considering what types of cloud computing resources are appropriate
for you
interested in modifying the AMI used in this workshop,
want to create your own AMI from scratch, or
want to use these lessons on a different cloud resources,
read the information and instructions below.
Choosing a cloud platform
The most important thing about The Cloud is choice - instead
of purchasing a physical computer, you can obtain on-demand computing at
almost any scale. This power comes with advantages and
disadvantages:
Advantages of Cloud Computing
Access large amounts of computing power on demand
Full administrative rights - install anything
Use pre-configured images (software already installed)
Disadvantages of Cloud Computing
Cloud computing costs money (you must keep track of your costs)
If you need help, you may not have a local system administrator
Images may be poorly documented (you may not be clear on what is
installed, or how to use it)
Cloud platform choices
There are several cloud providers to choose from. Some scientific
clouds may either be free or allocate resources competitively.
Commercial clouds are can be very powerful, but choice can be
overwhelming. We will cover as much as we you need to get through the
Data Carpentry lessons, but you will ultimately need to learn things not
covered here so see the documentation below:
You can launch any publicly available image by changing the AMI that
you load in step 4 on that page.
You can choose not to load an AMI at all, and install your own
software later by skipping step 4 on that page.
If you want to launch a different set of resources- more processors,
more disk space, different operating system, etc; you can choose a
different option at step 5.
For more detailed instructions, and how-tos for other changes
consult EC2
Getting Started.
Launching an instance on Atmosphere - These instructions are in beta
and not fully tested!
Prerequisites
You must have an iPlant account (register at https://user.cyverse.org/ ) - You
must also request access to Atmosphere (see documentationCyVerse requires Atmosphere users to have a valid .edu or .org
email address )
Search for the ‘TSW Workshop Williams 1.2’ image; Select this
image.
Click Launch and then select the following options in the launch
wizard:
Instance Name:Enter a name(optional)
Base Image Version: 1.0
Project: Choose an existing or create a new project.
Provider: iPlant Cloud - Tucson
Instance Size: small2
Click Launch.
Tip: You can select a larger instance, but you must
have sufficient resources (no exceeded quotas). If Atmosphere is at high
capacity, you may not be able to launch an instance if the instance size
exceeds what is currently free on the cloud provider
Your instance should be ready in 10-15 minutes. When your instance
status is listed as ‘active’ you will be able to connect.
Click on ‘Projects’ and select the project that contains your
instance.
Verifying that your instance status is ‘active’,
copy the IP address (e.g. 128.123.12.34) to your clipboard.
Open the terminal application and use ‘ssh’ to connect. Your
command will be:
BASH
$ ssh iplantusername@your.atmosphere.ipaddress
Your computer will be unable to verify the authenticity of the
host… type yes to continue connecting
When prompted for a password, enter your iPlant
username.
You should now be connected to your personal instance. You can
confirm this with the following commands;
whoami,pwd, which should yield the following
results:
BASH
Welcome to Ubuntu 12.04.2 LTS (GNU/Linux 3.2.0-37-virtual x86_64)New release '14.04.2 LTS' available.Run'do-release-upgrade' to upgrade to it._ _ _/\ ||_ _ __ ___ ___ ___ _ __ ||__ ___ _ __ ___/ _ \| __|'_ ` _ \ / _ \/ __| '_\|'_ \ / _ \ '__/ _ \ / ___ \ |_||||||(_)\__\ |_)||||__/||__//_/\_\__|_||_||_|\___/|___/ .__/|_||_|\___|_|\___||_|iPlant CollaborativeThe user manual is located here: http://goo.gl/2pT72For assistance, contact support@iplantcollaborative.org. Last login: Fri Aug 14 10:16:50 2015 from dhcp140-78.cshl.eduiplantusername@vm65-164:~$ whoamiiplantusernameiplantusername@vm65-164:~$ pwd/home/iplantusername
Note: In the above example ‘iplantusername’ will be
your actual iPlant username.
Click on ‘Projects’ and select the project that contains your
instance.
Verifying that your instance status is ‘active’,
copy the IP address (e.g. 128.123.12.34) to your clipboard.
Start PuTTY. In the section ‘Specify the destination you want to
connect to’ for ‘Host Name (or IP address)’ paste in the DNS address and
click ‘Open’
When prompted to login as, enter your iPlant username; you may be
notified that the authenticity of the host cannot be verified - if so,
ignore the warning an continue connecting
When prompted for a password enter your iPlant password.
You should now be connected to your personal instance. You can
confirm this with the following commands;
whoami,pwd, which should yield the following
results:
BASH
Welcome to Ubuntu 12.04.2 LTS (GNU/Linux 3.2.0-37-virtual x86_64)New release '14.04.2 LTS' available.Run'do-release-upgrade' to upgrade to it._ _ _/\ ||_ _ __ ___ ___ ___ _ __ ||__ ___ _ __ ___/ _ \| __|'_ ` _ \ / _ \/ __| '_\|'_ \ / _ \ '__/ _ \ / ___ \ |_||||||(_)\__\ |_)||||__/||__//_/\_\__|_||_||_|\___/|___/ .__/|_||_|\___|_|\___||_|iPlant CollaborativeThe user manual is located here: http://goo.gl/2pT72For assistance, contact support@iplantcollaborative.org. Last login: Fri Aug 14 10:16:50 2015 from dhcp140-78.cshl.eduiplantusername@vm65-164:~$ whoamiiplantusernameiplantusername@vm65-164:~$ pwd/home/iplantusername
Note: In the above example ‘iplantusername’ will be
your actual CyVerse username.
Bringing sample data into your Atmosphere instance
The sample dataset is NOT included on the Atmosphere
instance. The very first time you load the instance, you will need to
copy data from the public CyVerse Data Store into your instance using
the following instructions.
Setup iCommands
Prerequisites
You must be connected to your Atmosphere instance
iCommands will allow you to quickly transfer data into your
Atmosphere instance:
Initialize iCommands using the following command
BASH
$ iinit
You will then be asked to setup your account and will need to enter
the following information
Prompt
Entry
irodsHost
data.iplantcollaborative.org
port
1247
zone
iplant
irodsUserName
your iplant username
Current iRODS password
your iplant password
Verify that you have connected to your iPlant Data Store; view the
contents of your home directory using the following the ils
command:
using ls you should be able to verify you have
downloaded the dc_sampledata_lite directories and files.
Tip: You can use iCommands to move data between your
computer, a cloud instance, and the CyVerse Data Store. iCommands is
installed on the Data Carpentry Amazon AMI. You can download and see
documentation for iCommands here
Terminating your Atmosphere instance
When you are finished with your instance, you must terminate. Follow
the following steps.