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Commit 9a2681d3 authored by Matthieu Schaller's avatar Matthieu Schaller
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Implemented a new i/o scheme where each MPI ranks writes a file instead of...

Implemented a new i/o scheme where each MPI ranks writes a file instead of writing a single file for all the ranks.
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/*******************************************************************************
* This file is part of SWIFT.
* Copyright (c) 2019 Matthieu Schaller (schaller@strw.leidenuniv.nl)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
/* Config parameters. */
#include "../config.h"
#if defined(HAVE_HDF5) && defined(WITH_MPI)
/* Some standard headers. */
#include <hdf5.h>
#include <math.h>
#include <stddef.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
/* This object's header. */
#include "distributed_io.h"
/* Local includes. */
#include "black_holes_io.h"
#include "chemistry_io.h"
#include "common_io.h"
#include "cooling_io.h"
#include "dimension.h"
#include "engine.h"
#include "entropy_floor.h"
#include "error.h"
#include "fof_io.h"
#include "gravity_io.h"
#include "gravity_properties.h"
#include "hydro_io.h"
#include "hydro_properties.h"
#include "io_properties.h"
#include "kernel_hydro.h"
#include "memuse.h"
#include "part.h"
#include "part_type.h"
#include "star_formation_io.h"
#include "stars_io.h"
#include "tracers_io.h"
#include "units.h"
#include "velociraptor_io.h"
#include "xmf.h"
/**
* @brief Writes a data array in given HDF5 group.
*
* @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
* @param N The number of particles to write.
* @param internal_units The #unit_system used internally
* @param snapshot_units The #unit_system used in the snapshots
*
* @todo A better version using HDF5 hyper-slabs to write the file directly from
* the part array will be written once the structures have been stabilized.
*/
void write_distributed_array(const struct engine* e, hid_t grp,
const char* fileName,
const char* partTypeGroupName,
const struct io_props props, const size_t N,
const struct unit_system* internal_units,
const struct unit_system* snapshot_units) {
const size_t typeSize = io_sizeof_type(props.type);
const size_t num_elements = N * props.dimension;
/* message("Writing '%s' array...", props.name); */
/* Allocate temporary buffer */
void* temp = NULL;
if (swift_memalign("writebuff", (void**)&temp, IO_BUFFER_ALIGNMENT,
num_elements * typeSize) != 0)
error("Unable to allocate temporary i/o buffer");
/* Copy the particle data to the temporary buffer */
io_copy_temp_buffer(temp, e, props, N, internal_units, 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;
hsize_t shape[2];
hsize_t chunk_shape[2];
if (props.dimension > 1) {
rank = 2;
shape[0] = N;
shape[1] = props.dimension;
chunk_shape[0] = 1 << 20; /* Just a guess...*/
chunk_shape[1] = props.dimension;
} else {
rank = 1;
shape[0] = N;
shape[1] = 0;
chunk_shape[0] = 1 << 20; /* Just a guess...*/
chunk_shape[1] = 0;
}
/* Make sure the chunks are not larger than the dataset */
if (chunk_shape[0] > N) chunk_shape[0] = N;
/* Change shape of data space */
hid_t h_err = H5Sset_extent_simple(h_space, rank, shape, shape);
if (h_err < 0)
error("Error while changing data space 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);
/* Impose check-sum to verify data corruption */
h_err = H5Pset_fletcher32(h_prop);
if (h_err < 0)
error("Error while setting checksum options for field '%s'.", props.name);
/* Impose data compression */
if (e->snapshot_compression > 0) {
h_err = H5Pset_shuffle(h_prop);
if (h_err < 0)
error("Error while setting shuffling options for field '%s'.",
props.name);
h_err = H5Pset_deflate(h_prop, e->snapshot_compression);
if (h_err < 0)
error("Error while setting compression options for field '%s'.",
props.name);
}
/* Create dataset */
const hid_t h_data = H5Dcreate(grp, props.name, io_hdf5_type(props.type),
h_space, H5P_DEFAULT, h_prop, H5P_DEFAULT);
if (h_data < 0) error("Error while creating dataspace '%s'.", props.name);
/* Write temporary buffer to HDF5 dataspace */
h_err = H5Dwrite(h_data, io_hdf5_type(props.type), h_space, H5S_ALL,
H5P_DEFAULT, temp);
if (h_err < 0) error("Error while writing data array '%s'.", props.name);
/* Write unit conversion factors for this data set */
char buffer[FIELD_BUFFER_SIZE] = {0};
units_cgs_conversion_string(buffer, snapshot_units, props.units,
props.scale_factor_exponent);
float baseUnitsExp[5];
units_get_base_unit_exponents_array(baseUnitsExp, props.units);
io_write_attribute_f(h_data, "U_M exponent", baseUnitsExp[UNIT_MASS]);
io_write_attribute_f(h_data, "U_L exponent", baseUnitsExp[UNIT_LENGTH]);
io_write_attribute_f(h_data, "U_t exponent", baseUnitsExp[UNIT_TIME]);
io_write_attribute_f(h_data, "U_I exponent", baseUnitsExp[UNIT_CURRENT]);
io_write_attribute_f(h_data, "U_T exponent", baseUnitsExp[UNIT_TEMPERATURE]);
io_write_attribute_f(h_data, "h-scale exponent", 0.f);
io_write_attribute_f(h_data, "a-scale exponent", props.scale_factor_exponent);
io_write_attribute_s(h_data, "Expression for physical CGS units", buffer);
/* Write the actual number this conversion factor corresponds to */
const double factor =
units_cgs_conversion_factor(snapshot_units, props.units);
io_write_attribute_d(
h_data,
"Conversion factor to CGS (not including cosmological corrections)",
factor);
io_write_attribute_d(
h_data,
"Conversion factor to physical CGS (including cosmological corrections)",
factor * pow(e->cosmology->a, props.scale_factor_exponent));
#ifdef SWIFT_DEBUG_CHECKS
if (strlen(props.description) == 0)
error("Invalid (empty) description of the field '%s'", props.name);
#endif
/* Write the full description */
io_write_attribute_s(h_data, "Description", props.description);
/* Free and close everything */
swift_free("writebuff", temp);
H5Pclose(h_prop);
H5Dclose(h_data);
H5Sclose(h_space);
}
/**
* @brief Writes a snapshot distributed into multiple files.
*
* @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
*
* Creates a series of HDF5 output files (1 per MPI node) as a snapshot.
* Writes the particles contained in the engine.
* If such files already exist, it is erased and replaced by the new one.
* The companion XMF file is also updated accordingly.
*/
void write_output_distributed(struct engine* e, const char* baseName,
const struct unit_system* internal_units,
const struct unit_system* snapshot_units,
const int mpi_rank, const int mpi_size,
MPI_Comm comm, MPI_Info info) {
hid_t h_file = 0, h_grp = 0;
int numFiles = mpi_size;
const struct part* parts = e->s->parts;
const struct xpart* xparts = e->s->xparts;
const struct gpart* gparts = e->s->gparts;
const struct spart* sparts = e->s->sparts;
const struct bpart* bparts = e->s->bparts;
struct swift_params* params = e->parameter_file;
const int with_cosmology = e->policy & engine_policy_cosmology;
const int with_cooling = e->policy & engine_policy_cooling;
const int with_temperature = e->policy & engine_policy_temperature;
const int with_fof = e->policy & engine_policy_fof;
const int with_DM_background = e->s->with_DM_background;
#ifdef HAVE_VELOCIRAPTOR
const int with_stf = (e->policy & engine_policy_structure_finding) &&
(e->s->gpart_group_data != NULL);
#else
const int with_stf = 0;
#endif
/* Number of particles currently in the arrays */
const size_t Ntot = e->s->nr_gparts;
const size_t Ngas = e->s->nr_parts;
const size_t Nstars = e->s->nr_sparts;
const size_t Nblackholes = e->s->nr_bparts;
size_t Ndm_background = 0;
if (with_DM_background) {
Ndm_background = io_count_dm_background_gparts(gparts, Ntot);
}
/* Number of particles that we will write in this file.
* Recall that background particles are never inhibited and have no extras */
const size_t Ntot_written =
e->s->nr_gparts - e->s->nr_inhibited_gparts - e->s->nr_extra_gparts;
const size_t Ngas_written =
e->s->nr_parts - e->s->nr_inhibited_parts - e->s->nr_extra_parts;
const size_t Nstars_written =
e->s->nr_sparts - e->s->nr_inhibited_sparts - e->s->nr_extra_sparts;
const size_t Nblackholes_written =
e->s->nr_bparts - e->s->nr_inhibited_bparts - e->s->nr_extra_bparts;
const size_t Nbaryons_written =
Ngas_written + Nstars_written + Nblackholes_written;
const size_t Ndm_written =
Ntot_written > 0 ? Ntot_written - Nbaryons_written - Ndm_background : 0;
/* File name */
char fileName[FILENAME_BUFFER_SIZE];
if (e->snapshot_int_time_label_on)
snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%06i.%d.hdf5", baseName,
(int)round(e->time), mpi_rank);
else if (e->snapshot_invoke_stf) {
snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%04i.%d.hdf5", baseName,
e->stf_output_count, mpi_rank);
} else
snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%04i.%d.hdf5", baseName,
e->snapshot_output_count, mpi_rank);
/* Compute offset in the file and total number of particles */
const long long N[swift_type_count] = {Ngas_written, Ndm_written,
Ndm_background, 0,
Nstars_written, Nblackholes_written};
/* Gather the total number of particles to write */
long long N_total[swift_type_count] = {0};
MPI_Allreduce(N, N_total, swift_type_count, MPI_LONG_LONG_INT, MPI_SUM, comm);
/* First time, we need to create the XMF file */
if (e->snapshot_output_count == 0) xmf_create_file(baseName);
/* Open file */
/* message("Opening file '%s'.", fileName); */
h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
if (h_file < 0) error("Error while opening file '%s'.", fileName);
/* Open header to write simulation properties */
/* message("Writing file header..."); */
h_grp = H5Gcreate(h_file, "/Header", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating file header\n");
/* Convert basic output information to snapshot units */
const double factor_time =
units_conversion_factor(internal_units, snapshot_units, UNIT_CONV_TIME);
const double factor_length =
units_conversion_factor(internal_units, snapshot_units, UNIT_CONV_LENGTH);
const double dblTime = e->time * factor_time;
const double dim[3] = {e->s->dim[0] * factor_length,
e->s->dim[1] * factor_length,
e->s->dim[2] * factor_length};
/* Print the relevant information and print status */
io_write_attribute(h_grp, "BoxSize", DOUBLE, dim, 3);
io_write_attribute(h_grp, "Time", DOUBLE, &dblTime, 1);
const int dimension = (int)hydro_dimension;
io_write_attribute(h_grp, "Dimension", INT, &dimension, 1);
io_write_attribute(h_grp, "Redshift", DOUBLE, &e->cosmology->z, 1);
io_write_attribute(h_grp, "Scale-factor", DOUBLE, &e->cosmology->a, 1);
io_write_attribute_s(h_grp, "Code", "SWIFT");
time_t tm = time(NULL);
io_write_attribute_s(h_grp, "Snapshot date", ctime(&tm));
io_write_attribute_s(h_grp, "RunName", e->run_name);
/* GADGET-2 legacy values */
/* Number of particles of each type */
unsigned int numParticles[swift_type_count] = {0};
unsigned int numParticlesHighWord[swift_type_count] = {0};
for (int ptype = 0; ptype < swift_type_count; ++ptype) {
numParticles[ptype] = (unsigned int)N_total[ptype];
numParticlesHighWord[ptype] = (unsigned int)(N_total[ptype] >> 32);
}
io_write_attribute(h_grp, "NumPart_ThisFile", LONGLONG, N, swift_type_count);
io_write_attribute(h_grp, "NumPart_Total", UINT, numParticles,
swift_type_count);
io_write_attribute(h_grp, "NumPart_Total_HighWord", UINT,
numParticlesHighWord, swift_type_count);
double MassTable[swift_type_count] = {0};
io_write_attribute(h_grp, "MassTable", DOUBLE, MassTable, swift_type_count);
unsigned int flagEntropy[swift_type_count] = {0};
flagEntropy[0] = writeEntropyFlag();
io_write_attribute(h_grp, "Flag_Entropy_ICs", UINT, flagEntropy,
swift_type_count);
io_write_attribute_i(h_grp, "NumFilesPerSnapshot", numFiles);
io_write_attribute_i(h_grp, "ThisFile", mpi_rank);
/* Close header */
H5Gclose(h_grp);
/* Print the code version */
io_write_code_description(h_file);
/* Print the run's policy */
io_write_engine_policy(h_file, e);
/* Print the SPH parameters */
if (e->policy & engine_policy_hydro) {
h_grp = H5Gcreate(h_file, "/HydroScheme", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
if (h_grp < 0) error("Error while creating SPH group");
hydro_props_print_snapshot(h_grp, e->hydro_properties);
hydro_write_flavour(h_grp);
H5Gclose(h_grp);
}
/* Print the subgrid parameters */
h_grp = H5Gcreate(h_file, "/SubgridScheme", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
if (h_grp < 0) error("Error while creating subgrid group");
entropy_floor_write_flavour(h_grp);
cooling_write_flavour(h_grp, e->cooling_func);
chemistry_write_flavour(h_grp);
tracers_write_flavour(h_grp);
H5Gclose(h_grp);
/* Print the gravity parameters */
if (e->policy & engine_policy_self_gravity) {
h_grp = H5Gcreate(h_file, "/GravityScheme", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
if (h_grp < 0) error("Error while creating gravity group");
gravity_props_print_snapshot(h_grp, e->gravity_properties);
H5Gclose(h_grp);
}
/* Print the stellar parameters */
if (e->policy & engine_policy_stars) {
h_grp = H5Gcreate(h_file, "/StarsScheme", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
if (h_grp < 0) error("Error while creating stars group");
stars_props_print_snapshot(h_grp, e->stars_properties);
H5Gclose(h_grp);
}
/* Print the cosmological model */
h_grp =
H5Gcreate(h_file, "/Cosmology", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating cosmology group");
if (e->policy & engine_policy_cosmology)
io_write_attribute_i(h_grp, "Cosmological run", 1);
else
io_write_attribute_i(h_grp, "Cosmological run", 0);
cosmology_write_model(h_grp, e->cosmology);
H5Gclose(h_grp);
/* Print the runtime parameters */
h_grp =
H5Gcreate(h_file, "/Parameters", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating parameters group");
parser_write_params_to_hdf5(e->parameter_file, h_grp, 1);
H5Gclose(h_grp);
/* Print the runtime unused parameters */
h_grp = H5Gcreate(h_file, "/UnusedParameters", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
if (h_grp < 0) error("Error while creating parameters group");
parser_write_params_to_hdf5(e->parameter_file, h_grp, 0);
H5Gclose(h_grp);
/* Print the system of Units used in the spashot */
io_write_unit_system(h_file, snapshot_units, "Units");
/* Print the system of Units used internally */
io_write_unit_system(h_file, internal_units, "InternalCodeUnits");
/* Now write the top-level cell structure */
long long global_offsets[swift_type_count] = {0};
h_grp = H5Gcreate(h_file, "/Cells", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating cells group");
/* Write the location of the particles in the arrays */
io_write_cell_offsets(h_grp, e->s->cdim, e->s->dim, e->s->pos_dithering,
e->s->cells_top, e->s->nr_cells, e->s->width, e->nodeID,
N_total, global_offsets, internal_units,
snapshot_units);
H5Gclose(h_grp);
/* Tell the user if a conversion will be needed */
if (e->verbose) {
if (units_are_equal(snapshot_units, internal_units)) {
message("Snapshot and internal units match. No conversion needed.");
} else {
message("Conversion needed from:");
message("(Snapshot) Unit system: U_M = %e g.",
snapshot_units->UnitMass_in_cgs);
message("(Snapshot) Unit system: U_L = %e cm.",
snapshot_units->UnitLength_in_cgs);
message("(Snapshot) Unit system: U_t = %e s.",
snapshot_units->UnitTime_in_cgs);
message("(Snapshot) Unit system: U_I = %e A.",
snapshot_units->UnitCurrent_in_cgs);
message("(Snapshot) Unit system: U_T = %e K.",
snapshot_units->UnitTemperature_in_cgs);
message("to:");
message("(internal) Unit system: U_M = %e g.",
internal_units->UnitMass_in_cgs);
message("(internal) Unit system: U_L = %e cm.",
internal_units->UnitLength_in_cgs);
message("(internal) Unit system: U_t = %e s.",
internal_units->UnitTime_in_cgs);
message("(internal) Unit system: U_I = %e A.",
internal_units->UnitCurrent_in_cgs);
message("(internal) Unit system: U_T = %e K.",
internal_units->UnitTemperature_in_cgs);
}
}
/* 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 (numParticles[ptype] == 0) continue;
/* 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) error("Error while creating particle group.\n");
int num_fields = 0;
struct io_props list[100];
size_t Nparticles = 0;
struct part* parts_written = NULL;
struct xpart* xparts_written = NULL;
struct gpart* gparts_written = NULL;
struct velociraptor_gpart_data* gpart_group_data_written = NULL;
struct spart* sparts_written = NULL;
struct bpart* bparts_written = NULL;
/* Write particle fields from the particle structure */
switch (ptype) {
case swift_type_gas: {
if (Ngas == Ngas_written) {
/* No inhibted particles: easy case */
Nparticles = Ngas;
hydro_write_particles(parts, xparts, list, &num_fields);
num_fields += chemistry_write_particles(parts, list + num_fields);
if (with_cooling || with_temperature) {
num_fields += cooling_write_particles(
parts, xparts, list + num_fields, e->cooling_func);
}
if (with_fof) {
num_fields += fof_write_parts(parts, xparts, list + num_fields);
}
if (with_stf) {
num_fields +=
velociraptor_write_parts(parts, xparts, list + num_fields);
}
num_fields += tracers_write_particles(
parts, xparts, list + num_fields, with_cosmology);
num_fields +=
star_formation_write_particles(parts, xparts, list + num_fields);
} else {
/* Ok, we need to fish out the particles we want */
Nparticles = Ngas_written;
/* Allocate temporary arrays */
if (swift_memalign("parts_written", (void**)&parts_written,
part_align,
Ngas_written * sizeof(struct part)) != 0)
error("Error while allocating temporary memory for parts");
if (swift_memalign("xparts_written", (void**)&xparts_written,
xpart_align,
Ngas_written * sizeof(struct xpart)) != 0)
error("Error while allocating temporary memory for xparts");
/* Collect the particles we want to write */
io_collect_parts_to_write(parts, xparts, parts_written,
xparts_written, Ngas, Ngas_written);
/* Select the fields to write */
hydro_write_particles(parts_written, xparts_written, list,
&num_fields);
num_fields +=
chemistry_write_particles(parts_written, list + num_fields);
if (with_cooling || with_temperature) {
num_fields +=
cooling_write_particles(parts_written, xparts_written,
list + num_fields, e->cooling_func);
}
if (with_fof) {
num_fields += fof_write_parts(parts_written, xparts_written,
list + num_fields);
}
if (with_stf) {
num_fields += velociraptor_write_parts(
parts_written, xparts_written, list + num_fields);
}
num_fields += tracers_write_particles(
parts_written, xparts_written, list + num_fields, with_cosmology);
num_fields += star_formation_write_particles(
parts_written, xparts_written, list + num_fields);
}
} break;
case swift_type_dark_matter: {
if (Ntot == Ndm_written) {
/* This is a DM-only run without background or inhibited particles */
Nparticles = Ntot;
darkmatter_write_particles(gparts, list, &num_fields);
if (with_fof) {
num_fields += fof_write_gparts(gparts, list + num_fields);
}
if (with_stf) {
num_fields += velociraptor_write_gparts(e->s->gpart_group_data,
list + num_fields);
}
} else {
/* Ok, we need to fish out the particles we want */
Nparticles = Ndm_written;
/* Allocate temporary array */
if (swift_memalign("gparts_written", (void**)&gparts_written,
gpart_align,
Ndm_written * sizeof(struct gpart)) != 0)
error("Error while allocating temporary memory for gparts");
if (with_stf) {
if (swift_memalign(
"gpart_group_written", (void**)&gpart_group_data_written,
gpart_align,
Ndm_written * sizeof(struct velociraptor_gpart_data)) != 0)
error(
"Error while allocating temporary memory for gparts STF "
"data");
}
/* Collect the non-inhibited DM particles from gpart */
io_collect_gparts_to_write(gparts, e->s->gpart_group_data,
gparts_written, gpart_group_data_written,
Ntot, Ndm_written, with_stf);
/* Select the fields to write */
darkmatter_write_particles(gparts_written, list, &num_fields);
if (with_fof) {
num_fields += fof_write_gparts(gparts_written, list + num_fields);
}
if (with_stf) {
num_fields += velociraptor_write_gparts(gpart_group_data_written,
list + num_fields);
}
}
} break;
case swift_type_dark_matter_background: {
/* Ok, we need to fish out the particles we want */
Nparticles = Ndm_background;
/* Allocate temporary array */
if (swift_memalign("gparts_written", (void**)&gparts_written,
gpart_align,
Ndm_background * sizeof(struct gpart)) != 0)
error("Error while allocating temporart memory for gparts");
if (with_stf) {
if (swift_memalign(
"gpart_group_written", (void**)&gpart_group_data_written,
gpart_align,
Ndm_background * sizeof(struct velociraptor_gpart_data)) != 0)
error(
"Error while allocating temporart memory for gparts STF "
"data");
}
/* Collect the non-inhibited DM particles from gpart */
io_collect_gparts_background_to_write(
gparts, e->s->gpart_group_data, gparts_written,
gpart_group_data_written, Ntot, Ndm_background, with_stf);
/* Select the fields to write */
darkmatter_write_particles(gparts_written, list, &num_fields);
if (with_fof) {
num_fields += fof_write_gparts(gparts_written, list + num_fields);
}
if (with_stf) {
num_fields += velociraptor_write_gparts(gpart_group_data_written,
list + num_fields);
}
} break;
case swift_type_stars: {
if (Nstars == Nstars_written) {
/* No inhibted particles: easy case */
Nparticles = Nstars;
stars_write_particles(sparts, list, &num_fields, with_cosmology);
num_fields += chemistry_write_sparticles(sparts, list + num_fields);
num_fields += tracers_write_sparticles(sparts, list + num_fields,
with_cosmology);
if (with_fof) {
num_fields += fof_write_sparts(sparts, list + num_fields);
}
if (with_stf) {
num_fields += velociraptor_write_sparts(sparts, list + num_fields);
}
} else {
/* Ok, we need to fish out the particles we want */
Nparticles = Nstars_written;
/* Allocate temporary arrays */
if (swift_memalign("sparts_written", (void**)&sparts_written,
spart_align,
Nstars_written * sizeof(struct spart)) != 0)
error("Error while allocating temporary memory for sparts");
/* Collect the particles we want to write */
io_collect_sparts_to_write(sparts, sparts_written, Nstars,
Nstars_written);
/* Select the fields to write */
stars_write_particles(sparts_written, list, &num_fields,
with_cosmology);
num_fields +=
chemistry_write_sparticles(sparts_written, list + num_fields);
num_fields += tracers_write_sparticles(
sparts_written, list + num_fields, with_cosmology);
if (with_fof) {
num_fields += fof_write_sparts(sparts_written, list + num_fields);
}
if (with_stf) {
num_fields +=
velociraptor_write_sparts(sparts_written, list + num_fields);
}
}
} break;
case swift_type_black_hole: {
if (Nblackholes == Nblackholes_written) {
/* No inhibted particles: easy case */
Nparticles = Nblackholes;
black_holes_write_particles(bparts, list, &num_fields,
with_cosmology);
num_fields += chemistry_write_bparticles(bparts, list + num_fields);
if (with_fof) {
num_fields += fof_write_bparts(bparts, list + num_fields);
}
if (with_stf) {
num_fields += velociraptor_write_bparts(bparts, list + num_fields);
}
} else {
/* Ok, we need to fish out the particles we want */
Nparticles = Nblackholes_written;
/* Allocate temporary arrays */
if (swift_memalign("bparts_written", (void**)&bparts_written,
bpart_align,
Nblackholes_written * sizeof(struct bpart)) != 0)
error("Error while allocating temporary memory for bparts");
/* Collect the particles we want to write */
io_collect_bparts_to_write(bparts, bparts_written, Nblackholes,
Nblackholes_written);
/* Select the fields to write */
black_holes_write_particles(bparts_written, list, &num_fields,
with_cosmology);
num_fields +=
chemistry_write_bparticles(bparts_written, list + num_fields);
if (with_fof) {
num_fields += fof_write_bparts(bparts_written, list + num_fields);
}
if (with_stf) {
num_fields +=
velociraptor_write_bparts(bparts_written, list + num_fields);
}
}
} break;
default:
error("Particle Type %d not yet supported. Aborting", ptype);
}
/* Write everything that is not cancelled */
for (int i = 0; i < num_fields; ++i) {
/* Did the user cancel this field? */
char field[PARSER_MAX_LINE_SIZE];
sprintf(field, "SelectOutput:%.*s_%s", FIELD_BUFFER_SIZE, list[i].name,
part_type_names[ptype]);
int should_write = parser_get_opt_param_int(params, field, 1);
if (should_write)
write_distributed_array(e, h_grp, fileName, partTypeGroupName, list[i],
Nparticles, internal_units, snapshot_units);
}
/* Free temporary arrays */
if (parts_written) swift_free("parts_written", parts_written);
if (xparts_written) swift_free("xparts_written", xparts_written);
if (gparts_written) swift_free("gparts_written", gparts_written);
if (gpart_group_data_written)
swift_free("gpart_group_written", gpart_group_data_written);
if (sparts_written) swift_free("sparts_written", sparts_written);
if (bparts_written) swift_free("bparts_written", bparts_written);
/* Close particle group */
H5Gclose(h_grp);
}
/* message("Done writing particles..."); */
/* Close file */
H5Fclose(h_file);
e->snapshot_output_count++;
if (e->snapshot_invoke_stf) e->stf_output_count++;
}
#endif /* HAVE_HDF5 && WITH_MPI */
/*******************************************************************************
* This file is part of SWIFT.
* Copyright (c) 2019 Matthieu Schaller (schaller@strw.leidenuniv.nl)
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
#ifndef SWIFT_DISTRIBUTED_IO_H
#define SWIFT_DISTRIBUTED_IO_H
/* Config parameters. */
#include "../config.h"
#if defined(HAVE_HDF5) && defined(WITH_MPI)
/* MPI headers. */
#ifdef WITH_MPI
#include <mpi.h>
#endif
/* Includes. */
#include "engine.h"
#include "io_properties.h"
#include "part.h"
#include "units.h"
void write_output_distributed(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);
#endif /* HAVE_HDF5 && WITH_MPI */
#endif /* SWIFT_DISTRIBUTED_IO_H */
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