Linux Installation Instructions

Required software packages:

• Fortran 2003/2008 compiler: gfortran >= 7.x, intel >= 19

• Git source control management tool

• Message Passing Interface (MPI): E.g. MPICH2, Open MPI, etc.

• BLAS/LAPACK libraries

• Hierarchical Data Format HDF5

• PETSc git repository

• METIS/ParMETIS (for unstructured grids)

Installation Instructions

1. Install Git. Git is usually installed by default on most modern operating systems. It is usually available through your package manager.

2. Install a Fortran compiler (see bullets above), MPI, BLAS/LAPACK and HDF5 libraries (Note that petsc can be configured to download and install these libraries automatically. E.g. -\-download-mpich=yes or -\-download-openmpi=yes, -\-download-hdf5=yes, -\-download-f-blas-lapack=yes)

3. Install PETSc

   3.1. Clone petsc and check out the supported version:

   git clone https://gitlab.com/petsc/petsc petsc
   cd petsc
   git checkout v3.18.3
   

   3.2. Configure PETSc (see PETSc installation instructions).

   ./configure --with-mpi-dir=<dir> --with-hdf5-dir=<dir> --with-blas-lapack-dir=<dir>
   

   or

   ./configure --download-mpich=yes --download-hdf5=yes --download-hdf5-fortran-bindings=yes --download-fblaslapack=yes
   

   or (to add unstructured grid capability)

   ./configure --download-mpich=yes --download-hdf5=yes --download-hdf5-fortran-bindings=yes --download-fblaslapack=yes --download-metis=yes --download-parmetis=yes
   

   or (for most users, compile an optimized executable with full capability)

   ./configure --CFLAGS='-O3' --CXXFLAGS='-O3' --FFLAGS='-O3' --with-debugging=no --download-mpich=yes --download-hdf5=yes --download-hdf5-fortran-bindings=yes --download-fblaslapack=yes --download-metis=yes --download-parmetis=yes
   

   Note: To support HDF5 zlib compression, add --download-hdf5-configure-arguments="--with-zlib=yes" to the command line.

   3.3. Set the PETSC_DIR and PETSC_ARCH environment variables based on the PETSc installation location (PETSC_DIR) and architecture (PETSC_ARCH: hardware, compilers, etc.). See PETSc environment variables.

   The environmental variables can be set in your ~/.bashrc file by adding the following two lines somewhere in the file:

   export PETSC_DIR=/home/username/path_to_top_level_petsc
   export PETSC_ARCH=gnu-c-debug
   

   Note: You can check what your PETSC_ARCH actually is (the above is just an example) by opening up the directory where PETSc is installed and looking in the configure.log file for --PETSC_ARCH=. After you update your .bashrc file, either close the terminal and open a new one, or type source ./.bashrc for the changes to take effect.

   3.4. Compile PETSc

   cd $PETSC_DIR
   make all
   

   or even better follow the ‘make’ instructions printed at the end of configuration. E.g.

   xxx=========================================================================xxx
     Configure stage complete. Now build PETSc libraries with:
     make PETSC_DIR=/proj/geo002/petsc PETSC_ARCH=cray-xt4-pgi all
   xxx=========================================================================xxx
   

4. Download (clone) PFLOTRAN off Bitbucket.

git clone https://bitbucket.org/pflotran/pflotran

5. Compile PFLOTRAN (ensure that PETSC_DIR and PETSC_ARCH environment variables are properly defined, or PFLOTRAN will not compile)

cd pflotran/src/pflotran
git checkout maint/v4.0
make pflotran