sonarqube 5.2 MySQLTransactionRollbackException: Deadlock found when trying to get lock - sonarqube

Question

Using SonarQube 5.2 I’m seeing the following Deadlock issue:
05:48:22 ERROR: Error during Sonar runner execution
05:48:22 java.lang.IllegalStateException: Fail to execute request
[code=500, url=http://192.168.109.6/api/ce/submit?projectKey=CoprHD&projectName=CoprHD-controller&projectBranch=bugfix-COP-19001-hotfix]:
{"errors":[{"msg":"\n### Error updating database.
Cause: com.mysql.jdbc.exceptions.jdbc4.MySQLTransactionRollbackException:
Deadlock found when trying to get lock; try restarting transaction\n
### The error may involve org.sonar.db.user.RoleMapper.insertGroupRole-Inline\n### The error occurred while setting parameters\n
### SQL: INSERT INTO group_roles (group_id, resource_id, role) VALUES (?, ?, ?)\n
### Cause: com.mysql.jdbc.exceptions.jdbc4.MySQLTransactionRollbackException: Deadlock found when trying to get lock; try restarting transaction"}]}
05:48:22 at org.sonar.batch.report.ReportPublisher.uploadMultiPartReport(ReportPublisher.java:182)
05:48:22 at org.sonar.batch.report.ReportPublisher.sendOrDumpReport(ReportPublisher.java:151)
05:48:22 at org.sonar.batch.report.ReportPublisher.execute(ReportPublisher.java:115)
05:48:22 at org.sonar.batch.phases.PhaseExecutor.publishReportJob(PhaseExecutor.java:116)
05:48:22 at org.sonar.batch.phases.PhaseExecutor.execute(PhaseExecutor.java:106)
05:48:22 at org.sonar.batch.scan.ModuleScanContainer.doAfterStart(ModuleScanContainer.java:192)
05:48:22 at org.sonar.core.platform.ComponentContainer.startComponents(ComponentContainer.java:100)
05:48:22 at org.sonar.core.platform.ComponentContainer.execute(ComponentContainer.java:85)
05:48:22 at org.sonar.batch.scan.ProjectScanContainer.scan(ProjectScanContainer.java:258)
05:48:22 at org.sonar.batch.scan.ProjectScanContainer.scanRecursively(ProjectScanContainer.java:253)
05:48:22 at org.sonar.batch.scan.ProjectScanContainer.doAfterStart(ProjectScanContainer.java:243)
05:48:22 at org.sonar.core.platform.ComponentContainer.startComponents(ComponentContainer.java:100)
05:48:22 at org.sonar.core.platform.ComponentContainer.execute(ComponentContainer.java:85)
05:48:22 at org.sonar.batch.bootstrap.GlobalContainer.executeAnalysis(GlobalContainer.java:153)
05:48:22 at org.sonar.batch.bootstrapper.Batch.executeTask(Batch.java:110)
05:48:22 at org.sonar.runner.batch.BatchIsolatedLauncher.execute(BatchIsolatedLauncher.java:55)
05:48:22 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
05:48:22 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
05:48:22 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
05:48:22 at java.lang.reflect.Method.invoke(Method.java:606)
05:48:22 at org.sonar.runner.impl.IsolatedLauncherProxy.invoke(IsolatedLauncherProxy.java:61)
05:48:22 at com.sun.proxy.$Proxy0.execute(Unknown Source)
05:48:22 at org.sonar.runner.api.EmbeddedRunner.doExecute(EmbeddedRunner.java:275)
05:48:22 at org.sonar.runner.api.EmbeddedRunner.runAnalysis(EmbeddedRunner.java:166)
05:48:22 at org.sonar.runner.api.EmbeddedRunner.runAnalysis(EmbeddedRunner.java:153)
05:48:22 at org.sonar.runner.cli.Main.runAnalysis(Main.java:118)
05:48:22 at org.sonar.runner.cli.Main.execute(Main.java:80)
05:48:22 at org.sonar.runner.cli.Main.main(Main.java:66)
Searching for similar reports I found this reference which says the issue was resolved: https://jira.sonarsource.com/browse/SONAR-1945
I also found a reference that transaction-isolation should be changed from REPEATABLE-READ to READ-COMMITTED. Is this a reasonable thing to do with mysql for Sonar?
mysql> show variables like '%wait_timeout%';
+--------------------------+----------+
| Variable_name | Value |
+--------------------------+----------+
| innodb_lock_wait_timeout | 500 |
| lock_wait_timeout | 31536000 |
| wait_timeout | 28800 |
+--------------------------+----------+
3 rows in set (0.25 sec)
mysql> show variables like '%tx_isolation%';
+---------------+-----------------+
| Variable_name | Value |
+---------------+-----------------+
| tx_isolation | REPEATABLE-READ |
+---------------+-----------------+
1 row in set (0.00 sec)
mysql> SELECT ##GLOBAL.tx_isolation, ##tx_isolation;
+-----------------------+-----------------+
| ##GLOBAL.tx_isolation | ##tx_isolation |
+-----------------------+-----------------+
| REPEATABLE-READ | REPEATABLE-READ |
+-----------------------+-----------------+
For further info about the Deadlock issue, here is some data.
Does anyone know if this issue is something that should be tweaked in mysql or is this an issue that needs to be fixed in the SonarQube app?
mysql> show engine innodb status
=====================================
2015-12-18 07:42:25 7f61f03cd700 INNODB MONITOR OUTPUT
=====================================
Per second averages calculated from the last 31 seconds
-----------------
BACKGROUND THREAD
-----------------
srv_master_thread loops: 44635 srv_active, 0 srv_shutdown, 1284536 srv_idle
srv_master_thread log flush and writes: 1329157
----------
SEMAPHORES
----------
OS WAIT ARRAY INFO: reservation count 224853
OS WAIT ARRAY INFO: signal count 1727534
Mutex spin waits 1578113, rounds 7231747, OS waits 74673
RW-shared spins 483413, rounds 5257332, OS waits 110301
RW-excl spins 197945, rounds 3737144, OS waits 35005
Spin rounds per wait: 4.58 mutex, 10.88 RW-shared, 18.88 RW-excl
------------------------
LATEST DETECTED DEADLOCK
------------------------
2015-12-17 05:46:47 7f61f0594700
*** (1) TRANSACTION:
TRANSACTION 17641507, ACTIVE 0 sec inserting
mysql tables in use 1, locked 1
LOCK WAIT 8 lock struct(s), heap size 1184, 7 row lock(s), undo log entries 9
MySQL thread id 5021, OS thread handle 0x7f61f071a700, query id 33269201 localhost 127.0.0.1 sonar update
INSERT INTO group_roles (group_id, resource_id, role)
VALUES (null, 1515106, 'codeviewer')
*** (1) WAITING FOR THIS LOCK TO BE GRANTED:
RECORD LOCKS space id 310 page no 6 n bits 472 index `group_roles_resource` of table `sonar`.`group_roles` trx id 17641507 lock_mode X insert intention waiting
Record lock, heap no 1 PHYSICAL RECORD: n_fields 1; compact format; info bits 0
0: len 8; hex 73757072656d756d; asc supremum;;
*** (2) TRANSACTION:
TRANSACTION 17641509, ACTIVE 0 sec inserting
mysql tables in use 1, locked 1
7 lock struct(s), heap size 1184, 4 row lock(s), undo log entries 3
MySQL thread id 5005, OS thread handle 0x7f61f0594700, query id 33269204 localhost 127.0.0.1 sonar update
INSERT INTO group_roles (group_id, resource_id, role)
VALUES (1, 1515107, 'admin')
*** (2) HOLDS THE LOCK(S):
RECORD LOCKS space id 310 page no 6 n bits 472 index `group_roles_resource` of table `sonar`.`group_roles` trx id 17641509 lock_mode X
Record lock, heap no 1 PHYSICAL RECORD: n_fields 1; compact format; info bits 0
0: len 8; hex 73757072656d756d; asc supremum;;
*** (2) WAITING FOR THIS LOCK TO BE GRANTED:
RECORD LOCKS space id 310 page no 6 n bits 472 index `group_roles_resource` of table `sonar`.`group_roles` trx id 17641509 lock_mode X insert intention waiting
Record lock, heap no 1 PHYSICAL RECORD: n_fields 1; compact format; info bits 0
0: len 8; hex 73757072656d756d; asc supremum;;
*** WE ROLL BACK TRANSACTION (2)
------------
TRANSACTIONS
------------
Trx id counter 18864174
Purge done for trx's n:o
<pre>
LIST OF TRANSACTIONS FOR EACH SESSION:
---TRANSACTION 0, not started
MySQL thread id 7482, OS thread handle 0x7f61f03cd700, query id 38116433 localhost sonar init
show engine innodb status
---TRANSACTION 18864038, not started
MySQL thread id 7478, OS thread handle 0x7f61f3349700, query id 38115903 localhost 127.0.0.1 sonar cleaning up
---TRANSACTION 18864173, not started
MySQL thread id 7475, OS thread handle 0x7f61f040e700, query id 38116432 localhost 127.0.0.1 sonar cleaning up
--------
FILE I/O
--------
I/O thread 0 state: waiting for completed aio requests (insert buffer thread)
I/O thread 1 state: waiting for completed aio requests (log thread)
I/O thread 2 state: waiting for completed aio requests (read thread)
I/O thread 3 state: waiting for completed aio requests (read thread)
I/O thread 4 state: waiting for completed aio requests (read thread)
I/O thread 5 state: waiting for completed aio requests (read thread)
I/O thread 6 state: waiting for completed aio requests (write thread)
I/O thread 7 state: waiting for completed aio requests (write thread)
I/O thread 8 state: waiting for completed aio requests (write thread)
I/O thread 9 state: waiting for completed aio requests (write thread)
Pending normal aio reads: 0 [0, 0, 0, 0] , aio writes: 0 [0, 0, 0, 0] ,
ibuf aio reads: 0, log i/o's: 0, sync i/o's: 0
Pending flushes (fsync) log: 0; buffer pool: 0
7146308 OS file reads, 6478063 OS file writes, 1783568 OS fsyncs
0.00 reads/s, 0 avg bytes/read, 0.00 writes/s, 0.00 fsyncs/s
-------------------------------------
INSERT BUFFER AND ADAPTIVE HASH INDEX
-------------------------------------
Ibuf: size 1, free list len 3077, seg size 3079, 22965 merges
merged operations:
insert 45672, delete mark 7198683, delete 214896
discarded operations:
insert 0, delete mark 0, delete 0
Hash table size 6374777, node heap has 11107 buffer(s)
0.00 hash searches/s, 0.00 non-hash searches/s
---
LOG
---
Log sequence number 219765124434
Log flushed up to 219765124434
Pages flushed up to 219765124434
Last checkpoint at 219765124434
0 pending log writes, 0 pending chkp writes
1189792 log i/o's done, 0.00 log i/o's/second
----------------------
BUFFER POOL AND MEMORY
----------------------
Total memory allocated 3296722944; in additional pool allocated 0
Dictionary memory allocated 359878
Buffer pool size 196600
Free buffers 8192
Database pages 177301
Old database pages 65285
Modified db pages 0
Pending reads 0
Pending writes: LRU 0, flush list 0, single page 0
Pages made young 1567756, not young 296705943
0.00 youngs/s, 0.00 non-youngs/s
Pages read 7146255, created 1592527, written 5004155
0.00 reads/s, 0.00 creates/s, 0.00 writes/s
Buffer pool hit rate 1000 / 1000, young-making rate 0 / 1000 not 0 / 1000
Pages read ahead 0.00/s, evicted without access 0.00/s, Random read ahead 0.00/s
LRU len: 177301, unzip_LRU len: 0
I/O sum[0]:cur[0], unzip sum[0]:cur[0]