int thorium_transport_receive(struct thorium_transport *self, struct thorium_message *message)
{
int value;
if (self->transport_interface == NULL) {
return 0;
}
value = self->transport_interface->receive(self, message);
if (value) {
#ifdef THORIUM_TRANSPORT_DEBUG
printf("TRANSPORT RECEIVE Source %d Destination %d Tag %d Count %d\n",
thorium_message_source_node(message),
thorium_message_destination_node(message),
thorium_message_action(message),
thorium_message_count(message));
#endif
if (core_bitmap_get_bit_uint32_t(&self->flags, FLAG_PRINT_TRANSPORT_EVENTS)) {
thorium_transport_print_event(self, EVENT_TYPE_RECEIVE, message);
}
}
return value;
}
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_actor_pack_proxy_message(struct thorium_actor *self, struct thorium_message *message,
int real_source)
{
int real_tag;
int count;
int new_count;
void *buffer;
void *new_buffer;
int offset;
struct core_memory_pool *ephemeral_memory;
/*
* pack data in this order:
*
* - data (count bytes)
* - real_source
* - real_tag
*/
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
real_tag = thorium_message_action(message);
buffer = thorium_message_buffer(message);
count = thorium_message_count(message);
#ifdef DEBUG_BINOMIAL_TREE
printf("DEBUG_BINOMIAL_TREE pack_proxy_message count %d source %d action %x\n", count,
thorium_actor_name(self),
real_tag);
thorium_message_print(message);
#endif
new_count = count + sizeof(real_source) + sizeof(real_tag);
/* use slab allocator */
new_buffer = core_memory_pool_allocate(ephemeral_memory, new_count);
#ifdef THORIUM_ACTOR_DEBUG
printf("DEBUG12 core_memory_pool_allocate %p (pack proxy message)\n",
new_buffer);
#endif
if (count > 0)
core_memory_copy(new_buffer, buffer, count);
offset = count;
core_memory_copy((char *)new_buffer + offset, &real_source, sizeof(real_source));
offset += sizeof(real_source);
core_memory_copy((char *)new_buffer + offset, &real_tag, sizeof(real_tag));
offset += sizeof(real_tag);
thorium_message_init(message, ACTION_PROXY_MESSAGE, new_count, new_buffer);
thorium_message_set_source(message, real_source);
#if 0
/* free the old buffer
*/
core_memory_free(buffer);
buffer = NULL;
#endif
}
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);
}
int thorium_transport_send(struct thorium_transport *self, struct thorium_message *message)
{
int value;
if (self->transport_interface == NULL) {
return 0;
}
/*
* Send the message through the mock transport which is
* a transport profiler.
*/
if (core_bitmap_get_bit_uint32_t(&self->flags, FLAG_PROFILE)) {
thorium_transport_profiler_send_mock(&self->transport_profiler, message);
}
value = self->transport_interface->send(self, message);
if (value) {
#ifdef THORIUM_TRANSPORT_DEBUG
printf("TRANSPORT SEND Source %d Destination %d Tag %d Count %d\n",
thorium_message_source_node(message),
thorium_message_destination_node(message),
thorium_message_action(message),
thorium_message_count(message));
#endif
++self->active_request_count;
if (core_bitmap_get_bit_uint32_t(&self->flags, FLAG_PRINT_TRANSPORT_EVENTS)) {
thorium_transport_print_event(self, EVENT_TYPE_SEND, message);
}
}
return value;
}
void thorium_message_remove_metadata(struct thorium_message *self)
{
int count;
int metadata_size;
int all;
count = thorium_message_count(self);
metadata_size = thorium_message_metadata_size(self);
all = count - metadata_size;
thorium_message_set_count(self, all);
}
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));
}
int thorium_message_multiplexer_message_should_be_multiplexed(struct thorium_message_multiplexer *self,
struct thorium_message *message)
{
int buffer_size;
int threshold;
if (thorium_message_multiplexer_is_disabled(self))
return 0;
buffer_size = thorium_message_count(message);
threshold = self->buffer_size_in_bytes / 2;
return buffer_size <= threshold;
}
void thorium_actor_unpack_proxy_message(struct thorium_actor *self,
struct thorium_message *message)
{
int new_count;
int tag;
int source;
void *buffer;
int offset;
buffer = thorium_message_buffer(message);
new_count = thorium_message_count(message);
new_count -= sizeof(source);
new_count -= sizeof(tag);
offset = new_count;
source = *(int *)((char *)buffer + offset);
offset += sizeof(source);
tag = *(int *)((char *)buffer + offset);
#ifdef DEBUG_BINOMIAL_TREE
printf("DEBUG_BINOMIAL_TREE unpack_proxy_message real_count %d real_source %d real_action %x\n",
new_count, source, tag);
#endif
/*
* The action can not be ACTION_INVALID because it is invalid
* by convention.
*/
CORE_DEBUGGER_ASSERT(tag != ACTION_INVALID);
offset += sizeof(tag);
/*thorium_message_init(message, tag, new_count, buffer);*/
/*
* Change the tag, source, and count.
*/
thorium_message_set_source(message, source);
thorium_message_set_action(message, tag);
thorium_message_set_count(message, new_count);
#if 0
printf("DEBUG unpack_proxy_message... source %d tag %d count %d\n",
source, tag, new_count);
#endif
}
void biosal_assembly_graph_store_set_vertex_flag(struct thorium_actor *self,
struct thorium_message *message)
{
char *buffer;
int count;
int flag;
struct biosal_dna_kmer transport_kmer;
struct biosal_assembly_vertex *vertex;
struct biosal_assembly_graph_store *concrete_self;
struct core_memory_pool *ephemeral_memory;
int position;
concrete_self = thorium_actor_concrete_actor(self);
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
biosal_dna_kmer_init_empty(&transport_kmer);
buffer = thorium_message_buffer(message);
count = thorium_message_count(message);
position = 0;
position += biosal_dna_kmer_unpack(&transport_kmer, buffer, concrete_self->kmer_length,
ephemeral_memory, &concrete_self->transport_codec);
core_memory_copy(&flag, buffer + position, sizeof(flag));
position += sizeof(flag);
CORE_DEBUGGER_ASSERT_IS_EQUAL_INT(position, count);
CORE_DEBUGGER_ASSERT(flag >= BIOSAL_VERTEX_FLAG_START_VALUE);
CORE_DEBUGGER_ASSERT(flag <= BIOSAL_VERTEX_FLAG_END_VALUE);
if (flag == BIOSAL_VERTEX_FLAG_UNITIG) {
++concrete_self->unitig_vertex_count;
}
#if 0
printf("DEBUG ACTION_SET_VERTEX_FLAG %d\n", flag);
#endif
vertex = biosal_assembly_graph_store_find_vertex(self, &transport_kmer);
CORE_DEBUGGER_ASSERT_NOT_NULL(vertex);
biosal_dna_kmer_destroy(&transport_kmer, ephemeral_memory);
biosal_assembly_vertex_set_flag(vertex, flag);
thorium_actor_send_reply_empty(self, ACTION_SET_VERTEX_FLAG_REPLY);
}
/* \see http://www.mpich.org/static/docs/v3.1/www3/MPI_Isend.html */
int thorium_mpi1_pt2pt_transport_send(struct thorium_transport *self, struct thorium_message *message)
{
struct thorium_mpi1_pt2pt_transport *concrete_self;
char *buffer;
int count;
int destination;
int tag;
MPI_Request *request;
struct thorium_mpi1_pt2pt_active_request active_request;
int worker;
int result;
concrete_self = thorium_transport_get_concrete_transport(self);
worker = thorium_message_worker(message);
buffer = thorium_message_buffer(message);
count = thorium_message_count(message);
destination = thorium_message_destination_node(message);
tag = DUMMY_TAG;
thorium_mpi1_pt2pt_active_request_init(&active_request, buffer, worker);
request = thorium_mpi1_pt2pt_active_request_request(&active_request);
CORE_DEBUGGER_ASSERT(buffer == NULL || count > 0);
/* get return value */
result = MPI_Isend(buffer, count, concrete_self->datatype, destination, tag,
concrete_self->comm, request);
if (result != MPI_SUCCESS) {
return 0;
}
/* store the MPI_Request to test it later to know when
* the buffer can be reused
*/
/* \see http://blogs.cisco.com/performance/mpi_request_free-is-evil/
*/
/*MPI_Request_free(&request);*/
core_fast_queue_enqueue(&concrete_self->active_requests, &active_request);
return 1;
}
int thorium_message_unpack_double(struct thorium_message *message, int offset, double *value)
{
int bytes;
void *buffer;
double *pointer;
if (offset >= thorium_message_count(message)) {
return -1;
}
bytes = sizeof(double);
buffer = thorium_message_buffer(message);
pointer = (double *)((char *)buffer + offset);
*value = *pointer;
return bytes;
}
int thorium_message_unpack_int64_t(struct thorium_message *message, int offset, int64_t *value)
{
int bytes;
void *buffer;
int64_t *pointer;
if (offset >= thorium_message_count(message)) {
return -1;
}
bytes = sizeof(int64_t);
buffer = thorium_message_buffer(message);
pointer = (int64_t *)((char *)buffer + offset);
*value = *pointer;
return bytes;
}
int thorium_message_unpack_2_int(struct thorium_message *message, int *value1, int *value2)
{
int offset;
int count;
int required;
count = thorium_message_count(message);
required = sizeof(*value1) + sizeof(*value2);
if (required > count) {
return -1;
}
offset = 0;
offset += thorium_message_unpack_int(message, offset, value1);
offset += thorium_message_unpack_int(message, offset, value2);
return offset;
}
void biosal_input_stream_count_reply_mock(struct thorium_actor *self, struct thorium_message *message)
{
struct biosal_input_stream *concrete_self;
void *buffer;
int count;
struct core_vector mega_blocks;
char *file;
struct core_memory_pool *ephemeral_memory;
uint64_t result;
struct biosal_mega_block *block;
concrete_self = (struct biosal_input_stream *)thorium_actor_concrete_actor(self);
buffer = thorium_message_buffer(message);
count = thorium_message_count(message);
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
core_vector_init(&mega_blocks, 0);
core_vector_set_memory_pool(&mega_blocks, ephemeral_memory);
core_vector_unpack(&mega_blocks, buffer);
block = core_vector_at_last(&mega_blocks);
result = biosal_mega_block_get_entries(block);
#if 0
file = core_string_get(&concrete_self->file_for_parallel_counting);
#endif
file = concrete_self->file_name;
printf("%s/%d COUNT_IN_PARALLEL result for %s is %" PRIu64 "\n",
thorium_actor_script_name(self),
thorium_actor_name(self),
file,
result);
core_vector_destroy(&mega_blocks);
thorium_actor_send_buffer(self, concrete_self->controller,
ACTION_INPUT_COUNT_IN_PARALLEL_REPLY, count, buffer);
}
void biosal_input_stream_count_in_parallel_mock(struct thorium_actor *self, struct thorium_message *message)
{
struct biosal_input_stream *concrete_self;
void *buffer;
int count;
char *file;
concrete_self = (struct biosal_input_stream *)thorium_actor_concrete_actor(self);
buffer = thorium_message_buffer(message);
count = thorium_message_count(message);
file = concrete_self->file_name;
printf("%s/%d receives ACTION_INPUT_COUNT_IN_PARALLEL file %s\n",
thorium_actor_script_name(self),
thorium_actor_name(self),
file);
thorium_actor_send_to_self_buffer(self, ACTION_INPUT_COUNT, count, buffer);
}
void thorium_transport_print_event(struct thorium_transport *self, int type, struct thorium_message *message)
{
char *description;
int count;
int source_rank;
int destination_rank;
uint64_t time;
description = EVENT_STRING_SEND;
if (type == EVENT_TYPE_RECEIVE)
description = EVENT_STRING_RECEIVE;
count = thorium_message_count(message);
source_rank = thorium_message_source_node(message);
destination_rank = thorium_message_destination_node(message);
time = core_timer_get_nanoseconds(&self->timer);
time -= self->start_time;
printf("thorium_transport print_event time_nanoseconds= %" PRIu64 " type= %s source= %d destination= %d count= %d\n",
time, description,
source_rank, destination_rank, count);
}
void biosal_input_stream_push_sequences(struct thorium_actor *actor,
struct thorium_message *message)
{
struct biosal_input_command command;
void *buffer;
int store_name;
uint64_t store_first;
uint64_t store_last;
int sequences_to_read;
void *new_buffer;
int new_count;
struct thorium_message new_message;
void *buffer_for_sequence;
struct biosal_dna_sequence dna_sequence;
/*struct core_vector *command_entries;*/
int has_sequence;
int i;
struct biosal_input_stream *concrete_self;
#ifdef BIOSAL_INPUT_STREAM_DEBUG
int count;
int actual_count;
#endif
/* answer immediately
*/
thorium_actor_send_reply_empty(actor, ACTION_INPUT_PUSH_SEQUENCES_READY);
has_sequence = 1;
#ifdef BIOSAL_INPUT_STREAM_DEBUG
printf("DEBUG stream/%d biosal_input_stream_push_sequences entering...\n",
thorium_actor_name(actor));
#endif
buffer = thorium_message_buffer(message);
concrete_self = (struct biosal_input_stream *)thorium_actor_concrete_actor(actor);
biosal_input_command_init_empty(&command);
biosal_input_command_unpack(&command, buffer, thorium_actor_get_ephemeral_memory(actor),
&concrete_self->codec);
#ifdef BIOSAL_INPUT_STREAM_DEBUG
count = thorium_message_count(message);
printf("DEBUG biosal_input_stream_push_sequences after unpack, count %d:\n",
count);
biosal_input_command_print(&command);
#endif
store_name = biosal_input_command_store_name(&command);
store_first = biosal_input_command_store_first(&command);
store_last = biosal_input_command_store_last(&command);
sequences_to_read = store_last - store_first + 1;
#ifdef BIOSAL_INPUT_STREAM_DEBUG
printf("DEBUG biosal_input_stream_push_sequences received ACTION_INPUT_PUSH_SEQUENCES\n");
printf("DEBUG Command before sending it\n");
biosal_input_command_print(&command);
#endif
/*
* add sequences to the input command
*/
buffer_for_sequence = concrete_self->buffer_for_sequence;
/*command_entries = biosal_input_command_entries(&command);*/
i = 0;
/* TODO: actually load something
*/
while (sequences_to_read-- && has_sequence) {
has_sequence = biosal_input_proxy_get_sequence(&concrete_self->proxy,
buffer_for_sequence);
biosal_dna_sequence_init(&dna_sequence, buffer_for_sequence,
&concrete_self->codec, thorium_actor_get_ephemeral_memory(actor));
biosal_input_command_add_entry(&command, &dna_sequence, &concrete_self->codec,
thorium_actor_get_ephemeral_memory(actor));
biosal_dna_sequence_destroy(&dna_sequence, thorium_actor_get_ephemeral_memory(actor));
i++;
}
#ifdef BIOSAL_INPUT_STREAM_DEBUG
printf("DEBUG prepared %d sequences for command\n",
i);
biosal_input_command_print(&command);
#endif
new_count = biosal_input_command_pack_size(&command,
&concrete_self->codec);
new_buffer = thorium_actor_allocate(actor, new_count);
biosal_input_command_pack(&command, new_buffer, &concrete_self->codec);
#ifdef BIOSAL_INPUT_STREAM_DEBUG
actual_count = biosal_input_command_pack(&command, new_buffer);
printf("DEBUG123 new_count %d actual_count %d\n", new_count,
actual_count);
#endif
thorium_message_init(&new_message, ACTION_PUSH_SEQUENCE_DATA_BLOCK,
new_count, new_buffer);
#ifdef BIOSAL_INPUT_STREAM_DEBUG
printf("DEBUG biosal_input_stream_push_sequences sending ACTION_PUSH_SEQUENCE_DATA_BLOCK to %d\n",
store_name);
#endif
thorium_actor_send(actor, store_name, &new_message);
/*
* send sequences to store.
* The required information is the input command
*/
/*
thorium_actor_send_reply_empty(actor, ACTION_INPUT_PUSH_SEQUENCES_REPLY);
*/
/* free memory
*/
#ifdef BIOSAL_INPUT_STREAM_DEBUG
printf("DEBUG freeing %d entries\n",
(int)core_vector_size(command_entries));
#endif
biosal_input_command_destroy(&command, thorium_actor_get_ephemeral_memory(actor));
#if 0
for (i = 0; i < core_vector_size(command_entries); i++) {
a_sequence = (struct biosal_dna_sequence *)core_vector_at(command_entries, i);
biosal_dna_sequence_destroy(a_sequence, thorium_actor_get_ephemeral_memory(actor));
}
core_vector_destroy(command_entries);
#endif
#ifdef BIOSAL_INPUT_STREAM_DEBUG
printf("DEBUG biosal_input_stream_push_sequences EXIT\n");
#endif
}
/*
* Returns 1 if the message was multiplexed.
*
* This is O(1) in regard to the number of thorium nodes.
*/
int thorium_message_multiplexer_multiplex(struct thorium_message_multiplexer *self,
struct thorium_message *message)
{
/*
* If buffer is full, use thorium_node_send_with_transport
*
* get count
*
* if count is below or equal to the threshold
* multiplex the message.
* return 1
*
* return 0
*/
int count;
int current_size;
int maximum_size;
int action;
struct core_memory_pool *pool;
void *new_buffer;
int new_count;
void *buffer;
int destination_node;
int destination_actor;
int new_size;
int required_size;
struct thorium_multiplexed_buffer *real_multiplexed_buffer;
uint64_t time;
int next_node_in_route;
int source_node;
int current_node;
#ifdef DEBUG_MULTIPLEXER
thorium_printf("multiplex\n");
thorium_message_print(message);
#endif
if (CORE_BITMAP_GET_FLAG(self->flags, FLAG_DISABLED)) {
return 0;
}
action = thorium_message_action(message);
CORE_DEBUGGER_ASSERT(action != ACTION_INVALID);
#ifdef THORIUM_MULTIPLEXER_USE_ACTIONS_TO_SKIP
/*
* Don't multiplex already-multiplexed messages.
*/
if (thorium_multiplexer_policy_is_action_to_skip(self->policy, action)) {
return 0;
}
#endif
#ifdef CONFIG_MULTIPLEXER_USE_DECISION_MAKER
thorium_message_multiplexer_update_timeout(self);
#endif
++self->original_message_count;
count = thorium_message_count(message);
destination_node = thorium_message_destination_node(message);
source_node = message->routing_source;
current_node = self->node->name;
next_node_in_route = thorium_router_get_next_rank_in_route(&self->router,
source_node, current_node, destination_node);
/*
thorium_message_print(message);
thorium_printf("router: source_node %d current_node %d next_node_in_route %d"
" destination_node %d\n",
source_node, current_node,
next_node_in_route, destination_node);
*/
#ifdef CONFIG_USE_TOPOLOGY_AWARE_AGGREGATION
/*
* The next node in the route for this message is
* next_node_in_route.
*/
destination_node = next_node_in_route;
#endif
CORE_DEBUGGER_ASSERT(source_node >= 0);
real_multiplexed_buffer = core_vector_at(&self->buffers, destination_node);
CORE_DEBUGGER_ASSERT(real_multiplexed_buffer != NULL);
required_size = thorium_multiplexed_buffer_required_size(real_multiplexed_buffer, count);
buffer = thorium_message_buffer(message);
destination_actor = thorium_message_destination(message);
#ifdef DEBUG_MULTIPLEXER
thorium_printf("DEBUG multiplex count %d required_size %d action %x\n",
count, required_size, action);
#endif
/*
* Don't multiplex non-actor messages.
*/
if (destination_actor == THORIUM_ACTOR_NOBODY) {
return 0;
}
#ifdef CORE_DEBUGGER_ASSERT
if (real_multiplexed_buffer == NULL) {
thorium_printf("Error action %d destination_node %d destination_actor %d\n", action, destination_node,
destination_actor);
}
#endif
current_size = thorium_multiplexed_buffer_current_size(real_multiplexed_buffer);
maximum_size = thorium_multiplexed_buffer_maximum_size(real_multiplexed_buffer);
/*
* Don't multiplex large messages.
*/
if (required_size > maximum_size) {
#ifdef DEBUG_MULTIPLEXER
thorium_printf("too large required_size %d maximum_size %d\n", required_size, maximum_size);
#endif
return 0;
}
/*
thorium_printf("MULTIPLEX_MESSAGE\n");
*/
new_size = current_size + required_size;
/*
* Flush now if there is no space left for the <required_size> bytes
*/
if (new_size > maximum_size) {
#ifdef DEBUG_MULTIPLEXER
thorium_printf("thorium_message_multiplexer: must FLUSH thorium_message_multiplexer_multiplex required_size %d new_size %d maximum_size %d\n",
required_size, new_size, maximum_size);
#endif
thorium_message_multiplexer_flush(self, destination_node, FORCE_YES_SIZE);
current_size = thorium_multiplexed_buffer_current_size(real_multiplexed_buffer);
CORE_DEBUGGER_ASSERT(current_size == 0);
}
time = core_timer_get_nanoseconds(&self->timer);
/*
* If the buffer is empty before adding the data, it means that it is not
* in the list of buffers with content and it must be added.
*/
if (current_size == 0) {
thorium_multiplexed_buffer_set_time(real_multiplexed_buffer, time);
#ifdef THORIUM_MULTIPLEXER_TRACK_BUFFERS_WITH_CONTENT
core_set_add(&self->buffers_with_content, &destination_node);
#endif
/*
* Add it to the timeline.
*/
#ifdef THORIUM_MULTIPLEXER_USE_TREE
core_red_black_tree_add_key_and_value(&self->timeline, &time, &destination_node);
#elif defined(THORIUM_MULTIPLEXER_USE_HEAP)
core_binary_heap_insert(&self->timeline, &time, &destination_node);
#elif defined(THORIUM_MULTIPLEXER_USE_QUEUE)
core_queue_enqueue(&self->timeline, &destination_node);
#endif
}
/*
* The allocation of buffer is lazy.
* The current worker is an exporter of small message for the destination
* "destination_node".
*/
if (thorium_multiplexed_buffer_buffer(real_multiplexed_buffer) == NULL) {
pool = thorium_worker_get_outbound_message_memory_pool(self->worker);
new_count = self->buffer_size_in_bytes + THORIUM_MESSAGE_METADATA_SIZE;
new_buffer = core_memory_pool_allocate(pool, new_count);
thorium_multiplexed_buffer_set_buffer(real_multiplexed_buffer, new_buffer);
}
/*
thorium_printf("DEBUG worker_latency %d ns\n",
thorium_worker_latency(self->worker));
*/
thorium_multiplexed_buffer_append(real_multiplexed_buffer, count, buffer, time);
/*
* Try to flush. This only flushes something if the buffer is full.
*/
if (thorium_message_multiplexer_buffer_is_ready(self, real_multiplexed_buffer)) {
/*
* Try to flush here too. This is required in order to satisfy the
* technical requirement of a DOA limit.
*
* Obviously, don't flush if there is some outbound traffic congestion.
* Otherwise, there will be too many messages on the network.
*/
if (!thorium_worker_has_outbound_traffic_congestion(self->worker)) {
thorium_message_multiplexer_flush(self, destination_node, FORCE_YES_SIZE);
}
}
/*
* Verify invariant.
*/
CORE_DEBUGGER_ASSERT(thorium_multiplexed_buffer_current_size(real_multiplexed_buffer)<= maximum_size);
/*
* Inject the buffer into the worker too.
*/
return 1;
}
void biosal_assembly_graph_store_get_vertex(struct thorium_actor *self, struct thorium_message *message)
{
struct biosal_assembly_vertex vertex;
struct biosal_dna_kmer kmer;
void *buffer;
struct biosal_assembly_graph_store *concrete_self;
struct core_memory_pool *ephemeral_memory;
struct thorium_message new_message;
int new_count;
void *new_buffer;
struct biosal_assembly_vertex *canonical_vertex;
int is_canonical;
int path;
int position;
int count;
path = -1;
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
concrete_self = thorium_actor_concrete_actor(self);
buffer = thorium_message_buffer(message);
count = thorium_message_count(message);
biosal_dna_kmer_init_empty(&kmer);
position = 0;
position += biosal_dna_kmer_unpack(&kmer, buffer, concrete_self->kmer_length,
ephemeral_memory,
&concrete_self->transport_codec);
/*
* Check if a path index was provided too.
*/
if (position < count) {
position += thorium_message_unpack_int(message, position, &path);
}
CORE_DEBUGGER_ASSERT_IS_EQUAL_INT(position, count);
CORE_DEBUGGER_ASSERT(position == count);
canonical_vertex = biosal_assembly_graph_store_find_vertex(self, &kmer);
biosal_assembly_vertex_init_copy(&vertex, canonical_vertex);
is_canonical = biosal_dna_kmer_is_canonical(&kmer, concrete_self->kmer_length,
&concrete_self->transport_codec);
if (!is_canonical) {
biosal_assembly_vertex_invert_arcs(&vertex);
}
biosal_dna_kmer_destroy(&kmer, ephemeral_memory);
new_count = biosal_assembly_vertex_pack_size(&vertex);
new_buffer = thorium_actor_allocate(self, new_count);
biosal_assembly_vertex_pack(&vertex, new_buffer);
thorium_message_init(&new_message, ACTION_ASSEMBLY_GET_VERTEX_REPLY,
new_count, new_buffer);
thorium_actor_send_reply(self, &new_message);
thorium_message_destroy(&new_message);
}
void biosal_assembly_graph_store_push_arc_block(struct thorium_actor *self, struct thorium_message *message)
{
struct biosal_assembly_graph_store *concrete_self;
int size;
int i;
void *buffer;
int count;
struct biosal_assembly_arc_block input_block;
struct biosal_assembly_arc *arc;
struct core_memory_pool *ephemeral_memory;
struct core_vector *input_arcs;
char *sequence;
void *key;
#if 0
/*
* Don't do anything to rule out that this is the problem.
*/
thorium_actor_send_reply_empty(self, ACTION_ASSEMBLY_PUSH_ARC_BLOCK_REPLY);
return;
#endif
concrete_self = thorium_actor_concrete_actor(self);
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
sequence = core_memory_pool_allocate(ephemeral_memory, concrete_self->kmer_length + 1);
++concrete_self->received_arc_block_count;
count = thorium_message_count(message);
buffer = thorium_message_buffer(message);
biosal_assembly_arc_block_init(&input_block, ephemeral_memory, concrete_self->kmer_length,
&concrete_self->transport_codec);
biosal_assembly_arc_block_unpack(&input_block, buffer, concrete_self->kmer_length,
&concrete_self->transport_codec, ephemeral_memory);
input_arcs = biosal_assembly_arc_block_get_arcs(&input_block);
size = core_vector_size(input_arcs);
if (!concrete_self->printed_arc_size) {
printf("DEBUG ARC DELIVERY %d bytes, %d arcs\n",
count, size);
concrete_self->printed_arc_size = 1;
}
key = core_memory_pool_allocate(ephemeral_memory, concrete_self->key_length_in_bytes);
for (i = 0; i < size; i++) {
arc = core_vector_at(input_arcs, i);
#ifdef BIOSAL_ASSEMBLY_ADD_ARCS
biosal_assembly_graph_store_add_arc(self, arc, sequence, key);
#endif
++concrete_self->received_arc_count;
}
core_memory_pool_free(ephemeral_memory, key);
biosal_assembly_arc_block_destroy(&input_block, ephemeral_memory);
/*
*
* Add the arcs to the graph
*/
thorium_actor_send_reply_empty(self, ACTION_ASSEMBLY_PUSH_ARC_BLOCK_REPLY);
core_memory_pool_free(ephemeral_memory, sequence);
}
void biosal_assembly_graph_store_push_kmer_block(struct thorium_actor *self, struct thorium_message *message)
{
struct core_memory_pool *ephemeral_memory;
struct biosal_dna_kmer_frequency_block block;
struct biosal_assembly_vertex *bucket;
void *packed_kmer;
struct core_map_iterator iterator;
struct biosal_assembly_graph_store *concrete_self;
/*int tag;*/
void *key;
struct core_map *kmers;
struct biosal_dna_kmer kmer;
void *buffer;
int count;
struct biosal_dna_kmer encoded_kmer;
char *raw_kmer;
int period;
struct biosal_dna_kmer *kmer_pointer;
int *frequency;
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
concrete_self = thorium_actor_concrete_actor(self);
/*tag = thorium_message_action(message);*/
buffer = thorium_message_buffer(message);
count = thorium_message_count(message);
/*
* Handler for PUSH_DATA
*/
biosal_dna_kmer_frequency_block_init(&block, concrete_self->kmer_length,
ephemeral_memory, &concrete_self->transport_codec, 0);
biosal_dna_kmer_frequency_block_unpack(&block, buffer, ephemeral_memory,
&concrete_self->transport_codec);
key = core_memory_pool_allocate(ephemeral_memory, concrete_self->key_length_in_bytes);
kmers = biosal_dna_kmer_frequency_block_kmers(&block);
core_map_iterator_init(&iterator, kmers);
period = 2500000;
raw_kmer = core_memory_pool_allocate(thorium_actor_get_ephemeral_memory(self),
concrete_self->kmer_length + 1);
if (!concrete_self->printed_vertex_size) {
printf("DEBUG VERTEX DELIVERY %d bytes\n", count);
concrete_self->printed_vertex_size = 1;
}
while (core_map_iterator_has_next(&iterator)) {
/*
* add kmers to store
*/
core_map_iterator_next(&iterator, (void **)&packed_kmer, (void **)&frequency);
/* Store the kmer in 2 bit encoding
*/
biosal_dna_kmer_init_empty(&kmer);
biosal_dna_kmer_unpack(&kmer, packed_kmer, concrete_self->kmer_length,
ephemeral_memory,
&concrete_self->transport_codec);
kmer_pointer = &kmer;
if (concrete_self->codec_are_different) {
/*
* Get a copy of the sequence
*/
biosal_dna_kmer_get_sequence(kmer_pointer, raw_kmer, concrete_self->kmer_length,
&concrete_self->transport_codec);
biosal_dna_kmer_init(&encoded_kmer, raw_kmer, &concrete_self->storage_codec,
thorium_actor_get_ephemeral_memory(self));
kmer_pointer = &encoded_kmer;
}
biosal_dna_kmer_pack_store_key(kmer_pointer, key,
concrete_self->kmer_length, &concrete_self->storage_codec,
thorium_actor_get_ephemeral_memory(self));
#ifdef BIOSAL_DEBUG_ISSUE_540
if (strcmp(raw_kmer, "AGCTGGTAGTCATCACCAGACTGGAACAG") == 0
|| strcmp(raw_kmer, "CGCGATCTGTTGCTGGGCCTAACGTGGTA") == 0
|| strcmp(raw_kmer, "TACCACGTTAGGCCCAGCAACAGATCGCG") == 0) {
printf("Examine store key for %s\n", raw_kmer);
core_debugger_examine(key, concrete_self->key_length_in_bytes);
}
#endif
bucket = core_map_get(&concrete_self->table, key);
if (bucket == NULL) {
/* This is the first time that this kmer is seen.
*/
bucket = core_map_add(&concrete_self->table, key);
biosal_assembly_vertex_init(bucket);
#if 0
printf("DEBUG303 ADD_KEY");
biosal_dna_kmer_print(&encoded_kmer, concrete_self->kmer_length,
&concrete_self->storage_codec, ephemeral_memory);
#endif
}
if (concrete_self->codec_are_different) {
biosal_dna_kmer_destroy(&encoded_kmer,
thorium_actor_get_ephemeral_memory(self));
}
biosal_dna_kmer_destroy(&kmer, ephemeral_memory);
biosal_assembly_vertex_increase_coverage_depth(bucket, *frequency);
if (concrete_self->received >= concrete_self->last_received + period) {
printf("%s/%d received %" PRIu64 " kmers so far,"
" store has %" PRIu64 " canonical kmers, %" PRIu64 " kmers\n",
thorium_actor_script_name(self),
thorium_actor_name(self), concrete_self->received,
core_map_size(&concrete_self->table),
2 * core_map_size(&concrete_self->table));
concrete_self->last_received = concrete_self->received;
}
concrete_self->received += *frequency;
}
core_memory_pool_free(ephemeral_memory, key);
core_memory_pool_free(ephemeral_memory, raw_kmer);
core_map_iterator_destroy(&iterator);
biosal_dna_kmer_frequency_block_destroy(&block, thorium_actor_get_ephemeral_memory(self));
thorium_actor_send_reply_empty(self, ACTION_PUSH_KMER_BLOCK_REPLY);
}
void biosal_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 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_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);
}
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);
}
}
}
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 thorium_worker_work(struct thorium_worker *worker, struct thorium_actor *actor)
{
int dead;
int actor_name;
#ifdef THORIUM_WORKER_DEBUG
int tag;
int destination;
#endif
actor_name = thorium_actor_name(actor);
#ifdef THORIUM_WORKER_DEBUG_SCHEDULER
printf("WORK actor %d\n", actor_name);
#endif
/* the actor died while the work was queued.
*/
if (thorium_actor_dead(actor)) {
printf("NOTICE actor is dead already (thorium_worker_work)\n");
return;
}
#ifdef THORIUM_DISABLE_LOCKLESS_ACTORS
/* lock the actor to prevent another worker from making work
* on the same actor at the same time
*/
if (thorium_actor_trylock(actor) != CORE_LOCK_SUCCESS) {
#ifdef SHOW_FULL_RING_WARNINGS
printf("Warning: CONTENTION worker %d could not lock actor %d, returning the message...\n",
thorium_worker_name(worker),
actor_name);
#endif
return;
}
#endif
/* the actor died while this worker was waiting for the lock
*/
if (thorium_actor_dead(actor)) {
printf("DEBUG thorium_worker_work actor died while the worker was waiting for the lock.\n");
#ifdef THORIUM_WORKER_DEBUG
#endif
/*thorium_actor_unlock(actor);*/
return;
}
/* call the actor receive code
*/
thorium_actor_set_worker(actor, worker);
thorium_actor_work(actor);
/* Free ephemeral memory
*/
core_memory_pool_free_all(&worker->ephemeral_memory);
dead = thorium_actor_dead(actor);
if (dead) {
core_map_delete(&worker->actors, &actor_name);
if (core_bitmap_get_bit_uint32_t(&worker->flags,
FLAG_ENABLE_ACTOR_LOAD_PROFILER)) {
thorium_actor_write_profile(actor, &worker->load_profile_writer);
}
thorium_node_notify_death(worker->node, actor);
}
thorium_actor_set_worker(actor, NULL);
#ifdef THORIUM_WORKER_DEBUG_20140601
if (core_bitmap_get_bit_uint32_t(&worker->flags, FLAG_DEBUG)) {
printf("DEBUG worker/%d after dead call\n",
thorium_worker_name(worker));
}
#endif
#ifdef THORIUM_DISABLE_LOCKLESS_ACTORS
/* Unlock the actor.
* This does not do anything if a death notification
* was sent to the node
*/
thorium_actor_unlock(actor);
#endif
#ifdef THORIUM_WORKER_DEBUG
printf("thorium_worker_work Freeing buffer %p %i tag %i\n",
buffer, thorium_message_count(message),
thorium_message_action(message));
#endif
#ifdef THORIUM_WORKER_DEBUG_20140601
if (core_bitmap_get_bit_uint32_t(&worker->flags, FLAG_DEBUG)) {
printf("DEBUG worker/%d exiting thorium_worker_work\n",
thorium_worker_name(worker));
}
#endif
}
/*
* Returns 1 if the message was demultiplexed.
*
* This is O(1) in regard to the number of thorium nodes.
*/
int thorium_message_multiplexer_demultiplex(struct thorium_message_multiplexer *self,
struct thorium_message *message)
{
/*
* Algorithm:
*
* get tag.
* if tag is ACTION_MULTIPLEXER_MESSAGE
* for every enclosed message
* call thorium_node_prepare_received_message
* call thorium_node_dispatch_message()
* return 1
*
* return 0
*/
int count;
char *buffer;
struct thorium_message new_message;
int new_count;
void *new_buffer;
int position;
struct core_memory_pool *pool;
int messages;
int tag;
int source_node;
int destination_node;
int current_node;
int routing_destination;
#ifdef DEBUG_MULTIPLEXER
thorium_printf("demultiplex message\n");
thorium_message_print(message);
#endif
if (CORE_BITMAP_GET_FLAG(self->flags, FLAG_DISABLED)) {
return 0;
}
tag = thorium_message_action(message);
if (tag != ACTION_MULTIPLEXER_MESSAGE) {
return 0;
}
/*
thorium_printf("MULTIPLEXER demultiplex\n");
*/
messages = 0;
tracepoint(thorium_node, demultiplex_enter, self->node->name,
self->node->tick, messages);
source_node = thorium_message_source_node(message);
destination_node = thorium_message_destination_node(message);
/*
* Remove the metadata from the count.
*/
thorium_message_remove_metadata_from_count(message);
count = thorium_message_count(message);
buffer = thorium_message_buffer(message);
pool = thorium_worker_get_outbound_message_memory_pool(self->worker);
position = 0;
/*
* Inject a message for each enclosed message.
*/
while (position < count) {
core_memory_copy(&new_count, buffer + position, sizeof(new_count));
position += sizeof(new_count);
new_buffer = core_memory_pool_allocate(pool, new_count);
core_memory_copy(new_buffer, buffer + position, new_count);
thorium_message_init_with_nodes(&new_message, new_count, new_buffer,
source_node, destination_node);
thorium_node_prepare_received_message(self->node, &new_message);
/*
* For these demultiplexed messages, there are 2 outcomes:
*
* 1) the message must be delivered locally;
* 2) the message must be forward because this is a middle node in
* the route.
*/
/*
thorium_printf("demultiplex: \n");
thorium_message_print(&new_message);
thorium_printf("\n");
*/
/*
* Mark the message for recycling.
*/
thorium_message_set_worker(&new_message, thorium_worker_name(self->worker));
#ifdef CORE_DEBUGGER_ASSERT_ENABLED
if (thorium_message_action(&new_message) == ACTION_INVALID) {
thorium_printf("Error invalid action DEMUL Multiplexer position %d count %d new_count %d\n",
position, count, new_count);
thorium_message_print(&new_message);
}
#endif
CORE_DEBUGGER_ASSERT(thorium_message_action(&new_message) != ACTION_INVALID);
/*
thorium_printf("DEMULTIPLEX_MESSAGE\n");
*/
/*
thorium_printf("demultiplex, local delivery: \n");
thorium_message_print(&new_message);
*/
current_node = self->node->name;
routing_destination = new_message.routing_destination;
CORE_DEBUGGER_ASSERT(routing_destination >= 0);
/*
* This is a local delivery, nothing to see here.
*/
if (routing_destination == current_node) {
thorium_worker_send_local_delivery(self->worker, &new_message);
/*
* Otherwise, get the next node in the route and send the
* payload there since we can not do anything with it here.
*/
} else {
/*
* Export the message to another node.
* To do this, use an exporter worker.
*/
thorium_worker_send_for_multiplexer(self->worker,
&new_message);
}
/*
thorium_message_destroy(&new_message);
*/
position += new_count;
++messages;
}
CORE_DEBUGGER_ASSERT(messages > 0);
#ifdef DEBUG_MULTIPLEXER
thorium_printf("thorium_message_multiplexer_demultiplex %d messages\n",
messages);
#endif
tracepoint(thorium_node, demultiplex_exit, self->node->name,
self->node->tick, messages);
return 1;
}
