Installation problem using Docker

[debasishuiuc]

Hello, I am trying to install and compile pi-BEM using docker and have not been able to do so.

I used

docker run -v pwd:/pwd_to_your_own_directory/ -i -t mathlab/deal2lkit:latest bash

It successfully installed and then I tried installing pi-BEM but got the following error. Pleas help.

dealii@2dabcdcc27ca:$ git clone https://github.com/mathLab/pi-BEM.git
Cloning into 'pi-BEM'...
remote: Enumerating objects: 13, done.
remote: Counting objects: 100% (13/13), done.
remote: Compressing objects: 100% (12/12), done.
remote: Total 1886 (delta 4), reused 7 (delta 1), pack-reused 1873
Receiving objects: 100% (1886/1886), 803.27 KiB | 1.38 MiB/s, done.
Resolving deltas: 100% (1426/1426), done.
Checking connectivity... done.
dealii@2dabcdcc27ca:$ cd pi-BEM
dealii@2dabcdcc27ca:/pi-BEM$ mkdir build
dealii@2dabcdcc27ca:/pi-BEM$ cd build
dealii@2dabcdcc27ca:/pi-BEM/build$ cmake ../
-- Using the deal.II-9.0.0-pre installation found at /home/dealii/dealii-master
-- Include macro /home/dealii/dealii-master/share/deal.II/macros/macro_deal_ii_query_git_information.cmake
-- Include macro /home/dealii/dealii-master/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake
-- Include macro /home/dealii/dealii-master/share/deal.II/macros/macro_deal_ii_setup_target.cmake
-- Include macro /home/dealii/dealii-master/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake
-- Include macro /home/dealii/dealii-master/share/deal.II/macros/macro_deal_ii_add_test.cmake
-- Include macro /home/dealii/dealii-master/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/mpicc
-- Check for working C compiler: /usr/bin/mpicc -- 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/mpicxx
-- Check for working CXX compiler: /usr/bin/mpicxx -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Using the deal2lkit-9.0-pre installation found at /home/dealii/libs/deal2lkit-master
-- Include macro /home/dealii/libs/deal2lkit-master/share/deal2lkit/macros/macro_deal2lkit_initialize_cached_variables.cmake
-- Include macro /home/dealii/libs/deal2lkit-master/share/deal2lkit/macros/macro_deal2lkit_query_git_information.cmake
-- Include macro /home/dealii/libs/deal2lkit-master/share/deal2lkit/macros/macro_deal2lkit_setup_target.cmake
-- Include macro /home/dealii/libs/deal2lkit-master/share/deal2lkit/macros/macro_deal2lkit_invoke_autopilot.cmake
-- Found Release version of deal.II.
-- Found Release version of deal2lkit.
-- Configuring library bem_fma-lib
-- Configuring executable bem_fma_2d
-- Configuring executable bem_fma_3d
-- Found Debug version of deal.II.
-- Found Debug version of deal2lkit.
-- Configuring library bem_fma-lib.g
-- Configuring executable bem_fma_2d.g
-- Configuring executable bem_fma_3d.g
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dealii/pi-BEM/build
dealii@2dabcdcc27ca:/pi-BEM/build$ make -j4
Scanning dependencies of target bem_fma-lib
Scanning dependencies of target bem_fma-lib.g
[ 3%] Building CXX object CMakeFiles/bem_fma-lib.g.dir/source/local_expansion_coeff.cc.o
[ 6%] Building CXX object CMakeFiles/bem_fma-lib.g.dir/source/driver.cc.o
[ 10%] Building CXX object CMakeFiles/bem_fma-lib.dir/source/driver.cc.o
[ 13%] Building CXX object CMakeFiles/bem_fma-lib.dir/source/local_expansion_coeff.cc.o
[ 16%] Building CXX object CMakeFiles/bem_fma-lib.dir/source/computational_domain.cc.o
[ 20%] Building CXX object CMakeFiles/bem_fma-lib.g.dir/source/computational_domain.cc.o
In file included from /home/dealii/pi-BEM/source/../include/driver.h:66:0,
from /home/dealii/pi-BEM/source/driver.cc:1:
/home/dealii/pi-BEM/source/../include/bem_problem.h:23:44: fatal error: deal.II/lac/affine_constraints.h: No such file or directory
compilation terminated.
In file included from /home/dealii/pi-BEM/source/../include/driver.h:66:0,
from /home/dealii/pi-BEM/source/driver.cc:1:
/home/dealii/pi-BEM/source/../include/bem_problem.h:23:44: fatal error: deal.II/lac/affine_constraints.h: No such file or directory
compilation terminated.
CMakeFiles/bem_fma-lib.dir/build.make:62: recipe for target 'CMakeFiles/bem_fma-lib.dir/source/driver.cc.o' failed
make[2]: *** [CMakeFiles/bem_fma-lib.dir/source/driver.cc.o] Error 1
make[2]: *** Waiting for unfinished jobs....
CMakeFiles/bem_fma-lib.g.dir/build.make:62: recipe for target 'CMakeFiles/bem_fma-lib.g.dir/source/driver.cc.o' failed
make[2]: *** [CMakeFiles/bem_fma-lib.g.dir/source/driver.cc.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[ 23%] Building CXX object CMakeFiles/bem_fma-lib.g.dir/source/multipole_expansion.cc.o
In file included from /home/dealii/pi-BEM/source/computational_domain.cc:3:0:
/home/dealii/pi-BEM/source/../include/computational_domain.h:281:21: error: ‘NormalToMeshProjectionManifold’ is not a member of ‘dealii::OpenCASCADE’
std::shared_ptr<OpenCASCADE::NormalToMeshProjectionManifold<2, 3>>>
^
/home/dealii/pi-BEM/source/../include/computational_domain.h:281:21: error: ‘NormalToMeshProjectionManifold’ is not a member of ‘dealii::OpenCASCADE’
/home/dealii/pi-BEM/source/../include/computational_domain.h:281:68: error: wrong number of template arguments (2, should be 1)
std::shared_ptr<OpenCASCADE::NormalToMeshProjectionManifold<2, 3>>>
^
In file included from /usr/include/c++/5/bits/shared_ptr.h:52:0,
from /usr/include/c++/5/memory:82,
from /home/dealii/dealii-master/include/deal.II/bundled/boost/move/algorithm.hpp:33,
from /home/dealii/dealii-master/include/deal.II/bundled/boost/move/move.hpp:32,
from /home/dealii/dealii-master/include/deal.II/bundled/boost/variant/detail/move.hpp:28,
from /home/dealii/dealii-master/include/deal.II/bundled/boost/variant/detail/initializer.hpp:23,
from /home/dealii/dealii-master/include/deal.II/bundled/boost/variant/variant.hpp:30,
from /home/dealii/dealii-master/include/deal.II/bundled/boost/variant.hpp:17,
from /home/dealii/dealii-master/include/deal.II/base/table_handler.h:30,
from /home/dealii/dealii-master/include/deal.II/base/convergence_table.h:21,
from /home/dealii/pi-BEM/source/../include/computational_domain.h:9,
from /home/dealii/pi-BEM/source/computational_domain.cc:3:
/usr/include/c++/5/bits/shared_ptr_base.h:345:11: note: provided for ‘template class std::shared_ptr’
class shared_ptr;
^
In file included from /home/dealii/pi-BEM/source/computational_domain.cc:3:0:
/home/dealii/pi-BEM/source/../include/computational_domain.h:281:69: error: template argument 1 is invalid
std::shared_ptr<OpenCASCADE::NormalToMeshProjectionManifold<2, 3>>>
^
/home/dealii/pi-BEM/source/../include/computational_domain.h:281:69: error: template argument 2 is invalid
/home/dealii/pi-BEM/source/../include/computational_domain.h:281:71: error: expected unqualified-id before ‘>’ token
std::shared_ptr<OpenCASCADE::NormalToMeshProjectionManifold<2, 3>>>
^
/home/dealii/pi-BEM/source/computational_domain.cc: In member function ‘void ComputationalDomain::refine_and_resize(unsigned int)’:
/home/dealii/pi-BEM/source/computational_domain.cc:628:11: error: ‘normal_to_mesh_projectors’ was not declared in this scope
normal_to_mesh_projectors.push_back(
^
/home/dealii/pi-BEM/source/computational_domain.cc:629:30: error: ‘NormalToMeshProjectionManifold’ is not a member of ‘dealii::OpenCASCADE’
std::make_shared<OpenCASCADE::NormalToMeshProjectionManifold<2, 3>>(
^
/home/dealii/pi-BEM/source/computational_domain.cc:629:30: error: ‘NormalToMeshProjectionManifold’ is not a member of ‘dealii::OpenCASCADE’
/home/dealii/pi-BEM/source/computational_domain.cc:648:37: error: ‘normal_to_mesh_projectors’ was not declared in this scope
tria.set_manifold(1 + i, *normal_to_mesh_projectors[i]);
^
/home/dealii/pi-BEM/source/computational_domain.cc: In instantiation of ‘ComputationalDomain::~ComputationalDomain() [with int dim = 2]’:
/home/dealii/pi-BEM/source/computational_domain.cc:1191:16: required from here
/home/dealii/pi-BEM/source/computational_domain.cc:55:7: error: ‘class dealii::Triangulation<1, 2>’ has no member named ‘reset_manifold’
tria.reset_manifold(1 + i);
^
/home/dealii/pi-BEM/source/computational_domain.cc:60:7: error: ‘class dealii::Triangulation<1, 2>’ has no member named ‘reset_manifold’
tria.reset_manifold(11 + i);
^
/home/dealii/pi-BEM/source/computational_domain.cc:63:3: error: ‘class dealii::Triangulation<1, 2>’ has no member named ‘reset_manifold’
tria.reset_manifold(0);
^
/home/dealii/pi-BEM/source/computational_domain.cc: In instantiation of ‘ComputationalDomain::~ComputationalDomain() [with int dim = 3]’:
/home/dealii/pi-BEM/source/computational_domain.cc:1192:16: required from here
/home/dealii/pi-BEM/source/computational_domain.cc:55:7: error: ‘class dealii::Triangulation<2, 3>’ has no member named ‘reset_manifold’
tria.reset_manifold(1 + i);
^
/home/dealii/pi-BEM/source/computational_domain.cc:60:7: error: ‘class dealii::Triangulation<2, 3>’ has no member named ‘reset_manifold’
tria.reset_manifold(11 + i);
^
/home/dealii/pi-BEM/source/computational_domain.cc:63:3: error: ‘class dealii::Triangulation<2, 3>’ has no member named ‘reset_manifold’
tria.reset_manifold(0);
^
In file included from /home/dealii/pi-BEM/source/computational_domain.cc:3:0:
/home/dealii/pi-BEM/source/../include/computational_domain.h:281:21: error: ‘NormalToMeshProjectionManifold’ is not a member of ‘dealii::OpenCASCADE’
std::shared_ptr<OpenCASCADE::NormalToMeshProjectionManifold<2, 3>>>
^
/home/dealii/pi-BEM/source/../include/computational_domain.h:281:21: error: ‘NormalToMeshProjectionManifold’ is not a member of ‘dealii::OpenCASCADE’
/home/dealii/pi-BEM/source/../include/computational_domain.h:281:68: error: wrong number of template arguments (2, should be 1)
std::shared_ptr<OpenCASCADE::NormalToMeshProjectionManifold<2, 3>>>
^
In file included from /usr/include/c++/5/bits/shared_ptr.h:52:0,
from /usr/include/c++/5/memory:82,
from /home/dealii/dealii-master/include/deal.II/bundled/boost/move/algorithm.hpp:33,
from /home/dealii/dealii-master/include/deal.II/bundled/boost/move/move.hpp:32,
from /home/dealii/dealii-master/include/deal.II/bundled/boost/variant/detail/move.hpp:28,
from /home/dealii/dealii-master/include/deal.II/bundled/boost/variant/detail/initializer.hpp:23,
from /home/dealii/dealii-master/include/deal.II/bundled/boost/variant/variant.hpp:30,
from /home/dealii/dealii-master/include/deal.II/bundled/boost/variant.hpp:17,
from /home/dealii/dealii-master/include/deal.II/base/table_handler.h:30,
from /home/dealii/dealii-master/include/deal.II/base/convergence_table.h:21,
from /home/dealii/pi-BEM/source/../include/computational_domain.h:9,
from /home/dealii/pi-BEM/source/computational_domain.cc:3:
/usr/include/c++/5/bits/shared_ptr_base.h:345:11: note: provided for ‘template class std::shared_ptr’
class shared_ptr;
^
In file included from /home/dealii/pi-BEM/source/computational_domain.cc:3:0:
/home/dealii/pi-BEM/source/../include/computational_domain.h:281:69: error: template argument 1 is invalid
std::shared_ptr<OpenCASCADE::NormalToMeshProjectionManifold<2, 3>>>
^
/home/dealii/pi-BEM/source/../include/computational_domain.h:281:69: error: template argument 2 is invalid
/home/dealii/pi-BEM/source/../include/computational_domain.h:281:71: error: expected unqualified-id before ‘>’ token
std::shared_ptr<OpenCASCADE::NormalToMeshProjectionManifold<2, 3>>>
^
/home/dealii/pi-BEM/source/computational_domain.cc: In member function ‘void ComputationalDomain::refine_and_resize(unsigned int)’:
/home/dealii/pi-BEM/source/computational_domain.cc:628:11: error: ‘normal_to_mesh_projectors’ was not declared in this scope
normal_to_mesh_projectors.push_back(
^
/home/dealii/pi-BEM/source/computational_domain.cc:629:30: error: ‘NormalToMeshProjectionManifold’ is not a member of ‘dealii::OpenCASCADE’
std::make_shared<OpenCASCADE::NormalToMeshProjectionManifold<2, 3>>(
^
/home/dealii/pi-BEM/source/computational_domain.cc:629:30: error: ‘NormalToMeshProjectionManifold’ is not a member of ‘dealii::OpenCASCADE’
/home/dealii/pi-BEM/source/computational_domain.cc:648:37: error: ‘normal_to_mesh_projectors’ was not declared in this scope
tria.set_manifold(1 + i, *normal_to_mesh_projectors[i]);
^
/home/dealii/pi-BEM/source/computational_domain.cc: In instantiation of ‘ComputationalDomain::~ComputationalDomain() [with int dim = 2]’:
/home/dealii/pi-BEM/source/computational_domain.cc:1191:16: required from here
/home/dealii/pi-BEM/source/computational_domain.cc:55:7: error: ‘class dealii::Triangulation<1, 2>’ has no member named ‘reset_manifold’
tria.reset_manifold(1 + i);
^
/home/dealii/pi-BEM/source/computational_domain.cc:60:7: error: ‘class dealii::Triangulation<1, 2>’ has no member named ‘reset_manifold’
tria.reset_manifold(11 + i);
^
/home/dealii/pi-BEM/source/computational_domain.cc:63:3: error: ‘class dealii::Triangulation<1, 2>’ has no member named ‘reset_manifold’
tria.reset_manifold(0);
^
/home/dealii/pi-BEM/source/computational_domain.cc: In instantiation of ‘ComputationalDomain::ComputationalDomain() [with int dim = 3]’:
/home/dealii/pi-BEM/source/computational_domain.cc:1192:16: required from here
/home/dealii/pi-BEM/source/computational_domain.cc:55:7: error: ‘class dealii::Triangulation<2, 3>’ has no member named ‘reset_manifold’
tria.reset_manifold(1 + i);
^
/home/dealii/pi-BEM/source/computational_domain.cc:60:7: error: ‘class dealii::Triangulation<2, 3>’ has no member named ‘reset_manifold’
tria.reset_manifold(11 + i);
^
/home/dealii/pi-BEM/source/computational_domain.cc:63:3: error: ‘class dealii::Triangulation<2, 3>’ has no member named ‘reset_manifold’
tria.reset_manifold(0);
^
CMakeFiles/bem_fma-lib.dir/build.make:110: recipe for target 'CMakeFiles/bem_fma-lib.dir/source/computational_domain.cc.o' failed
make[2]: *** [CMakeFiles/bem_fma-lib.dir/source/computational_domain.cc.o] Error 1
CMakeFiles/Makefile2:136: recipe for target 'CMakeFiles/bem_fma-lib.dir/all' failed
make[1]: *** [CMakeFiles/bem_fma-lib.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
CMakeFiles/bem_fma-lib.g.dir/build.make:110: recipe for target 'CMakeFiles/bem_fma-lib.g.dir/source/computational_domain.cc.o' failed
make[2]: *** [CMakeFiles/bem_fma-lib.g.dir/source/computational_domain.cc.o] Error 1
CMakeFiles/Makefile2:284: recipe for target 'CMakeFiles/bem_fma-lib.g.dir/all' failed
make[1]: *** [CMakeFiles/bem_fma-lib.g.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2
dealii@2dabcdcc27ca:/pi-BEM/build$