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INSTALL.md

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MAST INSTALLATION

DEPENDENCY LIST

MAST depends on the following libraries:

  • PETSc (http://www.mcs.anl.gov/petsc/) MAST has been tested with PETSc version 3.6.3 and 3.7.7.

  • SLEPc (http://slepc.upv.es) This builds on top of PETSc and provides the eigensolvers. The version numbers are in sync with that of PETSc, so a 3.6.x/3.7.x version of this library should be used.

  • libMesh (http://libmesh.github.io) git clone git://github.com/libMesh/libmesh.git

  • MPI

  • LAPACK

  • BLAS

  • BOOST (http://www.boost.org)

  • BOOST unit test framework

  • EIGEN (http://eigen.tuxfamily.org/index.php?title=Main_Page)

  • PARMETIS/METIS (http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview) Both PETSc and libMesh use these libraries. PETSc can be requested to download and install a version of this library during compile time. libMesh includes these libraries in the contrib subdirectory, which it can compile and link to.

  • HDF5 (https://www.hdfgroup.org/HDF5/) This is used for the ExodusII output formats, which are efficiently read into Paraview. PETSc can be requested to download/build HDF5. libMesh also provides interfaces to Tecplot, and can be configured to build with Tecplot, in which case ExodusII becomes optional.

  • GCMMA Presently, this is the default optimization library. Please obtain it from the author of GCMMA at: krille@math.kth.se

  • libgfortran GCMMA is written in fortran. Hence, linking to GCMMA requires that MAST be linked to libgfortran.

CMAKE BUILD INSTRUCTIONS

  1. Download, build and install METIS and PARMETIS (PETSC can be request to install this during its configuration, which case skip this step.)
  2. Download, build and install PETSc with MPI support. Please make sure to build the shared verion of this library.
  3. Download, build and install SLEPc using the PETSc installation.
  4. Download libMesh. Configure libMesh. Following configuration options are used locally. Please change the options to suit your local system. Note that shared library is being build.
PETSC_DIR=/Users/manav/Documents/codes/numerical_lib/petsc/\
SLEPC_DIR=/Users/manav/Documents/codes/numerical_lib/slepc/\
FC=mpif90-openmpi-mp F77=mpif90-openmpi-mp  CC=mpicc-openmpi-mp\
CXX=mpicxx-openmpi-mp ./configure\
--prefix=${PWD}/../ --enable-mpi --disable-unique-id\
--enable-dependency-tracking --enable-fortran --enable-shared\
--enable-exceptions --disable-openmp --disable-default-comm-world\
--enable-tracefiles  --enable-amr  --enable-vsmoother\
--enable-periodic  --enable-dirichlet  --enable-parmesh\
--enable-nodeconstraint  --enable-ghosted  --enable-pfem\
--enable-ifem --enable-second --enable-xdr --enable-reference-counting\
--enable-perflog --enable-examples --enable-boost --disable-trilinos\
--disable-tbb --enable-sfc --disable-tecplot --disable-tecio\
--enable-metis --enable-parmetis --enable-tetgen --enable-triangle\
--disable-vtk --enable-hdf5 --enable-libHilbert --enable-nanoflann\
--enable-exodus --enable-netcdf --enable-petsc --enable-slepc\
--with-mpi=/opt/local --with-metis=internal --with-hdf5=/opt/local/\
--with-methods="opt dbg"\
  1. Build and install libMesh
  2. Create a subdirectory MAST_DIR/build/opt to build MAST. In the subdirectory, configure cmake build system using the following command. Please modify it based on your local system configuration. You can use -DCMAKE_BUILD_TYPE=Debug to build the debug version.
cmake ../ -Dlibmesh_dir=~/Documents/codes/libmesh \
-Dpetsc_dir=~/Documents/codes/numerical_lib/petsc \
-Dslepc_dir=~/Documents/codes/numerical_lib/slepc \
-Dboost_include_dir=/opt/local/include \
-Dmpi_include_dir=/opt/local/include/openmpi-mp \
-Dmpi_lib_dir=/opt/local/lib/openmpi-mp -Dlapack_lib_dir=/usr/lib \
-Dblas_lib_dir=/usr/lib -Dboost_lib_dir=/opt/local/lib \
-Dgcmma_lib_file=gcmma \
-Dgcmma_lib_dir=~/Documents/codes/numerical_lib/gcmma/build \
-Ddot_lib_file=dot \
-Ddot_lib_dir=~/Documents/codes/numerical_lib/optimization_codes/dot/build \
-Dnpsol_lib_file=npsol \
-Dnpsol_lib_dir=~/Documents/codes/numerical_lib/optimization_codes/npsol/build \
-Dfortran_lib_file=libgfortran.3.dylib \
-Dfortran_lib_dir=/opt/local/lib/libgcc \
-Dboost_test_lib=boost_unit_test_framework-mt \
-DCMAKE_Fortran_COMPILER=mpif90 -DCMAKE_BUILD_TYPE=Release \
-DCMAKE_CXX_FLAGS=-std=c++11 \
-DENABLE_GCMMA=ON \
-DENABLE_DOT=ON \
-DENABLE_NPSOL=ON

Note: CMAKE_BUILD_TYPE=Release builds an optimized version, while CMAKE_BUILD_TYPE=Debug builds the debug version of the code.

Note: GCMMA, DOT, NPSOL can be disabled by providing OFF as the compilation option above.

  1. Build the library using make mast

  2. Build one of the examples using. make example_driver

  3. Get instructions to run example by call it ./example_driver

CLion IDE

CLion is a C/C++ IDE produced by JetBrains (https://www.jetbrains.com/clion/) that leverages the CMake build process for project organization.

To develop/build MAST using CLion, CMake options that are typically supplied to the cmake terminal are provided in the preferences under Preferences > Build, Execution, Deployment > CMake in the CMake Options: box.

An example set of options is:

-DCMAKE_C_COMPILER=/usr/local/bin/mpicc
-DCMAKE_CXX_COMPILER=/usr/local/bin/mpicxx
-DCMAKE_FORTRAN_COMPILER=/usr/local/bin/mpifort
-Dlibmesh_dir=~/Code/libmesh-github-install
-Deigen_include_dir=/usr/local/include
-Dboost_include_dir=/usr/local/include
-Dboost_lib_dir=/usr/local/lib
-Dboost_test_lib=boost_unit_test_framework
-Dmpi_include_dir=/usr/local/include
-Dmpi_lib_dir=/usr/local/lib
-Dblas_lib_dir=/usr/lib
-Dlapack_lib_dir=/usr/lib
-Dpetsc_dir=~/Code/mast-multiphysics-deps2
-Dslepc_dir=~/Code/mast-multiphysics-deps2
-Dfortran_lib_dir=/usr/local/lib/gcc/7
-Dfortran_lib_file=libgfortran.dylib

You will want to use options corresponding to your own environment as described in the CMAKE BUILD INSTRUCTIONS section.