Error in compiling step-1

[X Zhu]

Hello Prof. Bangerth and developers,

I have already installed the deal.ii library (9.1.1-9build2) by apt package (just by "apt-get install libdeal.ii-dev") in my ubuntu 20.04LTS machine. I did compilations in step-1 and step-2, same errors occur.

The environment information is as follows:

*****

$ ldconfig -p |grep deal

   libdeal.ii.so.9.1.1 (libc6,x86-64) => /lib/x86_64-linux-gnu/libdeal.ii.so.9.1.1
   libdeal.ii.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libdeal.ii.so
   libdeal.ii.g.so.9.1.1 (libc6,x86-64) => /lib/x86_64-linux-gnu/libdeal.ii.g.so.9.1.1
   libdeal.ii.g.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libdeal.ii.g.so

$ export | grep deal
declare -x DEAL_II_DIR="/usr/include/deal.II"
declare -x PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/include/deal.II:/usr/include/deal.II"

$ ls /usr/include/deal.II/
algorithms       distributed  grid         matrix_free   numerics      physics
base             dofs         hp           meshworker    opencascade   sundials
boost_adaptors   fe           integrators  multigrid     optimization
differentiation  gmsh         lac          non_matching  particles

$ ls /usr/local/include/deal.II/
algorithms      cgal             gmsh         matrix_free   opencascade
arborx          differentiation  grid         meshworker    optimization
base            distributed      hp           multigrid     particles
boost_adaptors  dofs             integrators  non_matching  physics
bundled         fe               lac          numerics      sundials

$ ls /usr/local/lib/
cmake            libdeal_II.g.so.9.5.0-pre  libdeal_II.so.9.5.0-pre  python3.8
libdeal_II.g.so  libdeal_II.so              pkgconfig

**********

I copy the example files into another directory and run commands in step-2 folder:

************

$ cmake .
-- Using the deal.II-9.5.0-pre installation found at /usr/local (*** PS ***: I don't know why deal.ii-9.5.0 is involved.)
-- Include macro /usr/local/share/deal.II/macros/macro_deal_ii_add_test.cmake
-- Include macro /usr/local/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake
-- Include macro /usr/local/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake
-- Include macro /usr/local/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake
-- Include macro /usr/local/share/deal.II/macros/macro_deal_ii_query_git_information.cmake
-- Include macro /usr/local/share/deal.II/macros/macro_deal_ii_setup_target.cmake
-- The C compiler identification is GNU 9.4.0
-- The CXX compiler identification is GNU 9.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Autopilot invoked
###
#
#  Project  step-2  set up with  deal.II-9.5.0-pre  found at
#      /usr/local
#
#  CMAKE_BUILD_TYPE:          Debug
#
#  You can now run
#       $ make                - to compile and link the program
#       $ make run            - to (compile, link and) run the program
#
#       $ make debug          - to switch the build type to 'Debug'
#       $ make release        - to switch the build type to 'Release'
#
#       $ make edit_cache     - to change (cached) configuration variables
#                               and rerun the configure and generate phases of CMake
#
#       $ make strip_comments - to strip the source files in this
#                               directory off their comments; this is irreversible
#       $ make clean          - to remove the generated executable as well as
#                               all intermediate compilation files
#       $ make runclean       - to remove all output generated by the program
#       $ make distclean      - to clean the directory from _all_ generated
#                               files (includes clean, runclean and the removal
#                               of the generated build system)
#       $ make info           - to view this message again
#
#  Have a nice day!
#
###
-- Configuring done
-- Generating done
-- Build files have been written to: /media/zz/CE8C7223EFB7F02F/deal.ii_check/examples/step-2

$ make
Scanning dependencies of target step-2
[ 50%] Building CXX object CMakeFiles/step-2.dir/step-2.cc.o
In file included from /usr/local/include/deal.II/base/config.h:561,
                 from /usr/local/include/deal.II/grid/tria.h:20,
                 from /media/zhu/CE8C7223EFB7F02F/deal.ii_check/examples/step-2/step-2.cc:23:
/usr/local/include/deal.II/base/numbers.h:28:10: fatal error: Kokkos_Macros.hpp: No such file or directory
   28 | #include <Kokkos_Macros.hpp>
      |          ^~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/step-2.dir/build.make:63: CMakeFiles/step-2.dir/step-2.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:272: CMakeFiles/step-2.dir/all] Error 2
make: *** [Makefile:84: all] Error 2

****************

As the error shown in the above, I feel strange about another version 9.5.0 appearing in the compilation. I also do cmake by adding -DDEAL_II_DIR=/usr/local/include/deal.II or other directory like -DDEAL_II_DIR=/usr/include/deal.II (since the same /algorithms, /distributed, /grid, .. folders appear in this directory ), the error keeps the same.

So in this situation, what is the reason for this error and how to solve it? Thank you！

PS: Maybe I forgot I have installed it at the first then remove it incompletely, and installed it again. But I don't remember clearly. The clear impression is that I only use apt-get to install the deal.ii library.

Best，

Xianyun

[Jan Philipp Thiele]

ldconfig told you that the deal.II 9.1.1 shared object library is in /lib/x86_64-linux-gnu/
Additionally, there is an installation of deal.II 9.5.0-pre, which is the current development branch of deal.II, in /usr/local

This second one actually fits to apt-get install libdeal.ii-dev, so I'm not 100% sure if the 9.1.1 is a proper installation, for that There would have to be an include folder as well.

Additionally, fitting to the second installation the environment as well as the cmake variable DEAL_II_DIR are set to /usr/local which is why cmake only finds 9.5.0-pre.

You might try to set the cmake variable to the proper directory via -D DEAL_II_DIR, but you'd probably have to figure out where the matching include files are and set the variable to the parent directory of /include

If you installed, uninstalled and installed again I would not be sure whether the object libraries in /lib/x86_64-linux-gnu/ are still useable.

And I also think that on the first install you chose a different deal.II version.

I however, have never installed deal.II via apt so I don't know how to choose the correct version there, but if it was 9.1.1 before it might be in your Terminals call history.

Best,

Philipp

[X. Zhu]

Hello Jan and Prof. Bangerth,

Thanks for your reply. I fixed the issue by removing the package. After that, I can run step-1 by the "apt-get" version 9.1.1 and also by the git clone package (version 9.5.0). Thank you all.

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