The steps to properly compile PETSc on JURECA are this ones:
-
Purge the previous loaded packaged
module --force purge -
Load the needed packaged
module load Architecture/KNL
module load intel-para
module load CMake
The KNL (Intel Knights Landing) architecture allows to cross-compile PETSc -
Run the configure script (runPETScConfig)
./runPETScConfig
Disclaimer: This configure script has been created by looking for the options and flags the developers have used to compile a previous PETSc version on JURECA. If new flags are needed, one should load the default PETSc version
module load PETSc
and then go use the options defined at the compilation log file at
$PETSC_DIR/lib/petsc/conf/reconfigure-arch-linux2-c-opt.py. -
Run the PETSc make
make all
make test
Once PETSc is compiled, one can install PFLOTRAN setting up the newly compiled PETSc environmental variables:
export PETSC_DIR=/PETSc_install_dir
export PETSC_ARCH=name_given_to_the_compilation
Then, one can install PFLOTRAN as usual (make pflotran).
To run a model using PFLOTRAN on JURECA one can send a batch job using the run_JURECA.batch template