void PetscSetupUtils::CommonSetup()
{
InitialisePetsc();
// Check that the working directory is correct, or many tests will fail
std::string cwd = GetCurrentWorkingDirectory() + "/";
if (strcmp(cwd.c_str(), ChasteBuildRootDir()) != 0)
{
#define COVERAGE_IGNORE
// Change directory
std::cout << std::endl << "Changing directory from '" << cwd << "' to '" << ChasteBuildRootDir() << "'." << std::endl;
EXPECT0(chdir, ChasteBuildRootDir());
std::cout << "CWD now: " << GetCurrentWorkingDirectory() << std::endl;
#undef COVERAGE_IGNORE
}
#ifdef TEST_FOR_FPE
// Give all PETSc enabled tests the ability to trap for divide-by-zero
feenableexcept(FE_DIVBYZERO | FE_INVALID );
// Catch all SIGFPE signals and convert them to exceptions (before PETSc gets to them)
struct sigaction sa;
sa.sa_sigaction = FpeSignalToAbort;
sa.sa_flags = SA_RESETHAND|SA_SIGINFO;
sa.sa_restorer = 0;
sigaction(SIGFPE, &sa, NULL);
#endif
}
void CellMLToSharedLibraryConverter::ConvertCellmlToSo(const std::string& rCellmlFullPath,
const std::string& rCellmlFolder)
{
FileFinder tmp_folder;
FileFinder build_folder;
std::string old_cwd = GetCurrentWorkingDirectory();
// Check that the Chaste build tree exists
FileFinder chaste_root("", RelativeTo::ChasteBuildRoot);
if (!chaste_root.IsDir())
{
EXCEPTION("No Chaste build tree found at '" << chaste_root.GetAbsolutePath()
<< "' - you need the source to use CellML models directly in Chaste.");
}
FileFinder component_dir(mComponentName, RelativeTo::ChasteBuildRoot);
if (!component_dir.IsDir())
{
EXCEPTION("Unable to convert CellML model: required Chaste component '" << mComponentName
<< "' does not exist in '" << chaste_root.GetAbsolutePath() << "'.");
}
// Try the conversion
try
{
// Need to create a .so file from the CellML...
if (PetscTools::AmMaster())
{
// Create a temporary folder within heart/dynamic
std::stringstream folder_name;
folder_name << "dynamic/tmp_" << getpid() << "_" << time(NULL);
#ifdef CHASTE_CMAKE ///todo: #2656 - ignoring all cmake-specific code, revise after cmake transition
#define COVERAGE_IGNORE
tmp_folder.SetPath(component_dir.GetAbsolutePath() + "/" + folder_name.str(), RelativeTo::Absolute);
build_folder.SetPath(component_dir.GetAbsolutePath() + "/" + folder_name.str(), RelativeTo::Absolute);
#undef COVERAGE_IGNORE
#else
tmp_folder.SetPath(component_dir.GetAbsolutePath() + "/" + folder_name.str(), RelativeTo::Absolute);
build_folder.SetPath(component_dir.GetAbsolutePath() + "/build/" + ChasteBuildDirName() + "/" + folder_name.str(), RelativeTo::Absolute);
#endif
int ret = mkdir((tmp_folder.GetAbsolutePath()).c_str(), 0700);
if (ret != 0)
{
EXCEPTION("Failed to create temporary folder '" << tmp_folder.GetAbsolutePath() << "' for CellML conversion: "
<< strerror(errno));
}
// Copy the .cellml file (and any relevant others) into the temporary folder
FileFinder cellml_file(rCellmlFullPath, RelativeTo::Absolute);
FileFinder cellml_folder = cellml_file.GetParent();
std::string cellml_leaf_name = cellml_file.GetLeafNameNoExtension();
std::vector<FileFinder> cellml_files = cellml_folder.FindMatches(cellml_leaf_name + "*");
BOOST_FOREACH(const FileFinder& r_cellml_file, cellml_files)
{
r_cellml_file.CopyTo(tmp_folder);
}
#ifdef CHASTE_CMAKE ///todo: #2656 - ignoring all cmake-specific code, revise after cmake transition
#define COVERAGE_IGNORE
std::string cmake_lists_filename = tmp_folder.GetAbsolutePath() + "/CMakeLists.txt";
std::ofstream cmake_lists_filestream(cmake_lists_filename.c_str());
cmake_lists_filestream << "cmake_minimum_required(VERSION 2.8.10)\n" <<
"find_package(Chaste COMPONENTS " << mComponentName << ")\n" <<
"chaste_do_cellml(sources " << cellml_file.GetAbsolutePath() << " " << "ON)\n" <<
"set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})\n" <<
"include_directories(${Chaste_THIRD_PARTY_INCLUDE_DIRS} ${Chaste_INCLUDE_DIRS})\n" <<
"add_library(" << cellml_leaf_name << " SHARED " << "${sources})\n"
//"target_link_libraries(" << cellml_leaf_name << " ${Chaste_LIBRARIES})\n"
;
cmake_lists_filestream.close();
std::string cmake_args = " -DCMAKE_PREFIX_PATH=" + chaste_root.GetAbsolutePath() +
" -DCMAKE_BUILD_TYPE=" + ChasteBuildType() +
" -DBUILD_SHARED_LIBS=ON" +
" -DENABLE_CHASTE_TESTING=OFF" +
" -DChaste_USE_SHARED_LIBS=ON";
EXPECT0(chdir, tmp_folder.GetAbsolutePath());
EXPECT0(system, "cmake" + cmake_args + " .");
EXPECT0(system, "cmake --build . --config " + ChasteBuildType());
#undef COVERAGE_IGNORE
#else
// Change to Chaste source folder
EXPECT0(chdir, chaste_root.GetAbsolutePath());
// Run scons to generate C++ code and compile it to a .so
EXPECT0(system, "scons --warn=no-all dyn_libs_only=1 build=" + ChasteBuildType() + " " + tmp_folder.GetAbsolutePath());
#endif
FileFinder so_file(tmp_folder.GetAbsolutePath() + "/lib" + cellml_leaf_name + "." + msSoSuffix, RelativeTo::Absolute);
EXCEPT_IF_NOT(so_file.Exists());
// CD back
EXPECT0(chdir, old_cwd);
// Copy the .so to the same folder as the original .cellml file
FileFinder destination_folder(rCellmlFolder, RelativeTo::Absolute);
so_file.CopyTo(destination_folder);
if (mPreserveGeneratedSources)
{
// Copy generated source code as well
std::vector<FileFinder> generated_files = build_folder.FindMatches("*.?pp");
BOOST_FOREACH(const FileFinder& r_generated_file, generated_files)
{
r_generated_file.CopyTo(destination_folder);
}
}
// Delete the temporary folders
build_folder.DangerousRemove();
tmp_folder.DangerousRemove();
}
