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Matthieu Schaller authoredMatthieu Schaller authored
parallel_io.c 20.40 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 "parallel_io.h"
/* Local includes. */
#include "common_io.h"
#include "error.h"
/**
* @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 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.
*
* Calls #error() if an error occurs.
*/
void readArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N,
int dim, long long N_total, long long offset,
char* part_c, enum DATA_IMPORTANCE importance) {
hid_t h_data = 0, h_err = 0, h_type = 0, h_memspace = 0, h_filespace = 0,
h_plist_id = 0;
hsize_t shape[2], offsets[2];
htri_t exist = 0;
void* temp;
int i = 0, rank = 0;
const size_t typeSize = sizeOfType(type); const size_t copySize = typeSize * dim;
const size_t partSize = sizeof(struct part);
char* temp_c = 0;
/* Check whether the dataspace exists or not */
exist = H5Lexists(grp, name, 0);
if (exist < 0) {
error("Error while checking the existence of data set '%s'.", name);
} else if (exist == 0) {
if (importance == COMPULSORY) {
error("Compulsory data set '%s' not present in the file.", name);
} else {
for (i = 0; i < N; ++i) memset(part_c + i * partSize, 0, copySize);
return;
}
}
/* message( "Reading %s '%s' array...", importance == COMPULSORY ?
* "compulsory": "optional ", name); */
/* Open data space in file */
h_data = H5Dopen2(grp, name, H5P_DEFAULT);
if (h_data < 0) error("Error while opening data space '%s'.", name);
/* Check data type */
h_type = H5Dget_type(h_data);
if (h_type < 0) error("Unable to retrieve data type from the file");
/* if (!H5Tequal(h_type, hdf5Type(type))) */
/* error("Non-matching types between the code and the file"); */
/* Allocate temporary buffer */
temp = malloc(N * dim * typeSize);
if (temp == NULL) error("Unable to allocate memory for temporary buffer");
/* Prepare information for hyper-slab */
if (dim > 1) {
rank = 2;
shape[0] = N;
shape[1] = dim;
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 */
h_memspace = H5Screate_simple(rank, shape, NULL);
/* Select hyper-slab in file */
h_filespace = H5Dget_space(h_data);
H5Sselect_hyperslab(h_filespace, H5S_SELECT_SET, offsets, NULL, shape, NULL);
/* Set collective reading properties */
h_plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(h_plist_id, H5FD_MPIO_COLLECTIVE);
/* Read HDF5 dataspace in temporary buffer */
/* Dirty version that happens to work for vectors but should be improved */
/* Using HDF5 dataspaces would be better */
h_err = H5Dread(h_data, hdf5Type(type), h_memspace, h_filespace, h_plist_id,
temp);
if (h_err < 0) {
error("Error while reading data array '%s'.", name);
}
/* Copy temporary buffer to particle data */ temp_c = temp;
for (i = 0; i < N; ++i)
memcpy(part_c + i * partSize, &temp_c[i * copySize], copySize);
/* Free and close everything */
free(temp);
H5Pclose(h_plist_id);
H5Sclose(h_filespace);
H5Sclose(h_memspace);
H5Tclose(h_type);
H5Dclose(h_data);
}
/*-----------------------------------------------------------------------------
* Routines writing an output file
*-----------------------------------------------------------------------------*/
/**
* @brief Writes a data array in given HDF5 group.
*
* @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 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 N_total Total number of particles across all cores
* @param offset Offset in the array where this mpi task starts writing
* @param part_c A (char*) pointer on the first occurrence of the field of
*interest in the parts array
* @param us The UnitSystem currently in use
* @param convFactor The UnitConversionFactor for this array
*
* @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.
*
* Calls #error() if an error occurs.
*/
void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name,
enum DATA_TYPE type, int N, int dim, long long N_total,
int mpi_rank, long long offset, char* part_c,
struct UnitSystem* us,
enum UnitConversionFactor convFactor) {
hid_t h_data = 0, h_err = 0, h_memspace = 0, h_filespace = 0, h_plist_id = 0;
hsize_t shape[2], shape_total[2], offsets[2];
void* temp = 0;
int i = 0, rank = 0;
const size_t typeSize = sizeOfType(type);
const size_t copySize = typeSize * dim;
const size_t partSize = sizeof(struct part);
char* temp_c = 0;
char buffer[150];
/* message("Writing '%s' array...", name); */
/* Allocate temporary buffer */
temp = malloc(N * dim * sizeOfType(type));
if (temp == NULL) error("Unable to allocate memory for temporary buffer");
/* Copy particle data to temporary buffer */
temp_c = temp;
for (i = 0; i < N; ++i)
memcpy(&temp_c[i * copySize], part_c + i * partSize, copySize);
/* Create data space */
h_memspace = H5Screate(H5S_SIMPLE);
if (h_memspace < 0) {
error("Error while creating data space (memory) for field '%s'.", name); }
h_filespace = H5Screate(H5S_SIMPLE);
if (h_filespace < 0) {
error("Error while creating data space (file) for field '%s'.", name);
}
if (dim > 1) {
rank = 2;
shape[0] = N;
shape[1] = dim;
shape_total[0] = N_total;
shape_total[1] = dim;
offsets[0] = offset;
offsets[1] = 0;
} else {
rank = 1;
shape[0] = N;
shape[1] = 0;
shape_total[0] = N_total;
shape_total[1] = 0;
offsets[0] = offset;
offsets[1] = 0;
}
/* Change shape of memory data space */
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'.",
name);
}
/* Change shape of file data space */
h_err = H5Sset_extent_simple(h_filespace, rank, shape_total, NULL);
if (h_err < 0) {
error("Error while changing data space (file) shape for field '%s'.", name);
}
/* Create dataset */
h_data = H5Dcreate(grp, name, hdf5Type(type), h_filespace, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);
if (h_data < 0) {
error("Error while creating dataset '%s'.", name);
}
H5Sclose(h_filespace);
h_filespace = H5Dget_space(h_data);
H5Sselect_hyperslab(h_filespace, H5S_SELECT_SET, offsets, NULL, shape, NULL);
/* Create property list for collective dataset write. */
h_plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(h_plist_id, H5FD_MPIO_COLLECTIVE);
/* Write temporary buffer to HDF5 dataspace */
h_err = H5Dwrite(h_data, hdf5Type(type), h_memspace, h_filespace, h_plist_id,
temp);
if (h_err < 0) {
error("Error while writing data array '%s'.", name);
}
/* Write XMF description for this data set */
if (mpi_rank == 0) writeXMFline(xmfFile, fileName, name, N_total, dim, type);
/* Write unit conversion factors for this data set */
conversionString(buffer, us, convFactor);
writeAttribute_d(h_data, "CGS conversion factor",
conversionFactor(us, convFactor));
writeAttribute_f(h_data, "h-scale exponent", hFactor(us, convFactor));
writeAttribute_f(h_data, "a-scale exponent", aFactor(us, convFactor));
writeAttribute_s(h_data, "Conversion factor", buffer);
/* Free and close everything */
free(temp);
H5Dclose(h_data);
H5Pclose(h_plist_id);
H5Sclose(h_memspace);
H5Sclose(h_filespace);
}
/**
* @brief A helper macro to call the readArrayBackEnd function more easily.
*
* @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 on this MPI task.
* @param dim The dimension of the data (1 for scalar, 3 for vector)
* @param part The array of particles to fill
* @param N_total Total number of particles
* @param offset Offset in the array where this task starts reading
* @param field The name of the field (C code name as defined in part.h) to fill
* @param importance Is the data compulsory or not
*
*/
#define readArray(grp, name, type, N, dim, part, N_total, offset, field, \
importance) \
readArrayBackEnd(grp, name, type, N, dim, N_total, offset, \
(char*)(&(part[0]).field), importance)
/**
* @brief A helper macro to call the writeArrayBackEnd function more easily.
*
* @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 name The name of the array to write.
* @param type The #DATA_TYPE of the array.
* @param N The number of particles to write from this core.
* @param dim The dimension of the data (1 for scalar, 3 for vector)
* @param N_total Total number of particles across all cores
* @param mpi_rank The MPI task rank calling the function
* @param offset Offset in the array where this mpi task starts writing
* @param part A (char*) pointer on the first occurrence of the field of
*interest
*in the parts array
* @param field The name (code name) of the field to read from.
* @param us The UnitSystem currently in use
* @param convFactor The UnitConversionFactor for this array
*
*/
#define writeArray(grp, fileName, xmfFile, name, type, N, dim, part, N_total, \
mpi_rank, offset, field, us, convFactor) \
writeArrayBackEnd(grp, fileName, xmfFile, name, type, N, dim, N_total, \
mpi_rank, offset, (char*)(&(part[0]).field), us, \
convFactor)
/* Import the right hydro definition */
#include "hydro_io.h"
/**
* @brief Reads an HDF5 initial condition file (GADGET-3 type) in parallel
*
* @param fileName The file to read.
* @param dim (output) The dimension of the volume read from the file.
* @param parts (output) The array of #part read from the file.
* @param N (output) The number of particles read from the file.
* @param periodic (output) 1 if the volume is periodic, 0 if not.
*
* 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.
*
* Calls #error() if an error occurs.
*
*/
void read_ic_parallel(char* fileName, double dim[3], struct part** parts,
int* N, int* periodic, int mpi_rank, int mpi_size,
MPI_Comm comm, MPI_Info info) {
hid_t h_file = 0, h_grp = 0;
double boxSize[3] = {
0.0, -1.0, -1.0}; /* GADGET has only cubic boxes (in cosmological mode) */
int numParticles[6] = {
0}; /* GADGET has 6 particle types. We only keep the type 0*/
int numParticles_highWord[6] = {0};
long long offset = 0;
long long N_total = 0;
/* Open file */
/* message("Opening file '%s' as IC.", fileName); */
hid_t h_plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(h_plist_id, comm, info);
h_file = H5Fopen(fileName, H5F_ACC_RDONLY, h_plist_id);
if (h_file < 0) {
error("Error while opening file '%s'.", 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 */
readAttribute(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");
/* Read the relevant information and print status */
readAttribute(h_grp, "BoxSize", DOUBLE, boxSize);
readAttribute(h_grp, "NumPart_Total", UINT, numParticles);
readAttribute(h_grp, "NumPart_Total_HighWord", UINT, numParticles_highWord);
N_total = ((long long)numParticles[0]) +
((long long)numParticles_highWord[0] << 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 %d particles in a %speriodic box of size [%f %f %f].", */
/* N_total, (periodic ? "": "non-"), dim[0], dim[1], dim[2]); */
/* Divide the particles among the tasks. */
offset = mpi_rank * N_total / mpi_size;
*N = (mpi_rank + 1) * N_total / mpi_size - offset;
/* Close header */
H5Gclose(h_grp);
/* Allocate memory to store particles */
if (posix_memalign((void*)parts, part_align, *N * sizeof(struct part)) != 0)
error("Error while allocating memory for particles");
bzero(*parts, *N * sizeof(struct part));
/* message("Allocated %8.2f MB for particles.", *N * sizeof(struct part) /
* (1024.*1024.)); */
/* Open SPH particles group */
/* message("Reading particle arrays..."); */
h_grp = H5Gopen(h_file, "/PartType0", H5P_DEFAULT);
if (h_grp < 0) error("Error while opening particle group.\n");
/* Read particle fields into the particle structure */
hydro_read_particles(h_grp, *N, N_total, offset, *parts);
/* Close particle group */
H5Gclose(h_grp);
/* Close property handler */
H5Pclose(h_plist_id);
/* Close file */
H5Fclose(h_file);
/* message("Done Reading particles..."); */
}
/**
* @brief Writes an HDF5 output file (GADGET-3 type) with its XMF descriptor
*
* @param e The engine containing all the system.
* @param us The UnitSystem used for the conversion of units in the output
*
* Creates an HDF5 output file and writes the particles contained
* in the engine. If such a file already exists, it is erased and replaced
* by the new one.
* The companion XMF file is also updated accordingly.
*
* Calls #error() if an error occurs.
*
*/
void write_output_parallel(struct engine* e, struct UnitSystem* us,
int mpi_rank, int mpi_size, MPI_Comm comm,
MPI_Info info) {
hid_t h_file = 0, h_grp = 0, h_grpsph = 0;
int N = e->s->nr_parts;
int periodic = e->s->periodic;
unsigned int numParticles[6] = {N, 0};
unsigned int numParticlesHighWord[6] = {0};
unsigned int flagEntropy[6] = {0};
long long N_total = 0, offset = 0;
double offset_d = 0., N_d = 0., N_total_d = 0.;
int numFiles = 1;
struct part* parts = e->s->parts;
FILE* xmfFile = 0;
static int outputCount = 0;
/* File name */
char fileName[200];
sprintf(fileName, "output_%03i.hdf5", outputCount);
/* First time, we need to create the XMF file */
if (outputCount == 0 && mpi_rank == 0) createXMFfile();
/* Prepare the XMF file for the new entry */
if (mpi_rank == 0) xmfFile = prepareXMFfile();
/* Open HDF5 file */
hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(plist_id, comm, info);
h_file = H5Fcreate(fileName, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
if (h_file < 0) { error("Error while opening file '%s'.", fileName);
}
/* Compute offset in the file and total number of particles */
/* Done using double to allow for up to 2^50=10^15 particles */
N_d = (double)N;
MPI_Exscan(&N_d, &offset_d, 1, MPI_DOUBLE, MPI_SUM, comm);
N_total_d = offset_d + N_d;
MPI_Bcast(&N_total_d, 1, MPI_DOUBLE, mpi_size - 1, comm);
if (N_total_d > 1.e15)
error(
"Error while computing the offset for parallel output: Simulation has "
"more than 10^15 particles.\n");
N_total = (long long)N_total_d;
offset = (long long)offset_d;
/* Write the part of the XMF file corresponding to this specific output */
if (mpi_rank == 0) writeXMFheader(xmfFile, N_total, fileName, e->time);
/* 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 */
writeAttribute(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 */
writeAttribute(h_grp, "BoxSize", DOUBLE, e->s->dim, 3);
writeAttribute(h_grp, "NumPart_ThisFile", UINT, numParticles, 6);
double dblTime = e->time;
writeAttribute(h_grp, "Time", DOUBLE, &dblTime, 1);
/* GADGET-2 legacy values */
numParticles[0] = (unsigned int)N_total;
writeAttribute(h_grp, "NumPart_Total", UINT, numParticles, 6);
numParticlesHighWord[0] = (unsigned int)(N_total >> 32);
writeAttribute(h_grp, "NumPart_Total_HighWord", UINT, numParticlesHighWord,
6);
double MassTable[6] = {0., 0., 0., 0., 0., 0.};
writeAttribute(h_grp, "MassTable", DOUBLE, MassTable, 6);
writeAttribute(h_grp, "Flag_Entropy_ICs", UINT, flagEntropy, 6);
writeAttribute(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);
/* Close header */
H5Gclose(h_grp);
/* Print the code version */
writeCodeDescription(h_file);
/* Print the SPH parameters */
h_grpsph = H5Gcreate(h_file, "/SPH", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grpsph < 0) error("Error while creating SPH group");
writeSPHflavour(h_grpsph);
H5Gclose(h_grpsph);
/* Print the system of Units */
writeUnitSystem(h_file, us);
/* Create SPH particles group */
/* message("Writing particle arrays..."); */ h_grp =
H5Gcreate(h_file, "/PartType0", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_grp < 0) error("Error while creating particle group.\n");
/* Write particle fields from the particle structure */
hydro_write_particles(h_grp, fileName, xmfFile, N, N_total, mpi_rank, offset,
parts, us);
/* Close particle group */
H5Gclose(h_grp);
/* Write LXMF file descriptor */
if (mpi_rank == 0) writeXMFfooter(xmfFile);
/* message("Done writing particles..."); */
/* Close property descriptor */
H5Pclose(plist_id);
/* Close file */
H5Fclose(h_file);
++outputCount;
}
#endif /* HAVE_HDF5 */