-
Matthieu Schaller authored
Properties of the self-gravity scheme are now read from the YAML file. They are printed to stdout and to snapshots.
Matthieu Schaller authoredProperties of the self-gravity scheme are now read from the YAML file. They are printed to stdout and to snapshots.
serial_io.c 36.03 KiB
/*******************************************************************************
* This file is part of SWIFT.
* Copyright (c) 2012 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
* Matthieu Schaller (matthieu.schaller@durham.ac.uk).
*
* 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) && !defined(HAVE_PARALLEL_HDF5)
/* Some standard headers. */
#include <hdf5.h>
#include <math.h>
#include <mpi.h>
#include <stddef.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
/* This object's header. */
#include "serial_io.h"
/* Local includes. */
#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 "kernel_hydro.h"
#include "part.h"
#include "stars_io.h"
#include "units.h"
#include "xmf.h"
/*-----------------------------------------------------------------------------
* Routines reading an IC file
*-----------------------------------------------------------------------------*/
/**
* @brief Reads a data array from a given HDF5 group.
*
* @param grp The group from which to read.
* @param name The name of the array to read.
* @param type The #DATA_TYPE of the attribute.
* @param N The number of particles.
* @param dim The dimension of the data (1 for scalar, 3 for vector)
* @param part_c A (char*) pointer on the first occurrence of the field of
*interest in the parts array
* @param partSize The size in bytes of the particle structure.
* @param importance If COMPULSORY, the data must be present in the IC file. If
*OPTIONAL, the array will be zeroed when the data is not present. *
* @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 readArray(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) {
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 {
for (size_t i = 0; i < N; ++i)
memset(props.field + i * props.partSize, 0, copySize);
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);
/* Check data type */
const hid_t h_type = H5Dget_type(h_data);
if (h_type < 0) error("Unable to retrieve data type from the file");
/* if (!H5Tequal(h_type, hdf5_type(type))) */
/* error("Non-matching types between the code and the file"); */
/* 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 = temp;
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else {
float* temp_f = temp;
for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor;
}
}
/* Copy temporary buffer to particle data */
char* temp_c = 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);
H5Tclose(h_type);
H5Dclose(h_data);
}
/*-----------------------------------------------------------------------------
* Routines writing an output file
*-----------------------------------------------------------------------------*/
void prepareArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
char* partTypeGroupName, const struct io_props props,
unsigned long long N_total,
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);
}
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);
}
/* 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 data compression */
if (e->snapshotCompression > 0) {
h_err = H5Pset_deflate(h_prop, e->snapshotCompression);
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 XMF description for this data set */
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);
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 name The name of the array to write.
* @param type The #DATA_TYPE of the array.
* @param N The number of particles to write. * @param dim The dimension of the data (1 for scalar, 3 for vector)
* @param part_c A (char*) pointer on the first occurrence of the field of
*interest in the parts array
* @param partSize The size in bytes of the particle structure.
* @param us The unit_system currently in use
* @param convFactor The UnitConversionFactor for this arrayo
*/
void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
char* partTypeGroupName, const struct io_props props, size_t N,
long long N_total, int mpi_rank, long long offset,
const struct unit_system* internal_units,
const struct unit_system* snapshot_units) {
const size_t typeSize = io_sizeof_type(props.type);
const size_t copySize = typeSize * props.dimension;
const size_t num_elements = N * props.dimension;
/* message("Writing '%s' array...", props.name); */
/* Prepare the arrays in the file */
if (mpi_rank == 0)
prepareArray(e, grp, fileName, xmfFile, partTypeGroupName, props, N_total,
internal_units, snapshot_units);
/* Allocate temporary buffer */
void* temp = malloc(num_elements * io_sizeof_type(props.type));
if (temp == NULL) error("Unable to allocate memory for temporary buffer");
/* Copy particle data to temporary buffer */
if (props.convert_part == NULL &&
props.convert_gpart == NULL) { /* No conversion */
char* temp_c = temp;
for (size_t i = 0; i < N; ++i)
memcpy(&temp_c[i * copySize], props.field + i * props.partSize, copySize);
} else if (props.convert_part != NULL) { /* conversion (for parts)*/
float* temp_f = temp;
for (size_t i = 0; i < N; ++i)
temp_f[i] = props.convert_part(e, &props.parts[i]);
} else if (props.convert_gpart != NULL) { /* conversion (for gparts)*/
float* temp_f = temp;
for (size_t i = 0; i < N; ++i)
temp_f[i] = props.convert_gpart(e, &props.gparts[i]);
}
/* Unit conversion if necessary */
const double factor =
units_conversion_factor(internal_units, snapshot_units, props.units);
if (factor != 1.) {
/* message("Converting ! factor=%e", factor); */
if (io_is_double_precision(props.type)) {
double* temp_d = temp;
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else {
float* temp_f = temp;
for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor;
}
}
/* 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 */
free(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 sparts (output) Array of #spart 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 Nstars (output) The number of #spart read from the file on that node.
* @param periodic (output) 1 if the volume is periodic, 0 if not.
* @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_stars Are we reading star particles ?
* @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 dry_run If 1, don't read the particle. Only allocates the arrays.
*
* 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 spart** sparts, size_t* Ngas, size_t* Ngparts,
size_t* Nstars, int* periodic, int* flag_entropy,
int with_hydro, int with_gravity, int with_stars,
int mpi_rank, int mpi_size, MPI_Comm comm, MPI_Info info,
int dry_run) {
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};
/* GADGET has 6 particle types. We only keep the type 0 & 1 for now*/
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;
struct unit_system* ic_units = malloc(sizeof(struct unit_system));
/* 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 runtime parameters..."); */
h_grp = H5Gopen(h_file, "/RuntimePars", H5P_DEFAULT);
if (h_grp < 0) error("Error while opening runtime parameters\n");
/* Read the relevant information */
io_read_attribute(h_grp, "PeriodicBoundariesOn", INT, periodic);
/* Close runtime parameters */
H5Gclose(h_grp);
/* 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);
/* Read the relevant information and print status */
int flag_entropy_temp[6];
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);
for (int ptype = 0; ptype < swift_type_count; ++ptype)
N_total[ptype] =
(numParticles[ptype]) + (numParticles_highWord[ptype] << 32);
dim[0] = boxSize[0];
dim[1] = (boxSize[1] < 0) ? boxSize[0] : boxSize[1];
dim[2] = (boxSize[2] < 0) ? boxSize[0] : boxSize[2];
/* message("Found %lld particles in a %speriodic box of size [%f %f %f].",
*/
/* N_total, (periodic ? "": "non-"), dim[0], dim[1], dim[2]); */
fflush(stdout);
/* 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);
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);
}
/* 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(periodic, 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);
/* 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 (posix_memalign((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 star particles */
if (with_stars) {
*Nstars = N[swift_type_star];
if (posix_memalign((void*)sparts, spart_align,
*Nstars * sizeof(struct spart)) != 0)
error("Error while allocating memory for star particles");
bzero(*sparts, *Nstars * sizeof(struct spart));
}
/* Allocate memory to store all gravity particles */
if (with_gravity) {
Ndm = N[1];
*Ngparts = (with_hydro ? N[swift_type_gas] : 0) +
N[swift_type_dark_matter] +
(with_stars ? N[swift_type_star] : 0);
if (posix_memalign((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) {
h_file = H5Fopen(fileName, H5F_ACC_RDONLY, H5P_DEFAULT);
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[100];
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);
}
break;
case swift_type_dark_matter:
if (with_gravity) {
Nparticles = Ndm;
darkmatter_read_particles(*gparts, list, &num_fields);
}
break;
case swift_type_star:
if (with_stars) {
Nparticles = *Nstars;
star_read_particles(*sparts, list, &num_fields);
}
break;
default:
message("Particle Type %d not yet supported. Particles ignored",
ptype);
}
/* Read everything */
if (!dry_run)
for (int i = 0; i < num_fields; ++i)
readArray(h_grp, list[i], Nparticles, N_total[ptype], offset[ptype],
internal_units, ic_units);
/* Close particle group */
H5Gclose(h_grp);
}
/* Close file */
H5Fclose(h_file);
}
/* Wait for the read of the reading to complete */
MPI_Barrier(comm);
}
/* Prepare the DM particles */
if (!dry_run && with_gravity) io_prepare_dm_gparts(*gparts, Ndm);
/* Duplicate the hydro particles into gparts */
if (!dry_run && with_gravity && with_hydro)
io_duplicate_hydro_gparts(*parts, *gparts, *Ngas, Ndm);
/* Duplicate the star particles into gparts */
if (!dry_run && with_gravity && with_stars)
io_duplicate_star_gparts(*sparts, *gparts, *Nstars, Ndm + *Ngas);
/* 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 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_serial(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) {
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;
static int outputCount = 0;
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_%03i.hdf5", baseName,
outputCount);
/* 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 */
/* Do common stuff first */
if (mpi_rank == 0) {
/* First time, we need to create the XMF file */
if (outputCount == 0) xmf_create_file(baseName);
/* Prepare the XMF file for the new entry */
xmfFile = xmf_prepare_file(baseName);
/* Write the part corresponding to this specific output */
xmf_write_outputheader(xmfFile, fileName, e->time);
/* 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 runtime parameters..."); */
h_grp = H5Gcreate(h_file, "/RuntimePars", H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
if (h_grp < 0) error("Error while creating runtime parameters group\n");
/* Write the relevant information */
io_write_attribute(h_grp, "PeriodicBoundariesOn", INT, &periodic, 1);
/* Close runtime parameters */
H5Gclose(h_grp);
/* 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");
/* Print the relevant information and print status */
io_write_attribute(h_grp, "BoxSize", DOUBLE, e->s->dim, 3);
double dblTime = e->time;
io_write_attribute(h_grp, "Time", DOUBLE, &dblTime, 1);
int dimension = (int)hydro_dimension;
io_write_attribute(h_grp, "Dimension", INT, &dimension, 1);
/* 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_total,
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[6] = {0., 0., 0., 0., 0., 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(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);
/* Close header */
H5Gclose(h_grp);
/* Print the code version */
io_write_code_description(h_file);
/* 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);
writeSPHflavour(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 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);
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");
/* 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 (N_total[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");
}
/* Close particle group */
H5Gclose(h_grp);
}
/* Close file */ H5Fclose(h_file);
}
/* 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) {
h_file = H5Fopen(fileName, H5F_ACC_RDWR, H5P_DEFAULT);
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_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 = 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];
size_t Nparticles = 0;
/* Write particle fields from the particle structure */
switch (ptype) {
case swift_type_gas:
Nparticles = Ngas;
hydro_write_particles(parts, list, &num_fields);
break;
case swift_type_dark_matter:
/* Allocate temporary array */
if (posix_memalign((void*)&dmparts, gpart_align,
Ndm * sizeof(struct gpart)) != 0)
error("Error while allocating temporart memory for DM particles");
bzero(dmparts, Ndm * sizeof(struct gpart));
/* Collect the DM particles from gpart */
io_collect_dm_gparts(gparts, Ntot, dmparts, Ndm);
/* Write DM particles */
Nparticles = Ndm;
darkmatter_write_particles(dmparts, list, &num_fields);
break;
case swift_type_star:
Nparticles = Nstars;
star_write_particles(sparts, list, &num_fields);
break;
default:
error("Particle Type %d not yet supported. Aborting", ptype);
}
/* 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);
/* Free temporary array */
if (dmparts) {
free(dmparts);
dmparts = 0;
}
/* 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);
}
/* 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, outputCount, e->time);
/* message("Done writing particles..."); */
++outputCount;
}
#endif /* HAVE_HDF5 && HAVE_MPI */