void core_map_examine(struct core_map *self)
{
int key_size;
int value_size;
uint64_t size;
key_size = core_map_get_key_size(self);
value_size = core_map_get_value_size(self);
size = core_map_size(self);
printf("core_map_examine key_size %d value_size %d size %" PRIu64 "\n",
key_size, value_size, size);
}
void biosal_assembly_graph_store_push_data(struct thorium_actor *self, struct thorium_message *message)
{
struct biosal_assembly_graph_store *concrete_self;
int name;
int source;
concrete_self = thorium_actor_concrete_actor(self);
source = thorium_message_source(message);
concrete_self->source = source;
name = thorium_actor_name(self);
core_map_init(&concrete_self->coverage_distribution, sizeof(int), sizeof(uint64_t));
printf("%s/%d: local table has %" PRIu64" canonical kmers (%" PRIu64 " kmers)\n",
thorium_actor_script_name(self),
name, core_map_size(&concrete_self->table),
2 * core_map_size(&concrete_self->table));
core_memory_pool_examine(&concrete_self->persistent_memory);
core_map_iterator_init(&concrete_self->iterator, &concrete_self->table);
thorium_actor_send_to_self_empty(self, ACTION_YIELD);
}
void biosal_coverage_distribution_ask_to_stop(struct thorium_actor *self, struct thorium_message *message)
{
struct core_map_iterator iterator;
struct core_vector coverage_values;
struct biosal_coverage_distribution *concrete_actor;
uint64_t *frequency;
int *coverage;
concrete_actor = (struct biosal_coverage_distribution *)thorium_actor_concrete_actor(self);
core_map_iterator_init(&iterator, &concrete_actor->distribution);
core_vector_init(&coverage_values, sizeof(int));
while (core_map_iterator_has_next(&iterator)) {
#if 0
thorium_actor_log(self, "DEBUG EMIT iterator\n");
#endif
core_map_iterator_next(&iterator, (void **)&coverage,
(void **)&frequency);
#ifdef CORE_DEBUGGER_ASSERT_ENABLED
if (coverage == NULL) {
thorium_actor_log(self, "DEBUG map has %d buckets\n", (int)core_map_size(&concrete_actor->distribution));
}
#endif
CORE_DEBUGGER_ASSERT(coverage != NULL);
core_vector_push_back(&coverage_values, coverage);
}
core_vector_sort_int(&coverage_values);
core_map_iterator_destroy(&iterator);
core_vector_destroy(&coverage_values);
thorium_actor_ask_to_stop(self, message);
}
void biosal_assembly_graph_store_print_progress(struct thorium_actor *self)
{
struct biosal_assembly_graph_store *concrete_self;
uint64_t total;
uint64_t stride;
uint64_t current_value;
int steps;
float ratio;
char finished[] = " FINISHED";
char not_finished[] = "";
char *state;
concrete_self = thorium_actor_concrete_actor(self);
total = core_map_size(&concrete_self->table);
steps = 20;
stride = total / steps;
current_value = concrete_self->consumed_canonical_vertex_count;
if ((current_value == 0)
|| (current_value % stride == 0)
|| (current_value == total)) {
state = not_finished;
if (current_value == total) {
state = finished;
}
ratio = (0.0 + current_value) / total;
printf("%s/%d %.2f of vertices were consumed%s\n",
thorium_actor_script_name(self),
thorium_actor_name(self), ratio, state);
}
}
void biosal_assembly_graph_store_add_arc(struct thorium_actor *self,
struct biosal_assembly_arc *arc, char *sequence,
void *key)
{
struct biosal_assembly_graph_store *concrete_self;
struct biosal_dna_kmer *source;
struct biosal_dna_kmer real_source;
int destination;
int type;
struct biosal_assembly_vertex *vertex;
struct core_memory_pool *ephemeral_memory;
int is_canonical;
#if 0
/*
* Don't do anything just to see if this code
* is buggy.
*/
return;
#endif
#ifdef BIOSAL_ASSEMBLY_GRAPH_STORE_DEBUG_ARC
int verbose;
#endif
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
concrete_self = thorium_actor_concrete_actor(self);
#ifdef BIOSAL_ASSEMBLY_GRAPH_STORE_DEBUG_ARC
verbose = 0;
if (concrete_self->received_arc_count == 0) {
verbose = 1;
}
if (verbose) {
printf("DEBUG BioSAL::GraphStore::AddArc\n");
biosal_assembly_arc_print(arc, concrete_self->kmer_length, &concrete_self->transport_codec,
ephemeral_memory);
}
#endif
source = biosal_assembly_arc_source(arc);
destination = biosal_assembly_arc_destination(arc);
type = biosal_assembly_arc_type(arc);
/*
* Don't convert the data if the transport codec and the
* storage codec are the same.
*/
if (concrete_self->codec_are_different) {
biosal_dna_kmer_get_sequence(source, sequence, concrete_self->kmer_length,
&concrete_self->transport_codec);
biosal_dna_kmer_init(&real_source, sequence, &concrete_self->storage_codec,
ephemeral_memory);
source = &real_source;
}
biosal_dna_kmer_pack_store_key(source, key,
concrete_self->kmer_length, &concrete_self->storage_codec,
ephemeral_memory);
vertex = core_map_get(&concrete_self->table, key);
#ifdef CORE_DEBUGGER_ENABLE_ASSERT
if (vertex == NULL) {
printf("Error: vertex is NULL, key_length_in_bytes %d size %" PRIu64 "\n",
concrete_self->key_length_in_bytes,
core_map_size(&concrete_self->table));
}
#endif
CORE_DEBUGGER_ASSERT(vertex != NULL);
#ifdef BIOSAL_ASSEMBLY_GRAPH_STORE_DEBUG_ARC
if (verbose) {
printf("DEBUG BEFORE:\n");
biosal_assembly_vertex_print(vertex);
}
#endif
/*
* Inverse the arc if the source is not canonical
*/
is_canonical = biosal_dna_kmer_is_canonical(source, concrete_self->kmer_length,
&concrete_self->storage_codec);
if (!is_canonical) {
if (type == BIOSAL_ARC_TYPE_PARENT) {
type = BIOSAL_ARC_TYPE_CHILD;
} else if (type == BIOSAL_ARC_TYPE_CHILD) {
type = BIOSAL_ARC_TYPE_PARENT;
}
destination = biosal_dna_codec_get_complement(destination);
}
if (type == BIOSAL_ARC_TYPE_PARENT) {
biosal_assembly_vertex_add_parent(vertex, destination);
} else if (type == BIOSAL_ARC_TYPE_CHILD) {
biosal_assembly_vertex_add_child(vertex, destination);
}
#ifdef BIOSAL_ASSEMBLY_GRAPH_STORE_DEBUG_ARC
if (verbose) {
printf("DEBUG AFTER:\n");
biosal_assembly_vertex_print(vertex);
}
#endif
if (concrete_self->codec_are_different) {
biosal_dna_kmer_destroy(&real_source, ephemeral_memory);
}
}
void biosal_assembly_graph_store_push_kmer_block(struct thorium_actor *self, struct thorium_message *message)
{
struct core_memory_pool *ephemeral_memory;
struct biosal_dna_kmer_frequency_block block;
struct biosal_assembly_vertex *bucket;
void *packed_kmer;
struct core_map_iterator iterator;
struct biosal_assembly_graph_store *concrete_self;
/*int tag;*/
void *key;
struct core_map *kmers;
struct biosal_dna_kmer kmer;
void *buffer;
int count;
struct biosal_dna_kmer encoded_kmer;
char *raw_kmer;
int period;
struct biosal_dna_kmer *kmer_pointer;
int *frequency;
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
concrete_self = thorium_actor_concrete_actor(self);
/*tag = thorium_message_action(message);*/
buffer = thorium_message_buffer(message);
count = thorium_message_count(message);
/*
* Handler for PUSH_DATA
*/
biosal_dna_kmer_frequency_block_init(&block, concrete_self->kmer_length,
ephemeral_memory, &concrete_self->transport_codec, 0);
biosal_dna_kmer_frequency_block_unpack(&block, buffer, ephemeral_memory,
&concrete_self->transport_codec);
key = core_memory_pool_allocate(ephemeral_memory, concrete_self->key_length_in_bytes);
kmers = biosal_dna_kmer_frequency_block_kmers(&block);
core_map_iterator_init(&iterator, kmers);
period = 2500000;
raw_kmer = core_memory_pool_allocate(thorium_actor_get_ephemeral_memory(self),
concrete_self->kmer_length + 1);
if (!concrete_self->printed_vertex_size) {
printf("DEBUG VERTEX DELIVERY %d bytes\n", count);
concrete_self->printed_vertex_size = 1;
}
while (core_map_iterator_has_next(&iterator)) {
/*
* add kmers to store
*/
core_map_iterator_next(&iterator, (void **)&packed_kmer, (void **)&frequency);
/* Store the kmer in 2 bit encoding
*/
biosal_dna_kmer_init_empty(&kmer);
biosal_dna_kmer_unpack(&kmer, packed_kmer, concrete_self->kmer_length,
ephemeral_memory,
&concrete_self->transport_codec);
kmer_pointer = &kmer;
if (concrete_self->codec_are_different) {
/*
* Get a copy of the sequence
*/
biosal_dna_kmer_get_sequence(kmer_pointer, raw_kmer, concrete_self->kmer_length,
&concrete_self->transport_codec);
biosal_dna_kmer_init(&encoded_kmer, raw_kmer, &concrete_self->storage_codec,
thorium_actor_get_ephemeral_memory(self));
kmer_pointer = &encoded_kmer;
}
biosal_dna_kmer_pack_store_key(kmer_pointer, key,
concrete_self->kmer_length, &concrete_self->storage_codec,
thorium_actor_get_ephemeral_memory(self));
#ifdef BIOSAL_DEBUG_ISSUE_540
if (strcmp(raw_kmer, "AGCTGGTAGTCATCACCAGACTGGAACAG") == 0
|| strcmp(raw_kmer, "CGCGATCTGTTGCTGGGCCTAACGTGGTA") == 0
|| strcmp(raw_kmer, "TACCACGTTAGGCCCAGCAACAGATCGCG") == 0) {
printf("Examine store key for %s\n", raw_kmer);
core_debugger_examine(key, concrete_self->key_length_in_bytes);
}
#endif
bucket = core_map_get(&concrete_self->table, key);
if (bucket == NULL) {
/* This is the first time that this kmer is seen.
*/
bucket = core_map_add(&concrete_self->table, key);
biosal_assembly_vertex_init(bucket);
#if 0
printf("DEBUG303 ADD_KEY");
biosal_dna_kmer_print(&encoded_kmer, concrete_self->kmer_length,
&concrete_self->storage_codec, ephemeral_memory);
#endif
}
if (concrete_self->codec_are_different) {
biosal_dna_kmer_destroy(&encoded_kmer,
thorium_actor_get_ephemeral_memory(self));
}
biosal_dna_kmer_destroy(&kmer, ephemeral_memory);
biosal_assembly_vertex_increase_coverage_depth(bucket, *frequency);
if (concrete_self->received >= concrete_self->last_received + period) {
printf("%s/%d received %" PRIu64 " kmers so far,"
" store has %" PRIu64 " canonical kmers, %" PRIu64 " kmers\n",
thorium_actor_script_name(self),
thorium_actor_name(self), concrete_self->received,
core_map_size(&concrete_self->table),
2 * core_map_size(&concrete_self->table));
concrete_self->last_received = concrete_self->received;
}
concrete_self->received += *frequency;
}
core_memory_pool_free(ephemeral_memory, key);
core_memory_pool_free(ephemeral_memory, raw_kmer);
core_map_iterator_destroy(&iterator);
biosal_dna_kmer_frequency_block_destroy(&block, thorium_actor_get_ephemeral_memory(self));
thorium_actor_send_reply_empty(self, ACTION_PUSH_KMER_BLOCK_REPLY);
}
void biosal_assembly_graph_store_yield_reply(struct thorium_actor *self, struct thorium_message *message)
{
struct biosal_dna_kmer kmer;
void *key;
struct biosal_assembly_vertex *value;
int coverage;
int customer;
uint64_t *count;
int new_count;
void *new_buffer;
struct thorium_message new_message;
struct core_memory_pool *ephemeral_memory;
struct biosal_assembly_graph_store *concrete_self;
int i;
int max;
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
concrete_self = thorium_actor_concrete_actor(self);
customer = concrete_self->customer;
#if 0
printf("YIELD REPLY\n");
#endif
i = 0;
max = 1024;
key = NULL;
value = NULL;
while (i < max
&& core_map_iterator_has_next(&concrete_self->iterator)) {
core_map_iterator_next(&concrete_self->iterator, (void **)&key, (void **)&value);
biosal_dna_kmer_init_empty(&kmer);
biosal_dna_kmer_unpack(&kmer, key, concrete_self->kmer_length,
ephemeral_memory,
&concrete_self->storage_codec);
coverage = biosal_assembly_vertex_coverage_depth(value);
count = (uint64_t *)core_map_get(&concrete_self->coverage_distribution, &coverage);
if (count == NULL) {
count = (uint64_t *)core_map_add(&concrete_self->coverage_distribution, &coverage);
(*count) = 0;
}
/* increment for the lowest kmer (canonical) */
(*count)++;
biosal_dna_kmer_destroy(&kmer, ephemeral_memory);
++i;
}
/* yield again if the iterator is not at the end
*/
if (core_map_iterator_has_next(&concrete_self->iterator)) {
#if 0
printf("yield ! %d\n", i);
#endif
thorium_actor_send_to_self_empty(self, ACTION_YIELD);
return;
}
/*
printf("ready...\n");
*/
core_map_iterator_destroy(&concrete_self->iterator);
new_count = core_map_pack_size(&concrete_self->coverage_distribution);
new_buffer = thorium_actor_allocate(self, new_count);
core_map_pack(&concrete_self->coverage_distribution, new_buffer);
printf("SENDING %s/%d sends map to %d, %d bytes / %d entries\n",
thorium_actor_script_name(self),
thorium_actor_name(self),
customer, new_count,
(int)core_map_size(&concrete_self->coverage_distribution));
thorium_message_init(&new_message, ACTION_PUSH_DATA, new_count, new_buffer);
thorium_actor_send(self, customer, &new_message);
thorium_message_destroy(&new_message);
core_map_destroy(&concrete_self->coverage_distribution);
thorium_actor_send_empty(self, concrete_self->source,
ACTION_PUSH_DATA_REPLY);
}
void biosal_assembly_graph_store_print(struct thorium_actor *self)
{
struct core_map_iterator iterator;
struct biosal_dna_kmer kmer;
void *key;
struct biosal_assembly_vertex *value;
int coverage;
char *sequence;
struct biosal_assembly_graph_store *concrete_self;
int maximum_length;
int length;
struct core_memory_pool *ephemeral_memory;
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
concrete_self = thorium_actor_concrete_actor(self);
core_map_iterator_init(&iterator, &concrete_self->table);
printf("map size %d\n", (int)core_map_size(&concrete_self->table));
maximum_length = 0;
while (core_map_iterator_has_next(&iterator)) {
core_map_iterator_next(&iterator, (void **)&key, (void **)&value);
biosal_dna_kmer_init_empty(&kmer);
biosal_dna_kmer_unpack(&kmer, key, concrete_self->kmer_length,
thorium_actor_get_ephemeral_memory(self),
&concrete_self->storage_codec);
length = biosal_dna_kmer_length(&kmer, concrete_self->kmer_length);
/*
printf("length %d\n", length);
*/
if (length > maximum_length) {
maximum_length = length;
}
biosal_dna_kmer_destroy(&kmer, thorium_actor_get_ephemeral_memory(self));
}
/*
printf("MAx length %d\n", maximum_length);
*/
sequence = core_memory_pool_allocate(ephemeral_memory, maximum_length + 1);
sequence[0] = '\0';
core_map_iterator_destroy(&iterator);
core_map_iterator_init(&iterator, &concrete_self->table);
while (core_map_iterator_has_next(&iterator)) {
core_map_iterator_next(&iterator, (void **)&key, (void **)&value);
biosal_dna_kmer_init_empty(&kmer);
biosal_dna_kmer_unpack(&kmer, key, concrete_self->kmer_length,
thorium_actor_get_ephemeral_memory(self),
&concrete_self->storage_codec);
biosal_dna_kmer_get_sequence(&kmer, sequence, concrete_self->kmer_length,
&concrete_self->storage_codec);
coverage = biosal_assembly_vertex_coverage_depth(value);
printf("Sequence %s Coverage %d\n", sequence, coverage);
biosal_dna_kmer_destroy(&kmer, thorium_actor_get_ephemeral_memory(self));
}
core_map_iterator_destroy(&iterator);
core_memory_pool_free(ephemeral_memory, sequence);
}
int core_map_empty(struct core_map *self)
{
return core_map_size(self) == 0;
}
void biosal_sequence_partitioner_receive(struct thorium_actor *actor, struct thorium_message *message)
{
int tag;
int source;
int count;
void *buffer;
int bytes;
struct biosal_sequence_partitioner *concrete_actor;
struct biosal_partition_command command;
struct thorium_message response;
int command_number;
struct biosal_partition_command *active_command;
int stream_index;
struct biosal_partition_command *command_bucket;
int i;
thorium_message_get_all(message, &tag, &count, &buffer, &source);
concrete_actor = (struct biosal_sequence_partitioner *)thorium_actor_concrete_actor(actor);
if (tag == ACTION_SEQUENCE_PARTITIONER_SET_BLOCK_SIZE) {
thorium_message_unpack_int(message, 0, &concrete_actor->block_size);
thorium_actor_send_reply_empty(actor, ACTION_SEQUENCE_PARTITIONER_SET_BLOCK_SIZE_REPLY);
biosal_sequence_partitioner_verify(actor);
/*
printf("DEBUG biosal_sequence_partitioner_receive received block size\n");
*/
} else if (tag == ACTION_SEQUENCE_PARTITIONER_SET_ENTRY_VECTOR) {
/*
printf("DEBUG biosal_sequence_partitioner_receive unpacking vector, %d bytes\n",
count);
*/
core_vector_init(&concrete_actor->stream_entries, 0);
core_vector_unpack(&concrete_actor->stream_entries, buffer);
/*
printf("DEBUG after unpack\n");
*/
thorium_actor_send_reply_empty(actor, ACTION_SEQUENCE_PARTITIONER_SET_ENTRY_VECTOR_REPLY);
/*
printf("DEBUG biosal_sequence_partitioner_receive received received entry vector\n");
*/
biosal_sequence_partitioner_verify(actor);
} else if (tag == ACTION_SEQUENCE_PARTITIONER_SET_ACTOR_COUNT) {
thorium_message_unpack_int(message, 0, &concrete_actor->store_count);
thorium_actor_send_reply_empty(actor, ACTION_SEQUENCE_PARTITIONER_SET_ACTOR_COUNT_REPLY);
biosal_sequence_partitioner_verify(actor);
/*
printf("DEBUG biosal_sequence_partitioner_receive received received store count\n");
*/
} else if (tag == ACTION_SEQUENCE_PARTITIONER_GET_COMMAND) {
if (core_queue_dequeue(&concrete_actor->available_commands, &command)) {
bytes = biosal_partition_command_pack_size(&command);
/*
printf("DEBUG partitioner has command, packing %d bytes!\n", bytes);
*/
buffer = thorium_actor_allocate(actor, bytes);
biosal_partition_command_pack(&command, buffer);
thorium_message_init(&response, ACTION_SEQUENCE_PARTITIONER_GET_COMMAND_REPLY,
bytes, buffer);
thorium_actor_send_reply(actor, &response);
/* store the active command
*/
command_number = biosal_partition_command_name(&command);
command_bucket = (struct biosal_partition_command *)core_map_add(&concrete_actor->active_commands,
&command_number);
*command_bucket = command;
/* there may be other command available too !
*/
}
} else if (tag == ACTION_SEQUENCE_PARTITIONER_GET_COMMAND_REPLY_REPLY) {
/*
* take the name of the command, find it in the active
* command, generate a new command, and send ACTION_SEQUENCE_PARTITIONER_COMMAND_IS_READY
* as a reply
*/
thorium_message_unpack_int(message, 0, &command_number);
active_command = core_map_get(&concrete_actor->active_commands,
&command_number);
if (active_command == NULL) {
return;
}
stream_index = biosal_partition_command_stream_index(active_command);
active_command = NULL;
core_map_delete(&concrete_actor->active_commands,
&command_number);
biosal_sequence_partitioner_generate_command(actor, stream_index);
if (core_map_size(&concrete_actor->active_commands) == 0
&& core_queue_size(&concrete_actor->available_commands) == 0) {
thorium_actor_send_reply_empty(actor, ACTION_SEQUENCE_PARTITIONER_FINISHED);
}
} else if (tag == ACTION_ASK_TO_STOP
&& source == thorium_actor_supervisor(actor)) {
#ifdef BIOSAL_SEQUENCE_PARTITIONER_DEBUG
printf("DEBUG biosal_sequence_partitioner_receive ACTION_ASK_TO_STOP\n");
#endif
thorium_actor_send_to_self_empty(actor,
ACTION_STOP);
} else if (tag == ACTION_SEQUENCE_PARTITIONER_PROVIDE_STORE_ENTRY_COUNTS_REPLY) {
/* generate commands
*/
for (i = 0; i < core_vector_size(&concrete_actor->stream_entries); i++) {
biosal_sequence_partitioner_generate_command(actor, i);
}
}
}
int main(int argc, char **argv)
{
BEGIN_TESTS();
{
struct core_map big_map;
int kmer_length = 43;
struct biosal_dna_kmer kmer;
int count;
int run_test;
int coverage;
void *key;
int key_length;
int *bucket;
int i;
struct biosal_dna_codec codec;
struct core_memory_pool memory;
core_memory_pool_init(&memory, 1048576, -1);
biosal_dna_codec_init(&codec);
run_test = 1;
count = 100000000;
printf("STRESS TEST\n");
biosal_dna_kmer_init_mock(&kmer, kmer_length, &codec, &memory);
key_length = biosal_dna_kmer_pack_size(&kmer, kmer_length, &codec);
biosal_dna_kmer_destroy(&kmer, &memory);
core_map_init(&big_map, key_length, sizeof(coverage));
key = core_memory_allocate(key_length, -1);
i = 0;
while (i < count && run_test) {
biosal_dna_kmer_init_random(&kmer, kmer_length, &codec, &memory);
biosal_dna_kmer_pack_store_key(&kmer, key, kmer_length, &codec, &memory);
bucket = core_map_add(&big_map, key);
coverage = 99;
(*bucket) = coverage;
biosal_dna_kmer_destroy(&kmer, &memory);
if (i % 100000 == 0) {
printf("ADD %d/%d %" PRIu64 "\n", i, count,
core_map_size(&big_map));
}
i++;
}
core_map_destroy(&big_map);
core_memory_free(key, -1);
biosal_dna_codec_destroy(&codec);
core_memory_pool_destroy(&memory);
}
END_TESTS();
return 0;
}
void biosal_coverage_distribution_receive(struct thorium_actor *self, struct thorium_message *message)
{
int tag;
struct core_map map;
struct core_map_iterator iterator;
int *coverage_from_message;
uint64_t *count_from_message;
uint64_t *frequency;
int count;
void *buffer;
struct biosal_coverage_distribution *concrete_actor;
int name;
int source;
struct core_memory_pool *ephemeral_memory;
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
name = thorium_actor_name(self);
source = thorium_message_source(message);
concrete_actor = (struct biosal_coverage_distribution *)thorium_actor_concrete_actor(self);
tag = thorium_message_action(message);
count = thorium_message_count(message);
buffer = thorium_message_buffer(message);
if (tag == ACTION_PUSH_DATA) {
core_map_init(&map, 0, 0);
core_map_set_memory_pool(&map, ephemeral_memory);
core_map_unpack(&map, buffer);
core_map_iterator_init(&iterator, &map);
while (core_map_iterator_has_next(&iterator)) {
core_map_iterator_next(&iterator, (void **)&coverage_from_message,
(void **)&count_from_message);
#ifdef BIOSAL_COVERAGE_DISTRIBUTION_DEBUG
thorium_actor_log(self, "DEBUG DATA %d %d\n", (int)*coverage_from_message, (int)*count_from_message);
#endif
frequency = core_map_get(&concrete_actor->distribution, coverage_from_message);
if (frequency == NULL) {
frequency = core_map_add(&concrete_actor->distribution, coverage_from_message);
(*frequency) = 0;
}
(*frequency) += (*count_from_message);
}
core_map_iterator_destroy(&iterator);
thorium_actor_send_reply_empty(self, ACTION_PUSH_DATA_REPLY);
concrete_actor->actual++;
thorium_actor_log(self, "distribution/%d receives coverage data from producer/%d, %d entries / %d bytes %d/%d\n",
name, source, (int)core_map_size(&map), count,
concrete_actor->actual, concrete_actor->expected);
if (concrete_actor->expected != 0 && concrete_actor->expected == concrete_actor->actual) {
thorium_actor_log(self, "received everything %d/%d\n", concrete_actor->actual, concrete_actor->expected);
biosal_coverage_distribution_write_distribution(self);
thorium_actor_send_empty(self, concrete_actor->source,
ACTION_NOTIFY);
}
core_map_destroy(&map);
} else if (tag == ACTION_ASK_TO_STOP) {
biosal_coverage_distribution_ask_to_stop(self, message);
} else if (tag == ACTION_SET_EXPECTED_MESSAGE_COUNT) {
concrete_actor->source = source;
thorium_message_unpack_int(message, 0, &concrete_actor->expected);
thorium_actor_log(self, "distribution %d expects %d messages\n",
thorium_actor_name(self),
concrete_actor->expected);
thorium_actor_send_reply_empty(self, ACTION_SET_EXPECTED_MESSAGE_COUNT_REPLY);
}
}
void biosal_coverage_distribution_write_distribution(struct thorium_actor *self)
{
struct core_map_iterator iterator;
int *coverage;
uint64_t *canonical_frequency;
uint64_t frequency;
struct biosal_coverage_distribution *concrete_actor;
struct core_vector coverage_values;
struct core_vector_iterator vector_iterator;
struct core_buffered_file_writer descriptor;
struct core_buffered_file_writer descriptor_canonical;
struct core_string file_name;
struct core_string canonical_file_name;
int argc;
char **argv;
int name;
char *directory_name;
name = thorium_actor_name(self);
argc = thorium_actor_argc(self);
argv = thorium_actor_argv(self);
directory_name = biosal_command_get_output_directory(argc, argv);
/* Create the directory if it does not exist
*/
if (!core_directory_verify_existence(directory_name)) {
core_directory_create(directory_name);
}
core_string_init(&file_name, "");
core_string_append(&file_name, directory_name);
core_string_append(&file_name, "/");
core_string_append(&file_name, BIOSAL_COVERAGE_DISTRIBUTION_DEFAULT_OUTPUT_FILE);
core_string_init(&canonical_file_name, "");
core_string_append(&canonical_file_name, directory_name);
core_string_append(&canonical_file_name, "/");
core_string_append(&canonical_file_name, BIOSAL_COVERAGE_DISTRIBUTION_DEFAULT_OUTPUT_FILE_CANONICAL);
core_buffered_file_writer_init(&descriptor, core_string_get(&file_name));
core_buffered_file_writer_init(&descriptor_canonical, core_string_get(&canonical_file_name));
concrete_actor = (struct biosal_coverage_distribution *)thorium_actor_concrete_actor(self);
core_vector_init(&coverage_values, sizeof(int));
core_map_iterator_init(&iterator, &concrete_actor->distribution);
#ifdef BIOSAL_COVERAGE_DISTRIBUTION_DEBUG
thorium_actor_log(self, "map size %d\n", (int)core_map_size(&concrete_actor->distribution));
#endif
while (core_map_iterator_has_next(&iterator)) {
core_map_iterator_next(&iterator, (void **)&coverage, (void **)&canonical_frequency);
#ifdef BIOSAL_COVERAGE_DISTRIBUTION_DEBUG
thorium_actor_log(self, "DEBUG COVERAGE %d FREQUENCY %" PRIu64 "\n", *coverage, *frequency);
#endif
core_vector_push_back(&coverage_values, coverage);
}
core_map_iterator_destroy(&iterator);
core_vector_sort_int(&coverage_values);
#ifdef BIOSAL_COVERAGE_DISTRIBUTION_DEBUG
thorium_actor_log(self, "after sort ");
core_vector_print_int(&coverage_values);
thorium_actor_log(self, "\n");
#endif
core_vector_iterator_init(&vector_iterator, &coverage_values);
#if 0
core_buffered_file_writer_printf(&descriptor_canonical, "Coverage\tFrequency\n");
#endif
core_buffered_file_writer_printf(&descriptor, "Coverage\tFrequency\n");
#ifdef BIOSAL_COVERAGE_DISTRIBUTION_DEBUG
#endif
while (core_vector_iterator_has_next(&vector_iterator)) {
core_vector_iterator_next(&vector_iterator, (void **)&coverage);
canonical_frequency = (uint64_t *)core_map_get(&concrete_actor->distribution, coverage);
frequency = 2 * *canonical_frequency;
core_buffered_file_writer_printf(&descriptor_canonical, "%d %" PRIu64 "\n",
*coverage,
*canonical_frequency);
core_buffered_file_writer_printf(&descriptor, "%d\t%" PRIu64 "\n",
*coverage,
frequency);
}
core_vector_destroy(&coverage_values);
core_vector_iterator_destroy(&vector_iterator);
thorium_actor_log(self, "distribution %d wrote %s\n", name, core_string_get(&file_name));
thorium_actor_log(self, "distribution %d wrote %s\n", name, core_string_get(&canonical_file_name));
core_buffered_file_writer_destroy(&descriptor);
core_buffered_file_writer_destroy(&descriptor_canonical);
core_string_destroy(&file_name);
core_string_destroy(&canonical_file_name);
}
void thorium_worker_print_actors(struct thorium_worker *worker, struct thorium_balancer *scheduler)
{
struct core_map_iterator iterator;
int name;
int count;
struct thorium_actor *actor;
int producers;
int consumers;
int received;
int difference;
int script;
struct core_map distribution;
int frequency;
struct thorium_script *script_object;
int dead;
int node_name;
int worker_name;
int previous_amount;
node_name = thorium_node_name(worker->node);
worker_name = worker->name;
core_map_iterator_init(&iterator, &worker->actors);
printf("node/%d worker/%d %d queued messages, received: %d busy: %d load: %f ring: %d scheduled actors: %d/%d\n",
node_name, worker_name,
thorium_worker_get_scheduled_message_count(worker),
thorium_worker_get_sum_of_received_actor_messages(worker),
thorium_worker_is_busy(worker),
thorium_worker_get_scheduling_epoch_load(worker),
core_fast_ring_size_from_producer(&worker->actors_to_schedule),
thorium_scheduler_size(&worker->scheduler),
(int)core_map_size(&worker->actors));
core_map_init(&distribution, sizeof(int), sizeof(int));
while (core_map_iterator_get_next_key_and_value(&iterator, &name, NULL)) {
actor = thorium_node_get_actor_from_name(worker->node, name);
if (actor == NULL) {
continue;
}
dead = thorium_actor_dead(actor);
if (dead) {
continue;
}
count = thorium_actor_get_mailbox_size(actor);
received = thorium_actor_get_sum_of_received_messages(actor);
producers = core_map_size(thorium_actor_get_received_messages(actor));
consumers = core_map_size(thorium_actor_get_sent_messages(actor));
previous_amount = 0;
core_map_get_value(&worker->actor_received_messages, &name,
&previous_amount);
difference = received - previous_amount;;
if (!core_map_update_value(&worker->actor_received_messages, &name,
&received)) {
core_map_add_value(&worker->actor_received_messages, &name, &received);
}
printf(" [%s/%d] mailbox: %d received: %d (+%d) producers: %d consumers: %d\n",
thorium_actor_script_name(actor),
name, count, received,
difference,
producers, consumers);
script = thorium_actor_script(actor);
if (core_map_get_value(&distribution, &script, &frequency)) {
++frequency;
core_map_update_value(&distribution, &script, &frequency);
} else {
frequency = 1;
core_map_add_value(&distribution, &script, &frequency);
}
}
/*printf("\n");*/
core_map_iterator_destroy(&iterator);
core_map_iterator_init(&iterator, &distribution);
printf("node/%d worker/%d Frequency list\n", node_name, worker_name);
while (core_map_iterator_get_next_key_and_value(&iterator, &script, &frequency)) {
script_object = thorium_node_find_script(worker->node, script);
CORE_DEBUGGER_ASSERT(script_object != NULL);
printf("node/%d worker/%d Frequency %s => %d\n",
node_name,
worker->name,
thorium_script_name(script_object),
frequency);
}
core_map_iterator_destroy(&iterator);
core_map_destroy(&distribution);
}
