Installation

PETGEM is built with make against an existing PETSc installation. It targets Linux; a Docker image with the full dependency stack is provided.

Requirements

  • PETSc built with MPI and complex scalars. The configuration used by the project image is:

    ./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran \
            --download-mpich --download-fblaslapack \
            --with-scalar-type=complex --download-mumps --download-scalapack \
            --download-ptscotch --download-cmake --with-debugging=1 \
            --download-hdf5 --download-triangle

  • petsc4py (used by the Python preprocessing).

  • Gmsh - mesh generation.

  • Python 3 with numpy, h5py, meshio; matplotlib for the example post-processing scripts, pytest for the test suite.

  • Extrae - optional, for performance tracing (make USE_EXTRAE=1).

  • doxygen plus the packages in docs/requirements.txt - optional, to build the documentation.

PETSC_DIR and PETSC_ARCH must be set; the Makefile stops with an explicit error if PETSC_DIR does not point at a PETSc installation.

Docker

The image in docker/ provides PETSc (complex scalars), Gmsh, Extrae, and the Python stack:

git clone https://github.com/ocastilloreyes/petgem.git
cd petgem

docker build -t petgem-env -f docker/dockerfile.release .
docker run --rm -it -v $(pwd):/workspace -w /workspace petgem-env bash

# inside the container
make

See Quickstart for a first run.

Building

make builds all three binaries into build/:

  • build/fm.csem - forward kernel

  • build/im.csem - inverse kernel

  • build/petgem - dispatcher

With USE_EXTRAE=1 the binaries are suffixed .extrae (build/fm.csem.extrae, …). A single binary can be built on its own, e.g. make build/fm.csem.

Makefile targets

Target

Description

all (default)

Build fm.csem, im.csem, and petgem

clean

Remove build/ and object files

docs

Build the documentation (Doxygen XML + API stubs + Sphinx HTML)

clean_doc

Remove generated documentation artifacts

help

List targets and build options

Build options

Set as make <target> OPTION=1:

Option

Description

USE_EXTRAE=1

Build with Extrae instrumentation (requires EXTRAE_HOME)

USE_INTEL=1

Force Intel compiler flags. Auto-detected from PETSc’s $(PCC), so it is normally not needed; USE_INTEL=0 forces gcc-style flags.

V=1

Echo full compiler and linker command lines

NO_COLOR=1

Disable colored build output

Python helpers

The scripts under utils/ run directly from a clone - utils/preprocess.py adds the in-tree package to sys.path itself, so no install step is required:

python3 utils/preprocess.py -mode fm ...

To import the package as petgem from your own scripts:

pip install -e .