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Percona XtraDB Failure due to long Semaphore

abarotabarot ContributorCurrent User Role Novice
Hi,

3 of our 5 nodes in our Percona XtraDB cluster failed last night at the same time all reporting on a long semaphore waits. I have been asked to look at this as an emergency, could someone please help me assist troubleshoot this.

So far I have read that this is a bug due to the below setting being enabled.
innodb_adaptive_hash_index

Any help would be appreciated as this is out main production database system.

#################Node 3########################################
END OF INNODB MONITOR OUTPUT
============================
2019-04-05T11:13:52.608337Z 55825953 [Warning] WSREP: Percona-XtraDB-Cluster doesn't recommend use of DML command on a table (sportsGateway.DBControl) without an explicit primary key with pxc_strict_mode = PERMISSIVE
InnoDB: ###### Diagnostic info printed to the standard error stream
2019-04-05T11:14:07.082043Z 0 [ERROR] [FATAL] InnoDB: Semaphore wait has lasted > 600 seconds. We intentionally crash the server because it appears to be hung.
2019-04-05 04:14:07 0x7f1c4b8ea700 InnoDB: Assertion failure in thread 139759503451904 in file ut0ut.cc line 943
InnoDB: We intentionally generate a memory trap.
InnoDB: Submit a detailed bug report to http://bugs.mysql.com.
InnoDB: If you get repeated assertion failures or crashes, even
InnoDB: immediately after the mysqld startup, there may be
InnoDB: corruption in the InnoDB tablespace. Please refer to
InnoDB: http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
11:14:07 UTC - mysqld got signal 6 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.
Attempting to collect some information that could help diagnose the problem.
As this is a crash and something is definitely wrong, the information
collection process might fail.
Please help us make Percona XtraDB Cluster better by reporting any
bugs at https://jira.percona.com/projects/PXC/issues

################Node 4#############################################
END OF INNODB MONITOR OUTPUT
============================
InnoDB: ###### Diagnostic info printed to the standard error stream
2019-04-05T11:11:51.270754Z 0 [ERROR] [FATAL] InnoDB: Semaphore wait has lasted > 600 seconds. We intentionally crash the server because it appears to be hung.
2019-04-05 04:11:51 0x7f5047fff700 InnoDB: Assertion failure in thread 139982782068480 in file ut0ut.cc line 943
InnoDB: We intentionally generate a memory trap.
InnoDB: Submit a detailed bug report to http://bugs.mysql.com.
InnoDB: If you get repeated assertion failures or crashes, even
InnoDB: immediately after the mysqld startup, there may be
InnoDB: corruption in the InnoDB tablespace. Please refer to
InnoDB: http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.

############Node 1################################################
END OF INNODB MONITOR OUTPUT
============================
InnoDB: ###### Diagnostic info printed to the standard error stream
2019-04-05T11:13:27.690940Z 0 [ERROR] [FATAL] InnoDB: Semaphore wait has lasted > 600 seconds. We intentionally crash the server because it appears to be hung.
2019-04-05 04:13:27 0x7fd5aa2b8700 InnoDB: Assertion failure in thread 140555659740928 in file ut0ut.cc line 943
InnoDB: We intentionally generate a memory trap.
InnoDB: Submit a detailed bug report to http://bugs.mysql.com.
InnoDB: If you get repeated assertion failures or crashes, even
InnoDB: immediately after the mysqld startup, there may be
InnoDB: corruption in the InnoDB tablespace. Please refer to
InnoDB: http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
11:13:27 UTC - mysqld got signal 6 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.
Attempting to collect some information that could help diagnose the problem.
As this is a crash and something is definitely wrong, the information
collection process might fail.
Please help us make Percona XtraDB Cluster better by reporting any
bugs at https://jira.percona.com/projects/PXC/issues
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