Build configuration for MPI and PETSc

In OGS, the domain decomposition method (DDC) with MPI is used for parallel computing, and the PETSc package is employed to manage the partitioned vectors and matrices of the assembled global system of linear equations and to solve the assembled global system of linear equations as well.

To compiled OGS with PETSc, MPI c++ compiler wrappers like OpenMPI, MPICH ( has many derivatives, e.g intelMPI), and PETSc have to be installed as prerequisites.

Install MPI

MPI c++ compiler wrappers are essentially installed on most of Linux clusters and supercomputers, and they are usually managed by the environment module of operating system. What you have to do on that platforms is just to load a proper MPI wrapper module. On Linux powered laptop, PC, or work station, you can install OpenMPI or MPICH via the package manager of the Linux distribution, e.g. RPM of RedHat, pacman of Arch.

Install PETSc

If PETSc is not installed on your system, you can download the PETSc source code (https://petsc.org/release/download/), compile it and install by yourself according to the PETSc’s installation instruction on https://petsc.org/release/install/.

Here is an example of PETSc configuration:

./configure PETSC_ARCH=linux-fast  COPTFLAGS='-O3  --prefix=/home/me/opt/petsc --with-debugging=0 -march=native -mtune=native' CXXOPTFLAGS='-O3 -march=native -mtune=native' --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-fblaslapack --download-metis --download-parmetis --download-superlu_dist --download-scalapack --download-mumps  --download-hypre --with-c2html=0  --with-cxx-dialect=C++11 --with-cuda=0`

With that configuration, PETSc will be compiled without PETSc debugging model (--with-debugging=0), and installed to opt directory of the home directory. For Arch Linux, if you install PETSc package from AUR repository, please keep in mind that its option of --with-debugging is not set so far. This mean that PETSc is installed with PETSc debugging model by default. PETSc debugging model gives low performance. You can manually edit PKGBUILD of PETSc from AUR by adding the option of --with-debugging=0 before installation.

Please note that the PETSc package is preferred to build in release model regardless of OGS being built with release or debug preset because that you may not like to debug the source code of PETSc and want to have a better computational performance.

PESTSc is recommended to use on Linux. On Windows, it only runs on UNIX emulator Cygwin. A detailed description about how to use PETSc on Windows is available on this PETSc site: https://petsc.org/main/install/windows/.

One the frontends of EVE cluster of UFZ, your can load specified MPI, PETSc and other modules by command:

source [path to ogs source code]/scripts/env/eve/petsc.sh

Build configuration of OGS

For CMake configuration, the option of OGS_USE_PETSC must be set to true. It is -DOGS_USE_PETSC=ON for command line.

MPI C/C++ compiler has to be used for compilation. OGS_USE_MPI is set on automatically once OGS_USE_PETSC is on. On the platforms that the software is not managed by environment module, the standard C/C++ compiler is the default compiler. For such platforms, C/C++ compiler is better to be explicitly specified as MPI C/C++ compiler in CMake configuration in case the standard C/C++ compiler being used. If standard C/C++ compiler is used when OGS_USE_PETSC is switched on, the compilation will fail with missed library error.

For simplicity, you can first run CMake with MPI C/C++ compiler specified. For example:

cmake [path to source code] [-GNinja] -DOGS_USE_PETSC=ON -DCMAKE_C_COMPILER=/usr/bin/mpicc -DCMAKE_CXX_COMPILER=/usr/bin/mpic++

and then use ccmake or cmake-gui to configure further more CMake options.

The other basic build configurations are the same as that described in Build configuration.

Once the CMake configuration is done, you can run make or ninja (if -GNinja is set) to compile the source code as that for the compilation for serial computing code.


This article was written by Wenqing Wang. If you are missing something or you find an error please let us know.
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