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Type: Task
Resolution: Done
Fix Version/s: None
Affects Version/s: None
Component/s: None
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A Jenkins job is hanging doing a compact in an LSM tree.
http://mjc.homeunix.org:8180/job/wiredtiger-perf-med-lsm-compact/977/

Potentially relevant stack traces:

(gdb) thread apply all where

Thread 9 (Thread 0x7fdf97fff700 (LWP 26291)):
#0  pthread_cond_timedwait@@GLIBC_2.3.2 ()
    at ../nptl/sysdeps/unix/sysv/linux/x86_64/pthread_cond_timedwait.S:239
WT-1  0x000000000042386f in __wt_cond_wait (session=0x7fdf98041280, cond=0x7fdf98016160, 
    usecs=<value optimized out>) at ../src/os_posix/os_mtx.c:77
WT-2  0x0000000000444b88 in __evict_server (arg=0x7fdf98041280) at ../src/btree/bt_evict.c:194
WT-3  0x00007fdf98ca1ddb in start_thread (arg=0x7fdf97fff700) at pthread_create.c:301
WT-4  0x00007fdf989efa1d in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:115

Thread 6 (Thread 0x7fdf967fc700 (LWP 26294)):
#0  0x00007fdf989e8aa3 in select () at ../sysdeps/unix/syscall-template.S:82
WT-1  0x0000000000425958 in __wt_sleep (seconds=<value optimized out>, 
    micro_seconds=<value optimized out>) at ../src/os_posix/os_sleep.c:22
WT-2  0x000000000041eb77 in __wt_lsm_compact (session=0x7fdf98041a00, name=<value optimized out>, 
    skip=<value optimized out>) at ../src/lsm/lsm_tree.c:1134
WT-3  0x00000000004318c7 in __wt_schema_worker (session=0x7fdf98041a00, uri=0x7fdf75879060 "lsm:test", 
    file_func=0, name_func=0x41e910 <__wt_lsm_compact>, cfg=0x7fdf967fbd20, open_flags=0)
    at ../src/schema/schema_worker.c:37
WT-4  0x0000000000431deb in __wt_schema_worker (session=0x7fdf98041a00, uri=<value optimized out>, 
    file_func=0, name_func=0x41e910 <__wt_lsm_compact>, cfg=0x7fdf967fbd20, open_flags=0)
    at ../src/schema/schema_worker.c:86
WT-5  0x000000000043538a in __wt_session_compact (wt_session=0x7fdf98041a00, 
    uri=0x7fdf98020270 "table:test", config=<value optimized out>)
    at ../src/session/session_compact.c:229
WT-6  0x000000000044195f in __async_worker_execop (arg=0x7fdf98041a00)
    at ../src/async/async_worker.c:198
WT-7  __async_worker_op (arg=0x7fdf98041a00) at ../src/async/async_worker.c:253
WT-8  __wt_async_worker (arg=0x7fdf98041a00) at ../src/async/async_worker.c:310
WT-9  0x00007fdf98ca1ddb in start_thread (arg=0x7fdf967fc700) at pthread_create.c:301
WT-10 0x00007fdf989efa1d in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:115

Thread 5 (Thread 0x7fdf95ffb700 (LWP 26295)):
#0  0x00007fdf989e8aa3 in select () at ../sysdeps/unix/syscall-template.S:82
WT-1  0x0000000000425958 in __wt_sleep (seconds=<value optimized out>, 
---Type <return> to continue, or q <return> to quit---
    micro_seconds=<value optimized out>) at ../src/os_posix/os_sleep.c:22
WT-2  0x000000000041bece in __lsm_manager_run_server (arg=<value optimized out>)
    at ../src/lsm/lsm_manager.c:312
WT-3  __lsm_worker_manager (arg=<value optimized out>) at ../src/lsm/lsm_manager.c:377
WT-4  0x00007fdf98ca1ddb in start_thread (arg=0x7fdf95ffb700) at pthread_create.c:301
WT-5  0x00007fdf989efa1d in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:115

Thread 4 (Thread 0x7fdf957fa700 (LWP 26296)):
#0  pthread_cond_timedwait@@GLIBC_2.3.2 ()
    at ../nptl/sysdeps/unix/sysv/linux/x86_64/pthread_cond_timedwait.S:239
WT-1  0x000000000042386f in __wt_cond_wait (session=0x7fdf98042180, cond=0x7fdf98016080, 
    usecs=<value optimized out>) at ../src/os_posix/os_mtx.c:77
WT-2  0x000000000041f177 in __lsm_worker (arg=0x7fdf9800f0a0) at ../src/lsm/lsm_worker.c:149
WT-3  0x00007fdf98ca1ddb in start_thread (arg=0x7fdf957fa700) at pthread_create.c:301
WT-4  0x00007fdf989efa1d in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:115

Thread 3 (Thread 0x7fdf947ff700 (LWP 26297)):
#0  pthread_cond_timedwait@@GLIBC_2.3.2 ()
    at ../nptl/sysdeps/unix/sysv/linux/x86_64/pthread_cond_timedwait.S:239
WT-1  0x000000000042386f in __wt_cond_wait (session=0x7fdf98042400, cond=0x7fdf98016080, 
    usecs=<value optimized out>) at ../src/os_posix/os_mtx.c:77
WT-2  0x000000000041f177 in __lsm_worker (arg=0x7fdf9800f0c0) at ../src/lsm/lsm_worker.c:149
WT-3  0x00007fdf98ca1ddb in start_thread (arg=0x7fdf947ff700) at pthread_create.c:301
WT-4  0x00007fdf989efa1d in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:115

Thread 2 (Thread 0x7fdf93ffe700 (LWP 26298)):
#0  pthread_cond_timedwait@@GLIBC_2.3.2 ()
    at ../nptl/sysdeps/unix/sysv/linux/x86_64/pthread_cond_timedwait.S:239
WT-1  0x000000000042386f in __wt_cond_wait (session=0x7fdf98042680, cond=0x7fdf98016080, 
    usecs=<value optimized out>) at ../src/os_posix/os_mtx.c:77
WT-2  0x000000000041f177 in __lsm_worker (arg=0x7fdf9800f0e0) at ../src/lsm/lsm_worker.c:149
WT-3  0x00007fdf98ca1ddb in start_thread (arg=0x7fdf93ffe700) at pthread_create.c:301
WT-4  0x00007fdf989efa1d in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:115

Information:

(gdb) p /x lsm_tree->flags
$2 = 0x33
(gdb) list lsm.h:197
192		int freeing_old_chunks;		/* Whether chunks are being freed */
193		uint32_t merge_aggressiveness;	/* Increase amount of work per merge */
194	
195	#define	WT_LSM_TREE_ACTIVE		0x01	/* Workers are active */
196	#define	WT_LSM_TREE_COMPACT_FLUSH	0x02	/* Flushed for compact */
197	#define	WT_LSM_TREE_COMPACTING		0x04	/* Tree being compacted */
198	#define	WT_LSM_TREE_NEED_SWITCH		0x08	/* New chunk needs creating */
199	#define	WT_LSM_TREE_OPEN		0x10	/* The tree is open */
200	#define	WT_LSM_TREE_THROTTLE		0x20	/* Throttle updates */
201		uint32_t flags;
(gdb) p lsm_tree->chunk[0]
$4 = (WT_LSM_CHUNK *) 0x7fdf86045480
(gdb) p lsm_tree->chunk[1]
$5 = (WT_LSM_CHUNK *) 0x7fdf8640e580
(gdb) p *lsm_tree->chunk[0]
$6 = {uri = 0x7fdf3d5c3520 "file:test-000110.lsm", bloom_uri = 0x0, create_ts = {
    tv_sec = 1410541054, tv_nsec = 666855286}, count = 49624376, size = 6401531904, switch_txn = 0, 
  id = 110, generation = 3, refcnt = 0, bloom_busy = 0, empty = 0 '\000', evicted = 0 '\000', 
  flags = 4}
(gdb) p *lsm_tree->chunk[1]
$7 = {uri = 0x7fdf3df38ca0 "file:test-000106.lsm", bloom_uri = 0x0, create_ts = {
    tv_sec = 1410540986, tv_nsec = 133071004}, count = 375624, size = 0, switch_txn = 50001018, 
  id = 106, generation = 0, refcnt = 1, bloom_busy = 0, empty = 0 '\000', evicted = 0 '\000', 
  flags = 0}

There are only three entries in the app queue:

(gdb) p manager->appqh
$17 = {tqh_first = 0x7fdf948a93a0, tqh_last = 0x7fdf948a9460}
(gdb) p $17->tqh_first
$19 = (struct __wt_lsm_work_unit *) 0x7fdf948a93a0
(gdb) p *$19
$20 = {q = {tqe_next = 0x7fdf948a9400, tqe_prev = 0x7fdf9802be50}, flags = 2, 
  lsm_tree = 0x7fdf9808d000}
(gdb) p *$19->q.tqe_next
$21 = {q = {tqe_next = 0x7fdf948a9460, tqe_prev = 0x7fdf948a93a0}, flags = 4, 
  lsm_tree = 0x7fdf9808d000}
(gdb) p *$21->q.tqe_next
$22 = {q = {tqe_next = 0x0, tqe_prev = 0x7fdf948a9400}, flags = 1, lsm_tree = 0x7fdf9808d000}
(gdb) p *$22->q.tqe_next
Cannot access memory at address 0x0

One entry in the manager queue:

(gdb) p manager->managerqh
$18 = {tqh_first = 0x7fdf948a9280, tqh_last = 0x7fdf948a94a0}
(gdb) p *$18->tqh_first->q.tqe_next
$23 = {q = {tqe_next = 0x0, tqe_prev = 0x7fdf948a9280}, flags = 8, lsm_tree = 0x7fdf9808d000}
(gdb) p *$23->q.tqe_next

None in the switch queue.

The worker code is never retrieving a chunk to flush (chunk is always NULL at line 56 of lsm_worker.c).

The compact code is never pushing more forced flushes. I think it's a problem with:

                /*
                 * The flush flag is cleared when the the chunk has been
                 * flushed.  Continue to push forced flushes until the
                 * chunk is on disk.  Once it is on disk move to the compacting
                 * phase.
                 */
                if (flushing && !F_ISSET(lsm_tree, WT_LSM_TREE_COMPACT_FLUSH)) {
                        if (chunk != NULL &&
                            !F_ISSET(chunk, WT_LSM_CHUNK_ONDISK)) {
                                WT_ERR(__wt_verbose(session, WT_VERB_LSM,
                                    "Compact flush retry %s chunk %u",
                                    name, chunk->id));
                                F_SET(lsm_tree, WT_LSM_TREE_COMPACT_FLUSH);
                                WT_ERR(__wt_lsm_manager_push_entry(session,
                                    WT_LSM_WORK_FLUSH | WT_LSM_WORK_FORCE,
                                    lsm_tree));
                        } else {
                                if (ref) {
                                        WT_ASSERT(session, chunk != NULL);
                                        WT_ERR(__wt_verbose(session,
                                            WT_VERB_LSM,
                                            "Compact flush done %s chunk %u",
                                            name, chunk->id));
                                        (void)WT_ATOMIC_SUB(chunk->refcnt, 1);
                                }
                                flushing = ref = 0;
                                compacting = 1;
                                F_SET(lsm_tree, WT_LSM_TREE_COMPACTING);
                        }
                }

It should be

Unable to find source-code formatter for language: if. Available languages are: actionscript, ada, applescript, bash, c, c#, c++, cpp, css, erlang, go, groovy, haskell, html, java, javascript, js, json, lua, none, nyan, objc, perl, php, python, r, rainbow, ruby, scala, sh, sql, swift, visualbasic, xml, yaml

 (flushing && F_ISSET(lsm_tree, WT_LSM_TREE_COMPACT_FLUSH))

, but I need to think through the other implications of that change.

is related to

WT-1201 medium-lsm-multi failure in WT_CONNECTION::close

Closed

WT-1247 compaction still hanging

Closed

related to

WT-2 What does metadata look like?

Closed

WT-3 What file formats are required?

Closed

WT-4 Flexible cursor traversals

Closed

WT-5 How does pget work: is it necessary?

Closed

WT-6 Complex schema example

Closed

WT-7 Do we need the handle->err/errx methods?

Closed

WT-8 Do we need table load, bulk-load and/or dump methods?

Closed

WT-9 Does adding schema need to be transactional?

Closed

WT-10 Basic "getting started" tutorial

Closed

WT-1226 Fix a hang in LSM compact. Refs #1225

Closed

(7 related to)

Assignee:: Unassigned
Reporter:: Alexander Gorrod
Votes:: 0 Vote for this issue
Watchers:: 1 Start watching this issue

Created:: Sep 15 2014 12:18:46 AM UTC
Updated:: Apr 16 2015 08:44:16 PM UTC
Resolved:: Apr 09 2015 01:08:33 AM UTC

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