On Linux from source files¶

The following installation procedure describes how to install SLOTH from source files.

It is assumed that the user has a Unix environment with a recent GCC compiler (C++20 compatible), MPI libraries, CMake and Python 3. Obviously, Git is also needed to clone source files.

The following procedure is mainly based on the installation procedure of a parallel MPI version of MFEM. Only the installation of Voro++ (optional) is added.

System packages

On Ubuntu, most prerequisites can be installed with:

sudo apt-get install build-essential cmake git libopenmpi-dev openmpi-bin \
    python3 python3-sympy

Package names may differ on other distributions.

Installing on a supercomputer

For an installation on a supercomputer (modules, no internet access...), see the dedicated procedure on a cluster from source files.

Getting source files¶

The first step consists in cloning MFEM, METIS, HYPRE and, optionally, Voro++.

Clone of the default branch

The current installation procedure assumes that the clone of the source files is based on the default branch of each repository.
Users are free to consider different branches for their installation.

All sources are collected in a global directory called MFEM4SLOTH:

export MFEM4SLOTH=$HOME/MFEM4SLOTH   # absolute path, no trailing slash
mkdir -p $MFEM4SLOTH
cd $MFEM4SLOTH

MFEM¶

MFEM's source files are obtained by running the following command:

git clone https://github.com/mfem/mfem.git

HYPRE¶

HYPRE's source files are obtained by running the following command:

git clone https://github.com/hypre-space/hypre.git

METIS¶

METIS's source files are obtained by running the following commands:

git clone https://github.com/mfem/tpls.git
mv tpls/metis-4.0.3.tar.gz .
tar -zxvf metis-4.0.3.tar.gz
rm -fr metis-4.0.3.tar.gz tpls

Voro++ (optional)¶

Voro++ is only required if SLOTH is built with the --voro option. Its source files are obtained by running the following command:

git clone https://github.com/chr1shr/voro.git

Building dependencies¶

The second step consists in building METIS, HYPRE and, optionally, Voro++.

METIS¶

To build METIS, the following commands must be run:

cd $MFEM4SLOTH/metis-4.0.3
make OPTFLAGS=-Wno-error=implicit-function-declaration
cd ..
ln -s metis-4.0.3 metis-4.0

HYPRE¶

To build HYPRE, the following commands must be run:

cd $MFEM4SLOTH/hypre/src
./configure --disable-fortran
make -j N
cd ../..

where N is a user defined number of CPUs.

Voro++ (optional)¶

To build Voro++, the following commands must be run:

cd $MFEM4SLOTH/voro
cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$PWD/INSTALL
cmake --build build -j N
cmake --install build
cd ..

where N is a user defined number of CPUs.

Using Voro++ in SLOTH

Voro++ is not handled by the --mfem option. Its installation prefix must be given explicitly when building SLOTH:

bash ../envSloth.sh [OPTIONS] --mfem=$MFEM4SLOTH --voro=$MFEM4SLOTH/voro/INSTALL

Building MFEM with dependencies¶

Here, we assume that all dependencies are well built according to the previous directives. At this stage, MFEM can be installed by running the following commands:

cd $MFEM4SLOTH/mfem
make -j N parallel
make install PREFIX=$PWD/INSTALLDIR
cd ..

Checking the MFEM configuration

make parallel configures MFEM with MFEM_USE_MPI=YES and builds the library. The resulting configuration can be checked with:

grep -E "^MFEM_CXX|^MFEM_USE_MPI" config/config.mk

MFEM_CXX must be mpicxx and MFEM_USE_MPI must be YES. If a previous build exists, run make clean before make parallel.

Always reinstall after rebuilding MFEM

SLOTH reads the installed configuration (INSTALLDIR/share/mfem/config.mk), not config/config.mk. After any rebuild of MFEM, run make install PREFIX=$PWD/INSTALLDIR again, otherwise SLOTH keeps using the previous flags.

Installation directory

envSloth.sh --mfem=DIR expects MFEM to be installed in DIR/mfem/INSTALLDIR (with DIR/hypre and DIR/metis-4.0 next to it). The PREFIX above follows this convention.

SLOTH compilation¶

Once MFEM is installed, SLOTH can be built using the envSloth.sh shell script. This script loads MFEM, defines several environment variables, and compiles SLOTH.

Build SLOTH using the envSloth.sh shell script

The envSloth.sh shell script cannot be run directly from the root of the SLOTH repository. Users must create a separate build directory to compile SLOTH.

Installing Sympy

Please ensure that Sympy is installed. Sympy is a mandatory prerequisite to build SLOTH as it is used to handle physical properties.

Once MFEM and Sympy are installed, please run the following commands to build SLOTH:

mkdir build
cd build

bash ../envSloth.sh [OPTIONS]  --mfem=$MFEM4SLOTH

where $MFEM4SLOTH is the absolute path of the folder containing mfem/, hypre/ and metis-4.0/ (ie $HOME/MFEM4SLOTH in the current description, not the MFEM installation directory itself). If Voro++ has been built, add --voro=$MFEM4SLOTH/voro/INSTALL. [OPTIONS] are:

Build type (default: --release):
  --release          Release, with -march=native
  --portable         Release without -march=native (generic x86-64 target on x86)
  --debug | --coverage | --optim | --minsizerel | --relwithdebinfo

Dependencies:
  --mfem=DIR         local MFEM build (instead of spack on Linux / Homebrew on macOS)
  --exprtk=DIR       ExprTk (directory containing exprtk.hpp)
  --voro=DIR         Voro++ installation prefix
  --libtorch=DIR     LibTorch installation prefix
  --external=EXT_LIBDIR,EXT_LIBNAME
                     link Sloth with an external library

Other options:
  --shared           build Sloth as a shared library
  --install=DIR      installation directory (default: ../SlothInstall)
  --np=N             number of parallel compilation jobs (default: 4)
  -h | --help        print this help

Everything after "--" is passed unchanged to CMake, e.g.:
  bash ../envSloth.sh --exprtk=../../exprtk -- -DMATOOLS_VERBOSITY_LEVEL_1=ON

The up-to-date list is printed by bash ../envSloth.sh --help.

By default, this command builds a static library of SLOTH with release compiler options.

Building a shared library of SLOTH

The --shared option enables building a shared library of SLOTH. However, the user must ensure that the library type used for MFEM is compatible. Certain combinations of static and shared libraries may require specific compiler options, such as -fPIC.

The make command within the envSloth.sh script does not compile the tests. To compile tests after SLOTH has been built, run the following command:

make tests -j N

where N is a number of CPUs to use for building the tests in parallel.

Once the tests are compiled, users can verify the build by running all tests with ctest:

ctest -j N

SLOTH installation¶

Users can install the SLOTH library, headers, and scripts into the SlothInstall directory by running:

make install

Installing SLOTH in user-defined repository

By default, SLOTH is installed in a SlothInstall directory at the same level as the repository.

Users can specify another directory with the --install option of the envSloth.sh script.

Reinstalling after a dependency change

The installed CMake files (SlothInstall/lib/cmake/Sloth/SlothTargets.cmake) keep the link flags of MFEM at the time SLOTH was built. If MFEM is rebuilt, SLOTH must be rebuilt and reinstalled from an empty build directory.

Troubleshooting¶

Error	Cause	Fix
Compilation with `g++` instead of `mpicxx`	MPI not enabled in MFEM	`make clean`, then `make parallel` (not `make` alone)
`MFEM configuration file (share/mfem/config.mk) not found`	MFEM not installed, or `--mfem` points to the wrong folder	`make install PREFIX=$PWD/INSTALLDIR` in `mfem/`; `--mfem` must point to `MFEM4SLOTH`