void biosal_assembly_arc_classifier_receive(struct thorium_actor *self, struct thorium_message *message)
{
int tag;
void *buffer;
struct biosal_assembly_arc_classifier *concrete_self;
int size;
int i;
int *bucket;
int source;
int source_index;
if (thorium_actor_take_action(self, message)) {
return;
}
concrete_self = (struct biosal_assembly_arc_classifier *)thorium_actor_concrete_actor(self);
tag = thorium_message_action(message);
buffer = thorium_message_buffer(message);
source = thorium_message_source(message);
if (tag == ACTION_SET_CONSUMERS) {
core_vector_unpack(&concrete_self->consumers, buffer);
size = core_vector_size(&concrete_self->consumers);
core_vector_resize(&concrete_self->pending_requests, size);
for (i = 0; i < size; i++) {
core_vector_set_int(&concrete_self->pending_requests, i, 0);
}
thorium_actor_send_reply_empty(self, ACTION_SET_CONSUMERS_REPLY);
} else if (tag == ACTION_ASSEMBLY_PUSH_ARC_BLOCK_REPLY){
/*
* Decrease counter now.
*/
source_index = core_vector_index_of(&concrete_self->consumers, &source);
bucket = core_vector_at(&concrete_self->pending_requests, source_index);
--(*bucket);
--concrete_self->active_requests;
/*
* The previous value was maximum_pending_request_count + 1
*/
if (*bucket == concrete_self->maximum_pending_request_count) {
--concrete_self->consumer_count_above_threshold;
}
biosal_assembly_arc_classifier_verify_counters(self);
}
}
void biosal_input_controller_receive(struct thorium_actor *actor, struct thorium_message *message)
{
int tag;
int count;
char *file;
void *buffer;
struct biosal_input_controller *controller;
struct biosal_input_controller *concrete_actor;
int destination;
int script;
int stream;
char *local_file;
int i;
int name;
int source;
int destination_index;
struct thorium_message new_message;
int error;
int stream_index;
int64_t entries;
int64_t *bucket;
int *int_bucket;
int spawner;
int command_name;
int stream_name;
int consumer;
int consumer_index;
int *bucket_for_requests;
char *new_buffer;
int new_count;
int file_index;
struct core_vector mega_blocks;
struct core_vector_iterator vector_iterator;
struct biosal_mega_block *mega_block;
struct core_vector *vector_bucket;
struct core_vector block_counts;
uint64_t block_entries;
int mega_block_index;
uint64_t offset;
struct biosal_mega_block *block;
int acquaintance_index;
if (thorium_actor_take_action(actor, message)) {
return;
}
thorium_message_get_all(message, &tag, &count, &buffer, &source);
name = thorium_actor_name(actor);
controller = (struct biosal_input_controller *)thorium_actor_concrete_actor(actor);
concrete_actor = controller;
if (tag == ACTION_START) {
core_vector_init(&concrete_actor->spawners, 0);
core_vector_unpack(&concrete_actor->spawners, buffer);
core_vector_resize(&concrete_actor->stores_per_spawner,
core_vector_size(&concrete_actor->spawners));
for (i = 0; i < core_vector_size(&concrete_actor->spawners); i++) {
int_bucket = (int *)core_vector_at(&concrete_actor->stores_per_spawner, i);
*int_bucket = 0;
spawner = core_vector_at_as_int(&concrete_actor->spawners, i);
core_queue_enqueue(&concrete_actor->unprepared_spawners, &spawner);
}
concrete_actor->state = BIOSAL_INPUT_CONTROLLER_STATE_PREPARE_SPAWNERS;
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_LEVEL
printf("DEBUG preparing first spawner\n");
#endif
thorium_actor_send_to_self_empty(actor, ACTION_INPUT_CONTROLLER_PREPARE_SPAWNERS);
/*
thorium_dispatcher_print(thorium_actor_dispatcher(actor));
*/
} else if (tag == ACTION_ADD_FILE) {
file = (char *)buffer;
local_file = core_memory_allocate(strlen(file) + 1, MEMORY_CONTROLLER);
strcpy(local_file, file);
printf("controller %d ACTION_ADD_FILE %s\n",
thorium_actor_name(actor),
local_file);
core_vector_push_back(&concrete_actor->files, &local_file);
bucket = core_vector_at(&concrete_actor->files, core_vector_size(&concrete_actor->files) - 1);
local_file = *(char **)bucket;
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_LEVEL_2
printf("DEBUG11 ACTION_ADD_FILE %s %p bucket %p index %d\n",
local_file, local_file, (void *)bucket, core_vector_size(&concrete_actor->files) - 1);
#endif
thorium_actor_send_reply_empty(actor, ACTION_ADD_FILE_REPLY);
} else if (tag == ACTION_SPAWN_REPLY) {
if (concrete_actor->state == BIOSAL_INPUT_CONTROLLER_STATE_SPAWN_STORES) {
biosal_input_controller_add_store(actor, message);
return;
} else if (concrete_actor->state == BIOSAL_INPUT_CONTROLLER_STATE_PREPARE_SPAWNERS) {
concrete_actor->ready_spawners++;
thorium_message_unpack_int(message, 0, &name);
thorium_actor_send_empty(actor, name, ACTION_ASK_TO_STOP);
thorium_actor_send_to_self_empty(actor, ACTION_INPUT_CONTROLLER_PREPARE_SPAWNERS);
if (concrete_actor->ready_spawners == (int)core_vector_size(&concrete_actor->spawners)) {
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG
printf("DEBUG all spawners are prepared\n");
#endif
thorium_actor_send_to_supervisor_empty(actor, ACTION_START_REPLY);
}
return;
} else if (concrete_actor->state == BIOSAL_INPUT_CONTROLLER_STATE_SPAWN_PARTITIONER) {
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG
printf("DEBUG received spawn reply, state is spawn_partitioner\n");
#endif
thorium_message_unpack_int(message, 0, &concrete_actor->partitioner);
/* configure the partitioner
*/
destination = concrete_actor->partitioner;
thorium_actor_send_int(actor, destination,
ACTION_SEQUENCE_PARTITIONER_SET_BLOCK_SIZE,
concrete_actor->block_size);
thorium_actor_send_int(actor, destination,
ACTION_SEQUENCE_PARTITIONER_SET_ACTOR_COUNT,
core_vector_size(&concrete_actor->consumers));
core_vector_init(&block_counts, sizeof(uint64_t));
for (i = 0; i < core_vector_size(&concrete_actor->mega_block_vector); i++) {
block = (struct biosal_mega_block *)core_vector_at(&concrete_actor->mega_block_vector, i);
block_entries = biosal_mega_block_get_entries(block);
core_vector_push_back_uint64_t(&block_counts, block_entries);
}
new_count = core_vector_pack_size(&block_counts);
new_buffer = thorium_actor_allocate(actor, new_count);
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG
printf("DEBUG packed counts, %d bytes\n", count);
#endif
core_vector_pack(&block_counts, new_buffer);
thorium_message_init(&new_message, ACTION_SEQUENCE_PARTITIONER_SET_ENTRY_VECTOR,
new_count, new_buffer);
thorium_actor_send(actor, destination, &new_message);
core_vector_destroy(&block_counts);
return;
} else if (concrete_actor->state == BIOSAL_INPUT_CONTROLLER_STATE_SPAWN_READING_STREAMS) {
thorium_message_unpack_int(message, 0, &stream);
stream_index = stream;
mega_block_index = core_vector_size(&concrete_actor->reading_streams);
core_vector_push_back_int(&concrete_actor->reading_streams, stream_index);
core_vector_push_back_int(&concrete_actor->partition_commands, -1);
core_vector_push_back_int(&concrete_actor->stream_consumers, -1);
stream_index = core_vector_size(&concrete_actor->reading_streams) - 1;
mega_block = (struct biosal_mega_block *)core_vector_at(&concrete_actor->mega_block_vector,
mega_block_index);
offset = biosal_mega_block_get_offset(mega_block);
core_map_add_value(&concrete_actor->assigned_blocks,
&stream_index, &mega_block_index);
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_READING_STREAMS
printf("DEBUG setting offset to %" PRIu64 " for stream/%d\n",
offset, stream);
#endif
thorium_actor_send_uint64_t(actor, stream, ACTION_INPUT_STREAM_SET_START_OFFSET, offset);
return;
}
stream = *(int *)buffer;
file_index = core_vector_size(&concrete_actor->counting_streams);
local_file = *(char **)core_vector_at(&concrete_actor->files, file_index);
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_READING_STREAMS
printf("DEBUG actor %d receives stream %d from spawner %d for file %s\n",
name, stream, source,
local_file);
#endif
core_vector_push_back(&concrete_actor->counting_streams, &stream);
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_READING_STREAMS
printf("asking stream/%d to open %s\n", stream, local_file);
#endif
thorium_message_init(&new_message, ACTION_INPUT_OPEN, strlen(local_file) + 1, local_file);
#ifdef DEBUG_ISSUE_594
thorium_message_print(&new_message);
printf("SEND Buffer %s\n", local_file);
#endif
thorium_actor_send(actor, stream, &new_message);
thorium_message_destroy(&new_message);
if (core_vector_size(&concrete_actor->counting_streams) != core_vector_size(&concrete_actor->files)) {
thorium_actor_send_to_self_empty(actor, ACTION_INPUT_SPAWN);
}
#ifdef DEBUG_ISSUE_594
printf("EXIT Buffer %s\n", local_file);
#endif
} else if (tag == ACTION_INPUT_OPEN_REPLY) {
if (concrete_actor->state == BIOSAL_INPUT_CONTROLLER_STATE_SPAWN_READING_STREAMS) {
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_READING_STREAMS
printf("DEBUG receives open.reply for reading stream/%d\n", source);
#endif
concrete_actor->opened_streams++;
if (concrete_actor->opened_streams == core_vector_size(&concrete_actor->mega_block_vector)) {
thorium_actor_send_to_self_empty(actor, ACTION_INPUT_CONTROLLER_CREATE_STORES);
}
return;
}
concrete_actor->opened_streams++;
stream = source;
thorium_message_unpack_int(message, 0, &error);
if (error == BIOSAL_INPUT_ERROR_NO_ERROR) {
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_LEVEL_2
printf("DEBUG actor %d asks %d ACTION_INPUT_COUNT_IN_PARALLEL\n", name, stream);
#endif
thorium_actor_send_vector(actor, stream, ACTION_INPUT_COUNT_IN_PARALLEL,
&concrete_actor->spawners);
} else {
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_LEVEL_2
printf("DEBUG actor %d received error %d from %d\n", name, error, stream);
#endif
concrete_actor->counted++;
}
/* if all streams failed, notice supervisor */
if (concrete_actor->counted == core_vector_size(&concrete_actor->files)) {
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_LEVEL_2
#endif
printf("DEBUG %d: Error all streams failed.\n",
thorium_actor_name(actor));
thorium_actor_send_to_supervisor_empty(actor, ACTION_INPUT_DISTRIBUTE_REPLY);
}
/*
if (concrete_actor->opened_streams == core_vector_size(&concrete_actor->files)) {
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG
printf("DEBUG controller %d sends ACTION_INPUT_DISTRIBUTE_REPLY to supervisor %d [%d/%d]\n",
name, thorium_actor_supervisor(actor),
concrete_actor->opened_streams, core_vector_size(&concrete_actor->files));
#endif
}
*/
} else if (tag == ACTION_INPUT_COUNT_PROGRESS) {
stream_index = core_vector_index_of(&concrete_actor->counting_streams, &source);
local_file = core_vector_at_as_char_pointer(&concrete_actor->files, stream_index);
thorium_message_unpack_int64_t(message, 0, &entries);
bucket = (int64_t *)core_vector_at(&concrete_actor->counts, stream_index);
printf("controller/%d receives progress from stream/%d file %s %" PRIu64 " entries so far\n",
name, source, local_file, entries);
*bucket = entries;
} else if (tag == ACTION_INPUT_COUNT_IN_PARALLEL_REPLY) {
stream_index = core_vector_index_of(&concrete_actor->counting_streams, &source);
local_file = core_vector_at_as_char_pointer(&concrete_actor->files, stream_index);
core_vector_init(&mega_blocks, 0);
core_vector_unpack(&mega_blocks, buffer);
printf("DEBUG receive mega blocks from %d\n", source);
/*
* Update the file index for every mega block.
*/
core_vector_iterator_init(&vector_iterator, &mega_blocks);
bucket = (int64_t*)core_vector_at(&concrete_actor->counts, stream_index);
(*bucket) = 0;
while (core_vector_iterator_has_next(&vector_iterator)) {
core_vector_iterator_next(&vector_iterator, (void **)&mega_block);
printf("SETTING setting file to %d for mega block\n", stream_index);
biosal_mega_block_set_file(mega_block, stream_index);
entries = biosal_mega_block_get_entries_from_start(mega_block);
printf("Cataloging %d ENTRIES\n", (int)entries);
(*bucket) = entries;
biosal_mega_block_print(mega_block);
}
core_vector_iterator_destroy(&vector_iterator);
vector_bucket = (struct core_vector *)core_map_add(&concrete_actor->mega_blocks, &stream_index);
core_vector_init_copy(vector_bucket, &mega_blocks);
core_vector_destroy(&mega_blocks);
concrete_actor->counted++;
printf("controller/%d received from stream/%d for file %s %" PRIu64 " entries (final) %d/%d\n",
name, source, local_file, entries,
concrete_actor->counted, (int)core_vector_size(&concrete_actor->files));
thorium_actor_send_reply_empty(actor, ACTION_INPUT_CLOSE);
/* continue work here, tell supervisor about it */
if (concrete_actor->counted == core_vector_size(&concrete_actor->files)) {
thorium_actor_send_to_self_empty(actor, ACTION_INPUT_CONTROLLER_SPAWN_READING_STREAMS);
}
} else if (tag == ACTION_INPUT_DISTRIBUTE) {
core_timer_start(&concrete_actor->input_timer);
core_timer_start(&concrete_actor->counting_timer);
/* for each file, spawn a stream to count */
/* no files, return immediately
*/
if (core_vector_size(&concrete_actor->files) == 0) {
printf("Error: no file to distribute...\n");
thorium_actor_send_reply_empty(actor, ACTION_INPUT_DISTRIBUTE_REPLY);
return;
}
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_LEVEL_2
printf("DEBUG actor %d receives ACTION_INPUT_DISTRIBUTE\n", name);
#endif
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_LEVEL_2
printf("DEBUG send ACTION_INPUT_SPAWN to self\n");
#endif
thorium_actor_send_to_self_empty(actor, ACTION_INPUT_SPAWN);
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_LEVEL_2
printf("DEBUG resizing counts to %d\n", core_vector_size(&concrete_actor->files));
#endif
core_vector_resize(&concrete_actor->counts, core_vector_size(&concrete_actor->files));
for (i = 0; i < core_vector_size(&concrete_actor->counts); i++) {
bucket = (int64_t*)core_vector_at(&concrete_actor->counts, i);
*bucket = 0;
}
} else if (tag == ACTION_INPUT_SPAWN && source == name) {
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_LEVEL_2
printf("DEBUG ACTION_INPUT_SPAWN\n");
#endif
script = SCRIPT_INPUT_STREAM;
concrete_actor->state = BIOSAL_INPUT_CONTROLLER_STATE_SPAWN_STREAMS;
/* the next file name to send is the current number of streams */
i = core_vector_size(&concrete_actor->counting_streams);
destination_index = i % core_vector_size(&concrete_actor->spawners);
destination = *(int *)core_vector_at(&concrete_actor->spawners, destination_index);
thorium_message_init(message, ACTION_SPAWN, sizeof(script), &script);
thorium_actor_send(actor, destination, message);
bucket = core_vector_at(&concrete_actor->files, i);
local_file = *(char **)core_vector_at(&concrete_actor->files, i);
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_LEVEL_2
printf("DEBUG890 local_file %p bucket %p index %d\n", local_file, (void *)bucket,
i);
#endif
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG
printf("DEBUG actor %d spawns a stream for file %d/%d via spawner %d\n",
name, i, core_vector_size(&concrete_actor->files), destination);
#endif
/* also, spawn 4 stores on each node */
} else if (tag == ACTION_ASK_TO_STOP && ( source == thorium_actor_supervisor(actor)
|| source == thorium_actor_name(actor))) {
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_LEVEL_2
#endif
/* stop streams
*/
for (i = 0; i < core_vector_size(&concrete_actor->counting_streams); i++) {
stream = *(int *)core_vector_at(&concrete_actor->counting_streams, i);
thorium_actor_send_empty(actor, stream, ACTION_ASK_TO_STOP);
}
for (i = 0; i < core_vector_size(&concrete_actor->reading_streams); i++) {
stream = *(int *)core_vector_at(&concrete_actor->reading_streams, i);
thorium_actor_send_empty(actor, stream, ACTION_ASK_TO_STOP);
}
#if 0
/* stop data stores
*/
for (i = 0; i < core_vector_size(&concrete_actor->consumers); i++) {
store = core_vector_at_as_int(&concrete_actor->consumers, i);
thorium_actor_send_empty(actor, store, ACTION_ASK_TO_STOP);
}
#endif
/* stop partitioner
*/
if (concrete_actor->partitioner != THORIUM_ACTOR_NOBODY) {
thorium_actor_send_empty(actor,
concrete_actor->partitioner,
ACTION_ASK_TO_STOP);
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG
printf("DEBUG controller %d sends ACTION_ASK_TO_STOP_REPLY to %d\n",
thorium_actor_name(actor),
thorium_message_source(message));
#endif
}
thorium_actor_send_reply_empty(actor, ACTION_ASK_TO_STOP_REPLY);
/* stop self
*/
thorium_actor_send_to_self_empty(actor, ACTION_STOP);
thorium_actor_ask_to_stop(actor, message);
printf("DEBUG controller %d dies\n", name);
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG
#endif
} else if (tag == ACTION_INPUT_CONTROLLER_CREATE_PARTITION && source == name) {
spawner = *(int *)core_vector_at(&concrete_actor->spawners,
core_vector_size(&concrete_actor->spawners) / 2);
thorium_actor_send_int(actor, spawner, ACTION_SPAWN,
SCRIPT_SEQUENCE_PARTITIONER);
concrete_actor->state = BIOSAL_INPUT_CONTROLLER_STATE_SPAWN_PARTITIONER;
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG
printf("DEBUG input controller %d spawns a partitioner via spawner %d\n",
name, spawner);
#endif
} else if (tag == ACTION_SEQUENCE_PARTITIONER_COMMAND_IS_READY) {
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG
printf("DEBUG controller receives ACTION_SEQUENCE_PARTITIONER_COMMAND_IS_READY, asks for command\n");
#endif
thorium_actor_send_reply_empty(actor, ACTION_SEQUENCE_PARTITIONER_GET_COMMAND);
} else if (tag == ACTION_SEQUENCE_PARTITIONER_GET_COMMAND_REPLY) {
biosal_input_controller_receive_command(actor, message);
} else if (tag == ACTION_SEQUENCE_PARTITIONER_FINISHED) {
thorium_actor_send_empty(actor,
concrete_actor->partitioner,
ACTION_ASK_TO_STOP);
biosal_input_controller_verify_requests(actor, message);
} else if (tag == ACTION_SEQUENCE_PARTITIONER_PROVIDE_STORE_ENTRY_COUNTS) {
biosal_input_controller_receive_store_entry_counts(actor, message);
} else if (tag == ACTION_RESERVE_REPLY) {
concrete_actor->ready_consumers++;
printf("DEBUG marker ACTION_RESERVE_REPLY %d/%d\n",
concrete_actor->ready_consumers,
(int)core_vector_size(&concrete_actor->consumers));
if (concrete_actor->ready_consumers == core_vector_size(&concrete_actor->consumers)) {
concrete_actor->ready_consumers = 0;
printf("DEBUG all consumers are ready\n");
thorium_actor_send_empty(actor,
concrete_actor->partitioner,
ACTION_SEQUENCE_PARTITIONER_PROVIDE_STORE_ENTRY_COUNTS_REPLY);
}
} else if (tag == ACTION_INPUT_PUSH_SEQUENCES_READY) {
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG
printf("DEBUG biosal_input_controller_receive received ACTION_INPUT_PUSH_SEQUENCES_READY\n");
#endif
stream_name = source;
acquaintance_index = stream_name;
stream_index = core_vector_index_of(&concrete_actor->reading_streams, &acquaintance_index);
command_name = *(int *)core_vector_at(&concrete_actor->partition_commands,
stream_index);
thorium_actor_send_int(actor,
concrete_actor->partitioner,
ACTION_SEQUENCE_PARTITIONER_GET_COMMAND_REPLY_REPLY,
command_name);
} else if (tag == ACTION_INPUT_PUSH_SEQUENCES_REPLY) {
stream_name = source;
thorium_message_unpack_int(message, 0, &consumer);
consumer_index = core_vector_index_of(&concrete_actor->consumers,
&consumer);
bucket_for_requests = (int *)core_vector_at(&concrete_actor->consumer_active_requests, consumer_index);
(*bucket_for_requests)--;
biosal_input_controller_verify_requests(actor, message);
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_CONSUMERS
printf("DEBUG consumer # %d has %d active requests\n",
consumer_index, *bucket_for_requests);
#endif
} else if (tag == ACTION_SET_CONSUMERS) {
core_vector_init(&concrete_actor->consumers, 0);
core_vector_unpack(&concrete_actor->consumers, buffer);
printf("controller %d receives %d consumers\n",
thorium_actor_name(actor),
(int)core_vector_size(&concrete_actor->consumers));
for (i = 0; i < core_vector_size(&concrete_actor->consumers); i++) {
core_vector_push_back_int(&concrete_actor->consumer_active_requests, 0);
}
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG
core_vector_print_int(&concrete_actor->consumers);
printf("\n");
#endif
thorium_actor_send_reply_empty(actor, ACTION_SET_CONSUMERS_REPLY);
} else if (tag == ACTION_SET_BLOCK_SIZE) {
thorium_message_unpack_int(message, 0, &concrete_actor->block_size);
thorium_actor_send_reply_empty(actor, ACTION_SET_BLOCK_SIZE_REPLY);
} else if (tag == ACTION_SEQUENCE_STORE_READY) {
concrete_actor->filled_consumers++;
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG
printf("DEBUG ACTION_SEQUENCE_STORE_READY %d/%d\n", concrete_actor->filled_consumers,
(int)core_vector_size(&concrete_actor->consumers));
#endif
if (concrete_actor->filled_consumers == core_vector_size(&concrete_actor->consumers)) {
concrete_actor->filled_consumers = 0;
printf("DEBUG: all consumers are filled, sending ACTION_INPUT_DISTRIBUTE_REPLY\n");
core_timer_stop(&concrete_actor->input_timer);
core_timer_stop(&concrete_actor->distribution_timer);
core_timer_print_with_description(&concrete_actor->distribution_timer,
"Load input / Distribute input data");
core_timer_print_with_description(&concrete_actor->input_timer,
"Load input");
thorium_actor_send_to_supervisor_empty(actor, ACTION_INPUT_DISTRIBUTE_REPLY);
}
}
}
void spate_receive(struct thorium_actor *self, struct thorium_message *message)
{
thorium_actor_take_action(self, message);
}
void biosal_input_stream_receive(struct thorium_actor *actor, struct thorium_message *message)
{
int tag;
int source;
uint64_t count;
struct biosal_input_stream *concrete_self;
int i;
int has_sequence;
int sequences;
int sequence_index;
int buffer_size;
char *buffer;
char *read_buffer;
struct biosal_mega_block mega_block;
char *file_name_in_buffer;
if (thorium_actor_take_action(actor, message)) {
return;
}
concrete_self = thorium_actor_concrete_actor(actor);
tag = thorium_message_action(message);
source = thorium_message_source(message);
buffer = (char *)thorium_message_buffer(message);
/* Do nothing if there is an error.
* has_error returns the error to the source.
*/
/*
if (biosal_input_stream_has_error(actor, message)) {
return;
}
*/
if (tag == ACTION_INPUT_OPEN) {
#ifdef BIOSAL_INPUT_STREAM_DEBUG
printf("DEBUG ACTION_INPUT_OPEN\n");
#endif
if (concrete_self->open) {
concrete_self->error = BIOSAL_INPUT_ERROR_ALREADY_OPEN;
thorium_actor_send_reply_int(actor, ACTION_INPUT_OPEN_REPLY, concrete_self->error);
thorium_actor_send_to_self_empty(actor, ACTION_ASK_TO_STOP);
return;
}
concrete_self->open = 1;
/* TODO: find out the maximum read length in some way */
concrete_self->maximum_sequence_length = BIOSAL_INPUT_MAXIMUM_SEQUENCE_LENGTH;
concrete_self->buffer_for_sequence = (char *)core_memory_allocate(concrete_self->maximum_sequence_length, MEMORY_INPUT_STREAM);
/*biosal_input_stream_init(actor);*/
#ifdef BIOSAL_INPUT_STREAM_DEBUG
printf("DEBUG biosal_input_stream_receive open %s\n",
buffer);
#endif
/*core_memory_copy(&concrete_self->file_index, buffer, sizeof(concrete_self->file_index));*/
file_name_in_buffer = buffer;
printf("stream/%d (node/%d) opens file %s offset %" PRIu64 "\n", thorium_actor_name(actor),
thorium_actor_node_name(actor), file_name_in_buffer,
concrete_self->starting_offset);
#ifdef DEBUG_ISSUE_594
thorium_message_print(message);
printf("Buffer %s\n", buffer);
#endif
concrete_self->file_name = core_memory_allocate(strlen(file_name_in_buffer) + 1, MEMORY_INPUT_STREAM);
strcpy(concrete_self->file_name, file_name_in_buffer);
biosal_input_proxy_init(&concrete_self->proxy, concrete_self->file_name,
concrete_self->starting_offset, concrete_self->ending_offset);
concrete_self->proxy_ready = 1;
/* Die if there is an error...
*/
if (biosal_input_stream_has_error(actor, message)) {
#ifdef BIOSAL_INPUT_STREAM_DEBUG
printf("DEBUG has error\n");
#endif
thorium_actor_send_reply_int(actor, ACTION_INPUT_OPEN_REPLY, concrete_self->error);
thorium_actor_send_to_self_empty(actor, ACTION_ASK_TO_STOP);
return;
}
concrete_self->controller = source;
/* no error here... */
thorium_actor_send_reply_int(actor, ACTION_INPUT_OPEN_REPLY, concrete_self->error);
} else if (tag == ACTION_INPUT_COUNT) {
/* count a little bit and yield the worker */
if (concrete_self->count_customer == THORIUM_ACTOR_NOBODY) {
concrete_self->count_customer = source;
}
if (biosal_input_stream_check_open_error(actor, message)) {
thorium_actor_send_reply_int64_t(actor, ACTION_INPUT_COUNT_REPLY, concrete_self->error);
thorium_actor_send_to_self_empty(actor, ACTION_ASK_TO_STOP);
return;
}
#ifdef BIOSAL_INPUT_STREAM_DEBUG
printf("DEBUG ACTION_INPUT_COUNT received...\n");
#endif
i = 0;
/* continue counting ... */
has_sequence = 1;
while (i < concrete_self->granularity && has_sequence) {
has_sequence = biosal_input_proxy_get_sequence(&concrete_self->proxy,
concrete_self->buffer_for_sequence);
#if 0
printf("Sequence= %s\n", concrete_self->buffer_for_sequence);
#endif
i++;
}
sequences = biosal_input_proxy_size(&concrete_self->proxy);
#ifdef BIOSAL_INPUT_STREAM_DEBUG
printf("DEBUG ACTION_INPUT_COUNT sequences %d...\n", sequences);
#endif
if (!has_sequence || sequences % concrete_self->mega_block_size == 0) {
biosal_mega_block_init(&mega_block, -1, concrete_self->last_offset,
sequences - concrete_self->last_entries, sequences);
core_vector_push_back(&concrete_self->mega_blocks, &mega_block);
concrete_self->last_entries = sequences;
concrete_self->last_offset = biosal_input_proxy_offset(&concrete_self->proxy);
thorium_actor_send_int64_t(actor, concrete_self->controller, ACTION_INPUT_COUNT_PROGRESS, sequences);
}
if (has_sequence) {
/*printf("DEBUG yield\n");*/
thorium_actor_send_to_self_empty(actor, ACTION_YIELD);
/* notify the controller of our progress...
*/
} else {
thorium_actor_send_to_self_empty(actor, ACTION_INPUT_COUNT_READY);
}
} else if (tag == ACTION_YIELD_REPLY) {
if (biosal_input_stream_check_open_error(actor, message)) {
/*
* it is not clear that there can be an error when receiving YIELD.
error = concrete_self->error;
thorium_actor_send_reply_int(actor, ACTION_INPUT_COUNT_REPLY, error);
thorium_actor_send_to_self(actor, ACTION_ASK_TO_STOP);
*/
return;
}
thorium_actor_send_to_self_empty(actor, ACTION_INPUT_COUNT);
} else if (tag == ACTION_INPUT_COUNT_READY) {
if (biosal_input_stream_check_open_error(actor, message)) {
return;
}
count = biosal_input_proxy_size(&concrete_self->proxy);
thorium_actor_send_vector(actor, concrete_self->count_customer, ACTION_INPUT_COUNT_REPLY,
&concrete_self->mega_blocks);
printf("input_stream/%d on node/%d counted entries in %s, %" PRIu64 "\n",
thorium_actor_name(actor), thorium_actor_node_name(actor),
concrete_self->file_name, count);
} else if (tag == ACTION_INPUT_CLOSE) {
#ifdef BIOSAL_INPUT_STREAM_DEBUG
printf("DEBUG destroy proxy\n");
#endif
concrete_self->error = BIOSAL_INPUT_ERROR_NO_ERROR;
if (biosal_input_stream_check_open_error(actor, message)) {
concrete_self->error = BIOSAL_INPUT_ERROR_FILE_NOT_OPEN;
thorium_message_init(message, ACTION_INPUT_CLOSE_REPLY, sizeof(concrete_self->error),
&concrete_self->error);
thorium_actor_send(actor, source, message);
thorium_actor_send_to_self_empty(actor, ACTION_ASK_TO_STOP);
return;
}
thorium_message_init(message, ACTION_INPUT_CLOSE_REPLY, sizeof(concrete_self->error),
&concrete_self->error);
thorium_actor_send(actor, source, message);
thorium_actor_send_to_self_empty(actor, ACTION_ASK_TO_STOP);
#ifdef BIOSAL_INPUT_STREAM_DEBUG
printf("actor %d sending ACTION_INPUT_CLOSE_REPLY to %d\n",
thorium_actor_name(actor), source);
#endif
} else if (tag == ACTION_INPUT_GET_SEQUENCE) {
if (biosal_input_stream_check_open_error(actor, message)) {
/* the error management could be better. */
concrete_self->error = BIOSAL_INPUT_ERROR_FILE_NOT_OPEN;
thorium_message_init(message, ACTION_INPUT_GET_SEQUENCE_REPLY, sizeof(concrete_self->error),
&concrete_self->error);
thorium_actor_send(actor, source, message);
return;
}
sequence_index = biosal_input_proxy_size(&concrete_self->proxy);
/* TODO it would be clearer to use a struct to pack a int and a char []
* then to use the code below.
*/
read_buffer = concrete_self->buffer_for_sequence + sizeof(sequence_index);
has_sequence = biosal_input_proxy_get_sequence(&concrete_self->proxy,
read_buffer);
if (!has_sequence) {
thorium_message_init(message, ACTION_INPUT_GET_SEQUENCE_END, 0, NULL);
thorium_actor_send(actor, source, message);
return;
}
buffer_size = sizeof(sequence_index) + strlen(read_buffer) + 1;
core_memory_copy(concrete_self->buffer_for_sequence, &sequence_index, sizeof(sequence_index));
thorium_message_init(message, ACTION_INPUT_GET_SEQUENCE_REPLY,
buffer_size, concrete_self->buffer_for_sequence);
thorium_actor_send(actor, source, message);
} else if (tag == ACTION_INPUT_PUSH_SEQUENCES) {
biosal_input_stream_push_sequences(actor, message);
} else if (tag == ACTION_ASK_TO_STOP) {
thorium_actor_send_to_self_empty(actor, ACTION_STOP);
thorium_actor_send_range_empty(actor, &concrete_self->parallel_streams,
ACTION_ASK_TO_STOP);
thorium_actor_send_reply_empty(actor, ACTION_ASK_TO_STOP_REPLY);
} else if (tag == ACTION_INPUT_STREAM_RESET) {
/* fail silently
*/
if (!concrete_self->open) {
thorium_actor_send_reply_empty(actor, ACTION_INPUT_STREAM_RESET_REPLY);
return;
}
#ifdef BIOSAL_INPUT_STREAM_DEBUG
printf("DEBUG ACTION_INPUT_STREAM_RESET\n");
#endif
biosal_input_proxy_destroy(&concrete_self->proxy);
biosal_input_proxy_init(&concrete_self->proxy, concrete_self->file_name,
concrete_self->starting_offset,
concrete_self->ending_offset);
thorium_actor_send_reply_empty(actor, ACTION_INPUT_STREAM_RESET_REPLY);
} else if (tag == ACTION_PUSH_SEQUENCE_DATA_BLOCK_REPLY) {
thorium_actor_send_to_supervisor_int(actor, ACTION_INPUT_PUSH_SEQUENCES_REPLY,
source);
}
}
void biosal_assembly_graph_store_receive(struct thorium_actor *self, struct thorium_message *message)
{
int tag;
/*void *buffer;*/
struct biosal_assembly_graph_store *concrete_self;
double value;
struct biosal_dna_kmer kmer;
/*struct core_memory_pool *ephemeral_memory;*/
int customer;
int big_key_size;
int big_value_size;
if (thorium_actor_take_action(self, message)) {
return;
}
/*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);*/
if (tag == ACTION_SET_KMER_LENGTH) {
thorium_message_unpack_int(message, 0, &concrete_self->kmer_length);
biosal_dna_kmer_init_mock(&kmer, concrete_self->kmer_length,
&concrete_self->storage_codec, thorium_actor_get_ephemeral_memory(self));
concrete_self->key_length_in_bytes = biosal_dna_kmer_pack_size(&kmer,
concrete_self->kmer_length, &concrete_self->storage_codec);
biosal_dna_kmer_destroy(&kmer, thorium_actor_get_ephemeral_memory(self));
big_key_size = concrete_self->key_length_in_bytes;
big_value_size = sizeof(struct biosal_assembly_vertex);
core_map_init(&concrete_self->table, big_key_size,
big_value_size);
core_map_set_memory_pool(&concrete_self->table,
&concrete_self->persistent_memory);
printf("DEBUG big_key_size %d big_value_size %d\n", big_key_size, big_value_size);
/*
* Configure the map for better performance.
*/
core_map_disable_deletion_support(&concrete_self->table);
/*
* The threshold of the map is not very important because
* requests that hit the map have to first arrive as messages,
* which are slow.
*/
core_map_set_threshold(&concrete_self->table, 0.95);
thorium_actor_send_reply_empty(self, ACTION_SET_KMER_LENGTH_REPLY);
} else if (tag == ACTION_ASSEMBLY_GET_KMER_LENGTH) {
thorium_actor_send_reply_int(self, ACTION_ASSEMBLY_GET_KMER_LENGTH_REPLY,
concrete_self->kmer_length);
} else if (tag == ACTION_RESET) {
/*
* Reset the iterator.
*/
core_map_iterator_init(&concrete_self->iterator, &concrete_self->table);
printf("DEBUG unitig_vertex_count %d\n",
concrete_self->unitig_vertex_count);
thorium_actor_send_reply_empty(self, ACTION_RESET_REPLY);
} else if (tag == ACTION_SEQUENCE_STORE_REQUEST_PROGRESS_REPLY) {
thorium_message_unpack_double(message, 0, &value);
core_map_set_current_size_estimate(&concrete_self->table, value);
} else if (tag == ACTION_ASK_TO_STOP) {
printf("%s/%d received %d arc blocks\n",
thorium_actor_script_name(self),
thorium_actor_name(self),
concrete_self->received_arc_block_count);
thorium_actor_ask_to_stop(self, message);
} else if (tag == ACTION_SET_CONSUMER) {
thorium_message_unpack_int(message, 0, &customer);
printf("%s/%d will use coverage distribution %d\n",
thorium_actor_script_name(self),
thorium_actor_name(self), customer);
concrete_self->customer = customer;
thorium_actor_send_reply_empty(self, ACTION_SET_CONSUMER_REPLY);
} else if (tag == ACTION_PUSH_DATA) {
printf("%s/%d receives ACTION_PUSH_DATA\n",
thorium_actor_script_name(self),
thorium_actor_name(self));
biosal_assembly_graph_store_push_data(self, message);
} else if (tag == ACTION_STORE_GET_ENTRY_COUNT) {
thorium_actor_send_reply_uint64_t(self, ACTION_STORE_GET_ENTRY_COUNT_REPLY,
concrete_self->received);
} else if (tag == ACTION_GET_RECEIVED_ARC_COUNT) {
thorium_actor_send_reply_uint64_t(self, ACTION_GET_RECEIVED_ARC_COUNT_REPLY,
concrete_self->received_arc_count);
}
}
void framr_receive(actor_t *actor, message_t *message)
{
thorium_actor_take_action(actor, message);
}
