Installation didn't give any errors but when I tried make test, it failed all tests

[jap...@gmail.com]

Hello, 

I tried installing deal.ii today. Installation went fine without any errors however when I did make test, it failed all 6 tests. What should I do? Any help is highly appreciated. Thanks!

The error I get is as follows:

Running quicktests...

Test project /home/japan/dealii/build/tests/quick_tests

    Start 1: step.debug

1/6 Test #1: step.debug .......................***Failed    6.59 sec

make[7]: *** [tests/quick_tests/CMakeFiles/step.debug.run] Error 1

make[6]: *** [tests/quick_tests/CMakeFiles/step.debug.run.dir/all] Error 2

make[5]: *** [tests/quick_tests/CMakeFiles/step.debug.run.dir/rule] Error 2

make[4]: *** [step.debug.run] Error 2

Test step.debug: RUN

===============================   OUTPUT BEGIN  ===============================

[  0%] Built target kill-step.debug-OK

[  0%] Built target obj_non_matching_inst

[  2%] Built target obj_non_matching_debug

[ 11%] Built target obj_boost_serialization_debug

[ 11%] Built target obj_boost_system_debug

[ 13%] Built target obj_boost_iostreams_debug

[ 15%] Built target obj_muparser_debug

[ 15%] Built target expand_instantiations_exe

[ 20%] Built target obj_numerics_inst

[ 28%] Built target obj_numerics_debug

[ 37%] Built target obj_fe_inst

[ 48%] Built target obj_fe_debug

[ 51%] Built target obj_dofs_inst

[ 53%] Built target obj_dofs_debug

[ 57%] Built target obj_lac_inst

[ 66%] Built target obj_lac_debug

[ 68%] Built target obj_base_inst

[ 82%] Built target obj_base_debug

[ 86%] Built target obj_grid_inst

[ 88%] Built target obj_grid_debug

[ 88%] Built target obj_hp_inst

[ 91%] Built target obj_hp_debug

[ 93%] Built target obj_multigrid_inst

[ 95%] Built target obj_multigrid_debug

[ 97%] Built target obj_distributed_inst

[ 97%] Built target obj_distributed_debug

[ 97%] Built target obj_algorithms_inst

[ 97%] Built target obj_algorithms_debug

[ 97%] Built target obj_matrix_free_inst

[ 97%] Built target obj_matrix_free_debug

[ 97%] Built target obj_meshworker_inst

[ 97%] Built target obj_meshworker_debug

[ 97%] Built target obj_opencascade_inst

[100%] Built target obj_opencascade_debug

[100%] Built target obj_physics_inst

[100%] Built target obj_physics_debug

[100%] Built target obj_physics_elasticity_inst

[100%] Built target obj_physics_elasticity_debug

[100%] Built target deal_II.g

[100%] Built target step.debug

step.debug: RUN failed. Output:

./step.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by ./step.debug)

./step.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ./step.debug)

./step.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by ./step.debug)

./step.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./step.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./step.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./step.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./step.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/x86_64-linux-gnu/libtbb.so.2)

tests/quick_tests/CMakeFiles/step.debug.run.dir/build.make:57: recipe for target 'tests/quick_tests/CMakeFiles/step.debug.run' failed

CMakeFiles/Makefile2:10014: recipe for target 'tests/quick_tests/CMakeFiles/step.debug.run.dir/all' failed

CMakeFiles/Makefile2:10021: recipe for target 'tests/quick_tests/CMakeFiles/step.debug.run.dir/rule' failed

Makefile:3425: recipe for target 'step.debug.run' failed

step.debug: ******    RUN failed    *******

===============================    OUTPUT END   ===============================

Expected stage PASSED - aborting

CMake Error at /home/japan/dealii/cmake/scripts/run_test.cmake:140 (MESSAGE):

  *** abort

    Start 2: step.release

2/6 Test #2: step.release .....................***Failed    4.57 sec

make[7]: *** [tests/quick_tests/CMakeFiles/step.release.run] Error 1

make[6]: *** [tests/quick_tests/CMakeFiles/step.release.run.dir/all] Error 2

make[5]: *** [tests/quick_tests/CMakeFiles/step.release.run.dir/rule] Error 2

make[4]: *** [step.release.run] Error 2

Test step.release: RUN

===============================   OUTPUT BEGIN  ===============================

[  0%] Built target kill-step.release-OK

[  0%] Built target obj_non_matching_inst

[  0%] Built target obj_non_matching_release

[  9%] Built target obj_boost_serialization_release

[  9%] Built target obj_boost_system_release

[  9%] Built target obj_boost_iostreams_release

[  9%] Built target obj_muparser_release

[  9%] Built target expand_instantiations_exe

[ 14%] Built target obj_numerics_inst

[ 23%] Built target obj_numerics_release

[ 33%] Built target obj_fe_inst

[ 45%] Built target obj_fe_release

[ 47%] Built target obj_dofs_inst

[ 50%] Built target obj_dofs_release

[ 54%] Built target obj_lac_inst

[ 61%] Built target obj_lac_release

[ 64%] Built target obj_base_inst

[ 76%] Built target obj_base_release

[ 80%] Built target obj_grid_inst

[ 83%] Built target obj_grid_release

[ 83%] Built target obj_hp_inst

[ 85%] Built target obj_hp_release

[ 88%] Built target obj_multigrid_inst

[ 90%] Built target obj_multigrid_release

[ 92%] Built target obj_distributed_inst

[ 95%] Built target obj_distributed_release

[ 95%] Built target obj_algorithms_inst

[ 95%] Built target obj_algorithms_release

[ 95%] Built target obj_matrix_free_inst

[ 97%] Built target obj_matrix_free_release

[ 97%] Built target obj_meshworker_inst

[ 97%] Built target obj_meshworker_release

[ 97%] Built target obj_opencascade_inst

[ 97%] Built target obj_opencascade_release

[ 97%] Built target obj_physics_inst

[ 97%] Built target obj_physics_release

[ 97%] Built target obj_physics_elasticity_inst

[100%] Built target obj_physics_elasticity_release

[100%] Built target deal_II

[100%] Built target step.release

step.release: RUN failed. Output:

./step.release: /home/japan/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by ./step.release)

./step.release: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ./step.release)

./step.release: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by ./step.release)

./step.release: /home/japan/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /home/japan/dealii/build/lib/libdeal_II.so.9.0.0-pre)

./step.release: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/japan/dealii/build/lib/libdeal_II.so.9.0.0-pre)

./step.release: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/japan/dealii/build/lib/libdeal_II.so.9.0.0-pre)

./step.release: /home/japan/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/japan/dealii/build/lib/libdeal_II.so.9.0.0-pre)

./step.release: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/x86_64-linux-gnu/libtbb.so.2)

tests/quick_tests/CMakeFiles/step.release.run.dir/build.make:57: recipe for target 'tests/quick_tests/CMakeFiles/step.release.run' failed

CMakeFiles/Makefile2:9917: recipe for target 'tests/quick_tests/CMakeFiles/step.release.run.dir/all' failed

CMakeFiles/Makefile2:9924: recipe for target 'tests/quick_tests/CMakeFiles/step.release.run.dir/rule' failed

Makefile:3386: recipe for target 'step.release.run' failed

step.release: ******    RUN failed    *******

===============================    OUTPUT END   ===============================

Expected stage PASSED - aborting

CMake Error at /home/japan/dealii/cmake/scripts/run_test.cmake:140 (MESSAGE):

  *** abort

    Start 3: affinity.debug

3/6 Test #3: affinity.debug ...................***Failed    3.95 sec

make[7]: *** [tests/quick_tests/CMakeFiles/affinity.debug.run] Error 1

make[6]: *** [tests/quick_tests/CMakeFiles/affinity.debug.run.dir/all] Error 2

make[5]: *** [tests/quick_tests/CMakeFiles/affinity.debug.run.dir/rule] Error 2

make[4]: *** [affinity.debug.run] Error 2

Test affinity.debug: RUN

===============================   OUTPUT BEGIN  ===============================

[  0%] Built target kill-affinity.debug-OK

[  0%] Built target obj_non_matching_inst

[  2%] Built target obj_non_matching_debug

[ 11%] Built target obj_boost_serialization_debug

[ 11%] Built target obj_boost_system_debug

[ 13%] Built target obj_boost_iostreams_debug

[ 15%] Built target obj_muparser_debug

[ 15%] Built target expand_instantiations_exe

[ 20%] Built target obj_numerics_inst

[ 28%] Built target obj_numerics_debug

[ 37%] Built target obj_fe_inst

[ 48%] Built target obj_fe_debug

[ 51%] Built target obj_dofs_inst

[ 53%] Built target obj_dofs_debug

[ 57%] Built target obj_lac_inst

[ 66%] Built target obj_lac_debug

[ 68%] Built target obj_base_inst

[ 82%] Built target obj_base_debug

[ 86%] Built target obj_grid_inst

[ 88%] Built target obj_grid_debug

[ 88%] Built target obj_hp_inst

[ 91%] Built target obj_hp_debug

[ 93%] Built target obj_multigrid_inst

[ 95%] Built target obj_multigrid_debug

[ 97%] Built target obj_distributed_inst

[ 97%] Built target obj_distributed_debug

[ 97%] Built target obj_algorithms_inst

[ 97%] Built target obj_algorithms_debug

[ 97%] Built target obj_matrix_free_inst

[ 97%] Built target obj_matrix_free_debug

[ 97%] Built target obj_meshworker_inst

[ 97%] Built target obj_meshworker_debug

[ 97%] Built target obj_opencascade_inst

[100%] Built target obj_opencascade_debug

[100%] Built target obj_physics_inst

[100%] Built target obj_physics_debug

[100%] Built target obj_physics_elasticity_inst

[100%] Built target obj_physics_elasticity_debug

[100%] Built target deal_II.g

[100%] Built target affinity.debug

affinity.debug: RUN failed. Output:

./affinity.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ./affinity.debug)

./affinity.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./affinity.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./affinity.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./affinity.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./affinity.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/x86_64-linux-gnu/libtbb.so.2)

tests/quick_tests/CMakeFiles/affinity.debug.run.dir/build.make:57: recipe for target 'tests/quick_tests/CMakeFiles/affinity.debug.run' failed

CMakeFiles/Makefile2:9949: recipe for target 'tests/quick_tests/CMakeFiles/affinity.debug.run.dir/all' failed

CMakeFiles/Makefile2:9956: recipe for target 'tests/quick_tests/CMakeFiles/affinity.debug.run.dir/rule' failed

Makefile:3399: recipe for target 'affinity.debug.run' failed

affinity.debug: ******    RUN failed    *******

===============================    OUTPUT END   ===============================

Expected stage PASSED - aborting

CMake Error at /home/japan/dealii/cmake/scripts/run_test.cmake:140 (MESSAGE):

  *** abort

    Start 4: tbb.debug

4/6 Test #4: tbb.debug ........................***Failed    3.78 sec

make[7]: *** [tests/quick_tests/CMakeFiles/tbb.debug.run] Error 1

make[6]: *** [tests/quick_tests/CMakeFiles/tbb.debug.run.dir/all] Error 2

make[5]: *** [tests/quick_tests/CMakeFiles/tbb.debug.run.dir/rule] Error 2

make[4]: *** [tbb.debug.run] Error 2

Test tbb.debug: RUN

===============================   OUTPUT BEGIN  ===============================

[  0%] Built target kill-tbb.debug-OK

[  0%] Built target obj_non_matching_inst

[  2%] Built target obj_non_matching_debug

[ 11%] Built target obj_boost_serialization_debug

[ 11%] Built target obj_boost_system_debug

[ 13%] Built target obj_boost_iostreams_debug

[ 15%] Built target obj_muparser_debug

[ 15%] Built target expand_instantiations_exe

[ 20%] Built target obj_numerics_inst

[ 28%] Built target obj_numerics_debug

[ 37%] Built target obj_fe_inst

[ 48%] Built target obj_fe_debug

[ 51%] Built target obj_dofs_inst

[ 53%] Built target obj_dofs_debug

[ 57%] Built target obj_lac_inst

[ 66%] Built target obj_lac_debug

[ 68%] Built target obj_base_inst

[ 82%] Built target obj_base_debug

[ 86%] Built target obj_grid_inst

[ 88%] Built target obj_grid_debug

[ 88%] Built target obj_hp_inst

[ 91%] Built target obj_hp_debug

[ 93%] Built target obj_multigrid_inst

[ 95%] Built target obj_multigrid_debug

[ 97%] Built target obj_distributed_inst

[ 97%] Built target obj_distributed_debug

[ 97%] Built target obj_algorithms_inst

[ 97%] Built target obj_algorithms_debug

[ 97%] Built target obj_matrix_free_inst

[ 97%] Built target obj_matrix_free_debug

[ 97%] Built target obj_meshworker_inst

[ 97%] Built target obj_meshworker_debug

[ 97%] Built target obj_opencascade_inst

[100%] Built target obj_opencascade_debug

[100%] Built target obj_physics_inst

[100%] Built target obj_physics_debug

[100%] Built target obj_physics_elasticity_inst

[100%] Built target obj_physics_elasticity_debug

[100%] Built target deal_II.g

[100%] Built target tbb.debug

tbb.debug: RUN failed. Output:

./tbb.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by ./tbb.debug)

./tbb.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ./tbb.debug)

./tbb.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./tbb.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./tbb.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./tbb.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./tbb.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/x86_64-linux-gnu/libtbb.so.2)

tests/quick_tests/CMakeFiles/tbb.debug.run.dir/build.make:57: recipe for target 'tests/quick_tests/CMakeFiles/tbb.debug.run' failed

CMakeFiles/Makefile2:9788: recipe for target 'tests/quick_tests/CMakeFiles/tbb.debug.run.dir/all' failed

CMakeFiles/Makefile2:9795: recipe for target 'tests/quick_tests/CMakeFiles/tbb.debug.run.dir/rule' failed

Makefile:3334: recipe for target 'tbb.debug.run' failed

tbb.debug: ******    RUN failed    *******

===============================    OUTPUT END   ===============================

Expected stage PASSED - aborting

CMake Error at /home/japan/dealii/cmake/scripts/run_test.cmake:140 (MESSAGE):

  *** abort

    Start 5: lapack.debug

5/6 Test #5: lapack.debug .....................***Failed    9.65 sec

/home/japan/dealii/tests/quick_tests/lapack.cc: In function ‘int main()’:

/home/japan/dealii/tests/quick_tests/lapack.cc:100:25: error: variable ‘std::ofstream logfile’ has initializer but incomplete type

   std::ofstream logfile(logname.c_str());

                         ^

make[7]: *** [tests/quick_tests/CMakeFiles/lapack.debug.dir/lapack.cc.o] Error 1

make[6]: *** [tests/quick_tests/CMakeFiles/lapack.debug.dir/all] Error 2

make[5]: *** [tests/quick_tests/CMakeFiles/lapack.debug.run.dir/rule] Error 2

make[4]: *** [lapack.debug.run] Error 2

Test lapack.debug: BUILD

===============================   OUTPUT BEGIN  ===============================

lapack.debug: BUILD failed. Output:

[  0%] Built target kill-lapack.debug-OK

[  0%] Built target obj_non_matching_inst

[  2%] Built target obj_non_matching_debug

[ 10%] Built target obj_boost_serialization_debug

[ 10%] Built target obj_boost_system_debug

[ 13%] Built target obj_boost_iostreams_debug

[ 15%] Built target obj_muparser_debug

[ 15%] Built target expand_instantiations_exe

[ 19%] Built target obj_numerics_inst

[ 28%] Built target obj_numerics_debug

[ 36%] Built target obj_fe_inst

[ 47%] Built target obj_fe_debug

[ 50%] Built target obj_dofs_inst

[ 52%] Built target obj_dofs_debug

[ 56%] Built target obj_lac_inst

[ 65%] Built target obj_lac_debug

[ 67%] Built target obj_base_inst

[ 80%] Built target obj_base_debug

[ 84%] Built target obj_grid_inst

[ 86%] Built target obj_grid_debug

[ 86%] Built target obj_hp_inst

[ 89%] Built target obj_hp_debug

[ 91%] Built target obj_multigrid_inst

[ 93%] Built target obj_multigrid_debug

[ 95%] Built target obj_distributed_inst

[ 95%] Built target obj_distributed_debug

[ 95%] Built target obj_algorithms_inst

[ 95%] Built target obj_algorithms_debug

[ 95%] Built target obj_matrix_free_inst

[ 95%] Built target obj_matrix_free_debug

[ 95%] Built target obj_meshworker_inst

[ 95%] Built target obj_meshworker_debug

[ 95%] Built target obj_opencascade_inst

[ 97%] Built target obj_opencascade_debug

[ 97%] Built target obj_physics_inst

[ 97%] Built target obj_physics_debug

[ 97%] Built target obj_physics_elasticity_inst

[ 97%] Built target obj_physics_elasticity_debug

[ 97%] Built target deal_II.g

[100%] Building CXX object tests/quick_tests/CMakeFiles/lapack.debug.dir/lapack.cc.o

tests/quick_tests/CMakeFiles/lapack.debug.dir/build.make:62: recipe for target 'tests/quick_tests/CMakeFiles/lapack.debug.dir/lapack.cc.o' failed

CMakeFiles/Makefile2:10047: recipe for target 'tests/quick_tests/CMakeFiles/lapack.debug.dir/all' failed

CMakeFiles/Makefile2:9827: recipe for target 'tests/quick_tests/CMakeFiles/lapack.debug.run.dir/rule' failed

Makefile:3347: recipe for target 'lapack.debug.run' failed

lapack.debug: ******    BUILD failed    *******

===============================    OUTPUT END   ===============================

Expected stage PASSED - aborting

CMake Error at /home/japan/dealii/cmake/scripts/run_test.cmake:140 (MESSAGE):

  *** abort

    Start 6: umfpack.debug

6/6 Test #6: umfpack.debug ....................***Failed    3.83 sec

make[7]: *** [tests/quick_tests/CMakeFiles/umfpack.debug.run] Error 1

make[6]: *** [tests/quick_tests/CMakeFiles/umfpack.debug.run.dir/all] Error 2

make[5]: *** [tests/quick_tests/CMakeFiles/umfpack.debug.run.dir/rule] Error 2

make[4]: *** [umfpack.debug.run] Error 2

Test umfpack.debug: RUN

===============================   OUTPUT BEGIN  ===============================

[  0%] Built target kill-umfpack.debug-OK

[  0%] Built target obj_non_matching_inst

[  2%] Built target obj_non_matching_debug

[ 10%] Built target obj_boost_serialization_debug

[ 10%] Built target obj_boost_system_debug

[ 13%] Built target obj_boost_iostreams_debug

[ 15%] Built target obj_muparser_debug

[ 15%] Built target expand_instantiations_exe

[ 19%] Built target obj_numerics_inst

[ 28%] Built target obj_numerics_debug

[ 36%] Built target obj_fe_inst

[ 47%] Built target obj_fe_debug

[ 50%] Built target obj_dofs_inst

[ 52%] Built target obj_dofs_debug

[ 56%] Built target obj_lac_inst

[ 65%] Built target obj_lac_debug

[ 67%] Built target obj_base_inst

[ 80%] Built target obj_base_debug

[ 84%] Built target obj_grid_inst

[ 86%] Built target obj_grid_debug

[ 86%] Built target obj_hp_inst

[ 89%] Built target obj_hp_debug

[ 91%] Built target obj_multigrid_inst

[ 93%] Built target obj_multigrid_debug

[ 95%] Built target obj_distributed_inst

[ 95%] Built target obj_distributed_debug

[ 95%] Built target obj_algorithms_inst

[ 95%] Built target obj_algorithms_debug

[ 95%] Built target obj_matrix_free_inst

[ 95%] Built target obj_matrix_free_debug

[ 95%] Built target obj_meshworker_inst

[ 95%] Built target obj_meshworker_debug

[ 95%] Built target obj_opencascade_inst

[ 97%] Built target obj_opencascade_debug

[ 97%] Built target obj_physics_inst

[ 97%] Built target obj_physics_debug

[ 97%] Built target obj_physics_elasticity_inst

[ 97%] Built target obj_physics_elasticity_debug

[ 97%] Built target deal_II.g

[100%] Built target umfpack.debug

umfpack.debug: RUN failed. Output:

./umfpack.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by ./umfpack.debug)

./umfpack.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ./umfpack.debug)

./umfpack.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./umfpack.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./umfpack.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./umfpack.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/japan/dealii/build/lib/libdeal_II.g.so.9.0.0-pre)

./umfpack.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/x86_64-linux-gnu/libtbb.so.2)

tests/quick_tests/CMakeFiles/umfpack.debug.run.dir/build.make:57: recipe for target 'tests/quick_tests/CMakeFiles/umfpack.debug.run' failed

CMakeFiles/Makefile2:10144: recipe for target 'tests/quick_tests/CMakeFiles/umfpack.debug.run.dir/all' failed

CMakeFiles/Makefile2:10151: recipe for target 'tests/quick_tests/CMakeFiles/umfpack.debug.run.dir/rule' failed

Makefile:3477: recipe for target 'umfpack.debug.run' failed

umfpack.debug: ******    RUN failed    *******

===============================    OUTPUT END   ===============================

Expected stage PASSED - aborting

CMake Error at /home/japan/dealii/cmake/scripts/run_test.cmake:140 (MESSAGE):

  *** abort

0% tests passed, 6 tests failed out of 6

Total Test time (real) =  32.38 sec

The following tests FAILED:

 1 - step.debug (Failed)

 2 - step.release (Failed)

 3 - affinity.debug (Failed)

 4 - tbb.debug (Failed)

 5 - lapack.debug (Failed)

 6 - umfpack.debug (Failed)

Errors while running CTest

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

**                 Error: Some of the quick tests failed.                **

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

Please scroll up or check the file tests/quick_tests/quicktests.log for the

error messages. If you are unable to fix the problems, see the FAQ or write

to the mailing list linked at http://www.dealii.org

The affinity test can fail when you are linking in a library like BLAS

which uses OpenMP. Even without calling any BLAS functions, OpenMP messes

with the thread affinity which causes TBB to run single-threaded only. You

can fix this by exporting OMP_NUM_THREADS=1. Also see GOMP_CPU_AFFINITY 

and OMP_PROC_BIND.

CMake Error at /home/japan/dealii/tests/quick_tests/run.cmake:68 (MESSAGE):

tests/quick_tests/CMakeFiles/test.dir/build.make:57: recipe for target 'tests/quick_tests/CMakeFiles/test' failed

make[3]: *** [tests/quick_tests/CMakeFiles/test] Error 1

CMakeFiles/Makefile2:10273: recipe for target 'tests/quick_tests/CMakeFiles/test.dir/all' failed

make[2]: *** [tests/quick_tests/CMakeFiles/test.dir/all] Error 2

CMakeFiles/Makefile2:10280: recipe for target 'tests/quick_tests/CMakeFiles/test.dir/rule' failed

make[1]: *** [tests/quick_tests/CMakeFiles/test.dir/rule] Error 2

Makefile:3529: recipe for target 'test' failed

make: *** [test] Error 2

[Wolfgang Bangerth]

On 08/11/2017 06:42 PM, jap...@gmail.com wrote:
> step.debug: RUN failed. Output:
> ./step.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.9'
> not found (required by ./step.debug)
> ./step.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version
> `GLIBCXX_3.4.21' not found (required by ./step.debug)
> ./step.debug: /home/japan/anaconda3/lib/libstdc++.so.6: version
> `GLIBCXX_3.4.20' not found (required by ./step.debug)

These error messages typically indicate that either (i) you have multiple
compilers installed in your system and/or (ii) that deal.II or any of the
libraries it depends on (Trilinos, p4est, etc) were built with different
compilers or compiler versions. Could this be the case for you?

Best
W.

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

[drgeoff...@gmail.com]

I'm wondering if I could tag onto this message. I'm having a similar problem. Installed with no problems. However, when I run the tests, they all fail with the error:

symbol lookup error: /usr/lib/libumfpack.so.3.1.0: undefined symbol: amd_realloc

To Wolfgang's question... I have both gcc and g++ installed. I'm not sure if that could cause a conflict. The libraries, in particular the one in question, were installed using apt-get, so I didn't do any compiling on the machine. By the way, my platform is Ubuntu 14.04, if that is important. 

Thanks,

Geoff

[Wolfgang Bangerth]

On 08/12/2017 05:21 PM, drgeoff...@gmail.com wrote:
> I'm wondering if I could tag onto this message. I'm having a similar problem.
> Installed with no problems. However, when I run the tests, they all fail with
> the error:
>
> symbol lookup error: /usr/lib/libumfpack.so.3.1.0: undefined symbol: amd_realloc

That seems like a separate issue unless you also get the error messages about
the CXXABI or GLIBCXX version mismatch.

I think there was a question about your error on the mailing list a while ago.
Can you try to search for it?

[Japan Patel]

Hi Dr. Bangerth,

Thank you for your reply. You are right. When I checked for compilers I have two versions of each compilers. I don't know why that is....I do have petsc installed and I think that might have used different compilers. Is there a way to tell dealii to choose compilers?

I have the following:

$ dpkg --list | grep compiler

ii  g++                                         4:5.3.1-1ubuntu1                           amd64        GNU C++ compiler

ii  g++-5                                       5.4.0-6ubuntu1~16.04.4                     amd64        GNU C++ compiler

ii  gcc                                         4:5.3.1-1ubuntu1                           amd64        GNU C compiler

ii  gcc-5                                       5.4.0-6ubuntu1~16.04.4                     amd64        GNU C compiler

ii  gfortran                                    4:5.3.1-1ubuntu1                           amd64        GNU Fortran 95 compiler

ii  gfortran-5                                  5.4.0-6ubuntu1~16.04.4                     amd64        GNU Fortran compiler

ii  hardening-includes                          2.7ubuntu2                                 all          Makefile for enabling compiler flags for security hardening

ii  libllvm3.6v5:amd64                          1:3.6.2-3ubuntu2                           amd64        Modular compiler and toolchain technologies, runtime library

ii  libllvm3.8:amd64                            1:3.8-2ubuntu4                             amd64        Modular compiler and toolchain technologies, runtime library

ii  libllvm3.8:i386                             1:3.8-2ubuntu4                             i386         Modular compiler and toolchain technologies, runtime library

ii  libprotoc9v5:amd64                          2.6.1-1.3                                  amd64        protocol buffers compiler library

ii  libxkbcommon0:amd64                         0.5.0-1ubuntu2                             amd64        library interface to the XKB compiler - shared library

ii  protobuf-compiler                           2.6.1-1.3                                  amd64        compiler for protocol buffer definition files

Please advise on what to do next. I really appreciate your help!

Thanks!

[Denis Davydov]

Hi,

Usually, one compiles some MPI provider (i.e. Openmpi) and then use its compiler wrappers in majority of dealii' dependencies.

Alternativelt ou can give Spack https://github.com/dealii/dealii/wiki/deal.II-in-Spack a try which guarantees that the whole toolchain is consistent: a single version of a library is used in dependents and (by default) the same compiler is used to build everything.

Regards,
Denis

[Wolfgang Bangerth]

On 08/12/2017 07:22 PM, Japan Patel wrote:
>
> Thank you for your reply. You are right. When I checked for compilers I have
> two versions of each compilers. I don't know why that is....I do have petsc
> installed and I think that might have used different compilers. Is there a way
> to tell dealii to choose compilers?
>

You can also set the CXX environment variable to select a particular compiler
before running cmake. You may have to start from a new, empty, build directory
for this to work.

[drgeoff...@gmail.com]

Thanks. I was able to find the other thread regarding my problem and was able to use the correct cmake flags to get dealii to install correctly. Thank you for your help!

[Japan Patel]

Hey everyone,

Thanks Dr. Bangerth and thanks Denis!!

I was able to run step-1. I installed using spack. It took a while to download all the packages and install them but it was worth it as I was able to run an example problem which I wasn't able to before and all the packages are already linked which would have been a huge hassle had I installed them separately and then tried to link with dealii. Thank you so much for shipping dealii in this format. I really appreciate it! 

I think I can follow Dr. Bangerth's online lectures now and learn how to use dealii. 

Sincerely,

Japan

[Denis Davydov]

Hi Japan,

I am happy to hear that it worked and you resolved your problem!

Sincerely,

Denis.

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[kaleem iqbal]

Dear Prof. Wolfgang;

During running step-70. I found the following error  

Exception on processing:

--------------------------------------------------------
An error occurred in line <1360> of file </home/kaleem/deal.ii-candi/tmp/unpack/deal.II-v9.2.0/source/base/parameter_handler.cc> in function
    void dealii::ParameterHandler::print_parameters(const string&, dealii::ParameterHandler::OutputStyle) const
The violated condition was:
    out
Additional information:
    An input/output error has occurred. There are a number of reasons why this may be happening, both for reading and writing operations.

If this happens during an operation that tries to read data: First, you may be trying to read from a file that doesn't exist or that is not readable given its file permissions. Second, deal.II uses this error at times if it tries to read information from a file but where the information in the file does not correspond to the expected format. An example would be a truncated file, or a mesh file that contains not only sections that describe the vertices and cells, but also sections for additional data that deal.II does not understand.

If this happens during an operation that tries to write data: you may be trying to write to a file to which file or directory permissions do not allow you to write. A typical example is where you specify an output file in a directory that does not exist.
--------------------------------------------------------

Aborting!
----------------------------------------------------
CMakeFiles/run.dir/build.make:57: recipe for target 'CMakeFiles/run' failed
make[3]: *** [CMakeFiles/run] Error 1
CMakeFiles/Makefile2:131: recipe for target 'CMakeFiles/run.dir/all' failed
make[2]: *** [CMakeFiles/run.dir/all] Error 2
CMakeFiles/Makefile2:138: recipe for target 'CMakeFiles/run.dir/rule' failed
make[1]: *** [CMakeFiles/run.dir/rule] Error 2
Makefile:144: recipe for target 'run' failed
make: *** [run] Error 2
Please guide me

Regards

Kaleem iqbal

[heena patel]

Hi Iqbal,

                       Check this link below.

https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!searchin/dealii/step$2070$209.2$20version%7Csort:date/dealii/Y5Lgt9Gn0Zs/vNHTNDdaAwAJ

Regards,

Heena

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[Luca Heltai]

Take a look at your parameter file. It is probably trying to write output file to a directory that does not exist. 

Luca

Il giorno 30 lug 2020, alle ore 10:58, kaleem iqbal <kaleem...@gmail.com> ha scritto:



--

[kaleem iqbal]

Thanks heena. Simulation run now.

Regards

K Iqbal

[kaleem iqbal]

thanks for the reply. simulation run

To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/2E791A8D-2E6F-4FF2-A232-0ABDD68618BF%40gmail.com.

[kaleem iqbal]

I want to simulate FSI with elastic walls in bifurcation carotid arteries in 2D. is it possible to use that geometry?

[Wolfgang Bangerth]

On 7/30/20 3:59 AM, kaleem iqbal wrote:
> I want to simulate FSI with elastic walls in bifurcation carotid arteries in
> 2D. is it possible to use that geometry?

It is possible to use this geometry, but you need to generate a mesh for it.
(See step-49 for mesh generation.)