Remove a Submodule within git

For many git-based projects, submodules are useful in avoiding duplicate work and easing utility library updates.  There are times, however, when a submodule needs to be removed from a project.  Submodules aren’t removed with git rm submoduledir, they must be removed in a more tedious, manual fashion.  There are many unclear explanations of how to remove a submodule but I found one on Stack Overflow that’s concise, so I thought I’d share it.  The steps are as follows: Continue reading

Back-up and restore the database between two AWS EC2 instances

Hi all,

I must say there are couple of blogs and websites which have already done this, I mean to say the they must have explained the process of creating mysql dumps and restoring it back whenever there is a failure.

I had some other scenario where we manage multiple EC2 instances. Say the best practice is to manage a separate instance for production and another instance for testing or development or for internal usage for a organization. Continue reading

EC2 Instances: EBS-Backed Versus Instance Store

EC2 Instances: EBS-Backed Versus Instance Store

(or “What the heck is ephemeral storage?”)

The EC2 “Hardware”

When an EC2 instance is launched, a virtual machine is reserved for the instance to run. That virtual machine has particular specifications depending on the instance type: 32-bit or 64-bit CPU, number of virtual cores, size of hard drive, etc. Details about the instance specs is available at

When your EC2 instance is in a “running” state, that means that it’s running on the virtual machine, and this is what you get charged for. Continue reading

What is the difference between terminating and stopping an EC2 instance?

Background Information

Amazon supports the ability to terminate or stop a running instance. The ability to stop a running instance is only supported by instances that were launched with an EBS-based AMI. There are distinct differences between stopping and terminating an instance. It’s important to properly understand the implications of each action.

Note:  You cannot start/stop a Spot Instance.  Click here to see more information on this topic from AWS. Continue reading

Even More EC2 Goodies in the AWS Management Console

We’ve added some new features to the EC2 tab of the AWS Management Console to make it even more powerful and even easier to use.

You can now change the instance type of a stopped, EBS-backed EC2 instance. This means that you can scale up or scale down as your needs change. The new instance type must be compatible with the AMI that you used to boot the instance, so you can’t change from 32 bit to 64 bit or vice versa.

The Launch Instances Wizard now flags AMIs that will not incur any additional charges when used with an EC2 instance running within the AWS free usage tier: Continue reading

How to resize an Amazon EC2 AMI when boot disk is on EBS


Screwing around with the boot volume is part of our regular “explore around the edges” work before we get serious with how we are going to configure and orchestrate the new systems. The boot volume in this scenario does not have PV driver support and thus will perform slower than the actual ephemeral storage. Our need was for the boot volume to be big enough to hammer with bonnie++ – this is not something we’d do in a production scenario.


All of the cloud nerds at BioTeam are thrilled now that the Amazon Compute Cluster nodes have been publicly launched. If you missed the exciting news please visit the announcement post over at the AWS blog –

We’ve been madly banging on the new instance types and trying to (initially) perform some basic low level benchmarks before we go on to the cooler benchmarks where we run actual life science & informatics pipelines against the hot new gear. Using our Chef Server it’s trivial for us to orchestrate these new systems into working HPC clusters in just a matter of minutes. We plan to start blogging and demoing live deployment of elastic genome assembly pipelines and NextGen DNA sequencing instrument pipelines (like the Illumina software) on AWS soon. Continue reading

Add storage space to Amazon EC2 instance

Running out of storage space happens while working with Amazon EC2. There is two solutions allowing you not to recreate a new instance with more storage space. The first is to resize the EBS volume accordingly, and the second is to add a new EBS volume mounted on the instance. We’ll have a look on the latter in the case of an instance running Debian 6.0. Continue reading

How do I change the SSH Key on a running EC2 instance?

Background Information

Is it possible to change the SSH Key on a running EC2 instance? If so, how?



If you need to switch to a new SSH Key, RightScale recommends that you terminate the instance, change the associated SSH Key and launch the instance again.  Before terminating the instance or taking any corrective action, make sure you’ve saved any critical data that needs to be preserved.  So, if the instance has any attached EBS volumes, be sure to take snapshots of the volumes so that you can use them to restore your volume data on future instances.  However, any data saved on the instance’s local ephemeral drive will be lost once the instance is terminated. Continue reading

Change key pairs on AWS ec2 instance

For various security reasons it can be a good idea to change ssh keys. Amazon doesn’t actually let you change keys for a live instance. If you can easily restart your instance, that’s the best way to change the key pair. However, sometimes restarting an instance can be a much larger hassle than manually changing the keys. We recently ran into this very situation, so here’s a workaround: Continue reading