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 compile OGS with PETSc, MPI c++ compiler wrappers like OpenMPI, MPICH ( has many derivatives, e.g intelMPI) has to be installed as prerequisite.
PETSc is not supported on Windows system. As an alternative you can follow the instructions in Section Install PETSc manually and run PETSc using Cygwin or use Windows Subsystem For Linux (WSL). The latter option is recommended - using WSL. The manual of setting up OpenGeoSys in WSL can be found in our Windows Subsystem For Linux guide. After setting up WSL, please follow the Linux tab in this guide.
Before continuing with this guide, please follow all steps from the “Developer guide” articles: Set Up Prerequisites and Get the source code.
Please setup OpenGeoSys environment in WSL and proceed with instructions from Linux tab (recommended), or follow the Section Install PETSc manually from Windows tab (not recommended).
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. apt in Ubuntu, RPM in RedHat, pacman in ArchLinux.
On Ubuntu it is sufficient to install the package libopenmpi-dev.
Installation can be done using following command:
sudo apt install libopenmpi-devOn other distributions, the exact names of the packages can slightly differ. If this is the case, you can search for the correct names using the search function of your distributions package manager.
On MacOS machines, you can install OpenMPI using brew package manager:
brew install open-mpiThe easiest way of obtaining a working copy of OpenGeoSys with PETSc and MPI, is to use the release-petsc preset.
It will automatically download and compile a version of PETSc compatible with OpenGeoSys (if not system installed PETSc is found).
This could be done by running following commands inside of the folder containing OpenGeoSys source code:
cmake --preset release-petscand
cmake --build --preset release-petscThe release-petsc preset is based on the release preset.
It can be customized by passing additional variable with -D flags to cmake command.
If you want to install PETSc yourself, please see Section Install PETSc.
If settings of the preset release-petsc doesn’t suit your use case and you would like to enable PETSc in other preset, please follow the instructions in this section.
For CMake configuration, the option of OGS_USE_PETSC must be set to true.
A MPI C/C++ compiler has to be used for compilation.
You can specify it via the environment variables CC and CXX, e.g.:
CC=mpicc CXX=mpic++ cmake --preset my-preset [...]The other basic build configurations are the same as that described in Build configuration.
Once the CMake configuration is done, you can run ninja (or make) to compile the source code, same as compilation for the non-PETSc build.
The instructions from this section apply only if you want to install or compile PETSc yourself, instead of letting OpenGeoSys do it automatically.
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 with optimizations and without debugging info (--with-debugging=0), and installed to user’s opt 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.
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 usually build in release mode independent of the OGS’ release or debug build.
PETSc 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/release/install/windows/.
On the frontends of the UFZ EVE cluster the MPI, PETSc, and other required modules can be loaded with the following command:
source [path to ogs source code]/scripts/env/eve/petsc.shThis article was written by Wenqing Wang, Feliks Kiszkurno, Lars Bilke. If you are missing something or you find an error please let us know.
Generated with Hugo 0.117.0
in CI job 362666
|
Last revision: July 12, 2023
Commit: [PL/SSD] Rename x_dot to x_prev 04a8fec8
| Edit this page on