vector<Cparticle> *Cio_data::read(int timestep) {
H5PartFile *reader = H5PartOpenFile(filename.c_str(),H5PART_READ);
if (H5PartGetNumSteps(reader) < timestep) {
cerr << "There is not "<<timestep<<"timesteps in the file"<<endl;
H5PartCloseFile(reader);
exit(-1);
}
H5PartSetStep(reader,timestep);
int n = H5PartGetNumParticles(reader);
vector<Cparticle> *output = new vector<Cparticle>(n);
double r[NDIM][n],v[NDIM][n],mass[n],u[n];
for (int i=0; i<NDIM; i++) {
if (!H5PartReadDataFloat64(reader,dimNames[i],r[i])) {
cerr << "Error reading particle position data" << endl;
exit(-1);
}
}
for (int i=0; i<NDIM; i++) {
if (!H5PartReadDataFloat64(reader,vdimNames[i],v[i])) {
cerr << "Error reading particle velocity data" << endl;
exit(-1);
}
}
if (!(H5PartReadDataFloat64(reader,"mass",mass))&&
(H5PartReadDataFloat64(reader,"u",u))) {
cerr << "Error reading particle data in file" << endl;
exit(-1);
}
for (int i=0; i<n; i++) {
for (int j=0; j<NDIM; i++) {
(*output)[i].r[j] = r[j][i];
(*output)[i].v[j] = r[j][i];
}
(*output)[i].mass = mass[i];
(*output)[i].u = u[i];
}
H5PartCloseFile(reader);
return output;
}
void test_read2(void)
{
H5PartFile *file1;
H5PartFile *file2;
h5part_int64_t status;
TEST( "Opening file twice, read-only");
file1 = OPEN(FILENAME,H5PART_READ);
test_is_valid(file1);
file2 = OPEN(FILENAME,H5PART_READ);
test_is_valid(file2);
test_read_strided_data32(file1, NPARTICLES, NTIMESTEPS+1);
test_read_file_attribs(file2, 1);
status = H5PartCloseFile(file1);
RETURN(status, H5PART_SUCCESS, "H5PartCloseFile");
status = H5PartCloseFile(file2);
RETURN(status, H5PART_SUCCESS, "H5PartCloseFile");
}
void test_read4(void)
{
H5PartFile *file1;
H5PartFile *file2;
h5part_int64_t status;
TEST( "Opening file twice, read-only, lustre filesystem "
"MPI-IO Independent VFD, 64K alignment");
file1 = OPENALIGN(FILENAME,
H5PART_READ | H5PART_VFD_MPIIO_IND | H5PART_FS_LUSTRE,
65536);
test_is_valid(file1);
file2 = OPENALIGN(FILENAME,
H5PART_READ | H5PART_VFD_MPIIO_IND | H5PART_FS_LUSTRE,
65536);
test_is_valid(file2);
TEST("Redefining step name");
status = H5PartDefineStepName(file1, LONGNAME, 16);
RETURN(status, H5PART_SUCCESS, "H5PartDefineStepName");
status = H5PartDefineStepName(file2, LONGNAME, 16);
RETURN(status, H5PART_SUCCESS, "H5PartDefineStepName");
test_read_file_attribs(file1, 1);
status = H5PartSetStep(file2, NTIMESTEPS);
RETURN(status, H5PART_SUCCESS, "H5PartSetStep");
test_read_data64(file2, NPARTICLES, NTIMESTEPS-2);
status = H5PartCloseFile(file1);
RETURN(status, H5PART_SUCCESS, "H5PartCloseFile");
status = H5PartCloseFile(file2);
RETURN(status, H5PART_SUCCESS, "H5PartCloseFile");
}
void test_write4(void)
{
H5PartFile *file1;
H5PartFile *file2;
h5part_int64_t status;
TEST( "Opening file twice, write-append + read-only, "
"lustre filesystem, MPI-IO Independent VFD, 1K alignment");
file1 = OPENALIGN(FILENAME,
H5PART_APPEND | H5PART_VFD_MPIIO_IND | H5PART_FS_LUSTRE,
1024);
test_is_valid(file1);
file2 = OPENALIGN(FILENAME,
H5PART_READ | H5PART_VFD_MPIIO_IND | H5PART_FS_LUSTRE,
1024);
test_is_valid(file2);
TEST("Redefining step name");
status = H5PartDefineStepName(file1, LONGNAME, 16);
RETURN(status, H5PART_SUCCESS, "H5PartDefineStepName");
status = H5PartDefineStepName(file2, LONGNAME, 16);
RETURN(status, H5PART_SUCCESS, "H5PartDefineStepName");
status = H5PartSetChunkSize(file1, NPARTICLES);
RETURN(status, H5PART_SUCCESS, "H5PartSetChunkSize");
test_write_data64(file1, NPARTICLES, NTIMESTEPS-2);
test_write_file_attribs(file1, 1);
status = H5PartCloseFile(file1);
RETURN(status, H5PART_SUCCESS, "H5PartCloseFile");
status = H5PartCloseFile(file2);
RETURN(status, H5PART_SUCCESS, "H5PartCloseFile");
}
void test_read1(void)
{
H5PartFile *file1;
h5part_int64_t status;
TEST("Opening file once, read-only");
file1 = OPEN(FILENAME,H5PART_READ);
test_is_valid(file1);
test_read_file_attribs(file1, 0);
test_read_data32(file1, NPARTICLES, 1);
status = H5PartCloseFile(file1);
RETURN(status, H5PART_SUCCESS, "H5PartCloseFile");
}
void test_write1(void)
{
H5PartFile *file1;
h5part_int64_t status;
TEST("Opening file once, write-truncate");
file1 = OPEN(FILENAME,H5PART_WRITE);
test_is_valid(file1);
test_write_data32(file1, NPARTICLES, 1);
test_write_file_attribs(file1, 0);
status = H5PartCloseFile(file1);
RETURN(status, H5PART_SUCCESS, "H5PartCloseFile");
}
void test_read3(void)
{
H5PartFile *file1;
h5part_int64_t status;
TEST( "Opening file once, read-only, lustre filesystem, "
"MPI-POSIX VFD, 64KB alignment");
file1 = OPENALIGN(FILENAME,
H5PART_READ | H5PART_VFD_MPIPOSIX | H5PART_FS_LUSTRE,
65536);
test_is_valid(file1);
TEST("Redefining step name");
status = H5PartDefineStepName(file1, LONGNAME, 16);
RETURN(status, H5PART_SUCCESS, "H5PartDefineStepName");
test_read_strided_data64(file1, NPARTICLES, 0);
test_read_file_attribs(file1, 0);
status = H5PartCloseFile(file1);
RETURN(status, H5PART_SUCCESS, "H5PartCloseFile");
}
void test_write3(void)
{
H5PartFile *file1;
h5part_int64_t status;
TEST( "Opening file once, write-truncate, lustre filesyste, "
"MPI-POSIX VFD, 1KB alignment");
file1 = OPENALIGN(FILENAME,
H5PART_WRITE | H5PART_VFD_MPIPOSIX | H5PART_FS_LUSTRE,
1024);
test_is_valid(file1);
TEST("Redefining step name");
status = H5PartDefineStepName(file1, LONGNAME, 16);
RETURN(status, H5PART_SUCCESS, "H5PartDefineStepName");
test_write_strided_data64(file1, NPARTICLES, 0);
test_write_file_attribs(file1, 0);
status = H5PartCloseFile(file1);
RETURN(status, H5PART_SUCCESS, "H5PartCloseFile");
}
double write_data (float* data, int iter, Params* p)
{
int i,j;
double start_time;
double open_time;
double write_time;
double close_time;
double total_time;
double sum_time;
double open_mean;
double write_mean;
double close_mean;
double bandwidth;
float* segment;
char var_name[64];
char* filename;
H5PartFile* file;
h5part_int64_t status;
if (p->verbosity >= VERBOSITY_HIGH) {
printf ("rank %d: writing data\n", p->rank);
}
start_time = MPI_Wtime();
filename = (char*) malloc (strlen (p->filename) + 64);
sprintf (filename, "%s/%d.h5", p->filename, iter);
file = H5PartOpenFileParallelAlign (filename,
p->flags, MPI_COMM_WORLD, p->alignment);
if (!file) {
fprintf (stderr,
"rank %d: could not open H5Part file!\n", p->rank);
MPI_Barrier (MPI_COMM_WORLD);
exit (EXIT_FAILURE);
}
H5PartSetNumParticles (file, p->particles);
if (p->verbosity >= VERBOSITY_HIGH) {
printf ("rank %d: %ld particles\n", p->rank, p->particles);
}
open_time = MPI_Wtime() - start_time;
segment = data;
for (i=1; i<=p->segments; i++) {
status = H5PartSetStep (file, i);
if (status != H5PART_SUCCESS) {
fprintf (stderr, "rank %d: H5PartSetStep error!", p->rank);
}
for (j=0; j<p->blocks; j++) {
sprintf (var_name, "test%d", j);
status = H5PartWriteDataFloat32 (file, var_name, segment);
if (status != H5PART_SUCCESS) {
fprintf (stderr,
"rank %d: H5PartWriteDataFloat32 error!", p->rank);
}
segment += p->particles;
}
}
write_time = (MPI_Wtime() - start_time) - open_time;
H5PartCloseFile (file);
close_time = (MPI_Wtime() - start_time) - write_time - open_time;
total_time = open_time + write_time + close_time;
if (p->verbosity >= VERBOSITY_HIGH) {
printf ("rank %d: write\t%.3f\t%.3f\t%.3f\t%.3f\n", p->rank,
open_time, write_time, close_time, total_time);
}
MPI_Barrier (MPI_COMM_WORLD);
MPI_Reduce (&open_time, &sum_time, 1, MPI_DOUBLE,
MPI_SUM, 0, MPI_COMM_WORLD);
open_mean = sum_time / p->procs;
MPI_Reduce (&write_time, &sum_time, 1, MPI_DOUBLE,
MPI_SUM, 0, MPI_COMM_WORLD);
write_mean = sum_time / p->procs;
MPI_Reduce (&close_time, &sum_time, 1, MPI_DOUBLE,
MPI_SUM, 0, MPI_COMM_WORLD);
close_mean = sum_time / p->procs;
bandwidth = p->aggregate_size / total_time;
if (p->verbosity >= VERBOSITY_MEDIUM && p->rank == 0) {
printf ("write\t%.1f\t%.3f\t%.3f\t%.3f\t%.3f\n", bandwidth,
open_mean, write_mean, close_mean, total_time);
}
free (filename);
return bandwidth;
}
