Install PFLOTRAN on CHPC | Shuai Computational and Integrated Hydrology Group

Last updated: 2026-1-15

See this documentation for installation on Linux machine.

Setup environment

module load gcc/8.5.0 cmake/3.26.0

Install PETSc

Download Petsc from Bitbucket, and save it into directory petsc_v3.24.0, and checkout the latest version 3.24.0.

git clone https://gitlab.com/petsc/petsc.git petsc_v3.24.0
cd petsc_v3.24.0
git checkout v3.24.0

Set current dir as PETSC_DIR, define --PETSC_ARCH to any name, and a subdir with the same name will be created under the PETSC_DIR (eg.petsc_v3.20.2/notchpeak-gcc-8.5.0)

export PETSC_DIR=$PWD
export PETSC_ARCH=notchpeak-gcc-8.5.0

Configure PETSc

Use the recommended configuration. This will install a Fortran compiler, MPI, HDF5, and BLAS/LAPACK.

./configure --CC=$CC --CXX=$CXX --FC=$FC --F77=$F77 --COPTFLAGS='-O3' --CXXOPTFLAGS='-O3' --FOPTFLAGS='-O3 -Wno-unused-function' --with-debugging=no --download-mpich=yes --download-hdf5=yes --download-hdf5-fortran-bindings=yes --download-fblaslapack=yes --download-metis=yes --download-parmetis=yes --download-hdf5-configure-arguments="--with-zlib=yes"

This will download and install mpich-4.3.2rc2 and hdf5_1.14.6.

After configure, you will see something similar to the following message:

xxx=========================================================================xxx
 # Configure stage complete. Now build PETSc libraries with (gnumake build):
   make PETSC_DIR=/uufs/chpc.utah.edu/common/home/shuai-group1/pflotran/petsc_v3.24.0 PETSC_ARCH=notchpeak-gcc-8.5.0 all
xxx=========================================================================xxx

Follow the prompt to build PETSc:

 make PETSC_DIR=/uufs/chpc.utah.edu/common/home/shuai-group1/pflotran/petsc_v3.24.0 PETSC_ARCH=notchpeak-gcc-8.5.0 all

Download and compile PFLOTRAN

git clone https://bitbucket.org/pflotran/pflotran pflotran_master
cd pflotran_master
# optional. To checkout a specific version
# git checkout v6.0

cd src/pflotran && make -j4 pflotran # use parallel thread to compile? You can also try -j8, -j16... if more cores are available

WARNING

The pflotran version has to be compatible with the PETSc version used. E.g., PFLOTRAN v6.0 is compatible with PETSc v3.21.4, while current PFLOTRAN master branch is compatible with PETSc v3.24.x.

After compilation is complete, a new file named pflotran* executable is generated at current directory. You can also move this executable to another directory, e.g. ` ./bin/pflotran*, then you can export this directory to PATH`.

mkdir bin && cd bin && cp ../pflotran .

Fast compilation (use with caution)

Caution! This works if only a small change is made because the compilation will not rebuild all the dependencies.

make pflotran fast=1

Regression test

Do a regression test to see if pflotran if working. First, request an interactive node to run the regression test.

salloc -N 1 -n 2 -t 30 -A notchpeak-shared-short -p notchpeak-shared-short
mpirun -np 1 pflotran -pflotranin $PFLOTRAN_DIR/regression_tests/default/543/543_flow.in # need to use one core to run this example

Within seconds, the test model should finish, and the installation processes are done! 🎉

Create modulefile

Use module is a great way to organize compiled codes. Here is a sample that I used for PFLOTRAN on NERSC.

#%Module1.0#####################################################################
##
## modules modulefile
##
proc ModulesHelp { } {
    global mpi_bin

    puts stderr "\tPFLOTRAN pflotran/5.0 repository, opt build"
    puts stderr ""
}

module-whatis   "PFLOTRAN pflotran/5.0 repository, opt build"
# #############################################################################

module load cpu

setenv PFLOTRAN_DIR /PATH/TO/PFLOTRAN_DIR
setenv PETSC_DIR /PATH/TO/PETSC_DIR
setenv PETSC_ARCH perl-c-opt

prepend-path    PATH            $env(PFLOTRAN_DIR)/src/pflotran/bin
prepend-path    PATH            $env(PETSC_DIR)/$env(PETSC_ARCH)/bin
prepend-path    PYTHONPATH      $env(PFLOTRAN_DIR)/src/python

Update PFLOTRAN

make sure PETSC_DIR and PETSC_ARCH are in your environment

export PETSC_DIR=$PWD
export PETSC_ARCH=perl-c-opt

Pull the changes from remote repo

git pull

Recompile PFLOTRAN

cd pflotran/src/pflotran
make -j4 pflotran
# make pflotran fast=1

Common issues

module: command not found. This happened on an interactive node with zsh shell.
- To fix this, run source $LMOD_PKG/init/zsh prior to running any module command.
HDF5 error. This happened when running MPICH on NFS file system on CHPC. PFLOTRAN would run, but the resulting HDF5 file has no coordinate information (i.e., no meshes visible in ParaView).
- To fix this, set the environment variable HDF5_DO_MPI_FILE_SYNC=FALSE before running PFLOTRAN.

export HDF5_DO_MPI_FILE_SYNC=FALSE