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Glassfish Tuning and Thread Dumps

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Once you get into a production like stage with more data volume, more users, etc. you will find yourself pretty fast in the situation where Glassfish gets some hickups or slowness. An expected situation if you did not change the default parameters  out of the box which are chosen to make Glassfish to run even on a small box.

We ran into some kind of concurrency problems with JDBC pools and thread where Glassfish appeared to be hanging. One approach is to create thread dumps for the JVM.
With Glassfish we have a few options:

  1. jstack
    Run jps which returns you the list of applications running a JVM, choose the PID and execute
    jstack <PID>     or jstack -F <PID> > td.log
  2. asadmin
    Go the Glassfish_HOME/bin folder and execute
    ./asadmin --user admin generate-jvm-report --type=thread > threaddump.txt
  3. kill -3 <PID>
    Supposed to create a dump in the default log folder of Glassfish. Doesnt work for me.

With the (or better more than 1) file at hand you can evaluate them by hand or use some of the tools around. I am still struggling to make the tool analyzing my dumps. They simply open the files like a editor.

tda tool

tda tool

Some References

Enforce password for Ubuntu user on EC2 instances

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Using linux (Ubuntu) instances on Amazon EC2 is a quite safe thing to do, at least measured by the security provided by the platform (security groups, ACL, physical security,..). I recommend reading their security site here. At the end of the day the server is only as secure as you configure it, if you choose to open all ports running services with their default configurations and password settings, Amazon can’t help you.

When connecting to a Ubuntu server with ssh you need to provide the keyfile (somekeyfile.pem) that you can download when creating the key pair.

Key file

Key file

This 2048 bit key is required to login as regular ubuntu user. What I dislike is the fact that this user can sudo all, so once someone manage to get into you user account, he has root access too. I recommend to set a password for the ubuntu user and change the sudoers configuration.

Change the password for user ubuntu

Open the sudoers include file

sudo vi /etc/suderos.d/90-cloudimg-ubuntu or sudo vi /etc/sudoers

change last line from

ubuntu  ALL=(ALL) NOPASSWD:ALL

to

ubuntu ALL=(ALL) ALL

Monitoring Glassfish V3.1.2 Options

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There are 2 crucial phases you want to look under the hood of your running Glassfish or inside the JVM underneath: Performance Tuning and Health Monitoring during production.

With JMX (Java Management Extensions, Wikipedia) at hand, there are a few options to choose from.

JConsonsole

The graphical monitoring tool is great for local deployment, it allows you to connect to a JVM on the same host or a remote host. It creates line graphs for your for all relevant from the moment you connect, it is perfect to observe a server while you do some testing or other actions, though it does not record any values while you are not connected. I have a hard time to get it running on a remote server and I do not favour the ‘open’ approach (see previous blog entry) which allows anyone to access the JVM with the disabled authentication settings. I also had situations where the JVM was frozen and it was no longer possible to access the JVM for monitoring, here I would rather have snapshots before the problem started together with server.log.

JConsole

JConsole

Glassfish Rest Interface

Note: You need to enable the areas you want to monitor with the admin console (or the asadmin command line) because per default all are OFF. Continue reading →

Glassfish and https running secure applications

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By default Glassfish listens to http on port 8080 and https on port 8181.
It is better to listen to the default ports 80 for http and 443 for https, usually you dont want the user to enter port numbers as part of the URL.

Even the Glassfish Admin Console allows to change the ports (Configurations/Server Config/Network Config/Network Listener), certain server OS such as Ubuntu do not allow non-root users (you should run Glassfish as separate user !) to ports below 1024. We can achieve this by port rerouting with the iptables command (under Ubuntu)


iptables -A INPUT -p tcp --dport 80 -j ACCEPT
iptables -t nat -A PREROUTING -p tcp -m tcp --dport 80 -j REDIRECT --to-ports 8080
iptables -A INPUT -p tcp --dport 443 -j ACCEPT
iptables -t nat -A PREROUTING -p tcp -m tcp --dport 443 -j REDIRECT --to-ports 8181
iptables-save -c > /etc/iptables.rules
iptables-restore < /etc/iptables.rules

vi /etc/network/if-pre-up.d/iptablesload
#!/bin/sh
iptables-restore < /etc/iptables.rules
exit 0

Additionally you can get a proper SSL certificate to stop annoying the user with a no proper certificate warning. See previous tutorial here.

SSL Error

SSL Error (Chrome)

If you operate an enterprise application with a known URL to the users, unlike a regular website where the portal should be reached with regular http, I would completely disable regular http.

Disable http

Disable http

Glassfish V3.1.2 and SSL

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After almost 3 years (see previous post) I revisit the topic this time using the latest version og Glassfish 3.1.2 and GoDaddy as certificate provider. I created a certificate for a sub-domain (sub.whateverdomain.com) this time and make use of the extremly cheap 5.99 U$/year offer (no wildcard included)

Let me summarize the key steps here: Continue reading →

d3.js – Available Books

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D3 is my favourite visualization platform, though the learning curve is steeper because it is about selections, data mapping and transformation close to the DOM. D3 does not come with pre-defined visualizations like bar and piecharts. The website comes with lots of samples and tutorials are available as well. If you take the time to walk through them and experiment by yourself you will learn most. Still I enjoy reading books about technical topics with an end to end walk-through.

Currently there are 2 books about D3 both from O’Reilly and both have a similar introductory focus.

Getting Started with D3

d3a June 2012, 12.99 U$ (ebook)

The books does what its title promises, getting you started, It jumps right into D3 with sample applications and code. What I really like is the fact the author connects the visualizations to real life data (New York’s MTA transportation data) which makes the whole book more entertaining and tangible. It also provides a chapter about transition and interaction, even about layouts which make more exciting visualizations, like those we all know from the D3 websites sample page. Though it does not go into advanced details. At this reasonable price I would recommend the title.

Interactive Data Visualization for the Web

d3b

November 2012, 23.99 US (ebook)

This book is a bit more comprehensive than the first one, it starts with some more basic underlying technologies and provides the reader with an introduction to HTML, DOM, CSS and Javascripts. The chapters covering D3 are written lengthier providing slightly more details. It runs along the sample around a bar-charts and scatter-plots which turns dull after a while.  The early release I have seems to be incomplete, so I dont want to give a final verdict.

With D3 obviously getting more popular we will certainly see more books, hopefully covering advanced features and more visualization centric. I was asked if I like to write one but my D3 knowledge is way not comprehensive enough, I wish Mike Bostock would write one.

Post number 300 ! Thanks to the up to 1000 visitors a day.

Copy EC2 instance to another region

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Is it finally possible ? While the AMI import tool is long awaited for but only available for Windows, it is rather a big hazzle to transfer manually (see this) any other OS ( my last attempt in 2010).

Today Amazon announced the EBS Snapshot Copy Feature (across regions). The intention is certainly to allow easy migration of data to another region, as you can copy the snapshot, create a volume and attach it to an instance. I was curious to try if I can migrate my Ubuntu instance to another region and it worked. You can use both command-line as well the AWS web admin.

Running Ubuntu 12.04 Desktop on EC2

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To say it upfront: Usually there is no need to run an Ubuntu server with a desktop in the cloud. Whatever you do on the desktop you can do in a terminal too (assuming you dont want to use GIMP in the cloud). Here a little summary to get you started with a Precise Pangolin desktop running in the cloud.

Security: We will not use VNC, but NX. VNC is not secure (though can be tunnelled through SSH) and it works by sending compressed bitmaps of the screen, which is slower and less accurate than a NX server (X Server calls, Unix/Linux only)

Requirements: Amazon AWS account

Step-by-Step

  • Log into your AWS account
  • Optional: Create a security group with port 22 inbound only
    Security Group

    Security Group

    Port 22 only

    Port 22 only

    Continue reading →

Running EC2 spot instances

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or ‘ Save ultimately more money with AWS’

I use EC2 instances for test, development, demo and also for deployment to production. Amazon offers different types of instances, ranging from a micro instance (613 MB Ram and 2 CPU units) to a full fledge Cluster Compute Quadruple Extra Large Instance (60GB RAM and 33 CPU units). Of course a different price and paid per hour usage, available anytime.

All on demand Linux instances (Singapore):

  • Micro instance: U$ 0.02 per hour
  • Medium instance: U$ 0.34 per hour
  • High Mem/CPU instance: U$ 2.024 per hour

On top of this there are 3 different categories of instances (in contractual terms)

Some price comparison for a m1.Large instance we use for testing (7,5GB RAM and 4 CPU units)

  • On Demand (any time without any contractual obligations, we are using them currently)
    $0.340 per Hour > 1 month U$ 244.80 (fulltime 24h)
  • Reserved Instance (1 year term, one time payment U$ 276.00)
    U$ 0.196 per Hour > 1 month U$ 141.12 (3 months: U$ 699.36 vs on-demand U$ 734.40, 12 months: U$ 1969.44 vs. on-demand U$ 2937.60 = ~30% savings )
  • Spot Instance (depends on availability, you bid on a price range, if price exceeds your limit your instance shuts down)
    U$ 0.04 per Hour (as of December 5th 2012) > 1 month U$ 28.80

The spot instance, almost at 10% of the on-demand price, is extremely attractive and I am using it as test server.
Not suitable for production or demo purpose though.

The reserved instance starts to break even after 3 months full-time usage !

In order not to pay for instances running idle (at night, weekend) they auto-shutdown and the user can start them in a self provision fashion (for test, demo or training).

Interesting enough, the price fluctuation is very different in the AWS regions. Lets look at a m1.large instance type in the Ireleand  versus Singapore datacentre.

AWS Ireland

AWS Ireland

 

AWS Singapore

AWS Singapore

Obviously Singapore customers are not into this bidding concept, it remains permanently at 4cts while for Ireland the price jumps up to several Dollars !

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