Cluster from source files¶

The following installation procedure describes how to install SLOTH from source files on a supercomputer. Here, the description is based on an installation done on CCRT Topaze.

This procedure is mainly based on the installation procedure from source files on local computer.

Getting source files on local computer¶

The first step consists in cloning MFEM, METIS, HYPRE and SuiteSparse.

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.

cd $HOME
mkdir 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

SuiteSparse¶

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

git clone https://github.com/DrTimothyAldenDavis/SuiteSparse.git

Copy of source files on the supercomputer¶

Copy of the MFEM4SLOTH folder on the supercomputer by running the following command:

rsync --info=progress2 -e ssh -avz MFEM4SLOTH <login>@<remote_host>:$DEST_DIR

Building dependencies on the supercomputer¶

The second step consists in building METIS, HYPRE and SuiteSparse on the supercomputer. From now, all command are run on the supercomputer.

Load required modules¶

Before building dependencies, it is necessary to load some modules. Please keep in mind that versions depend on the targeted environment.

gnu, mpi, cmake are required to build MFEM with METIS, HYPRE and SuiteSparse. For SuiteSparse, blas and mpfr are also needed.

module load gnu/11.1.0
module load mpi/openmpi/4.1.4
module load cmake/3.29.6
module load blas/openblas/0.3.26
module load mpfr/4.2.0

Find available modules

The list of available modules can be obtained using the following command:

module avail [optional_string]

where an optional string can be specified to refine the search for modules. This string can be a partial name.

METIS¶

To build METIS, the following command must be run:

cd metis-4.0.3
make OPTFLAGS=-Wno-error=implicit-function-declaration
mkdir include
cp Lib/*.h include/
cd ..
ln -s metis-4.0.3 metis-4.0

The fourth instruction differs from the installation procedure from source files on local computer.

HYPRE¶

To build HYPRE, the following command must be run:

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

where N is a user defined number of CPUs.

SuiteSparse¶

To build SuiteSparse, the following commands must be run:

cd SuiteSparse/
make -j N
make install DESTDIR=$PWD/INSTALLDIR
mv INSTALLDIR/usr/local/lib64/* lib/
mv INSTALLDIR/usr/local/include/suitesparse/* include/
mv INSTALLDIR/usr/local/bin/* bin/
cd ..

where N is a user defined number of CPUs.

The fourth instruction differs from the installation procedure from source files on local computer.

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 mfem
make -j N parallel MFEM_USE_SUITESPARSE=YES 
make install PREFIX=INSTALLDIR
cd ..

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 command to build SLOTH:

mkdir build 
cd build

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

where $MFEM4SLOTH is a variable associated with the path towards the MFEM installation (ie $HOME/MFEM4SLOTH in the current description) and [OPTIONS] are:

    --release        Build with Release compiler options

    --optim          Build with Optim compiler options

    --debug          Build with Debug compiler options

    --coverage       Build with Coverage compiler options

    --minsizerel     Build with MinSizeRel compiler options

    --relwithdebinfo Build with RelWithDebInfo compiler options

    --external       Build SLOTH with an external package

    --shared         Build a shared library for Sloth

    --install        Specify the installation path for Sloth 
                     (default: a "SlothInstallation" directory at the same level as the repository)

    --np             Specify the number of CPUs to use for compilation (default: 4)

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 SlothInstallation directory by running:

make install

Installing SLOTH in user-defined repository

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

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