I have been using h5py for a while and I just tried installing the hdf5 library for making programs in C. (hdf5-1.12.0). I need some help setting it up properly. I am using Linux (via Windows WSL 2).
My understanding is that I can compile programs using the h5cc program. But when I try:
h5cc -o h5ex.out h5ex_d_chunk.c
h5cc cannot find any of the headers.
But as far as I can tell, hdf5 was installed to \usr\local\hdf5
Also, I tied fixing the include file problem but h5cc seems to be looking for the following directory for library files:
gcc: error: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl.a: No such file or directory
gcc: error: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.a: No such file or directory
Is there any advice on how I should fix this?
May 24, 2021, 2:14pm
Do you install the 1.12 binary yourself?
There will be a 1.12.1 release soon (release candidate this week).
h5cc internal details depends on the build system used to build the release.
Properly installing a given version of MPI is nontrivial, but you will get reasonable performance with installing openmpi v4.1 from source.
apt install flex
git clone https://github.com/open-mpi/ompi.git && cd ompi && git checkout v4.0.5
./autogen.pl && ./configure --prefix=/usr/local --with-libevent=/usr/local
git clone https://github.com/HDFGroup/hdf5.git && cd hdf5
git checkout hdf5-1_10_7
./configure --prefix=/usr/local -enable-parallel |grep 'Parallel HDF5'
make -j8 && sudo make install
H5CPP parallel (similar syntax to h5py)
git clone https://github.com/steven-varga/h5cpp.git
git checkout master
You can find then in
I installed the programs using the make script as described in the included INSTALL text file.
I did some more digging, and it seems like I had several h5cc programs installed, one by Python, one by myself, and one I don’t know where it came from. It seems this final one is configured to look for directories that don’t exist.
I was able to fix it by directly calling a different h5cc program.
Thanks for your response