance you could submit this as a PR?

here it is, in an even better form with improvement to FindSzip.cmake

#2833