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install_fenics.md

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Prerequisite

  • load the module of mpi like openmpi
  • Need ply module in python ;pip3 install ply
  • adjust LD_LIBRARY_PATH and INCLUDE for boost

pybind11

Python components

  • git clone dijitso, ffc, ufl, instant, fiat. Source links are found from fenics website
  • then do: git checkout 2018.1.0; python3 setup.py install. This will install components into pyhon3 folder
  • downgrade sympy as 1.1(pip3 install sympy==1.1)

Dolfin - boost 1.68 yielded incompatible libdolfin.so. Use 1.56

  • git clone dolfin. This is a stand-alone, not python3 component
  • export PETSC_DIR=/opt/libs/petsc/3.10.3
  • git checkout 2018.1.0; mkdir build; cd build; ccmake .. # setup prefix, eigen3 include, boost include, python3, swig, mpi lib, petsc

if scotch is to be connected, it must be compiled as shared library (*.so)

  • make -j 4; make install; cd ../python;
  • export pybind11_DIR=/opt/libs/pybind11/2.2.4/share/cmake/pybind11/
  • export DOLFIN_DIR=/usr/nic/apps/dolfin/2018.1.0/share/dolfin/cmake/
  • pip3 install .

when coupled with petsc

  • Error found saying SNESTEST is not declared. Disable the source code at {"test", {"Tool to verify Jacobian approximation", SNESTEST}},

mshr

  • git clone https://bitbucket.org/fenics-project/mshr.git
  • git checkout 2018.1.0; mkdir build; cd build;
  • ccmake .. # make CMAKE_INSTALL_PREFIX as dolfin install directory
  • make -j2; make install; cd ../python
  • export CPPFLAGS='-I/usr/nic/libs/boost/1.68.0_gcc485/include/' ; pip3 install .

Fenics