Installation issues

Asked by Sudhi Sharma Padillath Vasudevan

Hello Sir,

I am using Mac OS(High Seirra) and have pulled 2016.1.0 stable version of fenics inside a docker container. I wish to install DOLFWAVE inside this container along with fenics. I followed the steps as in you bitbucket repository : https://bitbucket.org/dolfwave/dolfwave-main/src/master/INSTALL

During make I get the following error ,

(Including only starting and final lines of error messsage)

 66%] Building CXX object src/CMakeFiles/dolfwave.dir/2hdforms/SymProj.cpp.o
[ 66%] Building CXX object src/CMakeFiles/dolfwave.dir/outputs/invariants.cpp.o
/home/fenics/shared/dolfwave/src/outputs/invariants.cpp: In member function ‘double dolfin::dolfwave::Dolfwave::Volume(const dolfin::Mesh&, dolfin::Expression&, std::__cxx11::string) cons’:
/home/fenics/shared/dolfwave/src/outputs/invariants.cpp:58:69: error: no matching function for call to ‘Vol::Form_M::Form_M(const dolfin::Mesh&, dolfin::Function&, dolfin::Expression&)’
     functional.reset(new Vol::Functional(mesh,(*eta_phi[4])[0],depth));

.....

.
.
.
.
/home/fenics/shared/dolfwave/src/outputs/../1hd1sforms/Inv3KdVBBMP2_1D.h:3605:7: note: candidate expects 1 argument, 3 provided
src/CMakeFiles/dolfwave.dir/build.make:1334: recipe for target 'src/CMakeFiles/dolfwave.dir/outputs/invariants.cpp.o' failed
make[2]: *** [src/CMakeFiles/dolfwave.dir/outputs/invariants.cpp.o] Error 1
CMakeFiles/Makefile2:213: recipe for target 'src/CMakeFiles/dolfwave.dir/all' failed
make[1]: *** [src/CMakeFiles/dolfwave.dir/all] Error 2
Makefile:127: recipe for target 'all' failed
make: *** [all] Error 2

Please help me to install it successfully.

Question information

Language:
English Edit question
Status:
Answered
For:
DOLFWAVE Edit question
Assignee:
No assignee Edit question
Last query:
Last reply:
Revision history for this message
Nuno Lopes (ndlopes) said :
#1

Hi, Dear Sudhi Sharma Padillath Vasudevan,

Unfortunately I'm not maintaining the code for some time now, so I'm not sure if I can help you.
However, did you tweaked the file dolfwave.conf in order to match your system?
I Just compiled the code in my osx (Mojave) and everything went ok.

What are the output of your dolfin-version and "ffc --version"? It should be 1.6.0.

Since the compilation went ok until 66%,
I'm guessing the problem is related with your FEniCS installation version vs Dolfwave.
In those times, the interface for some of dolfin and ffc libraries were changing fast.

I used to have Ubuntu and OSX installations,
In Ubuntu I used the dorsal installation of FEniCS but in OSX I use the binaries.

My script to config the bash in OSX is the following: (it replaces the dolfwave.conf)
Please change in order to match your system.

######################################################################
# .bash_profile
clear

#FEniCS_RESOURCES=`echo "$BASH_SOURCE" | sed -e 's|/share/fenics/fenics.conf||'`
FEniCS_RESOURCES="/Applications/FEniCS.app/Contents/Resources"

export PATH=$FEniCS_RESOURCES/bin:$PATH
export DYLD_FALLBACK_LIBRARY_PATH=$FEniCS_RESOURCES/lib:$FEniCS_RESOURCES/lib/vtk-5.10:$DYLD_FALLBACK_LIBRARY_PATH
export PYTHONPATH=$FEniCS_RESOURCES/lib/python2.7/site-packages:$FEniCS_RESOURCES/lib/vtk-5.10:$PYTHONPATH
export PKG_CONFIG_PATH=$FEniCS_RESOURCES/lib/pkgconfig:/usr/lib/pkgconfig:$PKG_CONFIG_PATH
export MANPATH=$FEniCS_RESOURCES/man:$FEniCS_RESOURCES/share/man:$MANPATH
export BOOST_DIR=$FEniCS_RESOURCES
export SWIG_LIB=$FEniCS_RESOURCES/share/swig/3.0.5
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export OPAL_PREFIX=$FEniCS_RESOURCES

OSX_VERSION=`sw_vers -productVersion | cut -d '.' -f 1 -f 2`

if [ -z "$FENICS_CONF_SILENT" ]; then
    # Clear screen
    clear

    # Set prompt
    export PS1="\[\033[01;32m\]\u@\[\033[01;31m\]FEniCS:\[\033[01;34m\]\W\$ \[\033[00m\]"

    # Set terminal title
    echo -n -e "\033]0;FEniCS\007"
fi

### DOLFWAVE CONFIG
export DOLFWAVE_ROOT=/Users/nuno/dolfwave-main
export FENICS_LIB_PATH=$FEniCS_RESOURCES/lib

export DYLD_FALLBACK_LIBRARY_PATH=${DOLFWAVE_ROOT}/src:$DYLD_FALLBACK_LIBRARY_PATH
export PATH=${DOLFWAVE_ROOT}/tools/run_and_log:$PWD/bin:$PATH
export DOLFWAVE_CMAKE_CONFIG_PATH=${DOLFWAVE_ROOT}/cmake
export DOLFWAVE_SOURCE_PATH=${DOLFWAVE_ROOT}/src
export DOLFWAVE_LIB_DYLIB=${DOLFWAVE_ROOT}/src/libdolfwave.dylib

# Variables to solve DSO Linkage problems
# Check the CMakeLists.txt in each demo
export DOLFIN_LIB_DYLIB=${FENICS_LIB_PATH}/libdolfin.dylib

######################################################

I hope it helps,
Moreover, could you please let me know what do you plan to do with dolfwave?

Cheers,
Nuno

Revision history for this message
Sudhi Sharma Padillath Vasudevan (sudhipv) said :
#2

Hello Sir,

What are the output of your dolfin-version and "ffc --version"? It should be 1.6.0.

Did you mean 16.1.0 ?? In one of the readme file i saw the compatible version is 2016.1.0.

My version output reads,

dolfin-version
2016.1.0
fenics@dbf88813b5ff:~/shared/dolfwave$ ffc --version
This is FFC, the FEniCS Form Compiler, version 2016.1.0.
UFC backend version 2016.1.0, signature 1b14b3cad537cb974523d529928ad9bde02ef657.
For further information, visit https://bitbucket.org/fenics-project/ffc/.

I am trying out the edited config file given by you, but it still fails at the same place. I think its related to the version itself.

Also,

I am working on quantifying uncertainty for high fidelity problems using domain decomposition based solvers.

I wish to try out examples from DOLFWAVE and see whether I can adopt my methods to solve these problems for non-linear time dependant cases.

Revision history for this message
Nuno Lopes (ndlopes) said :
#3

Hi,

It should be
"$dolfin-version
>>>1.6.0
$ffc --version
>>>This is FFC, the FEniCS Form Compiler, version 1.6.0.
>>>For further information, visit http://www.fenics.org/ffc/".

The FEniCS libraries were changing at the time...probably It should be a FEniCS version 2016.1 and not 2016.1.0.
And please if you decide to keep the effort, use the bitbucket repository.

Please, Let me know of you were able to install the libraries.

Revision history for this message
Sudhi Sharma Padillath Vasudevan (sudhipv) said :
#4

Hello Sir,

I have checked the fenics bit bucket repo to see the available versions and i got a version for 1.6.0

https://bitbucket.org/fenics-project/dolfin/downloads/

Now, my dolfin-version reads,

dolfin-version
1.6.0

ffc --version
This is FFC, the FEniCS Form Compiler, version 1.6.0.
For further information, visit http://www.fenics.org/ffc/.

But still, after cmake with FFC recompilation

make results in error,

 77%] Building CXX object src/CMakeFiles/dolfwave.dir/rungekutta/rk.cpp.o
[ 80%] Building CXX object src/CMakeFiles/dolfwave.dir/predictorcorrector/predictorcorrectora.cpp.o
[ 80%] Building CXX object src/CMakeFiles/dolfwave.dir/predictorcorrector/predictorcorrectorb.cpp.o
/home/fenics/shared/dolfwave/src/predictorcorrector/predictorcorrectorb.cpp: In member function ‘int dolfin::dolfwave::PredCorr::SolveLU(boost::shared_array<std::shared_ptr<dolfin::Vector> >&, boost::shared_array<std::shared_ptr<dolfin::Form> >&, dolfin::Matrix&, boost::shared_array<std::shared_ptr<dolfin::Function> >&, double, dolfin::DirichletBC&, bool, dolfin::PETScLUSolver&, dolfin::Matrix&, std::__cxx11::string)’:
/home/fenics/shared/dolfwave/src/predictorcorrector/predictorcorrectorb.cpp:66:36: error: ‘isnan’ was not declared in this scope
           if(Assert(!(isnan(l2error)||isinf(l2error)),__LINE__,
                                    ^
...
...
...
/usr/include/eigen3/Eigen/src/Core/GlobalFunctions.h:17:4: note: in definition of macro ‘EIGEN_ARRAY_DECLARE_GLOBAL_UNARY’
   (NAME)(const Eigen::ArrayBase<Derived>& x) { \
    ^
In file included from /usr/include/eigen3/Eigen/Core:302:0,
                 from /usr/include/eigen3/Eigen/SparseCore:11,
                 from /usr/include/eigen3/Eigen/Sparse:26,
                 from /home/fenics/build/include/dolfin/la/EigenMatrix.h:26,
                 from /home/fenics/build/include/dolfin/la/dolfin_la.h:24,
                 from /home/fenics/build/include/dolfin.h:22,
                 from /home/fenics/shared/dolfwave/src/predictorcorrector/predictorcorrectorb.cpp:16:
/usr/include/eigen3/Eigen/src/Core/MathFunctions.h:931:46: note: ‘Eigen::numext::isinf’
 template<typename T> EIGEN_DEVICE_FUNC bool (isinf) (const T &x) { return internal::isinf_impl(x); }
                                              ^
src/CMakeFiles/dolfwave.dir/build.make:1598: recipe for target 'src/CMakeFiles/dolfwave.dir/predictorcorrector/predictorcorrectorb.cpp.o' failed
make[2]: *** [src/CMakeFiles/dolfwave.dir/predictorcorrector/predictorcorrectorb.cpp.o] Error 1
CMakeFiles/Makefile2:213: recipe for target 'src/CMakeFiles/dolfwave.dir/all' failed
make[1]: *** [src/CMakeFiles/dolfwave.dir/all] Error 2
Makefile:127: recipe for target 'all' failed
make: *** [all] Error 2

My, dolfwave config file reads,

######################################################################
# .bash_profile
clear

#FEniCS_RESOURCES=`echo "$BASH_SOURCE" | sed -e 's|/share/fenics/fenics.conf||'`

FEniCS_RESOURCES = /home/fenics/build

#FEniCS_RESOURCES="/Applications/FEniCS.app/Contents/Resources"

export PATH=$FEniCS_RESOURCES/bin:$PATH
export DYLD_FALLBACK_LIBRARY_PATH=$FEniCS_RESOURCES/lib:$FEniCS_RESOURCES/lib/vtk-5.10:$DYLD_FALLBACK_LIBRARY_PATH
export PYTHONPATH=$FEniCS_RESOURCES/lib/python2.7/site-packages:$FEniCS_RESOURCES/lib/vtk-5.10:$PYTHONPATH
export PKG_CONFIG_PATH=$FEniCS_RESOURCES/lib/pkgconfig:/usr/lib/pkgconfig:$PKG_CONFIG_PATH
export MANPATH=$FEniCS_RESOURCES/man:$FEniCS_RESOURCES/share/man:$MANPATH
export BOOST_DIR=$FEniCS_RESOURCES
export SWIG_LIB=$FEniCS_RESOURCES/share/swig/3.0.5
export CC=/usr/bin/gcc
export CXX=/usr/bin/g++
export OPAL_PREFIX=$FEniCS_RESOURCES

OSX_VERSION=`sw_vers -productVersion | cut -d '.' -f 1 -f 2`

if [ -z "$FENICS_CONF_SILENT" ]; then
    # Clear screen
    clear

    # Set prompt
    export PS1="\[\033[01;32m\]\u@\[\033[01;31m\]FEniCS:\[\033[01;34m\]\W\$ \[\033[00m\]"

    # Set terminal title
    echo -n -e "\033]0;FEniCS\007"
fi

### DOLFWAVE CONFIG
export DOLFWAVE_ROOT=/home/fenics/shared/dolfwave
export FENICS_LIB_PATH=$FEniCS_RESOURCES/lib

export DYLD_FALLBACK_LIBRARY_PATH=${DOLFWAVE_ROOT}/src:$DYLD_FALLBACK_LIBRARY_PATH
export PATH=${DOLFWAVE_ROOT}/tools/run_and_log:$PWD/bin:$PATH
export DOLFWAVE_CMAKE_CONFIG_PATH=${DOLFWAVE_ROOT}/cmake
export DOLFWAVE_SOURCE_PATH=${DOLFWAVE_ROOT}/src
export DOLFWAVE_LIB_DYLIB=${DOLFWAVE_ROOT}/src/libdolfwave.dylib

# Variables to solve DSO Linkage problems
# Check the CMakeLists.txt in each demo
export DOLFIN_LIB_DYLIB=${FENICS_LIB_PATH}/libdolfin.dylib

######################################################

The way I download the fenics stable version through docker is :

docker run -ti -v $(pwd):/home/fenics/shared quay.io/fenicsproject/<image-name>:latest.

docker run -ti -v $(pwd):/home/fenics/shared quay.io/fenicsproject/stable:1.6.0

(https://bitbucket.org/fenics-project/docker/src/master/)

I don't know whether DOLFWAVE uses any other minor update version or not ?

Revision history for this message
Nuno Lopes (ndlopes) said :
#5

Hi,
Partially good news :)

Now that appears to be a Xcode, command-line tools, xctoolchain, installation issue.
If you google it you will find the isnan isinf issue on OSX.. Good luck.
/usr/include/eigen3/Eigen/src/Core/MathFunctions.h:931:46: note: ‘Eigen::numext::isinf’ ....

That lines are to avoid "infinite" or "not a number" in the iterative errors.
You could try to comment that lines in the code in order to see if the compilation continues to the end.

Nuno

Revision history for this message
Sudhi Sharma Padillath Vasudevan (sudhipv) said :
#6

Hello Sir,

After searching for a bit and adding some header files I was able to finally install the DOLFWAVE inside docker.

I also did

source dolfwave.conf

after that.

But now trying out the demos again gives some errors. May be I am missing some steps here.
Could you also please tell me how to run these demos ?

I tried cmake CMakeLists.txt and then make , but here again it gives error.

fenics@FEniCS:ZhaoP2$ make
[ 33%] Linking CXX executable 1HD_horizontalLandslide_ZhaoP2_demo
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/main.cpp.o: In function `main':
main.cpp:(.text+0x21e): undefined reference to `dolfin::dolfwave::Dolfwave::Dolfwave(int, double, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
main.cpp:(.text+0x30f): undefined reference to `dolfin::IntervalMesh::IntervalMesh(unsigned long, double, double)'
main.cpp:(.text+0x342): undefined reference to `dolfin::Constant::Constant(double)'
main.cpp:(.text+0x37b): undefined reference to `dolfin::dolfwave::Dolfwave::SpacesFunctionsVectorsInit(dolfin::Mesh&)'
main.cpp:(.text+0x39b): undefined reference to `dolfin::dolfwave::Dolfwave::BilinearFormInit(dolfin::Mesh&, dolfin::Expression&)'
main.cpp:(.text+0x3d9): undefined reference to `dolfin::dolfwave::Dolfwave::LinearFormsInit(dolfin::Expression&, dolfin::Expression&, dolfin::Expression&, dolfin::Expression&, dolfin::Expression&, dolfin::Expression&)'
main.cpp:(.text+0x3ec): undefined reference to `dolfin::dolfwave::Dolfwave::MatricesAssemble()'
main.cpp:(.text+0x400): undefined reference to `dolfin::dolfwave::Dolfwave::LUFactorization(bool)'
main.cpp:(.text+0x414): undefined reference to `dolfin::dolfwave::Dolfwave::Info(bool) const'
main.cpp:(.text+0x457): undefined reference to `dolfin::dolfwave::Dolfwave::RKInit(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
main.cpp:(.text+0x489): undefined reference to `dolfin::dolfwave::Dolfwave::SaveEta(unsigned int) const'
main.cpp:(.text+0x4ab): undefined reference to `dolfin::dolfwave::Dolfwave::DepthPlot(dolfin::Mesh const&, dolfin::Expression&, bool) const'
main.cpp:(.text+0x4ee): undefined reference to `dolfin::dolfwave::Dolfwave::RKSolve(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
main.cpp:(.text+0x52a): undefined reference to `dolfin::dolfwave::Dolfwave::PCInit(dolfin::Mesh const&, bool)'
main.cpp:(.text+0x54d): undefined reference to `dolfin::dolfwave::Dolfwave::MatricesAssemble()'
main.cpp:(.text+0x55c): undefined reference to `dolfin::dolfwave::Dolfwave::PCSolve()'
main.cpp:(.text+0x589): undefined reference to `dolfin::dolfwave::Dolfwave::PreviewEta(unsigned int) const'
main.cpp:(.text+0x59d): undefined reference to `dolfin::dolfwave::Dolfwave::SaveEta(unsigned int) const'
main.cpp:(.text+0x5bf): undefined reference to `dolfin::dolfwave::Dolfwave::DepthPlot(dolfin::Mesh const&, dolfin::Expression&, bool) const'
main.cpp:(.text+0x60d): undefined reference to `dolfin::dolfwave::Dolfwave::Volume(dolfin::Mesh const&, dolfin::Expression&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) const'
main.cpp:(.text+0x687): undefined reference to `dolfin::info(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ...)'
main.cpp:(.text+0x6cd): undefined reference to `dolfin::Constant::~Constant()'
main.cpp:(.text+0x8ba): undefined reference to `dolfin::Constant::~Constant()'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/main.cpp.o: In function `__static_initialization_and_destruction_0(int, int)':
main.cpp:(.text+0x967): undefined reference to `boost::system::generic_category()'
main.cpp:(.text+0x973): undefined reference to `boost::system::generic_category()'
main.cpp:(.text+0x97f): undefined reference to `boost::system::system_category()'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/main.cpp.o: In function `dolfin::IntervalMesh::~IntervalMesh()':
main.cpp:(.text._ZN6dolfin12IntervalMeshD2Ev[_ZN6dolfin12IntervalMeshD5Ev]+0x30): undefined reference to `dolfin::Mesh::~Mesh()'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/main.cpp.o: In function `dolfin::dolfwave::Dolfwave::~Dolfwave()':
main.cpp:(.text._ZN6dolfin8dolfwave8DolfwaveD2Ev[_ZN6dolfin8dolfwave8DolfwaveD5Ev]+0x14): undefined reference to `dolfin::dolfwave::Dolfwave::TimerStop()'
main.cpp:(.text._ZN6dolfin8dolfwave8DolfwaveD2Ev[_ZN6dolfin8dolfwave8DolfwaveD5Ev]+0x20): undefined reference to `dolfin::dolfwave::Dolfwave::FinalOutput() const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/main.cpp.o: In function `Depth::Depth(double const&)':
main.cpp:(.text._ZN5DepthC2ERKd[_ZN5DepthC5ERKd]+0x18): undefined reference to `dolfin::Expression::Expression()'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/main.cpp.o: In function `SourceEta::SourceEta(double const&)':
main.cpp:(.text._ZN9SourceEtaC2ERKd[_ZN9SourceEtaC5ERKd]+0x18): undefined reference to `dolfin::Expression::Expression()'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/main.cpp.o:(.rodata._ZTVN6dolfin12IntervalMeshE[_ZTVN6dolfin12IntervalMeshE]+0x20): undefined reference to `dolfin::Mesh::str[abi:cxx11](bool) const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/main.cpp.o:(.rodata._ZTIN6dolfin12IntervalMeshE[_ZTIN6dolfin12IntervalMeshE]+0x10): undefined reference to `typeinfo for dolfin::Mesh'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/main.cpp.o: In function `Depth::~Depth()':
main.cpp:(.text._ZN5DepthD2Ev[_ZN5DepthD5Ev]+0x2d): undefined reference to `dolfin::Expression::~Expression()'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/main.cpp.o: In function `SourceEta::~SourceEta()':
main.cpp:(.text._ZN9SourceEtaD2Ev[_ZN9SourceEtaD5Ev]+0x2d): undefined reference to `dolfin::Expression::~Expression()'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o: In function `__static_initialization_and_destruction_0(int, int)':
Depth.cpp:(.text+0x383): undefined reference to `boost::system::generic_category()'
Depth.cpp:(.text+0x38f): undefined reference to `boost::system::generic_category()'
Depth.cpp:(.text+0x39b): undefined reference to `boost::system::system_category()'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTV9SourceEta[_ZTV9SourceEta]+0x20): undefined reference to `dolfin::GenericFunction::evaluate(double*, double const*, ufc::cell const&) const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTV9SourceEta[_ZTV9SourceEta]+0x28): undefined reference to `dolfin::Expression::value_rank() const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTV9SourceEta[_ZTV9SourceEta]+0x30): undefined reference to `dolfin::Expression::value_dimension(unsigned long) const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTV9SourceEta[_ZTV9SourceEta]+0x38): undefined reference to `dolfin::Expression::eval(dolfin::Array<double>&, dolfin::Array<double> const&, ufc::cell const&) const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTV9SourceEta[_ZTV9SourceEta]+0x48): undefined reference to `dolfin::Expression::restrict(double*, dolfin::FiniteElement const&, dolfin::Cell const&, double const*, ufc::cell const&) const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTV9SourceEta[_ZTV9SourceEta]+0x50): undefined reference to `dolfin::Expression::compute_vertex_values(std::vector<double, std::allocator<double> >&, dolfin::Mesh const&) const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTV9SourceEta[_ZTV9SourceEta]+0x80): undefined reference to `dolfin::Variable::str[abi:cxx11](bool) const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTV5Depth[_ZTV5Depth]+0x20): undefined reference to `dolfin::GenericFunction::evaluate(double*, double const*, ufc::cell const&) const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTV5Depth[_ZTV5Depth]+0x28): undefined reference to `dolfin::Expression::value_rank() const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTV5Depth[_ZTV5Depth]+0x30): undefined reference to `dolfin::Expression::value_dimension(unsigned long) const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTV5Depth[_ZTV5Depth]+0x38): undefined reference to `dolfin::Expression::eval(dolfin::Array<double>&, dolfin::Array<double> const&, ufc::cell const&) const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTV5Depth[_ZTV5Depth]+0x48): undefined reference to `dolfin::Expression::restrict(double*, dolfin::FiniteElement const&, dolfin::Cell const&, double const*, ufc::cell const&) const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTV5Depth[_ZTV5Depth]+0x50): undefined reference to `dolfin::Expression::compute_vertex_values(std::vector<double, std::allocator<double> >&, dolfin::Mesh const&) const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTV5Depth[_ZTV5Depth]+0x80): undefined reference to `dolfin::Variable::str[abi:cxx11](bool) const'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTI9SourceEta[_ZTI9SourceEta]+0x10): undefined reference to `typeinfo for dolfin::Expression'
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/Depth.cpp.o:(.rodata._ZTI5Depth[_ZTI5Depth]+0x10): undefined reference to `typeinfo for dolfin::Expression'
collect2: error: ld returned 1 exit status
CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/build.make:120: recipe for target '1HD_horizontalLandslide_ZhaoP2_demo' failed
make[2]: *** [1HD_horizontalLandslide_ZhaoP2_demo] Error 1
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/all' failed
make[1]: *** [CMakeFiles/1HD_horizontalLandslide_ZhaoP2_demo.dir/all] Error 2
Makefile:83: recipe for target 'all' failed

Revision history for this message
Nuno Lopes (ndlopes) said :
#7

Hi,
I think the problem is due to the linkage of the libraries.
Check the CMakeFiles.txt in the demo dir and also try to adapt the previous bash script for FEniCs and Dolfwave configuration.
However, I wasn't never able to install Dolfwave with the docker version of FEniCS.

Good luck.

Can you help with this problem?

Provide an answer of your own, or ask Sudhi Sharma Padillath Vasudevan for more information if necessary.

To post a message you must log in.