diff options
Diffstat (limited to 'src')
25 files changed, 1839 insertions, 3403 deletions
diff --git a/src/H5FDioc.c b/src/H5FDioc.c index b00fb51..273ca0f 100644 --- a/src/H5FDioc.c +++ b/src/H5FDioc.c @@ -30,11 +30,21 @@ #include "H5Pprivate.h" /* Property lists */ #include "H5private.h" /* Generic Functions */ +#if 1 /* JRM */ /* For now, H5FDsubfiling_priv.h needs mercury. Since the code that needs it will \ + * move to its own header, just hack it for now. \ + */ +#include "mercury_thread.h" +#include "mercury_thread_mutex.h" +#include "mercury_thread_pool.h" +#endif /* JRM */ + #include "H5FDsubfiling_priv.h" /* The driver identification number, initialized at runtime */ -static hid_t H5FD_IOC_g = 0; +static hid_t H5FD_IOC_g = 0; +#if 0 /* JRM */ /* delete if all goes well */ extern volatile int sf_shutdown_flag; +#endif /* JRM */ /* * These macros check for overflow of various quantities. These macros @@ -227,6 +237,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5FD_ioc_init() */ +#if 0 /* JRM */ /* delete if all goes well */ /*------------------------------------------------------------------------- * Function: H5FD_ioc_set_shutdown_flag * @@ -246,6 +257,7 @@ H5FD_ioc_set_shutdown_flag(int flag) usleep(100); return; } /* end H5FD_ioc_set_shutdown_flag() */ +#endif /* JRM */ /*--------------------------------------------------------------------------- * Function: H5FD__ioc_term @@ -854,30 +866,30 @@ H5FD__ioc_open(const char *name, unsigned flags, hid_t ioc_fapl_id, haddr_t maxa else if (file_ptr->inode > 0) { /* No errors opening the subfiles */ subfiling_context_t *sf_context = get__subfiling_object(file_ptr->fa.common.context_id); - if (sf_context && sf_context->topology->rank_is_ioc) { - if (initialize_ioc_threads(sf_context) < 0) { - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "Unable to initialize IOC threads") + if (sf_context && sf_context->topology->rank_is_ioc) { + if (initialize_ioc_threads(sf_context) < 0) { + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "Unable to initialize IOC threads") + } } } } -} -else -{ - HDputs("We only support sec2 file opens at the moment."); - HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file = %s\n", name) -} + else { + HDputs("We only support sec2 file opens at the moment."); + HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file = %s\n", name) + } -ret_value = (H5FD_t *)file_ptr; + ret_value = (H5FD_t *)file_ptr; -done : if (NULL == ret_value) { - if (file_ptr) { - if (file_ptr->ioc_file) - H5FD_close(file_ptr->ioc_file); - H5FL_FREE(H5FD_ioc_t, file_ptr); - } -} /* end if error */ +done: + if (NULL == ret_value) { + if (file_ptr) { + if (file_ptr->ioc_file) + H5FD_close(file_ptr->ioc_file); + H5FL_FREE(H5FD_ioc_t, file_ptr); + } + } /* end if error */ -FUNC_LEAVE_NOAPI(ret_value) + FUNC_LEAVE_NOAPI(ret_value) } /* end H5FD__ioc_open() */ /*------------------------------------------------------------------------- @@ -1430,5 +1442,6 @@ H5FD_ioc_wait_thread_main(void) void H5FD_ioc_finalize_threads(void) { + return; } diff --git a/src/H5FDioc_threads.c b/src/H5FDioc_threads.c index 3a7ee84..0c3d23c 100644 --- a/src/H5FDioc_threads.c +++ b/src/H5FDioc_threads.c @@ -46,6 +46,12 @@ void __attribute__((destructor)) finalize_ioc_threads(void); int wait_for_thread_main(void); bool tpool_is_empty(void); +#if 1 /* JRM */ + +extern H5FD_ioc_io_queue_t io_queue_g; + +#endif /* JRM */ + /*------------------------------------------------------------------------- * Function: local ioc_thread_main * @@ -110,6 +116,15 @@ initialize_ioc_threads(void *_sf_context) char * envValue; double t_start = 0.0, t_end = 0.0; +#if 0 /* JRM */ /* delete this evenutually */ + HDprintf("\nworld_size = %d\n", world_size); +#endif /* JRM */ + +#if 1 /* JRM */ /* try doubling the size of the pool_request array */ + world_size *= 4; + alloc_size *= 4; +#endif /* JRM */ + assert(context_id != NULL); file_open_count = atomic_load(&sf_file_open_count); @@ -154,6 +169,16 @@ initialize_ioc_threads(void *_sf_context) goto err_exit; } +#if 1 /* JRM */ /* needed for new dispatch code */ + + status = hg_thread_mutex_init(&(io_queue_g.q_mutex)); + if (status) { + puts("hg_thread_mutex_init failed for io_queue_g.q_mutex"); + goto err_exit; + } + +#endif /* JRM */ + /* Allow experimentation with the number of helper threads */ if ((envValue = getenv("IOC_THREAD_POOL_COUNT")) != NULL) { int value_check = atoi(envValue); @@ -267,9 +292,13 @@ translate_opcode(io_op_t op) * *------------------------------------------------------------------------- */ +#if 0 /* JRM */ /* Original version -- expects sf_work_request_t * as its arguement */ static HG_THREAD_RETURN_TYPE handle_work_request(void *arg) { +#if 1 /* JRM */ + int curr_io_ops_pending; +#endif /* JRM */ int status = 0; hg_thread_ret_t ret = 0; sf_work_request_t * msg = (sf_work_request_t *)arg; @@ -298,6 +327,11 @@ handle_work_request(void *arg) } fflush(stdout); +#if 1 /* JRM */ + curr_io_ops_pending = atomic_fetch_sub(&sf_io_ops_pending, 1); + HDassert(curr_io_ops_pending > 0); +#endif /* JRM */ + atomic_fetch_sub(&sf_work_pending, 1); // atomic msg->in_progress = 0; if (msg->dependents) { @@ -315,6 +349,80 @@ handle_work_request(void *arg) return ret; } +#else /* JRM */ /* Modified version -- expects H5FD_ioc_io_queue_entry_t * as its argument */ + +static HG_THREAD_RETURN_TYPE +handle_work_request(void *arg) +{ +#if 1 /* JRM */ + int curr_io_ops_pending; +#endif /* JRM */ + int status = 0; + hg_thread_ret_t ret = 0; + H5FD_ioc_io_queue_entry_t *q_entry_ptr = (H5FD_ioc_io_queue_entry_t *)arg; + sf_work_request_t * msg = &(q_entry_ptr->wk_req); + int64_t file_context_id = msg->header[2]; + subfiling_context_t * sf_context = NULL; + + HDassert(q_entry_ptr); + HDassert(q_entry_ptr->magic == H5FD_IOC__IO_Q_ENTRY_MAGIC); + HDassert(q_entry_ptr->in_progress); + + sf_context = get__subfiling_object(file_context_id); + assert(sf_context != NULL); + + atomic_fetch_add(&sf_work_pending, 1); // atomic + msg->in_progress = 1; + switch (msg->tag) { + case WRITE_INDEP: + status = queue_write_indep(msg, msg->subfile_rank, msg->source, sf_context->sf_data_comm, + q_entry_ptr->counter); + break; + case READ_INDEP: + status = queue_read_indep(msg, msg->subfile_rank, msg->source, sf_context->sf_data_comm); + break; + default: + HDprintf("[ioc(%d)] received message tag(%x)from rank %d\n", msg->subfile_rank, msg->tag, + msg->source); + status = -1; + break; + } + fflush(stdout); + + atomic_fetch_sub(&sf_work_pending, 1); // atomic + + if (status < 0) { + HDprintf("[ioc(%d) %s]: request(%s) filename=%s from " + "rank(%d), size=%ld, offset=%ld FAILED\n", + msg->subfile_rank, __func__, translate_opcode((io_op_t)msg->tag), sf_context->sf_filename, + msg->source, msg->header[0], msg->header[1]); + + fflush(stdout); + } + +#if 1 /* JRM */ + curr_io_ops_pending = atomic_fetch_sub(&sf_io_ops_pending, 1); + if (curr_io_ops_pending <= 0) { + + HDprintf("\n\nhandle_work_request: curr_io_ops_pending = %d, op = %d, offset/len = %lld/%lld.\n\n", + curr_io_ops_pending, (msg->tag), (long long)(msg->header[1]), (long long)(msg->header[0])); + HDfflush(stdout); + } + + HDassert(curr_io_ops_pending > 0); +#endif /* JRM */ + + /* complete the I/O request */ + H5FD_ioc__complete_io_q_entry(q_entry_ptr); + + /* Check the I/O Queue to see if there are any dispatchable entries */ + H5FD_ioc__dispatch_elegible_io_q_entries(); + + return ret; +} + +#endif /* JRM */ /* Modified version -- expects H5FD_ioc_io_queue_entry_t * as its argument */ + void ioc__wait_for_serialize(void *_work) { @@ -425,6 +533,9 @@ check__overlap(void *_work, int current_index, int *conflict_id) int tpool_add_work(void *_work) { +#if 1 /* JRM */ + int curr_io_ops_pending; +#endif /* JRM */ static int work_index = 0; int conflict_id = -1; sf_work_request_t *work = (sf_work_request_t *)_work; @@ -448,6 +559,17 @@ tpool_add_work(void *_work) pool_request[work_index].func = handle_work_request; pool_request[work_index].args = work; +#if 1 /* JRM */ + curr_io_ops_pending = atomic_fetch_add(&sf_io_ops_pending, 1); + + HDassert(curr_io_ops_pending >= 0); + + if (curr_io_ops_pending >= pool_concurrent_max) { + + HDfprintf(stderr, "\n\n*** curr_io_ops_pending = %d >= pool_concurrent_max = %d ***\n\n", + curr_io_ops_pending, pool_concurrent_max); + } +#endif /* JRM */ hg_thread_pool_post(ioc_thread_pool, &pool_request[work_index++]); hg_thread_mutex_unlock(&ioc_mutex); return 0; @@ -538,3 +660,418 @@ wait_for_thread_main(void) } return 0; } + +/*------------------------------------------------------------------------- + * Function: H5FD_ioc_take_down_thread_pool + * + * Purpose: Destroy the thread pool if it exists. + * + * This function should only be called on shutdown after all + * pending I/O operations have completed. + * + * Return: void + * + * Programmer: JRM -- 10/27/21 + * + * Changes: None. + * + *------------------------------------------------------------------------- + */ +void +H5FD_ioc_take_down_thread_pool(void) +{ + HDassert(0 == atomic_load(&sf_io_ops_pending)); + + if (ioc_thread_pool != NULL) { + hg_thread_pool_destroy(ioc_thread_pool); + ioc_thread_pool = NULL; + } + + return; + +} /* H5FD_ioc_take_down_thread_pool() */ + +#if 1 /* JRM */ /* dispatch code -- move elsewhere? */ + +/*------------------------------------------------------------------------- + * Function: H5FD_ioc__alloc_io_q_entry + * + * Purpose: Allocate and initialize an instance of + * H5FD_ioc_io_queue_entry_t. Return pointer to the new + * instance on success, and NULL on failure. + * + * Return: Pointer to new instance of H5FD_ioc_io_queue_entry_t + * on success, and NULL on failure. + * + * Programmer: JRM -- 11/6/21 + * + * Changes: None. + * + *------------------------------------------------------------------------- + */ +/* TODO: update function when we decide how to handle error reporting in the IOCs */ +H5FD_ioc_io_queue_entry_t * +H5FD_ioc__alloc_io_q_entry(void) +{ + H5FD_ioc_io_queue_entry_t *q_entry_ptr = NULL; + + q_entry_ptr = (H5FD_ioc_io_queue_entry_t *)HDmalloc(sizeof(H5FD_ioc_io_queue_entry_t)); + + if (q_entry_ptr) { + + q_entry_ptr->magic = H5FD_IOC__IO_Q_ENTRY_MAGIC; + q_entry_ptr->next = NULL; + q_entry_ptr->prev = NULL; + q_entry_ptr->in_progress = FALSE; + q_entry_ptr->counter = 0; + + /* will memcpy the wk_req field, so don't bother to initialize */ + /* will initialize thread_wk field before use */ + +#if H5FD_IOC__COLLECT_STATS + q_entry_ptr->q_time = 0; + q_entry_ptr->dispatch_time = 0; +#endif /* H5FD_IOC__COLLECT_STATS */ + } + + return (q_entry_ptr); + +} /* H5FD_ioc__alloc_io_q_entry() */ + +/*------------------------------------------------------------------------- + * Function: H5FD_ioc__complete_io_q_entry + * + * Purpose: Update the IOC I/O Queue for the completion of an I/O + * request. + * + * To do this: + * + * 1) Remove the entry from the I/O Queue + * + * 2) If so configured, update statistics + * + * 3) Discard the instance of H5FD_ioc_io_queue_entry_t. + * + * Return: void. + * + * Programmer: JRM -- 11/7/21 + * + * Changes: None. + * + *------------------------------------------------------------------------- + */ +/* TODO: update function when we decide how to handle error reporting in the IOCs */ +/* TODO: Update for per file I/O Queue */ +void +H5FD_ioc__complete_io_q_entry(H5FD_ioc_io_queue_entry_t *entry_ptr) +{ +#if 0 /* H5FD_IOC__COLLECT_STATS */ + uint64_t queued_time; + uint64_t execution_time; +#endif /* H5FD_IOC__COLLECT_STATS */ + + HDassert(entry_ptr); + HDassert(entry_ptr->magic == H5FD_IOC__IO_Q_ENTRY_MAGIC); + + /* must obtain io_queue_g mutex before deleting and updating stats */ + hg_thread_mutex_lock(&(io_queue_g.q_mutex)); + + HDassert(io_queue_g.magic == H5FD_IOC__IO_Q_MAGIC); + HDassert(io_queue_g.num_pending + io_queue_g.num_in_progress == io_queue_g.q_len); + HDassert(io_queue_g.num_in_progress > 0); + + H5FD_IOC__Q_REMOVE(&io_queue_g, entry_ptr); + + io_queue_g.num_in_progress--; + + HDassert(io_queue_g.num_pending + io_queue_g.num_in_progress == io_queue_g.q_len); + +#if H5FD_IOC__COLLECT_STATS +#if 0 /* no place to collect this yet */ + /* Compute the queued and execution time */ + queued_time = entry_ptr->dispatch_time - entry_ptr->q_time; + execution_time = H5_now_usec() = entry_ptr->dispatch_time; +#endif + + io_queue_g.requests_completed++; + + entry_ptr->q_time = H5_now_usec(); + +#endif /* H5FD_IOC__COLLECT_STATS */ + + hg_thread_mutex_unlock(&(io_queue_g.q_mutex)); + + HDassert(entry_ptr->wk_req.buffer == NULL); + + H5FD_ioc__free_io_q_entry(entry_ptr); + + entry_ptr = NULL; + + return; + +} /* H5FD_ioc__complete_io_q_entry() */ + +/*------------------------------------------------------------------------- + * Function: H5FD_ioc__dispatch_elegible_io_q_entries + * + * Purpose: Scan the IOC I/O Queue for dispatchable entries, and + * dispatch any such entries found. + * + * Do this by scanning the I/O queue from head to tail for + * entries that: + * + * 1) Have not already been dispatched + * + * 2) Either: + * + * a) do not intersect with any prior entries on the + * I/O queue, or + * + * b) Are read requests, and all intersections are with + * prior read requests. + * + * Dispatch any such entries found. + * + * Do this to maintain the POSIX semantics required by + * HDF5. + * + * Return: void. + * + * Programmer: JRM -- 11/7/21 + * + * Changes: None. + * + *------------------------------------------------------------------------- + */ +/* TODO: update function when we decide how to handle error reporting in the IOCs */ +/* TODO: Update for per file I/O Queue */ +/* TODO: Keep an eye on statistics and optimize this algorithm if necessary. While it is O(N) + * where N is the number of elements in the I/O Queue if there are are no-overlaps, it + * can become O(N**2) in the worst case. + */ +void +H5FD_ioc__dispatch_elegible_io_q_entries(void) +{ + hbool_t conflict_detected; + int64_t entry_offset; + int64_t entry_len; + int64_t scan_offset; + int64_t scan_len; + H5FD_ioc_io_queue_entry_t *entry_ptr = NULL; + H5FD_ioc_io_queue_entry_t *scan_ptr = NULL; + + hg_thread_mutex_lock(&(io_queue_g.q_mutex)); + + HDassert(io_queue_g.magic == H5FD_IOC__IO_Q_MAGIC); + + entry_ptr = io_queue_g.q_head; + + /* sanity check on first element in the I/O queue */ + HDassert((entry_ptr == NULL) || (entry_ptr->prev == NULL)); + + while ((entry_ptr) && (io_queue_g.num_pending > 0)) { + + HDassert(entry_ptr->magic == H5FD_IOC__IO_Q_ENTRY_MAGIC); + + if (!entry_ptr->in_progress) { + + entry_offset = entry_ptr->wk_req.header[1]; + entry_len = entry_ptr->wk_req.header[0]; + + conflict_detected = FALSE; + + scan_ptr = entry_ptr->prev; + + HDassert((scan_ptr == NULL) || (scan_ptr->magic == H5FD_IOC__IO_Q_ENTRY_MAGIC)); + + while ((scan_ptr) && (!conflict_detected)) { + + /* check for overlaps */ + scan_offset = scan_ptr->wk_req.header[1]; + scan_len = scan_ptr->wk_req.header[0]; + + /* at present, I/O requests are scalar -- i.e. single blocks specified by offset and length. + * when this changes, this if statment will have to be updated accordingly. + */ + if (!(((scan_offset + scan_len) < entry_offset) || + ((entry_offset + entry_len) < scan_offset))) { + + /* the two request overlap -- unless they are both reads, we have detected a conflict */ + + /* TODO: update this if statement when we add collective I/O */ + if ((entry_ptr->wk_req.tag != READ_INDEP) || (scan_ptr->wk_req.tag != READ_INDEP)) { + + conflict_detected = TRUE; + } + } + + scan_ptr = scan_ptr->prev; + } + + if (!conflict_detected) { /* dispatch I/O request */ + + HDassert(scan_ptr == NULL); + HDassert(!entry_ptr->in_progress); + + entry_ptr->in_progress = TRUE; + + HDassert(io_queue_g.num_pending > 0); + + io_queue_g.num_pending--; + io_queue_g.num_in_progress++; + + HDassert(io_queue_g.num_pending + io_queue_g.num_in_progress == io_queue_g.q_len); + + entry_ptr->thread_wk.func = handle_work_request; + entry_ptr->thread_wk.args = entry_ptr; + +#if H5FD_IOC__COLLECT_STATS + if (io_queue_g.num_in_progress > io_queue_g.max_num_in_progress) { + + io_queue_g.max_num_in_progress = io_queue_g.num_in_progress; + } + + io_queue_g.requests_dispatched++; + + entry_ptr->dispatch_time = H5_now_usec(); + +#endif /* H5FD_IOC__COLLECT_STATS */ + + hg_thread_pool_post(ioc_thread_pool, &(entry_ptr->thread_wk)); + } + } + + entry_ptr = entry_ptr->next; + } + + hg_thread_mutex_unlock(&(io_queue_g.q_mutex)); + +} /* H5FD_ioc__dispatch_elegible_io_q_entries() */ + +/*------------------------------------------------------------------------- + * Function: H5FD_ioc__free_io_q_entry + * + * Purpose: Free the supplied instance of H5FD_ioc_io_queue_entry_t. + * + * Verify that magic field is set to + * H5FD_IOC__IO_Q_ENTRY_MAGIC, and that the next and prev + * fields are NULL. + * + * Return: void. + * + * Programmer: JRM -- 11/6/21 + * + * Changes: None. + * + *------------------------------------------------------------------------- + */ +/* TODO: update function when we decide how to handle error reporting in the IOCs */ +void +H5FD_ioc__free_io_q_entry(H5FD_ioc_io_queue_entry_t *q_entry_ptr) +{ + /* use assertions for error checking, since the following should never fail. */ + + HDassert(q_entry_ptr); + HDassert(q_entry_ptr->magic == H5FD_IOC__IO_Q_ENTRY_MAGIC); + HDassert(q_entry_ptr->next == NULL); + HDassert(q_entry_ptr->prev == NULL); + HDassert(q_entry_ptr->wk_req.buffer == NULL); + + q_entry_ptr->magic = 0; + + HDfree(q_entry_ptr); + + q_entry_ptr = NULL; + + return; + +} /* H5FD_ioc__free_c_io_q_entry() */ + +/*------------------------------------------------------------------------- + * Function: H5FD_ioc__queue_io_q_entry + * + * Purpose: Add an I/O request to the tail of the IOC I/O Queue. + * + * To do this, we must: + * + * 1) allocate a new instance of H5FD_ioc_io_queue_entry_t + * + * 2) Initialize the new instance and copy the supplied + * instance of sf_work_request_t into it. + * + * 3) Append it to the IOC I/O queue. + * + * Note that this does not dispatch the request even if it + * is eligible for immediate dispatch. This is done with + * a call to H5FD_ioc__dispatch_elegible_io_q_entries(). + * + * Return: void. + * + * Programmer: JRM -- 11/7/21 + * + * Changes: None. + * + *------------------------------------------------------------------------- + */ +/* TODO: update function when we decide how to handle error reporting in the IOCs */ +/* TODO: Update for per file I/O Queue */ +void +H5FD_ioc__queue_io_q_entry(sf_work_request_t *wk_req_ptr) +{ + H5FD_ioc_io_queue_entry_t *entry_ptr = NULL; + + HDassert(wk_req_ptr); + HDassert(io_queue_g.magic == H5FD_IOC__IO_Q_MAGIC); + + entry_ptr = H5FD_ioc__alloc_io_q_entry(); + + HDassert(entry_ptr); + HDassert(entry_ptr->magic == H5FD_IOC__IO_Q_ENTRY_MAGIC); + + HDmemcpy((void *)(&(entry_ptr->wk_req)), (const void *)wk_req_ptr, sizeof(sf_work_request_t)); + + /* must obtain io_queue_g mutex before appending */ + hg_thread_mutex_lock(&(io_queue_g.q_mutex)); + + entry_ptr->counter = io_queue_g.req_counter++; + + io_queue_g.num_pending++; + + H5FD_IOC__Q_APPEND(&io_queue_g, entry_ptr); + + HDassert(io_queue_g.num_pending + io_queue_g.num_in_progress == io_queue_g.q_len); + +#if H5FD_IOC__COLLECT_STATS + + entry_ptr->q_time = H5_now_usec(); + + if (io_queue_g.q_len > io_queue_g.max_q_len) { + + io_queue_g.max_q_len = io_queue_g.q_len; + } + + if (io_queue_g.num_pending > io_queue_g.max_num_pending) { + + io_queue_g.max_num_pending = io_queue_g.num_pending; + } + + if (entry_ptr->wk_req.tag == READ_INDEP) { + + io_queue_g.ind_read_requests++; + } + else if (entry_ptr->wk_req.tag == WRITE_INDEP) { + + io_queue_g.ind_write_requests++; + } + + io_queue_g.requests_queued++; + +#endif /* H5FD_IOC__COLLECT_STATS */ + + hg_thread_mutex_unlock(&(io_queue_g.q_mutex)); + + return; + +} /* H5FD_ioc__queue_io_q_entry() */ + +#endif /* JRM */ /* dispatch code -- move elsewhere? */ diff --git a/src/H5FDsubfile_int.c b/src/H5FDsubfile_int.c index 0d231fa..ecf706f 100644 --- a/src/H5FDsubfile_int.c +++ b/src/H5FDsubfile_int.c @@ -71,7 +71,7 @@ static stat_record_t subfiling_stats[TOTAL_STAT_COUNT]; #define SF_READ_WAIT_TIME (subfiling_stats[READ_WAIT].total / (double)subfiling_stats[READ_WAIT].op_count) #define SF_QUEUE_DELAYS (subfiling_stats[QUEUE_STAT].total) -#define SF_ALIGNMENT 8 +#define SF_ALIGNMENT 8 static void maybe_initialize_statistics(void) @@ -460,7 +460,9 @@ close__subfiles(subfiling_context_t *sf_context, uint64_t fid) HDassert((sf_context != NULL)); t0 = MPI_Wtime(); -#if MPI_VERSION >= 3 && MPI_SUBVERSION >= 1 +/* TODO: can't use comm world here -- must use communicator set in the file open */ +//#if MPI_VERSION >= 3 && MPI_SUBVERSION >= 1 +#if 0 /* JRM */ /* Just use regular barrier */ MPI_Request b_req = MPI_REQUEST_NULL; int mpi_status = MPI_Ibarrier(MPI_COMM_WORLD, &b_req); if (mpi_status == MPI_SUCCESS) { @@ -502,6 +504,7 @@ close__subfiles(subfiling_context_t *sf_context, uint64_t fid) * currently open, we can shutdown the IO concentrator * as part of the file close. */ +#if 0 /* JRM */ /* delete this if all goes well */ if (file_open_count == 1) { /* Shutdown the main IOC thread */ H5FD_ioc_set_shutdown_flag(1); @@ -514,9 +517,37 @@ close__subfiles(subfiling_context_t *sf_context, uint64_t fid) t1 = t2; t_main_exit = t2 - t1; H5FD_ioc_finalize_threads(); + + t2 = MPI_Wtime(); + } +#else /* JRM */ + if (file_open_count == 1) { + + HDassert(0 == atomic_load(&sf_shutdown_flag)); + + /* Shutdown the main IOC thread */ + atomic_init(&sf_shutdown_flag, 1); + + /* Allow ioc_main to exit.*/ + do { + + usleep(20); + + } while (0 != atomic_load(&sf_shutdown_flag)); + + t1 = MPI_Wtime(); + H5FD_ioc_wait_thread_main(); + t2 = MPI_Wtime(); + t1 = t2; + t_main_exit = t2 - t1; + + H5FD_ioc_take_down_thread_pool(); + t2 = MPI_Wtime(); } +#endif /* JRM */ + t_finalize_threads = t2 - t1; if ((subfile_fid = sf_context->sf_fid) > 0) { @@ -654,8 +685,10 @@ sf_write_data(int fd, int64_t file_offset, void *data_buffer, int64_t data_size, ssize_t written = 0; while (bytes_remaining) { if ((written = pwrite(fd, this_data, (size_t)bytes_remaining, file_offset)) < 0) { + int saved_errno = errno; struct stat statbuf; perror("pwrite failed!"); + HDprintf("\nerrno = %d (%s)\n\n", saved_errno, strerror(saved_errno)); fstat(fd, &statbuf); HDprintf("[ioc(%d) %s] pwrite(fd, data, bytes_remaining=%ld, " "file_offset=%ld), fd=%d, st_size=%ld\n", @@ -1502,7 +1535,11 @@ H5FD__open_subfiles(void *_config_info, uint64_t h5_file_id, int flags) /* Ensure that the IOC service won't exit * as we prepare to start up.. */ +#if 0 /* JRM */ /* delete if all goes well */ H5FD_ioc_set_shutdown_flag(0); +#else /* JRM */ + atomic_init(&sf_shutdown_flag, 0); +#endif /* JRM */ /* If we're actually using the IOCs, we will * start the service threads on the identified diff --git a/src/H5FDsubfile_mpi.c b/src/H5FDsubfile_mpi.c index 2204d8d..d6f7cdf 100644 --- a/src/H5FDsubfile_mpi.c +++ b/src/H5FDsubfile_mpi.c @@ -43,6 +43,13 @@ atomic_int sf_file_refcount = 0; atomic_int sf_ioc_fini_refcount = 0; atomic_int sf_ioc_ready = 0; atomic_int sf_shutdown_flag = 0; +#if 1 /* JRM */ +/* sf_io_ops_pending is use to track the number of I/O operations pending so that we can wait + * until all I/O operations have been serviced before shutting down the worker thread pool. + * The value of this variable must always be non-negative. + */ +atomic_int sf_io_ops_pending = 0; +#endif /* JRM */ /* * Structure definitions to enable async io completions @@ -106,9 +113,38 @@ int client_op_index = 0; int client_op_size = 0; client_xfer_info_t *client_ops = NULL; +#if 1 /* JRM */ /* Find a better place for this */ +H5FD_ioc_io_queue_t io_queue_g = { + /* magic = */ H5FD_IOC__IO_Q_MAGIC, + /* q_head = */ NULL, + /* q_tail = */ NULL, + /* num_pending = */ 0, + /* num_in_progress = */ 0, + /* q_len = */ 0, + /* req_counter = */ 0, + /* q_mutex = */ + PTHREAD_MUTEX_INITIALIZER +#if H5FD_IOC__COLLECT_STATS + /* comma to allow further initializers */, + /* max_q_len = */ 0, + /* max_num_pending = */ 0, + /* max_num_in_progress = */ 0, + /* ind_read_requests = */ 0, + /* ind_write_requests = */ 0, + /* requests_queued = */ 0, + /* requests_dispatched = */ 0, + /* requests_completed = */ 0 +#endif /* H5FD_IOC__COLLECT_STATS */ +}; +#endif /* JRM */ /* Find a better place for this */ + /* const char *sf_subfile_prefix = "."; */ -#define MAX_WORK_PER_RANK 2 +#if 0 /* JRM */ +#define MAX_WORK_PER_RANK 2 +#else /* JRM */ +#define MAX_WORK_PER_RANK 4 /* just to see if this changes anything */ +#endif /* JRM */ #define K(n) ((n)*1024) #define M(n) ((n) * (1024 * 1024)) #define DEFAULT_STRIPE_SIZE M(32) @@ -955,6 +991,7 @@ async_completion(void *arg) * Changes: Initial Version/None. *------------------------------------------------------------------------- */ +#if 0 /* JRM */ /* original version */ static int write__independent_async(int n_io_concentrators, hid_t context_id, int64_t offset, int64_t elements, int H5_ATTR_PARALLEL_UNUSED dtype_extent, const void *data, io_req_t **io_req) @@ -1064,8 +1101,167 @@ write__independent_async(int n_io_concentrators, hid_t context_id, int64_t offse sf_io_request->prev = sf_io_request->next = NULL; /* Start the actual data transfer */ +#if 1 /* JRM */ /* experiment with MPI_Issend() */ status = MPI_Isend(data, (int)elements, MPI_BYTE, io_concentrator[ioc_start], WRITE_INDEP_DATA, sf_context->sf_data_comm, &sf_io_request->completion_func.io_args.io_req); +#else /* JRM */ +#if 1 /* JRM */ /* experiment with MPI_Send */ + status = MPI_Issend(data, (int)elements, MPI_BYTE, io_concentrator[ioc_start], WRITE_INDEP_DATA, + sf_context->sf_data_comm, &sf_io_request->completion_func.io_args.io_req); +#else /* JRM */ + status = MPI_Send(data, (int)elements, MPI_BYTE, io_concentrator[ioc_start], WRITE_INDEP_DATA, + sf_context->sf_data_comm); +#endif /* JRM */ +#endif /* JRM */ + + /* When we actually have the async IO support, + * the request should be queued before we + * return to the caller. + * Having queued the IO operation, we might want to + * get additional work started before allowing the + * queued IO requests to make further progress and/or + * to complete, so we just return to the caller. + */ + + if (status == MPI_SUCCESS) { + sf_io_request->completion_func.pending = 1; + *io_req = sf_io_request; + } + else { + puts("MPI_Isend must have failed!"); + free(sf_io_request); + *io_req = NULL; + } + return status; +} /* end write__independent_async() */ + +#else /* JRM */ /* modified to use IOC supplied tag for data send */ + +static int +write__independent_async(int n_io_concentrators, hid_t context_id, int64_t offset, int64_t elements, + int H5_ATTR_PARALLEL_UNUSED dtype_extent, const void *data, io_req_t **io_req) +{ + + int ack = 0, active_sends = 0, n_waiting = 0, status = 0; + int64_t stripe_size, ioc_row, start_id, ioc_start, ioc_offset; + int * io_concentrator = NULL; + io_req_t * sf_io_request = NULL; + MPI_Request ackrequest; + int64_t msg[3] = { + 0, + }; + + subfiling_context_t *sf_context = get__subfiling_object(context_id); + assert(sf_context != NULL); + + /* Calculate the IOC that we'll send the IO request to */ + stripe_size = sf_context->sf_stripe_size; + + start_id = offset / stripe_size; + ioc_row = start_id / n_io_concentrators; + ioc_offset = (offset % stripe_size) + (ioc_row * stripe_size); + ioc_start = start_id % n_io_concentrators; + + io_concentrator = sf_context->topology->io_concentrator; + assert(io_concentrator != NULL); + + /* Make sure that we can return a request structure + * if everything is working correctly + */ + assert(io_req); + + /* Prepare an IO request. + * This gets sent to the ioc identified by the file offset. + * (see above: Calculate the IOC)) + */ + msg[0] = elements; + msg[1] = ioc_offset; + msg[2] = context_id; +#ifdef VERBOSE + printf("[%s ioc(%ld)] elements=%ld, offset=%ld, file_offset=%ld\n", __func__, ioc_start, elements, offset, + ioc_offset); + fflush(stdout); +#endif + status = MPI_Send(msg, 3, MPI_INT64_T, io_concentrator[ioc_start], WRITE_INDEP, sf_context->sf_msg_comm); + if (status != MPI_SUCCESS) { + int len; + char estring[MPI_MAX_ERROR_STRING]; + MPI_Error_string(status, estring, &len); + printf("[%d] ERROR! MPI_Send of %ld bytes to %d returned an " + "error(%s)\n", + WORLD_RANK(sf_context), sizeof(msg), io_concentrator[ioc_start], estring); + fflush(stdout); + return -1; + } + else + active_sends++; + /* + * We wait for memory to be allocated on the target IOC so that we can + * start sending user data. Once memory is allocated, we will receive + * an ACK (or NACK) message from the IOC to allow us to proceed. + */ + /* On ACK, IOC will send tag to be used for data send -- need this to + * distinguish between multiple concurrent writes from a single rank. + */ + status = MPI_Irecv(&ack, 1, MPI_INT, io_concentrator[ioc_start], WRITE_INDEP_ACK, + sf_context->sf_data_comm, &ackrequest); + + if (status != MPI_SUCCESS) { + printf("[%d %s] MPI_Irecv failed\n", WORLD_RANK(sf_context), __func__); + fflush(stdout); + return -1; + } + + n_waiting = active_sends; + + while (n_waiting) { + int flag = 0; + status = MPI_Test(&ackrequest, &flag, MPI_STATUS_IGNORE); + if (status == MPI_SUCCESS) { + if (flag == 0) + usleep(0); + else { + n_waiting--; + if (ack == 0) { /* NACK */ + printf("%s - Received NACK!\n", __func__); + } + } + } + } + + /* At this point in the new implementation, we should queue + * the async write so that when the top level VFD tells us + * to complete all pending IO requests, we have all the info + * we need to accomplish that. + */ + sf_io_request = (io_req_t *)malloc(sizeof(io_req_t)); + assert(sf_io_request); + + sf_io_request->completion_func.io_args.ioc = (int)ioc_start; + sf_io_request->completion_func.io_args.context_id = context_id; + sf_io_request->completion_func.io_args.offset = offset; + sf_io_request->completion_func.io_args.elements = elements; + sf_io_request->completion_func.io_args.data = cast_to_void(data); + sf_io_request->completion_func.io_args.io_req = MPI_REQUEST_NULL; + sf_io_request->completion_func.io_function = async_completion; + sf_io_request->completion_func.pending = 0; + + sf_io_request->prev = sf_io_request->next = NULL; + /* Start the actual data transfer */ + +#if 1 /* JRM */ /* experiment with MPI_Issend() */ + /* use ack from IOC as the tag for the send */ + status = MPI_Isend(data, (int)elements, MPI_BYTE, io_concentrator[ioc_start], ack, + sf_context->sf_data_comm, &sf_io_request->completion_func.io_args.io_req); +#else /* JRM */ +#if 1 /* JRM */ /* experiment with MPI_Send */ + status = MPI_Issend(data, (int)elements, MPI_BYTE, io_concentrator[ioc_start], WRITE_INDEP_DATA, + sf_context->sf_data_comm, &sf_io_request->completion_func.io_args.io_req); +#else /* JRM */ + status = MPI_Send(data, (int)elements, MPI_BYTE, io_concentrator[ioc_start], WRITE_INDEP_DATA, + sf_context->sf_data_comm); +#endif /* JRM */ +#endif /* JRM */ /* When we actually have the async IO support, * the request should be queued before we @@ -1088,6 +1284,8 @@ write__independent_async(int n_io_concentrators, hid_t context_id, int64_t offse return status; } /* end write__independent_async() */ +#endif /* JRM */ /* modified to use IOC supplied tag for data send */ + /* * Function: H5FD__write_vector_internal * @@ -1105,7 +1303,7 @@ write__independent_async(int n_io_concentrators, hid_t context_id, int64_t offse */ herr_t H5FD__write_vector_internal(hid_t h5_fid, hssize_t count, haddr_t addrs[], size_t sizes[], - const void *bufs[] /* data_in */) + const void *bufs[] /* in */) { herr_t ret_value = SUCCEED; hssize_t status = 0, k = 0; @@ -1161,8 +1359,10 @@ H5FD__write_vector_internal(hid_t h5_fid, hssize_t count, haddr_t addrs[], size_ * We can can now try to complete those before returning * to the caller for the next set of IO operations. */ +#if 1 /* JRM */ /* experiment with synchronous send */ if (sf_async_reqs[0]->completion_func.io_function) ret_value = (*sf_async_reqs[0]->completion_func.io_function)(mpi_reqs); +#endif /* JRM */ if (active_reqs) free(active_reqs); @@ -1188,7 +1388,7 @@ errors: */ herr_t H5FD__read_vector_internal(hid_t h5_fid, hssize_t count, haddr_t addrs[], size_t sizes[], - void *bufs[] /* data_out */) + void *bufs[] /* out */) { herr_t ret_value = SUCCEED; hssize_t status = 0, k = 0; @@ -1265,6 +1465,7 @@ sf_truncate(hid_t h5_fid, haddr_t H5_ATTR_PARALLEL_UNUSED addr) return 0; } +#if 1 /* JRM */ /* delete this if all goes well */ int sf_shutdown_local_ioc(hid_t fid) { @@ -1276,7 +1477,40 @@ sf_shutdown_local_ioc(hid_t fid) } return 0; } +#else /* JRM */ + +/*------------------------------------------------------------------------- + * Function: sf_shutdown_local_ioc() + * + * Purpose: Set the sf_shutdown_flag, and wait until the local + * I/O Concentrator shuts down. + * + * Return: Void + * + * Errors: None + * + * Programmer: JRM -- 10/26/21 + * + * Changes: None. + * + *------------------------------------------------------------------------- + */ +void +sf_shutdown_local_ioc(hid_t fid) +{ + hid_t context_id = fid_map_to_context((uint64_t)fid); + subfiling_context_t *sf_context = get__subfiling_object(context_id); + assert(sf_context != NULL); + if (sf_context->topology->rank_is_ioc) { + atomic_fetch_add(&sf_shutdown_flag, 1); + } + return; + +} /* sf_shutdown_local_ioc() */ +#endif /* JRM */ + +#if 0 /* JRM */ /* original version of ioc_main() */ /*------------------------------------------------------------------------- * Function: Public/IOC ioc_main * @@ -1381,9 +1615,22 @@ ioc_main(int64_t context_id) atomic_init(&sf_ioc_fini_refcount, 0); atomic_init(&sf_shutdown_flag, 0); atomic_init(&sf_ioc_ready, 1); +#if 1 /* JRM */ + /* this variable is incremented by tpool_add_work(), and decremented when the + * received I/O request is completed. + * + * On shutdown, we must wait until this field is decremented to zero before + * taking down the thread pool. + */ + atomic_init(&sf_io_ops_pending, 0); +#endif /* JRM */ shutdown_requested = 0; +#if 0 /* JRM */ while (!shutdown_requested || sf_work_pending) { +#else /* JRM */ + while ( ( ! shutdown_requested ) || ( 0 < atomic_load(&sf_io_ops_pending) ) || sf_work_pending) { +#endif /* JRM */ flag = 0; ret = MPI_Iprobe(MPI_ANY_SOURCE, MPI_ANY_TAG, context->sf_msg_comm, &flag, &status); if ((ret == MPI_SUCCESS) && (flag != 0)) { @@ -1394,6 +1641,14 @@ ioc_main(int64_t context_id) int source = status.MPI_SOURCE; int tag = status.MPI_TAG; +#if 1 /* JRM */ + if ( ( tag != READ_INDEP ) && ( tag != WRITE_INDEP ) ) { + + HDprintf("\n\nioc_main: recieved non READ_INDEP / WRITE_INDEP mssg. tag = %d.\n\n", tag); + HDfflush(stdout); + } +#endif /* JRM */ + MPI_Get_count(&status, MPI_BYTE, &count); if (count > request_size) { msg = (sf_work_request_t *)malloc((size_t)count); @@ -1456,12 +1711,145 @@ ioc_main(int64_t context_id) return 0; } +#else /* JRM */ /* re-written version of ioc_main() */ + +int +ioc_main(int64_t context_id) +{ + int subfile_rank; + int flag, ret; + int max_work_depth; + int shutdown_requested; + MPI_Status status, msg_status; + sf_work_request_t wk_req; + useconds_t delay = 20; + subfiling_context_t *context = get__subfiling_object(context_id); + double queue_start_time; + + assert(context != NULL); + /* We can't have opened any files at this point.. + * The file open approach has changed so that the normal + * application rank (hosting this thread) does the file open. + * We can simply utilize the file descriptor (which should now + * represent an open file). + */ + + subfile_rank = context->sf_group_rank; + + /* zero out the wk_req, since the received message will typically be smaller + * than sizeof(sf_work_request_t). + */ + HDmemset(&wk_req, 0, sizeof(sf_work_request_t)); + + /* Initialize atomic vars */ + /* JRM */ /* delete most of these? */ + atomic_init(&sf_workinprogress, 0); + atomic_init(&sf_work_pending, 0); + atomic_init(&sf_file_close_count, 0); + atomic_init(&sf_file_refcount, 0); + atomic_init(&sf_ioc_fini_refcount, 0); + atomic_init(&sf_shutdown_flag, 0); + atomic_init(&sf_ioc_ready, 1); +#if 1 /* JRM */ + /* this variable is incremented by tpool_add_work(), and decremented when the + * received I/O request is completed. + * + * On shutdown, we must wait until this field is decremented to zero before + * taking down the thread pool. + */ + atomic_init(&sf_io_ops_pending, 0); +#endif /* JRM */ + shutdown_requested = 0; + + while ((!shutdown_requested) || (0 < atomic_load(&sf_io_ops_pending)) || sf_work_pending) { + + flag = 0; + ret = MPI_Iprobe(MPI_ANY_SOURCE, MPI_ANY_TAG, context->sf_msg_comm, &flag, &status); + if ((ret == MPI_SUCCESS) && (flag != 0)) { + sf_work_request_t *msg = NULL; + int count; + int index = 0; + int request_size = (int)sizeof(sf_work_request_t); + int source = status.MPI_SOURCE; + int tag = status.MPI_TAG; + +#if 1 /* JRM */ + if ((tag != READ_INDEP) && (tag != WRITE_INDEP)) { + + HDprintf("\n\nioc_main: recieved non READ_INDEP / WRITE_INDEP mssg. tag = %d.\n\n", tag); + HDfflush(stdout); + } +#endif /* JRM */ + + MPI_Get_count(&status, MPI_BYTE, &count); + + /* convert this assert to a proper error message once we decide how to handle error + * reporting from the I/O concentrator. + */ + HDassert(count <= sizeof(sf_work_request_t)); + + /* zero out the wk_req, since the received message will typically be smaller + * than sizeof(sf_work_request_t). + */ + HDmemset(&wk_req, 0, sizeof(sf_work_request_t)); + + ret = MPI_Recv(&wk_req, count, MPI_BYTE, source, tag, context->sf_msg_comm, &msg_status); + + if (MPI_SUCCESS == ret) { + + int howmany = 0; + + MPI_Get_count(&msg_status, MPI_BYTE, &howmany); + + if (howmany != count) { + printf("%s: MPI_Recv completed %d bytes of %d\n", __func__, howmany, count); + fflush(stdout); + } + } + + queue_start_time = MPI_Wtime(); + + if (ret == MPI_SUCCESS) { + + int curr_io_ops_pending; + + wk_req.tag = tag; + wk_req.source = source; + wk_req.subfile_rank = subfile_rank; + wk_req.start_time = queue_start_time; + wk_req.buffer = NULL; + + curr_io_ops_pending = atomic_fetch_add(&sf_io_ops_pending, 1); + + HDassert(curr_io_ops_pending >= 0); + + H5FD_ioc__queue_io_q_entry(&wk_req); + + H5FD_ioc__dispatch_elegible_io_q_entries(); + } + } + else { + usleep(delay); + } + shutdown_requested = atomic_load(&sf_shutdown_flag); + } + + /* Reset the shutdown flag */ + atomic_init(&sf_shutdown_flag, 0); + + return 0; + +} /* ioc_main() */ + +#endif /* JRM */ /* re-written versin of ioc_main() */ + /* ========================================= Private helper functions ========================================= */ +#if 0 /* JRM */ /* original version */ static int send_ack__(int target, int subfile_rank, int tag, MPI_Comm comm) { @@ -1476,6 +1864,27 @@ send_ack__(int target, int subfile_rank, int tag, MPI_Comm comm) #endif return ret; } +#else /* JRM */ /* version modified to send expected data send tag */ + +static int +send_ack__(int target, int subfile_rank, int tag, MPI_Comm comm, int ack) +{ + + HDassert(ack > 0); + + int ret = MPI_Send(&ack, 1, MPI_INT, target, tag, comm); +#ifndef NDEBUG + if (sf_verbose_flag) { + if (sf_logfile) { + fprintf(sf_logfile, "[ioc(%d): Sending ACK to MPI_rank(%d)\n", subfile_rank, target); + } + } +#endif + return ret; + +} /* send_ack__() */ + +#endif /* JRM */ /* version modified to send expected data send tag */ static int send_nack__(int target, int subfile_rank, int tag, MPI_Comm comm) @@ -1521,10 +1930,14 @@ from the thread pool threads... * *------------------------------------------------------------------------- */ +#if 0 /* JRM */ /* original version */ int queue_write_indep(sf_work_request_t *msg, int subfile_rank, int source, MPI_Comm comm) { int fd; +#if 1 /* JRM */ + int actual_bytes_received; +#endif /* JRM */ char * recv_buffer = NULL; int ret = MPI_SUCCESS; MPI_Status msg_status; @@ -1572,6 +1985,21 @@ queue_write_indep(sf_work_request_t *msg, int subfile_rank, int source, MPI_Comm send_ack__(source, subfile_rank, WRITE_INDEP_ACK, comm); ret = MPI_Recv(recv_buffer, (int)data_size, MPI_BYTE, source, WRITE_INDEP_DATA, comm, &msg_status); +#if 1 /* JRM */ + if ( MPI_SUCCESS != MPI_Get_count(&msg_status, MPI_BYTE, &actual_bytes_received) ) { + + HDprintf("\n\nqueue_write_indep(): can't get actual bytes receive.\n\n"); + HDfflush(stdout); + + } else if ( actual_bytes_received != data_size ) { + + HDprintf("\n\nqueue_write_indep(): message size mismatch -- expected = %ld, actual = %d.\n\n", + data_size, actual_bytes_received); + HDfflush(stdout); + + } +#endif /* JRM */ + t_end = MPI_Wtime(); t_wait = t_end - t_start; sf_write_wait_time += t_wait; @@ -1635,6 +2063,140 @@ queue_write_indep(sf_work_request_t *msg, int subfile_rank, int source, MPI_Comm return 0; } +#else /* JRM */ /* version modified for new dispatch code */ + +int +queue_write_indep(sf_work_request_t *msg, int subfile_rank, int source, MPI_Comm comm, int counter) +{ + int fd; +#if 1 /* JRM */ + int actual_bytes_received; +#endif /* JRM */ + int rcv_tag = ((counter & 0xFFFF) << 12) | WRITE_INDEP_DATA; + char * recv_buffer = NULL; + int ret = MPI_SUCCESS; + MPI_Status msg_status; + int64_t data_size = msg->header[0]; + int64_t file_offset = msg->header[1]; + int64_t file_context_id = msg->header[2]; + double t_start, t_end; + double t_write, t_wait, t_queue_delay; + subfiling_context_t *sf_context = get__subfiling_object(file_context_id); + int64_t stripe_id = file_offset + data_size; + haddr_t sf_eof; + assert(sf_context != NULL); + + sf_eof = (haddr_t)(stripe_id % sf_context->sf_stripe_size); + stripe_id /= sf_context->sf_stripe_size; + sf_eof += (haddr_t)((stripe_id * sf_context->sf_blocksize_per_stripe) + sf_context->sf_base_addr); + + /* flag that we've attempted to write data to the file */ + sf_context->sf_write_count++; + /* For debugging performance */ + sf_write_ops++; + + t_start = MPI_Wtime(); + t_queue_delay = t_start - msg->start_time; + +#ifndef NDEBUG + if (sf_verbose_flag) { + if (sf_logfile) { + fprintf(sf_logfile, + "[ioc(%d) %s]: msg from %d: datasize=%ld\toffset=%ld, " + "queue_delay = %lf seconds\n", + subfile_rank, __func__, source, data_size, file_offset, t_queue_delay); + } + } +#endif + + if (recv_buffer == NULL) { + if ((recv_buffer = (char *)malloc((size_t)data_size)) == NULL) { + perror("malloc"); + send_nack__(source, subfile_rank, WRITE_INDEP_ACK, comm); + return -1; + } + } + + send_ack__(source, subfile_rank, WRITE_INDEP_ACK, comm, rcv_tag); + ret = MPI_Recv(recv_buffer, (int)data_size, MPI_BYTE, source, rcv_tag, comm, &msg_status); + +#if 1 /* JRM */ + if (MPI_SUCCESS != MPI_Get_count(&msg_status, MPI_BYTE, &actual_bytes_received)) { + + HDprintf("\n\nqueue_write_indep(): can't get actual bytes receive.\n\n"); + HDfflush(stdout); + } + else if (actual_bytes_received != data_size) { + + HDprintf("\n\nqueue_write_indep(): message size mismatch -- expected = %ld, actual = %d.\n\n", + data_size, actual_bytes_received); + HDfflush(stdout); + } +#endif /* JRM */ + + t_end = MPI_Wtime(); + t_wait = t_end - t_start; + sf_write_wait_time += t_wait; + t_start = t_end; +#ifndef NDEBUG + if (sf_verbose_flag) { + if (sf_logfile) { + fprintf(sf_logfile, "[ioc(%d) %s] MPI_Recv(%ld bytes, from = %d) status = %d\n", subfile_rank, + __func__, data_size, source, ret); + } + } +#endif + + if (ret != MPI_SUCCESS) { + int len; + char estring[MPI_MAX_ERROR_STRING]; + MPI_Error_string(ret, estring, &len); + printf("[ioc(%d) %s] MPI_ERROR(%d)! MPI_Recv of %ld bytes from %d " + "returned an error(%s)\n", + subfile_rank, __func__, msg_status.MPI_ERROR, data_size, source, estring); + fflush(stdout); + return ret; + } + + fd = sf_context->sf_fid; + + if (fd < 0) { + printf("[ioc(%d)] WARNING: %s called while subfile_fid = %d (closed)\n", subfile_rank, __func__, fd); + fflush(stdout); + } + else { + if (sf_write_data(fd, file_offset, recv_buffer, data_size, subfile_rank) < 0) { + free(recv_buffer); + recv_buffer = NULL; + printf("[ioc(%d) %s] sf_write_data returned an error!\n", subfile_rank, __func__); + fflush(stdout); + return -1; + } + t_end = MPI_Wtime(); + t_write = t_end - t_start; + sf_pwrite_time += t_write; + } + + sf_queue_delay_time += t_queue_delay; + + /* Done... */ + if (sf_eof > sf_context->sf_eof) + sf_context->sf_eof = sf_eof; + +#ifdef VERBOSE + printf("[ioc(%d)] %s local sf_eof = %ld sf_context=%p\n", subfile_rank, __func__, sf_context->sf_eof, + (void *)sf_context); + fflush(stdout); +#endif + if (recv_buffer) { + free(recv_buffer); + } + return 0; + +} /* queue_write_indep() */ + +#endif /* JRM */ /* version modified for new dispatch code */ + /*------------------------------------------------------------------------- * Function: Public/IOC queue_read_indep * @@ -1655,6 +2217,93 @@ queue_write_indep(sf_work_request_t *msg, int subfile_rank, int source, MPI_Comm * *------------------------------------------------------------------------- */ +#if 0 /* JRM */ /* original version */ +int +queue_read_indep(sf_work_request_t *msg, int subfile_rank, int source, MPI_Comm comm) +{ + int fd; + char * send_buffer = NULL; + int ret = MPI_SUCCESS; + int64_t data_size = msg->header[0]; + int64_t file_offset = msg->header[1]; + int64_t file_context_id = msg->header[2]; + double t_start, t_end; + double t_read, t_queue_delay; + + subfiling_context_t *sf_context = get__subfiling_object(file_context_id); + assert(sf_context != NULL); + + sf_context->sf_read_count++; + /* For debugging performance */ + sf_read_ops++; + + t_start = MPI_Wtime(); + t_queue_delay = t_start - msg->start_time; + + fd = sf_context->sf_fid; + if (fd < 0) { + printf("[ioc(%d) %s] subfile(%d) file descriptor not valid\n", subfile_rank, __func__, fd); + return -1; + } + +#ifndef NDEBUG + if (sf_verbose_flag && (sf_logfile != NULL)) { + fprintf(sf_logfile, + "[ioc(%d) %s] msg from %d: datasize=%ld\toffset=%ld " + "queue_delay=%lf seconds\n", + subfile_rank, __func__, source, data_size, file_offset, t_queue_delay); + } +#endif + if ((send_buffer = (char *)malloc((size_t)data_size)) == NULL) { + perror("malloc"); + return -1; + } + + if (sf_read_data(fd, file_offset, send_buffer, data_size, subfile_rank) < 0) { + printf("[%d] %s - sf_read_data fd=%d for source(%d) returned an error!\n", subfile_rank, __func__, fd, + source); + fflush(stdout); + /* + * Should send a zero(0) byte message to the client to prevent + * it from hanging... + */ + MPI_Send(send_buffer, 0, MPI_BYTE, source, READ_INDEP_DATA, comm); + free(send_buffer); + return -1; + } + + ret = MPI_Send(send_buffer, (int)data_size, MPI_BYTE, source, READ_INDEP_DATA, comm); + if (ret != MPI_SUCCESS) { + int len; + char estring[MPI_MAX_ERROR_STRING]; + MPI_Error_string(ret, estring, &len); + printf("[ioc(%d)] ERROR! MPI_Send of %ld bytes to %d returned an " + "error(%s)\n", + subfile_rank, data_size, source, estring); + fflush(stdout); + return ret; + } + t_end = MPI_Wtime(); + t_read = t_end - t_start; + sf_pread_time += t_read; + sf_queue_delay_time += t_queue_delay; + +#ifndef NDEBUG + if (sf_verbose_flag && (sf_logfile != NULL)) { + fprintf(sf_logfile, "[ioc(%d)] MPI_Send to source(%d) completed\n", subfile_rank, source); + } +#endif + + if (send_buffer) { + free(send_buffer); + send_buffer = NULL; + } + + return 0; +} /* end queue_read_indep() */ + +#else /* JRM */ /* version modified for new dispatch code */ + int queue_read_indep(sf_work_request_t *msg, int subfile_rank, int source, MPI_Comm comm) { @@ -1739,6 +2388,8 @@ queue_read_indep(sf_work_request_t *msg, int subfile_rank, int source, MPI_Comm return 0; } /* end queue_read_indep() */ +#endif /* JRM */ /* version modified for new dispatch code */ + /* --------------------------------------------------- * Helper function for subfiling_open_file() see below * Subfiles should be located in the same directory @@ -1824,7 +2475,7 @@ get__subfile_name(subfiling_context_t *sf_context, int64_t h5_file_id, int subfi int subfiling_open_file(sf_work_request_t *msg, int subfile_rank, int flags) { - int errors = 0; + int errors = 0; char filepath[PATH_MAX]; char linebuf[PATH_MAX]; diff --git a/src/H5FDsubfiling.c b/src/H5FDsubfiling.c index b19df57..cd7739d 100644 --- a/src/H5FDsubfiling.c +++ b/src/H5FDsubfiling.c @@ -898,8 +898,8 @@ done: static herr_t H5FD__subfiling_close(H5FD_t *_file) { - H5FD_subfiling_t *file_ptr = (H5FD_subfiling_t *)_file; - herr_t ret_value = SUCCEED; /* Return value */ + H5FD_subfiling_t * file_ptr = (H5FD_subfiling_t *)_file; + herr_t ret_value = SUCCEED; /* Return value */ subfiling_context_t *sf_context = NULL; FUNC_ENTER_NOAPI_NOINIT @@ -1017,13 +1017,18 @@ done: * Purpose: Set the flags that this VFL driver is capable of supporting. * (listed in H5FDpublic.h) * + * For now, duplicate the flags used for the MPIO VFD. + * Revisit this when we have a version of the subfiling VFD + * that is usable in serial builds. + * * Return: SUCCEED (Can't fail) * - * Programmer: Quincey Koziol - * Friday, August 25, 2000 + * Programmer: John Mainzer + * 11/15/21 * *------------------------------------------------------------------------- */ +#if 0 /* JRM */ /* original version -- delete if all goes well */ static herr_t H5FD__subfiling_query(const H5FD_t *_file, unsigned long *flags /* out */) { @@ -1062,6 +1067,28 @@ H5FD__subfiling_query(const H5FD_t *_file, unsigned long *flags /* out */) FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5FD_subfiling_query() */ +#else /* JRM */ /* new version copied from MPIO VFD */ + +static herr_t +H5FD__subfiling_query(const H5FD_t H5_ATTR_UNUSED *_file, unsigned long *flags /* out */) +{ + FUNC_ENTER_STATIC_NOERR + + /* Set the VFL feature flags that this driver supports */ + if (flags) { + *flags = 0; + *flags |= H5FD_FEAT_AGGREGATE_METADATA; /* OK to aggregate metadata allocations */ + *flags |= H5FD_FEAT_AGGREGATE_SMALLDATA; /* OK to aggregate "small" raw data allocations */ + // *flags |= H5FD_FEAT_HAS_MPI; /* This driver uses MPI */ + *flags |= H5FD_FEAT_ALLOCATE_EARLY; /* Allocate space early instead of late */ + *flags |= H5FD_FEAT_DEFAULT_VFD_COMPATIBLE; /* VFD creates a file which can be opened with the default + VFD */ + } + + FUNC_LEAVE_NOAPI(SUCCEED) +} /* end H5FD__mpio_query() */ + +#endif /* JRM */ /* new version copied from MPIO VFD */ /*------------------------------------------------------------------------- * Function: H5FD_subfiling_get_eoa @@ -1577,15 +1604,15 @@ H5FD__subfiling_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_AT size, /* (in) IO size */ 1); /* (in) data extent of the 'type' assumes byte */ #else /* JRM */ - count = init__indep_io(sf_context, /* We use the context to look up config info */ + count = init__indep_io(sf_context, /* We use the context to look up config info */ max_depth, ioc_total, (int64_t *)source_data_offset, /* (out) Memory offset */ (int64_t *)sf_data_size, /* (out) Length of this contiguous block */ (int64_t *)sf_offset, /* (out) File offset */ - &ioc_start, /* (out) IOC index corresponding to starting offset */ - &ioc_count, /* (out) number of actual IOCs used */ - offset, /* (in) Starting file offset */ - (int64_t)size, /* (in) IO size */ - 1); /* (in) data extent of the 'type' assumes byte */ + &ioc_start, /* (out) IOC index corresponding to starting offset */ + &ioc_count, /* (out) number of actual IOCs used */ + offset, /* (in) Starting file offset */ + (int64_t)size, /* (in) IO size */ + 1); /* (in) data extent of the 'type' assumes byte */ #endif /* JRM */ next = ioc_start; @@ -1626,7 +1653,7 @@ H5FD__subfiling_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_AT #if 0 /* JRM */ int vectorlen = ioc_count; #else /* JRM */ - uint32_t vectorlen = (uint32_t)ioc_count; + uint32_t vectorlen = (uint32_t)ioc_count; #endif /* JRM */ /* @@ -1725,7 +1752,9 @@ done: /*------------------------------------------------------------------------- * Function: H5FD__subfile_read_vector (internal function) * - * Purpose: Perform count reads from the specified file at the offsets + * Purpose: Vector Read function for the sub-filing VFD. + * + * Perform count reads from the specified file at the offsets * provided in the addrs array, with the lengths and memory * types provided in the sizes and types arrays. Data read * is returned in the buffers provided in the bufs array. @@ -1741,10 +1770,21 @@ done: * Failure: FAIL * The contents of supplied buffers are undefined. * - * Programmer: JRM -- 6/10/20 + * Programmer: RAW -- ??/??/21 * * Changes: None. * + * Notes: Thus function doesn't actually implement vector read. + * Instead, it comverts the vector read call into a series + * of scalar read calls. Fix this when time permits. + * + * Also, it didn't support the sizes and types optimization. + * I implemented a version of this which is more generous + * than that currently defined in the RFC. This is good + * enough for now, but the final version should follow + * the RFC. + * JRM -- 10/5/21 + * *------------------------------------------------------------------------- */ static herr_t @@ -1787,10 +1827,64 @@ H5FD__subfiling_read_vector(H5FD_t *_file, hid_t dxpl_id, uint32_t count, H5FD_m /* Set DXPL for operation */ H5CX_set_dxpl(dxpl_id); + + /* TODO: setup real support for vector I/O */ if (file_ptr->fa.require_ioc) { - int k; + + hbool_t extend_sizes = FALSE; + hbool_t extend_types = FALSE; + int k; + size_t size; + H5FD_mem_t type; + haddr_t eoa; + + HDassert((count == 0) || (sizes[0] != 0)); + HDassert((count == 0) || (types[0] != H5FD_MEM_NOLIST)); + + /* Note that the following code does not let the sub-filing VFD participate + * in collective calls when thre is no data to write. This is not an issue + * now, as we don't do anything special with collective operations. However + * this needs to be fixed. + */ for (k = 0; k < (int)count; k++) { - if (H5FD__subfiling_read(_file, types[k], dxpl_id, addrs[k], sizes[k], bufs[k]) != SUCCEED) + + if (!extend_sizes) { + + if (sizes[k] == 0) { + + extend_sizes = TRUE; + size = sizes[k - 1]; + } + else { + + size = sizes[k]; + } + } + + if (!extend_types) { + + if (types[k] == H5FD_MEM_NOLIST) { + + extend_types = TRUE; + type = types[k - 1]; + } + else { + + type = types[k]; + } + } + + if (HADDR_UNDEF == (eoa = H5FD__subfiling_get_eoa(_file, type))) + HGOTO_ERROR(H5E_VFL, H5E_CANTINIT, FAIL, "driver get_eoa request failed") + + if ((addrs[k] + size) > eoa) + + HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, + "addr overflow, addrs[%d] = %llu, sizes[%d] = %llu, eoa = %llu", (int)k, + (unsigned long long)(addrs[k]), (int)k, (unsigned long long)size, + (unsigned long long)eoa) + + if (H5FD__subfiling_read(_file, type, dxpl_id, addrs[k], size, bufs[k]) != SUCCEED) HGOTO_ERROR(H5E_VFL, H5E_READERROR, FAIL, "file vector read request failed") } } @@ -1826,10 +1920,21 @@ done: * input arguments are not valid, or the actual * subfiling writes have failed for some reason. * - * Programmer: JRM -- 6/10/20 + * Programmer: RAW -- ??/??/21 * * Changes: None. * + * Notes: Thus function doesn't actually implement vector write. + * Instead, it comverts the vector write call into a series + * of scalar read calls. Fix this when time permits. + * + * Also, it didn't support the sizes and types optimization. + * I implemented a version of this which is more generous + * than that currently defined in the RFC. This is good + * enough for now, but the final version should follow + * the RFC. + * JRM -- 10/5/21 + * *------------------------------------------------------------------------- */ static herr_t @@ -1873,9 +1978,61 @@ H5FD__subfiling_write_vector(H5FD_t *_file, hid_t dxpl_id, uint32_t count, H5FD_ } /* Call the subfiling IOC write*/ if (file_ptr->fa.require_ioc) { - int k; + + hbool_t extend_sizes = FALSE; + hbool_t extend_types = FALSE; + int k; + size_t size; + H5FD_mem_t type; + haddr_t eoa; + + HDassert((count == 0) || (sizes[0] != 0)); + HDassert((count == 0) || (types[0] != H5FD_MEM_NOLIST)); + + /* Note that the following code does not let the sub-filing VFD participate + * in collective calls when thre is no data to write. This is not an issue + * now, as we don't do anything special with collective operations. However + * this needs to be fixed. + */ for (k = 0; k < (int)count; k++) { - if (H5FD__subfiling_write(_file, types[k], dxpl_id, addrs[k], sizes[k], bufs[k]) != SUCCEED) + + if (!extend_sizes) { + + if (sizes[k] == 0) { + + extend_sizes = TRUE; + size = sizes[k - 1]; + } + else { + + size = sizes[k]; + } + } + + if (!extend_types) { + + if (types[k] == H5FD_MEM_NOLIST) { + + extend_types = TRUE; + type = types[k - 1]; + } + else { + + type = types[k]; + } + } + + if (HADDR_UNDEF == (eoa = H5FD__subfiling_get_eoa(_file, type))) + HGOTO_ERROR(H5E_VFL, H5E_CANTINIT, FAIL, "driver get_eoa request failed") + + if ((addrs[k] + size) > eoa) + + HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, + "addr overflow, addrs[%d] = %llu, sizes[%d] = %llu, eoa = %llu", (int)k, + (unsigned long long)(addrs[k]), (int)k, (unsigned long long)size, + (unsigned long long)eoa) + + if (H5FD__subfiling_write(_file, type, dxpl_id, addrs[k], size, bufs[k]) != SUCCEED) HGOTO_ERROR(H5E_VFL, H5E_WRITEERROR, FAIL, "file vector write request failed") } } diff --git a/src/H5FDsubfiling.h b/src/H5FDsubfiling.h index 93a2b0a..c7ab265 100644 --- a/src/H5FDsubfiling.h +++ b/src/H5FDsubfiling.h @@ -20,6 +20,14 @@ #ifndef H5FDsubfiling_H #define H5FDsubfiling_H +#if 1 /* JRM */ /* For now, H5FDsubfiling_priv.h needs mercury. Since the code that needs it will \ + * move to its own header, just hack it for now. \ + */ +#include "mercury_thread.h" +#include "mercury_thread_mutex.h" +#include "mercury_thread_pool.h" +#endif /* JRM */ + #include "H5FDsubfiling_priv.h" #define H5FD_SUBFILING (H5FD_subfiling_init()) @@ -113,6 +121,8 @@ * The full pathname of the user HDF5 file. * +WARNING -- this code is commented out + #define H5FD_SUBFILING_PATH_MAX 4096 typedef struct config_common_t { @@ -234,13 +244,20 @@ H5_DLL herr_t H5FD__write_vector(hid_t h5_fid, hssize_t count, haddr_t *addrs, h H5_DLL int H5FD__truncate(hid_t h5_fid, haddr_t addr); H5_DLL int H5FD__shutdown_local_ioc(hid_t fid); H5_DLL void manage_client_logfile(int client_rank, int flag_value); +#if 0 /* JRM */ H5_DLL int initialize_ioc_threads(void *sf_context); +#endif /* JRM */ H5_DLL herr_t H5FD__write_vector_internal(hid_t h5_fid, hssize_t count, haddr_t addrs[], size_t sizes[], const void *bufs[] /* data_in */); H5_DLL herr_t H5FD__read_vector_internal(hid_t h5_fid, hssize_t count, haddr_t addrs[], size_t sizes[], void *bufs[] /* data_out */); +#if 0 /* JRM */ H5_DLL int queue_write_indep(sf_work_request_t *msg, int subfile_rank, int source, MPI_Comm comm); +#else /* JRM */ +H5_DLL int queue_write_indep(sf_work_request_t *msg, int subfile_rank, int source, MPI_Comm comm, + int counter); +#endif /* JRM */ H5_DLL int queue_read_indep(sf_work_request_t *msg, int subfile_rank, int source, MPI_Comm comm); diff --git a/src/H5FDsubfiling_priv.h b/src/H5FDsubfiling_priv.h index 4753423..4ca63d0 100644 --- a/src/H5FDsubfiling_priv.h +++ b/src/H5FDsubfiling_priv.h @@ -213,11 +213,24 @@ typedef struct _info_header { /* Header for a driver info message */ /* Bit 3 SET indicates collectives */ #define COLL_FUNC (0x1 << 3) +#if 0 /* JRM */ /* original version */ + #define ACK_PART (0x0acc << 8) #define DATA_PART (0xd8da << 8) #define READY (0xfeed << 8) #define COMPLETED (0xfed1 << 8) +#else /* JRM */ /* reduce size to make space for counters to disambiguate multiple concurrent requests from \ + same rank */ + +#define ACK_PART (0x01 << 8) +#define DATA_PART (0x02 << 8) +#define READY (0x04 << 8) +#define COMPLETED (0x08 << 8) + +#endif /* JRM */ /* reduce size to make space for counters to disambiguate multiple concurrent requests from \ + same rank */ + #define READ_INDEP (READ_OP) #define READ_COLL (COLL_FUNC | READ_OP) #define WRITE_INDEP (WRITE_OP) @@ -363,6 +376,377 @@ extern int sf_verbose_flag; extern atomic_int sf_work_pending; extern atomic_int sf_file_open_count; extern atomic_int sf_file_close_count; +extern atomic_int sf_shutdown_flag; +extern atomic_int sf_io_ops_pending; + +#if 1 /* JRM */ /* this belongs in an IOC private header file */ + +#define H5FD_IOC__COLLECT_STATS TRUE + +/**************************************************************************** + * + * IOC I/O Queue management macros: + * + * The following macros perform the necessary operations on the IOC I/O + * Queue, which is implemented as a doubly linked list of instances of + * H5FD_ioc_io_queue_entry_t. + * + * WARNING: q_ptr->q_mutex must be held when these macros are executed.. + * + * At present, the necessary operations are append (insert an entry at the + * end of the queue), and delete (remove an entry from the queue). + * + * At least initially, all sanity checking is done with asserts, as the + * the existing I/O concentrator code is not well integrated into the HDF5 + * error reporting system. This will have to be revisited for a production + * version, but it should be suficient for now. + * + * JRM -- 11/2/21 + * + ****************************************************************************/ + +/* clang-format off */ + +#define H5FD_IOC__Q_APPEND(q_ptr, entry_ptr) \ +do { \ + HDassert(q_ptr); \ + HDassert((q_ptr)->magic == H5FD_IOC__IO_Q_MAGIC); \ + HDassert((((q_ptr)->q_len == 0) && ((q_ptr)->q_head == NULL) && ((q_ptr)->q_tail == NULL)) || \ + (((q_ptr)->q_len > 0) && ((q_ptr)->q_head != NULL) && ((q_ptr)->q_tail != NULL))); \ + HDassert(entry_ptr); \ + HDassert((entry_ptr)->magic == H5FD_IOC__IO_Q_ENTRY_MAGIC); \ + HDassert((entry_ptr)->next == NULL); \ + HDassert((entry_ptr)->prev == NULL); \ + HDassert((entry_ptr)->in_progress == FALSE); \ + \ + if ( ((q_ptr)->q_head) == NULL ) \ + { \ + ((q_ptr)->q_head) = (entry_ptr); \ + ((q_ptr)->q_tail) = (entry_ptr); \ + } \ + else \ + { \ + ((q_ptr)->q_tail)->next = (entry_ptr); \ + (entry_ptr)->prev = ((q_ptr)->q_tail); \ + ((q_ptr)->q_tail) = (entry_ptr); \ + } \ + ((q_ptr)->q_len)++; \ +} while ( FALSE ) /* H5FD_IOC__Q_APPEND() */ + +#define H5FD_IOC__Q_REMOVE(q_ptr, entry_ptr) \ +do { \ + HDassert(q_ptr); \ + HDassert((q_ptr)->magic == H5FD_IOC__IO_Q_MAGIC); \ + HDassert((((q_ptr)->q_len == 1) && ((q_ptr)->q_head ==((q_ptr)->q_tail)) && ((q_ptr)->q_head == (entry_ptr))) || \ + (((q_ptr)->q_len > 0) && ((q_ptr)->q_head != NULL) && ((q_ptr)->q_tail != NULL))); \ + HDassert(entry_ptr); \ + HDassert((entry_ptr)->magic == H5FD_IOC__IO_Q_ENTRY_MAGIC); \ + HDassert((((q_ptr)->q_len == 1) && ((entry_ptr)->next == NULL) && ((entry_ptr)->prev == NULL)) || \ + (((q_ptr)->q_len > 1) && (((entry_ptr)->next != NULL) || ((entry_ptr)->prev != NULL)))); \ + HDassert((entry_ptr)->in_progress == TRUE); \ + \ + { \ + if ( (((q_ptr)->q_head)) == (entry_ptr) ) \ + { \ + (((q_ptr)->q_head)) = (entry_ptr)->next; \ + if ( (((q_ptr)->q_head)) != NULL ) \ + (((q_ptr)->q_head))->prev = NULL; \ + } \ + else \ + { \ + (entry_ptr)->prev->next = (entry_ptr)->next; \ + } \ + if (((q_ptr)->q_tail) == (entry_ptr) ) \ + { \ + ((q_ptr)->q_tail) = (entry_ptr)->prev; \ + if ( ((q_ptr)->q_tail) != NULL ) \ + ((q_ptr)->q_tail)->next = NULL; \ + } \ + else \ + { \ + (entry_ptr)->next->prev = (entry_ptr)->prev; \ + } \ + (entry_ptr)->next = NULL; \ + (entry_ptr)->prev = NULL; \ + ((q_ptr)->q_len)--; \ + } \ +} while ( FALSE ) /* H5FD_IOC__Q_REMOVE() */ + +/* clang-format on */ + +/**************************************************************************** + * + * structure H5FD_ioc_io_queue_entry + * + * magic: Unsigned 32 bit integer always set to H5FD_IOC__IO_Q_ENTRY_MAGIC. + * This field is used to validate pointers to instances of + * H5FD_ioc_io_queue_entry_t. + * + * next: Next pointer in the doubly linked list used to implement + * the IOC I/O Queue. This field points to the next entry + * in the queue, or NULL if there is no next entry. + * + * prev: Prev pointer in the doubly linked list used to implement + * the IOC I/O Queue. This field points to the previous entry + * in the queue, or NULL if there is no previous entry. + * + * in_progress: Boolean flag that must be FALSE when the entry is insterted + * into the IOC I/O Queue, and set to TRUE when the entry is dispatched + * to the worker thread pool for execution. + * + * When in_progress is FALS, the enty is said to be pending. + * + * counter: uint32_t containing a serial number assigned to this IOC + * I/O Queue entry. Note that this will roll over on long + * computations, and thus is not in general unique. + * + * The counter fields is used to construct a tag to distinguish + * multiple concurrent I/O requests from a give rank, and thus + * this should not be a problem as long as there is sufficient + * time between roll overs. As only the lower bits of the counter + * are used in tag construction, this is more frequent than the + * size of the counter field would suggest -- albeit hopefully + * still infrequent enough. + * + * wk_req: Instance of sf_work_request_t. Replace with individual + * fields when convenient. + * + * + * Statistics: + * + * The following fields are only defined if H5FD_IOC__COLLECT_STATS is TRUE. + * They are intended to allow collection of basic statistics on the + * behaviour of the IOC I/O Queue for purposes of debugging and performance + * optimization. + * + * q_time: uint64_t containing the time the entry was place on the + * IOC I/O Queue in usec after the UNIX epoch. + * + * This value is used to compute the queue wait time, and the + * total processing time for the entry. + * + * dispatch_time: uint64_t containing the time the entry is dispatched in + * usec after the UNIX epoch. This field is undefined if the + * entry is pending. + * + * This value is used to compute the execution time for the + * entry. + * + ****************************************************************************/ + +#define H5FD_IOC__IO_Q_ENTRY_MAGIC 0x1357 + +typedef struct H5FD_ioc_io_queue_entry { + + uint32_t magic; + struct H5FD_ioc_io_queue_entry *next; + struct H5FD_ioc_io_queue_entry *prev; + hbool_t in_progress; + uint32_t counter; + + /* rework these fileds */ /* JRM */ + sf_work_request_t wk_req; + struct hg_thread_work thread_wk; + + /* statistics */ +#if H5FD_IOC__COLLECT_STATS + + uint64_t q_time; + uint64_t dispatch_time; + +#endif /* H5FD_IOC__COLLECT_STATS */ + +} H5FD_ioc_io_queue_entry_t; + +#if 0 /* JRM */ /* keep this copy for convenience for now */ +typedef struct { + /* {Datasize, Offset, FileID} */ + int64_t header[3]; /* The basic RPC input plus */ + int tag; /* the supplied OPCODE tag */ + int source; /* Rank of who sent the message */ + int subfile_rank; /* The IOC rank */ + hid_t context_id; /* context to be used to complete */ + double start_time; /* the request, + time of receipt */ + /* from which we calc Time(queued) */ + void *buffer; /* for writes, we keep the buffer */ + /* around for awhile... */ + volatile int in_progress; /* Not used! */ + volatile int serialize; /* worker thread needs to wait while true */ + volatile int dependents; //* If current work item has dependents */ + int depend_id; /* work queue index of the dependent */ +} sf_work_request_t; + +struct hg_thread_work { + hg_thread_func_t func; + void * args; + HG_QUEUE_ENTRY(hg_thread_work) entry; /* Internal */ +}; + +#endif /* JRM */ + +/**************************************************************************** + * + * structure H5FD_ioc_io_queue + * + * This is a temporary structure -- its fields should be moved to an I/O + * concentrator Catchall structure eventualy. + * + * The fields of this structure support the io queue used to receive and + * sequence I/O requests for execution by the worker threads. The rules + * for sequencing are as follows: + * + * 1) Non-overlaping I/O requests must be fed to the worker threads in + * the order received, and may execute concurrently + * + * 2) Overlaping read requests must be fed to the worker threads in + * the order received, but may execute concurrently. + * + * 3) If any pair of I/O requests overlap, and at least one is a write + * request, they must be executed in strict arrival order, and the + * first must complete before the second starts. + * + * Due to the strict ordering requirment in rule 3, entries must be + * inserted at the tail of the queue in receipt order, and retained on + * the queue until completed. Entries in the queue are marked pending + * when inserted on the queue, in progress when handed to a worker + * thread, and deleted from the queue when completed. + * + * The dispatch algorith is as follows: + * + * 1) Set X equal to the element at the head of the queue. + * + * 2) If X is pending, and there exists no prior element (i.e. between X + * and the head of the queue) that intersects with X, goto 5). + * + * 3) If X is pending, X is a read, and all prior intersecting elements + * are reads, goto 5). + * + * 4) If X is in progress, or if any prior intersecting element is a + * write, or if X is a write, set X equal to its successor in the + * queue (i.e. the next element further down the queue from the head) + * and goto 2) If there is no next element, exit without dispatching + * any I/O request. + * + * 5) If we get to 5, X must be pending. Mark it in progress, and + * dispatch it. If the number of in progress entries is less than + * the number of worker threads, and X has a successor in the queue, + * set X equal to its predecessor, and goto 2). Otherwise exit without + * dispatching further I/O requests. + * + * Note that the above dispatch algorithm doesn't address collective + * I/O requests -- this should be OK for now, but it will have to + * addressed prior to production release. + * + * On I/O request completion, worker threads must delete their assigned + * I/O requests from the queue, check to see if there are any pending + * requests, and trigger the dispatch algorithm if there are. + * + * The fileds in the structure are discussed individually below. + * + * magic: Unsigned 32 bit integer always set to H5FD_IOC__IO_Q_MAGIC. + * This field is used to validate pointers to instances of + * H5C_t. + * + * q_head: Pointer to the head of the doubly linked list of entries in + * the I/O queue. + * + * This field is NULL if the I/O queue is empty. + * + * q_tail: Pointer to the tail of the doubly linked list of entries in + * the I/O queue. + * + * This field is NULL if the I/O queue is empty. + * + * num_pending: Number of I/O request pending on the I/O queue. + * + * num_in_progress: Number of I/O requests in progress on the I/O queue. + * + * q_len: Number of I/O requests on the I/O queue. Observe that q_len + * must equal (num_pending + num_in_progress). + * + * req_counter: unsigned 16 bit integer used to provide a "unique" tag for + * each I/O request. This value is incremented by 1, and then + * passed to the worker thread where its lower bits are incorporated + * into the tag used to disambiguate multiple, concurrent I/O + * requests from a single rank. The value is 32 bits, as MPI tags + * are limited to 32 bits. The value is unsigned as it is expected + * to wrap around once its maximum value is reached. + * + * q_mutex: Mutex used to ensure that only one thread accesses the IOC I/O + * Queue at once. This mutex must be held to access of modifiy + * all fields of the + * + * + * Statistics: + * + * The following fields are only defined if H5FD_IOC__COLLECT_STATS is TRUE. + * They are intended to allow collection of basic statistics on the + * behaviour of the IOC I/O Queue for purposes of debugging and performance + * optimization. + * + * max_q_len: Maximum number of requests residing on the IOC I/O Queue at + * any point in time in the current run. + * + * max_num_pending: Maximum number of pending rquests residing on the IOC + * I/O Queue at any point in time in the current run. + * + * max_num_in_progress: Maximum number of in progress rquests residing on + * the IOC I/O Queue at any point in time in the current run. + * + * ind_read_requests: Number of independent read requests received by the + * IOC to date. + * + * ind_write_requests Number of independent write requests received by the + * IOC to date. + * + * requests_queued: Number of I/O requests received and placed on the IOC + * I/O queue. + * + * requests_dispatched: Number of I/O requests dispatched for execution by + * the worker threads. + * + * requests_completed: Number of I/O requests completed by the worker threads. + * Observe that on file close, requests_queued, requests_dispatched, + * and requests_completed should be equal. + * + ****************************************************************************/ + +#define H5FD_IOC__IO_Q_MAGIC 0x2468 + +typedef struct H5FD_ioc_io_queue { + + uint32_t magic; + H5FD_ioc_io_queue_entry_t *q_head; + H5FD_ioc_io_queue_entry_t *q_tail; + int32_t num_pending; + int32_t num_in_progress; + int32_t q_len; + uint32_t req_counter; + hg_thread_mutex_t q_mutex; + + /* statistics */ +#if H5FD_IOC__COLLECT_STATS + int32_t max_q_len; + int32_t max_num_pending; + int32_t max_num_in_progress; + int64_t ind_read_requests; + int64_t ind_write_requests; + int64_t requests_queued; + int64_t requests_dispatched; + int64_t requests_completed; +#endif /* H5FD_IOC__COLLECT_STATS */ + +} H5FD_ioc_io_queue_t; + +H5_DLL void H5FD_ioc_take_down_thread_pool(void); + +H5_DLL H5FD_ioc_io_queue_entry_t *H5FD_ioc__alloc_io_q_entry(void); +H5_DLL void H5FD_ioc__complete_io_q_entry(H5FD_ioc_io_queue_entry_t *entry_ptr); +H5_DLL void H5FD_ioc__dispatch_elegible_io_q_entries(void); +H5_DLL void H5FD_ioc__free_io_q_entry(H5FD_ioc_io_queue_entry_t *q_entry_ptr); +H5_DLL void H5FD_ioc__queue_io_q_entry(sf_work_request_t *wk_req_ptr); + +#endif /* JRM */ #ifdef __cplusplus } diff --git a/src/mercury/src/util/.deps/.dirstamp b/src/mercury/src/util/.deps/.dirstamp deleted file mode 100644 index e69de29..0000000 --- a/src/mercury/src/util/.deps/.dirstamp +++ /dev/null diff --git a/src/mercury/src/util/.deps/mercury_atomic_queue.Plo b/src/mercury/src/util/.deps/mercury_atomic_queue.Plo deleted file mode 100644 index 481e5f0..0000000 --- a/src/mercury/src/util/.deps/mercury_atomic_queue.Plo +++ /dev/null @@ -1,357 +0,0 @@ -mercury/src/util/mercury_atomic_queue.lo: \ - mercury/src/util/mercury_atomic_queue.c /usr/include/stdc-predef.h \ - mercury/src/util/mercury_atomic_queue.h \ - mercury/src/util/mercury_atomic.h mercury/src/util/mercury_util_config.h \ - /usr/lib/gcc/x86_64-redhat-linux/8/include/stddef.h \ - /usr/lib/gcc/x86_64-redhat-linux/8/include/stdint.h \ - /usr/include/stdint.h /usr/include/bits/libc-header-start.h \ - /usr/include/features.h /usr/include/sys/cdefs.h \ - /usr/include/bits/wordsize.h /usr/include/bits/long-double.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/bits/wchar.h /usr/include/bits/stdint-intn.h \ - /usr/include/bits/stdint-uintn.h \ - /usr/lib/gcc/x86_64-redhat-linux/8/include/stdatomic.h \ - mercury/src/util/mercury_mem.h \ - /usr/lib/gcc/x86_64-redhat-linux/8/include/immintrin.h \ - /usr/lib/gcc/x86_64-redhat-linux/8/include/mmintrin.h \ - /usr/lib/gcc/x86_64-redhat-linux/8/include/xmmintrin.h \ - /usr/lib/gcc/x86_64-redhat-linux/8/include/mm_malloc.h \ - 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