Skip to content
Snippets Groups Projects
Commit b503350c authored by Peter W. Draper's avatar Peter W. Draper
Browse files

Merge branch 'parallel_io_improvements' into 'master' 

Parallel io improvements

See merge request !497
parents 00eb15b5 12bab1d7
No related branches found
No related tags found
1 merge request!497Parallel io improvements
Hide whitespace changes
Inline Side-by-side
Showing
with 311 additions and 222 deletions
src/parallel_io.c
+ 311
− 222
View file @ b503350c
......@@ -240,19 +240,103 @@ void readArray(hid_t grp, struct io_props props, size_t N, long long N_total,
* Routines writing an output file
*-----------------------------------------------------------------------------*/
/**
* @brief Prepares an array in the snapshot.
*
* @param e The #engine we are writing from.
* @param grp The HDF5 grp to write to.
* @param fileName The name of the file we are writing to.
* @param xmfFile The (opened) XMF file we are appending to.
* @param partTypeGroupName The name of the group we are writing to.
* @param props The #io_props of the field to write.
* @param N_total The total number of particles to write in this array.
* @param snapshot_units The units used for the data in this snapshot.
*/
void prepareArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
char* partTypeGroupName, struct io_props props,
long long N_total, const struct unit_system* snapshot_units) {
/* Create data space */
const hid_t h_space = H5Screate(H5S_SIMPLE);
if (h_space < 0)
error("Error while creating data space for field '%s'.", props.name);
int rank = 0;
hsize_t shape[2];
hsize_t chunk_shape[2];
if (props.dimension > 1) {
rank = 2;
shape[0] = N_total;
shape[1] = props.dimension;
chunk_shape[0] = 1 << 16; /* Just a guess...*/
chunk_shape[1] = props.dimension;
} else {
rank = 1;
shape[0] = N_total;
shape[1] = 0;
chunk_shape[0] = 1 << 16; /* Just a guess...*/
chunk_shape[1] = 0;
}
/* Make sure the chunks are not larger than the dataset */
if (chunk_shape[0] > N_total) chunk_shape[0] = N_total;
/* Change shape of data space */
hid_t h_err = H5Sset_extent_simple(h_space, rank, shape, NULL);
if (h_err < 0)
error("Error while changing data space shape for field '%s'.", props.name);
/* Create property list for collective dataset write. */
const hid_t h_plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(h_plist_id, H5FD_MPIO_COLLECTIVE);
/* Set chunk size */
/* h_err = H5Pset_chunk(h_prop, rank, chunk_shape); */
/* if (h_err < 0) { */
/* error("Error while setting chunk size (%llu, %llu) for field '%s'.", */
/* chunk_shape[0], chunk_shape[1], props.name); */
/* } */
/* Create dataset */
const hid_t h_data =
H5Dcreate(grp, props.name, io_hdf5_type(props.type), h_space, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);
if (h_data < 0) error("Error while creating dataspace '%s'.", props.name);
/* Write unit conversion factors for this data set */
char buffer[FIELD_BUFFER_SIZE];
units_cgs_conversion_string(buffer, snapshot_units, props.units);
io_write_attribute_d(
h_data, "CGS conversion factor",
units_cgs_conversion_factor(snapshot_units, props.units));
io_write_attribute_f(h_data, "h-scale exponent",
units_h_factor(snapshot_units, props.units));
io_write_attribute_f(h_data, "a-scale exponent",
units_a_factor(snapshot_units, props.units));
io_write_attribute_s(h_data, "Conversion factor", buffer);
/* Add a line to the XMF */
xmf_write_line(xmfFile, fileName, partTypeGroupName, props.name, N_total,
props.dimension, props.type);
/* Close everything */
H5Pclose(h_plist_id);
H5Dclose(h_data);
H5Sclose(h_space);
}
/**
* @brief Writes a chunk of data in an open HDF5 dataset
*
* @param e The #engine we are writing from.
* @param h_data The HDF5 dataset to write to.
* @param h_plist_id the parallel HDF5 properties.
* @param props The #io_props of the field to read.
* @param props The #io_props of the field to write.
* @param N The number of particles to write.
* @param offset Offset in the array where this mpi task starts writing.
* @param internal_units The #unit_system used internally.
* @param snapshot_units The #unit_system used in the snapshots.
*/
void writeArray_chunk(struct engine* e, hid_t h_data, hid_t h_plist_id,
void writeArray_chunk(struct engine* e, hid_t h_data,
const struct io_props props, size_t N, long long offset,
const struct unit_system* internal_units,
const struct unit_system* snapshot_units) {
......@@ -338,7 +422,7 @@ void writeArray_chunk(struct engine* e, hid_t h_data, hid_t h_plist_id,
/* Write temporary buffer to HDF5 dataspace */
h_err = H5Dwrite(h_data, io_hdf5_type(props.type), h_memspace, h_filespace,
h_plist_id, temp);
H5P_DEFAULT, temp);
if (h_err < 0) {
error("Error while writing data array '%s'.", props.name);
}
......@@ -367,7 +451,6 @@ void writeArray_chunk(struct engine* e, hid_t h_data, hid_t h_plist_id,
* @param e The #engine we are writing from.
* @param grp The group in which to write.
* @param fileName The name of the file in which the data is written.
* @param xmfFile The FILE used to write the XMF description.
* @param partTypeGroupName The name of the group containing the particles in
* the HDF5 file.
* @param props The #io_props of the field to read
......@@ -378,7 +461,7 @@ void writeArray_chunk(struct engine* e, hid_t h_data, hid_t h_plist_id,
* @param internal_units The #unit_system used internally.
* @param snapshot_units The #unit_system used in the snapshots.
*/
void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
void writeArray(struct engine* e, hid_t grp, char* fileName,
char* partTypeGroupName, struct io_props props, size_t N,
long long N_total, int mpi_rank, long long offset,
const struct unit_system* internal_units,
......@@ -390,62 +473,9 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
const ticks tic = getticks();
#endif
/* Work out properties of the array in the file */
int rank;
hsize_t shape_total[2];
hsize_t chunk_shape[2];
if (props.dimension > 1) {
rank = 2;
shape_total[0] = N_total;
shape_total[1] = props.dimension;
chunk_shape[0] = 1 << 16; /* Just a guess...*/
chunk_shape[1] = props.dimension;
} else {
rank = 1;
shape_total[0] = N_total;
shape_total[1] = 0;
chunk_shape[0] = 1 << 16; /* Just a guess...*/
chunk_shape[1] = 0;
}
/* Make sure the chunks are not larger than the dataset */
if (chunk_shape[0] > (hsize_t)N_total) chunk_shape[0] = N_total;
/* Create the space in the file */
hid_t h_filespace = H5Screate(H5S_SIMPLE);
if (h_filespace < 0) {
error("Error while creating data space (file) for field '%s'.", props.name);
}
/* Change shape of file data space */
hid_t h_err = H5Sset_extent_simple(h_filespace, rank, shape_total, NULL);
if (h_err < 0) {
error("Error while changing data space (file) shape for field '%s'.",
props.name);
}
/* Dataset properties */
const hid_t h_prop = H5Pcreate(H5P_DATASET_CREATE);
/* Set chunk size */
/* h_err = H5Pset_chunk(h_prop, rank, chunk_shape); */
/* if (h_err < 0) { */
/* error("Error while setting chunk size (%llu, %llu) for field '%s'.", */
/* chunk_shape[0], chunk_shape[1], props.name); */
/* } */
/* Create dataset */
const hid_t h_data = H5Dcreate(grp, props.name, io_hdf5_type(props.type),
h_filespace, H5P_DEFAULT, h_prop, H5P_DEFAULT);
if (h_data < 0) {
error("Error while creating dataset '%s'.", props.name);
}
H5Sclose(h_filespace);
/* Create property list for collective dataset write. */
const hid_t h_plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(h_plist_id, H5FD_MPIO_COLLECTIVE);
/* Open dataset */
const hid_t h_data = H5Dopen(grp, props.name, H5P_DEFAULT);
if (h_data < 0) error("Error while opening dataset '%s'.", props.name);
/* Given the limitations of ROM-IO we will need to write the data in chunk of
HDF5_PARALLEL_IO_MAX_BYTES bytes per node until all the nodes are done. */
......@@ -458,8 +488,8 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
/* Write the first chunk */
const size_t this_chunk = (N > max_chunk_size) ? max_chunk_size : N;
writeArray_chunk(e, h_data, h_plist_id, props, this_chunk, offset,
internal_units, snapshot_units);
writeArray_chunk(e, h_data, props, this_chunk, offset, internal_units,
snapshot_units);
/* Compute how many items are left */
if (N > max_chunk_size) {
......@@ -482,27 +512,8 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
message("Need to redo one iteration for array '%s'", props.name);
}
/* Write XMF description for this data set */
if (mpi_rank == 0)
xmf_write_line(xmfFile, fileName, partTypeGroupName, props.name, N_total,
props.dimension, props.type);
/* Write unit conversion factors for this data set */
char buffer[FIELD_BUFFER_SIZE];
units_cgs_conversion_string(buffer, snapshot_units, props.units);
io_write_attribute_d(
h_data, "CGS conversion factor",
units_cgs_conversion_factor(snapshot_units, props.units));
io_write_attribute_f(h_data, "h-scale exponent",
units_h_factor(snapshot_units, props.units));
io_write_attribute_f(h_data, "a-scale exponent",
units_a_factor(snapshot_units, props.units));
io_write_attribute_s(h_data, "Conversion factor", buffer);
/* Close everything */
H5Pclose(h_prop);
H5Dclose(h_data);
H5Pclose(h_plist_id);
#ifdef IO_SPEED_MEASUREMENT
MPI_Barrier(MPI_COMM_WORLD);
......@@ -797,128 +808,47 @@ void read_ic_parallel(char* fileName, const struct unit_system* internal_units,
}
/**
* @brief Writes an HDF5 output file (GADGET-3 type) with
*its XMF descriptor
*
* @param e The engine containing all the system.
* @param baseName The common part of the snapshot file name.
* @param internal_units The #unit_system used internally
* @param snapshot_units The #unit_system used in the snapshots
* @param mpi_rank The MPI rank of this node.
* @param mpi_size The number of MPI ranks.
* @param comm The MPI communicator.
* @param info The MPI information object
*
* Creates an HDF5 output file and writes the particles
* contained in the engine. If such a file already exists, it is
* erased and replaced by the new one.
* The companion XMF file is also updated accordingly.
*
* Calls #error() if an error occurs.
* @brief Prepares a file for a parallel write.
*
* @param e The #engine.
* @param baseName The base name of the snapshots.
* @param N_total The total number of particles of each type to write.
* @param internal_units The #unit_system used internally.
* @param snapshot_units The #unit_system used in the snapshots.
*/
void write_output_parallel(struct engine* e, const char* baseName,
const struct unit_system* internal_units,
const struct unit_system* snapshot_units,
int mpi_rank, int mpi_size, MPI_Comm comm,
MPI_Info info) {
void prepare_file(struct engine* e, const char* baseName, long long N_total[6],
const struct unit_system* internal_units,
const struct unit_system* snapshot_units) {
hid_t h_file = 0, h_grp = 0;
const size_t Ngas = e->s->nr_parts;
const size_t Nstars = e->s->nr_sparts;
const size_t Ntot = e->s->nr_gparts;
int periodic = e->s->periodic;
int numFiles = 1;
struct part* parts = e->s->parts;
struct gpart* gparts = e->s->gparts;
struct gpart* dmparts = NULL;
struct spart* sparts = e->s->sparts;
FILE* xmfFile = 0;
/* Number of unassociated gparts */
const size_t Ndm = Ntot > 0 ? Ntot - (Ngas + Nstars) : 0;
/* File name */
char fileName[FILENAME_BUFFER_SIZE];
snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%04i.hdf5", baseName,
e->snapshotOutputCount);
int periodic = e->s->periodic;
int numFiles = 1;
/* First time, we need to create the XMF file */
if (e->snapshotOutputCount == 0 && mpi_rank == 0) xmf_create_file(baseName);
if (e->snapshotOutputCount == 0) xmf_create_file(baseName);
/* Prepare the XMF file for the new entry */
if (mpi_rank == 0) xmfFile = xmf_prepare_file(baseName);
/* Prepare some file-access properties */
hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
/* Set some MPI-IO parameters */
// MPI_Info_set(info, "IBM_largeblock_io", "true");
MPI_Info_set(info, "romio_cb_write", "enable");
MPI_Info_set(info, "romio_ds_write", "disable");
/* Activate parallel i/o */
hid_t h_err = H5Pset_fapl_mpio(plist_id, comm, info);
if (h_err < 0) error("Error setting parallel i/o");
/* Align on 4k pages. */
h_err = H5Pset_alignment(plist_id, 1024, 4096);
if (h_err < 0) error("Error setting Hdf5 alignment");
/* Disable meta-data cache eviction */
H5AC_cache_config_t mdc_config;
mdc_config.version = H5AC__CURR_CACHE_CONFIG_VERSION;
h_err = H5Pget_mdc_config(plist_id, &mdc_config);
if (h_err < 0) error("Error getting the MDC config");
xmfFile = xmf_prepare_file(baseName);
mdc_config.evictions_enabled = 0; /* false */
mdc_config.incr_mode = H5C_incr__off;
mdc_config.decr_mode = H5C_decr__off;
mdc_config.flash_incr_mode = H5C_flash_incr__off;
h_err = H5Pset_mdc_config(plist_id, &mdc_config);
if (h_err < 0) error("Error setting the MDC config");
/* Use parallel meta-data writes */
#if H5_VERSION_GE(1, 10, 0)
h_err = H5Pset_all_coll_metadata_ops(plist_id, 1);
if (h_err < 0) error("Error setting collective meta-data on all ops");
h_err = H5Pset_coll_metadata_write(plist_id, 1);
if (h_err < 0) error("Error setting collective meta-data writes");
#endif
/* HDF5 File name */
char fileName[FILENAME_BUFFER_SIZE];
snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%04i.hdf5", baseName,
e->snapshotOutputCount);
/* Open HDF5 file with the chosen parameters */
h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
if (h_file < 0) {
error("Error while opening file '%s'.", fileName);
}
/* Compute offset in the file and total number of particles */
size_t N[swift_type_count] = {Ngas, Ndm, 0, 0, Nstars, 0};
long long N_total[swift_type_count] = {0};
long long offset[swift_type_count] = {0};
MPI_Exscan(&N, &offset, swift_type_count, MPI_LONG_LONG_INT, MPI_SUM, comm);
for (int ptype = 0; ptype < swift_type_count; ++ptype)
N_total[ptype] = offset[ptype] + N[ptype];
/* The last rank now has the correct N_total. Let's
* broadcast from there */
MPI_Bcast(&N_total, 6, MPI_LONG_LONG_INT, mpi_size - 1, comm);
/* Now everybody konws its offset and the total number of
* particles of each type */
hid_t h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
if (h_file < 0) error("Error while opening file '%s'.", fileName);
/* Write the part of the XMF file corresponding to this
* specific output */
if (mpi_rank == 0) xmf_write_outputheader(xmfFile, fileName, e->time);
#ifdef IO_SPEED_MEASUREMENT
MPI_Barrier(MPI_COMM_WORLD);
ticks tic = getticks();
#endif
xmf_write_outputheader(xmfFile, fileName, e->time);
/* Open header to write simulation properties */
/* message("Writing runtime parameters..."); */
h_grp =
hid_t h_grp =
H5Gcreate(h_file, "/RuntimePars", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating runtime parameters group\n");
......@@ -1008,10 +938,200 @@ void write_output_parallel(struct engine* e, const char* baseName,
/* Print the system of Units used internally */
io_write_unit_system(h_file, internal_units, "InternalCodeUnits");
/* Loop over all particle types */
for (int ptype = 0; ptype < swift_type_count; ptype++) {
/* Don't do anything if no particle of this kind */
if (N_total[ptype] == 0) continue;
/* Add the global information for that particle type to
* the XMF meta-file */
xmf_write_groupheader(xmfFile, fileName, N_total[ptype],
(enum part_type)ptype);
/* Create the particle group in the file */
char partTypeGroupName[PARTICLE_GROUP_BUFFER_SIZE];
snprintf(partTypeGroupName, PARTICLE_GROUP_BUFFER_SIZE, "/PartType%d",
ptype);
h_grp = H5Gcreate(h_file, partTypeGroupName, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
if (h_grp < 0)
error("Error while opening particle group %s.", partTypeGroupName);
int num_fields = 0;
struct io_props list[100];
/* Write particle fields from the particle structure */
switch (ptype) {
case swift_type_gas:
hydro_write_particles(parts, list, &num_fields);
num_fields += chemistry_write_particles(parts, list + num_fields);
break;
case swift_type_dark_matter:
darkmatter_write_particles(gparts, list, &num_fields);
break;
case swift_type_star:
star_write_particles(sparts, list, &num_fields);
break;
default:
error("Particle Type %d not yet supported. Aborting", ptype);
}
/* Prepare everything */
for (int i = 0; i < num_fields; ++i)
prepareArray(e, h_grp, fileName, xmfFile, partTypeGroupName, list[i],
N_total[ptype], snapshot_units);
/* Close particle group */
H5Gclose(h_grp);
/* Close this particle group in the XMF file as well */
xmf_write_groupfooter(xmfFile, (enum part_type)ptype);
}
/* Write LXMF file descriptor */
xmf_write_outputfooter(xmfFile, e->snapshotOutputCount, e->time);
/* Close the file for now */
H5Fclose(h_file);
}
/**
* @brief Writes an HDF5 output file (GADGET-3 type) with
*its XMF descriptor
*
* @param e The engine containing all the system.
* @param baseName The common part of the snapshot file name.
* @param internal_units The #unit_system used internally
* @param snapshot_units The #unit_system used in the snapshots
* @param mpi_rank The MPI rank of this node.
* @param mpi_size The number of MPI ranks.
* @param comm The MPI communicator.
* @param info The MPI information object
*
* Creates an HDF5 output file and writes the particles
* contained in the engine. If such a file already exists, it is
* erased and replaced by the new one.
* The companion XMF file is also updated accordingly.
*
* Calls #error() if an error occurs.
*
*/
void write_output_parallel(struct engine* e, const char* baseName,
const struct unit_system* internal_units,
const struct unit_system* snapshot_units,
int mpi_rank, int mpi_size, MPI_Comm comm,
MPI_Info info) {
const size_t Ngas = e->s->nr_parts;
const size_t Nstars = e->s->nr_sparts;
const size_t Ntot = e->s->nr_gparts;
struct part* parts = e->s->parts;
struct gpart* gparts = e->s->gparts;
struct gpart* dmparts = NULL;
struct spart* sparts = e->s->sparts;
/* Number of unassociated gparts */
const size_t Ndm = Ntot > 0 ? Ntot - (Ngas + Nstars) : 0;
/* Compute offset in the file and total number of particles */
size_t N[swift_type_count] = {Ngas, Ndm, 0, 0, Nstars, 0};
long long N_total[swift_type_count] = {0};
long long offset[swift_type_count] = {0};
MPI_Exscan(&N, &offset, swift_type_count, MPI_LONG_LONG_INT, MPI_SUM, comm);
for (int ptype = 0; ptype < swift_type_count; ++ptype)
N_total[ptype] = offset[ptype] + N[ptype];
/* The last rank now has the correct N_total. Let's
* broadcast from there */
MPI_Bcast(&N_total, 6, MPI_LONG_LONG_INT, mpi_size - 1, comm);
/* Now everybody konws its offset and the total number of
* particles of each type */
#ifdef IO_SPEED_MEASUREMENT
ticks tic = getticks();
#endif
/* Rank 0 prepares the file */
if (mpi_rank == 0)
prepare_file(e, baseName, N_total, internal_units, snapshot_units);
MPI_Barrier(MPI_COMM_WORLD);
#ifdef IO_SPEED_MEASUREMENT
if (engine_rank == 0)
message("Writing HDF5 header took %.3f %s.",
message("Preparing file on rank 0 took %.3f %s.",
clocks_from_ticks(getticks() - tic), clocks_getunit());
tic = getticks();
#endif
/* HDF5 File name */
char fileName[FILENAME_BUFFER_SIZE];
snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%04i.hdf5", baseName,
e->snapshotOutputCount);
/* Prepare some file-access properties */
hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
/* Set some MPI-IO parameters */
// MPI_Info_set(info, "IBM_largeblock_io", "true");
MPI_Info_set(info, "romio_cb_write", "enable");
MPI_Info_set(info, "romio_ds_write", "disable");
/* Activate parallel i/o */
hid_t h_err = H5Pset_fapl_mpio(plist_id, comm, info);
if (h_err < 0) error("Error setting parallel i/o");
/* Align on 4k pages. */
h_err = H5Pset_alignment(plist_id, 1024, 4096);
if (h_err < 0) error("Error setting Hdf5 alignment");
/* Disable meta-data cache eviction */
H5AC_cache_config_t mdc_config;
mdc_config.version = H5AC__CURR_CACHE_CONFIG_VERSION;
h_err = H5Pget_mdc_config(plist_id, &mdc_config);
if (h_err < 0) error("Error getting the MDC config");
mdc_config.evictions_enabled = 0; /* false */
mdc_config.incr_mode = H5C_incr__off;
mdc_config.decr_mode = H5C_decr__off;
mdc_config.flash_incr_mode = H5C_flash_incr__off;
h_err = H5Pset_mdc_config(plist_id, &mdc_config);
if (h_err < 0) error("Error setting the MDC config");
/* Use parallel meta-data writes */
#if H5_VERSION_GE(1, 10, 0)
h_err = H5Pset_all_coll_metadata_ops(plist_id, 1);
if (h_err < 0) error("Error setting collective meta-data on all ops");
h_err = H5Pset_coll_metadata_write(plist_id, 1);
if (h_err < 0) error("Error setting collective meta-data writes");
#endif
#ifdef IO_SPEED_MEASUREMENT
MPI_Barrier(MPI_COMM_WORLD);
if (engine_rank == 0)
message("Setting parallel HDF5 access properties took %.3f %s.",
clocks_from_ticks(getticks() - tic), clocks_getunit());
tic = getticks();
#endif
/* Open HDF5 file with the chosen parameters */
hid_t h_file = H5Fopen(fileName, H5F_ACC_RDWR, plist_id);
if (h_file < 0) {
error("Error while opening file '%s'.", fileName);
}
#ifdef IO_SPEED_MEASUREMENT
MPI_Barrier(MPI_COMM_WORLD);
if (engine_rank == 0)
message("Opening HDF5 file took %.3f %s.",
clocks_from_ticks(getticks() - tic), clocks_getunit());
tic = getticks();
......@@ -1056,21 +1176,13 @@ void write_output_parallel(struct engine* e, const char* baseName,
/* Don't do anything if no particle of this kind */
if (N_total[ptype] == 0) continue;
/* Add the global information for that particle type to
* the XMF meta-file */
if (mpi_rank == 0)
xmf_write_groupheader(xmfFile, fileName, N_total[ptype],
(enum part_type)ptype);
/* Open the particle group in the file */
char partTypeGroupName[PARTICLE_GROUP_BUFFER_SIZE];
snprintf(partTypeGroupName, PARTICLE_GROUP_BUFFER_SIZE, "/PartType%d",
ptype);
h_grp = H5Gcreate(h_file, partTypeGroupName, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
if (h_grp < 0) {
hid_t h_grp = H5Gopen(h_file, partTypeGroupName, H5P_DEFAULT);
if (h_grp < 0)
error("Error while opening particle group %s.", partTypeGroupName);
}
int num_fields = 0;
struct io_props list[100];
......@@ -1113,9 +1225,9 @@ void write_output_parallel(struct engine* e, const char* baseName,
/* Write everything */
for (int i = 0; i < num_fields; ++i)
writeArray(e, h_grp, fileName, xmfFile, partTypeGroupName, list[i],
Nparticles, N_total[ptype], mpi_rank, offset[ptype],
internal_units, snapshot_units);
writeArray(e, h_grp, fileName, partTypeGroupName, list[i], Nparticles,
N_total[ptype], mpi_rank, offset[ptype], internal_units,
snapshot_units);
/* Free temporary array */
if (dmparts) {
......@@ -1139,16 +1251,6 @@ void write_output_parallel(struct engine* e, const char* baseName,
tic = getticks();
#endif
/* Close this particle group in the XMF file as well */
if (mpi_rank == 0) xmf_write_groupfooter(xmfFile, (enum part_type)ptype);
#ifdef IO_SPEED_MEASUREMENT
MPI_Barrier(MPI_COMM_WORLD);
if (engine_rank == 0)
message("Writing XMF group footer took %.3f %s.",
clocks_from_ticks(getticks() - tic), clocks_getunit());
#endif
}
#ifdef IO_SPEED_MEASUREMENT
......@@ -1156,19 +1258,6 @@ void write_output_parallel(struct engine* e, const char* baseName,
tic = getticks();
#endif
/* Write LXMF file descriptor */
if (mpi_rank == 0)
xmf_write_outputfooter(xmfFile, e->snapshotOutputCount, e->time);
#ifdef IO_SPEED_MEASUREMENT
MPI_Barrier(MPI_COMM_WORLD);
if (engine_rank == 0)
message("Writing XMF output footer took %.3f %s.",
clocks_from_ticks(getticks() - tic), clocks_getunit());
tic = getticks();
#endif
/* message("Done writing particles..."); */
/* Close property descriptor */
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment