This page describes how to install libMesh/MAST on Ubuntu 18.04 (Eoan Ermine) using dependencies from the standard package manager.

It is written for someone who has limited experience compiling software on Linux and contains details a more advanced user likely won't need.

Dependencies

Installing libMesh/MAST on Ubuntu 18.04 (Bionic Beaver) is relatively simple if you are able to use Ubuntu's Advanced Packaging Tool (APT) since all of the dependencies are provided in the standard package repositories. To do so we assume you have sudo privileges on your system and it is connected to the internet. If you are not a privileged user, ask an administrator to install these dependencies or consider manually compiling/installing the dependencies in your home directory.

To install all of the dependencies, simply execute the following commands in the terminal/shell. Some of the packages will install a number of required sub-dependencies.

sudo apt-get install -y git m4
sudo apt-get install -y gcc gfortran
sudo apt-get install -y libblas-dev
sudo apt-get install -y liblapack-dev liblapack-doc liblapack-doc-man
sudo apt-get install -y mpi-default-dev libopenmpi-dev openmpi-doc
sudo apt-get install -y petsc-dev libpetsc3.7-dev libpetsc3.7.7 libpetsc3.7.7-dbg libpetsc3.7.7-dev petsc3.7.7-doc
sudo apt-get install -y slepc-dev libslepc3.7-dev libslepc3.7.4 libslepc3.7.4-dev slepc3.7.4-doc
sudo apt-get install -y libmetis-dev libmetis5-dbg libmetis-doc
sudo apt-get install -y libparmetis-dev parmetis-doc
sudo apt-get install -y libboost-all-dev libboost-doc
sudo apt-get install -y libeigen3-dev libeigen3-doc
sudo apt-get install -y libglpk-dev glpk-utils glpk-doc
sudo apt-get install -y libnlopt-dev libnlopt0
sudo apt-get install -y libvtk6-dev libvtk6.3 vtk6

CMake

We utilize some newer features in CMake and require a more recent version (3.13) than is included in the default APT repositories (3.10) for Ubuntu 18.04. The following code adds Kitware's (CMake maintainers) APT repository and installs the most recent version of CMake.

sudo apt-get install -y apt-transport-https ca-certificates gnupg software-properties-common wget
wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null | gpg --dearmor - | sudo tee /etc/apt/trusted.gpg.d/kitware.gpg >/dev/null
sudo apt-add-repository 'deb https://apt.kitware.com/ubuntu/ bionic main'
sudo apt-get update
sudo apt-get -y install cmake

libMesh

When using dependencies from Ubuntu 19.10's standard package repository, only a recent version of libMesh can be built. Any official libMesh "release" up to and include v1.5.1 will fail to build with linking errors related to a conflict between the Ubuntu apt provided metis (which the provided PETSc package requires) and the metis that libMesh builds itself. This issue was resolved in libMesh repository commit df1e2b7 by adding the ability for libMesh to properly use an external metis. The MAST developers currently provide a version of libMesh v1.5.1 that have the fixes for the build patched in.

As a result, we need to build libMesh from the v1.5.1_with_build_updates branch of jdeaton's fork of the official libMesh repository. To do this we first clone the forked repository from GitHub, then checkout the appropriate branch of the code. From the directory where you want to build libMesh, execute the following in the terminal/shell, which will clone libMesh into a new directory libmesh:

git clone https://github.com/jdeaton/libmesh.git
cd libmesh
git checkout v1.5.1_with_build_updates
git submodule init
git submodule update

libMesh compilation/installation follows the common Makefile-based configure, make, make install process that is common on Linux/Unix systems. Before beginning, we set a few environment variables by executing the following commands from inside the libmesh directory in the terminal/shell. libMesh_INSTALL_DIR specifies where the products of the libMesh build process will be installed. By default, text below specifies a directory that will be alongside libmesh named libmesh_install. You may change this if you wish. NP specifies the number of parallel jobs to use during compilation.

export libMesh_INSTALL_DIR="$(cd ..; pwd)/libmesh_install"

export NP=4

We recommend compiling libMesh in a dedicated build directory to keep from cluttering the main libMesh repository. From inside the libmesh directory, create a build directory and navigate into it with:

mkdir build

cd build

We can now configure the libMesh build by pasting the entire contents of the following snippet into the shell/terminal. By default, libMesh will configure optimized, development, and debug versions of the library.

PETSC_DIR=/usr/lib/petsc \
SLEPC_DIR=/usr/lib/slepc \
../configure \
  --prefix=${libMesh_INSTALL_DIR} \
  --disable-strict-lgpl \
  --enable-triangle=yes \
  --enable-tetgen=yes \
  --with-metis=/usr/lib/x86_64-linux-gnu \
  --with-metis-include=/usr/include \
  --with-eigen-include=/usr/include \
  --with-glpk-include=/usr/include \
  --with-glpk-lib=/usr/lib/x86_64-linux-gnu \
  --with-nlopt-include=/usr/include \
  --with-nlopt-lib=/usr/lib/x86_64-linux-gnu \
  --with-vtk-include=/usr/include/vtk-6.3 \
  --with-vtk-lib=/usr/lib/x86_64-linux-gnu

If the configuration was successful, you should have the following output under Optional Packages:

Optional Packages:
  boost............................ : yes
  capnproto........................ : no
  cppunit.......................... : no
  curl............................. : no
  eigen............................ : yes
  exodus........................... : yes
     version....................... : v5.22
  fparser.......................... : yes
     build from version............ : release
  glpk............................. : yes
  gmv.............................. : yes
  gzstream......................... : yes
  hdf5............................. : no
  laspack.......................... : yes
  libhilbert....................... : yes
  metaphysicl...................... : yes
  metis............................ : yes
  mpi.............................. : yes
  nanoflann........................ : yes
  nemesis.......................... : yes
     version....................... : v5.22
  netcdf........................... : yes
     version....................... : 4
  nlopt............................ : yes
  parmetis......................... : yes
  petsc............................ : yes
     version....................... : 3.7.7
  qhull............................ : yes
  sfcurves......................... : yes
  slepc............................ : yes
     version....................... : 3.7.4
  thread model..................... : pthread
  c++ rtti ........................ : yes
  tecio............................ : yes
  tecplot...(vendor binaries)...... : no
  tetgen........................... : yes
  triangle......................... : yes
  trilinos......................... : no
  vtk.............................. : yes
     version....................... : 6.3.0

We can now compile the libMesh binaries by executing in the terminal/shell, which will take some time:

make -j ${NP}

Optionally, you can now test compiled libraries by executing make check in the terminal/shell. This will compile and run a number of example cases provided in the libMesh source. Note that this will take a long time and since you are using standard, well-maintained dependencies it is probably not necessary.

Finally, we will install the products of the libMesh compilation by simply executing the following, which will place all of the necessary libMesh files for MAST into the directory specified above with libMesh_INSTALL_DIR. Optionally, after this is complete, you can test the installed binaries using make checkinstall. Again, this takes quite a while and is likely not necessary with this standard installation.

make install

The important directories from the installed contents are:

${libMesh_INSTALL_DIR}/bin - libMesh utility programs
${libMesh_INSTALL_DIR}/contrib - third-party utility programs bundled with libMesh
${libMesh_INSTALL_DIR}/examples - source code for libMesh examples and wrapper scripts to run them
${libMesh_INSTALL_DIR}/include - development headers for libMesh and bundled third-party packages
${libMesh_INSTALL_DIR}/lib - libraries for libMesh and bundled third-party packages
${libMesh_INSTALL_DIR}/share - single element reference meshes

MAST

The following instructions describe how to configure and compile the MAST library, some example programs, and the unit tests. In this guide, we don't build support for Cython, the pyNastran interface, interfaces to commercial/licensed optimizers (DOT, SNOPT, GCMMA) or the documentation.

Since MAST is in a state of ongoing development, we will build it from the master branch on the GitHub repository so we have the most up-to-date changes. If you have forked MAST, substitute the remote URL for you fork in the git clone line.

We begin by cloning the repository from inside the directory of your choice:

git clone https://github.com/MASTmultiphysics/mast-multiphysics

cd mast-multiphysics

We again recommend building in a dedicated build directory to keep from cluttering the main repository. From inside the mast-multiphysics directory, create a build directory and navigate into it with:

mkdir build

cd build

The build process for MAST differs slightly from libMesh since we utilize CMake to generate Makefiles rather than a configure script. This is done by executing the following commands in the terminal/shell from inside the build directory. CMake will perform some inspections of your system, locate dependencies, and create the Makefiles necessary to build MAST in the build directory.

cmake .. \
  -DCMAKE_BUILD_TYPE=Debug \
  -DCMAKE_C_COMPILER=mpicc \
  -DCMAKE_CXX_COMPILER=mpic++ \
  -DCMAKE_Fortran_COMPILER=mpifort \
  -DlibMesh_DIR=${libMesh_INSTALL_DIR} \
  -DPETSc_DIR=/usr/lib/petsc \
  -DSLEPc_DIR=/usr/lib/slepc \
  -DEIGEN3_ROOT=/usr/include/eigen3 \
  -DBOOST_ROOT=/usr \
  -DBUILD_DOC=OFF \
  -DENABLE_DOT=OFF \
  -DENABLE_GCMMA=OFF \
  -DENABLE_SNOPT=OFF\
  -DENABLE_NASTRANIO=OFF \
  -DENABLE_CYTHON=OFF

Note that the above commands create a Debug version of the MAST library (using the *_dbg versions of libMesh). This is required if you want to utilize a C++ debugger (such as gdb) and includes a significant amount of diagnostic/debug output. For more performance, an optimized/Release version can be built by changing the -DCMAKE_BUILD_TYPE CMake variable to Release.

After CMake configuration completes, you can build the MAST library (libmast), several example problems, and unit tests by simply executing the following in the terminal/shell.

make -j ${NP}

Todo:

Contact libMesh developers to resolve inability of libMesh configuration process to find Ubuntu repository provided HDF5 headers/libraries (openmpi/serial).

Update page with next release of libMesh after v1.5.1 that will incorporate changes to deal with metis conflicts.

Update the guide to include building support for pyNastran, Cython, and generating the documentation locally.