Code Generation for PDEs tutorial

See merge request !326

Frederik Hennig authored Aug 14, 2020 and Markus Holzer committed Aug 14, 2020

- Added folder 'codegen' to 'apps/tutorials'
- Implemented heat equation code generation in python
- Implemented C++ application for running the generated code
- Added CMake build files for code generation tutorial

Update CMakeLists.txt

See merge request !328

Disable dlopen trick on OpenMPI >= 3.0.0

See merge request !325

Suppress signedness warning in GPUField.impl.h

See merge request !322

DistanceComputations.h: include "core/logging/Logging.h"

See merge request !321

DistanceComputations.h uses logging macros but does not include the
header unconditionally.

nrOfGhostLayers_ is unsigned while all cell_idx_t calculations are
signed.

Inline pe_coupling::overlapFractionPe

See merge request !315

change docu image to gcc

See merge request !324

Fluctuating MRT: propagate the RNG counter to all copies of the lattice model

See merge request !320

If a process started by mpiexec finishes too quickly, sometimes some of the other processes are not started.
It is unclear whether this is an OpenMPI or macOS bug, but appears significantly more often since moving from macOS 10.13 to 10.15. OpenMPI 4.0.1 and 3.0.0 both show the issue on macOS 10.15.

Michael Kuron authored Jul 29, 2020 and Dominik Thoennes committed Jul 30, 2020

Workaround for https://github.com/open-mpi/ompi/issues/5798

Update CMake boost python logic and std::filesystem usage

See merge request !319

The two-argument version was removed late in the standardization process

We need to have at least one other required library, otherwise FindBoost will consider itself successful even if it didn't find anything.
Also, add Python 3.8 support by using the Python version numbers as library version numbers.

Adapting flake8 formatig for python files

See merge request !317

[BUGFIX] caching of buffers can lead to dead locks

See merge request !318

If load balancing changes the neighborhood, caching of receive
buffers can lead to dead locks.

Unify python code style

See merge request !306

fixed smaller formatting issues in mesa_pd

See merge request !311

OpenMP support is now switchable within the generation script

See merge request !313

[API] improved interface of merge sqlitedb script

See merge request !314

Since MSVC only has beta support for OpenMP 2.0 firstprivate
cannot be used for these compilers. However, firstprivate
is necessary for a reasonably safe implementation of OpenMP
in MESA-PD. The solution is to move OpenMP support to the
generator and disable OpenMP for the checked in version.
The waLBerla OpenMP guards are removed as they are no longer
needed. It is now assumed that if MESA-PD is generated with
OpenMP support it is about to be used. If OpenMP is disabled
with CMake warnings will pop up about undefined pragmas.

Defining this function in a header without inline/static specifier may
lead to ODR violations.