From af2dc556811810c0592b0941b5c6fc62d8088295 Mon Sep 17 00:00:00 2001
From: loikki <loic.hausammann@protonmail.com>
Date: Sat, 21 Aug 2021 17:36:14 +0200
Subject: [PATCH] Format + fix error in return value
---
examples/reader_example.py | 2 +-
src/index_file.cpp | 44 ++++++++++----------
src/index_file.hpp | 14 +++----
src/reader.cpp | 78 +++++++++++++++++++----------------
src/reader_generate_index.cpp | 3 +-
5 files changed, 75 insertions(+), 66 deletions(-)
diff --git a/examples/reader_example.py b/examples/reader_example.py
index 84ea32e..8177b19 100644
--- a/examples/reader_example.py
+++ b/examples/reader_example.py
@@ -63,7 +63,7 @@ for f in args.files:
filename = f[:-5]
else:
raise Exception("It seems that you are not providing a logfile (.dump)")
- with csds.Reader(filename, verbose=0, number_index=10,
+ with csds.Reader(filename, verbose=2, number_index=10,
restart_init=False, use_cache=True) as reader:
# Check the time limits
diff --git a/src/index_file.cpp b/src/index_file.cpp
index dea6188..61f0713 100644
--- a/src/index_file.cpp
+++ b/src/index_file.cpp
@@ -65,18 +65,17 @@ IndexFile::IndexFile(const std::string filename, int verbose) {
MapFile(filename, 0, verbose);
/* Read times */
- pmIndex->ReadData(csds_index_time_offset, csds_index_time_size,
- &mTime);
+ pmIndex->ReadData(csds_index_time_offset, csds_index_time_size, &mTime);
pmIndex->ReadData(csds_index_integer_time_offset,
- csds_index_integer_time_size, &mIntegerTime);
+ csds_index_integer_time_size, &mIntegerTime);
/* Read the number of particles. */
pmIndex->ReadData(csds_index_npart_offset, csds_index_npart_size,
- mNParts.data());
+ mNParts.data());
/* Read whether the file is sorted. */
pmIndex->ReadData(csds_index_is_sorted_offset, csds_index_is_sorted_size,
- &mIsSorted);
+ &mIsSorted);
/* Compute the position of the history of new particles. */
size_t count = 0;
@@ -116,8 +115,8 @@ void IndexFile::WriteSorted() {
const char is_sorted = 1;
/* Write the value */
- pmIndex->WriteData(csds_index_is_sorted_offset,
- csds_index_is_sorted_size, &is_sorted);
+ pmIndex->WriteData(csds_index_is_sorted_offset, csds_index_is_sorted_size,
+ &is_sorted);
mIsSorted = true;
}
@@ -138,8 +137,7 @@ struct index_data *IndexFile::GetData(enum part_type type) const {
}
const size_t type_offset = count * sizeof(struct index_data);
- const char *ret =
- pmIndex->GetMap() + csds_index_data_offset + type_offset;
+ const char *ret = pmIndex->GetMap() + csds_index_data_offset + type_offset;
return (struct index_data *)ret;
}
@@ -153,7 +151,7 @@ struct index_data *IndexFile::GetData(enum part_type type) const {
struct index_data *IndexFile::GetCreatedHistory(enum part_type type) const {
/* Get the position after the previous array. */
- char *ret = (char *) GetData(csds_type_count);
+ char *ret = (char *)GetData(csds_type_count);
/* Get the offset of particles of this type by skipping entries of lower
* types. */
@@ -178,7 +176,7 @@ struct index_data *IndexFile::GetCreatedHistory(enum part_type type) const {
struct index_data *IndexFile::GetRemovedHistory(enum part_type type) const {
/* Get the position after the previous array. */
- char *ret = (char *) GetCreatedHistory(csds_type_count);
+ char *ret = (char *)GetCreatedHistory(csds_type_count);
/* Get the offset of particles of this type by skipping entries of lower
* types. */
@@ -218,8 +216,7 @@ bool IndexFile::ContainsTimeArray() {
* @param sorted Does the file needs to be sorted?
* @param verbose the verbose level
*/
-void IndexFile::MapFile(const std::string filename,
- int sorted, int verbose) {
+void IndexFile::MapFile(const std::string filename, int sorted, int verbose) {
/* Un-map previous file */
if (pmIndex != NULL) {
csds_error("Trying to remap.");
@@ -232,8 +229,8 @@ void IndexFile::MapFile(const std::string filename,
}
/* Map the index file */
pmIndex = new MappedFile(filename,
- /* read_only */ 0,
- /* track_mmap */ 0);
+ /* read_only */ 0,
+ /* track_mmap */ 0);
/* Sort the file */
for (int i = 0; i < csds_type_count; i++) {
if (mNParts[i] != 0) {
@@ -256,7 +253,7 @@ void IndexFile::MapFile(const std::string filename,
/* Map the index file */
pmIndex = new MappedFile(filename, /* read_only */ 1,
- /* track_mmap */ 0);
+ /* track_mmap */ 0);
}
/**
@@ -280,8 +277,10 @@ IndexFile::~IndexFile() {
*
* @return Did we find the particle?
*/
-bool IndexFile::GetOffset(int64_t id, enum part_type type, uint64_t &offset) const {
+bool IndexFile::GetOffset(int64_t id, enum part_type type,
+ uint64_t &offset) const {
+#ifdef CSDS_DEBUG_CHECKS
/* Ensure that the file is sorted according to the ids. */
if (!mIsSorted) {
csds_error("The index file should be already sorted.");
@@ -290,19 +289,20 @@ bool IndexFile::GetOffset(int64_t id, enum part_type type, uint64_t &offset) con
if (mNParts[type] == 0) {
csds_error("Trying to find a particle in an empty index.");
}
+#endif
/* Get the data structure. */
struct index_data *data = GetData(type);
/* Search for the value (binary search) */
struct index_data value = {.id = id, .offset = 0};
- struct index_data *it = std::lower_bound(data, data + mNParts[type],
- value, CompareIndexDataId);
+ struct index_data *it =
+ std::lower_bound(data, data + mNParts[type], value, CompareIndexDataId);
/* Check if we found the particle */
if (it->id == id) {
offset = it->offset;
- return false;
+ return true;
}
/* Try to find it in the history */
@@ -311,10 +311,10 @@ bool IndexFile::GetOffset(int64_t id, enum part_type type, uint64_t &offset) con
for (uint64_t i = 0; i < mNPartsCreated[type]; i++) {
if (data[i].id == id) {
offset = data[i].offset;
- return false;
+ return true;
}
}
/* The particle was not found */
- return true;
+ return false;
}
diff --git a/src/index_file.hpp b/src/index_file.hpp
index 0357c9c..0e7d966 100644
--- a/src/index_file.hpp
+++ b/src/index_file.hpp
@@ -41,8 +41,7 @@ class IndexFile {
~IndexFile();
bool ContainsTimeArray();
- void MapFile(const std::string filename,
- int sorted, int verbose);
+ void MapFile(const std::string filename, int sorted, int verbose);
bool GetOffset(int64_t id, enum part_type type, uint64_t &offset) const;
// TODO convert the 3 functions into particle accessor (e.g. return const&)
@@ -50,9 +49,11 @@ class IndexFile {
struct index_data *GetCreatedHistory(enum part_type type) const;
struct index_data *GetRemovedHistory(enum part_type type) const;
- double GetTime() const {return mTime;}
- integertime_t GetIntegerTime() const {return mIntegerTime;}
- uint64_t GetNumberParticles(enum part_type type) const {return mNParts[type];}
+ double GetTime() const { return mTime; }
+ integertime_t GetIntegerTime() const { return mIntegerTime; }
+ uint64_t GetNumberParticles(enum part_type type) const {
+ return mNParts[type];
+ }
uint64_t GetNumberCreatedParticles(enum part_type type) const {
return mNPartsCreated[type];
}
@@ -70,11 +71,10 @@ class IndexFile {
return d1.id < d2.id;
}
-protected:
+ protected:
void SortFile();
void WriteSorted();
-
/* Time of the index file */
double mTime;
diff --git a/src/reader.cpp b/src/reader.cpp
index 351879b..bca92e0 100644
--- a/src/reader.cpp
+++ b/src/reader.cpp
@@ -201,13 +201,13 @@ void Reader::SetTime(double time) {
/* Read the file */
this->mIndex.index_prev = new IndexFile(filename_prev, this->mVerbose);
- this->mIndex.index_prev->MapFile(
- filename_prev, /* sorted */ 1, this->mVerbose);
+ this->mIndex.index_prev->MapFile(filename_prev, /* sorted */ 1,
+ this->mVerbose);
if ((int)index_ind != this->mIndex.n_files - 1) {
this->mIndex.index_next = new IndexFile(filename_next, this->mVerbose);
- this->mIndex.index_next->MapFile(
- filename_next, /* sorted */ 1, this->mVerbose);
+ this->mIndex.index_next->MapFile(filename_next, /* sorted */ 1,
+ this->mVerbose);
}
/* Get the offset of the time chunk */
@@ -243,7 +243,7 @@ size_t Reader::CountNumberNewParticles(enum part_type part_type) {
/* Get the history of created particles. */
struct index_data *data =
- this->mIndex.index_next->GetCreatedHistory(part_type);
+ this->mIndex.index_next->GetCreatedHistory(part_type);
/* Do we have any new particle? */
if (this->mIndex.index_next->GetNumberCreatedParticles(part_type) == 0 ||
@@ -253,7 +253,8 @@ size_t Reader::CountNumberNewParticles(enum part_type part_type) {
/* Get the last created particle */
// TODO move inside index file
- uint64_t nparts = this->mIndex.index_next->GetNumberCreatedParticles(part_type);
+ uint64_t nparts =
+ this->mIndex.index_next->GetNumberCreatedParticles(part_type);
struct index_data value = {.id = 0, .offset = threshold};
struct index_data *it = std::lower_bound(data, data + nparts, value,
IndexFile::CompareIndexDataOffset);
@@ -297,7 +298,7 @@ size_t Reader::CountNumberRemovedParticles(enum part_type part_type) {
/* Get the history of created particles. */
struct index_data *data =
- this->mIndex.index_next->GetRemovedHistory(part_type);
+ this->mIndex.index_next->GetRemovedHistory(part_type);
/* Do we have any new particle? */
if (this->mIndex.index_next->GetNumberRemovedParticles(part_type) == 0 ||
@@ -306,7 +307,8 @@ size_t Reader::CountNumberRemovedParticles(enum part_type part_type) {
}
/* Get the last created particle */
- const uint64_t nparts = this->mIndex.index_next->GetNumberCreatedParticles(part_type);
+ const uint64_t nparts =
+ this->mIndex.index_next->GetNumberCreatedParticles(part_type);
struct index_data value = {.id = 0, .offset = threshold};
struct index_data *it = std::lower_bound(data, data + nparts, value,
IndexFile::CompareIndexDataOffset);
@@ -343,7 +345,8 @@ void Reader::GetNumberParticles(
std::array<uint64_t, csds_type_count> &n_parts,
const std::array<bool, csds_type_count> &read_types) {
- const bool final_index = this->mIndex.index_prev->GetTime() == this->GetTimeEnd();
+ const bool final_index =
+ this->mIndex.index_prev->GetTime() == this->GetTimeEnd();
for (size_t i = 0; i < n_parts.size(); i++) {
/* Should we skip this type of particles? */
@@ -360,19 +363,22 @@ void Reader::GetNumberParticles(
/* Here we simply need to count the number of particles removed between
the two last time records */
struct index_data *removed =
- this->mIndex.index_prev->GetRemovedHistory((part_type)i);
- size_t size_max = this->mIndex.index_prev->GetNumberRemovedParticles((part_type)i);
+ this->mIndex.index_prev->GetRemovedHistory((part_type)i);
+ size_t size_max =
+ this->mIndex.index_prev->GetNumberRemovedParticles((part_type)i);
struct index_data value = {.id = 0, .offset = this->mTime.time_offset};
- struct index_data *it = std::upper_bound(
- removed, removed + size_max, value, IndexFile::CompareIndexDataOffset);
+ struct index_data *it =
+ std::upper_bound(removed, removed + size_max, value,
+ IndexFile::CompareIndexDataOffset);
n_parts[i] = size_max - (it - removed);
/* In between the last two records, we also store the particles active
in the last step, therefore we need to count the particles created */
struct index_data *created =
- this->mIndex.index_prev->GetCreatedHistory((part_type)i);
- size_max = this->mIndex.index_prev->GetNumberCreatedParticles((part_type)i);
+ this->mIndex.index_prev->GetCreatedHistory((part_type)i);
+ size_max =
+ this->mIndex.index_prev->GetNumberCreatedParticles((part_type)i);
it = std::upper_bound(created, created + size_max, value,
IndexFile::CompareIndexDataOffset);
@@ -382,8 +388,9 @@ void Reader::GetNumberParticles(
else {
/* Count the number of particles present in the last index file. */
const uint64_t count_prev =
- final_index ? this->mIndex.index_prev->GetNumberRemovedParticles((part_type)i)
- : this->mIndex.index_prev->GetNumberParticles((part_type)i);
+ final_index
+ ? this->mIndex.index_prev->GetNumberRemovedParticles((part_type)i)
+ : this->mIndex.index_prev->GetNumberParticles((part_type)i);
/* Count the number of particles that have been created since last index.
*/
const uint64_t count_new =
@@ -609,9 +616,7 @@ void Reader::ReadAllParticlesSingleType(
struct index_data *data = this->mIndex.index_prev->GetData(type);
struct index_data *data_created =
- have_next_index
- ? this->mIndex.index_next->GetCreatedHistory(type)
- : NULL;
+ have_next_index ? this->mIndex.index_next->GetCreatedHistory(type) : NULL;
/* Current index to read */
size_t current_index = 0;
@@ -758,8 +763,8 @@ void Reader::ReadParticlesFromIdsSingleType(
/* Get the offset */
size_t offset = 0;
- bool found = this->mIndex.index_prev->GetOffset(
- (int64_t)ids[i], type, offset);
+ bool found =
+ this->mIndex.index_prev->GetOffset((int64_t)ids[i], type, offset);
/* Deal with the particles not found */
if (!found) {
@@ -912,7 +917,6 @@ int Reader::UpdateSingleParticle(size_t index, enum part_type type, double time,
csds_error("Found particles that do not correspond.");
}
#endif
-
if (flag == csds_flag_change_type || flag == csds_flag_mpi_exit ||
flag == csds_flag_delete) {
return 1;
@@ -1019,6 +1023,7 @@ void Reader::UpdateParticlesSingleType(
/* Update the particles */
const int64_t initial_size_cache = this->mCache[type].Size();
+
for (int64_t part = 0; part < initial_size_cache; part++) {
/* Get the current particle index */
size_t ind = this->mCache[type].GetCurrentIndexAndIncrement();
@@ -1046,8 +1051,9 @@ void Reader::UpdateParticlesSingleType(
if (have_next_index &&
current_field.GetField() == field_enum_particles_ids) {
struct index_data *next_removed =
- this->mIndex.index_next->GetRemovedHistory(type);
- for (size_t i = 0; i < this->mIndex.index_next->GetNumberRemovedParticles(type);
+ this->mIndex.index_next->GetRemovedHistory(type);
+ for (size_t i = 0;
+ i < this->mIndex.index_next->GetNumberRemovedParticles(type);
i++) {
/* Stop as soon as we reach the correct time */
if (next_removed[i].offset > offset_time) break;
@@ -1058,10 +1064,11 @@ void Reader::UpdateParticlesSingleType(
/* Ensures that it is not simply a transitioning particle */
struct index_data *next_created =
- this->mIndex.index_next->GetCreatedHistory(type);
+ this->mIndex.index_next->GetCreatedHistory(type);
bool found = false;
for (size_t j = 0;
- j < this->mIndex.index_next->GetNumberCreatedParticles(type); j++) {
+ j < this->mIndex.index_next->GetNumberCreatedParticles(type);
+ j++) {
/* Stop as soon as we reach the correct time */
if (next_created[j].offset > offset_time) break;
@@ -1088,7 +1095,7 @@ void Reader::UpdateParticlesSingleType(
/* Check if we need to update the cache with the previous index file */
size_t offset_index =
- this->mLog->times.GetIndexFromTime(this->mIndex.index_prev->GetTime());
+ this->mLog->times.GetIndexFromTime(this->mIndex.index_prev->GetTime());
offset_index = this->mLog->times[offset_index].offset;
const bool do_previous =
this->mCache[type].GetLastTimeOffset() < offset_index;
@@ -1097,22 +1104,23 @@ void Reader::UpdateParticlesSingleType(
struct index_data *prev_created =
this->mIndex.index_prev->GetCreatedHistory(type);
struct index_data *next_created =
- have_next_index
- ? this->mIndex.index_next->GetCreatedHistory(type)
- : NULL;
+ have_next_index ? this->mIndex.index_next->GetCreatedHistory(type) : NULL;
/* Go to the last particle created */
struct index_data *index_data = do_previous ? prev_created : next_created;
const size_t size_next =
- have_next_index ? this->mIndex.index_next->GetNumberCreatedParticles(type) : 0;
+ have_next_index ? this->mIndex.index_next->GetNumberCreatedParticles(type)
+ : 0;
size_t size_max =
- do_previous ? this->mIndex.index_prev->GetNumberCreatedParticles(type) : size_next;
+ do_previous ? this->mIndex.index_prev->GetNumberCreatedParticles(type)
+ : size_next;
/* Get the last created particle */
struct index_data value = {.id = 0,
.offset = this->mCache[type].GetLastTimeOffset()};
- struct index_data *it = std::upper_bound(
- index_data, index_data + size_max, value, IndexFile::CompareIndexDataOffset);
+ struct index_data *it =
+ std::upper_bound(index_data, index_data + size_max, value,
+ IndexFile::CompareIndexDataOffset);
size_t center = it - index_data;
/* Create a temporary buffer */
diff --git a/src/reader_generate_index.cpp b/src/reader_generate_index.cpp
index 105ed34..2adf4ca 100644
--- a/src/reader_generate_index.cpp
+++ b/src/reader_generate_index.cpp
@@ -698,7 +698,8 @@ void Reader::GenerateIndexFiles(int number_index, int current_index) {
/* Loop over all the particle types */
for (int i = 0; i < csds_type_count; i++) {
/* Allocate the array for the current state */
- current_state[i].reserve(hashmap_overallocation * index.GetNumberParticles((part_type)i));
+ current_state[i].reserve(hashmap_overallocation *
+ index.GetNumberParticles((part_type)i));
/* Copy the index file into the arrays. */
for (size_t p = 0; p < index.GetNumberParticles((part_type)i); p++) {
--
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