void seissol::checkpoint::posix::Wavefield::write(double time, int timestepWaveField)
{
EPIK_TRACER("CheckPoint_write");
SCOREP_USER_REGION("CheckPoint_write", SCOREP_USER_REGION_TYPE_FUNCTION);
logInfo(rank()) << "Checkpoint backend: Writing.";
// Start at the beginning
checkErr(lseek64(file(), 0, SEEK_SET));
// Write the header
EPIK_USER_REG(r_write_header, "checkpoint_write_header");
SCOREP_USER_REGION_DEFINE(r_write_header);
EPIK_USER_START(r_write_header);
SCOREP_USER_REGION_BEGIN(r_write_header, "checkpoint_write_header", SCOREP_USER_REGION_TYPE_COMMON);
WavefieldHeader header;
header.time = time;
header.timestepWaveField = timestepWaveField;
writeHeader(file(), header);
EPIK_USER_END(r_write_header);
SCOREP_USER_REGION_END(r_write_header);
// Save data
EPIK_USER_REG(r_write_wavefield, "checkpoint_write_wavefield");
SCOREP_USER_REGION_DEFINE(r_write_wavefield);
EPIK_USER_START(r_write_wavefield);
SCOREP_USER_REGION_BEGIN(r_write_wavefield, "checkpoint_write_wavefield", SCOREP_USER_REGION_TYPE_COMMON);
// Convert to char* to do pointer arithmetic
const char* buffer = reinterpret_cast<const char*>(dofs());
unsigned long left = numDofs()*sizeof(real);
if (alignment()) {
left = (left + alignment() - 1) / alignment();
left *= alignment();
}
while (left > 0) {
unsigned long written = ::write(file(), buffer, left);
if (written <= 0)
checkErr(written, left);
buffer += written;
left -= written;
}
EPIK_USER_END(r_write_wavefield);
SCOREP_USER_REGION_END(r_write_wavefield);
// Finalize the checkpoint
finalizeCheckpoint();
logInfo(rank()) << "Checkpoint backend: Writing. Done.";
}
void seissol::checkpoint::posix::Wavefield::write(double time, int timestepWaveField)
{
EPIK_TRACER("CheckPoint_write");
SCOREP_USER_REGION("CheckPoint_write", SCOREP_USER_REGION_TYPE_FUNCTION);
logInfo(rank()) << "Writing check point.";
// Skip identifier
checkErr(lseek64(file(), sizeof(unsigned long), SEEK_SET));
// Write the header
EPIK_USER_REG(r_write_header, "checkpoint_write_header");
SCOREP_USER_REGION_DEFINE(r_write_header);
EPIK_USER_START(r_write_header);
SCOREP_USER_REGION_BEGIN(r_write_header, "checkpoint_write_header", SCOREP_USER_REGION_TYPE_COMMON);
checkErr(::write(file(), &time, sizeof(time)), sizeof(time));
checkErr(::write(file(), ×tepWaveField, sizeof(timestepWaveField)),
sizeof(timestepWaveField));
EPIK_USER_END(r_write_header);
SCOREP_USER_REGION_END(r_write_header);
// Save data
EPIK_USER_REG(r_write_wavefield, "checkpoint_write_wavefield");
SCOREP_USER_REGION_DEFINE(r_write_wavefield);
EPIK_USER_START(r_write_wavefield);
SCOREP_USER_REGION_BEGIN(r_write_wavefield, "checkpoint_write_wavefield", SCOREP_USER_REGION_TYPE_COMMON);
// Convert to char* to do pointer arithmetic
const char* buffer = reinterpret_cast<const char*>(dofs());
unsigned long left = numDofs()*sizeof(real);
while (left > 0) {
unsigned long written = ::write(file(), buffer, left);
if (written <= 0)
checkErr(written, left);
buffer += written;
left -= written;
}
EPIK_USER_END(r_write_wavefield);
SCOREP_USER_REGION_END(r_write_wavefield);
// Finalize the checkpoint
finalizeCheckpoint();
logInfo(rank()) << "Writing check point. Done.";
}
void seissol::checkpoint::mpio::WavefieldAsync::writePrepare(double time, int timestepWaveField)
{
EPIK_TRACER("CheckPoint_writePrepare");
SCOREP_USER_REGION("CheckPoint_writePrepare", SCOREP_USER_REGION_TYPE_FUNCTION);
// Write the header
writeHeader(time, timestepWaveField);
// Create copy of the dofs
memcpy(m_dofsCopy, dofs(), numDofs()*sizeof(real));
// Save data
EPIK_USER_REG(r_write_wavefield, "checkpoint_write_begin_wavefield");
SCOREP_USER_REGION_DEFINE(r_write_wavefield);
EPIK_USER_START(r_write_wavefield);
SCOREP_USER_REGION_BEGIN(r_write_wavefield, "checkpoint_write_begin_wavefield", SCOREP_USER_REGION_TYPE_COMMON);
checkMPIErr(setDataView(file()));
checkMPIErr(MPI_File_write_all_begin(file(), m_dofsCopy, numDofs(), MPI_DOUBLE));
EPIK_USER_END(r_write_wavefield);
SCOREP_USER_REGION_END(r_write_wavefield);
m_started = true;
logInfo(rank()) << "Checkpoint backend: Writing. Done.";
}
void seissol::checkpoint::mpio::FaultAsync::writePrepare(int timestepFault)
{
EPIK_TRACER("CheckPointFault_writePrepare");
SCOREP_USER_REGION("CheckPointFault_writePrepare", SCOREP_USER_REGION_TYPE_FUNCTION);
if (numSides() == 0)
return;
// Write the header
writeHeader(timestepFault);
// Create copy of the data
for (unsigned int i = 0; i < NUM_VARIABLES; i++)
memcpy(&m_dataCopy[i*numSides()*numBndGP()],
data(i), numSides()*numBndGP()*sizeof(double));
// Save data
EPIK_USER_REG(r_write_wavefield, "checkpoint_write_begin_fault");
SCOREP_USER_REGION_DEFINE(r_write_fault);
EPIK_USER_START(r_write_wavefield);
SCOREP_USER_REGION_BEGIN(r_write_fault, "checkpoint_write_begin_fault", SCOREP_USER_REGION_TYPE_COMMON);
checkMPIErr(setDataView(file()));
checkMPIErr(MPI_File_write_all_begin(file(), m_dataCopy, numSides() * numBndGP() * NUM_VARIABLES, MPI_DOUBLE));
EPIK_USER_END(r_write_fault);
SCOREP_USER_REGION_END(r_write_fault);
m_started = true;
logInfo(rank()) << "Writing fault check point. Done.";
}
void seissol::checkpoint::mpio::Wavefield::write(double time, int timestepWaveField)
{
EPIK_TRACER("CheckPoint_write");
SCOREP_USER_REGION("CheckPoint_write", SCOREP_USER_REGION_TYPE_FUNCTION);
logInfo(rank()) << "Writing check point.";
// Write the header
writeHeader(time, timestepWaveField);
// Save data
EPIK_USER_REG(r_write_wavefield, "checkpoint_write_wavefield");
SCOREP_USER_REGION_DEFINE(r_write_wavefield);
EPIK_USER_START(r_write_wavefield);
SCOREP_USER_REGION_BEGIN(r_write_wavefield, "checkpoint_write_wavefield", SCOREP_USER_REGION_TYPE_COMMON);
checkMPIErr(setDataView(file()));
checkMPIErr(MPI_File_write_all(file(), dofs(), numDofs(), MPI_DOUBLE, MPI_STATUS_IGNORE));
EPIK_USER_END(r_write_wavefield);
SCOREP_USER_REGION_END(r_write_wavefield);
// Finalize the checkpoint
finalizeCheckpoint();
logInfo(rank()) << "Writing check point. Done.";
}
void seissol::checkpoint::h5::Fault::write(int timestepFault)
{
EPIK_TRACER("CheckPointFault_write");
SCOREP_USER_REGION("CheckPointFault_write", SCOREP_USER_REGION_TYPE_FUNCTION);
if (numSides() == 0)
return;
logInfo(rank()) << "Writing fault check point.";
// Create array with all pointers
EPIK_USER_REG(r_write_fault, "checkpoint_write_fault");
SCOREP_USER_REGION_DEFINE(r_write_fault);
EPIK_USER_START(r_write_fault);
SCOREP_USER_REGION_BEGIN(r_write_fault, "checkpoint_write_fault", SCOREP_USER_REGION_TYPE_COMMON);
// Attributes
checkH5Err(H5Awrite(m_h5timestepFault[odd()], H5T_NATIVE_INT, ×tepFault));
// Set memory and file space
hsize_t fStart[2] = {fileOffset(), 0};
hsize_t count[2] = {numSides(), numBndGP()};
hid_t h5memSpace = H5Screate_simple(2, count, 0L);
checkH5Err(h5memSpace);
checkH5Err(H5Sselect_all(h5memSpace));
checkH5Err(H5Sselect_hyperslab(m_h5fSpaceData, H5S_SELECT_SET, fStart, 0L, count, 0L));
for (unsigned int i = 0; i < NUM_VARIABLES; i++) {
checkH5Err(H5Dwrite(m_h5data[odd()][i], H5T_NATIVE_DOUBLE, h5memSpace, m_h5fSpaceData,
h5XferList(), data(i)));
}
checkH5Err(H5Sclose(h5memSpace));
EPIK_USER_END(r_write_fault);
SCOREP_USER_REGION_END(r_write_fault);
// Finalize the checkpoint
finalizeCheckpoint();
logInfo(rank()) << "Writing fault check point. Done.";
}
void seissol::checkpoint::h5::Wavefield::write(double time, int waveFieldTimeStep)
{
EPIK_TRACER("CheckPoint_write");
SCOREP_USER_REGION("CheckPoint_write", SCOREP_USER_REGION_TYPE_FUNCTION);
logInfo(rank()) << "Writing check point.";
EPIK_USER_REG(r_header, "checkpoint_write_header");
SCOREP_USER_REGION_DEFINE(r_header);
EPIK_USER_START(r_header);
SCOREP_USER_REGION_BEGIN(r_header, "checkpoint_write_header", SCOREP_USER_REGION_TYPE_COMMON);
// Time
checkH5Err(H5Awrite(m_h5time[odd()], H5T_NATIVE_DOUBLE, &time));
// Wavefield writer
checkH5Err(H5Awrite(m_h5timestepWavefield[odd()], H5T_NATIVE_INT, &waveFieldTimeStep));
EPIK_USER_END(r_header);
SCOREP_USER_REGION_END(r_header);
// Save data
EPIK_USER_REG(r_write_wavefield, "checkpoint_write_wavefield");
SCOREP_USER_REGION_DEFINE(r_write_wavefield);
EPIK_USER_START(r_write_wavefield);
SCOREP_USER_REGION_BEGIN(r_write_wavefield, "checkpoint_write_wavefield", SCOREP_USER_REGION_TYPE_COMMON);
// Write the wave field
unsigned int offset = 0;
hsize_t fStart = fileOffset();
hsize_t count = dofsPerIteration();
hid_t h5memSpace = H5Screate_simple(1, &count, 0L);
checkH5Err(h5memSpace);
checkH5Err(H5Sselect_all(h5memSpace));
for (unsigned int i = 0; i < totalIterations()-1; i++) {
checkH5Err(H5Sselect_hyperslab(m_h5fSpaceData, H5S_SELECT_SET, &fStart, 0L, &count, 0L));
checkH5Err(H5Dwrite(m_h5data[odd()], H5T_NATIVE_DOUBLE, h5memSpace, m_h5fSpaceData,
h5XferList(), &const_cast<real*>(dofs())[offset]));
// We are finished in less iterations, read data twice
// so everybody needs the same number of iterations
if (i < iterations()-1) {
fStart += count;
offset += count;
}
}
checkH5Err(H5Sclose(h5memSpace));
// Save reminding data in the last iteration
count = numDofs() - (iterations() - 1) * count;
h5memSpace = H5Screate_simple(1, &count, 0L);
checkH5Err(h5memSpace);
checkH5Err(H5Sselect_all(h5memSpace));
checkH5Err(H5Sselect_hyperslab(m_h5fSpaceData, H5S_SELECT_SET, &fStart, 0L, &count, 0L));
checkH5Err(H5Dwrite(m_h5data[odd()], H5T_NATIVE_DOUBLE, h5memSpace, m_h5fSpaceData,
h5XferList(), &dofs()[offset]));
checkH5Err(H5Sclose(h5memSpace));
EPIK_USER_END(r_write_wavefield);
SCOREP_USER_REGION_END(r_write_wavefield);
// Finalize the checkpoint
finalizeCheckpoint();
logInfo(rank()) << "Writing check point. Done.";
}
