diff --git a/Applications/ApplicationsLib/CMakeLists.txt b/Applications/ApplicationsLib/CMakeLists.txt
index 701c66a4c58918e3921934ed248a42f9ba381ba7..64bb9c8717445ea5e5994728959e5d14fd50af23 100644
--- a/Applications/ApplicationsLib/CMakeLists.txt
+++ b/Applications/ApplicationsLib/CMakeLists.txt
@@ -10,6 +10,10 @@ target_link_libraries(ApplicationsLib
PRIVATE MathLib MeshLib MeshGeoToolsLib NumLib
)
+if(OGS_USE_PYTHON)
+ target_include_directories(ApplicationsLib PRIVATE ${PYTHON_INCLUDE_DIRS})
+endif()
+
# Set cpp definitions if the cmake option is enabled for the given process.
foreach(process ${ProcessesList})
if(OGS_BUILD_PROCESS_${process})
diff --git a/Applications/ApplicationsLib/ProjectData.cpp b/Applications/ApplicationsLib/ProjectData.cpp
index 58b077d4a0af2460de993c2f215b890aaed47997..de782c13f956efde4b975147ad9a0efd64d8fa6d 100644
--- a/Applications/ApplicationsLib/ProjectData.cpp
+++ b/Applications/ApplicationsLib/ProjectData.cpp
@@ -18,6 +18,10 @@
#include <logog/include/logog.hpp>
+#ifdef OGS_USE_PYTHON
+#include <pybind11/eval.h>
+#endif
+
#include "BaseLib/Algorithm.h"
#include "BaseLib/FileTools.h"
@@ -162,6 +166,21 @@ ProjectData::ProjectData(BaseLib::ConfigTree const& project_config,
{
_mesh_vec = readMeshes(project_config, project_directory);
+#ifdef OGS_USE_PYTHON
+ if (auto const python_script =
+ project_config.getConfigParameterOptional<std::string>(
+ "python_script"))
+ {
+ namespace py = pybind11;
+ auto const script_path =
+ BaseLib::copyPathToFileName(*python_script, project_directory);
+
+ // Evaluate in scope of main module
+ py::object scope = py::module::import("__main__").attr("__dict__");
+ py::eval_file(script_path, scope);
+ }
+#endif // OGS_USE_PYTHON
+
//! \ogs_file_param{prj__curves}
parseCurves(project_config.getConfigSubtreeOptional("curves"));
diff --git a/Applications/CLI/CMakeLists.txt b/Applications/CLI/CMakeLists.txt
index c2410af0547a690a67d35040746b99cf947c35b4..998ac84220bb3144c299669aaaf317c5674b1763 100644
--- a/Applications/CLI/CMakeLists.txt
+++ b/Applications/CLI/CMakeLists.txt
@@ -5,6 +5,46 @@ target_link_libraries(ogs
PRIVATE BaseLib ApplicationsLib
)
+if(OGS_USE_PYTHON)
+ # Troubleshooting:
+ # If you get linker errors, such as ogs.cpp:(.text+0xb4): Warnung: undefinierter Verweis auf »_Py_ZeroStruct«
+ # it could be that OGS is compiled with the wrong Python version.
+ # I (Ch. Leh.) observed the following: The symbol _Py_ZeroStruct could not be found in /usr/lib/libpython3.6m.so (I intended to compile OGS with Python3).
+ # It's apparently a Python2 symbol (present in /usr/lib/libpython2.7.so)
+ # The compiler command-line was the following:
+ # /usr/bin/g++ ... -DvtkRenderingVolume_AUTOINIT="1(vtkRenderingVolumeOpenGL2)" \
+ # -I/usr/include/vtk -I/usr/include/python2.7 -I/usr/include/freetype2 \
+ # -I/usr/include/libxml2 ... -I/.../BaseLib ... \
+ # -isystem /usr/include/python3.6m ... -o CMakeFiles/ogs.dir/ogs.cpp.o \
+ # -c /.../Applications/CLI/ogs.cpp
+ # In particular, the Python2 include path comes before the Python3 include path.
+ # Compiling OGS with Python2 solved the issue.
+ # I assume (this is only a guess!) that VTK pulls in Python2 dependencies (on my system).
+ # I assume that this is related to https://github.com/ufz/ogs/pull/2158.
+ # Workaround: Always make sure that OGS is compiled with the same Python version as VTK.
+ # TODO: Find out how to properly address the issue.
+
+ # Performance warning from
+ # https://github.com/pybind/pybind11/blob/master/docs/compiling.rst:
+ # Since pybind11 is a metatemplate library, it is crucial that certain compiler
+ # flags are provided to ensure high quality code generation. In contrast to the
+ # pybind11_add_module() command, the CMake interface library only provides the
+ # minimal set of parameters to ensure that the code using pybind11 compiles, but
+ # it does not pass these extra compiler flags (i.e. this is up to you).
+ # TODO: Enable further compiler/linker flags.
+ target_link_libraries(ogs PRIVATE pybind11::embed)
+
+ add_library(ogs_python_bindings STATIC ogs_python_bindings.cpp)
+ target_link_libraries(ogs_python_bindings PRIVATE pybind11::embed)
+ target_include_directories(ogs_python_bindings PRIVATE ${PYTHON_INCLUDE_DIRS})
+
+ target_link_libraries(ogs PRIVATE ogs_python_bindings)
+
+ if(BUILD_SHARED_LIBS)
+ target_compile_definitions(ogs_python_bindings OGS_BUILD_SHARED_LIBS)
+ endif()
+endif()
+
if(OGS_USE_PETSC)
target_link_libraries(ogs PRIVATE ${PETSC_LIBRARIES})
endif()
diff --git a/Applications/CLI/ogs.cpp b/Applications/CLI/ogs.cpp
index 1a7dbc096a267bedfe71c3135d74e77dfddc1e36..f9ceb6a55bac2e23c5598f815f2be3788559b749 100644
--- a/Applications/CLI/ogs.cpp
+++ b/Applications/CLI/ogs.cpp
@@ -10,8 +10,8 @@
*
*/
-#include <chrono>
#include <tclap/CmdLine.h>
+#include <chrono>
#ifndef _WIN32
#ifdef __APPLE__
@@ -42,7 +42,9 @@
#include "NumLib/NumericsConfig.h"
-int main(int argc, char *argv[])
+#include "ogs_python_bindings.h"
+
+int main(int argc, char* argv[])
{
// Parse CLI arguments.
TCLAP::CmdLine cmd(
@@ -65,34 +67,32 @@ int main(int argc, char *argv[])
"PROJECT FILE");
cmd.add(project_arg);
- TCLAP::ValueArg<std::string> outdir_arg(
- "o", "output-directory",
- "the output directory to write to",
- false,
- "",
- "output directory");
+ TCLAP::ValueArg<std::string> outdir_arg("o", "output-directory",
+ "the output directory to write to",
+ false, "", "output directory");
cmd.add(outdir_arg);
- TCLAP::ValueArg<std::string> log_level_arg(
- "l", "log-level",
- "the verbosity of logging messages: none, error, warn, info, debug, all",
- false,
+ TCLAP::ValueArg<std::string> log_level_arg("l", "log-level",
+ "the verbosity of logging "
+ "messages: none, error, warn, "
+ "info, debug, all",
+ false,
#ifdef NDEBUG
- "info",
+ "info",
#else
- "all",
+ "all",
#endif
- "log level");
+ "log level");
cmd.add(log_level_arg);
TCLAP::SwitchArg nonfatal_arg("",
- "config-warnings-nonfatal",
- "warnings from parsing the configuration file will not trigger program abortion");
+ "config-warnings-nonfatal",
+ "warnings from parsing the configuration "
+ "file will not trigger program abortion");
cmd.add(nonfatal_arg);
- TCLAP::SwitchArg unbuffered_cout_arg("",
- "unbuffered-std-out",
- "use unbuffered standard output");
+ TCLAP::SwitchArg unbuffered_cout_arg("", "unbuffered-std-out",
+ "use unbuffered standard output");
cmd.add(unbuffered_cout_arg);
#ifndef _WIN32 // TODO: On windows floating point exceptions are not handled
@@ -124,6 +124,11 @@ int main(int argc, char *argv[])
#endif // __APPLE__
#endif // _WIN32
+#ifdef OGS_USE_PYTHON
+ pybind11::scoped_interpreter guard = ApplicationsLib::setupEmbeddedPython();
+ (void)guard;
+#endif
+
BaseLib::RunTime run_time;
{
@@ -167,7 +172,9 @@ int main(int argc, char *argv[])
if (auto t = project_config->getConfigSubtreeOptional("insitu"))
{
//! \ogs_file_param{prj__insitu__scripts}
- InSituLib::Initialize(t->getConfigSubtree("scripts"), BaseLib::extractPath(project_arg.getValue()));
+ InSituLib::Initialize(
+ t->getConfigSubtree("scripts"),
+ BaseLib::extractPath(project_arg.getValue()));
isInsituConfigured = true;
}
#else
@@ -196,11 +203,11 @@ int main(int argc, char *argv[])
#ifdef USE_INSITU
if (isInsituConfigured)
InSituLib::Finalize();
- #endif
+#endif
INFO("[time] Execution took %g s.", run_time.elapsed());
#if defined(USE_PETSC)
- controller->Finalize(1) ;
+ controller->Finalize(1);
#endif
} // This nested scope ensures that everything that could possibly
// possess a ConfigTree is destructed before the final check below is
@@ -209,7 +216,9 @@ int main(int argc, char *argv[])
BaseLib::ConfigTree::assertNoSwallowedErrors();
ogs_status = solver_succeeded ? EXIT_SUCCESS : EXIT_FAILURE;
- } catch (std::exception& e) {
+ }
+ catch (std::exception& e)
+ {
ERR(e.what());
ogs_status = EXIT_FAILURE;
}
diff --git a/Applications/CLI/ogs_python_bindings.cpp b/Applications/CLI/ogs_python_bindings.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..12c0225bf053f874acdb93390faa48bf6da2482e
--- /dev/null
+++ b/Applications/CLI/ogs_python_bindings.cpp
@@ -0,0 +1,38 @@
+#ifdef OGS_USE_PYTHON
+
+#include <pybind11/embed.h>
+
+#include "ogs_python_bindings.h"
+
+#ifndef OGS_BUILD_SHARED_LIBS
+extern "C" PyObject* pybind11_init_impl_OpenGeoSys();
+
+// Hackish trick that hopefully ensures that the linker won't strip the symbol
+// pointed to by p from the library being built.
+template <typename T>
+void mark_used(T p)
+{
+ volatile T vp = (volatile T)p;
+ vp = vp;
+}
+
+#endif // OGS_BUILD_SHARED_LIBS
+
+namespace ApplicationsLib
+{
+pybind11::scoped_interpreter setupEmbeddedPython()
+{
+#ifndef OGS_BUILD_SHARED_LIBS
+ // pybind11_init_impl_OpenGeoSys is the function initializing the embedded
+ // OpenGeoSys Python module. The name is generated by pybind11. If it is not
+ // obvious that this symbol is actually used, the linker might remove it
+ // under certain circumstances.
+ mark_used(&pybind11_init_impl_OpenGeoSys);
+#endif
+
+ return pybind11::scoped_interpreter{};
+}
+
+} // namespace ApplicationsLib
+
+#endif // OGS_USE_PYTHON
diff --git a/Applications/CLI/ogs_python_bindings.h b/Applications/CLI/ogs_python_bindings.h
new file mode 100644
index 0000000000000000000000000000000000000000..c4b1e2a9442bc55800a9a5b5d8410f1ab2428279
--- /dev/null
+++ b/Applications/CLI/ogs_python_bindings.h
@@ -0,0 +1,15 @@
+#pragma once
+
+#ifdef OGS_USE_PYTHON
+
+#include <pybind11/embed.h>
+
+namespace ApplicationsLib
+{
+/// Sets up an embedded Python interpreter and makes sure that the OpenGeoSys
+/// Python module is not removed by the linker.
+pybind11::scoped_interpreter setupEmbeddedPython();
+
+} // namespace ApplicationsLib
+
+#endif // OGS_USE_PYTHON
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3d87e8ba12738e631d4dfbb34c53744ff2ab4dc4..d183b58ad142567857f6cc3daa539fcaa6f691f6 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -210,6 +210,8 @@ option(OGS_ENABLE_ELEMENT_PYRAMID "Build FEM elements for pyramids." ON)
option(OGS_CHECK_HEADER_COMPILATION "Check header for standalone compilation." OFF)
+option(OGS_USE_PYTHON "Interface with python" OFF)
+
###################
### Definitions ###
###################
@@ -259,12 +261,16 @@ if(OGS_USE_EIGEN)
add_definitions(-DEIGEN_INITIALIZE_MATRICES_BY_NAN)
endif()
endif()
-
if(MSVC AND OGS_32_BIT)
add_definitions(-DEIGEN_MAX_ALIGN_BYTES=0 -DEIGEN_DONT_ALIGN)
endif()
# End Eigen
+if(OGS_USE_PYTHON)
+ add_definitions(-DOGS_USE_PYTHON)
+ find_package(pybind11 REQUIRED)
+endif()
+
if (OGS_FATAL_ABORT)
add_definitions(-DOGS_FATAL_ABORT)
endif()