void biosal_assembly_vertex_set_flag(struct biosal_assembly_vertex *self, int flag)
{
CORE_DEBUGGER_ASSERT(flag >= BIOSAL_VERTEX_FLAG_START_VALUE);
CORE_DEBUGGER_ASSERT(flag <= BIOSAL_VERTEX_FLAG_END_VALUE);
CORE_BITMAP_SET_FLAG(self->flags, flag);
}
int core_simple_queue_enqueue(struct core_simple_queue *self, void *data)
{
struct core_simple_queue_item *new_item;
/*
* Allocate an item and copy the data.
*/
new_item = core_simple_queue_allocate_item(self);
CORE_DEBUGGER_ASSERT(new_item != NULL);
CORE_DEBUGGER_ASSERT(new_item->data_ != NULL);
CORE_DEBUGGER_ASSERT(new_item->next_ == NULL);
core_memory_copy(new_item->data_, data, self->bytes_per_unit_);
++self->size_;
/*
* The queue is empty.
*/
if (self->head_ == NULL && self->tail_ == NULL) {
self->tail_ = new_item;
self->head_ = self->tail_;
return 1;
}
/*
* Otherwise, there is at least one element in the queue.
*/
self->tail_->next_ = new_item;
self->tail_ = new_item;
return 1;
}
int core_dynamic_hash_table_iterator_next(struct core_dynamic_hash_table_iterator *self, void **key, void **value)
{
if (!core_dynamic_hash_table_iterator_has_next(self)) {
return 0;
}
CORE_DEBUGGER_ASSERT(core_dynamic_hash_table_state(self->list, self->index) ==
CORE_HASH_TABLE_BUCKET_OCCUPIED);
if (key != NULL) {
*key = core_dynamic_hash_table_key(self->list, self->index);
#ifdef CORE_DEBUGGER_ASSERT
CORE_DEBUGGER_ASSERT(*key != NULL);
#endif
}
if (value != NULL) {
*value = core_dynamic_hash_table_value(self->list, self->index);
#ifdef CORE_DEBUGGER_ASSERT
CORE_DEBUGGER_ASSERT(*value != NULL);
#endif
}
self->index++;
return 1;
}
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);
*/
}
int biosal_dna_kmer_get_symbol(struct biosal_dna_kmer *self, int position,
int kmer_length, struct biosal_dna_codec *codec)
{
CORE_DEBUGGER_ASSERT(position >= 0);
CORE_DEBUGGER_ASSERT(position < kmer_length);
return biosal_dna_codec_get_nucleotide_code(codec, self->encoded_data, position);
}
void thorium_worker_pool_assign_worker_to_actor(struct thorium_worker_pool *pool, int name)
{
int worker_index;
#ifdef THORIUM_WORKER_POOL_USE_LEAST_BUSY
int score;
#endif
#ifdef THORIUM_WORKER_POOL_USE_SCRIPT_ROUND_ROBIN
int script;
struct thorium_actor *actor;
#endif
/*
printf("DEBUG Needs to do actor placement\n");
*/
/* assign this actor to the least busy actor
*/
worker_index = -1;
#ifdef THORIUM_WORKER_POOL_USE_LEAST_BUSY
worker_index = thorium_balancer_select_worker_least_busy(&pool->scheduler, &score);
#elif defined(THORIUM_WORKER_POOL_USE_SCRIPT_ROUND_ROBIN)
actor = thorium_node_get_actor_from_name(pool->node, name);
/*
* Somehow this actor dead a while ago.
*/
if (actor == NULL) {
return;
}
/* The actor can't be dead if it does not have an initial
* placement...
*/
CORE_DEBUGGER_ASSERT(actor != NULL);
script = thorium_actor_script(actor);
worker_index = thorium_balancer_select_worker_script_round_robin(&pool->balancer, script);
#endif
CORE_DEBUGGER_ASSERT(worker_index >= 0);
#ifdef THORIUM_WORKER_POOL_DEBUG
printf("ASSIGNING %d to %d\n", name, worker_index);
#endif
thorium_balancer_set_actor_worker(&pool->balancer, name, worker_index);
}
/*
*This is called from within the actor running inside this worker.
*/
void thorium_worker_free_message(struct thorium_worker *worker, struct thorium_message *message)
{
int source_worker;
void *buffer;
buffer = thorium_message_buffer(message);
source_worker = thorium_message_worker(message);
if (source_worker == worker->name) {
/* This is from the current worker
*/
core_memory_pool_free(&worker->outbound_message_memory_pool, buffer);
#ifdef THORIUM_WORKER_DEBUG_INJECTION
++worker->counter_freed_outbound_buffers_from_self;
#endif
} else {
/* This is from another fellow local worker
* or from another BIOSAL node altogether.
*/
CORE_DEBUGGER_ASSERT(thorium_message_buffer(message) != NULL);
thorium_worker_enqueue_message_for_triage(worker, message);
}
}
int thorium_mpi1_request_test(struct thorium_mpi1_request *self)
{
MPI_Status status;
int flag;
int result;
int count;
flag = 0;
result = MPI_Test(&self->request, &flag, &status);
if (result != MPI_SUCCESS) {
return 0;
}
if (!flag) {
return 0;
}
result = MPI_Get_count(&status, MPI_BYTE, &count);
CORE_DEBUGGER_ASSERT(count >= 0);
if (result != MPI_SUCCESS) {
return 0;
}
self->source = status.MPI_SOURCE;
self->tag = status.MPI_TAG;
self->count = count;
return 1;
}
void thorium_transport_destroy(struct thorium_transport *self)
{
/*
* Print the report if requested.
*/
if (core_bitmap_get_bit_uint32_t(&self->flags, FLAG_PROFILE)) {
thorium_transport_profiler_print_report(&self->transport_profiler);
}
thorium_transport_profiler_destroy(&self->transport_profiler);
CORE_DEBUGGER_ASSERT(thorium_transport_get_active_request_count(self) == 0);
if (self->transport_interface != NULL) {
self->transport_interface->destroy(self);
core_memory_free(self->concrete_transport, MEMORY_TRANSPORT);
self->concrete_transport = NULL;
}
self->node = NULL;
self->rank = -1;
self->size = -1;
core_timer_destroy(&self->timer);
}
int thorium_worker_enqueue_message_for_triage(struct thorium_worker *worker, struct thorium_message *message)
{
#ifdef THORIUM_WORKER_DEBUG_INJECTION
int worker_name;
#endif
CORE_DEBUGGER_ASSERT(thorium_message_buffer(message) != NULL);
if (!core_fast_ring_push_from_producer(&worker->clean_message_ring_for_triage, message)) {
#ifdef SHOW_FULL_RING_WARNINGS
printf("thorium_worker: Warning: ring is full, clean_message_ring_for_triage action= %x\n",
thorium_message_action(message));
#endif
core_fast_queue_enqueue(&worker->clean_message_queue_for_triage, message);
#ifdef THORIUM_WORKER_DEBUG_INJECTION
} else {
/*
* Update software counters.
*/
worker_name = thorium_message_worker(message);
if (worker_name >= 0) {
++worker->counter_injected_outbound_buffers_other_local_workers;
} else {
++worker->counter_injected_inbound_buffers_from_thorium_core;
}
#endif
}
return 1;
}
void core_fasta_input_init(struct biosal_input_format *input)
{
char *file;
struct core_fasta_input *fasta;
uint64_t offset;
fasta = (struct core_fasta_input *)biosal_input_format_implementation(input);
file = biosal_input_format_file(input);
CORE_DEBUGGER_ASSERT(input->operations != NULL);
#if 0
printf("DEBUG BEFORE faulty call.\n");
#endif
offset = biosal_input_format_start_offset(input);
core_buffered_reader_init(&fasta->reader, file, offset);
fasta->buffer = NULL;
fasta->next_header = NULL;
fasta->has_header = 0;
fasta->has_first = 0;
}
int core_dynamic_hash_table_iterator_has_next(struct core_dynamic_hash_table_iterator *self)
{
uint64_t size;
if (self->list == NULL) {
return 0;
}
size = core_dynamic_hash_table_buckets(self->list);
if (size == 0) {
return 0;
}
while (self->index < size
&& core_dynamic_hash_table_state(self->list, self->index) !=
CORE_HASH_TABLE_BUCKET_OCCUPIED) {
self->index++;
}
if (self->index >= size) {
return 0;
}
/* Make sure that the pointed bucket is occupied
*/
CORE_DEBUGGER_ASSERT(core_dynamic_hash_table_state(self->list, self->index) ==
CORE_HASH_TABLE_BUCKET_OCCUPIED);
return 1;
}
void thorium_message_init(struct thorium_message *self, int action, int count,
void *buffer)
{
CORE_DEBUGGER_ASSERT(action != THORIUM_MESSAGE_INVALID_ACTION);
self->action= action;
self->buffer = buffer;
self->count = count;
self->source_actor = -1;
self->destination_actor = -1;
/* ranks are set with thorium_node_resolve */
self->source_node = -1;
self->destination_node = -1;
#ifdef THORIUM_MESSAGE_USE_ROUTING
self->routing_source = -1;
self->routing_destination = -1;
#endif
self->worker = -1;
thorium_message_set_type(self, THORIUM_MESSAGE_TYPE_NONE);
#ifdef THORIUM_MESSAGE_ENABLE_TRACEPOINTS
thorium_message_initialize_tracepoints(self);
#endif
}
/* This can only be called from the PRODUCER
*/
int thorium_worker_enqueue_actor(struct thorium_worker *worker, struct thorium_actor *actor)
{
int value;
CORE_DEBUGGER_ASSERT(actor != NULL);
value = core_fast_ring_push_from_producer(&worker->actors_to_schedule, &actor);
#ifdef SHOW_FULL_RING_WARNINGS
if (!value) {
printf("thorium_worker: Warning: ring is full, actors_to_schedule\n");
}
#endif
/*
* Do a wake up if necessary when scheduling an actor in
* the scheduling queue.
*/
if (value && worker->waiting_is_enabled) {
/*
* This call checks if the thread is currently waiting.
* If it is currently waiting, then a signal is sent
* to tell the operating system to wake up the thread so that
* it continues its good work for the actor computation in thorium.
*/
thorium_worker_signal(worker);
}
return value;
}
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);
}
void thorium_worker_evict_actor(struct thorium_worker *worker, int actor_name)
{
struct thorium_actor *actor;
int name;
struct core_fast_queue saved_actors;
int count;
int value;
core_set_add(&worker->evicted_actors, &actor_name);
core_map_delete(&worker->actors, &actor_name);
core_fast_queue_init(&saved_actors, sizeof(struct thorium_actor *));
/* evict the actor from the scheduling queue
*/
while (thorium_scheduler_dequeue(&worker->scheduler, &actor)) {
name = thorium_actor_name(actor);
if (name != actor_name) {
core_fast_queue_enqueue(&saved_actors,
&actor);
}
}
while (core_fast_queue_dequeue(&saved_actors, &actor)) {
thorium_scheduler_enqueue(&worker->scheduler, actor);
}
core_fast_queue_destroy(&saved_actors);
/* Evict the actor from the ring
*/
count = core_fast_ring_size_from_consumer(&worker->actors_to_schedule);
while (count-- && core_fast_ring_pop_from_consumer(&worker->actors_to_schedule,
&actor)) {
name = thorium_actor_name(actor);
if (name != actor_name) {
/*
* This can not fail logically.
*/
value = core_fast_ring_push_from_producer(&worker->actors_to_schedule,
&actor);
CORE_DEBUGGER_ASSERT(value);
}
}
core_map_iterator_destroy(&worker->actor_iterator);
core_map_iterator_init(&worker->actor_iterator, &worker->actors);
}
void thorium_actor_send_range_default(struct thorium_actor *actor, struct core_vector *actors,
int first, int last,
struct thorium_message *message)
{
int use_binomial_tree;
struct core_vector destinations;
struct core_memory_pool *ephemeral_memory;
int name;
int action;
action = thorium_message_action(message);
use_binomial_tree = 0;
#ifdef USE_BINOMIAL_TREE
/*
* ACTION_ASK_TO_STOP basically kills actors (if they agree to).
* It is a bad idea to use a binomial tree to send this death signal
* since intermediate actors can die before acting as relays.
*/
if (action != ACTION_ASK_TO_STOP)
use_binomial_tree = 1;
#endif
if (!use_binomial_tree) {
thorium_actor_send_range_loop(actor, actors, first, last, message);
return;
}
tracepoint(thorium_binomial_tree, send_range, message, (int)core_vector_size(actors));
/*
* Otherwise, use the binomial tree code path. This algorithm is better since it distributed
* the sending operations intot a binomial tree where there are a lot of intermediate
* actors (to be exact, the number of intermediate actors is close to log2(actors.size)).
*/
ephemeral_memory = thorium_actor_get_ephemeral_memory(actor);
core_vector_init(&destinations, sizeof(int));
core_vector_set_memory_pool(&destinations, ephemeral_memory);
CORE_DEBUGGER_ASSERT(core_vector_empty(&destinations));
core_vector_copy_range(actors, first, last, &destinations);
/*
* Set the source now.
*/
name = thorium_actor_name(actor);
thorium_message_set_source(message, name);
thorium_actor_send_range_binomial_tree(actor, &destinations, message);
core_vector_destroy(&destinations);
}
void thorium_cfs_scheduler_destroy(struct thorium_scheduler *self)
{
struct thorium_cfs_scheduler *concrete_self;
concrete_self = self->concrete_self;
core_red_black_tree_destroy(&concrete_self->tree);
CORE_DEBUGGER_ASSERT(core_memory_pool_profile_balance_count(&concrete_self->pool) == 0);
core_memory_pool_destroy(&concrete_self->pool);
}
void core_dynamic_hash_table_delete(struct core_dynamic_hash_table *self, void *key)
{
void *bucket;
if (!self->resize_in_progress) {
core_hash_table_delete(self->current, key);
CORE_DEBUGGER_ASSERT(core_dynamic_hash_table_get(self, key) == NULL);
return;
}
/* if the resizing is completed, everything is in current
*/
if (core_dynamic_hash_table_resize(self)) {
core_hash_table_delete(self->current, key);
CORE_DEBUGGER_ASSERT(core_dynamic_hash_table_get(self, key) == NULL);
return;
}
/* First look for the key in
* the next table
*/
bucket = core_hash_table_get(self->next, key);
if (bucket != NULL) {
core_hash_table_delete(self->next, key);
CORE_DEBUGGER_ASSERT(core_dynamic_hash_table_get(self, key) == NULL);
return;
}
core_hash_table_delete(self->current, key);
CORE_DEBUGGER_ASSERT(core_dynamic_hash_table_get(self, key) == NULL);
}
void thorium_multiplexed_buffer_append(struct thorium_multiplexed_buffer *self,
int count, void *buffer, uint64_t time)
{
void *multiplexed_buffer;
void *destination_in_buffer;
int required_size;
++self->counter_original_message_count;
CORE_DEBUGGER_ASSERT(self->buffer_ != NULL);
required_size = thorium_multiplexed_buffer_required_size(self, count);
/*
* Make sure there is enough space.
*/
CORE_DEBUGGER_ASSERT(self->maximum_size_ - self->current_size_ >= required_size);
multiplexed_buffer = self->buffer_;
destination_in_buffer = ((char *)multiplexed_buffer) + self->current_size_;
/*
* Append <count><buffer> to the <multiplexed_buffer>
*/
core_memory_copy(destination_in_buffer, &count, sizeof(count));
core_memory_copy((char *)destination_in_buffer + sizeof(count),
buffer, count);
/*
* Add the message.
*/
CORE_DEBUGGER_ASSERT(self->current_size_ <= self->maximum_size_);
self->current_size_ += required_size;
++self->message_count_;
CORE_DEBUGGER_ASSERT(self->message_count_ >= 1);
thorium_multiplexed_buffer_profile(self, time);
}
int thorium_worker_dequeue_message_for_triage(struct thorium_worker *worker, struct thorium_message *message)
{
int value;
value = core_fast_ring_pop_from_consumer(&worker->clean_message_ring_for_triage, message);
#ifdef CORE_DEBUGGER_ENABLE_ASSERT
if (value) {
CORE_DEBUGGER_ASSERT(thorium_message_buffer(message) != NULL);
}
#endif
return value;
}
void core_string_swap_c_string(char *sequence, int i, int j)
{
char value;
CORE_DEBUGGER_ASSERT(sequence != NULL);
value = sequence[i];
sequence[i] = sequence[j];
sequence[j] = value;
#ifdef DEBUG_STRING
printf("SWAP %d %d result %s\n", i, j, sequence);
#endif
}
struct biosal_assembly_vertex *biosal_assembly_graph_store_find_vertex(struct thorium_actor *self,
struct biosal_dna_kmer *kmer)
{
struct core_memory_pool *ephemeral_memory;
struct biosal_assembly_graph_store *concrete_self;
char *sequence;
struct biosal_dna_kmer storage_kmer;
char *key;
struct biosal_assembly_vertex *canonical_vertex;
ephemeral_memory = thorium_actor_get_ephemeral_memory(self);
concrete_self = thorium_actor_concrete_actor(self);
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);
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);
canonical_vertex = core_map_get(&concrete_self->table, key);
#ifdef CORE_DEBUGGER_ASSERT
if (canonical_vertex == NULL) {
printf("not found Seq = %s name %d kmerlength %d key_length %d hash %" PRIu64 "\n", sequence,
thorium_actor_name(self),
concrete_self->kmer_length,
concrete_self->key_length_in_bytes,
biosal_dna_kmer_hash(&storage_kmer, concrete_self->kmer_length,
&concrete_self->storage_codec));
}
#endif
CORE_DEBUGGER_ASSERT(canonical_vertex != NULL);
core_memory_pool_free(ephemeral_memory, sequence);
core_memory_pool_free(ephemeral_memory, key);
biosal_dna_kmer_destroy(&storage_kmer, ephemeral_memory);
return canonical_vertex;
}
void biosal_assembly_graph_store_mark_as_used(struct thorium_actor *self,
struct biosal_assembly_vertex *vertex, int source, int path)
{
struct biosal_assembly_graph_store *concrete_self;
CORE_DEBUGGER_ASSERT(source >= 0);
CORE_DEBUGGER_ASSERT(path >= 0);
concrete_self = thorium_actor_concrete_actor(self);
if (!biosal_assembly_vertex_get_flag(vertex, BIOSAL_VERTEX_FLAG_USED)) {
biosal_assembly_vertex_set_flag(vertex, BIOSAL_VERTEX_FLAG_USED);
++concrete_self->consumed_canonical_vertex_count;
biosal_assembly_graph_store_print_progress(self);
}
#if 0
printf("%s set last_actor %d last_path_index %d\n",
thorium_actor_script_name(self),
source, path);
#endif
biosal_assembly_vertex_set_last_actor(vertex, source, path);
}
int thorium_fifo_scheduler_enqueue(struct thorium_scheduler *self, struct thorium_actor *actor)
{
int priority;
struct core_fast_queue *selected_queue;
struct thorium_fifo_scheduler *queue;
queue = self->concrete_self;
CORE_DEBUGGER_ASSERT(actor != NULL);
priority = thorium_actor_get_priority(actor);
selected_queue = thorium_fifo_scheduler_select_queue(queue, priority);
return core_fast_queue_enqueue(selected_queue, &actor);
}
void core_vector_destroy(struct core_vector *self)
{
if (self->data != NULL) {
core_memory_pool_free(self->memory, self->data);
++self->profile_free_calls;
self->data = NULL;
}
CORE_DEBUGGER_ASSERT(self->profile_allocate_calls == self->profile_free_calls);
self->element_size = 0;
self->maximum_size = 0;
self->size = 0;
core_vector_set_memory_pool(self, NULL);
}
void *core_vector_at(struct core_vector *self, int64_t index)
{
#if 0
CORE_DEBUGGER_ASSERT(index < self->size);
#endif
if (index >= self->size) {
return NULL;
}
if (index < 0) {
return NULL;
}
return ((char *)self->data) + index * self->element_size;
}
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_input_format_init(struct biosal_input_format *input, void *implementation,
struct biosal_input_format_interface *operations, char *file,
uint64_t start_offset, uint64_t end_offset)
{
biosal_input_format_interface_init_fn_t handler;
FILE *descriptor;
#if 0
printf("DEBUG biosal_input_format_init\n");
#endif
input->implementation = implementation;
CORE_DEBUGGER_ASSERT(operations != NULL);
input->operations = operations;
input->sequences = 0;
input->file = file;
input->error = BIOSAL_INPUT_ERROR_NO_ERROR;
input->start_offset = start_offset;
input->end_offset = end_offset;
descriptor = fopen(input->file, "r");
if (descriptor == NULL) {
input->error = BIOSAL_INPUT_ERROR_FILE_NOT_FOUND;
return;
} else {
fclose(descriptor);
}
#if 0
printf("DEBUG INPUT_FORMAT %s from %" PRIu64 " to %" PRIu64 "\n",
file, start_offset, end_offset);
#endif
handler = biosal_input_format_interface_get_init(input->operations);
handler(input);
#if 0
printf("DEBUG after concrete init\n");
#endif
}
/* \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;
}