diff --git a/src/parallel_io.c b/src/parallel_io.c
index d17b7e99e5ec0bb97d87eb1dc50e4a5d40a37f01..03b13aa63f65ad2c0dbe27110ed5cd276ca50b65 100644
--- a/src/parallel_io.c
+++ b/src/parallel_io.c
@@ -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 */