Problem installing Dealii-9.0.0

[Felipe Orellana]

Hello,

    My name is Felipe. I am trying to install dealii-9.0.0 on my local cluster.

    After commanding  

cmake -DCMAKE_INSTALL_PREFIX=/path2install /path2source

 with my desired directories (which btw, are the same directory, just  /home/Felipe/BIGSOFTWARE/dealii-9.0.0/ ), the system progresses well for almost a minute.. but then I get an error and the installation stops. I paste the error message below.

    What is there missing in my system?

    Are there any flags that I could add/write to avoid these errors?

I would appreciate your help,

cheers,

Felipe

-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_scalapack.cmake
-- DEAL_II_WITH_SCALAPACK has unmet configuration requirements: DEAL_II_WITH_MPI has to be set to "ON".
-- DEAL_II_WITH_SCALAPACK has unmet configuration requirements: DEAL_II_WITH_LAPACK has to be set to "ON".
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_slepc.cmake
-- DEAL_II_WITH_SLEPC has unmet configuration requirements: DEAL_II_WITH_PETSC has to be set to "ON".
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_sundials.cmake
-- SUNDIALS_LIB_IDAS not found! Call:
--     FIND_LIBRARY(SUNDIALS_LIB_IDAS NAMES sundials_idas HINTS PATH_SUFFIXES lib lib64 lib)
-- SUNDIALS_LIB_IDA not found! Call:
--     FIND_LIBRARY(SUNDIALS_LIB_IDA NAMES sundials_ida HINTS PATH_SUFFIXES lib lib64 lib)
-- SUNDIALS_LIB_ARKODE not found! Call:
--     FIND_LIBRARY(SUNDIALS_LIB_ARKODE NAMES sundials_arkode HINTS PATH_SUFFIXES lib lib64 lib)
-- SUNDIALS_LIB_KINSOL not found! Call:
--     FIND_LIBRARY(SUNDIALS_LIB_KINSOL NAMES sundials_kinsol HINTS PATH_SUFFIXES lib lib64 lib)
-- SUNDIALS_LIB_SER not found! Call:
--     FIND_LIBRARY(SUNDIALS_LIB_SER NAMES sundials_nvecserial HINTS PATH_SUFFIXES lib lib64 li

-- SUNDIALS_INCLUDE_DIR not found! Call:
--     FIND_PATH(SUNDIALS_INCLUDE_DIR sundials/sundials_nvector.h HINTS PATH_SUFFIXES include)
--   SUNDIALS_LIBRARIES: *** Required variable "SUNDIALS_LIB_IDA" set to NOTFOUND ***
--   SUNDIALS_INCLUDE_DIRS: *** Required variable "SUNDIALS_INCLUDE_DIR" set to NOTFOUND ***
--   SUNDIALS_USER_INCLUDE_DIRS: *** Required variable "SUNDIALS_INCLUDE_DIR" set to NOTFOUND ***
-- Could NOT find SUNDIALS
-- DEAL_II_WITH_SUNDIALS has unmet external dependencies.
--
-- Include /home/Felipe/BIGSOFTWARE/

dealii-9.0.0/cmake/setup_cpack.cmake
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/setup_custom_targets.cmake
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/setup_finalize.cmake
-- Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG
-- Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG - Failed
CMake Error at cmake/setup_finalize.cmake:95 (MESSAGE):
 

    Configuration error: Cannot compile a test program with the final set of
    compiler and linker flags:
      CXX flags (DEBUG): -pedantic -fPIC -Wall -Wextra -Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Wswitch -Woverloaded-virtual -Wno-deprecated-declarations -Wno-literal-suffix -std=c++11 -Wno-parentheses -Wno-unused-local-typedefs -Og -ggdb -Wa,--compress-debug-sections
      LD flags  (DEBUG): -Wl,--as-needed -rdynamic -fuse-ld=gold pthread -ggdb
      LIBRARIES (DEBUG): m;dl;/usr/lib64/libz.so;rt;
   
Call Stack (most recent call first):
  cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
  CMakeLists.txt:132 (VERBOSE_INCLUDE)

-- Configuring incomplete, errors occurred!
See also "/home/Felipe/BIGSOFTWARE/dealii-9.0.0/build/CMakeFiles/CMakeOutput.log".

[Bruno Turcksin]

Felipe,

Can you post everything that deal.II prints on the screen.

Best,

Bruno

[Felipe Orellana]

 Hello Bruno,

   Thanks for replying.

  Here I post the output:

    cmake -DCMAKE_INSTALL_PREFIX=/home/Felipe/BIGSOFTWARE/dealii-9.0.0/ /home/Felipe/BIGSOFTWARE/dealii-9.0.0
-- This is CMake 3.16.0-rc3
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/setup_external_macros.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_add_flags.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_check_compiler_setup.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_check_cxx_compiler_bug.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_check_mpi_interface.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_clear_cmake_required.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_configure_feature.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_deal_ii_add_definitions.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_deal_ii_add_library.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_deal_ii_add_test.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_deal_ii_find_file.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_deal_ii_find_library.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_deal_ii_find_path.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_deal_ii_find_program.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_deal_ii_initialize_cached_variables.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_deal_ii_insource_setup_target.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_deal_ii_invoke_autopilot.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_deal_ii_package_handle.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_deal_ii_pickup_tests.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_deal_ii_query_git_information.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_deal_ii_setup_target.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_decorate_with_stars.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_enable_if_links.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_enable_if_supported.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_enable_language_optional.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_evaluate_expression.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_expand_instantiations.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_filter_system_libraries.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_find_package.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_find_system_library.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_item_matches.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_purge_feature.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_push_cmake_required.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_register_feature.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_remove_duplicates.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_replace_flag.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_reset_cmake_required.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_set_if_empty.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_setup_source_list.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_setup_unity_target.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_strip_flag.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_switch_library_preference.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_to_string.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_to_string_and_add_prefix.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_unset_if_changed.cmake
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/macros/macro_verbose_include.cmake
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/setup_cached_variables.cmake
-- Prepending ${CUDA_NVCC_FLAGS} to ${DEAL_II_CUDA_FLAGS}
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/setup_deal_ii.cmake
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/setup_compiler_flags.cmake
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/setup_compiler_flags_gnu.cmake
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/bundled/setup_bundled.cmake
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/checks/check_01_cpu_features.cmake
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/checks/check_01_cxx_features.cmake
-- Using C++ version flag "-std=c++11"
-- DEAL_II_WITH_CXX17 and DEAL_II_WITH_CXX14 are both disabled
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/checks/check_02_compiler_features.cmake
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/checks/check_02_system_features.cmake
-- Performing Test m_LIBRARY
-- Performing Test m_LIBRARY - Success
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/checks/check_03_compiler_bugs.cmake
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_1_cuda.cmake
-- DEAL_II_WITH_CUDA is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_1_lapack.cmake
-- DEAL_II_WITH_LAPACK is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_1_mpi.cmake
-- DEAL_II_WITH_MPI is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_1_threads.cmake
-- TBB_LIBRARY not found! Call:
--     FIND_LIBRARY(TBB_LIBRARY NAMES tbb HINTS PATH_SUFFIXES lib lib64 lib)
-- TBB_DEBUG_LIBRARY not found! Call:
--     FIND_LIBRARY(TBB_DEBUG_LIBRARY NAMES tbb_debug HINTS PATH_SUFFIXES lib lib64 lib)
-- TBB_INCLUDE_DIR not found! Call:
--     FIND_PATH(TBB_INCLUDE_DIR tbb/tbb_stddef.h HINTS PATH_SUFFIXES include include/tbb tbb)
--   TBB_LIBRARIES: *** Required variable "TBB_LIBRARY" set to NOTFOUND ***
--   TBB_INCLUDE_DIRS: *** Required variable "TBB_INCLUDE_DIR" set to NOTFOUND ***
--   TBB_USER_INCLUDE_DIRS: *** Required variable "TBB_INCLUDE_DIR" set to NOTFOUND ***
-- Could NOT find TBB
-- DEAL_II_WITH_THREADS has unmet external dependencies.
-- DEAL_II_WITH_THREADS successfully set up with bundled packages.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_1_zlib.cmake
--   ZLIB_VERSION: 1.2.7
--   ZLIB_LIBRARIES: /usr/lib64/libz.so
--   ZLIB_INCLUDE_DIRS: /usr/include
-- Found ZLIB
-- DEAL_II_WITH_ZLIB successfully set up with external dependencies.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_2_boost.cmake
-- Could NOT find Boost: Found unsuitable version "1.53.0", but required is at least "1.59" (found /usr/include)
--   BOOST_LIBRARIES: *** Required variable "Boost_LIBRARIES" empty ***
--   BOOST_INCLUDE_DIRS: /usr/include
--   BOOST_USER_INCLUDE_DIRS: /usr/include
-- Could NOT find BOOST
-- DEAL_II_WITH_BOOST has unmet external dependencies.
-- DEAL_II_WITH_BOOST successfully set up with bundled packages.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_2_metis.cmake
-- DEAL_II_WITH_METIS is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_2_trilinos.cmake
-- DEAL_II_WITH_TRILINOS is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_2_umfpack.cmake
-- DEAL_II_WITH_UMFPACK is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_3_petsc.cmake
-- DEAL_II_WITH_PETSC is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_adolc.cmake
-- DEAL_II_WITH_ADOLC is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_arpack.cmake
-- DEAL_II_WITH_ARPACK is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_assimp.cmake
-- DEAL_II_WITH_ASSIMP is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_gmsh.cmake
-- DEAL_II_WITH_GMSH is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_gsl.cmake
-- DEAL_II_WITH_GSL is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_hdf5.cmake
-- DEAL_II_WITH_HDF5 is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_muparser.cmake
-- MUPARSER_LIBRARY not found! Call:
--     FIND_LIBRARY(MUPARSER_LIBRARY NAMES muparser muparserd HINTS PATH_SUFFIXES lib lib64 lib)
-- MUPARSER_INCLUDE_DIR not found! Call:
--     FIND_PATH(MUPARSER_INCLUDE_DIR muParserDef.h HINTS PATH_SUFFIXES include)
--   MUPARSER_LIBRARIES: *** Required variable "MUPARSER_LIBRARY" set to NOTFOUND ***
--   MUPARSER_INCLUDE_DIRS: *** Required variable "MUPARSER_INCLUDE_DIR" set to NOTFOUND ***
-- Could NOT find MUPARSER
-- DEAL_II_WITH_MUPARSER has unmet external dependencies.
-- DEAL_II_WITH_MUPARSER successfully set up with bundled packages.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_nanoflann.cmake
-- DEAL_II_WITH_NANOFLANN is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_netcdf.cmake
-- DEAL_II_WITH_NETCDF is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_opencascade.cmake
-- DEAL_II_WITH_OPENCASCADE is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_p4est.cmake
-- DEAL_II_WITH_P4EST is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_scalapack.cmake
-- DEAL_II_WITH_SCALAPACK is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_slepc.cmake
-- DEAL_II_WITH_SLEPC is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/configure/configure_sundials.cmake
-- DEAL_II_WITH_SUNDIALS is set to off.
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/setup_cpack.cmake

--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/setup_custom_targets.cmake
--
-- Include /home/Felipe/BIGSOFTWARE/dealii-9.0.0/cmake/setup_finalize.cmake

CMake Error at cmake/setup_finalize.cmake:95 (MESSAGE):
 

    Configuration error: Cannot compile a test program with the final set of
    compiler and linker flags:
      CXX flags (DEBUG): -pedantic -fPIC -Wall -Wextra -Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Wswitch -Woverloaded-virtual -Wno-deprecated-declarations -Wno-literal-suffix -std=c++11 -Wno-parentheses -Wno-unused-local-typedefs -Og -ggdb -Wa,--compress-debug-sections
      LD flags  (DEBUG): -Wl,--as-needed -rdynamic -fuse-ld=gold pthread -ggdb
      LIBRARIES (DEBUG): m;dl;/usr/lib64/libz.so;rt;
   

 

Call Stack (most recent call first):
  cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
  CMakeLists.txt:132 (VERBOSE_INCLUDE)


-- Configuring incomplete, errors occurred!
See also "/home/Felipe/BIGSOFTWARE/dealii-9.0.0/build/CMakeFiles/CMakeOutput.log".

See also "/home/Felipe/BIGSOFTWARE/dealii-9.0.0/build/CMakeFiles/CMakeError.log".
[Felipe@mu01 build]$

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[Bruno Turcksin]

Felipe,

Le lun. 10 févr. 2020 à 08:49, Felipe Orellana
<felipeorell...@gmail.com> a écrit :

> Here I post the output:

Can you redo it in a clean directory. The output from CMake is
different the first time you run it. Also which compiler are you
using?

Best,

Bruno

[Felipe Orellana]

 Bruno !

     Thanks for replying so swiftly.

     Yes, I had forgotten to recreate the dir from scratch to avoid carrying trash.. I recreated a new building directory, did it from there, I attach a log file with the corresponding output.

     My compilers (g++, gcc):  gcc version 4.8.5 20150623 (Red Hat 4.8.5-28) (GCC)      

     The log also reads '-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes '

     Also, I am using CMake 3.16.0-rc3.

    The log file accuses several failed tests on Deal_II.. the first one online 106:

    -- Performing Test DEAL_II_HAVE_FLAG_Wplacement_new - Failed

cheers many,

Felipe

    

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[Bruno Turcksin]

Felipe,

So this is a strange bug. The problem is from the flag
-Woverloaded-virtual With gcc 4.8 and 4.9 As you can see the flag
alone works https://wandbox.org/permlink/GLbCK7qVqfScXrZp but if I add
another flag it won't compile
https://wandbox.org/permlink/4Lw7aNqGlJkik6SL If you have access to
gcc 5 or later, I would advise you to use that instead. You can also
try the latest version of deal.II maybe we don't use that flag
anymore.

Best,

Bruno

Le lun. 10 févr. 2020 à 09:47, Felipe Orellana

> You received this message because you are subscribed to a topic in the Google Groups "deal.II User Group" group.
> To unsubscribe from this topic, visit https://groups.google.com/d/topic/dealii/SQ6QW-jNzP8/unsubscribe.
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[Daniel Arndt]

So this is a strange bug. The problem is from the flag
-Woverloaded-virtual With gcc 4.8 and 4.9 As you can see the flag
alone works https://wandbox.org/permlink/GLbCK7qVqfScXrZp but if I add
another flag it won't compile
https://wandbox.org/permlink/4Lw7aNqGlJkik6SL If you have access to
gcc 5 or later, I would advise you to use that instead. You can also
try the latest version of deal.II maybe we don't use that flag
anymore.

The problem here are the additional quotes in the compiler arguments, see https://godbolt.org/z/bwDjWy.

Felipe, could you also send the file CMakeErrors.log?

Best,

Daniel

[Bruno Turcksin]

Le lun. 10 févr. 2020 à 10:41, Daniel Arndt <d.arnd...@gmail.com> a écrit :
> The problem here are the additional quotes in the compiler arguments, see https://godbolt.org/z/bwDjWy.

Strange, I get that problem with gcc 4.8 and 4.9 but it works with the
other versions of gcc.

Bruno

[Felipe Orellana]

  Hello Dan,

       Thanks for your attention.

        I attach the CMakeError.log

        The first error is: c++: error: unrecognized command line option '-Wplacement-new'

       Maybe there is a chain sequence, so all sprouts from it..

cheers many,

Felipe

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[Daniel Arndt]

Felipe,

The relevant error is at the end of the file:

Linking CXX executable cmTC_9dc5e
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_9dc5e.dir/link.txt --verbose=1
/usr/bin/c++   -DDEAL_II_HAVE_USABLE_FLAGS_DEBUG -pedantic -fPIC -Wall -Wextra -Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Wswitch -Woverloaded-virtual -Wno-deprecated-declarations -Wno-literal-suffix -std=c++11 -Wno-parentheses -Wno-unused-local-typedefs -Og -ggdb -Wa,--compress-debug-sections    -rdynamic CMakeFiles/cmTC_9dc5e.dir/src.cxx.o  -o cmTC_9dc5e  -rdynamic -fuse-ld=gold pthread -ggdb -lm -ldl /usr/lib64/libz.so -lrt
c++: error: pthread: No such file or directory

This is the issue described in https://github.com/dealii/dealii/issues/9116 and fixed in https://github.com/dealii/dealii/pull/9117.

Best,

Daniel

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[Felipe Orellana]

Hi Dan and Bruno,

     I have followed the thread 9117 for solving this problem, by adding the recommended flag:

    

IF(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.16.0")

LIST(TRANSFORM CMAKE_THREAD_LIBS_INIT PREPEND "-l")

ENDIF()

 which is what I understood from thread 9117 (which btw is not very well written).

But I have not succeeded in compiling. The errors posted are similar:

    -- Performing Test DEAL_II_HAVE_FLAG_Wplacement_new - Failed

     When reading the file 'configure_1_threads.cmake' I found inside my directory dealii-9.0.0/cmake/configure

..

       I wonder where exactly I should add the corresponding 3-lines-instruction flag. I tried two target places inside the script, the two that seemed to me as relevant and appropriate.. which are right below the 'ADD FLAGS' locations..

 I attach the  virgin version of 'configure_1_threads.cmake'.

  what should I do?

      Am I interpreting thread 9117 correctly?

      Am I adding the flags where they should be?

      Is dealii 9.0.0 good for the purpose?

cheers,

Felipe

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[Bruno Turcksin]

Felipe,

Le mar. 11 févr. 2020 à 08:29, Felipe Orellana <felipeorell...@gmail.com> a écrit :

Hi Dan and Bruno,

     I have followed the thread 9117 for solving this problem, by adding the recommended flag:

    

IF(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.16.0")

LIST(TRANSFORM CMAKE_THREAD_LIBS_INIT PREPEND "-l")

ENDIF()

Why didn't you copy/paste the patch? Also you could just use CMake 3.15. This should fix your problem.

But I have not succeeded in compiling. The errors posted are similar:

    -- Performing Test DEAL_II_HAVE_FLAG_Wplacement_new - Failed

That's not really a  problem. This test just checks if your compiler supports -Wplacement-new if it doesn't, we won't use the flag. So that test can fail safely.

When you reconfigure deal.II, you should do it in a clean directory or at least remove cmake's cache.

Best,

Bruno

[Felipe Orellana]

 Hi Bruno,

      Thanks a lot for your response.

  1) YW: When you reconfigure deal.II, you should do it in a clean directory or at least remove cmake's cache..

       Clearly, every time I recompile, I do it from a newly created build directory.

  2)  I am not understanding well here:

    YW:  Why didn't you copy/paste the patch?

    What is 'the patch'  ..how can access that text?,

          if I click on Tamiko's post, the web cannot find the site, cannot find the commit.

YW: Also you could just use CMake 3.15. This should fix your problem.

    

    I do not have CMake 3.15..in my cluster, I installed 3.16 sometime ago. For 3.15 I would need to install one from scratch.

    I think this problem can be bypassed with 3.16 just by using the flags correctly.. that's what i understand from the flag..

cheers many,

Felipe

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[Bruno Turcksin]

Le mar. 11 févr. 2020 à 09:03, Felipe Orellana <felipeorell...@gmail.com> a écrit :

  2)  I am not understanding well here:

    YW:  Why didn't you copy/paste the patch?

    What is 'the patch'  ..how can access that text?,

          if I click on Tamiko's post, the web cannot find the site, cannot find the commit.

Here it is  https://github.com/dealii/dealii/commit/336319966b484889bbdd1da58623293b93980628.patch

Bruno

[Felipe Orellana]

 Hi Bruno, and Dan,

            Great !  I successfully installed dealii 9.0.0. on my cluster. I paste below the finishing line and the tests it passed.

          Thanks a lot for your crucial support.

          Thanks Bruno for your specific instructions.

 I guess any subsequent potential issues could be just due to linking and pointing to this library software.

cheers many,

Felipe

    -- Installing: /home/Felipe/BIGSOFTWARE/dealii-9.0.0/examples/step-9/step-9.release
-- Set runtime path of "/home/Felipe/BIGSOFTWARE/dealii-9.0.0/examples/step-9/step-9.release" to "/home/Felipe/BIGSOFTWARE/dealii-9.0.0/lib"

   [Felipe@mu01 build]$ make test
Scanning dependencies of target test
[100%] Running quicktests...
Test project /home/Felipe/BIGSOFTWARE/dealii-9.0.0/build/tests/quick_tests
    Start 1: step.debug
1/5 Test #1: step.debug .......................   Passed   21.94 sec
    Start 2: step.release
2/5 Test #2: step.release .....................   Passed   19.10 sec
    Start 3: affinity.debug
3/5 Test #3: affinity.debug ...................   Passed   13.06 sec
    Start 4: tbb.debug
4/5 Test #4: tbb.debug ........................   Passed   11.88 sec
    Start 5: boost_zlib.debug
5/5 Test #5: boost_zlib.debug .................   Passed   13.69 sec

100% tests passed, 0 tests failed out of 5

Total Test time (real) =  79.67 sec
Built target test

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