diff --git a/logger/Makefile.am b/logger/Makefile.am
index f18e11a8ca6eefa2e4edb4fbf946930250dacbf3..29fc5213dc997dee014ac183e7241ed9f6605f55 100644
--- a/logger/Makefile.am
+++ b/logger/Makefile.am
@@ -48,11 +48,11 @@ SUBDIRS = tests
# List required headers
include_HEADERS = logger_header.h logger_loader_io.h logger_particle.h logger_time.h logger_tools.h logger_reader.h \
- logger_index.h logger_logfile.h
+ logger_logfile.h
# Common source files
AM_SOURCES = logger_header.c logger_loader_io.c logger_particle.c logger_time.c logger_tools.c logger_reader.c \
- logger_index.c logger_logfile.c
+ logger_logfile.c
if HAVEPYTHON
AM_SOURCES += logger_python_wrapper.c
endif
diff --git a/logger/logger_loader_io.c b/logger/logger_loader_io.c
index e879dea0f25da9e3385910c6545f612211dc918a..f18f9bb7eb2eaf88ba11eaf916c0a68a27cfd2d2 100644
--- a/logger/logger_loader_io.c
+++ b/logger/logger_loader_io.c
@@ -59,7 +59,8 @@ void *logger_loader_io_mmap_file(char *filename, size_t *file_size,
else
fd = open(filename, O_RDWR);
- if (fd == -1) error("Unable to open file %s (%s).", filename, strerror(errno));
+ if (fd == -1)
+ error("Unable to open file %s (%s).", filename, strerror(errno));
/* get the file size. */
*file_size = logger_loader_io_get_file_size(fd);
diff --git a/logger/logger_particle.c b/logger/logger_particle.c
index b159b521a0df1831008791e5540861d788a065b2..6809e0edf6125e66cbb8807cc98eeb31b5e04ecd 100644
--- a/logger/logger_particle.c
+++ b/logger/logger_particle.c
@@ -154,8 +154,10 @@ size_t logger_particle_read(struct logger_particle *part,
}
}
- /* Get the time of current record. */
- if (times->next) {
+ /* Get the time of current record.
+ This check is required for the manipulating the file before
+ the initialization of the time_array. */
+ if (times->size != 0) {
part->time = time_array_get_time(times, offset);
} else
part->time = -1;
diff --git a/logger/logger_reader.h b/logger/logger_reader.h
index 3a964aea29e5f72253080f23f6a105bfab7740eb..c4a3ba8912676cf332344e6ec4ebd2943a8afa79 100644
--- a/logger/logger_reader.h
+++ b/logger/logger_reader.h
@@ -47,7 +47,6 @@
#ifndef __LOGGER_LOGGER_READER_H__
#define __LOGGER_LOGGER_READER_H__
-#include "logger_index.h"
#include "logger_loader_io.h"
#include "logger_logfile.h"
#include "logger_particle.h"
@@ -66,9 +65,6 @@ struct logger_reader {
/* Time of each index file. #TODO */
double *times;
- /* Information contained in the index file. */
- struct logger_index index;
-
/* Informations contained in the file header. */
struct logger_logfile log;
diff --git a/logger/logger_time.c b/logger/logger_time.c
index a88745876acea9c7f4f4736afb82fec5be450b22..125c7ea94b3866daedcd1391df3c9f7d98736a26 100644
--- a/logger/logger_time.c
+++ b/logger/logger_time.c
@@ -21,6 +21,51 @@
#include "logger_logfile.h"
#include "logger_reader.h"
+/**
+ * @brief Check if enough space is available and increase it if required.
+ *
+ * @param t The #time_array.
+ */
+void time_array_ensure_size(struct time_array *t) {
+ /* Check if we still have some place. */
+ if (t->size < t->capacity) return;
+
+ /* Increase the size */
+ t->capacity *= 2;
+
+ t->time = realloc(t->time, sizeof(double) * t->capacity);
+ if (t->time == NULL) error("Failed to realloc time memory.");
+
+ t->int_time = realloc(t->int_time, sizeof(integertime_t) * t->capacity);
+ if (t->int_time == NULL) error("Failed to realloc integer time memory.");
+
+ t->offset = realloc(t->offset, sizeof(size_t) * t->capacity);
+ if (t->offset == NULL) error("Failed to realloc offset memory.");
+}
+
+/**
+ * @brief Add an element to the #time_array.
+ *
+ * @param t The #time_array.
+ * @param int_time The time in integer.
+ * @param time The time in double.
+ * @param offset The offset of the record.
+ */
+void time_array_append(struct time_array *t, const integertime_t int_time,
+ const double time, const size_t offset) {
+
+ /* Increase the available space if required */
+ time_array_ensure_size(t);
+
+ /* Copy the values */
+ t->time[t->size] = time;
+ t->int_time[t->size] = int_time;
+ t->offset[t->size] = offset;
+
+ /* Increase the size used. */
+ t->size += 1;
+}
+
/**
* @brief read a time record.
*
@@ -95,8 +140,19 @@ size_t time_offset_first_record(const struct header *h) {
* @param t #time_array to initialize.
*/
void time_array_init(struct time_array *t) {
- t->next = NULL;
- t->prev = NULL;
+ /* Allocate the arrays */
+ t->int_time = malloc(sizeof(integertime_t) * LOGGER_TIME_INIT_SIZE);
+ if (t->int_time == NULL) error("Failed to initialize the integer times.");
+
+ t->time = malloc(sizeof(double) * LOGGER_TIME_INIT_SIZE);
+ if (t->time == NULL) error("Failed to initialize the times.");
+
+ t->offset = malloc(sizeof(size_t) * LOGGER_TIME_INIT_SIZE);
+ if (t->offset == NULL) error("Failed to initialize the offsets.");
+
+ /* Initialize the sizes */
+ t->size = 0;
+ t->capacity = LOGGER_TIME_INIT_SIZE;
}
/**
@@ -108,9 +164,6 @@ void time_array_init(struct time_array *t) {
void time_array_populate(struct time_array *t, struct logger_logfile *log) {
/* Initialize a few variables. */
- t->next = NULL;
- t->prev = NULL;
-
integertime_t int_time = 0;
double time = 0;
@@ -121,81 +174,69 @@ void time_array_populate(struct time_array *t, struct logger_logfile *log) {
size_t offset = time_offset_first_record(&log->header);
while (offset < file_size) {
/* read current time record and store it. */
- t->offset = offset;
size_t tmp_offset = offset;
time_read(&int_time, &time, log->reader, tmp_offset);
- t->int_time = int_time;
- t->time = time;
+ time_array_append(t, int_time, time, offset);
/* get next record. */
int test = tools_get_next_record(&log->header, log->log.map, &offset,
log->log.file_size);
if (test == -1) break;
-
- /* allocate next time_array. */
- struct time_array *tmp = malloc(sizeof(struct time_array));
- tmp->prev = t;
- tmp->next = NULL;
- t->next = tmp;
- t = tmp;
}
-
- /* free unused time_array. */
- struct time_array *tmp = t->prev;
- tmp->next = NULL;
- free(t);
}
/**
- * @brief access the time of a given record (by its offset)
+ * @brief access the time of a given record (by its offset).
*
- * @param t #time_array to access
- * @param offset offset of the record
+ * @param t #time_array to access.
+ * @param offset offset of the record.
*
- * @return integer time of the record
+ * @return integer time of the record.
*/
integertime_t time_array_get_integertime(struct time_array *t,
const size_t offset) {
- const struct time_array *tmp = time_array_get_time_array(t, offset);
- return tmp->int_time;
+ size_t ind = time_array_get_index(t, offset);
+ return t->int_time[ind];
}
/**
- * @brief access the time of a given record (by its offset)
+ * @brief access the time of a given record (by its offset).
*
- * @param t #time_array to access
- * @param offset offset of the record
+ * @param t #time_array to access.
+ * @param offset offset of the record.
*
- * @return time of the record
+ * @return time of the record.
*/
double time_array_get_time(const struct time_array *t, const size_t offset) {
- const struct time_array *tmp = time_array_get_time_array(t, offset);
- return tmp->time;
+ size_t ind = time_array_get_index(t, offset);
+ return t->time[ind];
}
/**
- * @brief access the #time_array of a given record (by its offset)
+ * @brief Find the index of the last time record written before a given offset.
*
* @param t #time_array to access.
* @param offset offset of the record.
*
- * @return pointer to the requested #time_array
+ * @return The index of the last time record.
*/
-struct time_array *time_array_get_time_array(const struct time_array *t,
- const size_t offset) {
+size_t time_array_get_index(const struct time_array *t, const size_t offset) {
#ifdef SWIFT_DEBUG_CHECKS
if (!t) error("NULL pointer.");
#endif
- const struct time_array *tmp;
+
/* Find the time_array with the correct offset. */
- for (tmp = t; tmp->next && tmp->offset <= offset; tmp = tmp->next) {
- }
+ for (size_t i = 1; i < t->size; i++) {
+ if (offset < t->offset[i]) {
+ return i - 1;
+ }
- /* If providing the offset of a time_array, need to give it back. */
- if (tmp->offset == offset) return (struct time_array *)tmp;
+ else if (offset == t->offset[i])
+ return i;
+ }
- return (struct time_array *)tmp->prev;
+ error("Unable to find the required offset.");
}
/**
@@ -204,11 +245,19 @@ struct time_array *time_array_get_time_array(const struct time_array *t,
* @param t #time_array to free
*/
void time_array_free(struct time_array *t) {
- struct time_array *tmp;
- for (tmp = t; t->next; t = tmp) {
- tmp = t->next;
- free(t);
- }
+ /* Free the arrays */
+ free(t->int_time);
+ t->int_time = NULL;
+
+ free(t->time);
+ t->time = NULL;
+
+ free(t->offset);
+ t->offset = NULL;
+
+ /* Reset the counters */
+ t->size = 0;
+ t->capacity = 0;
}
/**
@@ -217,21 +266,18 @@ void time_array_free(struct time_array *t) {
* @param t #time_array to print
*/
void time_array_print(const struct time_array *t) {
- size_t threshold = 4;
+ const size_t threshold = 4;
- size_t n = time_array_count(t);
+ size_t n = t->size;
size_t up_threshold = n - threshold;
- printf("Times (size %lu): [%lli (%g)", n, t->int_time, t->time);
+ printf("Times (size %lu): [%lli (%g)", n, t->int_time[0], t->time[0]);
/* Loop over all elements. */
for (size_t i = 1; i < n; i++) {
- if (!t->next) error("Next pointer not initialized %zi.", i);
-
- t = t->next;
/* Skip the times at the center of the array. */
if (i < threshold || i > up_threshold)
- printf(", %lli (%g)", t->int_time, t->time);
+ printf(", %lli (%g)", t->int_time[i], t->time[i]);
if (i == threshold) printf(", ...");
}
@@ -245,37 +291,20 @@ void time_array_print(const struct time_array *t) {
* @param t #time_array to print
*/
void time_array_print_offset(const struct time_array *t) {
- size_t threshold = 4;
+ const size_t threshold = 4;
- size_t n = time_array_count(t);
+ size_t n = t->size;
size_t up_threshold = n - threshold;
- printf("Times (size %lu): [%lu", n, t->offset);
+ printf("Times (size %lu): [%lu", n, t->offset[0]);
/* Loop over all elements. */
for (size_t i = 1; i < n; i++) {
- t = t->next;
/* Skip the offset in the middle of the array. */
- if (i < threshold || i > up_threshold) printf(", %lu", t->offset);
+ if (i < threshold || i > up_threshold) printf(", %lu", t->offset[i]);
if (i == threshold) printf(", ...");
}
printf("]\n");
}
-
-/**
- * @brief count number of element in #time_array
- *
- * @param t #time_array to count
- *
- * @return number of element
- */
-size_t time_array_count(const struct time_array *t) {
- size_t count = 1;
- for (const struct time_array *tmp = t; tmp->next; tmp = tmp->next) {
- count += 1;
- }
-
- return count;
-}
diff --git a/logger/logger_time.h b/logger/logger_time.h
index 09bf85ff96c53358ce6111be01ca3307463720fe..272746b6ed4406fe70e45ac16f137c4c37048fc7 100644
--- a/logger/logger_time.h
+++ b/logger/logger_time.h
@@ -27,6 +27,8 @@ typedef long long integertime_t;
struct logger_reader;
+#define LOGGER_TIME_INIT_SIZE 1024
+
/**
* @brief This structure contains all the time record.
*
@@ -39,28 +41,27 @@ struct logger_reader;
*
* The time step of an offset can be obtained with
* #time_array_get_integertime, #time_array_get_time and
- * #time_array_get_time_array.
- *
- * The size of the time array can be accessed with
- * #time_array_count.
+ * #time_array_get_index.
*/
struct time_array {
- /* Pointer to next element. */
- void *next;
+ /* Integertime of the records. */
+ integertime_t *int_time;
- /* Pointer to prev element. */
- void *prev;
+ /* Double time of the records. */
+ double *time;
- /* Integertime of this time record. */
- integertime_t int_time;
+ /* Offset in the file of the time records. */
+ size_t *offset;
- /* Double time of this time record. */
- double time;
+ /* Number of element in the arrays. */
+ size_t size;
- /* Offset in the file of this time record. */
- size_t offset;
+ /* Maximum number of element available */
+ size_t capacity;
};
+void time_array_append(struct time_array *t, const integertime_t int_time,
+ const double time, const size_t offset);
size_t time_read(integertime_t *int_time, double *time,
const struct logger_reader *reader, size_t offset);
@@ -72,8 +73,7 @@ integertime_t time_array_get_integertime(struct time_array *t,
double time_array_get_time(const struct time_array *t, const size_t offset);
-struct time_array *time_array_get_time_array(const struct time_array *t,
- const size_t offset);
+size_t time_array_get_index(const struct time_array *t, const size_t offset);
void time_array_free(struct time_array *t);
@@ -81,8 +81,6 @@ void time_array_print(const struct time_array *t);
void time_array_print_offset(const struct time_array *t);
-size_t time_array_count(const struct time_array *t);
-
size_t time_offset_first_record(const struct header *h);
#endif // __LOGGER_LOGGER_TIMELINE_H__
diff --git a/logger/tests/Makefile.am b/logger/tests/Makefile.am
index 4d2f181bfde15a285e833393e1c55c6936755de4..dd94462b8b98b0a089d0f959b81c603c29911a76 100644
--- a/logger/tests/Makefile.am
+++ b/logger/tests/Makefile.am
@@ -20,17 +20,18 @@ AM_CFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/logger $(HDF5_CPPFLAGS) $(GSL_IN
AM_LDFLAGS = ../../src/.libs/libswiftsim.a ../.libs/liblogger.a $(HDF5_LDFLAGS) $(HDF5_LIBS) $(FFTW_LIBS) $(TCMALLOC_LIBS) $(JEMALLOC_LIBS) $(TBBMALLOC_LIBS) $(GRACKLE_LIBS) $(GSL_LIBS) $(PROFILER_LIBS)
# List of programs and scripts to run in the test suite
-TESTS = testLogfileHeader testLogfileReader
+TESTS = testLogfileHeader testLogfileReader testTimeArray
# List of test programs to compile
-check_PROGRAMS = testLogfileHeader testLogfileReader
+check_PROGRAMS = testLogfileHeader testLogfileReader testTimeArray
# Rebuild tests when SWIFT is updated.
-$(check_PROGRAMS): ../../src/.libs/libswiftsim.a
+$(check_PROGRAMS): ../../src/.libs/libswiftsim.a ../.libs/liblogger.a
# Sources for the individual programs
testLogfileHeader_SOURCES = testLogfileHeader.c
testLogfileReader_SOURCES = testLogfileReader.c
+testTimeArray_SOURCES = testTimeArray.c
# Files necessary for distribution
EXTRA_DIST = testLogfileHeader.yml testLogfileReader.yml
diff --git a/logger/tests/testTimeArray.c b/logger/tests/testTimeArray.c
new file mode 100644
index 0000000000000000000000000000000000000000..602cdccad7b370c39f190bb3ae4fc345ccdebb25
--- /dev/null
+++ b/logger/tests/testTimeArray.c
@@ -0,0 +1,76 @@
+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Copyright (C) 2019 Loic Hausammann (loic.hausammann@epfl.ch)
+ *
+ * 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/>.
+ *
+ ******************************************************************************/
+
+#include "logger_time.h"
+#include <time.h>
+#include <stdlib.h>
+
+#define NUMBER_OF_ELEMENT 10000
+#define TIME_BASE 0.04
+#define OFFSET_BASE 1000
+
+int main(int argc, char *argv[]) {
+
+ if (NUMBER_OF_ELEMENT < LOGGER_TIME_INIT_SIZE) {
+ error("Not testing the reallocation.");
+ }
+
+ srand(100);
+ /* Initialize the time array */
+ struct time_array times;
+ time_array_init(×);
+
+ /* Add elements */
+ for(size_t i = 0; i < NUMBER_OF_ELEMENT; i++) {
+ integertime_t int_time = i;
+ double time = i * TIME_BASE;
+ size_t offset = i * OFFSET_BASE;
+
+ time_array_append(×, int_time, time, offset);
+ }
+
+ /* Check the elements */
+ for(size_t i = 0; i < NUMBER_OF_ELEMENT; i++) {
+ integertime_t int_time = i;
+ double time = i * TIME_BASE;
+ size_t offset = i * OFFSET_BASE;
+
+ /* Ensure that we can get the correct offset when looking
+ in between the records. */
+ int r = rand() % OFFSET_BASE;
+ size_t read_offset = offset + r;
+
+ /* The offset cannot be larger than the largest one */
+ if (i == NUMBER_OF_ELEMENT - 1) {
+ read_offset = offset;
+ }
+
+ /* Get the index from the offset */
+ size_t ind = time_array_get_index(×, read_offset);
+
+ /* Check the values obtained */
+ assert(i == ind);
+ assert(int_time == times.int_time[ind]);
+ assert(time == times.time[ind]);
+ assert(offset == times.offset[ind]);
+ }
+
+
+ return 0;
+}