From bbba0624261c9164161a62a2ee10af907b957a2d Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Thu, 3 Dec 2020 09:37:04 +0100
Subject: [PATCH] [CMake] Introduced option OGS_USE_XDMF (defaults to OFF).
Makes hdf5 and libxml2 dependencies optional.
---
CMakeLists.txt | 5 +++
MeshLib/CMakeLists.txt | 8 +++-
MeshLib/IO/writeMeshToFile.cpp | 2 +
ProcessLib/Output/Output.cpp | 8 ++++
ProcessLib/Output/Output.h | 6 +++
ProcessLib/Output/ProcessOutput.cpp | 6 +++
Tests/CMakeLists.txt | 4 +-
ThirdParty/CMakeLists.txt | 68 ++++++++++++++---------------
scripts/ci/jobs/code-quality.yml | 2 +-
scripts/cmake/ConanSetup.cmake | 32 ++++++++------
10 files changed, 89 insertions(+), 52 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 928bf041b43..72339dbf4ea 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -110,6 +110,7 @@ option(OGS_INSITU "Builds OGS with insitu visualization capabilities." OFF)
option(OGS_USE_LIS "Use Lis" OFF)
option(OGS_USE_PETSC "Use PETSc routines" OFF)
option(OGS_USE_NETCDF "Add NetCDF support." OFF)
+option(OGS_USE_XDMF "Add Xdmf file IO support" OFF)
# Eigen
option(OGS_USE_EIGEN "Use Eigen linear solver" ON)
@@ -237,6 +238,10 @@ if(OGS_USE_EIGEN)
endif()
# End Eigen
+if(OGS_USE_XDMF)
+ add_definitions(-DOGS_USE_XDMF)
+endif()
+
if(OGS_FATAL_ABORT)
add_definitions(-DOGS_FATAL_ABORT)
endif()
diff --git a/MeshLib/CMakeLists.txt b/MeshLib/CMakeLists.txt
index c328d33c7cd..e73de0542b3 100644
--- a/MeshLib/CMakeLists.txt
+++ b/MeshLib/CMakeLists.txt
@@ -12,7 +12,9 @@ append_source_files(SOURCES Elements)
append_source_files(SOURCES IO)
append_source_files(SOURCES IO/Legacy)
append_source_files(SOURCES IO/VtkIO)
-append_source_files(SOURCES IO/XDMF)
+if(OGS_USE_XDMF)
+ append_source_files(SOURCES IO/XDMF)
+endif()
append_source_files(SOURCES MeshQuality)
append_source_files(SOURCES Vtk)
@@ -26,7 +28,9 @@ ogs_add_library(MeshLib ${SOURCES})
target_link_libraries(
MeshLib
- PUBLIC BaseLib GeoLib GitInfoLib MathLib ${VTK_LIBRARIES} OgsXdmf
+ PUBLIC
+ BaseLib GeoLib GitInfoLib MathLib ${VTK_LIBRARIES}
+ $<$<TARGET_EXISTS:OgsXdmf>:OgsXdmf>
PRIVATE spdlog::spdlog)
if(OGS_USE_MPI AND TARGET MPI::MPI_CXX)
diff --git a/MeshLib/IO/writeMeshToFile.cpp b/MeshLib/IO/writeMeshToFile.cpp
index 2d1165e5012..86dda37ec86 100644
--- a/MeshLib/IO/writeMeshToFile.cpp
+++ b/MeshLib/IO/writeMeshToFile.cpp
@@ -42,6 +42,7 @@ int writeMeshToFile(const MeshLib::Mesh& mesh,
}
return 0;
}
+#ifdef OGS_USE_XDMF
if (file_path.extension().string() == ".xdmf")
{
auto writer =
@@ -56,6 +57,7 @@ int writeMeshToFile(const MeshLib::Mesh& mesh,
return 0;
}
+#endif
ERR("writeMeshToFile(): Unknown mesh file format in file {:s}.",
file_path.string());
return -1;
diff --git a/ProcessLib/Output/Output.cpp b/ProcessLib/Output/Output.cpp
index bd4035eec12..c2b4e1f9af0 100644
--- a/ProcessLib/Output/Output.cpp
+++ b/ProcessLib/Output/Output.cpp
@@ -227,6 +227,7 @@ struct Output::OutputFile
}
};
+#ifdef OGS_USE_XDMF
void Output::outputMeshXdmf(OutputFile const& output_file,
MeshLib::Mesh const& mesh,
int const timestep,
@@ -245,6 +246,7 @@ void Output::outputMeshXdmf(OutputFile const& output_file,
}
_mesh_xdmf_writer->writeStep(timestep, t);
}
+#endif
void Output::outputMesh(OutputFile const& output_file,
MeshLib::IO::PVDFile* const pvd_file,
@@ -313,12 +315,18 @@ void Output::doOutputAlways(Process const& process,
}
else if (_output_file_type == ProcessLib::OutputType::xdmf)
{
+#ifdef OGS_USE_XDMF
OutputFile const file(_output_directory, _output_file_type,
_output_file_prefix, "", mesh.getName(),
timestep, t, _output_file_data_mode,
_output_file_compression);
outputMeshXdmf(file, mesh, timestep, t);
+#else
+ OGS_FATAL(
+ "Trying to write Xdmf file but OGS was not built with "
+ "Xdmf-support.");
+#endif
}
};
diff --git a/ProcessLib/Output/Output.h b/ProcessLib/Output/Output.h
index 23d6ceec6ed..e75f35c88d6 100644
--- a/ProcessLib/Output/Output.h
+++ b/ProcessLib/Output/Output.h
@@ -14,7 +14,9 @@
#include <utility>
#include "MeshLib/IO/VtkIO/PVDFile.h"
+#ifdef OGS_USE_XDMF
#include "MeshLib/IO/XDMF/Xdmf3Writer.h"
+#endif
#include "ProcessOutput.h"
namespace ProcessLib
@@ -89,13 +91,17 @@ private:
MeshLib::Mesh const& mesh,
int const timestep,
double const t) const;
+#ifdef OGS_USE_XDMF
void outputMeshXdmf(OutputFile const& output_file,
MeshLib::Mesh const& mesh,
int const timestep,
double const t);
+#endif
private:
+#ifdef OGS_USE_XDMF
std::unique_ptr<MeshLib::IO::Xdmf3Writer> _mesh_xdmf_writer;
+#endif
std::string const _output_directory;
OutputType const _output_file_type;
std::string const _output_file_prefix;
diff --git a/ProcessLib/Output/ProcessOutput.cpp b/ProcessLib/Output/ProcessOutput.cpp
index d84278f8a69..5297b79d2f9 100644
--- a/ProcessLib/Output/ProcessOutput.cpp
+++ b/ProcessLib/Output/ProcessOutput.cpp
@@ -285,11 +285,17 @@ void makeOutput(std::string const& file_name, MeshLib::Mesh const& mesh,
case OutputType::xdmf:
{
+#ifdef OGS_USE_XDMF
MeshLib::IO::Xdmf3Writer writer(
file_name, MeshLib::IO::transformGeometry(mesh),
MeshLib::IO::transformTopology(mesh),
MeshLib::IO::transformAttributes(mesh), time_step);
writer.writeStep(time_step, time);
+#else
+ OGS_FATAL(
+ "Trying to write Xdmf file but OGS was not built with "
+ "Xdmf-support.");
+#endif
}
}
diff --git a/Tests/CMakeLists.txt b/Tests/CMakeLists.txt
index 350ed3570d5..f3e902b7904 100644
--- a/Tests/CMakeLists.txt
+++ b/Tests/CMakeLists.txt
@@ -1,5 +1,7 @@
### xdmfdiff ###
-add_subdirectory(xdmfdiff)
+if(OGS_USE_XDMF)
+ add_subdirectory(xdmfdiff)
+endif()
### testrunner ###
include(${PROJECT_SOURCE_DIR}/scripts/cmake/OGSEnabledElements.cmake)
diff --git a/ThirdParty/CMakeLists.txt b/ThirdParty/CMakeLists.txt
index 14bdd3ae703..c42ad6743d4 100644
--- a/ThirdParty/CMakeLists.txt
+++ b/ThirdParty/CMakeLists.txt
@@ -88,42 +88,42 @@ if(OGS_BUILD_UTILS)
list(APPEND DISABLE_WARNINGS_TARGETS ogs_metis mpmetis)
endif()
-# Xdmf
-find_package(ZLIB REQUIRED) # ZLIB is a HDF5 dependency
-set(XDMF_LIBNAME OgsXdmf CACHE INTERNAL "")
-add_subdirectory(xdmf)
-target_include_directories(${XDMF_LIBNAME} PUBLIC
- ${PROJECT_SOURCE_DIR}/ThirdParty/xdmf
- ${PROJECT_BINARY_DIR}/ThirdParty/xdmf
-)
-if(OGS_USE_CONAN AND UNIX AND APPLE)
- find_package(Iconv REQUIRED)
+if(OGS_USE_XDMF)
+ find_package(ZLIB REQUIRED) # ZLIB is a HDF5 dependency
+ set(XDMF_LIBNAME OgsXdmf CACHE INTERNAL "")
+ add_subdirectory(xdmf)
+ target_include_directories(${XDMF_LIBNAME} PUBLIC
+ ${PROJECT_SOURCE_DIR}/ThirdParty/xdmf
+ ${PROJECT_BINARY_DIR}/ThirdParty/xdmf
+ )
+ if(OGS_USE_CONAN AND UNIX AND APPLE)
+ find_package(Iconv REQUIRED)
+ endif()
+
+ if(MSVC AND OGS_USE_CONAN)
+ # Hack: Conan HDF5 not found on Windows
+ target_link_libraries(${XDMF_LIBNAME} ${CONAN_LIBS})
+ else()
+ target_link_libraries(${XDMF_LIBNAME} Boost::boost ${Iconv_LIBRARIES} ZLIB::ZLIB)
+ endif()
+ target_include_directories(${XDMF_LIBNAME}Core PUBLIC
+ ${PROJECT_SOURCE_DIR}/ThirdParty/xdmf/core
+ ${PROJECT_BINARY_DIR}/ThirdParty/xdmf/core
+ )
+ find_package(LibXml2 REQUIRED) # LibXml2 is a XdmfCore dependency
+ target_link_libraries(${XDMF_LIBNAME}Core PUBLIC LibXml2::LibXml2)
+
+ set_target_properties(${XDMF_LIBNAME} ${XDMF_LIBNAME}Core PROPERTIES
+ RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_BINDIR}
+ LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}
+ ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}
+ )
+ if(BUILD_SHARED_LIBS)
+ install(TARGETS ${XDMF_LIBNAME} ${XDMF_LIBNAME}Core LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
+ endif()
+ list(APPEND DISABLE_WARNINGS_TARGETS ${XDMF_LIBNAME} ${XDMF_LIBNAME}Core)
endif()
-if(MSVC AND OGS_USE_CONAN)
- # Hack: Conan HDF5 not found on Windows
- target_link_libraries(${XDMF_LIBNAME} ${CONAN_LIBS})
-else()
- target_link_libraries(${XDMF_LIBNAME} Boost::boost ${Iconv_LIBRARIES} ZLIB::ZLIB)
-endif()
-target_include_directories(${XDMF_LIBNAME}Core PUBLIC
- ${PROJECT_SOURCE_DIR}/ThirdParty/xdmf/core
- ${PROJECT_BINARY_DIR}/ThirdParty/xdmf/core
-)
-find_package(LibXml2 REQUIRED) # LibXml2 is a XdmfCore dependency
-target_link_libraries(${XDMF_LIBNAME}Core PUBLIC LibXml2::LibXml2)
-
-set_target_properties(${XDMF_LIBNAME} ${XDMF_LIBNAME}Core PROPERTIES
- RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_BINDIR}
- LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}
- ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}
-)
-if(BUILD_SHARED_LIBS)
- install(TARGETS ${XDMF_LIBNAME} ${XDMF_LIBNAME}Core LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
-endif()
-list(APPEND DISABLE_WARNINGS_TARGETS ${XDMF_LIBNAME} ${XDMF_LIBNAME}Core)
-# Xdmf end
-
foreach(TARGET ${DISABLE_WARNINGS_TARGETS})
target_compile_options(${TARGET} PRIVATE
$<$<OR:$<CXX_COMPILER_ID:Clang>,$<CXX_COMPILER_ID:AppleClang>,$<CXX_COMPILER_ID:GNU>>:-w>
diff --git a/scripts/ci/jobs/code-quality.yml b/scripts/ci/jobs/code-quality.yml
index d7f4021b5c6..59916cf3f8b 100644
--- a/scripts/ci/jobs/code-quality.yml
+++ b/scripts/ci/jobs/code-quality.yml
@@ -8,7 +8,7 @@ cppcheck:
script:
- >
cmake .. -G Ninja -DCMAKE_BUILD_TYPE=Release -DOGS_USE_CONAN=OFF
- -DOGS_USE_UNITY_BUILDS=OFF -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
+ -DOGS_USE_UNITY_BUILDS=OFF -DOGS_USE_XDMF=ON -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
- bash cppcheck.sh
artifacts:
reports:
diff --git a/scripts/cmake/ConanSetup.cmake b/scripts/cmake/ConanSetup.cmake
index a2eab45b23b..bec3c0476b4 100644
--- a/scripts/cmake/ConanSetup.cmake
+++ b/scripts/cmake/ConanSetup.cmake
@@ -35,8 +35,6 @@ set(CONAN_REQUIRES
boost/${ogs.minimum_version.boost}@conan/stable
eigen/${ogs.minimum_version.eigen}@conan/stable
vtk/${ogs.tested_version.vtk}@bilke/stable
- hdf5/${ogs.tested_version.hdf5}
- libxml2/${ogs.tested_version.libxml2}
CACHE INTERNAL ""
)
@@ -47,9 +45,6 @@ set(CONAN_OPTIONS
vtk:iolegacy=True
CACHE INTERNAL ""
)
-if(UNIX AND NOT APPLE)
- list(APPEND CONAN_OPTIONS libxml2:iconv=False)
-endif()
if((UNIX AND NOT APPLE) AND BUILD_SHARED_LIBS)
set(CONAN_OPTIONS ${CONAN_OPTIONS} vtk:fPIC=True)
@@ -59,6 +54,24 @@ if(OGS_USE_MPI)
set(CONAN_OPTIONS ${CONAN_OPTIONS} vtk:mpi_minimal=True)
endif()
+if(OGS_USE_XDMF)
+ list(APPEND CONAN_REQUIRES
+ hdf5/${ogs.tested_version.hdf5}
+ libxml2/${ogs.tested_version.libxml2}
+ )
+ if(UNIX AND NOT APPLE)
+ list(APPEND CONAN_OPTIONS libxml2:iconv=False)
+ endif()
+ if(MSVC)
+ # Hack: Conan HDF5 not found on Windows
+ # Use custom FindHDF5 with forced values from Conan
+ list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/scripts/cmake/conan/win-hdf5")
+ else()
+ # Hack: Suppress hdf5 compiler wrapper checks
+ set(HDF5_C_COMPILER_EXECUTABLE "OFF" CACHE INTERNAL "")
+ endif()
+endif()
+
if(OGS_USE_PETSC)
set(CONAN_REQUIRES ${CONAN_REQUIRES} petsc/${ogs.minimum_version.petsc}@bilke/testing)
if(OGS_CONAN_USE_SYSTEM_OPENMPI)
@@ -194,12 +207,3 @@ endif()
if(OGS_USE_PETSC)
set(PETSC_DIR ${CONAN_PETSC_ROOT} CACHE INTERNAL "")
endif()
-
-if(MSVC)
- # Hack: Conan HDF5 not found on Windows
- # Use custom FindHDF5 with forced values from Conan
- list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/scripts/cmake/conan/win-hdf5")
-else()
- # Hack: Suppress hdf5 compiler wrapper checks
- set(HDF5_C_COMPILER_EXECUTABLE "OFF" CACHE INTERNAL "")
-endif()
--
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