Category Archives: Databases Administration

Covering NoSQL, Relational Database, Data Visualization, and Reporting.

MySQL Error: 1062 ‘Duplicate entry’ Error

The all too common MySQL ‘Duplicate entry’ Error.

mysql> show slave status\G;
*************************** 1. row ***************************
               Slave_IO_State: Waiting for master to send event
                  Master_Host: master-mysql.local
                  Master_User: repl
                  Master_Port: 3306
                Connect_Retry: 60
              Master_Log_File: mysql-bin.004768
          Read_Master_Log_Pos: 1022786917
               Relay_Log_File: relay-bin.001728
                Relay_Log_Pos: 929659721
        Relay_Master_Log_File: mysql-bin.004768
             Slave_IO_Running: Yes
            Slave_SQL_Running: No
              Replicate_Do_DB: 
          Replicate_Ignore_DB: information_schema,mysql
           Replicate_Do_Table: 
       Replicate_Ignore_Table:
      Replicate_Wild_Do_Table: 
  Replicate_Wild_Ignore_Table: 
                   Last_Errno: 1062
                   Last_Error: Error 'Duplicate entry 'xyz' for key 'PRIMARY'' on query. Default database: 'db'. Query: 'INSERT INTO  data  (   id,   version ) VALUES  (279598012, 5)'
                 Skip_Counter: 0
          Exec_Master_Log_Pos: 929659575
              Relay_Log_Space: 1022787256
              Until_Condition: None
               Until_Log_File: 
                Until_Log_Pos: 0
           Master_SSL_Allowed: No
           Master_SSL_CA_File: 
           Master_SSL_CA_Path: 
              Master_SSL_Cert: 
            Master_SSL_Cipher: 
               Master_SSL_Key: 
        Seconds_Behind_Master: NULL
Master_SSL_Verify_Server_Cert: No
                Last_IO_Errno: 0
                Last_IO_Error: 
               Last_SQL_Errno: 1062
               Last_SQL_Error:Error 'Duplicate entry 'xyz' for key 'PRIMARY'' on query. Default database: 'db'. Query: 'INSERT INTO  data  (   id,   version ) VALUES  (279598012, 5)'
  Replicate_Ignore_Server_Ids: 
             Master_Server_Id: 10147115
1 row in set (0.00 sec)

The easy way to deal with this is to verify this it is a replication entry and running the following command.

mysql> SET GLOBAL SQL_SLAVE_SKIP_COUNTER=1; START SLAVE;

However, if you have what seems to be a large number of duplicate entry error and don’t feel like skipping the entries one by one or you just don’t want replication to stop for this error. You can add the following to the /etc/my.cnf

slave-skip-errors = 1062

And restart the MySQL services. This will skip all the Duplicate entry errors until it’s removed and the MySQL is restarted.

Keep in mind, that this error can indicate other issues with the MySQL service or system, before skipping the error completely.

Installing MariaDB 10.1 on CentOS 6.8

MariaDB is a fork of the MySQL; it is notable for being led by the original developers of MySQL and is community-developed. The original developers forked it due to concerns over its acquisition by Oracle.

MariaDB intends to be a “drop-in” replacement for MySQL, ensuring capability with library binary and matching with MySQL APIs and commands. Making it extremely easy for current MySQL User/Administrator to switch over with little to no difference in how they use it.

It includes the XtraDB storage engine an enhanced version of the InnoDB storage engine. XtraDB is designed to better scale on modern hardware and includes a variety of other features useful in high-performance environments. To top it off XtraDB is backwards compatible with the standard InnoDB, make it a good “drop-in” replacement.

Installational is pretty straight forward and very similar to installing MySQL. I prefer to install package with yum. So the first thing it to add the MariaDB yum repo.

Pick your favorite editor and added the following file.
/etc/yum.repos.d/MariaDB.repo

# MariaDB 10.1 CentOS repository list - created 2017-03-03 18:33 UTC
# http://downloads.mariadb.org/mariadb/repositories/
[mariadb]
name = MariaDB
baseurl = http://yum.mariadb.org/10.1/centos6-amd64
gpgkey=https://yum.mariadb.org/RPM-GPG-KEY-MariaDB
gpgcheck=1

Now run the following.

[rhosto@localhost ~]$ sudo yum clean all

[rhosto@localhost ~]$ sudo yum install MariaDB-server MariaDB-client

Now we can start the service.

[rhosto@localhost ~]$ sudo service mysql start

Next I strongly recommend running ‘/usr/bin/mysql_secure_installation’. Which will set the MariaDB root user password and give you the option of removing the test databases and anonymous user created by default.

[rhosto@localhost ~]$ sudo /usr/bin/mysql_secure_installation

NOTE: RUNNING ALL PARTS OF THIS SCRIPT IS RECOMMENDED FOR ALL MariaDB
SERVERS IN PRODUCTION USE! PLEASE READ EACH STEP CAREFULLY!

In order to log into MariaDB to secure it, we'll need the current
password for the root user. If you've just installed MariaDB, and
you haven't set the root password yet, the password will be blank,
so you should just press enter here.

Enter current password for root (enter for none): 
OK, successfully used password, moving on...

Setting the root password ensures that nobody can log into the MariaDB
root user without the proper authorisation.

Set root password? [Y/n] y
New password: 
Re-enter new password: 
Password updated successfully!
Reloading privilege tables..
... Success!


By default, a MariaDB installation has an anonymous user, allowing anyone
to log into MariaDB without having to have a user account created for
them. This is intended only for testing, and to make the installation
go a bit smoother. You should remove them before moving into a
production environment.

Remove anonymous users? [Y/n] Y
... Success!

Normally, root should only be allowed to connect from 'localhost'. This
ensures that someone cannot guess at the root password from the network.

Disallow root login remotely? [Y/n] Y
... Success!

By default, MariaDB comes with a database named 'test' that anyone can
access. This is also intended only for testing, and should be removed
before moving into a production environment.

Remove test database and access to it? [Y/n] Y
- Dropping test database...
... Success!
- Removing privileges on test database...
... Success!

Reloading the privilege tables will ensure that all changes made so far
will take effect immediately.

Reload privilege tables now? [Y/n] Y
... Success!

Cleaning up...

All done! If you've completed all of the above steps, your MariaDB
installation should now be secure.

Thanks for using MariaDB!

Now verify that it will startup on reboot.

[rhosto@localhost ~]$ sudo chkconfig --list mysql
mysql 0:off 1:off 2:on 3:on 4:on 5:on 6:off

And you are good to go.

[rhosto@localhost ~]$ mysql -u root -p
Enter password: 
Welcome to the MariaDB monitor. Commands end with ; or \g.
Your MariaDB connection id is 11
Server version: 10.1.21-MariaDB MariaDB Server

Copyright (c) 2000, 2016, Oracle, MariaDB Corporation Ab and others.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

MariaDB [(none)]>

Querying Apache Hadoop Resource Manager with Python.

Querying Apache Hadoop Resource Manager with Python.

I was recently asked to write a script that would monitor the running application on the Apache Hadoop Resource Manager.

I wonder over to the Apache Hadoop Cluster Application Statistics API. The API allows to query most of the information that you see in the WEB UI. Information such as status on the cluster, metrics on the cluster, scheduler information, information about nodes in the cluster, and information about applications on the cluster.

I first start by querying the cluster info.

import urllib2
import json

resource_manager = 'http://resourcemanager:8088'

info_url = resource_manager+"/ws/v1/cluster/info"

request = urllib2.Request(info_url)

'''
If you prefer to work with xml replace json below with xml
'''
request.add_header('Accept', 'application/json')

response = urllib2.urlopen(request)
data = json.loads(response.read())

print json.dumps(data, sort_keys=True, indent=4, separators=(',', ': '))

returns the following:

{
"clusterInfo": {
"haState": "ACTIVE",
"hadoopBuildVersion": "2.6.0-cdh5.7.0 from c00978c67b0d3fe9f3b896b5030741bd40bf541a by jenkins source checksum b2eabfa328e763c88cb14168f9b372",
"hadoopVersion": "2.6.0-cdh5.7.0",
"hadoopVersionBuiltOn": "2016-03-23T18:36Z",
"id": 1478120586043,
"resourceManagerBuildVersion": "2.6.0-cdh5.7.0 from c00978c67b0d3fe9f3b896b5030741bd40bf541a by jenkins source checksum deb0fdfede32bbbb9cfbda6aa7e380",
"resourceManagerVersion": "2.6.0-cdh5.7.0",
"resourceManagerVersionBuiltOn": "2016-03-23T18:43Z",
"rmStateStoreName": "org.apache.hadoop.yarn.server.resourcemanager.recovery.NullRMStateStore",
"startedOn": 1478120586043,
"state": "STARTED"
}
}

Now onto what I need to do, querying the Resource Manager about running applications. The Cluster Applications API allow you to collect information on resources, which represents an application. There are multiple parameters that can be specified to retrieve data. For a list of parameters go to Cluster_Applications_API

I however just need the information on running applications. Which looks something like.

import urllib2
import json

resource_manager = 'http://dvcdhnn02:8088'

info_url = resource_manager+"/ws/v1/cluster/apps?states=running"

request = urllib2.Request(info_url)

'''
If you prefer to work with xml replace json below with xml
'''
request.add_header('Accept', 'application/json')

response = urllib2.urlopen(request)
data = json.loads(response.read())

print json.dumps(data, sort_keys=True, indent=4, separators=(',', ': '))

which returns something like:

{
"apps": {
"app": [
{
"allocatedMB": 24576,
"allocatedVCores": 3,
"amContainerLogs": "http://resourcemanager:8042/node/containerlogs/container_1478120586043_15232_01_000001/hdfs",
"amHostHttpAddress": "resourcemanager:8042",
"applicationTags": "",
"applicationType": "MAPREDUCE",
"clusterId": 1478120586043,
"diagnostics": "",
"elapsedTime": 18009,
"finalStatus": "UNDEFINED",
"finishedTime": 0,
"id": "application_1478120586043_15232",
"logAggregationStatus": "NOT_START",
"memorySeconds": 431865,
"name": "SELECT 1 AS `number_of_records...TIMESTAMP))(Stage-1)",
"numAMContainerPreempted": 0,
"numNonAMContainerPreempted": 0,
"preemptedResourceMB": 0,
"preemptedResourceVCores": 0,
"progress": 54.07485,
"queue": "root.hdfs",
"runningContainers": 3,
"startedTime": 1479156085020,
"state": "RUNNING",
"trackingUI": "ApplicationMaster",
"trackingUrl": "http://resourcemanager:8088/proxy/application_1478120586043_15232/",
"user": "hdfs",
"vcoreSeconds": 51
}
]
}
}

straight forward and simple to use.

Resizing InnoDB Logs

If you have already created your database and you change the setting for “innodb_log_file_size=###M” and restart here you database and get an error that looks something like

InnoDB: Error: log file ./ib_logfile0 is of different size 0 5242880 bytes

Here what you need to do.
1.) Make sure your database shutdown clean.
2.) Move(not delete) any existing ib_logfile[#] to a safe place.
3.) edit the “innodb_log_file_size=###M” setting in your my.cnf.
4.) Restart your database and check your log file to make sure there were no errors.
5.) Check to make sure the new ib_logfile[#] are the right size.

MongoDB Script for counting records in collections in all the databases

Here is a quick script. I wrote for a co-worker.

var host = "localhost"
var port = 27000
var dbslist = db.adminCommand('listDatabases');

for( var d = 0; d < dbslist.databases.length; d++) {
     var db = connect(host+":"+port+"/"+dbslist.databases[d].name);
     var collections = db.getCollectionNames();
     for(var i = 0; i < collections.length; i++){
         var name = collections[i];
         if(name.substr(0, 6) != 'system') {
            print("\t"+dbslist.databases[d].name+"."+name + ' = ' + db[name].count() + ' records');
         }
     }
}