-
Loic Hausammann authoredLoic Hausammann authored
logger.c 21.85 KiB
/*******************************************************************************
* This file is part of SWIFT.
* Copyright (c) 2017 Pedro Gonnet (pedro.gonnet@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"
#ifdef HAVE_POSIX_FALLOCATE /* Are we on a sensible platform? */
#ifdef WITH_LOGGER
/* Some standard headers. */
#include <hdf5.h>
#include <math.h>
#include <stdint.h>
#include <stdlib.h>
#include <string.h>
/* This object's header. */
#include "logger.h"
/* Local headers. */
#include "atomic.h"
#include "dump.h"
#include "engine.h"
#include "error.h"
#include "part.h"
#include "units.h"
/*
* Thoses are definitions from the format and therefore should not be changed!
*/
/* number of bytes for a mask */
// TODO change this to number of bits
#define logger_mask_size 1
/* number of bits for chunk header */
#define logger_header_bytes 8
/* number bytes for an offset */
#define logger_offset_size logger_header_bytes - logger_mask_size
/* number of bytes for the version information */
#define logger_version_size 20
/* number of bytes for the labels in the header */
#define logger_label_size 20
/* number of bytes for the number in the header */
#define logger_number_size 4
char logger_version[logger_version_size] = "0.1";
const struct mask_data logger_mask_data[logger_count_mask] = {
/* Particle's position */
{3 * sizeof(double), 1 << logger_x, "positions"}, /* Particle's velocity */
{3 * sizeof(float), 1 << logger_v, "velocities"},
/* Particle's acceleration */
{3 * sizeof(float), 1 << logger_a, "accelerations"},
/* Particle's entropy */
{sizeof(float), 1 << logger_u, "entropy"},
/* Particle's smoothing length */
{sizeof(float), 1 << logger_h, "smoothing length"},
/* Particle's density */
{sizeof(float), 1 << logger_rho, "density"},
/* Particle's constants: mass (float) and ID (long long) */
{sizeof(float) + sizeof(long long), 1 << logger_consts, "consts"},
/* Simulation time stamp: integertime and double time (e.g. scale
factor or time) */
{sizeof(integertime_t) + sizeof(double), 1 << logger_timestamp,
"timestamp"}};
/**
* @brief Write the header of a chunk (offset + mask).
*
* This is maybe broken for big(?) endian.
*
* @param buff The writing buffer
* @param mask The mask to write
* @param offset The old offset
* @param offset_new The new offset
*
* @return updated buff
*/
char *logger_write_chunk_header(char *buff, const unsigned int *mask,
const size_t *offset, const size_t offset_new) {
/* write mask */
memcpy(buff, mask, logger_mask_size);
buff += logger_mask_size;
/* write offset */
size_t diff_offset = offset_new - *offset;
memcpy(buff, &diff_offset, logger_offset_size);
buff += logger_offset_size;
return buff;
}
/**
* @brief Write to the dump
*
* @param d #dump file
* @param offset (return) offset of the data
* @param size number of bytes to write
* @param p pointer to the data
*/
void logger_write_data(struct dump *d, size_t *offset, size_t size,
const void *p) {
/* get buffer */
char *buff = dump_get(d, size, offset);
/* write data to the buffer */
memcpy(buff, p, size);
/* Update offset to end of chunk */
*offset += size;
}
/**
* @brief Compute the size of a message given its mask.
*
* @param mask The mask that will be used to dump a #part or #gpart.
*
* @return The size of the logger message in bytes.
*/int logger_compute_chunk_size(unsigned int mask) {
/* Start with 8 bytes for the header. */
int size = logger_mask_size + logger_offset_size;
/* Is this a particle or a timestep? */
if (mask & logger_mask_data[logger_timestamp].mask) {
/* The timestamp should not contain any other bits. */
if (mask != logger_mask_data[logger_timestamp].mask)
error("Timestamps should not include any other data.");
/* A timestamp consists of an unsigned long long int. */
size += logger_mask_data[logger_timestamp].size;
} else {
for (int i = 0; i < logger_count_mask; i++) {
if (mask & logger_mask_data[i].mask) {
size += logger_mask_data[i].size;
}
}
}
return size;
}
/**
* @brief log all particles in the engine.
*
* @param log The #logger
* @param e The #engine
*/
void logger_log_all(struct logger *log, const struct engine *e) {
/* Ensure that enough space is available */
logger_ensure_size(log, e->total_nr_parts, e->total_nr_gparts, 0);
#ifdef SWIFT_DEBUG_CHECKS
message("Need to implement stars");
#endif
/* some constants */
const struct space *s = e->s;
const unsigned int mask =
logger_mask_data[logger_x].mask | logger_mask_data[logger_v].mask |
logger_mask_data[logger_a].mask | logger_mask_data[logger_u].mask |
logger_mask_data[logger_h].mask | logger_mask_data[logger_rho].mask |
logger_mask_data[logger_consts].mask;
/* loop over all parts */
for (long long i = 0; i < e->total_nr_parts; i++) {
logger_log_part(log, &s->parts[i], mask,
&s->xparts[i].logger_data.last_offset);
s->xparts[i].logger_data.steps_since_last_output = 0;
}
/* loop over all gparts */
if (e->total_nr_gparts > 0) error("Not implemented");
/* loop over all sparts */
// TODO
}
/**
* @brief Dump a #part to the log.
*
* @param log The #logger
* @param p The #part to dump.
* @param mask The mask of the data to dump.
* @param offset Pointer to the offset of the previous log of this particle; * (return) offset of this log.
*/
void logger_log_part(struct logger *log, const struct part *p,
unsigned int mask, size_t *offset) {
/* Make sure we're not writing a timestamp. */
if (mask & logger_mask_data[logger_timestamp].mask)
error("You should not log particles as timestamps.");
/* Start by computing the size of the message. */
const int size = logger_compute_chunk_size(mask);
/* Allocate a chunk of memory in the dump of the right size. */
size_t offset_new;
char *buff = (char *)dump_get(&log->dump, size, &offset_new);
/* Write the header. */
buff = logger_write_chunk_header(buff, &mask, offset, offset_new);
/* Particle position as three doubles. */
if (mask & logger_mask_data[logger_x].mask) {
memcpy(buff, p->x, logger_mask_data[logger_x].size);
buff += logger_mask_data[logger_x].size;
}
/* Particle velocity as three floats. */
if (mask & logger_mask_data[logger_v].mask) {
memcpy(buff, p->v, logger_mask_data[logger_v].size);
buff += logger_mask_data[logger_v].size;
}
/* Particle accelleration as three floats. */
if (mask & logger_mask_data[logger_a].mask) {
memcpy(buff, p->a_hydro, logger_mask_data[logger_a].size);
buff += logger_mask_data[logger_a].size;
}
#if defined(GADGET2_SPH)
/* Particle internal energy as a single float. */
if (mask & logger_mask_data[logger_u].mask) {
memcpy(buff, &p->entropy, logger_mask_data[logger_u].size);
buff += logger_mask_data[logger_u].size;
}
/* Particle smoothing length as a single float. */
if (mask & logger_mask_data[logger_h].mask) {
memcpy(buff, &p->h, logger_mask_data[logger_h].size);
buff += logger_mask_data[logger_h].size;
}
/* Particle density as a single float. */
if (mask & logger_mask_data[logger_rho].mask) {
memcpy(buff, &p->rho, logger_mask_data[logger_rho].size);
buff += logger_mask_data[logger_rho].size;
}
/* Particle constants, which is a bit more complicated. */
if (mask & logger_mask_data[logger_consts].mask) {
// TODO make it dependent of logger_mask_data
memcpy(buff, &p->mass, sizeof(float));
buff += sizeof(float);
memcpy(buff, &p->id, sizeof(long long));
buff += sizeof(long long);
}
#endif
/* Update the log message offset. */
*offset = offset_new;}
/**
* @brief Dump a #gpart to the log.
*
* @param log The #logger
* @param p The #gpart to dump.
* @param mask The mask of the data to dump.
* @param offset Pointer to the offset of the previous log of this particle;
* (return) offset of this log.
*/
void logger_log_gpart(struct logger *log, const struct gpart *p,
unsigned int mask, size_t *offset) {
/* Make sure we're not writing a timestamp. */
if (mask & logger_mask_data[logger_timestamp].mask)
error("You should not log particles as timestamps.");
/* Make sure we're not looging fields not supported by gparts. */
if (mask &
(logger_mask_data[logger_u].mask | logger_mask_data[logger_rho].mask))
error("Can't log SPH quantities for gparts.");
/* Start by computing the size of the message. */
const int size = logger_compute_chunk_size(mask);
/* Allocate a chunk of memory in the dump of the right size. */
size_t offset_new;
char *buff = (char *)dump_get(&log->dump, size, &offset_new);
/* Write the header. */
buff = logger_write_chunk_header(buff, &mask, offset, offset_new);
/* Particle position as three doubles. */
if (mask & logger_mask_data[logger_x].mask) {
memcpy(buff, p->x, logger_mask_data[logger_x].size);
buff += logger_mask_data[logger_x].size;
}
/* Particle velocity as three floats. */
if (mask & logger_mask_data[logger_v].mask) {
memcpy(buff, p->v_full, logger_mask_data[logger_v].size);
buff += logger_mask_data[logger_v].size;
}
/* Particle accelleration as three floats. */
if (mask & logger_mask_data[logger_a].mask) {
memcpy(buff, p->a_grav, logger_mask_data[logger_a].size);
buff += logger_mask_data[logger_a].size;
}
/* Particle constants, which is a bit more complicated. */
if (mask & logger_mask_data[logger_consts].mask) {
// TODO make it dependent of logger_mask_data
memcpy(buff, &p->mass, sizeof(float));
buff += sizeof(float);
memcpy(buff, &p->id_or_neg_offset, sizeof(long long));
buff += sizeof(long long);
}
/* Update the log message offset. */
*offset = offset_new;
}
/**
* @brief write a timestamp
*
* @param log The #logger
* @param timestamp time to write
* @param time time or scale factor * @param offset Pointer to the offset of the previous log of this particle;
* (return) offset of this log.
*/
void logger_log_timestamp(struct logger *log, integertime_t timestamp,
double time, size_t *offset) {
struct dump *dump = &log->dump;
/* Start by computing the size of the message. */
const int size =
logger_compute_chunk_size(logger_mask_data[logger_timestamp].mask);
/* Allocate a chunk of memory in the dump of the right size. */
size_t offset_new;
char *buff = (char *)dump_get(dump, size, &offset_new);
/* Write the header. */
unsigned int mask = logger_mask_data[logger_timestamp].mask;
buff = logger_write_chunk_header(buff, &mask, offset, offset_new);
/* Store the timestamp. */
// TODO make it dependent of logger_mask_data
memcpy(buff, ×tamp, sizeof(integertime_t));
buff += sizeof(integertime_t);
/* Store the time */
memcpy(buff, &time, sizeof(double));
/* Update the log message offset. */
*offset = offset_new;
}
/**
* @brief Ensure that the buffer is large enough for a step.
*
* Check if logger parameters are large enough to write all particles
* and ensure that enough space is available in the buffer.
*
* @param log The #logger
* @param total_nr_parts total number of part
* @param total_nr_gparts total number of gpart
* @param total_nr_sparts total number of spart
*/
void logger_ensure_size(struct logger *log, size_t total_nr_parts,
size_t total_nr_gparts, size_t total_nr_sparts) {
/* count part memory */
size_t limit = log->max_chunk_size;
limit *= total_nr_parts;
/* count gpart memory */
if (total_nr_gparts > 0) error("Not implemented");
/* count spart memory */
if (total_nr_sparts > 0) error("Not implemented");
/* ensure enough space in dump */
dump_ensure(&log->dump, limit, log->buffer_scale * limit);
}
/**
* @brief intialize the logger structure
*
* @param log The #logger
* @param params The #swift_params
*/
void logger_init(struct logger *log, struct swift_params *params) {
/* read parameters */
log->delta_step = parser_get_param_int(params, "Logger:delta_step");
size_t buffer_size = parser_get_opt_param_float(params, "Logger:initial_buffer_size", 0.5) *
1e9;
log->buffer_scale =
parser_get_opt_param_float(params, "Logger:buffer_scale", 10);
parser_get_param_string(params, "Logger:basename", log->base_name);
/* set initial value of parameters */
log->timestamp_offset = 0;
/* generate dump filename */
char logger_name_file[PARSER_MAX_LINE_SIZE];
strcpy(logger_name_file, log->base_name);
strcat(logger_name_file, ".dump");
/* Compute max size for a particle chunk */
int max_size = logger_offset_size + logger_mask_size;
/* Loop over all fields except timestamp */
for (int i = 0; i < logger_count_mask - 1; i++) {
max_size += logger_mask_data[i].size;
}
log->max_chunk_size = max_size;
/* init dump */
dump_init(&log->dump, logger_name_file, buffer_size);
}
/**
* @brief Close dump file and desallocate memory
*
* @param log The #logger
*/
void logger_clean(struct logger *log) { dump_close(&log->dump); }
/**
* @brief Write a file header to a logger file
*
* @param log The #logger
* @param dump The #dump in which to log the particle data.
*
*/
void logger_write_file_header(struct logger *log, const struct engine *e) {
/* get required variables */
struct dump *dump = &log->dump;
size_t file_offset = dump->file_offset;
if (file_offset != 0)
error(
"The logger is not empty."
"This function should be called before writing anything in the logger");
/* Write version information */
logger_write_data(dump, &file_offset, logger_version_size, &logger_version);
/* write offset direction */
const int reversed = 0;
logger_write_data(dump, &file_offset, logger_number_size, &reversed);
/* placeholder to write the offset of the first log here */
char *skip_header = dump_get(dump, logger_offset_size, &file_offset);
/* write number of bytes used for names */
const int label_size = logger_label_size;
logger_write_data(dump, &file_offset, logger_number_size, &label_size);
/* write number of masks */
int count_mask = logger_count_mask;
logger_write_data(dump, &file_offset, logger_number_size, &count_mask);
/* write masks */
// loop over all mask type
for (int i = 0; i < logger_count_mask; i++) {
// mask name
logger_write_data(dump, &file_offset, logger_label_size,
&logger_mask_data[i].name);
// mask size
logger_write_data(dump, &file_offset, logger_number_size,
&logger_mask_data[i].size);
}
/* last step: write first offset */
memcpy(skip_header, &file_offset, logger_offset_size);
}
/**
* @brief read chunk header
*
* @param buff The reading buffer
* @param mask The mask to read
* @param offset (return) the offset pointed by this chunk (absolute)
* @param offset_cur The current chunk offset
*
* @return Number of bytes read
*/
__attribute__((always_inline)) INLINE static int logger_read_chunk_header(
const char *buff, unsigned int *mask, size_t *offset, size_t cur_offset) {
memcpy(mask, buff, logger_mask_size);
buff += logger_mask_size;
*offset = 0;
memcpy(offset, buff, logger_offset_size);
*offset = cur_offset - *offset;
return logger_mask_size + logger_offset_size;
}
/**
* @brief Read a logger message and store the data in a #part.
*
* @param p The #part in which to store the values.
* @param offset Pointer to the offset of the logger message in the buffer,
* will be overwritten with the offset of the previous message.
* @param buff Pointer to the start of an encoded logger message.
*
* @return The mask containing the values read.
*/
int logger_read_part(struct part *p, size_t *offset, const char *buff) {
/* Jump to the offset. */
buff = &buff[*offset];
/* Start by reading the logger mask for this entry. */
const size_t cur_offset = *offset;
unsigned int mask = 0;
buff += logger_read_chunk_header(buff, &mask, offset, cur_offset);
/* We are only interested in particle data. */
if (mask & logger_mask_data[logger_timestamp].mask)
error("Trying to read timestamp as particle.");
/* Particle position as three doubles. */
if (mask & logger_mask_data[logger_x].mask) {
memcpy(p->x, buff, logger_mask_data[logger_x].size);
buff += logger_mask_data[logger_x].size;
}
/* Particle velocity as three floats. */ if (mask & logger_mask_data[logger_v].mask) {
memcpy(p->v, buff, logger_mask_data[logger_v].size);
buff += logger_mask_data[logger_v].size;
}
/* Particle accelleration as three floats. */
if (mask & logger_mask_data[logger_a].mask) {
memcpy(p->a_hydro, buff, logger_mask_data[logger_a].size);
buff += logger_mask_data[logger_a].size;
}
#if defined(GADGET2_SPH)
/* Particle internal energy as a single float. */
if (mask & logger_mask_data[logger_u].mask) {
memcpy(&p->entropy, buff, logger_mask_data[logger_u].size);
buff += logger_mask_data[logger_u].size;
}
/* Particle smoothing length as a single float. */
if (mask & logger_mask_data[logger_h].mask) {
memcpy(&p->h, buff, logger_mask_data[logger_h].size);
buff += logger_mask_data[logger_h].size;
}
/* Particle density as a single float. */
if (mask & logger_mask_data[logger_rho].mask) {
memcpy(&p->rho, buff, logger_mask_data[logger_rho].size);
buff += logger_mask_data[logger_rho].size;
}
/* Particle constants, which is a bit more complicated. */
if (mask & logger_mask_data[logger_rho].mask) {
// TODO make it dependent of logger_mask_data
memcpy(&p->mass, buff, sizeof(float));
buff += sizeof(float);
memcpy(&p->id, buff, sizeof(long long));
buff += sizeof(long long);
}
#endif
/* Finally, return the mask of the values we just read. */
return mask;
}
/**
* @brief Read a logger message and store the data in a #gpart.
*
* @param p The #gpart in which to store the values.
* @param offset Pointer to the offset of the logger message in the buffer,
* will be overwritten with the offset of the previous message.
* @param buff Pointer to the start of an encoded logger message.
*
* @return The mask containing the values read.
*/
int logger_read_gpart(struct gpart *p, size_t *offset, const char *buff) {
/* Jump to the offset. */
buff = &buff[*offset];
/* Start by reading the logger mask for this entry. */
const size_t cur_offset = *offset;
unsigned int mask = 0;
buff += logger_read_chunk_header(buff, &mask, offset, cur_offset);
/* We are only interested in particle data. */
if (mask & logger_mask_data[logger_timestamp].mask)
error("Trying to read timestamp as particle.");
/* We can't store all part fields in a gpart. */
if (mask &
(logger_mask_data[logger_u].mask | logger_mask_data[logger_rho].mask))
error("Trying to read SPH quantities into a gpart.");
/* Particle position as three doubles. */
if (mask & logger_mask_data[logger_x].mask) {
memcpy(p->x, buff, logger_mask_data[logger_x].size);
buff += logger_mask_data[logger_x].size;
}
/* Particle velocity as three floats. */
if (mask & logger_mask_data[logger_v].mask) {
memcpy(p->v_full, buff, logger_mask_data[logger_v].size);
buff += logger_mask_data[logger_v].size;
}
/* Particle accelleration as three floats. */
if (mask & logger_mask_data[logger_a].mask) {
memcpy(p->a_grav, buff, logger_mask_data[logger_a].size);
buff += logger_mask_data[logger_a].size;
}
/* Particle constants, which is a bit more complicated. */
if (mask & logger_mask_data[logger_rho].mask) {
// TODO make it dependent of logger_mask_data
memcpy(&p->mass, buff, sizeof(float));
buff += sizeof(float);
memcpy(&p->id_or_neg_offset, buff, sizeof(long long));
buff += sizeof(long long);
}
/* Finally, return the mask of the values we just read. */
return mask;
}
/**
* @brief Read a logger message for a timestamp.
*
* @param t The timestamp in which to store the value.
* @param offset Pointer to the offset of the logger message in the buffer,
* will be overwritten with the offset of the previous message.
* @param buff Pointer to the start of an encoded logger message.
*
* @return The mask containing the values read.
*/
int logger_read_timestamp(unsigned long long int *t, double *time,
size_t *offset, const char *buff) {
/* Jump to the offset. */
buff = &buff[*offset];
/* Start by reading the logger mask for this entry. */
const size_t cur_offset = *offset;
unsigned int mask = 0;
buff += logger_read_chunk_header(buff, &mask, offset, cur_offset);
/* We are only interested in timestamps. */
if (!(mask & logger_mask_data[logger_timestamp].mask))
error("Trying to read timestamp from a particle.");
/* Make sure we don't have extra fields. */
if (mask != logger_mask_data[logger_timestamp].mask)
error("Timestamp message contains extra fields.");
/* Copy the timestamp value from the buffer. */
// TODO make it dependent of logger_mask_data
memcpy(t, buff, sizeof(unsigned long long int));
buff += sizeof(unsigned long long int);
/* Copy the timestamp value from the buffer. */
memcpy(time, buff, sizeof(double));
/* Finally, return the mask of the values we just read. */
return mask;
}
#endif /* WITH_LOGGER */
#endif /* HAVE_POSIX_FALLOCATE */