mirror of
https://github.com/netdata/netdata.git
synced 2025-04-13 17:19:11 +00:00
Add commands to check and fix database corruption (#11828)
* Set a flag to do aclk sync thread shutdown Attempt to dequeue a cmd in case the queue is full and someone is blocked * Drop tables and recreate instead of deleting * Add commands to check the database -W check-database, fix-database, compact-database * Split the database setup to config and cleanup part * Add checks during database setup and cleanup to detect corruption to the dimension and chart tables * Add full database check and refactor code * Change commands to better indicate that the operations refer to the sqlite metadata database (not the metrics dbengine database) * Add check for table being null (request for entire database check) * Rename command for better clarity
This commit is contained in:
Stelios Fragkakis
GitHub
parent
e2bdee968e
commit
0586829ee6
6 changed files with 267 additions and 27 deletions
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@ -44,6 +44,9 @@ void netdata_cleanup_and_exit(int ret) {
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// stop everything
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info("EXIT: stopping static threads...");
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#ifdef ENABLE_NEW_CLOUD_PROTOCOL
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aclk_sync_exit_all();
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#endif
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cancel_main_threads();
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// free the database
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@ -360,13 +363,16 @@ int help(int exitcode) {
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" -W stacksize=N Set the stacksize (in bytes).\n\n"
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" -W debug_flags=N Set runtime tracing to debug.log.\n\n"
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" -W unittest Run internal unittests and exit.\n\n"
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" -W sqlite-check Check metadata database integrity and exit.\n\n"
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" -W sqlite-fix Check metadata database integrity, fix if needed and exit.\n\n"
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" -W sqlite-compact Reclaim metadata database unused space and exit.\n\n"
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#ifdef ENABLE_DBENGINE
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" -W createdataset=N Create a DB engine dataset of N seconds and exit.\n\n"
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" -W stresstest=A,B,C,D,E,F\n"
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" Run a DB engine stress test for A seconds,\n"
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" with B writers and C readers, with a ramp up\n"
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" time of D seconds for writers, a page cache\n"
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" size of E MiB, an optional disk space limit"
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" size of E MiB, an optional disk space limit\n"
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" of F MiB and exit.\n\n"
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#endif
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" -W set section option value\n"
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@ -801,6 +807,20 @@ int main(int argc, char **argv) {
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char* createdataset_string = "createdataset=";
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char* stresstest_string = "stresstest=";
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#endif
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if(strcmp(optarg, "sqlite-check") == 0) {
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sql_init_database(DB_CHECK_INTEGRITY);
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return 0;
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}
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if(strcmp(optarg, "sqlite-fix") == 0) {
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sql_init_database(DB_CHECK_FIX_DB);
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return 0;
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}
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if(strcmp(optarg, "sqlite-compact") == 0) {
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sql_init_database(DB_CHECK_RECLAIM_SPACE);
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return 0;
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}
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if(strcmp(optarg, "unittest") == 0) {
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if(unit_test_buffer()) return 1;
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@ -690,7 +690,7 @@ int rrd_init(char *hostname, struct rrdhost_system_info *system_info) {
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if (gap_when_lost_iterations_above < 1)
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gap_when_lost_iterations_above = 1;
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if (unlikely(sql_init_database())) {
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if (unlikely(sql_init_database(DB_CHECK_NONE))) {
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if (default_rrd_memory_mode == RRD_MEMORY_MODE_DBENGINE)
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fatal("Failed to initialize SQLite");
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info("Skipping SQLITE metadata initialization since memory mode is not db engine");
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@ -97,7 +97,7 @@ int aclk_database_enq_cmd_noblock(struct aclk_database_worker_config *wc, struct
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/* wait for free space in queue */
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uv_mutex_lock(&wc->cmd_mutex);
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if ((queue_size = wc->queue_size) == ACLK_DATABASE_CMD_Q_MAX_SIZE) {
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if ((queue_size = wc->queue_size) == ACLK_DATABASE_CMD_Q_MAX_SIZE || wc->is_shutting_down) {
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uv_mutex_unlock(&wc->cmd_mutex);
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return 1;
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}
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@ -118,6 +118,10 @@ void aclk_database_enq_cmd(struct aclk_database_worker_config *wc, struct aclk_d
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/* wait for free space in queue */
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uv_mutex_lock(&wc->cmd_mutex);
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if (wc->is_shutting_down) {
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uv_mutex_unlock(&wc->cmd_mutex);
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return;
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}
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while ((queue_size = wc->queue_size) == ACLK_DATABASE_CMD_Q_MAX_SIZE) {
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uv_cond_wait(&wc->cmd_cond, &wc->cmd_mutex);
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}
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@ -142,10 +146,12 @@ struct aclk_database_cmd aclk_database_deq_cmd(struct aclk_database_worker_confi
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uv_mutex_lock(&wc->cmd_mutex);
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queue_size = wc->queue_size;
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if (queue_size == 0) {
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if (queue_size == 0 || wc->is_shutting_down) {
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memset(&ret, 0, sizeof(ret));
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ret.opcode = ACLK_DATABASE_NOOP;
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ret.completion = NULL;
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if (wc->is_shutting_down)
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uv_cond_signal(&wc->cmd_cond);
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} else {
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/* dequeue command */
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ret = wc->cmd_queue.cmd_array[wc->cmd_queue.head];
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@ -156,7 +162,6 @@ struct aclk_database_cmd aclk_database_deq_cmd(struct aclk_database_worker_confi
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wc->cmd_queue.head + 1 : 0;
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}
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wc->queue_size = queue_size - 1;
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/* wake up producers */
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uv_cond_signal(&wc->cmd_cond);
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}
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@ -184,6 +189,30 @@ int aclk_worker_enq_cmd(char *node_id, struct aclk_database_cmd *cmd)
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return (wc == NULL);
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}
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void aclk_sync_exit_all()
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{
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rrd_wrlock();
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RRDHOST *host = localhost;
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while(host) {
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struct aclk_database_worker_config *wc = host->dbsync_worker;
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if (wc) {
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wc->is_shutting_down = 1;
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(void) aclk_database_deq_cmd(wc);
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uv_cond_signal(&wc->cmd_cond);
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}
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host = host->next;
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}
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rrd_unlock();
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uv_mutex_lock(&aclk_async_lock);
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struct aclk_database_worker_config *wc = aclk_thread_head;
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while (wc) {
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wc->is_shutting_down = 1;
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wc = wc->next;
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}
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uv_mutex_unlock(&aclk_async_lock);
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}
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int aclk_start_sync_thread(void *data, int argc, char **argv, char **column)
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{
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char uuid_str[GUID_LEN + 1];
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@ -313,7 +342,7 @@ void aclk_database_worker(void *arg)
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struct aclk_database_cmd cmd;
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unsigned cmd_batch_size;
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aclk_database_init_cmd_queue(wc);
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//aclk_database_init_cmd_queue(wc);
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char threadname[NETDATA_THREAD_NAME_MAX+1];
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if (wc->host)
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@ -347,9 +376,9 @@ void aclk_database_worker(void *arg)
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timer_req.data = wc;
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fatal_assert(0 == uv_timer_start(&timer_req, timer_cb, TIMER_PERIOD_MS, TIMER_PERIOD_MS));
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wc->retry_count = 0;
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// wc->retry_count = 0;
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wc->node_info_send = (wc->host && !localhost);
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aclk_add_worker_thread(wc);
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// aclk_add_worker_thread(wc);
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info("Starting ACLK sync thread for host %s -- scratch area %lu bytes", wc->host_guid, sizeof(*wc));
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memset(&cmd, 0, sizeof(cmd));
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@ -359,11 +388,10 @@ void aclk_database_worker(void *arg)
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if (!wc->chart_payload_count)
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info("%s: No pending charts and dimensions detected during startup", wc->host_guid);
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#endif
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wc->chart_updates = 0;
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wc->startup_time = now_realtime_sec();
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wc->cleanup_after = wc->startup_time + ACLK_DATABASE_CLEANUP_FIRST;
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wc->rotation_after = wc->startup_time + ACLK_DATABASE_ROTATION_DELAY;
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wc->alert_updates = 0;
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debug(D_ACLK_SYNC,"Node %s reports pending message count = %u", wc->node_id, wc->chart_payload_count);
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while (likely(!netdata_exit)) {
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@ -498,7 +526,7 @@ void aclk_database_worker(void *arg)
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uv_close((uv_handle_t *)&timer_req, NULL);
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/* cleanup operations of the event loop */
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info("Shutting down ACLK sync event loop.");
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//info("Shutting down ACLK sync event loop for %s", wc->host_guid);
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/*
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* uv_async_send after uv_close does not seem to crash in linux at the moment,
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@ -508,7 +536,7 @@ void aclk_database_worker(void *arg)
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uv_close((uv_handle_t *)&wc->async, NULL);
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uv_run(loop, UV_RUN_DEFAULT);
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info("Shutting down ACLK sync event loop complete.");
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info("Shutting down ACLK sync event loop complete for host %s", wc->host_guid);
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/* TODO: don't let the API block by waiting to enqueue commands */
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uv_cond_destroy(&wc->cmd_cond);
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/* uv_mutex_destroy(&wc->cmd_mutex); */
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@ -597,6 +625,11 @@ void sql_create_aclk_table(RRDHOST *host, uuid_t *host_uuid, uuid_t *node_id)
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strcpy(wc->host_guid, host_guid);
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if (node_id && !uuid_is_null(*node_id))
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uuid_unparse_lower(*node_id, wc->node_id);
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wc->chart_updates = 0;
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wc->alert_updates = 0;
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wc->retry_count = 0;
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aclk_database_init_cmd_queue(wc);
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aclk_add_worker_thread(wc);
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fatal_assert(0 == uv_thread_create(&(wc->thread), aclk_database_worker, wc));
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#else
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UNUSED(host);
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@ -193,6 +193,7 @@ struct aclk_database_worker_config {
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int node_info_send;
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int chart_pending;
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int chart_reset_count;
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volatile unsigned is_shutting_down;
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struct aclk_database_worker_config *next;
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};
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@ -227,4 +228,5 @@ void sql_check_aclk_table_list(struct aclk_database_worker_config *wc);
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void sql_delete_aclk_table_list(struct aclk_database_worker_config *wc, struct aclk_database_cmd cmd);
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void sql_maint_aclk_sync_database(struct aclk_database_worker_config *wc, struct aclk_database_cmd cmd);
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int claimed();
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void aclk_sync_exit_all();
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#endif //NETDATA_SQLITE_ACLK_H
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@ -12,6 +12,10 @@ const char *database_config[] = {
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"chart_type int, memory_mode int, history_entries);",
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"CREATE TABLE IF NOT EXISTS dimension(dim_id blob PRIMARY KEY, chart_id blob, id text, name text, "
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"multiplier int, divisor int , algorithm int, options text);",
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"DROP TABLE IF EXISTS chart_active;",
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"DROP TABLE IF EXISTS dimension_active;",
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"CREATE TABLE IF NOT EXISTS chart_active(chart_id blob PRIMARY KEY, date_created int);",
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"CREATE TABLE IF NOT EXISTS dimension_active(dim_id blob primary key, date_created int);",
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"CREATE TABLE IF NOT EXISTS metadata_migration(filename text, file_size, date_created int);",
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@ -45,8 +49,10 @@ const char *database_config[] = {
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"INSERT INTO chart_hash_map (chart_id, hash_id) values (new.chart_id, new.hash_id) "
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"on conflict (chart_id, hash_id) do nothing; END; ",
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"delete from chart_active;",
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"delete from dimension_active;",
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NULL
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};
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const char *database_cleanup[] = {
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"delete from chart where chart_id not in (select chart_id from dimension);",
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"delete from host where host_id not in (select host_id from chart);",
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"delete from chart_label where chart_id not in (select chart_id from chart);",
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@ -180,18 +186,153 @@ void store_active_dimension(uuid_t *dimension_uuid)
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return;
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}
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static int check_table_integrity_cb(void *data, int argc, char **argv, char **column)
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{
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int *status = data;
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UNUSED(argc);
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UNUSED(column);
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info("---> %s", argv[0]);
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*status = (strcmp(argv[0], "ok") != 0);
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return 0;
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}
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static int check_table_integrity(char *table)
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{
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int status = 0;
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char *err_msg = NULL;
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char wstr[255];
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if (table) {
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info("Checking table %s", table);
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snprintfz(wstr, 254, "PRAGMA integrity_check(%s);", table);
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}
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else {
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info("Checking entire database");
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strcpy(wstr,"PRAGMA integrity_check;");
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}
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int rc = sqlite3_exec(db_meta, wstr, check_table_integrity_cb, (void *) &status, &err_msg);
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if (rc != SQLITE_OK) {
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error_report("SQLite error during database integrity check for %s, rc = %d (%s)",
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table ? table : "the entire database", rc, err_msg);
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sqlite3_free(err_msg);
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}
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return status;
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}
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const char *rebuild_chart_commands[] = {
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"BEGIN TRANSACTION; ",
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"DROP INDEX IF EXISTS ind_c1;" ,
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"DROP TABLE IF EXISTS chart_backup; " ,
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"CREATE TABLE chart_backup AS SELECT * FROM chart; " ,
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"DROP TABLE chart; ",
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"CREATE TABLE IF NOT EXISTS chart(chart_id blob PRIMARY KEY, host_id blob, type text, id text, "
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"name text, family text, context text, title text, unit text, plugin text, "
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"module text, priority int, update_every int, chart_type int, memory_mode int, history_entries); ",
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"INSERT INTO chart SELECT DISTINCT * FROM chart_backup; ",
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"DROP TABLE chart_backup; " ,
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"CREATE INDEX IF NOT EXISTS ind_c1 on chart (host_id, id, type, name);",
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"COMMIT TRANSACTION;",
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NULL
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};
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static void rebuild_chart()
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{
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int rc;
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char *err_msg = NULL;
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info("Rebuilding chart table");
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for (int i = 0; rebuild_chart_commands[i]; i++) {
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info("Executing %s", rebuild_chart_commands[i]);
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rc = sqlite3_exec(db_meta, rebuild_chart_commands[i], 0, 0, &err_msg);
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if (rc != SQLITE_OK) {
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error_report("SQLite error during database setup, rc = %d (%s)", rc, err_msg);
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error_report("SQLite failed statement %s", rebuild_chart_commands[i]);
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sqlite3_free(err_msg);
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}
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}
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return;
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}
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const char *rebuild_dimension_commands[] = {
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"BEGIN TRANSACTION; ",
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"DROP INDEX IF EXISTS ind_d1;" ,
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"DROP TABLE IF EXISTS dimension_backup; " ,
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"CREATE TABLE dimension_backup AS SELECT * FROM dimension; " ,
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"DROP TABLE dimension; " ,
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"CREATE TABLE IF NOT EXISTS dimension(dim_id blob PRIMARY KEY, chart_id blob, id text, name text, "
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"multiplier int, divisor int , algorithm int, options text);" ,
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"INSERT INTO dimension SELECT distinct * FROM dimension_backup; " ,
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"DROP TABLE dimension_backup; " ,
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"CREATE INDEX IF NOT EXISTS ind_d1 on dimension (chart_id, id, name);",
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"COMMIT TRANSACTION;",
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NULL
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};
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void rebuild_dimension()
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{
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int rc;
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char *err_msg = NULL;
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info("Rebuilding dimension table");
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for (int i = 0; rebuild_dimension_commands[i]; i++) {
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info("Executing %s", rebuild_dimension_commands[i]);
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rc = sqlite3_exec(db_meta, rebuild_dimension_commands[i], 0, 0, &err_msg);
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if (rc != SQLITE_OK) {
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error_report("SQLite error during database setup, rc = %d (%s)", rc, err_msg);
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error_report("SQLite failed statement %s", rebuild_dimension_commands[i]);
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sqlite3_free(err_msg);
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}
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}
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return;
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}
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static int attempt_database_fix()
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{
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info("Closing database and attempting to fix it");
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int rc = sqlite3_close(db_meta);
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if (rc != SQLITE_OK)
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error_report("Failed to close database, rc = %d", rc);
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info("Attempting to fix database");
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db_meta = NULL;
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return sql_init_database(DB_CHECK_FIX_DB | DB_CHECK_CONT);
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}
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static int init_database_batch(int rebuild, int init_type, const char *batch[])
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{
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int rc;
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char *err_msg = NULL;
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for (int i = 0; batch[i]; i++) {
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debug(D_METADATALOG, "Executing %s", batch[i]);
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rc = sqlite3_exec(db_meta, batch[i], 0, 0, &err_msg);
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if (rc != SQLITE_OK) {
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error_report("SQLite error during database %s, rc = %d (%s)", init_type ? "cleanup" : "setup", rc, err_msg);
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error_report("SQLite failed statement %s", batch[i]);
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sqlite3_free(err_msg);
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if (SQLITE_CORRUPT == rc) {
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if (!rebuild)
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return attempt_database_fix();
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rc = check_table_integrity(NULL);
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if (rc)
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error_report("Databse integrity errors reported");
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}
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return 1;
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}
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}
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return 0;
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}
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/*
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* Initialize the SQLite database
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* Return 0 on success
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*/
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int sql_init_database(void)
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int sql_init_database(db_check_action_type_t rebuild)
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{
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char *err_msg = NULL;
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char sqlite_database[FILENAME_MAX + 1];
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int rc;
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fatal_assert(0 == uv_mutex_init(&sqlite_transaction_lock));
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snprintfz(sqlite_database, FILENAME_MAX, "%s/netdata-meta.db", netdata_configured_cache_dir);
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rc = sqlite3_open(sqlite_database, &db_meta);
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if (rc != SQLITE_OK) {
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@ -201,18 +342,55 @@ int sql_init_database(void)
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return 1;
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}
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|
||||
info("SQLite database %s initialization", sqlite_database);
|
||||
if (rebuild & (DB_CHECK_INTEGRITY | DB_CHECK_FIX_DB)) {
|
||||
int errors_detected = 0;
|
||||
if (!(rebuild & DB_CHECK_CONT))
|
||||
info("Running database check on %s", sqlite_database);
|
||||
|
||||
for (int i = 0; database_config[i]; i++) {
|
||||
debug(D_METADATALOG, "Executing %s", database_config[i]);
|
||||
rc = sqlite3_exec(db_meta, database_config[i], 0, 0, &err_msg);
|
||||
if (rc != SQLITE_OK) {
|
||||
error_report("SQLite error during database setup, rc = %d (%s)", rc, err_msg);
|
||||
error_report("SQLite failed statement %s", database_config[i]);
|
||||
sqlite3_free(err_msg);
|
||||
return 1;
|
||||
if (check_table_integrity("chart")) {
|
||||
errors_detected++;
|
||||
if (rebuild & DB_CHECK_FIX_DB)
|
||||
rebuild_chart();
|
||||
else
|
||||
error_report("Errors reported -- run with -W sqlite-fix");
|
||||
}
|
||||
|
||||
if (check_table_integrity("dimension")) {
|
||||
errors_detected++;
|
||||
if (rebuild & DB_CHECK_FIX_DB)
|
||||
rebuild_dimension();
|
||||
else
|
||||
error_report("Errors reported -- run with -W sqlite-fix");
|
||||
}
|
||||
|
||||
if (!errors_detected) {
|
||||
if (check_table_integrity(NULL))
|
||||
error_report("Errors reported");
|
||||
}
|
||||
}
|
||||
|
||||
if (rebuild & DB_CHECK_RECLAIM_SPACE) {
|
||||
if (!(rebuild & DB_CHECK_CONT))
|
||||
info("Reclaiming space of %s", sqlite_database);
|
||||
rc = sqlite3_exec(db_meta, "VACUUM;", 0, 0, &err_msg);
|
||||
if (rc != SQLITE_OK) {
|
||||
error_report("Failed to execute VACUUM rc = %d (%s)", rc, err_msg);
|
||||
sqlite3_free(err_msg);
|
||||
}
|
||||
}
|
||||
|
||||
if (rebuild && !(rebuild & DB_CHECK_CONT))
|
||||
return 1;
|
||||
|
||||
info("SQLite database %s initialization", sqlite_database);
|
||||
|
||||
if (init_database_batch(rebuild, 0, &database_config[0]))
|
||||
return 1;
|
||||
|
||||
if (init_database_batch(rebuild, 0, &database_cleanup[0]))
|
||||
return 1;
|
||||
|
||||
fatal_assert(0 == uv_mutex_init(&sqlite_transaction_lock));
|
||||
info("SQLite database initialization completed");
|
||||
return 0;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -16,6 +16,13 @@ struct node_instance_list {
|
|||
int hops;
|
||||
};
|
||||
|
||||
typedef enum db_check_action_type {
|
||||
DB_CHECK_NONE = 0x0000,
|
||||
DB_CHECK_INTEGRITY = 0x0001,
|
||||
DB_CHECK_FIX_DB = 0x0002,
|
||||
DB_CHECK_RECLAIM_SPACE = 0x0004,
|
||||
DB_CHECK_CONT = 0x00008
|
||||
} db_check_action_type_t;
|
||||
|
||||
#define SQLITE_INSERT_DELAY (50) // Insert delay in case of lock
|
||||
|
||||
|
|
@ -49,7 +56,7 @@ struct node_instance_list {
|
|||
return 1; \
|
||||
}
|
||||
|
||||
extern int sql_init_database(void);
|
||||
extern int sql_init_database(db_check_action_type_t rebuild);
|
||||
extern void sql_close_database(void);
|
||||
|
||||
extern int sql_store_host(uuid_t *guid, const char *hostname, const char *registry_hostname, int update_every, const char *os, const char *timezone, const char *tags);
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue