/*******************************************************************************
* This file is part of SWIFT.
* Copyright (c) 2012 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
* 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 .
*
******************************************************************************/
/* Config parameters. */
#include
#if defined(HAVE_HDF5) && defined(WITH_MPI) && !defined(HAVE_PARALLEL_HDF5)
/* Some standard headers. */
#include
#include
#include
#include
#include
#include
#include
#include
/* This object's header. */
#include "serial_io.h"
/* Local includes. */
#include "black_holes_io.h"
#include "chemistry_io.h"
#include "common_io.h"
#include "dimension.h"
#include "engine.h"
#include "error.h"
#include "gravity_io.h"
#include "gravity_properties.h"
#include "hydro_io.h"
#include "hydro_properties.h"
#include "io_properties.h"
#include "memuse.h"
#include "mhd_io.h"
#include "output_list.h"
#include "output_options.h"
#include "part.h"
#include "part_type.h"
#include "rt_io.h"
#include "sink_io.h"
#include "star_formation_io.h"
#include "stars_io.h"
#include "tools.h"
#include "units.h"
#include "version.h"
#include "xmf.h"
/* Max number of entries that can be written for a given particle type */
static const int io_max_size_output_list = 100;
/**
* @brief Reads a data array from a given HDF5 group.
*
* @param grp The group from which to read.
* @param props The #io_props of the field to read
* @param N The number of particles to read on this rank.
* @param N_total The total number of particles on all ranks.
* @param offset The offset position where this rank starts reading.
* @param internal_units The #unit_system used internally
* @param ic_units The #unit_system used in the ICs
* @param cleanup_h Are we removing h-factors from the ICs?
* @param cleanup_sqrt_a Are we cleaning-up the sqrt(a) factors in the Gadget
* IC velocities?
* @param h The value of the reduced Hubble constant to use for cleaning.
* @param a The current value of the scale-factor.
*
* @todo A better version using HDF5 hyper-slabs to read the file directly into
* the part array will be written once the structures have been stabilized.
*/
void read_array_serial(hid_t grp, const struct io_props props, size_t N,
long long N_total, long long offset,
const struct unit_system* internal_units,
const struct unit_system* ic_units, int cleanup_h,
int cleanup_sqrt_a, double h, double a) {
const size_t typeSize = io_sizeof_type(props.type);
const size_t copySize = typeSize * props.dimension;
const size_t num_elements = N * props.dimension;
/* Check whether the dataspace exists or not */
const htri_t exist = H5Lexists(grp, props.name, 0);
if (exist < 0) {
error("Error while checking the existence of data set '%s'.", props.name);
} else if (exist == 0) {
if (props.importance == COMPULSORY) {
error("Compulsory data set '%s' not present in the file.", props.name);
} else {
/* Create a single instance of the default value */
float* temp = (float*)malloc(copySize);
for (int i = 0; i < props.dimension; ++i) temp[i] = props.default_value;
/* Copy it everywhere in the particle array */
for (size_t i = 0; i < N; ++i)
memcpy(props.field + i * props.partSize, temp, copySize);
free(temp);
return;
}
}
/* message( "Reading %s '%s' array...", importance == COMPULSORY ? */
/* "compulsory": "optional ", name); */
/* fflush(stdout); */
/* Open data space */
const hid_t h_data = H5Dopen(grp, props.name, H5P_DEFAULT);
if (h_data < 0) error("Error while opening data space '%s'.", props.name);
/* Allocate temporary buffer */
void* temp = malloc(num_elements * typeSize);
if (temp == NULL) error("Unable to allocate memory for temporary buffer");
/* Prepare information for hyper-slab */
hsize_t shape[2], offsets[2];
int rank;
if (props.dimension > 1) {
rank = 2;
shape[0] = N;
shape[1] = props.dimension;
offsets[0] = offset;
offsets[1] = 0;
} else {
rank = 2;
shape[0] = N;
shape[1] = 1;
offsets[0] = offset;
offsets[1] = 0;
}
/* Create data space in memory */
const hid_t h_memspace = H5Screate_simple(rank, shape, NULL);
/* Select hyper-slab in file */
const hid_t h_filespace = H5Dget_space(h_data);
H5Sselect_hyperslab(h_filespace, H5S_SELECT_SET, offsets, NULL, shape, NULL);
/* Read HDF5 dataspace in temporary buffer */
/* Dirty version that happens to work for vectors but should be improved */
/* Using HDF5 dataspaces would be better */
const hid_t h_err = H5Dread(h_data, io_hdf5_type(props.type), h_memspace,
h_filespace, H5P_DEFAULT, temp);
if (h_err < 0) error("Error while reading data array '%s'.", props.name);
/* Unit conversion if necessary */
const double factor =
units_conversion_factor(ic_units, internal_units, props.units);
if (factor != 1. && exist != 0) {
/* message("Converting ! factor=%e", factor); */
if (io_is_double_precision(props.type)) {
double* temp_d = (double*)temp;
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else {
float* temp_f = (float*)temp;
#ifdef SWIFT_DEBUG_CHECKS
float maximum = 0.f;
float minimum = FLT_MAX;
#endif
/* Loop that converts the Units */
for (size_t i = 0; i < num_elements; ++i) {
#ifdef SWIFT_DEBUG_CHECKS
/* Find the absolute minimum and maximum values */
const float abstemp_f = fabsf(temp_f[i]);
if (abstemp_f != 0.f) {
maximum = max(maximum, abstemp_f);
minimum = min(minimum, abstemp_f);
}
#endif
/* Convert the float units */
temp_f[i] *= factor;
}
#ifdef SWIFT_DEBUG_CHECKS
/* The two possible errors: larger than float or smaller
* than float precision. */
if (factor * maximum > FLT_MAX) {
error("Unit conversion results in numbers larger than floats");
} else if (factor * minimum < FLT_MIN) {
error("Numbers smaller than float precision");
}
#endif
}
}
/* Clean-up h if necessary */
const float h_factor_exp = units_h_factor(internal_units, props.units);
if (cleanup_h && h_factor_exp != 0.f && exist != 0) {
/* message("Multipltying '%s' by h^%f=%f", props.name, h_factor_exp,
* h_factor); */
if (io_is_double_precision(props.type)) {
double* temp_d = (double*)temp;
const double h_factor = pow(h, h_factor_exp);
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= h_factor;
} else {
float* temp_f = (float*)temp;
const float h_factor = pow(h, h_factor_exp);
for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= h_factor;
}
}
/* Clean-up a if necessary */
if (cleanup_sqrt_a && a != 1. && (strcmp(props.name, "Velocities") == 0)) {
if (io_is_double_precision(props.type)) {
double* temp_d = (double*)temp;
const double vel_factor = sqrt(a);
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= vel_factor;
} else {
float* temp_f = (float*)temp;
const float vel_factor = sqrt(a);
for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= vel_factor;
}
}
/* Copy temporary buffer to particle data */
char* temp_c = (char*)temp;
for (size_t i = 0; i < N; ++i)
memcpy(props.field + i * props.partSize, &temp_c[i * copySize], copySize);
/* Free and close everything */
free(temp);
H5Sclose(h_filespace);
H5Sclose(h_memspace);
H5Dclose(h_data);
}
void prepare_array_serial(
const struct engine* e, hid_t grp, const char* fileName, FILE* xmfFile,
const char* partTypeGroupName, const struct io_props props,
const unsigned long long N_total,
const enum lossy_compression_schemes lossy_compression,
const struct unit_system* internal_units,
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);
/* Decide what chunk size to use based on compression */
int log2_chunk_size = 20;
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 << log2_chunk_size;
chunk_shape[1] = props.dimension;
} else {
rank = 1;
shape[0] = N_total;
shape[1] = 0;
chunk_shape[0] = 1 << log2_chunk_size;
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, shape);
if (h_err < 0)
error("Error while changing data space shape for field '%s'.", props.name);
/* Dataset type */
hid_t h_type = H5Tcopy(io_hdf5_type(props.type));
/* Dataset properties */
hid_t h_prop = H5Pcreate(H5P_DATASET_CREATE);
/* Set chunk size if have some particles */
if (N_total > 0) {
h_err = H5Pset_chunk(h_prop, rank, chunk_shape);
if (h_err < 0)
error("Error while setting chunk size (%llu, %llu) for field '%s'.",
(unsigned long long)chunk_shape[0],
(unsigned long long)chunk_shape[1], props.name);
}
/* Are we imposing some form of lossy compression filter? */
char comp_buffer[32] = "None";
if (lossy_compression != compression_write_lossless)
set_hdf5_lossy_compression(&h_prop, &h_type, lossy_compression, props.name,
comp_buffer);
/* Impose GZIP and shuffle data compression */
if (e->snapshot_compression > 0 && N_total > 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);
}
/* Impose check-sum to verify data corruption */
if (N_total > 0) {
h_err = H5Pset_fletcher32(h_prop);
if (h_err < 0)
error("Error while setting checksum options for field '%s'.", props.name);
}
/* Create dataset */
const hid_t h_data = H5Dcreate(grp, props.name, h_type, h_space, H5P_DEFAULT,
h_prop, H5P_DEFAULT);
if (h_data < 0) error("Error while creating dataspace '%s'.", props.name);
/* Write XMF description for this data set */
if (xmfFile != NULL)
xmf_write_line(xmfFile, fileName, /*distributed=*/0, partTypeGroupName,
props.name, N_total, props.dimension, props.type);
/* 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);
io_write_attribute_s(h_data, "Lossy compression filter", comp_buffer);
io_write_attribute_b(h_data, "Value stored as physical", props.is_physical);
io_write_attribute_b(h_data, "Property can be converted to comoving",
props.is_convertible_to_comoving);
/* 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);
/* Close everything */
H5Tclose(h_type);
H5Pclose(h_prop);
H5Dclose(h_data);
H5Sclose(h_space);
}
/**
* @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 N_total The total number of particles on all ranks.
* @param offset The offset position where this rank starts writing.
* @param lossy_compression Lossy compression filter to apply.
* @param mpi_rank The MPI rank of this node
* @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_array_serial(const struct engine* e, hid_t grp, char* fileName,
FILE* xmfFile, const char* partTypeGroupName,
const struct io_props props, const size_t N,
const long long N_total, const int mpi_rank,
const long long offset,
const enum lossy_compression_schemes lossy_compression,
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); */
/* Prepare the arrays in the file */
if (mpi_rank == 0)
prepare_array_serial(e, grp, fileName, xmfFile, partTypeGroupName, props,
N_total, lossy_compression, internal_units,
snapshot_units);
/* 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);
/* Construct information for the hyper-slab */
int rank;
hsize_t shape[2];
hsize_t offsets[2];
if (props.dimension > 1) {
rank = 2;
shape[0] = N;
shape[1] = props.dimension;
offsets[0] = offset;
offsets[1] = 0;
} else {
rank = 1;
shape[0] = N;
shape[1] = 0;
offsets[0] = offset;
offsets[1] = 0;
}
/* Create data space in memory */
const hid_t h_memspace = H5Screate(H5S_SIMPLE);
if (h_memspace < 0)
error("Error while creating data space (memory) for field '%s'.",
props.name);
/* Change shape of memory data space */
hid_t h_err = H5Sset_extent_simple(h_memspace, rank, shape, NULL);
if (h_err < 0)
error("Error while changing data space (memory) shape for field '%s'.",
props.name);
/* Open pre-existing data set */
const hid_t h_data = H5Dopen(grp, props.name, H5P_DEFAULT);
if (h_data < 0) error("Error while opening dataset '%s'.", props.name);
/* Select data space in that data set */
const hid_t h_filespace = H5Dget_space(h_data);
H5Sselect_hyperslab(h_filespace, H5S_SELECT_SET, offsets, NULL, shape, NULL);
/* Write temporary buffer to HDF5 dataspace */
h_err = H5Dwrite(h_data, io_hdf5_type(props.type), h_memspace, h_filespace,
H5P_DEFAULT, temp);
if (h_err < 0) error("Error while writing data array '%s'.", props.name);
/* Free and close everything */
swift_free("writebuff", temp);
H5Dclose(h_data);
H5Sclose(h_memspace);
H5Sclose(h_filespace);
}
/**
* @brief Reads an HDF5 initial condition file (GADGET-3 type)
*
* @param fileName The file to read.
* @param internal_units The system units used internally
* @param dim (output) The dimension of the volume read from the file.
* @param parts (output) The array of #part (gas particles) read from the file.
* @param gparts (output) The array of #gpart read from the file.
* @param sinks (output) Array of #sink particles.
* @param sparts (output) Array of #spart particles.
* @param bparts (output) Array of #bpart particles.
* @param Ngas (output) The number of #part read from the file on that node.
* @param Ngparts (output) The number of #gpart read from the file on that node.
* @param Ngparts_background (output) The number of background #gpart (type 2)
* @param Nnuparts (output) The number of neutrino #gpart (type 6)
* read from the file on that node.
* @param Nsinks (output) The number of #sink read from the file on that node.
* @param Nstars (output) The number of #spart read from the file on that node.
* @param Nblackholes (output) The number of #bpart read from the file on that
* node.
* @param flag_entropy (output) 1 if the ICs contained Entropy in the
* InternalEnergy field
* @param with_hydro Are we reading gas particles ?
* @param with_gravity Are we reading/creating #gpart arrays ?
* @param with_sink Are we reading sink particles ?
* @param with_stars Are we reading star particles ?
* @param with_black_holes Are we reading black hole particles ?
* @param with_cosmology Are we running with cosmology ?
* @param cleanup_h Are we cleaning-up h-factors from the quantities we read?
* @param cleanup_sqrt_a Are we cleaning-up the sqrt(a) factors in the Gadget
* IC velocities?
* @param h The value of the reduced Hubble constant to use for correction.
* @param a The current value of the scale-factor.
* @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
* @param n_threads The number of threads to use for local operations.
* @param dry_run If 1, don't read the particle. Only allocates the arrays.
* @param remap_ids Are we ignoring the ICs' IDs and remapping them to [1, N[ ?
* @param ics_metadata Will store metadata group copied from the ICs file
*
* Opens the HDF5 file fileName and reads the particles contained
* in the parts array. N is the returned number of particles found
* in the file.
*
* @warning Can not read snapshot distributed over more than 1 file !!!
* @todo Read snapshots distributed in more than one file.
*
*/
void read_ic_serial(char* fileName, const struct unit_system* internal_units,
double dim[3], struct part** parts, struct gpart** gparts,
struct sink** sinks, struct spart** sparts,
struct bpart** bparts, size_t* Ngas, size_t* Ngparts,
size_t* Ngparts_background, size_t* Nnuparts,
size_t* Nsinks, size_t* Nstars, size_t* Nblackholes,
int* flag_entropy, const int with_hydro,
const int with_gravity, const int with_sink,
const int with_stars, const int with_black_holes,
const int with_cosmology, const int cleanup_h,
const int cleanup_sqrt_a, double h, double a,
const int mpi_rank, int mpi_size, MPI_Comm comm,
MPI_Info info, const int n_threads, const int dry_run,
const int remap_ids, struct ic_info* ics_metadata) {
hid_t h_file = 0, h_grp = 0;
/* GADGET has only cubic boxes (in cosmological mode) */
double boxSize[3] = {0.0, -1.0, -1.0};
long long numParticles[swift_type_count] = {0};
long long numParticles_highWord[swift_type_count] = {0};
size_t N[swift_type_count] = {0};
long long N_total[swift_type_count] = {0};
long long offset[swift_type_count] = {0};
int dimension = 3; /* Assume 3D if nothing is specified */
size_t Ndm = 0;
size_t Ndm_background = 0;
size_t Ndm_neutrino = 0;
struct unit_system* ic_units =
(struct unit_system*)malloc(sizeof(struct unit_system));
/* Initialise counters */
*Ngas = 0, *Ngparts = 0, *Ngparts_background = 0, *Nstars = 0,
*Nblackholes = 0, *Nsinks = 0, *Nnuparts = 0;
/* First read some information about the content */
if (mpi_rank == 0) {
/* Open file */
/* message("Opening file '%s' as IC.", fileName); */
h_file = H5Fopen(fileName, H5F_ACC_RDONLY, H5P_DEFAULT);
if (h_file < 0)
error("Error while opening file '%s' for initial read.", fileName);
/* Open header to read simulation properties */
/* message("Reading file header..."); */
h_grp = H5Gopen(h_file, "/Header", H5P_DEFAULT);
if (h_grp < 0) error("Error while opening file header\n");
/* Check the dimensionality of the ICs (if the info exists) */
const hid_t hid_dim = H5Aexists(h_grp, "Dimension");
if (hid_dim < 0)
error("Error while testing existance of 'Dimension' attribute");
if (hid_dim > 0) io_read_attribute(h_grp, "Dimension", INT, &dimension);
if (dimension != hydro_dimension)
error("ICs dimensionality (%dD) does not match code dimensionality (%dD)",
dimension, (int)hydro_dimension);
/* Check whether the number of files is specified (if the info exists) */
const hid_t hid_files = H5Aexists(h_grp, "NumFilesPerSnapshot");
int num_files = 1;
if (hid_files < 0)
error(
"Error while testing the existance of 'NumFilesPerSnapshot' "
"attribute");
if (hid_files > 0)
io_read_attribute(h_grp, "NumFilesPerSnapshot", INT, &num_files);
if (num_files != 1)
error(
"ICs are split over multiples files (%d). SWIFT cannot handle this "
"case. The script /tools/combine_ics.py is availalbe in the "
"repository "
"to combine files into a valid input file.",
num_files);
/* Read the relevant information and print status */
int flag_entropy_temp[swift_type_count];
io_read_attribute(h_grp, "Flag_Entropy_ICs", INT, flag_entropy_temp);
*flag_entropy = flag_entropy_temp[0];
io_read_attribute(h_grp, "BoxSize", DOUBLE, boxSize);
io_read_attribute(h_grp, "NumPart_Total", LONGLONG, numParticles);
io_read_attribute(h_grp, "NumPart_Total_HighWord", LONGLONG,
numParticles_highWord);
/* Check that the user is not doing something silly when they e.g. restart
* from a snapshot by asserting that the current scale-factor (from
* parameter file) and the redshift in the header are consistent */
if (with_cosmology) {
io_assert_valid_header_cosmology(h_grp, a);
}
for (int ptype = 0; ptype < swift_type_count; ++ptype)
N_total[ptype] =
(numParticles[ptype]) + (numParticles_highWord[ptype] << 32);
/* Get the box size if not cubic */
dim[0] = boxSize[0];
dim[1] = (boxSize[1] < 0) ? boxSize[0] : boxSize[1];
dim[2] = (boxSize[2] < 0) ? boxSize[0] : boxSize[2];
/* Change box size in the 1D and 2D case */
if (hydro_dimension == 2)
dim[2] = min(dim[0], dim[1]);
else if (hydro_dimension == 1)
dim[2] = dim[1] = dim[0];
/* Convert the box size if we want to clean-up h-factors */
if (cleanup_h) {
dim[0] /= h;
dim[1] /= h;
dim[2] /= h;
}
/* message("Found %lld particles in a %speriodic box of size [%f %f %f].",
N_total, (periodic ? "": "non-"), dim[0], dim[1], dim[2]); */
/* Close header */
H5Gclose(h_grp);
/* Read the unit system used in the ICs */
if (ic_units == NULL) error("Unable to allocate memory for IC unit system");
io_read_unit_system(h_file, ic_units, internal_units, mpi_rank);
if (units_are_equal(ic_units, internal_units)) {
message("IC and internal units match. No conversion needed.");
} else {
message("Conversion needed from:");
message("(ICs) Unit system: U_M = %e g.", ic_units->UnitMass_in_cgs);
message("(ICs) Unit system: U_L = %e cm.",
ic_units->UnitLength_in_cgs);
message("(ICs) Unit system: U_t = %e s.", ic_units->UnitTime_in_cgs);
message("(ICs) Unit system: U_I = %e A.",
ic_units->UnitCurrent_in_cgs);
message("(ICs) Unit system: U_T = %e K.",
ic_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);
}
/* Read metadata from ICs file */
ic_info_read_hdf5(ics_metadata, h_file);
/* Close file */
H5Fclose(h_file);
}
/* Convert the dimensions of the box */
for (int j = 0; j < 3; j++)
dim[j] *=
units_conversion_factor(ic_units, internal_units, UNIT_CONV_LENGTH);
/* Now need to broadcast that information to all ranks. */
MPI_Bcast(flag_entropy, 1, MPI_INT, 0, comm);
MPI_Bcast(N_total, swift_type_count, MPI_LONG_LONG_INT, 0, comm);
MPI_Bcast(dim, 3, MPI_DOUBLE, 0, comm);
MPI_Bcast(ic_units, sizeof(struct unit_system), MPI_BYTE, 0, comm);
ic_info_struct_broadcast(ics_metadata, 0);
/* Divide the particles among the tasks. */
for (int ptype = 0; ptype < swift_type_count; ++ptype) {
offset[ptype] = mpi_rank * N_total[ptype] / mpi_size;
N[ptype] = (mpi_rank + 1) * N_total[ptype] / mpi_size - offset[ptype];
}
/* Allocate memory to store SPH particles */
if (with_hydro) {
*Ngas = N[0];
if (swift_memalign("parts", (void**)parts, part_align,
*Ngas * sizeof(struct part)) != 0)
error("Error while allocating memory for SPH particles");
bzero(*parts, *Ngas * sizeof(struct part));
}
/* Allocate memory to store sinks particles */
if (with_sink) {
*Nsinks = N[swift_type_sink];
if (swift_memalign("sinks", (void**)sinks, sink_align,
*Nsinks * sizeof(struct sink)) != 0)
error("Error while allocating memory for sink particles");
bzero(*sinks, *Nsinks * sizeof(struct sink));
}
/* Allocate memory to store stars particles */
if (with_stars) {
*Nstars = N[swift_type_stars];
if (swift_memalign("sparts", (void**)sparts, spart_align,
*Nstars * sizeof(struct spart)) != 0)
error("Error while allocating memory for stars particles");
bzero(*sparts, *Nstars * sizeof(struct spart));
}
/* Allocate memory to store stars particles */
if (with_black_holes) {
*Nblackholes = N[swift_type_black_hole];
if (swift_memalign("bparts", (void**)bparts, bpart_align,
*Nblackholes * sizeof(struct bpart)) != 0)
error("Error while allocating memory for black hole particles");
bzero(*bparts, *Nblackholes * sizeof(struct bpart));
}
/* Allocate memory to store all gravity particles */
if (with_gravity) {
Ndm = N[swift_type_dark_matter];
Ndm_background = N[swift_type_dark_matter_background];
Ndm_neutrino = N[swift_type_neutrino];
*Ngparts = (with_hydro ? N[swift_type_gas] : 0) +
N[swift_type_dark_matter] +
N[swift_type_dark_matter_background] + N[swift_type_neutrino] +
(with_sink ? N[swift_type_sink] : 0) +
(with_stars ? N[swift_type_stars] : 0) +
(with_black_holes ? N[swift_type_black_hole] : 0);
*Ngparts_background = Ndm_background;
*Nnuparts = Ndm_neutrino;
if (swift_memalign("gparts", (void**)gparts, gpart_align,
*Ngparts * sizeof(struct gpart)) != 0)
error("Error while allocating memory for gravity particles");
bzero(*gparts, *Ngparts * sizeof(struct gpart));
}
/* message("Allocated %8.2f MB for particles.", *N * sizeof(struct part) / */
/* (1024.*1024.)); */
/* message("BoxSize = %lf", dim[0]); */
/* message("NumPart = [%zd, %zd] Total = %zd", *Ngas, Ndm, *Ngparts); */
/* For dry runs, only need to do this on rank 0 */
if (dry_run) mpi_size = 1;
/* Now loop over ranks and read the data */
for (int rank = 0; rank < mpi_size; ++rank) {
/* Is it this rank's turn to read ? */
if (rank == mpi_rank) {
/* Set the minimal API version to avoid issues with advanced features */
hid_t h_props = H5Pcreate(H5P_FILE_ACCESS);
herr_t err =
H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
HDF5_HIGHEST_FILE_FORMAT_VERSION);
if (err < 0) error("Error setting the hdf5 API version");
h_file = H5Fopen(fileName, H5F_ACC_RDONLY, h_props);
if (h_file < 0)
error("Error while opening file '%s' on rank %d.", fileName, mpi_rank);
/* 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[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 = 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[io_max_size_output_list];
bzero(list, io_max_size_output_list * sizeof(struct io_props));
size_t Nparticles = 0;
/* Read particle fields into the particle structure */
switch (ptype) {
case swift_type_gas:
if (with_hydro) {
Nparticles = *Ngas;
hydro_read_particles(*parts, list, &num_fields);
num_fields += mhd_read_particles(*parts, list + num_fields);
num_fields += chemistry_read_particles(*parts, list + num_fields);
num_fields += rt_read_particles(*parts, list + num_fields);
}
break;
case swift_type_dark_matter:
if (with_gravity) {
Nparticles = Ndm;
darkmatter_read_particles(*gparts, list, &num_fields);
}
break;
case swift_type_dark_matter_background:
if (with_gravity) {
Nparticles = Ndm_background;
darkmatter_read_particles(*gparts + Ndm, list, &num_fields);
}
break;
case swift_type_neutrino:
if (with_gravity) {
Nparticles = Ndm_neutrino;
darkmatter_read_particles(*gparts + Ndm + Ndm_background, list,
&num_fields);
}
break;
case swift_type_sink:
if (with_sink) {
Nparticles = *Nsinks;
sink_read_particles(*sinks, list, &num_fields);
}
break;
case swift_type_stars:
if (with_stars) {
Nparticles = *Nstars;
stars_read_particles(*sparts, list, &num_fields);
num_fields +=
star_formation_read_particles(*sparts, list + num_fields);
num_fields += rt_read_stars(*sparts, list + num_fields);
}
break;
case swift_type_black_hole:
if (with_black_holes) {
Nparticles = *Nblackholes;
black_holes_read_particles(*bparts, list, &num_fields);
}
break;
default:
if (mpi_rank == 0)
message("Particle Type %d not yet supported. Particles ignored",
ptype);
}
/* Read everything */
if (!dry_run)
for (int i = 0; i < num_fields; ++i) {
/* If we are remapping ParticleIDs later, don't need to read them.
*/
if (remap_ids && strcmp(list[i].name, "ParticleIDs") == 0) continue;
/* Read array. */
read_array_serial(h_grp, list[i], Nparticles, N_total[ptype],
offset[ptype], internal_units, ic_units,
cleanup_h, cleanup_sqrt_a, h, a);
}
/* Close particle group */
H5Gclose(h_grp);
}
/* Close file */
H5Fclose(h_file);
H5Pclose(h_props);
}
/* Wait for the read of the reading to complete */
MPI_Barrier(comm);
}
/* If we are remapping ParticleIDs later, start by setting them to 1. */
if (remap_ids) io_set_ids_to_one(*gparts, *Ngparts);
/* Duplicate the parts for gravity */
if (!dry_run && with_gravity) {
/* Let's initialise a bit of thread parallelism here */
struct threadpool tp;
threadpool_init(&tp, n_threads);
/* Prepare the DM particles */
io_prepare_dm_gparts(&tp, *gparts, Ndm);
/* Prepare the DM background particles */
io_prepare_dm_background_gparts(&tp, *gparts + Ndm, Ndm_background);
/* Prepare the DM neutrino particles */
io_prepare_dm_neutrino_gparts(&tp, *gparts + Ndm + Ndm_background,
Ndm_neutrino);
/* Duplicate the hydro particles into gparts */
if (with_hydro)
io_duplicate_hydro_gparts(&tp, *parts, *gparts, *Ngas,
Ndm + Ndm_background + Ndm_neutrino);
/* Duplicate the sink particles into gparts */
if (with_sink)
io_duplicate_sinks_gparts(&tp, *sinks, *gparts, *Nsinks,
Ndm + Ndm_background + Ndm_neutrino + *Ngas);
/* Duplicate the stars particles into gparts */
if (with_stars)
io_duplicate_stars_gparts(
&tp, *sparts, *gparts, *Nstars,
Ndm + Ndm_background + Ndm_neutrino + *Ngas + *Nsinks);
/* Duplicate the black holes particles into gparts */
if (with_black_holes)
io_duplicate_black_holes_gparts(
&tp, *bparts, *gparts, *Nblackholes,
Ndm + Ndm_background + Ndm_neutrino + *Ngas + *Nsinks + *Nstars);
threadpool_clean(&tp);
}
/* message("Done Reading particles..."); */
/* Clean up */
free(ic_units);
}
/**
* @brief Writes an HDF5 output file (GADGET-3 type) with its XMF descriptor
*
* @param e The engine containing all the system.
* @param internal_units The #unit_system used internally
* @param snapshot_units The #unit_system used in the snapshots
* @param fof Is this a snapshot related to a stand-alone FOF call?
* @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_serial(struct engine* e,
const struct unit_system* internal_units,
const struct unit_system* snapshot_units,
const int fof, const int mpi_rank, const int mpi_size,
MPI_Comm comm, MPI_Info info) {
hid_t h_file = 0, h_grp = 0, h_props = 0;
int numFiles = 1;
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;
const struct sink* sinks = e->s->sinks;
struct output_options* output_options = e->output_options;
struct output_list* output_list = e->output_list_snapshots;
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 = e->s->with_DM;
const int with_DM_background = e->s->with_DM_background;
const int with_neutrinos = e->s->with_neutrinos;
const int with_hydro = (e->policy & engine_policy_hydro) ? 1 : 0;
const int with_stars = (e->policy & engine_policy_stars) ? 1 : 0;
const int with_black_hole = (e->policy & engine_policy_black_holes) ? 1 : 0;
const int with_sink = (e->policy & engine_policy_sinks) ? 1 : 0;
#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
const int with_rt = e->policy & engine_policy_rt;
FILE* xmfFile = 0;
/* 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 Nsinks = e->s->nr_sinks;
const size_t Nstars = e->s->nr_sparts;
const size_t Nblackholes = e->s->nr_bparts;
// const size_t Nbaryons = Ngas + Nstars;
// const size_t Ndm = Ntot > 0 ? Ntot - Nbaryons : 0;
/* Determine if we are writing a reduced snapshot, and if so which
* output selection type to use. Can just create a copy of this on
* each rank. */
char current_selection_name[FIELD_BUFFER_SIZE] =
select_output_header_default_name;
if (output_list) {
/* Users could have specified a different Select Output scheme for each
* snapshot. */
output_list_get_current_select_output(output_list, current_selection_name);
}
/* File name */
char fileName[FILENAME_BUFFER_SIZE];
char xmfFileName[FILENAME_BUFFER_SIZE];
char snapshot_subdir_name[FILENAME_BUFFER_SIZE];
char snapshot_base_name[FILENAME_BUFFER_SIZE];
output_options_get_basename(output_options, current_selection_name,
e->snapshot_subdir, e->snapshot_base_name,
snapshot_subdir_name, snapshot_base_name);
io_get_snapshot_filename(
fileName, xmfFileName, output_list, e->snapshot_invoke_stf,
e->stf_output_count, e->snapshot_output_count, e->snapshot_subdir,
snapshot_subdir_name, e->snapshot_base_name, snapshot_base_name);
/* Create the directory */
if (mpi_rank == 0) safe_checkdir(snapshot_subdir_name, /*create=*/1);
/* Do we want to sub-sample any of the arrays */
int subsample[swift_type_count];
float subsample_fraction[swift_type_count];
for (int i = 0; i < swift_type_count; ++i) {
subsample[i] = 0;
subsample_fraction[i] = 1.f;
}
output_options_get_subsampling(
output_options, current_selection_name, e->snapshot_subsample,
e->snapshot_subsample_fraction, subsample, subsample_fraction);
/* Is any particle type being subsampled? */
int subsample_any = 0;
for (int i = 0; i < swift_type_count; ++i) {
subsample_any += subsample[i];
if (!subsample[i]) subsample_fraction[i] = 1.f;
}
/* Number of particles that we will write */
size_t Ngas_written, Ndm_written, Ndm_background, Ndm_neutrino,
Nsinks_written, Nstars_written, Nblackholes_written;
if (subsample[swift_type_gas]) {
Ngas_written = io_count_gas_to_write(e->s, /*subsample=*/1,
subsample_fraction[swift_type_gas],
e->snapshot_output_count);
} else {
Ngas_written =
e->s->nr_parts - e->s->nr_inhibited_parts - e->s->nr_extra_parts;
}
if (subsample[swift_type_stars]) {
Nstars_written = io_count_stars_to_write(
e->s, /*subsample=*/1, subsample_fraction[swift_type_stars],
e->snapshot_output_count);
} else {
Nstars_written =
e->s->nr_sparts - e->s->nr_inhibited_sparts - e->s->nr_extra_sparts;
}
if (subsample[swift_type_black_hole]) {
Nblackholes_written = io_count_black_holes_to_write(
e->s, /*subsample=*/1, subsample_fraction[swift_type_black_hole],
e->snapshot_output_count);
} else {
Nblackholes_written =
e->s->nr_bparts - e->s->nr_inhibited_bparts - e->s->nr_extra_bparts;
}
if (subsample[swift_type_sink]) {
Nsinks_written = io_count_sinks_to_write(
e->s, /*subsample=*/1, subsample_fraction[swift_type_sink],
e->snapshot_output_count);
} else {
Nsinks_written =
e->s->nr_sinks - e->s->nr_inhibited_sinks - e->s->nr_extra_sinks;
}
Ndm_written = io_count_dark_matter_to_write(
e->s, subsample[swift_type_dark_matter],
subsample_fraction[swift_type_dark_matter], e->snapshot_output_count);
if (with_DM_background) {
Ndm_background = io_count_background_dark_matter_to_write(
e->s, subsample[swift_type_dark_matter_background],
subsample_fraction[swift_type_dark_matter_background],
e->snapshot_output_count);
} else {
Ndm_background = 0;
}
if (with_neutrinos) {
Ndm_neutrino = io_count_neutrinos_to_write(
e->s, subsample[swift_type_neutrino],
subsample_fraction[swift_type_neutrino], e->snapshot_output_count);
} else {
Ndm_neutrino = 0;
}
/* Total number of fields to write per ptype */
int numFields[swift_type_count] = {0};
for (int ptype = 0; ptype < swift_type_count; ++ptype) {
numFields[ptype] = output_options_get_num_fields_to_write(
output_options, current_selection_name, ptype);
}
/* Compute offset in the file and total number of particles */
size_t N[swift_type_count] = {
Ngas_written, Ndm_written, Ndm_background, Nsinks_written,
Nstars_written, Nblackholes_written, Ndm_neutrino};
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, swift_type_count, MPI_LONG_LONG_INT, mpi_size - 1, comm);
/* List what fields to write.
* Note that we want to want to write a 0-size dataset for some species
* in case future snapshots will contain them (e.g. star formation) */
const int to_write[swift_type_count] = {
with_hydro, with_DM, with_DM_background, with_sink,
with_stars, with_black_hole, with_neutrinos
};
/* Now everybody knows its offset and the total number of particles of each
* type */
/* Do common stuff first */
if (mpi_rank == 0) {
/* First time, we need to create the XMF file */
if (e->snapshot_output_count == 0) xmf_create_file(xmfFileName);
/* Prepare the XMF file for the new entry */
xmfFile = xmf_prepare_file(xmfFileName);
/* Write the part corresponding to this specific output */
xmf_write_outputheader(xmfFile, fileName, e->time);
/* Set the minimal API version to avoid issues with advanced features */
h_props = H5Pcreate(H5P_FILE_ACCESS);
herr_t err = H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
HDF5_HIGHEST_FILE_FORMAT_VERSION);
if (err < 0) error("Error setting the hdf5 API version");
/* Open file */
/* message("Opening file '%s'.", fileName); */
h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, h_props);
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");
io_write_attribute_s(h_grp, "RunName", e->run_name);
io_write_attribute_s(h_grp, "System", hostname());
io_write_attribute(h_grp, "Shift", DOUBLE, e->s->initial_shift, 3);
/* Write out the particle types */
io_write_part_type_names(h_grp);
/* Write out the time-base */
if (with_cosmology) {
io_write_attribute_d(h_grp, "TimeBase_dloga", e->time_base);
const double delta_t =
cosmology_get_timebase(e->cosmology, e->ti_current);
io_write_attribute_d(h_grp, "TimeBase_dt", delta_t);
} else {
io_write_attribute_d(h_grp, "TimeBase_dloga", 0);
io_write_attribute_d(h_grp, "TimeBase_dt", e->time_base);
}
/* Store the time at which the snapshot was written */
time_t tm = time(NULL);
struct tm* timeinfo = localtime(&tm);
char snapshot_date[64];
strftime(snapshot_date, 64, "%T %F %Z", timeinfo);
io_write_attribute_s(h_grp, "SnapshotDate", snapshot_date);
/* GADGET-2 legacy values: Number of particles of each type */
long long numParticlesThisFile[swift_type_count] = {0};
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);
if (numFields[ptype] == 0) {
numParticlesThisFile[ptype] = 0;
} else {
numParticlesThisFile[ptype] = N_total[ptype];
}
}
io_write_attribute(h_grp, "NumPart_ThisFile", LONGLONG,
numParticlesThisFile, 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);
io_write_attribute(h_grp, "TotalNumberOfParticles", LONGLONG, N_total,
swift_type_count);
double MassTable[swift_type_count] = {0};
io_write_attribute(h_grp, "MassTable", DOUBLE, MassTable, swift_type_count);
io_write_attribute(h_grp, "InitialMassTable", DOUBLE,
e->s->initial_mean_mass_particles, 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(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);
io_write_attribute_i(h_grp, "ThisFile", 0);
io_write_attribute_s(h_grp, "SelectOutput", current_selection_name);
io_write_attribute_i(h_grp, "Virtual", 0);
io_write_attribute(h_grp, "CanHaveTypes", INT, to_write, swift_type_count);
if (subsample_any) {
io_write_attribute_s(h_grp, "OutputType", "SubSampled");
io_write_attribute(h_grp, "SubSampleFractions", FLOAT, subsample_fraction,
swift_type_count);
} else {
io_write_attribute_s(h_grp, "OutputType", "FullVolume");
}
/* Close header */
H5Gclose(h_grp);
/* Copy metadata from ICs to the file */
ic_info_write_hdf5(e->ics_metadata, h_file);
/* Write all the meta-data */
io_write_meta_data(h_file, e, internal_units, snapshot_units, fof);
/* Loop over all particle types */
for (int ptype = 0; ptype < swift_type_count; ptype++) {
/* Don't do anything if there are
* (a) no particles of this kind in this run, or
* (b) if we have disabled every field of this particle type. */
if (!to_write[ptype] || numFields[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");
/* Add an alias name for convenience */
char aliasName[PARTICLE_GROUP_BUFFER_SIZE];
snprintf(aliasName, PARTICLE_GROUP_BUFFER_SIZE, "/%sParticles",
part_type_names[ptype]);
hid_t h_err = H5Lcreate_soft(partTypeGroupName, h_grp, aliasName,
H5P_DEFAULT, H5P_DEFAULT);
if (h_err < 0) error("Error while creating alias for particle group.\n");
/* Write the number of particles as an attribute */
io_write_attribute_ll(h_grp, "NumberOfParticles", N_total[ptype]);
io_write_attribute_ll(h_grp, "TotalNumberOfParticles", N_total[ptype]);
/* Close particle group */
H5Gclose(h_grp);
}
/* Close file */
H5Fclose(h_file);
H5Pclose(h_props);
}
/* Now write the top-level cell structure */
hid_t h_file_cells = 0, h_grp_cells = 0, h_props_cells = 0;
if (mpi_rank == 0) {
/* Set the minimal API version to avoid issues with advanced features */
h_props_cells = H5Pcreate(H5P_FILE_ACCESS);
herr_t err =
H5Pset_libver_bounds(h_props_cells, HDF5_LOWEST_FILE_FORMAT_VERSION,
HDF5_HIGHEST_FILE_FORMAT_VERSION);
if (err < 0) error("Error setting the hdf5 API version");
/* Open the snapshot on rank 0 */
h_file_cells = H5Fopen(fileName, H5F_ACC_RDWR, h_props_cells);
if (h_file_cells < 0)
error("Error while opening file '%s' on rank %d.", fileName, mpi_rank);
/* Create the group we want in the file */
h_grp_cells = H5Gcreate(h_file_cells, "/Cells", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
if (h_grp_cells < 0) error("Error while creating cells group");
}
/* Write the location of the particles in the arrays */
io_write_cell_offsets(h_grp_cells, e->s->cdim, e->s->dim, e->s->cells_top,
e->s->nr_cells, e->s->width, mpi_rank,
/*distributed=*/0, subsample, subsample_fraction,
e->snapshot_output_count, N_total, offset, to_write,
numFields, internal_units, snapshot_units);
/* Close everything */
if (mpi_rank == 0) {
H5Gclose(h_grp_cells);
H5Fclose(h_file_cells);
H5Pclose(h_props_cells);
}
/* Now loop over ranks and write the data */
for (int rank = 0; rank < mpi_size; ++rank) {
/* Is it this rank's turn to write ? */
if (rank == mpi_rank) {
/* Set the minimal API version to avoid issues with advanced features */
h_props = H5Pcreate(H5P_FILE_ACCESS);
herr_t err =
H5Pset_libver_bounds(h_props, HDF5_LOWEST_FILE_FORMAT_VERSION,
HDF5_HIGHEST_FILE_FORMAT_VERSION);
if (err < 0) error("Error setting the hdf5 API version");
h_file = H5Fopen(fileName, H5F_ACC_RDWR, h_props);
if (h_file < 0)
error("Error while opening file '%s' on rank %d.", fileName, mpi_rank);
/* Loop over all particle types */
for (int ptype = 0; ptype < swift_type_count; ptype++) {
/* Don't do anything if there are
* (a) no particles of this kind in this run, or
* (b) if we have disabled every field of this particle type. */
if (!to_write[ptype] || numFields[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, /*distributed=*/0,
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 = 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[io_max_size_output_list];
bzero(list, io_max_size_output_list * sizeof(struct io_props));
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;
struct sink* sinks_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;
/* Select the fields to write */
io_select_hydro_fields(parts, xparts, with_cosmology,
with_cooling, with_temperature, with_fof,
with_stf, with_rt, e, &num_fields, list);
} 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,
subsample[swift_type_gas], subsample_fraction[swift_type_gas],
e->snapshot_output_count, Ngas, Ngas_written);
/* Select the fields to write */
io_select_hydro_fields(parts_written, xparts_written,
with_cosmology, with_cooling,
with_temperature, with_fof, with_stf,
with_rt, e, &num_fields, list);
}
} break;
case swift_type_dark_matter: {
if (Ntot == Ndm_written) {
/* This is a DM-only run without background or inhibited particles
* or neutrinos */
Nparticles = Ntot;
/* Select the fields to write */
io_select_dm_fields(gparts, e->s->gpart_group_data, with_fof,
with_stf, e, &num_fields, list);
} 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, subsample[swift_type_dark_matter],
subsample_fraction[swift_type_dark_matter],
e->snapshot_output_count, Ntot, Ndm_written, with_stf);
/* Select the fields to write */
io_select_dm_fields(gparts_written, gpart_group_data_written,
with_fof, with_stf, e, &num_fields, list);
}
} 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,
subsample[swift_type_dark_matter_background],
subsample_fraction[swift_type_dark_matter_background],
e->snapshot_output_count, Ntot, Ndm_background, with_stf);
/* Select the fields to write */
io_select_dm_fields(gparts_written, gpart_group_data_written,
with_fof, with_stf, e, &num_fields, list);
} break;
case swift_type_neutrino: {
/* Ok, we need to fish out the particles we want */
Nparticles = Ndm_neutrino;
/* Allocate temporary array */
if (swift_memalign("gparts_written", (void**)&gparts_written,
gpart_align,
Ndm_neutrino * 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_neutrino * 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_neutrino_to_write(
gparts, e->s->gpart_group_data, gparts_written,
gpart_group_data_written, subsample[swift_type_neutrino],
subsample_fraction[swift_type_neutrino],
e->snapshot_output_count, Ntot, Ndm_neutrino, with_stf);
/* Select the fields to write */
io_select_neutrino_fields(gparts_written, gpart_group_data_written,
with_fof, with_stf, e, &num_fields, list);
} break;
case swift_type_sink: {
if (Nsinks == Nsinks_written) {
/* No inhibted particles: easy case */
Nparticles = Nsinks;
/* Select the fields to write */
io_select_sink_fields(sinks, with_cosmology, with_fof, with_stf,
e, &num_fields, list);
} else {
/* Ok, we need to fish out the particles we want */
Nparticles = Nsinks_written;
/* Allocate temporary arrays */
if (swift_memalign("sinks_written", (void**)&sinks_written,
sink_align,
Nsinks_written * sizeof(struct sink)) != 0)
error("Error while allocating temporary memory for sinks");
/* Collect the particles we want to write */
io_collect_sinks_to_write(
sinks, sinks_written, subsample[swift_type_sink],
subsample_fraction[swift_type_sink], e->snapshot_output_count,
Nsinks, Nsinks_written);
/* Select the fields to write */
io_select_sink_fields(sinks_written, with_cosmology, with_fof,
with_stf, e, &num_fields, list);
}
} break;
case swift_type_stars: {
if (Nstars == Nstars_written) {
/* No inhibted particles: easy case */
Nparticles = Nstars;
/* Select the fields to write */
io_select_star_fields(sparts, with_cosmology, with_fof, with_stf,
with_rt, e, &num_fields, list);
} 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, subsample[swift_type_stars],
subsample_fraction[swift_type_stars],
e->snapshot_output_count, Nstars, Nstars_written);
/* Select the fields to write */
io_select_star_fields(sparts_written, with_cosmology, with_fof,
with_stf, with_rt, e, &num_fields, list);
}
} break;
case swift_type_black_hole: {
if (Nblackholes == Nblackholes_written) {
/* No inhibted particles: easy case */
Nparticles = Nblackholes;
/* Select the fields to write */
io_select_bh_fields(bparts, with_cosmology, with_fof, with_stf, e,
&num_fields, list);
} 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, subsample[swift_type_black_hole],
subsample_fraction[swift_type_black_hole],
e->snapshot_output_count, Nblackholes, Nblackholes_written);
/* Select the fields to write */
io_select_bh_fields(bparts_written, with_cosmology, with_fof,
with_stf, e, &num_fields, list);
}
} break;
default:
error("Particle Type %d not yet supported. Aborting", ptype);
}
/* Verify we are not going to crash when writing below */
if (num_fields >= io_max_size_output_list)
error("Too many fields to write for particle type %d", ptype);
for (int i = 0; i < num_fields; ++i) {
if (!list[i].is_used) error("List of field contains an empty entry!");
if (!list[i].dimension)
error("Dimension of field '%s' is <= 1!", list[i].name);
}
/* Did the user specify a non-standard default for the entire particle
* type? */
const enum lossy_compression_schemes compression_level_current_default =
output_options_get_ptype_default_compression(
output_options->select_output, current_selection_name,
(enum part_type)ptype, e->verbose);
/* Write everything that is not cancelled */
int num_fields_written = 0;
for (int i = 0; i < num_fields; ++i) {
/* Did the user cancel this field? */
const enum lossy_compression_schemes compression_level =
output_options_get_field_compression(
output_options, current_selection_name, list[i].name,
(enum part_type)ptype, compression_level_current_default,
e->verbose);
if (compression_level != compression_do_not_write) {
write_array_serial(e, h_grp, fileName, xmfFile, partTypeGroupName,
list[i], Nparticles, N_total[ptype], mpi_rank,
offset[ptype], compression_level, internal_units,
snapshot_units);
num_fields_written++;
}
}
if (mpi_rank == 0) {
/* Only write this now that we know exactly how many fields there are.
*/
io_write_attribute_i(h_grp, "NumberOfFields", num_fields_written);
}
/* Free temporary array */
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", sparts_written);
if (sinks_written) swift_free("sinks_written", sinks_written);
/* Close particle group */
H5Gclose(h_grp);
/* Close this particle group in the XMF file as well */
if (mpi_rank == 0)
xmf_write_groupfooter(xmfFile, (enum part_type)ptype);
}
/* Close file */
H5Fclose(h_file);
H5Pclose(h_props);
}
/* Wait for the read of the reading to complete */
MPI_Barrier(comm);
}
/* Write footer of LXMF file descriptor */
if (mpi_rank == 0)
xmf_write_outputfooter(xmfFile, e->snapshot_output_count, e->time);
/* message("Done writing particles..."); */
e->snapshot_output_count++;
if (e->snapshot_invoke_stf) e->stf_output_count++;
}
#endif /* HAVE_HDF5 && HAVE_MPI */