High CPU Usage
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@Sebastian-Roth The more I look into this the more I’m going to blame mysql and the ISAM table format for the OP’s issue. ISAM uses table locking for updates to the data, where INNODB uses row level locking for updates. SO if you have 10 systems updating the fog
history
table that is in ISAM format, one system will have update access while 9 will be placed in a blocked status until the first system finishes its update action. When the first finishes, then the second in line will get its chance and so on. I think with FOG 1.6.x stream we should setup the innodb as the default table engine. Understand we NEED to do a lot more bench marking on this issue, but I think with the help of the OP and other large FOG deployments we can get a better understanding of what it will take to make FOG go faster… -
@george1421 Relevant github issue for further discussion and thoughts on MyISAM -> InnoDB specifically: https://github.com/FOGProject/fogproject/issues/370
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@Sebastian-Roth
Thanks for your reply, I have changed the client checkin time from 60 to 600 (10mins) and has made a huge difference (picture below)Client Maxsize: 204800000
Grace Timeout: 60
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@Arrowtron I have some ideas of what we can do here if you are willing to help the FOG Project team.
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@george1421 said in High CPU Usage:
@Arrowtron I have some ideas of what we can do here if you are willing to help the FOG Project team.
Yes can do, let me know what information you need
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@Arrowtron Well, what I would like to do is make it worse to make it better. The meaning is to reset as much of the fixes you’ve done to this point to put it back to what way FOG was installed. This includes any adjustments suggested by the mysql tuner script. We need to have it as close to as installed as possible. Also reset the fog client check in time.
Run it in the as installed configuration for a few hours during your peak business time. Use top and sort by processor usage. Grab a screen shot of the top screen.
Shutdown apache
Lets make sure we have a good backup of the mysql server before doing anything. From the fog server linux command prompt key in
mysqldump -u root -p --all-databases > all-databases-backup.sql
login to the mysql command line tool with
mysql -u root -p fog
You will need to use the password you created for the root database user when you installed fog. If you don’t know the password that could be a problem. The older version of FOG had a black password for the mysql root user. Understand I’m usingmysql
to mean both mysql and mariadb. The command line tool is the same.At db prompt paste in this command.
SELECT TABLE_NAME,ENGINE FROM information_schema.TABLES WHERE TABLE_SCHEMA = 'fog' and ENGINE = 'MyISAM';
You should see an output that looks like this
+------------------------+--------+ | TABLE_NAME | ENGINE | +------------------------+--------+ | LDAPServers | MyISAM | | clientUpdates | MyISAM | | dirCleaner | MyISAM | | globalSettings | MyISAM | | greenFog | MyISAM | | groupMembers | MyISAM | | groups | MyISAM | | history | MyISAM | | hookEvents | MyISAM | | hostAutoLogOut | MyISAM | | hostMAC | MyISAM | | hostScreenSettings | MyISAM | | hosts | MyISAM | | imageGroupAssoc | MyISAM | | imagePartitionTypes | MyISAM | | imageTypes | MyISAM | | images | MyISAM | | imagingLog | MyISAM | | inventory | MyISAM | | ipxeTable | MyISAM | | keySequence | MyISAM | | location | MyISAM | | locationAssoc | MyISAM | | moduleStatusByHost | MyISAM | | modules | MyISAM | | multicastSessions | MyISAM | | multicastSessionsAssoc | MyISAM | | nfsFailures | MyISAM | | nfsGroupMembers | MyISAM | | nfsGroups | MyISAM | | notifyEvents | MyISAM | | os | MyISAM | | oui | MyISAM | | plugins | MyISAM | | powerManagement | MyISAM | | printerAssoc | MyISAM | | printers | MyISAM | | pxeMenu | MyISAM | | scheduledTasks | MyISAM | | schemaVersion | MyISAM | | snapinAssoc | MyISAM | | snapinGroupAssoc | MyISAM | | snapinJobs | MyISAM | | snapinTasks | MyISAM | | snapins | MyISAM | | supportedOS | MyISAM | | taskLog | MyISAM | | taskStates | MyISAM | | taskTypes | MyISAM | | tasks | MyISAM | | userCleanup | MyISAM | | userTracking | MyISAM | | users | MyISAM | | virus | MyISAM | | wolbroadcast | MyISAM | +------------------------+--------+ 55 rows in set (0.00 sec)
If your tables show innodb then we have to stop because your database is not in the default state.
If your database files say MyISAM then proceed and paste in these lines. You can do them in one block paste in. Just make sure the last line is entered too.
ALTER TABLE LDAPServers ENGINE=InnoDB; ALTER TABLE clientUpdates ENGINE=InnoDB; ALTER TABLE dirCleaner ENGINE=InnoDB; ALTER TABLE globalSettings ENGINE=InnoDB; ALTER TABLE greenFog ENGINE=InnoDB; ALTER TABLE groupMembers ENGINE=InnoDB; ALTER TABLE groups ENGINE=InnoDB; ALTER TABLE history ENGINE=InnoDB; ALTER TABLE hookEvents ENGINE=InnoDB; ALTER TABLE hostAutoLogOut ENGINE=InnoDB; ALTER TABLE hostMAC ENGINE=InnoDB; ALTER TABLE hostScreenSettings ENGINE=InnoDB; ALTER TABLE hosts ENGINE=InnoDB; ALTER TABLE imageGroupAssoc ENGINE=InnoDB; ALTER TABLE imagePartitionTypes ENGINE=InnoDB; ALTER TABLE imageTypes ENGINE=InnoDB; ALTER TABLE images ENGINE=InnoDB; ALTER TABLE imagingLog ENGINE=InnoDB; ALTER TABLE inventory ENGINE=InnoDB; ALTER TABLE ipxeTable ENGINE=InnoDB; ALTER TABLE keySequence ENGINE=InnoDB; ALTER TABLE location ENGINE=InnoDB; ALTER TABLE locationAssoc ENGINE=InnoDB; ALTER TABLE moduleStatusByHost ENGINE=InnoDB; ALTER TABLE modules ENGINE=InnoDB; ALTER TABLE multicastSessions ENGINE=InnoDB; ALTER TABLE multicastSessionsAssoc ENGINE=InnoDB; ALTER TABLE nfsFailures ENGINE=InnoDB; ALTER TABLE nfsGroupMembers ENGINE=InnoDB; ALTER TABLE nfsGroups ENGINE=InnoDB; ALTER TABLE notifyEvents ENGINE=InnoDB; ALTER TABLE os ENGINE=InnoDB; ALTER TABLE oui ENGINE=InnoDB; ALTER TABLE plugins ENGINE=InnoDB; ALTER TABLE powerManagement ENGINE=InnoDB; ALTER TABLE printerAssoc ENGINE=InnoDB; ALTER TABLE printers ENGINE=InnoDB; ALTER TABLE pxeMenu ENGINE=InnoDB; ALTER TABLE scheduledTasks ENGINE=InnoDB; ALTER TABLE schemaVersion ENGINE=InnoDB; ALTER TABLE snapinAssoc ENGINE=InnoDB; ALTER TABLE snapinGroupAssoc ENGINE=InnoDB; ALTER TABLE snapinJobs ENGINE=InnoDB; ALTER TABLE snapinTasks ENGINE=InnoDB; ALTER TABLE snapins ENGINE=InnoDB; ALTER TABLE supportedOS ENGINE=InnoDB; ALTER TABLE taskLog ENGINE=InnoDB; ALTER TABLE taskStates ENGINE=InnoDB; ALTER TABLE taskTypes ENGINE=InnoDB; ALTER TABLE tasks ENGINE=InnoDB; ALTER TABLE userCleanup ENGINE=InnoDB; ALTER TABLE userTracking ENGINE=InnoDB; ALTER TABLE users ENGINE=InnoDB; ALTER TABLE virus ENGINE=InnoDB; ALTER TABLE wolbroadcast ENGINE=InnoDB;
Once that is done run the same query again to make sure all of the tables now say innodb
SELECT TABLE_NAME,ENGINE FROM information_schema.TABLES WHERE TABLE_SCHEMA = 'fog';
If they are all innodb then you can exit the mysql program if I missed one then run the
ALTER TABLE
command on those missing tables. Please not any table I missed.At this point reboot the FOG server.
When the fog server comes back up make sure the web ui works as expected. Let the FOG server run for a few hours then again capture a snapshot for the settings using
top
. Post the results here.This next test is to let the FOG server run for a week using the innodb format then rerun the mysql tuner script. DON’T apply the settings, but post the results here. Let us look at the recommendations before you apply them to the FOG server’s database.
In the end what we need to know is the change in performance by simply changing the database engine from isam to innodb format. Also to see the recommendations provided by mysqltuner. I have some default settings for the innodb that I would start out with, but they may not be right for all situation.
Let me say we do need help from FOG Admins who have either unique target hardware or large installations that can’t be simulated easily. With your help I feel strongly that we can improve FOG’s performance and move everyone’s FOG install in a positive direction.
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@Arrowtron How is this testing going? Do you see measured improvements in performance?
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@george1421 Sorry didn’t get to you sooner, few work things came up
I have changed the client polling back to 60 seconds and left for a day, screenshot taken at peak time with roughly ~600 PC’s online (with FOG service installed)
Made a VM snapshot at this point* - can revert back if needed
I ran into a few issues with the following tables, they wouldn’t change to InnoDB engine, seems like a corrupt row in that table
I have restarted the server and appears to be loading the web/dashboard - however very slow
I’ll keep this running and let you know if things improve, although those tables that haven’t been changed seem like important tables to change.
Let me know how I should proceed -
@george1421 I haven’t heard back from you, here are the results after 7 days
There are roughly 597 PC’s online with FOG service Installed
As stated from previous reply, there were a few tables that didn’t change to MyISAM
The client polling is 60 seconds>> MySQLTuner 1.7.19 - Major Hayden <major@mhtx.net> >> Bug reports, feature requests, and downloads at http://mysqltuner.com/ >> Run with '--help' for additional options and output filtering [--] Skipped version check for MySQLTuner script [OK] Logged in using credentials from Debian maintenance account. [OK] Currently running supported MySQL version 5.7.28-0ubuntu0.19.04.2 [OK] Operating on 64-bit architecture -------- Log file Recommendations ---------------------------------------------- -------------------- [OK] Log file /var/log/mysql/error.log exists [--] Log file: /var/log/mysql/error.log(0B) [OK] Log file /var/log/mysql/error.log is readable. [!!] Log file /var/log/mysql/error.log is empty [OK] Log file /var/log/mysql/error.log is smaller than 32 Mb [OK] /var/log/mysql/error.log doesn't contain any warning. [OK] /var/log/mysql/error.log doesn't contain any error. [--] 0 start(s) detected in /var/log/mysql/error.log [--] 0 shutdown(s) detected in /var/log/mysql/error.log -------- Storage Engine Statistics --------------------------------------------- -------------------- [--] Status: +ARCHIVE +BLACKHOLE +CSV -FEDERATED +InnoDB +MEMORY +MRG_MYISAM +My ISAM +PERFORMANCE_SCHEMA [--] Data in InnoDB tables: 14.7M (Tables: 50) [--] Data in MyISAM tables: 1002.6K (Tables: 5) [OK] Total fragmented tables: 0 -------- Analysis Performance Metrics ------------------------------------------ -------------------- [--] innodb_stats_on_metadata: OFF [OK] No stat updates during querying INFORMATION_SCHEMA. -------- CVE Security Recommendations ------------------------------------------ -------------------- [--] Skipped due to --cvefile option undefined -------- Performance Metrics --------------------------------------------------- -------------------- [--] Up for: 7d 20h 30m 0s (494M q [728.806 qps], 11M conn, TX: 439G, RX: 106G) [--] Reads / Writes: 98% / 2% [--] Binary logging is disabled [--] Physical Memory : 3.8G [--] Max MySQL memory : 2.7G [--] Other process memory: 0B [--] Total buffers: 192.0M global + 17.1M per thread (151 max threads) [--] P_S Max memory usage: 72B [--] Galera GCache Max memory usage: 0B [OK] Maximum reached memory usage: 1.1G (29.54% of installed RAM) [OK] Maximum possible memory usage: 2.7G (70.22% of installed RAM) [OK] Overall possible memory usage with other process is compatible with memory available [OK] Slow queries: 0% (0/494M) [OK] Highest usage of available connections: 37% (57/151) [OK] Aborted connections: 0.00% (8/11267058) [!!] name resolution is active : a reverse name resolution is made for each new connection and can reduce performance [!!] Query cache may be disabled by default due to mutex contention. [!!] Query cache efficiency: 0.0% (0 cached / 454M selects) [OK] Query cache prunes per day: 0 [OK] Sorts requiring temporary tables: 0% (9 temp sorts / 139M sorts) [OK] No joins without indexes [!!] Temporary tables created on disk: 97% (11M on disk / 11M total) [OK] Thread cache hit rate: 98% (209K created / 11M connections) [OK] Table cache hit rate: 96% (977 open / 1K opened) [OK] table_definition_cache(1400) is upper than number of tables(334) [OK] Open file limit used: 2% (144/5K) [OK] Table locks acquired immediately: 99% (101M immediate / 101M locks) -------- Performance schema ---------------------------------------------------- -------------------- [--] Memory used by P_S: 72B [--] Sys schema is installed. -------- ThreadPool Metrics ---------------------------------------------------- -------------------- [--] ThreadPool stat is disabled. -------- MyISAM Metrics -------------------------------------------------------- -------------------- [!!] Key buffer used: 18.7% (3M used / 16M cache) [OK] Key buffer size / total MyISAM indexes: 16.0M/238.0K [OK] Read Key buffer hit rate: 100.0% (235M cached / 76 reads) [!!] Write Key buffer hit rate: 83.1% (154 cached / 128 writes) -------- InnoDB Metrics -------------------------------------------------------- -------------------- [--] InnoDB is enabled. [--] InnoDB Thread Concurrency: 0 [OK] InnoDB File per table is activated [OK] InnoDB buffer pool / data size: 128.0M/14.7M [!!] Ratio InnoDB log file size / InnoDB Buffer pool size (75 %): 48.0M * 2/128. 0M should be equal to 25% [OK] InnoDB buffer pool instances: 1 [--] Number of InnoDB Buffer Pool Chunk : 1 for 1 Buffer Pool Instance(s) [OK] Innodb_buffer_pool_size aligned with Innodb_buffer_pool_chunk_size & Innodb _buffer_pool_instances [OK] InnoDB Read buffer efficiency: 100.00% (9450445390 hits/ 9450446365 total) [!!] InnoDB Write Log efficiency: 59.83% (3030357 hits/ 5065232 total) [OK] InnoDB log waits: 0.00% (0 waits / 2034875 writes) -------- AriaDB Metrics -------------------------------------------------------- -------------------- [--] AriaDB is disabled. -------- TokuDB Metrics -------------------------------------------------------- -------------------- [--] TokuDB is disabled. -------- XtraDB Metrics -------------------------------------------------------- -------------------- [--] XtraDB is disabled. -------- Galera Metrics -------------------------------------------------------- -------------------- [--] Galera is disabled. -------- Replication Metrics --------------------------------------------------- -------------------- [--] Galera Synchronous replication: NO [--] No replication slave(s) for this server. [--] Binlog format: ROW [--] XA support enabled: ON [--] Semi synchronous replication Master: Not Activated [--] Semi synchronous replication Slave: Not Activated [--] This is a standalone server -------- Recommendations ------------------------------------------------------- -------------------- General recommendations: Set up a Secure Password for root@localhost user: SET PASSWORD FOR 'root'@'S pecificDNSorIp' = PASSWORD('secure_password'); Restrict Host for 'fogstorage'@% to fogstorage@SpecificDNSorIp UPDATE mysql.user SET host ='SpecificDNSorIp' WHERE user='fogstorage' AND ho st ='%'; FLUSH PRIVILEGES; Configure your accounts with ip or subnets only, then update your configurat ion with skip-name-resolve=1 When making adjustments, make tmp_table_size/max_heap_table_size equal Reduce your SELECT DISTINCT queries which have no LIMIT clause Before changing innodb_log_file_size and/or innodb_log_files_in_group read t his: https://bit.ly/2TcGgtU Variables to adjust: query_cache_size (=0) query_cache_type (=0) query_cache_limit (> 1M, or use smaller result sets) tmp_table_size (> 16M) max_heap_table_size (> 16M) innodb_log_file_size should be (=16M) if possible, so InnoDB total log files size equals to 25% of buffer pool size.
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@Arrowtron I’m sorry this dropped off my radar. We need to get the errors converting the tables fixed.
Will you log into the sql server console with
mysql -u root
or if mysql root user has a password withmysql -u root -p
At the mysql server command prompt key in
SELECT @@GLOBAL.sql_mode global, @@SESSION.sql_mode session
and post the output.Also look in the /etc/my.cnf file for sql server and look for a line with a keyword of
sql_mode =
post the results of that option.If its not in that file you can find all of the config files with this command
/usr/sbin/mysqld --verbose --help | grep -A 1 "Default options"
ref: https://thehikashop.com/blog/8-fix-incorrect-date-value-0000-00-00-in-mysql
ref: https://www.sitepoint.com/quick-tip-how-to-permanently-change-sql-mode-in-mysql/ -
mysql> SELECT @@GLOBAL.sql_mode global, @@SESSION.sql_mode session; +-------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+ | global | session | +-------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+ | ONLY_FULL_GROUP_BY,STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION | ONLY_FULL_GROUP_BY,STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION | +-------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+ 1 row in set (0.01 sec)
/etc/my.cnf doesn’t exist
/usr/sbin/mysqld --verbose --help | grep -A 1 “Default options”
Default options are read from the following files in the given order: /etc/my.cnf /etc/mysql/my.cnf ~/.my.cnf
nano /etc/mysql/my.cnf
!includedir /etc/mysql/conf.d/ !includedir /etc/mysql/mysql.conf.d/
~/.my.cnf doesn’t exist
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@Arrowtron said in High CPU Usage:
/etc/mysql/conf.d/
will you confirm there are no files in this location?
This is the problem why those date codes are being rejected.
ONLY_FULL_GROUP_BY,STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION
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@george1421 said in High CPU Usage:
/etc/mysql/conf.d/
2 files in that location
mysqldump.cnf
[mysqldump] quick quote-names max_allowed_packet = 16M
mysql.cnf
[mysql]
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@george1421 said in High CPU Usage:
STRICT_TRANS_TABLES
Interesting find. Hmmm, just did a quick test. This is not the case on Debian 9 (MariaDB 10.1.44). But Ubuntu (20.04 - pre release testing) with MySQL 8.0.19 does have the same
sql_mode
that as we see from the OP’s Ubuntu 18.04 install. I will see if I can figure out why they have it in Ubuntu. -
@Sebastian-Roth said in High CPU Usage:
I will see if I can figure out why they have it in Ubuntu.
It looks like its the defaults compiled into the sql server because the OP doesn’t have that value specifically set. So now we need to come up with the correct line to exclude that value from the sql server options. Once we get that turned off we can then convert the rest of the tables to innodb format. I do think it is a great find too because that value would have stopped the creation of the fog tables if we defaulted to the innodb engine.
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@george1421 said in High CPU Usage:
So now we need to come up with the correct line to exclude that value from the sql server options.
Definitely worth a try though I am not sure how we will handle this “for the mass”. Sure we can mess with DB settings but I am afraid of doing this and causing a lot more issues than we had before. But we’ll see. Probably we’ll find a god solution to that somehow.
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@Sebastian-Roth I had some more time to look into this and I admit, “I couldn’t see the forest because of the trees”.
This is what the OP posted as the global configuration.
mysql> SELECT @@GLOBAL.sql_mode global, @@SESSION.sql_mode session; +-------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+ | global | session | +-------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+ | ONLY_FULL_GROUP_BY,STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION | ONLY_FULL_GROUP_BY,STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION | +-------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+ 1 row in set (0.01 sec)
This is the error he received when he tried to alter the table.
mysql> ALTER TABLE hosts ENGINE=InnoDB; ERROR 1067 (42000): Invalid default value for 'hostSecTime'
If we describe table hosts this is what we see.
MariaDB [fog]> describe hosts; +------------------+---------------+------+-----+---------------------+----------------+ | Field | Type | Null | Key | Default | Extra | +------------------+---------------+------+-----+---------------------+----------------+ | hostID | int(11) | NO | PRI | NULL | auto_increment | | hostName | varchar(16) | NO | UNI | NULL | | | hostDesc | longtext | NO | | NULL | | | hostIP | varchar(25) | NO | MUL | NULL | | | hostImage | int(11) | NO | | NULL | | | hostBuilding | int(11) | NO | | NULL | | | hostCreateDate | timestamp | NO | | CURRENT_TIMESTAMP | | | hostLastDeploy | datetime | NO | | NULL | | | hostCreateBy | varchar(50) | NO | | NULL | | | hostUseAD | char(1) | NO | MUL | NULL | | | hostADDomain | varchar(250) | NO | | NULL | | | hostADOU | longtext | NO | | NULL | | | hostADUser | varchar(250) | NO | | NULL | | | hostADPass | varchar(250) | NO | | NULL | | | hostADPassLegacy | longtext | NO | | NULL | | | hostProductKey | longtext | YES | | NULL | | | hostPrinterLevel | varchar(2) | NO | | NULL | | | hostKernelArgs | varchar(250) | NO | | NULL | | | hostKernel | varchar(250) | NO | | NULL | | | hostDevice | varchar(250) | NO | | NULL | | | hostInit | longtext | YES | | NULL | | | hostPending | enum('0','1') | NO | | NULL | | | hostPubKey | longtext | NO | | NULL | | | hostSecToken | longtext | NO | | NULL | | | hostSecTime | timestamp | NO | | 0000-00-00 00:00:00 | | | hostPingCode | varchar(20) | YES | | NULL | | | hostExitBios | longtext | YES | | NULL | | | hostExitEfi | longtext | YES | | NULL | | | hostEnforce | enum('0','1') | NO | | 1 | | +------------------+---------------+------+-----+---------------------+----------------+ 29 rows in set (0.02 sec)
So the issue is (maybe) not the STRICT_TRANS_TABLES like I originally thought, but the two values just after those of NO_ZERO_IN_DATE,NO_ZERO_DATE
With that in mind we might consider changing the default values for the tables from
0000-00-00 00:00:00
to something more memorable such as1980-01-01 00:00:00
I don’t know the impact on FOG’s internal program if it uses
0000-00-00 00:00:00
as anything significant or its just a value other than NULL. This seems to be an issue with mysql it doesn’t look like mariadb has these value but does introduce strict_trans_table in 10.2.4 and later. ref: https://mariadb.com/kb/en/sql-mode/ -
@george1421 Hi George, let me know if you need me to do anything further
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@Arrowtron ok i will follow up in about 30 minutes with a test we can try.