I've previously installed the Quantum Espresso (QEsp) binaries using "apt install" on an Ubuntu 16.04.7 LTS distro. This has worked fine, except that calculations don't produce .hdf5 output, which I need to transfer the data to Mathematica/Python/etc. So now I'm compiling from source.
According to , QEsp needs a special flag at compile time in order for it to have HDF5 support. In other words, someone could run the command
However for me, this produces the output:
The following libraries have been found: BLAS_LIBS=-L/opt/intel/mkl/lib/intel64 -lmkl_gf_lp64 -lmkl_sequential -lmkl_core LAPACK_LIBS= FFT_LIBS= HDF5_LIBS=
which I'm pretty sure means that HDF5_LIBS were not found. According to , if this happens, I need only specify the include and lib locations using the commands
./configure -with-hdf5-libs=<options> -with-hdf5-include=<path>
where "<options>" and "<path>" are placeholders for the necessary directories. If I run the command
as per the instructions of , I get the following output:
x86_64-conda_cos6-linux-gnu-gfortran -I/home/eugenio/miniconda3/include -L/home/eugenio/miniconda3/lib /home/eugenio/miniconda3/lib/libhdf5hl_fortran.a /home/eugenio/miniconda3/lib/libhdf5_hl.a /home/eugenio/miniconda3/lib/libhdf5_fortran.a /home/eugenio/miniconda3/lib/libhdf5.a -L/home/eugenio/miniconda3/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-rpath,/home/eugenio/miniconda3/lib -L/home/eugenio/miniconda3/lib -lrt -lpthread -lz -ldl -lm -Wl,-rpath -Wl,/home/eugenio/miniconda3/lib
How do I properly specify the include and lib directories, given the above output? How will I know that I have done this correctly, and that it will compile with HDF5 support?
I've unsuccessfully tried a number of different rearrangements, and have heeded the warning in  that "directories in the list must be separated by spaces"... I'm pretty sure I'm doing this part incorrectly.