Installing 9.2.0 with HDF5

[Curro Trigo]

Hello:

I'm trying to install deal II 9.2.0 on Ubuntu 20.04.2 LTS realease. And I succeded.

But if I try to install it with HDF5 activated I get errors like those shown below in the cmake process (while executing 'cmake -DDEAL_II_DIR=/home/curro/dealii-9.2.0/ ../'):

-- Include /home/curro/dealii-9.2.0/cmake/configure/configure_hdf5.cmake

-- HDF5_INCLUDE_DIR not found! Call:

--     FIND_PATH(HDF5_INCLUDE_DIR hdf5.h HINTS PATH_SUFFIXES hdf5 hdf5/include include/hdf5 include)

-- HDF5_LIBRARY not found! Call:

--     FIND_LIBRARY(HDF5_LIBRARY NAMES hdf5 HINTS PATH_SUFFIXES hdf5/lib lib lib64 lib)

-- HDF5_HL_LIBRARY not found! Call:

--     FIND_LIBRARY(HDF5_HL_LIBRARY NAMES hdf5_hl HINTS PATH_SUFFIXES lib lib64 lib)

-- HDF5_PUBCONF not found! Call:

--     FIND_FILE(HDF5_PUBCONF NAMES H5pubconf.h H5pubconf-64.h HINTS HDF5_INCLUDE_DIR-NOTFOUND PATH_SUFFIXES hdf5 hdf5/include include/hdf5 include)

--   HDF5_LIBRARIES: *** Required variable "HDF5_HL_LIBRARY" set to NOTFOUND ***

--   HDF5_INCLUDE_DIRS: *** Required variable "HDF5_INCLUDE_DIR" set to NOTFOUND ***

--   HDF5_USER_INCLUDE_DIRS: *** Required variable "HDF5_INCLUDE_DIR" set to NOTFOUND ***

-- Could NOT find HDF5

-- DEAL_II_WITH_HDF5 has unmet external dependencies.

I've downloaded from 'https://www.hdfgroup.org/' the file 'hdf5-1.12.0-linux-centos7-x86_64-shared-production.tar.gz'. And I have expanded it. Also, I've set the environment variable LD_LIBRARY_PATH to the folder where I've expanded it. With no success.

Any help will be welcome. Thanks a lot in advance.

Curro Trigo

[Wolfgang Bangerth]

On 3/21/21 1:41 PM, Curro Trigo wrote:
>
> I've downloaded from 'https://www.hdfgroup.org/' the file
> 'hdf5-1.12.0-linux-centos7-x86_64-shared-production.tar.gz'. And I have
> expanded it. Also, I've set the environment variable LD_LIBRARY_PATH to the
> folder where I've expanded it. With no success.

You also need files such as hdf5.h, i.e., header files and not just the libraries.

I would suspect that there is an ubuntu package for hdf5. It would probably be
easier if you installed that through the regular package manager, than do it
by hand.

Best
W.

--
------------------------------------------------------------------------
Wolfgang Bangerth email: bang...@colostate.edu
www: http://www.math.colostate.edu/~bangerth/

[Francisco Trigo]

Hello again,

 

The problem is when I type 'apt-cache search hdf5' I get 103 packages (attached to this e-mail) in Ubuntu related to hdf5. Which ones do I have to select?

 

I've selected these four packages:

 

  hdf5-helpers 

  libhdf5-103

  libhdf5-cpp-103

  libhdf5-dev

 

with the same result:

 

-- Include /home/curro/dealii-9.2.0/cmake/configure/configure_hdf5.cmake

-- HDF5_INCLUDE_DIR not found! Call:

--     FIND_PATH(HDF5_INCLUDE_DIR hdf5.h HINTS /usr/lib/x86_64-linux-gnu/hdf5 PATH_SUFFIXES hdf5 hdf5/include include/hdf5 include)

-- HDF5_LIBRARY not found! Call:

--     FIND_LIBRARY(HDF5_LIBRARY NAMES hdf5 HINTS /usr/lib/x86_64-linux-gnu/hdf5 PATH_SUFFIXES hdf5/lib lib lib64 lib)

-- HDF5_HL_LIBRARY not found! Call:

--     FIND_LIBRARY(HDF5_HL_LIBRARY NAMES hdf5_hl HINTS /usr/lib/x86_64-linux-gnu/hdf5 PATH_SUFFIXES lib lib64 lib)

-- HDF5_PUBCONF not found! Call:

--     FIND_FILE(HDF5_PUBCONF NAMES H5pubconf.h H5pubconf-64.h HINTS HDF5_INCLUDE_DIR-NOTFOUND /usr/lib/x86_64-linux-gnu/hdf5 PATH_SUFFIXES hdf5 hdf5/include include/hdf5 include)

--   HDF5_LIBRARIES: *** Required variable "HDF5_HL_LIBRARY" set to NOTFOUND ***

--   HDF5_INCLUDE_DIRS: *** Required variable "HDF5_INCLUDE_DIR" set to NOTFOUND ***

--   HDF5_USER_INCLUDE_DIRS: *** Required variable "HDF5_INCLUDE_DIR" set to NOTFOUND ***

-- Could NOT find HDF5

-- DEAL_II_WITH_HDF5 has unmet external dependencies.

 

Any suggestion?

 

Thank you!

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[simon...@gmail.com]

Hi,
Can you try this:

cmake -DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/serial ..


Because, as far as I can tell, the "hint" that is currently in configure_hdf5.cmake isn't good enough.

Best,
Simon

[Francisco Trigo]

Hello Simon;

 

Your advice has worked fine, I had already tried what you suggested but I missed the final “/serial” of the path. With the complete path finally HDF5 has been detected successfully.

 

Definitively configure_hdf5.cmake is not good enough.

 

For the sake of completion, I installed these Ubuntu packages: ‘libhdf5-103’ and ‘libhdf5-dev’, but ‘hdf5-helpers’ and ‘libhdf5-cpp-103’ also installed automatically.

 

Thank you very much indeed, Simon.

 

Curro

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