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Need Help Improving Speed on Large MySQL Database

Posted on 2012-09-05
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Last Modified: 2012-09-15
Hello,

I have a large MySQL database (about 6GB).  I'm running on a cloud server that stores the MySQL data on a SAN.  I have a VB.NET Windows application that processes large files (50MB-100MB) into the DB (inserts and updates).  I am running at 80% of RAM (total RAM is 2GB), so I am not paging.

My performance is somewhat slow, and I was wondering whether I am using the best InnoDB parameters.  Here's what I'm using:

innodb_additional_mem_pool_size=6M
innodb_flush_log_at_trx_commit=0
innodb_log_buffer_size=3M
innodb_buffer_pool_size=900M
innodb_log_file_size=57M
innodb_thread_concurrency=12

Should any of these values be altered?

Thanks, Stu Engelman
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Question by:stuengelman
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LVL 81

Expert Comment

by:arnold
ID: 38371095
How much resources memory, does the cloud MySQL server have?
Is the server on which you are processing these data files also cloud based?
Does the MySQL cloud provide you with access the phpmyadmin? Phpmyadmin can help optimize MySQL.
Indecies, etc. might be impacting your performance rather than the settings you referenced.
The other isssue might be network related from the system on which the data is crunch to the cloud MySQL.

When performing updates are you using conditional or do you do select, update type of interactions?
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Author Comment

by:stuengelman
ID: 38371112
Hi Arnold,

I have 2GB of RAM on my cloud server.

The input data is on the server.

I do not have phpmyadmin.

I only created indicies for fields I use in WHERE and ORDER BY clauses.

There shouldn't be any data crunch issues, as the program, input data, and DB are all on the cloud.  I.e., nothing is being transmitted over the internet.

I'm doing SELECT, INSERT, and UPDATE statements.

Thanks, Stu
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by:arnold
ID: 38371212
Do you have an option to add phpmyadmin?
Your database is 6gb while your total available memory is 2GB.
Not clear whether the entire 6gb is contained within multiple tables or you have a single table of that size.

What is the issue that you are seeing? Do you have performance issues on reads? Etc.
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Author Comment

by:stuengelman
ID: 38371248
Hi Arnold,

I don't think there is an option to add phpmyadmin.

The DB will ultimately be much bigger than 6GB, so I can't keep increasing RAM so the entire DB can be contained in core.

The DB right now has a single table.

Not sure whether the speed issue is due to SELECTS, INSERTS, or UPDATES, or some combination of these.

Stu
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Expert Comment

by:arnold
ID: 38371809
Adjusting parameters you reference deals with resource management based on the number of incoming simultaneous connections.
When tunning it is often helpful to know what is being impacted.
http://www.mysqlperformanceblog.com/2007/11/01/innodb-performance-optimization-basics/
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Author Comment

by:stuengelman
ID: 38374227
Hi Arnold,

Testing out the recommendations in the link now.

Will report back shortly.

Thanks again,

Stu
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Author Comment

by:stuengelman
ID: 38374539
Hi Arnold,

Here are my new settings based on the advice in the link:

innodb_file_per_table
innodb_additional_mem_pool_size=6M
innodb_flush_log_at_trx_commit=2
innodb_log_buffer_size=4M
innodb_buffer_pool_size=1000M
innodb_log_file_size=500M
innodb_thread_concurrency=8

I'm still running very slowly, and I'm only using 80% of RAM as before, so I know I'm not paging.

Can you recommend any changes to the above configurations, or anything else I might do?

Thanks, Stu
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arnold earned 2000 total points
ID: 38374731
You are writing into the database, are you writing each row at a time or are you submitting the updates all at once?
80% memory at all times does not negate the possibility that your system is swapping.
You have a 6GB database table which can not be kept in memory of a 2GB system.
The app you are running and the database server share the same resources (memory) in particular.
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Author Comment

by:stuengelman
ID: 38374862
Hi Arnold,

The run has two parts.  The first part reads large CSV's (around 100MB each) via a streamreader object and processes each row into the DB one at a time via an INSERT or UPDATE command.  The second part reads the entire DB (a few selected fields) via a single SELECT statement, and performs cleanups to the selected fields (individual UPDATES for each row requiring one).  The second part ran somewhat faster than the first part when the DB was small, but that may not be the case any more (I don't know).  I'm wondering whether the second part might be speeded up by using less RAM (i.e., using OFFSET and LIMIT to process sequential SELECT statements that QUERY the table in chunks of 25,000 or 50,000 records at a time).

You are correct that the application, the MySQL runtime engine, and the SAN all share the same total available memory of 2GB (unless the SAN has dedicated RAM).  You are also correct that there is caching; it's odd that the 20% of free RAM is exactly what the utilized cache space is.  Maybe there is some background service running on the cloud to prevent RAM freespace from going under 20%.

When the application wasn't running, I tried running "SELECT COUNT(*) FROM tablename;" in MySQL Query Browser.  It just kept running for 15-20 minutes without returning an answer (after which I shut Query Browser down), leading me to believe I still have some major InnoDB configuration setting issue.

Stu
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Author Comment

by:stuengelman
ID: 38374937
Arnold,

I think I just noticed something very major.

Right now the system is processing a CSV in the "part 1" phase (using the terminology of my prior post).

The MySQL runtime engine is performing disk I/O on the table at a rate of 2.5MBPS, but the application is processing CSV reads at only 2.5KBPS.  In other words, for every byte I read in from the CSV, MySQL is performing 1000 times that much I/O on the MySQL data and index information.

Hopefully this information will be helpful at pointing you to a solution (possibly one or more InnoDB settings that need to be changed).

Stu
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Expert Comment

by:arnold
ID: 38375063
I do not think the issue is with the innodb variable settings. The issue is that it has to sweep in portions of the database for the scans.

select count(column_with_index) from table_name
Let it run at the conclusion it should tell you how long it took within the MySQL server.
Running "explain query" should tell the query plan.
How much memory is being used by the MySQL server process?

show session status where variable_name like "innodb%"
Run the same replacing session with global.
Phpmyadmin uses the status report to recommend settings changes to improve performance as well as point out items that might be the issue.
Phpmyadmin is a php based GUI interface into MySQL.
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Author Comment

by:stuengelman
ID: 38376679
Hi Arnold,

select count(column_with_index) from table_name took 754 seconds (column_with_index was the physical index) using MySQL Query Browser with the application not running.  The (extended) query plan was: "id","select_type","table","type","possible_keys","key","key_len","ref","rows","filtered","Extra"1,"SIMPLE","rawdata","index","","city","257","",11562740,100.00,"Using index"

select count(column_with_index) from table_name took 92 seconds (column_with_index was a logical index this time) using MySQL Query Browser with the application not running.  The (extended) query plan was: "id","select_type","table","type","possible_keys","key","key_len","ref","rows","filtered","Extra"1,"SIMPLE","rawdata","index","","city","257","",11562740,100.00,"Using index"

The MySQL server process is using 1.2GB of RAM.

It looks like session status requires command line input.  What EXE do I invoke to bring up the required command window?  Should I run session status with the application running or not running?

Do you think I need Phpmyadmin?  Can I buy this and install it on a Windows O/S?  Are there any alternatives if Phpmyadmin cannot run on Windows?

Thanks, Stu
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Expert Comment

by:arnold
ID: 38376890
Phpmyadmin is a web interface based on php. In iis you would need to add php support. Both php and phpmyadmin are open source
http://www.iis-aid.com/articles/how_to_guides/install_and_configure_phpmyadmin_iis

It is clear you are resource bound, additional memory will likely improve performance.

Use perfmon on the system to get paging data/memory use data.
The I/O you previously reported is fine, I.e. every query you run on the MySQL has to scan through the 6gb, while your read in a "line" at a time into the application.
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Author Comment

by:stuengelman
ID: 38377003
Hi Arnold,

It looks like PHP is already installed on the server, so I just have to install Phpmyadmin (it doesn't look like that is there).

Will look at getting extra memory.

Memory use as mentioned when running my application was 80% of total 2GB of RAM, plus 400MB in cache.

Stu
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Expert Comment

by:arnold
ID: 38377030
Sorry,

The application you are using should be able to get session status data provided you maintain a is Nile connection versus connect/disconnect.
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Author Comment

by:stuengelman
ID: 38377032
Hi Arnold,

Just to be sure on the Phpmyadmin, do you know what the name of its EXE is?

Thanks, Stu
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Expert Comment

by:arnold
ID: 38377043
Check properties of computer/advanced settings/performance/advanced
Processor prioritize tin for programs and system cache should also be prioritized for programs.applications.
What is the size of the paging file? Opening up tasks manager look at the performance ratio.
Increasing the size of the page file may help somewhat.
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Expert Comment

by:arnold
ID: 38377162
phpmyadmin is a PHP based web site, no executable.
You need to make sure you have php for windows installed.
http://php.iis.net/

A significant portion of your 2GB ram is used up by the windows operating system.

The organization of the data in a single table is likely a contributing issue as well.

Do you have this setup on your local workstation where you can test?
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Author Comment

by:stuengelman
ID: 38377300
Hi Arnold,

I set CPU priority to "Applications".

The paging space used is about 300MB when I am not running anything other than standard background services, and 400MB when I run my application.

My total page space is set to 2GB; what should I increase this to?

Thanks, Stu
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Author Comment

by:stuengelman
ID: 38377313
Arnold,

PHP for windows is already installed on the server.  The problem is that I don't know how to invoke phpmyadmin.

Stu
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Author Comment

by:stuengelman
ID: 38377317
Arnold,

In re "The application you are using should be able to get session status data provided you maintain a is Nile connection versus connect/disconnect." - I don't follow what you're saying.  Please explain in more simple terms.

Thanks, Stu
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Author Comment

by:stuengelman
ID: 38377322
Arnold,

In re "Do you have this setup on your local workstation where you can test?" - Yes, I have the system on my PC as well.

Stu
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Expert Comment

by:arnold
ID: 38378286
What is the performance on the local pc like? Look at the resources available on the pc versus on the cloud.
CPU/memory/paging file

Usually when you look at the paging file it tells you what you have it set to and what the system recommends.

Re application connect/disconnect.
When your application runs does it establish a connection to MySQL and keeps it while reading in the data stream then generating requests on the single connection (single session) or does your application establishes a connection when it is ready with a data insert/update?

Are you able to run the application on the local pc and insert the data into the cloud server as a way to compare whether both applications are dependent on the MySQL
Network related tasks.
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Expert Comment

by:arnold
ID: 38378292
Additionally, you can run phpmyadmin remotely I.e. MySQL server/login within the phpmyadmin configuration.
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Author Comment

by:stuengelman
ID: 38378416
Hi Arnold,

The performance on the PC was excellent, but that was because I was only using about 20 small test input input files.  There's no comparison to be made to the server because the server DB table/index space is now at 7GB (3GB for data, and 4GB for indicies).

As mentioned earlier, the application runs in two parts (processing input into the DB, and then "scrubbing" certain fields on the PC).  The first part uses a single connection.  The second part uses two connections, one to query the DB, and another to make UPDATES where necessary as the first cursor progresses.

Running the server application on my PC against the data on the cloud is certainly possible, but this adds overhead as all SQL commands would have to travel over the net.  I do have more RAM on my PC than the server, but this is not relevant as the application only takes up 10MB of memory (most of the RAM demand is coming from the MySQL daemon).  I could in theory run the MySQL daemon on my PC too, pointing to the server DB; this method would likely be extremely slow as all INSERT and UPDATE information would have to be pumped over the web (also, MySQL is not optimized to run fast on non-server O/S's; MS MSDE ("MS SQL Lite") is alot better for this, but MSDE couldn't handle the data/index load here).

What are the precise steps for invoking phpmyadmin remotely, and then exactly what should I do once I'm in?

Thanks, Stu
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Expert Comment

by:arnold
ID: 38378485
How many indecies do you have.
Show create table
To see the columns and their definitions along with index references.
When you insert, update the indecies have to be updated.
Once you add it as a subdirectory of a site http://servername/phpmyadmin
Once he web page loads, you would use the MySQL defined username, password.
Then you will see multiple selections one of which is performance or status.
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Author Comment

by:stuengelman
ID: 38378525
Hi Arnold,

I have one physical index, and six logical indices.

CREATE TABLE `rawdata` (
  `email` varchar(255) NOT NULL DEFAULT '',
  `first` varchar(255) NOT NULL DEFAULT '',
  `last` varchar(255) NOT NULL DEFAULT '',
  `street1` varchar(255) NOT NULL DEFAULT '',
  `street2` varchar(255) NOT NULL DEFAULT '',
  `street` varchar(255) DEFAULT NULL,
  `city` varchar(255) NOT NULL DEFAULT '',
  `state` varchar(255) NOT NULL DEFAULT '',
  `zip5` varchar(255) NOT NULL DEFAULT '',
  `zip4` varchar(255) NOT NULL DEFAULT '',
  `zip` varchar(255) DEFAULT NULL,
  `phone` varchar(255) NOT NULL DEFAULT '',
  `sex` varchar(255) NOT NULL DEFAULT '',
  `dob` varchar(255) DEFAULT NULL,
  `stamp` varchar(255) NOT NULL DEFAULT '',
  `category` varchar(255) NOT NULL DEFAULT '',
  `spamcode` varchar(255) NOT NULL DEFAULT '',
  `spamdate` varchar(255) NOT NULL DEFAULT '',
  PRIMARY KEY (`email`),
  KEY `city` (`city`),
  KEY `state` (`state`),
  KEY `zip` (`zip`),
  KEY `sex` (`sex`),
  KEY `dob` (`dob`),
  KEY `category` (`category`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;

"Once you add it as a subdirectory of a site http://servername/phpmyadmin" - Please explain exactly what steps I should take.  I'm not following this.

"Once the web page loads, you would use the MySQL defined username, password." - What do I do to get the web page to load.

"Then you will see multiple selections one of which is performance or status." - I assume the idea is to start the application, and then login to phpmyadmin and get the performance or status information to you.  Correct?

Thanks, Stu
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Expert Comment

by:arnold
ID: 38378549
On you workstation, you can setup IIS.
The default location for iis install is c:\inetpub\wwwroot
Which is accessible as http://localhost or http://127.0.0.1

You then follow the directions in php.iis.net to install php for windows and then configure the local iis to handle php pages. You then get phpmyadmin from phpmyadmin.net. Using 7zip (open source)if you do not already have an uncompressing tool (winzip, winrar,7zip, etc) into
c:\inetpub\wwwroot effectively being

c:\inetpub\wwwroot\phpmyadmin which will be accessible as http://127.0.0.1/phpmyadmin
Within phpmyadmin there is a configuration file where you would need to put in the serverIP

When you access the interface, you will be prompted with a login where you would need to use MySQL credentials to login.

You can test it first to access your local MySQL instance first. Once that works, you can alter the configuration to point to the cloud MySQL.
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Expert Comment

by:arnold
ID: 38378673
Another thought. Your database/table design could be improved through breaking out the cities, states, street, sex (should be a set of two options)
The varchar(255)  

Do you have the workbench from MySQL on your pc system?
You should consider breaking this up.
Using foreign keys to tie one to the other. Using triggers to maintain data consistency.
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Author Comment

by:stuengelman
ID: 38378676
Hi Arnold,

I think we're making this a little too complex.

Basically, I need to know first how to determine whether or not phpmyadmin is installed on my server.  PHP 5 itself is installed, but I need to know specifically whether phpmyadmin is installed and how to launch it.

I downloaded a phpmyadmin installer to my PC, which I can upload to the server and install there if phpmyadmin is not already there.  In that case, I would just need to know how to launch it.

Thanks, Stu
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Author Comment

by:stuengelman
ID: 38378679
Hi Arnold,

Right now I have too much code to alter the table design, as the code would have to be altered to accomodate the schema changes.

Stu
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Expert Comment

by:arnold
ID: 38378686
Using a web browser you would access the local URL Http://localserver/phpmyadmin
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Author Comment

by:stuengelman
ID: 38378696
"Using a web browser you would access the local URL Http://localserver/phpmyadmin " - I got "Internet Explorer cannot display the webpage"

I assume I should now upload the phpmyadmin installer and run it?
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Expert Comment

by:arnold
ID: 38378721
Before you upload see f you can set it up locally.
Add iis on your workstation
Install php.
Configure iis to serve up php pages
Confirm iis works http://localserver where you should see an iis welcome screen confirming it is installed and working.
Then use th phpmyadmin installer to install.
The see if he interface works http://localserver/phpmyadmin
You can then either install it in he cloud or reconfigure the local to talk to the cloud mysql
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Author Comment

by:stuengelman
ID: 38379058
Hi Arnold,

I unzipped the phpmyadmin package, and found it had no actual installer.  Some articles I read convinced me that quite alot of manual adjustments have to be made to configure it properly before using it.  It really looks like more trouble than it's worth.

I had an idea I wanted to share with you.  I was thinking of setting the isolation level to SERIALIZABLE to prevent data quality issues in another system that reads the DB table for extraction purposes.  I admit that this will slow things down more, but what if at the same time I used transactions (START TRANSACTION and COMMIT) in the DB Loader application (the one we've been discussing) so that each individual INSERT and UPDATE wasn't physically touching the DB table.  The basic idea is that I would have a counter in each of the two portions of the DB Loader discussed above so that say about 100MB of data would be queued until the table is impacted.  E.g., if each CSV input row had an average of 200 bytes, then COMMITS wouldn't occur until 500,000 underlying row commands (INSERTS and UPDATES) are ready to be processed.  Since I'm already running at 80% of RAM with the DB Loader, I might have to throttle back the RAM allocated to the MySQL daemon by the 100MB to prevent more paging, but this would only be a 10% reduction (I'm at 1GB now in my InnoDB setting for maximum MySQL engine RAM).

Any opinions?

Thanks, Stu
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Expert Comment

by:arnold
ID: 38379245
Using a transaction will not help since you would be doing select/inserts.in an unrelated data you would be making things worse.

The configuration of the phpmyadmin is minimal, it has a config file where you would specify the MySQL server ip, and use cookies.

The information and suggestions it provides is well worth it.
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Author Comment

by:stuengelman
ID: 38379812
OK,

The phpmyadmin package when unzipped appears to have no installer.  When I unzip it everything appears to be ordinary files and binaries.  What path would I put it in?  I still want to run it on the server (Win 2008 R2).

Thanks, Stu
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Expert Comment

by:arnold
ID: 38379822
You copy the php content to the c:\inetpub\wwwroot\ location.

This is a PHP based web site.

Do you have IIS installed and working (IIS also uses memory which is why due to the limited amount of memory available on the cloud server, I am trying to get you to run the phpmyadmin remotely)?
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Author Comment

by:stuengelman
ID: 38379843
What is "location"?  What value do I use for this?

I do have both IIS and PHP 5 installed on the server; that's why placing phpmyadmin would make things easier for me.

I assume after placing phpmyadmin on the server, I do an "Application Create" from the Properties dialog of the folder (i.e., convert the folder into an IIS domain).  Correct?

Thanks, Stu
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Author Comment

by:stuengelman
ID: 38379852
I think I'm following on location now - I simply call the folder phpmyadmin and then convert the folder into a web domain.
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Expert Comment

by:BigSchmuh
ID: 38383833
Did you try evaluating the time you/we are spending on this versus the price of enhancing your DBMS server to 8GB ($220) ram ?
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Expert Comment

by:arnold
ID: 38383973
The index is as large as or larger then the data.
The table designs reflects a large amount of data duplication. (city, state) sex instead of limiting to two or several options, allows for user errors, expanding the option from M, F to  male, female, man, woman, etc.varchar255.

This is more of a learning experience that will help the asker in the future with database design, performance troubleshooting and performance optimization.
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Author Comment

by:stuengelman
ID: 38384071
Hi Arnold,

After much work, I finally got phpmyadmin installed on the server.  Please provide instructions for what to do after I log in (e.g., should my application be running, what phpmyadmin utilities should I use and how do I navigate to them, what information from phpmyadmin do I need to pass to you for inspection, etc.).

Your point on the extra RAM is well taken.  The issue is my client will have to pay $30 month for each extra gig at his current host.  This is very pricey and he will not go up another $180 per month to get to 8GB unless and until the business is proven viable.

Thanks, Stu
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Expert Comment

by:arnold
ID: 38384977
Stu, once you login, there is a performance/status option.
This is the one you would use. The phpmyadmin uses mysql internal status collection data.
show global session status, etc.
modify the config.sample.inc.php and save it as config.inc.php
if you do not have a password on the root account, within the config.inc.php change the line dealing with no password to true from false which is the default.
$cfg['Servers'][$i]['AllowNoPassword'] = true

upon login using root/password or root/no_password.

Status selection is where the different parameters on the performance of your system but be seen.
All status variables Items in red provide an explanation and at time suggestions what changes should be considered to address what this item references. i.e. adjust tmp index table, etc.
where you will see Advisor where you can run an analyzer for additional suggestions.
If you have slow query response, there is a way to configure mysql to log slow queries so that you can review them and possibly fix it.
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Author Comment

by:stuengelman
ID: 38386204
Hi Arnold,

Thanks for the instructions.  Will try them today and report back.

Stu
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Author Comment

by:stuengelman
ID: 38391260
Hi Arnold,

I first created config.inc.php by copying from config.sample.inc.php.

Then on invoking http://localhost/phpmyadmin from MSIE, I get the error message:

"phpMyAdmin - Error. The mysqli extension is missing. Please check your PHP configuration. <a href="Documentation.html#faqmysql" target="documentation"><img src="themes/dot.gif" title="Documentation" alt="Documentation" class="icon ic_b_help" /></a>"

Please advise.

Thanks, Stu
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Expert Comment

by:arnold
ID: 38391324
There are two suggestions to deal with the issue
http://sourceforge.net/projects/phpmyadmin/forums/forum/72909/topic/5109957
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Author Comment

by:stuengelman
ID: 38400628
Hi Arnold,

So far no luck with phpMyAdmin.

I'm going to do a test with more RAM and adjusting my InnoDB buffer settings.

I'll let you know if it helps.

Stu
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Expert Comment

by:arnold
ID: 38400913
You should try setting up phpmyadmin locally.  Once it works, you can configure config.inc.php to include referencd to the cloud MySQL server which you could access using your local phpmyadmin setup and ....
The difficulty is that many tunning scripts/process are available for MySQL on Linux/unix and no so much that I've seen for windows.
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Author Comment

by:stuengelman
ID: 38400941
Hi Arnold,

The documentation for configuring phpmyadmin is very complex, and I'm honestly just getting lost in it.  I don't think spending more time on phpmyadmin will be productive for me.

I added an extra core and another 4GB of RAM.  I also upped my buffer pool and log file sizes for InnoDB significantly.  The system is running faster now, but I won't really know how much faster until the MySQL daemon gets up to the full 2GB I just increased it to.  When you start a run against MySQL, the runtime engine goes very slowly from its idle starting point of about 130MB of RAM to the max you set it at (2GB per my latest settings).

I'll let you know how it goes.

Thanks, Stu
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Author Comment

by:stuengelman
ID: 38402361
Hi Arnold,

The new hardware setup, along with associated changes to InnoDB settings, increased my speed 50%.  I think I can get at least another 50% by making some efficiency improvements to my .NET code.  I actually throttled back to one core and 4GB of RAM, as CPU utilization is low and RAM utilization is only 70% at 4GB of RAM.  No doubt the 70% RAM utilization will cause paging issues because the Windows garbage collector is slow and causes memory leaks, so I'll probably also try out a third party memory manager if I can find one compatible with the server O/S.

Thanks so much for all the hard work you put into this, and all your great ideas.

Stu
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Author Closing Comment

by:stuengelman
ID: 38402362
Fantastic expert.  He really knows his topic, and had alot of great advice.
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