void process_ping(struct thorium_actor *self, struct thorium_message *message)
{
int count;
char *buffer;
int buffer_size;
uint64_t *bucket;
uint64_t expected_checksum;
uint64_t actual_checksum;
struct process *concrete_self;
concrete_self = (struct process *)thorium_actor_concrete_actor(self);
buffer = thorium_message_buffer(message);
count = thorium_message_count(message);
buffer_size = count - sizeof(expected_checksum);
bucket = (uint64_t *)(buffer + buffer_size);
expected_checksum = *bucket;
actual_checksum = core_hash_data_uint64_t(buffer, buffer_size, SEED);
if (expected_checksum != actual_checksum) {
printf("TRANSPORT FAILED source: %d (%d) destination: %d (%d) tag: ACTION_PING count: %d"
" expected_checksum: %" PRIu64 " actual_checksum: %" PRIu64 "\n",
thorium_message_source(message),
thorium_message_source_node(message),
thorium_message_destination(message),
thorium_message_destination_node(message),
count,
expected_checksum, actual_checksum);
++concrete_self->failed;
} else {
++concrete_self->passed;
}
thorium_actor_send_reply_empty(self, ACTION_PING_REPLY);
}
void thorium_message_get_all(struct thorium_message *message, int *tag, int *count, void **buffer, int *source)
{
*tag = thorium_message_action(message);
*count = thorium_message_count(message);
*buffer = thorium_message_buffer(message);
*source = thorium_message_source(message);
}
void thorium_actor_send_then(struct thorium_actor *self, int destination,
struct thorium_message *message, thorium_actor_receive_fn_t handler)
{
CORE_DEBUGGER_ASSERT(destination != THORIUM_ACTOR_NOBODY);
CORE_DEBUGGER_ASSERT(NAME() != THORIUM_ACTOR_NOBODY);
thorium_actor_send(self, destination, message);
int parent_actor = thorium_message_source(message);
int parent_message = thorium_message_get_identifier(message);
/*
*/
LOG("XXX ASK... registering message %d:%d", parent_actor, parent_message);
/*
* Register the information so that the callback is invoked
* when the response arrives.
*
* the key is parent_actor + parent_message and the value is handler.
*/
thorium_actor_add_action_with_parent(self, parent_actor, parent_message,
handler);
/*
printf("NOT_IMPLEMENTED src %d dst %d msgid %d:%d" "\n",
thorium_actor_name(self),
destination,
parent_actor,
parent_message);
*/
}
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 thorium_message_init_copy(struct thorium_message *self, struct thorium_message *old_message)
{
thorium_message_init(self,
thorium_message_action(old_message),
thorium_message_count(old_message),
thorium_message_buffer(old_message));
thorium_message_set_source(self,
thorium_message_source(old_message));
thorium_message_set_destination(self,
thorium_message_destination(old_message));
}
void buddy_receive(struct thorium_actor *actor, struct thorium_message *message)
{
int tag;
int source;
int name;
name = thorium_actor_name(actor);
source = thorium_message_source(message);
tag = thorium_message_action(message);
if (tag == ACTION_BUDDY_BOOT) {
printf("ACTION_BUDDY_BOOT\n");
thorium_actor_print(actor);
thorium_message_init(message, ACTION_BUDDY_BOOT_REPLY, 0, NULL);
thorium_actor_send(actor, source, message);
} else if (tag == ACTION_BUDDY_HELLO) {
printf("ACTION_BUDDY_HELLO\n");
/* pin the actor to the worker for no reason !
*/
/*
thorium_actor_send_to_self_empty(actor, ACTION_PIN_TO_WORKER);
*/
thorium_message_init(message, ACTION_BUDDY_HELLO_REPLY, 0, NULL);
thorium_actor_send(actor, source, message);
} else if (tag == ACTION_ASK_TO_STOP) {
printf("BUDDY_DIE\n");
printf("buddy_receive Actor %i received a message (%i BUDDY_DIE) from actor %i\n",
name, tag, source);
/*
thorium_actor_send_to_self_empty(actor, ACTION_UNPIN_FROM_WORKER);
*/
thorium_message_init(message, ACTION_STOP, 0, NULL);
thorium_actor_send(actor, name, message);
}
}
void biosal_assembly_graph_store_get_summary(struct thorium_actor *self, struct thorium_message *message)
{
struct biosal_assembly_graph_store *concrete_self;
int source;
source = thorium_message_source(message);
concrete_self = thorium_actor_concrete_actor(self);
concrete_self->summary_in_progress = 1;
concrete_self->source_for_summary = source;
thorium_actor_add_action_with_condition(self, ACTION_YIELD_REPLY,
biosal_assembly_graph_store_yield_reply_summary,
&concrete_self->summary_in_progress, 1);
core_map_iterator_init(&concrete_self->iterator, &concrete_self->table);
thorium_actor_send_to_self_empty(self, ACTION_YIELD);
}
void spate_ask_to_stop(struct thorium_actor *self, struct thorium_message *message)
{
int source;
struct spate *concrete_self;
concrete_self = (struct spate *)thorium_actor_concrete_actor(self);
source = thorium_message_source(message);
if (!spate_must_print_help(self)) {
thorium_actor_log(self, "spate %d stops", thorium_actor_name(self));
}
#if 0
thorium_actor_ask_to_stop(self, message);
#endif
/*
* Check if the source is an initial actor because each initial actor
* is its own supervisor.
*/
if (core_vector_index_of(&concrete_self->initial_actors, &source) >= 0) {
thorium_actor_send_to_self_empty(self, ACTION_STOP);
}
if (concrete_self->is_leader) {
if (concrete_self->assembly_graph_builder != THORIUM_ACTOR_NOBODY)
thorium_actor_send_empty(self, concrete_self->assembly_graph_builder,
ACTION_ASK_TO_STOP);
if (concrete_self->assembly_graph_builder != THORIUM_ACTOR_NOBODY)
thorium_actor_send_empty(self, concrete_self->manager_for_sequence_stores,
ACTION_ASK_TO_STOP);
if (!spate_must_print_help(self)) {
core_timer_stop(&concrete_self->timer);
core_timer_print_with_description(&concrete_self->timer, "Total");
}
}
}
void biosal_input_controller_set_offset_reply(struct thorium_actor *self, struct thorium_message *message)
{
int stream_index;
int acquaintance_index;
int source;
int block_index;
struct biosal_mega_block *block;
struct biosal_input_controller *concrete_actor;
int file_index;
char *file_name;
struct thorium_message new_message;
source = thorium_message_source(message);
acquaintance_index = source;
concrete_actor = (struct biosal_input_controller *)thorium_actor_concrete_actor(self);
stream_index = core_vector_index_of(&concrete_actor->reading_streams, &acquaintance_index);
block_index = core_map_get_int(&concrete_actor->assigned_blocks, &stream_index);
#ifdef BIOSAL_INPUT_CONTROLLER_DEBUG_READING_STREAMS
printf("DEBUG got reply from stream/%d for offset, stream_index %d block_index %d\n", source,
stream_index, block_index);
#endif
block = (struct biosal_mega_block *)core_vector_at(&concrete_actor->mega_block_vector,
block_index);
file_index = biosal_mega_block_get_file(block);
file_name = *(char **)core_vector_at(&concrete_actor->files, file_index);
printf("DEBUG send ACTION_INPUT_OPEN %s\n", file_name);
thorium_message_init(&new_message, ACTION_INPUT_OPEN, strlen(file_name) + 1, file_name);
thorium_actor_send_reply(self, &new_message);
thorium_message_destroy(&new_message);
}
void framr_hello_reply(actor_t *actor, message_t *message)
{
message_t new_message;
int name;
int source;
int boss;
framr_t *self;
struct core_vector *spawners;
self = thorium_actor_concrete_actor(actor);
name = thorium_actor_name(actor);
source = thorium_message_source(message);
spawners = &self->spawners;
pm("Actor %d is satisfied with a reply from the neighbor %d.\n", name, source);
boss = core_vector_at_as_int(spawners, 0);
thorium_message_init(&new_message, ACTION_NOTIFY, 0, NULL);
thorium_actor_send(actor, boss, &new_message);
thorium_message_destroy(&new_message);
}
void biosal_input_controller_add_store(struct thorium_actor *actor, struct thorium_message *message)
{
int source;
int store;
int index;
struct biosal_input_controller *concrete_actor;
int *bucket;
/*
printf("DEBUG biosal_input_controller_add_store\n");
*/
concrete_actor = (struct biosal_input_controller *)thorium_actor_concrete_actor(actor);
source = thorium_message_source(message);
thorium_message_unpack_int(message, 0, &store);
index = core_vector_index_of(&concrete_actor->spawners, &source);
/*
printf("DEBUG biosal_input_controller_add_store index %d\n", index);
*/
bucket = core_vector_at(&concrete_actor->stores_per_spawner, index);
/* the content of the bucket is initially the total number of
* stores that are desired for this spawner.
*/
*bucket = (*bucket - 1);
core_vector_push_back(&concrete_actor->consumers, &store);
thorium_actor_send_to_self_empty(actor, ACTION_INPUT_CONTROLLER_CREATE_STORES);
/*
printf("DEBUG remaining to spawn: %d (before returning)\n", *bucket);
*/
}
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 reader_receive(struct thorium_actor *actor, struct thorium_message *message)
{
int tag;
int argc;
char **argv;
/*int i;*/
int name;
struct reader *reader1;
int source;
uint64_t count;
void *buffer;
int sequences;
int script;
int sequence_index;
char *received_sequence;
int error;
reader1 = (struct reader *)thorium_actor_concrete_actor(actor);
tag = thorium_message_action(message);
source = thorium_message_source(message);
buffer = thorium_message_buffer(message);
name = thorium_actor_name(actor);
if (tag == ACTION_START) {
core_vector_init(&reader1->spawners, 0);
core_vector_unpack(&reader1->spawners, buffer);
argc = thorium_actor_argc(actor);
argv = thorium_actor_argv(actor);
name = thorium_actor_name(actor);
reader1->last_report = 0;
/*
printf("actor %i received %i arguments\n", name, argc);
for (i = 0; i < argc ;i++) {
printf(" argument %i : %s\n", i, argv[i]);
}
*/
if (core_vector_index_of(&reader1->spawners, &name) != 0) {
thorium_message_init(message, ACTION_STOP, 0, NULL);
thorium_actor_send(actor, name, message);
return;
}
if (argc == 1) {
thorium_message_init(message, ACTION_STOP, 0, NULL);
thorium_actor_send(actor, name, message);
return;
}
reader1->sequence_reader = thorium_actor_spawn(actor, SCRIPT_INPUT_STREAM);
reader1->file = argv[argc - 1];
thorium_message_init(message, ACTION_INPUT_OPEN, strlen(reader1->file) + 1,
reader1->file);
printf("actor %i: asking actor %i to count entries in %s\n",
name, reader1->sequence_reader, reader1->file);
thorium_actor_send(actor, reader1->sequence_reader, message);
} else if (tag == ACTION_INPUT_COUNT_PROGRESS) {
sequences = *(int64_t *)buffer;
if (sequences < reader1->last_report + 10000000) {
return;
}
printf("Actor %i received a progress report from actor %i: %i\n",
name, source, sequences);
reader1->last_report = sequences;
} else if (tag == ACTION_INPUT_OPEN_REPLY && !reader1->counted) {
thorium_message_unpack_int(message, 0, &error);
if (error == BIOSAL_INPUT_ERROR_NO_ERROR) {
printf("Successfully opened file.\n");
thorium_actor_send_reply_empty(actor, ACTION_INPUT_COUNT);
} else if (error == BIOSAL_INPUT_ERROR_FILE_NOT_FOUND) {
printf("Error, file not found! \n");
thorium_actor_send_to_self_empty(actor, ACTION_STOP);
} else if (error == BIOSAL_INPUT_ERROR_FORMAT_NOT_SUPPORTED) {
printf("Error, format not supported! \n");
thorium_actor_send_to_self_empty(actor, ACTION_STOP);
}
} else if (tag == ACTION_INPUT_COUNT_REPLY) {
count = *(int64_t*)thorium_message_buffer(message);
printf("actor %i: file has %" PRIu64 " items\n", name, count);
thorium_message_init(message, ACTION_INPUT_CLOSE, 0, NULL);
thorium_actor_send(actor, source, message);
reader1->counted = 1;
} else if (tag == ACTION_INPUT_CLOSE_REPLY && !reader1->pulled) {
/* not necessary, it is already dead. */
thorium_actor_send_reply_empty(actor, ACTION_ASK_TO_STOP);
printf("actor %d received ACTION_INPUT_CLOSE_REPLY from actor %d, asking it to stop"
" with ACTION_ASK_TO_STOP\n", name, source);
/*
thorium_message_init(message, ACTION_STOP, 0, NULL);
thorium_actor_send(actor, name, message);
return;
*/
script = SCRIPT_INPUT_STREAM;
thorium_message_init(message, ACTION_SPAWN, sizeof(script), &script);
thorium_actor_send(actor, name, message);
} else if (tag == ACTION_INPUT_CLOSE_REPLY && reader1->pulled) {
thorium_actor_send_reply_empty(actor, ACTION_ASK_TO_STOP);
thorium_actor_send_to_self_empty(actor, ACTION_STOP);
} else if (tag == ACTION_ASK_TO_STOP_REPLY && reader1->pulled) {
/* this tag will never arrive here */
thorium_message_init(message, ACTION_STOP, 0, NULL);
thorium_actor_send(actor, name, message);
} else if (tag == ACTION_SPAWN_REPLY && source == name) {
reader1->sequence_reader = *(int *)buffer;
printf("actor %d tells actor %d to open %s to pull sequences from the file\n",
name, reader1->sequence_reader, reader1->file);
thorium_message_init(message, ACTION_INPUT_OPEN,
strlen(reader1->file) + 1, reader1->file);
thorium_actor_send(actor, reader1->sequence_reader, message);
} else if (tag == ACTION_INPUT_OPEN_REPLY && reader1->counted) {
thorium_message_init(message, ACTION_INPUT_GET_SEQUENCE, 0, NULL);
thorium_actor_send(actor, source, message);
} else if (tag == ACTION_INPUT_GET_SEQUENCE_REPLY) {
sequence_index = *(int *)buffer;
received_sequence = (char*)buffer + sizeof(sequence_index);
/*
printf("DEBUG %d %s\n", sequence_index, received_sequence);
*/
if (sequence_index == 123456) {
printf("actor %d says that sequence %d is %s.\n",
name, sequence_index, received_sequence);
} else if (sequence_index % 100000 == 0) {
printf("actor %d is pulling sequences from fellow local actor %d,"
" %d sequences pulled so far !\n",
name, reader1->sequence_reader, sequence_index);
}
if (sequence_index < 1000000) {
thorium_message_init(message, ACTION_INPUT_GET_SEQUENCE, 0, NULL);
thorium_actor_send(actor, source, message);
} else {
thorium_message_init(message, ACTION_INPUT_CLOSE, 0, NULL);
thorium_actor_send(actor, source, message);
reader1->pulled = 1;
}
} else if (tag == ACTION_INPUT_GET_SEQUENCE_END) {
printf("actor %d: reached the end...\n", name);
thorium_message_init(message, ACTION_INPUT_CLOSE, 0, NULL);
thorium_actor_send(actor, source, message);
reader1->pulled = 1;
}
}
void frame_receive(struct thorium_actor *actor, struct thorium_message *message)
{
int tag;
int name;
void *buffer;
struct frame *concrete_actor;
int other;
struct core_vector initial_actors;
struct core_vector *acquaintance_vector;
int source;
source = thorium_message_source(message);
concrete_actor = (struct frame *)thorium_actor_concrete_actor(actor);
tag = thorium_message_action(message);
name = thorium_actor_name(actor);
buffer = thorium_message_buffer(message);
acquaintance_vector = &concrete_actor->acquaintance_vector;
if (tag == ACTION_START) {
core_vector_init(&initial_actors, sizeof(int));
core_vector_unpack(&initial_actors, buffer);
core_vector_push_back_vector(acquaintance_vector, &initial_actors);
core_vector_destroy(&initial_actors);
other = thorium_actor_spawn(actor, thorium_actor_script(actor));
core_vector_push_back_int(acquaintance_vector, other);
thorium_actor_send_empty(actor, other, ACTION_PING);
printf("actor %d sends ACTION_PING to new actor %d\n",
name, other);
} else if (tag == ACTION_PING) {
/* new acquaintance
*/
core_vector_push_back(acquaintance_vector, &source);
printf("actor %d (value %d) receives ACTION_PING from actor %d\n",
name, concrete_actor->value, source);
printf("Acquaintances of actor %d: ", name);
core_vector_print_int(acquaintance_vector);
printf("\n");
thorium_actor_send_reply_empty(actor, ACTION_PING_REPLY);
} else if (tag == ACTION_PING_REPLY) {
concrete_actor->pings++;
printf("actor %d receives ACTION_PING_REPLY from actor %d\n",
name, source);
/* kill the system
*/
if (concrete_actor->migrated_other && concrete_actor->pings == 2) {
thorium_actor_send_reply_empty(actor, ACTION_ASK_TO_STOP);
thorium_actor_send_to_self_empty(actor, ACTION_ASK_TO_STOP);
return;
}
/* migrate other actor
*/
printf("actor %d asks actor %d to migrate using actor %d as spawner\n",
name, source, name);
printf("Acquaintances of actor %d: ", name);
core_vector_print_int(acquaintance_vector);
printf("\n");
thorium_actor_send_reply_int(actor, ACTION_MIGRATE, name);
/* send a message to other while it is migrating.
* this is supposed to work !
*/
printf("actor %d sends ACTION_PING to %d while it is migrating\n",
name, source);
thorium_actor_send_reply_empty(actor, ACTION_PING);
concrete_actor->migrated_other = 1;
} else if (tag == ACTION_MIGRATE_REPLY) {
thorium_message_unpack_int(message, 0, &other);
printf("actor %d received migrated actor %d\n", name, other);
printf("Acquaintances of actor %d: ", name);
core_vector_print_int(acquaintance_vector);
printf("\n");
/* it is possible that the ACTION_PING went through
* before the migration
*/
if (concrete_actor->pings == 2) {
thorium_actor_send_reply_empty(actor, ACTION_ASK_TO_STOP);
thorium_actor_send_to_self_empty(actor, ACTION_ASK_TO_STOP);
}
} else if (tag == ACTION_PACK) {
thorium_actor_send_reply_int(actor, ACTION_PACK_REPLY, concrete_actor->value);
} else if (tag == ACTION_UNPACK) {
thorium_message_unpack_int(message, 0, &concrete_actor->value);
thorium_actor_send_reply_empty(actor, ACTION_UNPACK_REPLY);
} else if (tag == ACTION_ASK_TO_STOP) {
printf("actor %d received ACTION_ASK_TO_STOP, value: %d ",
name, concrete_actor->value);
printf("acquaintance vector: ");
core_vector_print_int(acquaintance_vector);
printf("\n");
thorium_actor_send_to_self_empty(actor, ACTION_STOP);
}
}
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_assembly_arc_classifier_push_arc_block(struct thorium_actor *self, struct thorium_message *message)
{
struct biosal_assembly_arc_classifier *concrete_self;
int source;
struct biosal_assembly_arc_block input_block;
struct biosal_assembly_arc_block *output_block;
struct core_vector output_blocks;
struct core_memory_pool *ephemeral_memory;
int consumer_count;
struct core_vector *input_arcs;
struct core_vector *output_arcs;
int size;
int i;
struct biosal_assembly_arc *arc;
void *buffer;
int count;
struct biosal_dna_kmer *kmer;
int consumer_index;
int arc_count;
int consumer;
struct thorium_message new_message;
int new_count;
void *new_buffer;
int *bucket;
int maximum_pending_requests;
int maximum_buffer_length;
int reservation;
count = thorium_message_count(message);
buffer = thorium_message_buffer(message);
if (count == 0) {
printf("Error, count is 0 (classifier_push_arc_block)\n");
return;
}
concrete_self = (struct biosal_assembly_arc_classifier *)thorium_actor_concrete_actor(self);
source = thorium_message_source(message);
consumer_count = core_vector_size(&concrete_self->consumers);
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
CORE_DEBUGGER_LEAK_DETECTION_BEGIN(ephemeral_memory, classify_arcs);
core_vector_init(&output_blocks, sizeof(struct biosal_assembly_arc_block));
core_vector_set_memory_pool(&output_blocks, ephemeral_memory);
biosal_assembly_arc_block_init(&input_block, ephemeral_memory, concrete_self->kmer_length,
&concrete_self->codec);
#ifdef BIOSAL_ASSEMBLY_ARC_CLASSIFIER_DEBUG
printf("UNPACKING\n");
#endif
biosal_assembly_arc_block_unpack(&input_block, buffer, concrete_self->kmer_length,
&concrete_self->codec, ephemeral_memory);
#ifdef BIOSAL_ASSEMBLY_ARC_CLASSIFIER_DEBUG
printf("OK\n");
#endif
input_arcs = biosal_assembly_arc_block_get_arcs(&input_block);
/*
* Configure the ephemeral memory reservation.
*/
arc_count = core_vector_size(input_arcs);
reservation = (arc_count / consumer_count) * 2;
core_vector_resize(&output_blocks, consumer_count);
CORE_DEBUGGER_ASSERT(!core_memory_pool_has_double_free(ephemeral_memory));
/*
* Initialize output blocks.
* There is one for each destination.
*/
for (i = 0; i < consumer_count; i++) {
output_block = core_vector_at(&output_blocks, i);
biosal_assembly_arc_block_init(output_block, ephemeral_memory, concrete_self->kmer_length,
&concrete_self->codec);
biosal_assembly_arc_block_reserve(output_block, reservation);
}
size = core_vector_size(input_arcs);
/*
* Classify every arc in the input block
* and put them in output blocks.
*/
#ifdef BIOSAL_ASSEMBLY_ARC_CLASSIFIER_DEBUG
printf("ClassifyArcs arc_count= %d\n", size);
#endif
CORE_DEBUGGER_ASSERT(!core_memory_pool_has_double_free(ephemeral_memory));
for (i = 0; i < size; i++) {
arc = core_vector_at(input_arcs, i);
kmer = biosal_assembly_arc_source(arc);
consumer_index = biosal_dna_kmer_store_index(kmer, consumer_count,
concrete_self->kmer_length, &concrete_self->codec,
ephemeral_memory);
output_block = core_vector_at(&output_blocks, consumer_index);
/*
* Make a copy of the arc and copy it.
* It will be freed
*/
biosal_assembly_arc_block_add_arc_copy(output_block, arc,
concrete_self->kmer_length, &concrete_self->codec,
ephemeral_memory);
}
/*
* Input arcs are not needed anymore.
*/
biosal_assembly_arc_block_destroy(&input_block, ephemeral_memory);
CORE_DEBUGGER_ASSERT(!core_memory_pool_has_double_free(ephemeral_memory));
/*
* Finally, send these output blocks to consumers.
*/
maximum_pending_requests = 0;
maximum_buffer_length = 0;
/*
* Figure out the maximum buffer length tor
* messages.
*/
for (i = 0; i < consumer_count; i++) {
output_block = core_vector_at(&output_blocks, i);
new_count = biosal_assembly_arc_block_pack_size(output_block, concrete_self->kmer_length,
&concrete_self->codec);
if (new_count > maximum_buffer_length) {
maximum_buffer_length = new_count;
}
}
#if 0
printf("POOL_BALANCE %d\n",
core_memory_pool_profile_balance_count(ephemeral_memory));
#endif
for (i = 0; i < consumer_count; i++) {
output_block = core_vector_at(&output_blocks, i);
output_arcs = biosal_assembly_arc_block_get_arcs(output_block);
arc_count = core_vector_size(output_arcs);
/*
* Don't send an empty message.
*/
if (arc_count > 0) {
/*
* Allocation is not required because new_count <= maximum_buffer_length
*/
new_count = biosal_assembly_arc_block_pack_size(output_block, concrete_self->kmer_length,
&concrete_self->codec);
new_buffer = thorium_actor_allocate(self, maximum_buffer_length);
CORE_DEBUGGER_ASSERT(new_count <= maximum_buffer_length);
biosal_assembly_arc_block_pack(output_block, new_buffer, concrete_self->kmer_length,
&concrete_self->codec);
thorium_message_init(&new_message, ACTION_ASSEMBLY_PUSH_ARC_BLOCK,
new_count, new_buffer);
consumer = core_vector_at_as_int(&concrete_self->consumers, i);
/*
* Send the message.
*/
thorium_actor_send(self, consumer, &new_message);
thorium_message_destroy(&new_message);
/* update event counters for control.
*/
bucket = core_vector_at(&concrete_self->pending_requests, i);
++(*bucket);
++concrete_self->active_requests;
if (*bucket > maximum_pending_requests) {
maximum_pending_requests = *bucket;
}
if (*bucket > concrete_self->maximum_pending_request_count) {
++concrete_self->consumer_count_above_threshold;
}
}
CORE_DEBUGGER_ASSERT(!core_memory_pool_has_double_free(ephemeral_memory));
#if 0
printf("i = %d\n", i);
#endif
/*
* Destroy output block.
*/
biosal_assembly_arc_block_destroy(output_block,
ephemeral_memory);
CORE_DEBUGGER_LEAK_CHECK_DOUBLE_FREE(ephemeral_memory);
CORE_DEBUGGER_ASSERT(!core_memory_pool_has_double_free(ephemeral_memory));
}
core_vector_destroy(&output_blocks);
CORE_DEBUGGER_ASSERT(!core_memory_pool_has_double_free(ephemeral_memory));
CORE_DEBUGGER_LEAK_CHECK_DOUBLE_FREE(ephemeral_memory);
/*
* Check if a response must be sent now.
*/
++concrete_self->received_blocks;
concrete_self->source = source;
/*
* Only send a direct reply if there is enough memory.
*
* As long as maximum_pending_requests is lower than maximum_pending_request_count,
* there is still space for at least one additional request.
*/
if (maximum_pending_requests < concrete_self->maximum_pending_request_count
&& core_memory_has_enough_bytes()) {
thorium_actor_send_empty(self, concrete_self->source,
ACTION_ASSEMBLY_PUSH_ARC_BLOCK_REPLY);
} else {
concrete_self->producer_is_waiting = 1;
}
CORE_DEBUGGER_LEAK_DETECTION_END(ephemeral_memory, classify_arcs);
}
void biosal_input_stream_count_reply(struct thorium_actor *self, struct thorium_message *message)
{
struct biosal_input_stream *concrete_self;
void *buffer;
uint64_t result;
struct biosal_mega_block *block;
int i;
int size;
struct core_vector *vector;
int source_index;
int source;
int j;
uint64_t total;
concrete_self = (struct biosal_input_stream *)thorium_actor_concrete_actor(self);
buffer = thorium_message_buffer(message);
source = thorium_message_source(message);
source_index = core_vector_index_of(&concrete_self->parallel_streams, &source);
vector = core_vector_at(&concrete_self->parallel_mega_blocks, source_index);
core_vector_unpack(vector, buffer);
block = core_vector_at_last(vector);
result = biosal_mega_block_get_entries(block);
concrete_self->total_entries += result;
++concrete_self->finished_parallel_stream_count;
printf("DEBUG count_reply %d/%d\n",
concrete_self->finished_parallel_stream_count,
(int)core_vector_size(&concrete_self->parallel_streams));
/*
* Send back an array of mega blocks when it is done.
*/
if (concrete_self->finished_parallel_stream_count ==
core_vector_size(&concrete_self->parallel_streams)) {
/*
* Transfer mega blocks
* to main vector.
*/
size = core_vector_size(&concrete_self->parallel_streams);
for (i = 0; i < size; i++) {
/*
* This is easy to do because they are already sorted.
*
* With one parallel stream, there is nothing else to do.
*
* Otherwise, mega blocks with correct entries_from_start
* need to be created (the entries fields are only for
* the stuff between 2 offsets so they are already
* correct.
*/
vector = core_vector_at(&concrete_self->parallel_mega_blocks,
i);
#if 0
printf("ParallelStream %d\n", i);
#endif
for (j = 0; j < core_vector_size(vector); j++) {
block = core_vector_at(vector, j);
biosal_mega_block_print(block);
}
core_vector_push_back_vector(&concrete_self->mega_blocks,
vector);
}
/*
* Update total
*/
total = 0;
for (i = 0; i < core_vector_size(&concrete_self->mega_blocks); i++) {
block = core_vector_at(&concrete_self->mega_blocks, i);
total += biosal_mega_block_get_entries(block);
biosal_mega_block_set_entries_from_start(block, total);
}
/*
* Destroy mega block vectors.
*/
for (i = 0; i < size; i++) {
vector = core_vector_at(&concrete_self->parallel_mega_blocks,
i);
core_vector_destroy(vector);
}
core_vector_resize(&concrete_self->parallel_mega_blocks, 0);
printf("DEBUG send ACTION_INPUT_COUNT_IN_PARALLEL_REPLY to %d\n",
concrete_self->controller);
thorium_actor_send_vector(self, concrete_self->controller,
ACTION_INPUT_COUNT_IN_PARALLEL_REPLY,
&concrete_self->mega_blocks);
}
}
void thorium_worker_send(struct thorium_worker *worker, struct thorium_message *message)
{
void *buffer;
int count;
void *old_buffer;
old_buffer = thorium_message_buffer(message);
/*
* Allocate a buffer if the actor provided a NULL buffer or if it
* provided its own buffer.
*/
if (old_buffer == NULL
|| old_buffer != worker->zero_copy_buffer) {
count = thorium_message_count(message);
/* use slab allocator */
buffer = thorium_worker_allocate(worker, count);
/* according to
* http://stackoverflow.com/questions/3751797/can-i-call-core_memory_copy-and-core_memory_move-with-number-of-bytes-set-to-zero
* memcpy works with a count of 0, but the addresses must be valid
* nonetheless
*
* Copy the message data.
*/
if (count > 0) {
#ifdef DISPLAY_COPY_WARNING
printf("thorium_worker: Warning, not using zero-copy path, action %x count %d source %d destination %d\n",
thorium_message_action(message), count, thorium_message_source(message),
thorium_message_destination(message));
#endif
core_memory_copy(buffer, old_buffer, count);
}
thorium_message_set_buffer(message, buffer);
}
/*
* Always write metadata.
*/
thorium_message_write_metadata(message);
#ifdef THORIUM_WORKER_DEBUG_INJECTION
++worker->counter_allocated_outbound_buffers;
#endif
#ifdef THORIUM_WORKER_DEBUG_MEMORY
printf("ALLOCATE %p\n", buffer);
#endif
#ifdef THORIUM_WORKER_DEBUG
printf("[thorium_worker_send] allocated %i bytes (%i + %i) for buffer %p\n",
all, count, metadata_size, buffer);
printf("thorium_worker_send old buffer: %p\n",
thorium_message_buffer(message));
#endif
#ifdef THORIUM_BUG_594
if (thorium_message_action(©) == 30202) {
printf("DEBUG-594 thorium_worker_send\n");
thorium_message_print(©);
}
#endif
#ifdef THORIUM_WORKER_DEBUG_20140601
if (thorium_message_action(message) == 1100) {
printf("DEBUG thorium_worker_send 1100\n");
}
#endif
/* if the destination is on the same node,
* handle that directly here to avoid locking things
* with the node.
*/
thorium_worker_enqueue_message(worker, message);
worker->zero_copy_buffer = NULL;
}
void table_receive(struct thorium_actor *actor, struct thorium_message *message)
{
int tag;
int source;
int name;
int remote;
struct thorium_message spawn_message;
int script;
int new_actor;
void *buffer;
struct table *table1;
table1 = (struct table *)thorium_actor_concrete_actor(actor);
source = thorium_message_source(message);
tag = thorium_message_action(message);
name = thorium_actor_name(actor);
buffer = thorium_message_buffer(message);
if (tag == ACTION_START) {
printf("Actor %i receives ACTION_START from actor %i\n",
name, source);
core_vector_init(&table1->spawners, 0);
core_vector_unpack(&table1->spawners, buffer);
remote = core_vector_index_of(&table1->spawners, &name) + 1;
remote %= core_vector_size(&table1->spawners);
script = SCRIPT_TABLE;
thorium_message_init(&spawn_message, ACTION_SPAWN, sizeof(script), &script);
thorium_actor_send(actor, *(int *)core_vector_at(&table1->spawners, remote), &spawn_message);
/*
printf("sending notification\n");
thorium_message_init(message, ACTION_TABLE_NOTIFY, 0, NULL);
thorium_actor_send(actor, 0, message);
*/
} else if (tag == ACTION_SPAWN_REPLY) {
new_actor= *(int *)buffer;
printf("Actor %i receives ACTION_SPAWN_REPLY from actor %i,"
" new actor is %d\n",
name, source, new_actor);
thorium_message_init(message, ACTION_TABLE_DIE2, 0, NULL);
thorium_actor_send(actor, new_actor, message);
thorium_message_init(message, ACTION_TABLE_NOTIFY, 0, NULL);
thorium_actor_send(actor, core_vector_at_as_int(&table1->spawners, 0), message);
} else if (tag == ACTION_TABLE_DIE2) {
printf("Actor %i receives ACTION_TABLE_DIE2 from actor %i\n",
name, source);
if (name < core_vector_size(&table1->spawners)) {
return;
}
thorium_message_init(message, ACTION_STOP, 0, NULL);
thorium_actor_send(actor, name, message);
} else if (tag == ACTION_TABLE_DIE) {
printf("Actor %i receives ACTION_TABLE_DIE from actor %i\n",
name, source);
thorium_message_init(message, ACTION_STOP, 0, NULL);
thorium_actor_send(actor, name, message);
} else if (tag == ACTION_TABLE_NOTIFY) {
printf("Actor %i receives ACTION_TABLE_NOTIFY from actor %i\n",
name, source);
table1->done++;
if (table1->done == core_vector_size(&table1->spawners)) {
printf("actor %d kills %d to %d\n",
name, 0, (int)core_vector_size(&table1->spawners) - 1);
thorium_message_init(message, ACTION_TABLE_DIE, 0, NULL);
thorium_actor_send_range(actor, &table1->spawners, message);
}
}
}
/*
* Basically, this actor does this:
* - spawn visitors
* - let them visit stuff
* - kill them.
* - spawn walkers
* - let them walk
* - kill the walkers
* - return OK
*/
void biosal_unitig_manager_receive(struct thorium_actor *self, struct thorium_message *message)
{
struct biosal_unitig_manager *concrete_self;
int tag;
void *buffer;
int spawner;
int expected;
int script;
int actor_count;
int source;
struct core_string file_name;
char *directory;
int argc;
char **argv;
char *path;
tag = thorium_message_action(message);
source = thorium_message_source(message);
buffer = thorium_message_buffer(message);
concrete_self = (struct biosal_unitig_manager *)thorium_actor_concrete_actor(self);
if (tag == ACTION_START) {
core_vector_unpack(&concrete_self->spawners, buffer);
spawner = thorium_actor_get_random_spawner(self, &concrete_self->spawners);
concrete_self->state = STATE_SPAWN_WRITER;
thorium_actor_send_int(self, spawner, ACTION_SPAWN, SCRIPT_WRITER_PROCESS);
} else if (tag == ACTION_SPAWN_REPLY
&& concrete_self->state == STATE_SPAWN_WRITER) {
thorium_message_unpack_int(message, 0, &concrete_self->writer_process);
/*
* open the file now.
*/
argc = thorium_actor_argc(self);
argv = thorium_actor_argv(self);
directory = core_command_get_output_directory(argc, argv);
core_string_init(&file_name, directory);
core_string_append(&file_name, "/");
core_string_append(&file_name, "unitigs.fasta");
path = core_string_get(&file_name);
thorium_actor_send_buffer(self, concrete_self->writer_process,
ACTION_OPEN, strlen(path) + 1, path);
core_string_destroy(&file_name);
} else if (tag == ACTION_OPEN_REPLY
&& source == concrete_self->writer_process) {
/*
* Spawn visitors.
*/
concrete_self->state = STATE_VISITORS;
thorium_actor_send_to_self_empty(self, ACTION_PING);
} else if (tag == ACTION_PING) {
spawner = thorium_actor_get_random_spawner(self, &concrete_self->spawners);
thorium_actor_send_int(self, spawner, ACTION_SPAWN, SCRIPT_MANAGER);
} else if (tag == ACTION_SPAWN_REPLY) {
thorium_message_unpack_int(message, 0, &concrete_self->manager);
script = SCRIPT_UNITIG_VISITOR;
if (concrete_self->state == STATE_WALKERS) {
script = SCRIPT_UNITIG_WALKER;
}
thorium_actor_send_int(self, concrete_self->manager, ACTION_MANAGER_SET_SCRIPT,
script);
} else if (tag == ACTION_ASK_TO_STOP) {
thorium_actor_send_empty(self, concrete_self->writer_process,
ACTION_ASK_TO_STOP);
thorium_actor_send_empty(self, concrete_self->manager,
ACTION_ASK_TO_STOP);
thorium_actor_send_to_self_empty(self, ACTION_STOP);
thorium_actor_send_reply_empty(self, ACTION_ASK_TO_STOP_REPLY);
} else if (tag == ACTION_MANAGER_SET_SCRIPT_REPLY) {
actor_count = UNITIG_VISITOR_COUNT_PER_WORKER;
if (concrete_self->state == STATE_WALKERS)
actor_count = UNITIG_WALKER_COUNT_PER_WORKER;
thorium_actor_send_reply_int(self, ACTION_MANAGER_SET_ACTORS_PER_WORKER,
actor_count);
} else if (tag == ACTION_MANAGER_SET_ACTORS_PER_WORKER_REPLY) {
thorium_actor_send_reply_vector(self, ACTION_START,
&concrete_self->spawners);
} else if (tag == ACTION_START_REPLY
&& concrete_self->state == STATE_VISITORS
&& core_vector_size(&concrete_self->visitors) == 0) {
core_vector_unpack(&concrete_self->visitors, buffer);
printf("DEBUG the system has %d visitors\n",
(int)core_vector_size(&concrete_self->visitors));
thorium_actor_send_to_supervisor_empty(self, ACTION_START_REPLY);
} else if (tag == ACTION_START_REPLY
&& concrete_self->state == STATE_WALKERS
&& core_vector_size(&concrete_self->walkers) == 0) {
core_vector_unpack(&concrete_self->walkers, buffer);
printf("DEBUG the system has %d walkers\n",
(int)core_vector_size(&concrete_self->walkers));
core_timer_start(&concrete_self->timer);
concrete_self->completed = 0;
thorium_actor_send_range_int(self, &concrete_self->walkers,
ACTION_SET_CONSUMER, concrete_self->writer_process);
thorium_actor_send_range_vector(self, &concrete_self->walkers,
ACTION_START, &concrete_self->graph_stores);
} else if (tag == ACTION_SET_PRODUCERS) {
core_vector_unpack(&concrete_self->graph_stores, buffer);
core_timer_start(&concrete_self->timer);
concrete_self->completed = 0;
thorium_actor_send_range_vector(self, &concrete_self->visitors,
ACTION_START, &concrete_self->graph_stores);
} else if (tag == ACTION_START_REPLY && concrete_self->state == STATE_VISITORS) {
++concrete_self->completed;
expected = core_vector_size(&concrete_self->visitors);
if (concrete_self->completed % UNITIG_VISITOR_COUNT_PER_WORKER == 0
|| concrete_self->completed == expected) {
printf("PROGRESS unitig visitors %d/%d\n",
concrete_self->completed,
expected);
}
if (concrete_self->completed == expected) {
core_timer_stop(&concrete_self->timer);
core_timer_print_with_description(&concrete_self->timer, "Visit vertices for unitigs");
/*
* Stop the visitor manager and all visitors too.
*/
thorium_actor_send_empty(self, concrete_self->manager, ACTION_ASK_TO_STOP);
/*
* Reset graph stores.
*/
thorium_actor_send_range_empty(self, &concrete_self->graph_stores,
ACTION_RESET);
concrete_self->completed = 0;
}
} else if (tag == ACTION_RESET_REPLY) {
++concrete_self->completed;
expected = core_vector_size(&concrete_self->graph_stores);
if (concrete_self->completed == expected) {
concrete_self->completed = 0;
concrete_self->state = STATE_WALKERS;
/*
* Go back at the beginning.
*/
thorium_actor_send_to_self_empty(self, ACTION_PING);
}
} else if (tag == ACTION_START_REPLY && concrete_self->state == STATE_WALKERS) {
++concrete_self->completed;
expected = core_vector_size(&concrete_self->walkers);
if (concrete_self->completed % UNITIG_WALKER_COUNT_PER_WORKER == 0
|| concrete_self->completed == expected) {
printf("PROGRESS unitig walkers %d/%d\n",
concrete_self->completed,
expected);
}
if (concrete_self->completed == expected) {
core_timer_stop(&concrete_self->timer);
core_timer_print_with_description(&concrete_self->timer, "Walk for unitigs");
thorium_actor_send_to_supervisor_empty(self, ACTION_SET_PRODUCERS_REPLY);
}
}
}
void biosal_assembly_graph_store_mark_vertex_as_visited(struct thorium_actor *self, struct thorium_message *message)
{
struct biosal_assembly_graph_store *concrete_self;
char *buffer;
int source;
int path_index;
char *sequence;
struct core_memory_pool *ephemeral_memory;
struct biosal_dna_kmer kmer;
struct biosal_dna_kmer storage_kmer;
struct biosal_assembly_vertex *canonical_vertex;
int position;
void *key;
int force;
force = 1;
position = 0;
concrete_self = thorium_actor_concrete_actor(self);
source = thorium_message_source(message);
buffer = thorium_message_buffer(message);
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
/*
* Get the kmer.
*/
biosal_dna_kmer_init_empty(&kmer);
position += biosal_dna_kmer_unpack(&kmer, buffer, concrete_self->kmer_length,
ephemeral_memory, &concrete_self->transport_codec);
sequence = core_memory_pool_allocate(ephemeral_memory, concrete_self->kmer_length + 1);
biosal_dna_kmer_get_sequence(&kmer, sequence, concrete_self->kmer_length,
&concrete_self->transport_codec);
biosal_dna_kmer_init(&storage_kmer, sequence, &concrete_self->storage_codec,
ephemeral_memory);
/*
* Get store key
*/
key = core_memory_pool_allocate(ephemeral_memory, concrete_self->key_length_in_bytes);
biosal_dna_kmer_pack_store_key(&storage_kmer, key, concrete_self->kmer_length, &concrete_self->storage_codec,
ephemeral_memory);
/* Get vertex. */
canonical_vertex = core_map_get(&concrete_self->table, key);
biosal_dna_kmer_destroy(&kmer, ephemeral_memory);
biosal_dna_kmer_destroy(&storage_kmer, ephemeral_memory);
core_memory_pool_free(ephemeral_memory, key);
core_memory_pool_free(ephemeral_memory, sequence);
position += thorium_message_unpack_int(message, position, &path_index);
/*
* At this point, mark the vertex with flag BIOSAL_VERTEX_FLAG_USED
* so that any other actor that attempt to grab it will have to communicate
* with the actor.
*/
/*
* This is a good idea to always update with the last one.
*/
if (force || !biosal_assembly_vertex_get_flag(canonical_vertex, BIOSAL_VERTEX_FLAG_USED)) {
biosal_assembly_graph_store_mark_as_used(self, canonical_vertex, source, path_index);
}
#if 0
#endif
thorium_actor_send_reply_empty(self, ACTION_MARK_VERTEX_AS_VISITED_REPLY);
}
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 core_writer_process_receive(struct thorium_actor *self, struct thorium_message *message)
{
int action;
int count;
int source;
char *buffer;
char *file_name;
struct core_writer_process *concrete_self;
concrete_self = thorium_actor_concrete_actor(self);
action = thorium_message_action(message);
count = thorium_message_count(message);
buffer = thorium_message_buffer(message);
source = thorium_message_source(message);
if (action == ACTION_OPEN) {
if (concrete_self->has_file) {
thorium_actor_log(self, "actor error, already open, can not open\n");
return;
}
file_name = buffer;
core_buffered_file_writer_init(&concrete_self->writer, file_name);
concrete_self->has_file = 1;
thorium_actor_send_reply_empty(self, ACTION_OPEN_REPLY);
} else if (action == ACTION_WRITE) {
core_buffered_file_writer_write(&concrete_self->writer, buffer, count);
thorium_actor_send_reply_empty(self, ACTION_WRITE_REPLY);
} else if (action == ACTION_CLOSE) {
if (!concrete_self->has_file) {
thorium_actor_log(self, "Error, can not close a file that is not open\n");
return;
}
core_buffered_file_writer_destroy(&concrete_self->writer);
concrete_self->has_file = 0;
thorium_actor_send_reply_empty(self, ACTION_CLOSE_REPLY);
} else if (action == ACTION_ASK_TO_STOP
&& source == thorium_actor_supervisor(self)) {
/*
* Close the file if it is open
* right now.
*/
if (concrete_self->has_file) {
core_buffered_file_writer_destroy(&concrete_self->writer);
concrete_self->has_file = 0;
}
thorium_actor_send_to_self_empty(self, ACTION_STOP);
thorium_actor_send_reply_empty(self, ACTION_ASK_TO_STOP_REPLY);
}
}
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);
}
}
static void source_receive(struct thorium_actor *self, struct thorium_message *message)
{
int action;
void *buffer;
int leader;
int source;
int count;
struct source *concrete_self;
int name;
concrete_self = (struct source *)thorium_actor_concrete_actor(self);
action = thorium_message_action(message);
buffer = thorium_message_buffer(message);
source = thorium_message_source(message);
name = thorium_actor_name(self);
count = thorium_message_count(message);
if (action == ACTION_ASK_TO_STOP) {
thorium_actor_log(self, "sent %d ACTION_PING messages\n",
concrete_self->message_count);
thorium_actor_send_to_self_empty(self, ACTION_STOP);
} else if (action == ACTION_NOTIFY) {
#ifdef LATENCY_PROBE_USE_MULTIPLEXER
thorium_actor_send_to_self_empty(self, ACTION_ENABLE_MULTIPLEXER);
#endif
CORE_DEBUGGER_ASSERT(core_vector_empty(&concrete_self->targets));
core_vector_unpack(&concrete_self->targets, buffer);
if (source_is_important(self)) {
printf("%d (node %d worker %d) has %d targets\n", thorium_actor_name(self),
thorium_actor_node_name(self),
thorium_actor_worker_name(self),
(int)core_vector_size(&concrete_self->targets));
}
concrete_self->leader = source;
source_send_ping(self);
} else if (action == ACTION_PING_REPLY) {
CORE_DEBUGGER_ASSERT(count == 0);
++concrete_self->message_count;
CORE_DEBUGGER_ASSERT_IS_EQUAL_INT(count, 0);
CORE_DEBUGGER_ASSERT_IS_NULL(buffer);
if (concrete_self->message_count % PERIOD == 0 || concrete_self->event_count < 500) {
if (source_is_important(self)) {
printf("progress %d %d/%d\n",
name, concrete_self->message_count, concrete_self->event_count);
}
}
if (concrete_self->message_count == concrete_self->event_count) {
leader = concrete_self->leader;
thorium_actor_send_empty(self, leader, ACTION_NOTIFY_REPLY);
if (source_is_important(self))
printf("%d (ACTION_PING sent: %d)"
" sends ACTION_NOTIFY_REPLY to %d\n", thorium_actor_name(self),
concrete_self->message_count,
leader);
} else {
source_send_ping(self);
}
}
}