Error built with HDF5 1.8.18

[bxwllzz]

HDF5 is built from source. When configure matio, it reported can't found HDF5:

./configure --enable-mat73=yes --with-hdf5=/home/pi/matio/CMake-hdf5-1.8.18/HDF5-1.8.18-Linux/HDF_Group/HDF5/1.8.18 --with-default-file-ver=7.3
...
checking for HDF5 software...  no
...   
MATIO Configuration Summary       
==============================================================
           C Compiler: gcc
               CFLAGS:  -g -O2
     Shared Libraries: yes
     Static Libraries: yes
  default MAT version: MAT_FT_MAT73

Features --------------------------------------------
  MAT v7.3 file support: no
Extended sparse support: yes

Packages --------------------------------------------
                 zlib: -lz
                 hdf5: 
               MATLAB: 

config.log:

...
configure:15844: checking for HDF5 software
configure:15881: gcc -o conftest -I/home/pi/matio/CMake-hdf5-1.8.18/HDF5-1.8.18-Linux/HDF_Group/HDF5/1.8.18/include  -g -O2   conftest.c -L/home/pi/matio/CMake-hdf5-1.8.18/HDF5-1.8.18-Linux/HDF_Group/HDF5/1.8.18/lib -lhdf5 -lz -lm  >&5
/home/pi/matio/CMake-hdf5-1.8.18/HDF5-1.8.18-Linux/HDF_Group/HDF5/1.8.18/lib/libhdf5.a(H5PL.c.o): In function `H5PL_term_interface':
H5PL.c:(.text+0x32c): undefined reference to `dlclose'
/home/pi/matio/CMake-hdf5-1.8.18/HDF5-1.8.18-Linux/HDF_Group/HDF5/1.8.18/lib/libhdf5.a(H5PL.c.o): In function `H5PL_load':
H5PL.c:(.text+0x5e8): undefined reference to `dlsym'
H5PL.c:(.text+0x7ac): undefined reference to `dlopen'
H5PL.c:(.text+0x7bc): undefined reference to `dlsym'
H5PL.c:(.text+0x934): undefined reference to `dlclose'
H5PL.c:(.text+0x99c): undefined reference to `dlerror'
H5PL.c:(.text+0xca4): undefined reference to `dlclose'
/home/pi/matio/CMake-hdf5-1.8.18/HDF5-1.8.18-Linux/HDF_Group/HDF5/1.8.18/lib/libhdf5.a(H5Z.c.o): In function `H5Z_init_interface':
H5Z.c:(.text+0x958): undefined reference to `SZ_encoder_enabled'
/home/pi/matio/CMake-hdf5-1.8.18/HDF5-1.8.18-Linux/HDF_Group/HDF5/1.8.18/lib/libhdf5.a(H5Zszip.c.o): In function `H5Z_filter_szip':
H5Zszip.c:(.text+0x104): undefined reference to `SZ_BufftoBuffDecompress'
H5Zszip.c:(.text+0x19c): undefined reference to `SZ_BufftoBuffCompress'
collect2: error: ld returned 1 exit status
...

Fix is change HDF5_LIBS in matio_hdf5.m4 From "-L${HDF5_DIR}/lib -lhdf5" To "-L${HDF5_DIR}/lib -lhdf5 -ldl -lszip"

[emmenlau]

Hmm, I guess it needs a slightly more clever fix, because its really not clear if HDF5 was built with szip support or not? One solution is of course pkg-config that was meant exactly for this kind of problem. An alternative might be to try without szip and add -ldl -lszip as a fallback if linking fails without it? Just my two cents...

[tbeu]

I regularly build HDF5 from source and test it on Travis CI and never met the issue. Can you please provide yout HDF5 config (call).

[emmenlau]

@tbeu are you building hdf5 against the (optional) szip library?

[tbeu]

No, I don't since it is not needed (by matio to have the szip support for hdf5).

[emmenlau]

This is the reason. I think many people build hdf5 with szip because its one of the "official" filters. Maybe even the official Windows dll is linked against szip? In any case, I would not add -ldl -lszipas a default, but it might be good to have a way to add it for users who need it. @bxwllzz did you try adding it to LD_LIBS or LD_FLAGS when running configure?

[tbeu]

OK, I will check it if I configure hdf5 with --with-szlib.

[bxwllzz]

I build HDF5 with cmake as HDF5 - Building HDF5-1.8 With CMake which is "RECOMMENDED by HDF5". Following the Build Instructions in that page, I run build-unix.sh to built HDF5. I just noticed it says These files will build the static HDF5 C and C++ libraries with SZIP and ZLIB compression included. But I stiil don't know how to use cmake to build HDF5 without SZIP?

@emmenlau Adding -ldl -lszip to LD_LIBS or LD_FLAGS when running configure didn't solve this problem.

[emmenlau]

@bxwllzz I did not test this myself but here are cmake instructions from HDF5: https://support.hdfgroup.org/HDF5/release/chgcmkbuild.html According to my understanding -DHDF5_ENABLE_SZIP_SUPPORT=OFF should disable SZIP. If you want to be double sure, add also -DHDF5_ENABLE_SZIP_ENCODING=OFF. I did not test it, but it seems promising. Does it help?

[bxwllzz]

@emmenlau build-unix.sh run ctest -S HDF5config.cmake,BUILD_GENERATOR=Unix -C Release -V -O hdf5.log In HDF5config.cmake, I found some options:

...
### disable ext libs building
#set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF")
#set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF")
#set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_ENCODING:BOOL=OFF")
...

After uncomment these lines, I can make HDF5 without SZIP. Thanks for your advice.

[tbeu]

It is all working for me - using plain configure and not cmake.

curl https://support.hdfgroup.org/ftp/lib-external/szip/2.1.1/src/szip-2.1.1.tar.gz -O -J
tar -zxf szip-2.1.1.tar.gz
cd szip-2.1.1
./configure --quiet CFLAGS="-w"
make install -C src
cd ..
git clone --depth 1 --branch hdf5_1_8_18 https://bitbucket.hdfgroup.org/scm/hdffv/hdf5.git hdf5_1_8_18
cd hdf5_1_8_18
./configure --quiet --enable-shared --disable-production --enable-debug=all --with-pic --disable-deprecated-symbols --disable-hl --disable-strict-format-checks --disable-clear-file-buffers --disable-instrument --disable-parallel --disable-trace --with-default-api-version=v18 --with-szlib=~/szip-2.1.1/szip CFLAGS="-w"
make install -C src

[tbeu]

You can run cmake -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF -DHDF5_ENABLE_SZIP_ENCODING:BOOL=OFF ./ to disable szlib in hdf5.