I tried to duplicate, but failed.
Is it possible for you to use regular gcc instead of mpicc just to see
if mpicc or its linker is the problem?
=Dennis Heimbigner
Unidata
On 10/10/2021 11:10 PM, Vesselin Kolev via netcdfgroup wrote:
Hello Liao and thank you for the replay!
The error pops up regardless the MPI affinity. For instance, if I
compile the HDF5 library as a serial code:
LDFLAGS="-L/opt/software/zlib/1.2.11/lib"
CFLAGS="-I/opt/software/zlib/1.2.11/include"
CXXFLAGS="-I/opt/software/zlib/1.2.11/include"
FCLAGS="-I/opt/software/zlib/1.2.11/include"
ZLIB_ROOT=/opt/software/zlib/1.2.11 FC=gfortran FCFLAGS="-Ofast"
CC=gcc CFLAGS="-Ofast" CXX=g++ CXXFLAGS="-Ofast" cmake ..
-DCMAKE_INSTALL_PREFIX=/opt/software/hdf/5/1.12.1-gcc_11-zlib_1-api_v18-nojava
-DHDF5_ENABLE_THREADSAFE=OFF -DHDF5_BUILD_CPP_LIB=ON
-DHDF5_BUILD_FORTRAN=ON -DHDF5_BUILD_HL_LIB=ON -DHDF5_BUILD_JAVA=OFF
-DHDF5_ENABLE_Z_LIB_SUPPORT=ON -DBUILD_SHARED_LIBS=ON
-DDEFAULT_API_VERSION=v18
I still get the same error while trying to compile NetCDF-c.:
../liblib/.libs/libnetcdf.so: undefined reference to `H5Pset_fapl_http'
../liblib/.libs/libnetcdf.so: undefined reference to `H5FD_http_init'
Note that H5Pset_fapl_http and H5FD_http_init are defined in
libhdf5/H5FDhttp.c:
https://fossies.org/dox/netcdf-c-4.8.0/H5FDhttp_8c.html
Both H5Pset_fapl_http and H5FD_http_init are referenced in
libhdf5/.libs/libnchdf5.a:
nm libhdf5/.libs/libnchdf5.a | grep http
U H5Pset_fapl_http
U H5FD_http_init
and it seems like H5FDhttp.c goes into the set of compiled files:
nm libhdf5/.libs/libnchdf5.a | grep ".o" | grep http
libnchdf5_la-H5FDhttp.o:
Hence, the question is why that content cannot be read during the
linking process.
Thank you very much in advance for your answer.
Best,
Vesselin Kolev
On 10/10/2021 22:37, Wei-Keng Liao wrote:
Your HDF5 was configured to be installed under folder:
/opt/software/hdf/5/1.10.7-gcc_11-zlib_1-api_v18-mpich_3
But you are using a different folder in your NetCDF configuration.
/opt/software/hdf/5/1.10.7-gcc_11-zlib_1-api_v18-nojava
In addition, your HDF5 was built using mpicc/mpifort, but
you are using gcc to build NetCDF. I suggest you to use the
same compilers.
Wei-keng
On Oct 10, 2021, at 4:17 AM, Vesselin Kolev via netcdfgroup
<netcdfgroup@xxxxxxxxxxxxxxxx> wrote:
Hello Everyone,
I face very strange problem when compiling NetCDF-C 4.8.0 against
HDF5-1.10.7 and HDF5-1.12.1.
Note that HDF5 is compiled in the following manner:
LDFLAGS="-L/opt/software/zlib/1.2.11/lib"
CFLAGS="-I/opt/software/zlib/1.2.11/include"
CXXFLAGS="-I/opt/software/zlib/1.2.11/include"
FCLAGS="-I/opt/software/zlib/1.2.11/include"
ZLIB_ROOT=/opt/software/zlib/1.2.11 FC=mpifort FCFLAGS="-Ofast"
CC=mpicc CFLAGS="-Ofast" CXX=mpic++ CXXFLAGS="-Ofast" cmake ..
-DCMAKE_INSTALL_PREFIX=/opt/software/hdf/5/1.10.7-gcc_11-zlib_1-api_v18-mpich_3
-DHDF5_ENABLE_THREADSAFE=OFF -DHDF5_BUILD_CPP_LIB=OFF
-DHDF5_BUILD_FORTRAN=ON -DHDF5_BUILD_HL_LIB=ON -DHDF5_BUILD_JAVA=OFF
-DHDF5_ENABLE_Z_LIB_SUPPORT=ON -DBUILD_SHARED_LIBS=ON
-DDEFAULT_API_VERSION=v18 -DHDF5_ENABLE_PARALLEL=ON
using GCC 11.0.3. Also note, that the HDF5 compilation passed the
post-compilation tests without any fail.
But if I try to compile NetCDF-C agains that particular compilation
of HDF5:
LDFLAGS="-L/opt/software/hdf/5/1.10.7-gcc_11-zlib_1-api_v18-nojava/lib"
CC=gcc CFLAGS="-Ofast
-I/opt/software/hdf/5/1.10.7-gcc_11-zlib_1-api_v18-nojava/include"
./configure
--prefix=/opt/software/netcdf-c/4/4.8.0-gcc_11_hdf5_1.10.7
--enable-mmap --enable-byterange
I get the following error:
../liblib/.libs/libnetcdf.so: undefined reference to `H5Pset_fapl_http'
../liblib/.libs/libnetcdf.so: undefined reference to `H5FD_http_init'
Any suggestions where to look for the source of the problem are
greatly welcomed.
Thank you very much in advance!
Best,
Vesselin Kolev
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