PetscSetupUtils.cpp

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*/
 
#include "PetscSetupUtils.hpp"
 
#include <cassert>
#include <cstdlib>
#include <cstring>
#include <iostream>
#include <petsc.h>
 
#include "ChasteBuildRoot.hpp"
#include "ChasteSyscalls.hpp"
#include "Citations.hpp"
#include "CommandLineArguments.hpp"
#include "Exception.hpp"
#include "GetCurrentWorkingDirectory.hpp"
#include "PetscException.hpp"
#include "PetscTools.hpp"
 
#include "PetscAndChasteCitations.hpp"
 
#ifdef TEST_FOR_FPE
#include <fenv.h>
#include <signal.h>
 
void FpeSignalToAbort(int sig_num, siginfo_t* info, void* context)
{
    if (info->si_code == FPE_FLTDIV)
    {
        std::cerr << "SIGFPE: floating point exception was divide by zero.\n";
    }
    else if (info->si_code == FPE_FLTINV)
    {
        std::cerr << "SIGFPE: floating point exception was an invalid operation (like 0.0/0.0).\n";
    }
    else
    {
        std::cerr << "SIGFPE: unexpected error code.\n";
    }
}
#endif
 
void PetscSetupUtils::InitialisePetsc()
{
    // The CommandLineArguments instance is filled in by the cxxtest test suite runner.
    CommandLineArguments* p_args = CommandLineArguments::Instance();
    PETSCEXCEPT(PetscInitialize(p_args->p_argc, p_args->p_argv, CHASTE_PETSC_NULLPTR, CHASTE_PETSC_NULLPTR));
    // Work around what seems to be an Intel compiler bug/quirk that makes the cache stale,
    // by using an explicit reset to ensure all code is aware we're running in parallel.
    PetscTools::ResetCache();
}
 
void PetscSetupUtils::CommonSetup()
{
    InitialisePetsc();
 
    if ((PETSC_VERSION_MAJOR < 3) || (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR < 5)) // PETSc 3.4 or earlier
    {
        // Add some PETSc citations if we're not using the built-in citation mechanisms
        Citations::Register(PetscCitation1, &PetscCite1);
        Citations::Register(PetscCitation2, &PetscCite2);
    }
    // Add main Chaste citation
    Citations::Register(ChasteCitation, &ChasteCite);
 
    // Check that the working directory is correct, or many tests will fail
    std::string cwd = GetCurrentWorkingDirectory() + "/";
    if (strcmp(cwd.c_str(), ChasteSourceRootDir()) != 0)
    {
        // Change directory
        std::cout << std::endl
                  << "Changing directory from '" << cwd << "' to '" << ChasteSourceRootDir() << "'." << std::endl;
        EXPECT0(chdir, ChasteSourceRootDir());
        std::cout << "CWD now: " << GetCurrentWorkingDirectory() << std::endl;
    }
 
#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 PetscSetupUtils::CommonFinalize()
{
    // This does nothing if we are on a new PETSc, just allows Chaste to print citations instead in this case
    Citations::Print();
 
    PETSCEXCEPT(PetscFinalize());
}
 
void PetscSetupUtils::ResetStatusCache()
{
    PetscTools::ResetCache();
}