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#1 | Configure with hdf5 datum

Fri Sep 23, 2022 6:15 am

Ragab

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Posts:	2
Registered since:	09.23.2022

Previously, I successfully installed FLEUR without hdf5 and it worked well. Now I would like to install it with hdf5 to get outputs as the same in the 2022 FLEUR Hands-on tutorial.
For this purpose I used:

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FC=mpiifort CC=mpiicc ./configure.sh -includedir /usr/local/hdf5/include -libdir /usr/local/libxc/lib -includedir /usr/local/libxc/include -libdir /usr/local/hdf5/lib

The configure results are:

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/usr/bin/docker->fleur_MPI
-- Found Python3: /opt/intel/oneapi/intelpython/latest/bin/python3.9 (found version "3.9.10") found components: Interpreter
Python3 found:TRUE
Python3 path:/opt/intel/oneapi/intelpython/latest/bin/python3.9
The python executable used for the testscan be overwritten with the juDFT_PYTHON environment variable
 

************************Summary***************************
Compiler   :  /opt/intel/oneapi/mpi/2021.6.0/bin/mpiifort
Compiler ID:  Intel
Flags      :  -I/usr/local/libxc/include -I/usr/local/hdf5/include -mkl -qopenmp -assume byterecl -no-wrap-margin -r8 -qopenmp
Use OpenMP :  ON
Libraries  :  -lmkl_scalapack_lp64;-lmkl_blacs_intelmpi_lp64;-L/usr/local/hdf5/lib;-L/usr/local/libxc/lib;/usr/lib64/libxml2.so
 
These Libraries are required:
  XML Library found       :     TRUE
  LAPACK Library found    :     TRUE
These Libraries are optional:
  ELPA (one node) Library found :
  FFT from MKL found            :     TRUE
  FFT from FFTW found           :     TRUE
  SpFFT found                   :     FALSE
  LibXC Library found           :     FALSE
  HDF5 Library found            :     TRUE
  Wannier90 1.2 Library found   :     FALSE
  Wannier90-4   Library found   :
  Wannier90-5   Library found   :
  EDSolver Library found        :     FALSE
  MAGMA Library found           :     FALSE
  progress thread compiled      :     TRUE
  MPI Library found             :     TRUE
    SCALAPACK Library found     :     TRUE
    ELPA Library found          :     FALSE
    ChASE Library found         :     FALSE
  Compile GPU version           :     FALSE
 

Compile serial version        :     FALSE
Compile parallel version      :     TRUE
 

Git describe  : MaX-R6.0-3-g5518b73
Git hash      : 5518b7393f32c3bc4aa1bd3f1f6cb16a220adf51
Doxygen found : YES
************************-------***************************
-- Configuring done
-- Generating done
-- Build files have been written to: /rhome/pkgs/4fleur/build
/rhome/pkgs/4fleur
Configuration finished
You should change into directory build
run 'make' or 'make -j'
 

and I got the executable files. But when I tried to inpgen to generate a FLEUR input I got the following errors:

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/rhome/pkgs/4fleur/build/inpgen: error while loading shared libraries: libhdf5_fortran.so.1000: cannot open shared object file: No such file or directory
/rhome/pkgs/4fleur/build/inpgen: error while loading shared libraries: libhdf5_fortran.so.1000: cannot open shared object file: No such file or directory
/rhome/pkgs/4fleur/build/inpgen: error while loading shared libraries: libhdf5_fortran.so.1000: cannot open shared object file: No such file or directory
/rhome/pkgs/4fleur/build/inpgen: error while loading shared libraries: libhdf5_fortran.so.1000: cannot open shared object file: No such file or directory
 

Could you please tell me what is the problem?

Thanks.

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#2 | RE: Configure with hdf5 datum

Fri Sep 23, 2022 11:06 am (Last edited: Fri Sep 23, 2022 11:06 am)

Gregor

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Posts:	175
Registered since:	04.07.2021

You compiled Fleur correctly, don't worry. It is just that at runtime it also has to be known where to find the library you want to link to. For this there exists an environment variable LD_LIBRARY_PATH. You have to also put the path for the HDF5 library into that environment variable. If I see it correctly this means that you should invoke a command like

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export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/hdf5/lib

if you are using a bash shell or a z shell. In other terminal shells this will look slightly differently. I suggest to put that line into your .bashrc or .zshrc file if you use one of these shells. With this you don't have to type it in each time before you want to start FLEUR.

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#3 | RE: Configure with hdf5 datum

Fri Sep 23, 2022 11:27 am

Thank you so much, Gregor. This command has solved the problem.

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