2. Installation & Setup¶
This section describes the requirements and procedure to be followed to install the ExTASY package.
Pre-requisites.The following are the minimal requirements to install the ExTASY module.
- python >= 2.7
- virtualenv >= 1.11
- pip >= 1.5
- Password-less ssh login to Stampede and/or Archer machine (help )
The easiest way to install ExTASY is to create virtualenv. This way, ExTASY and its dependencies can easily be installed in user-space without clashing with potentially incompatible system-wide packages.
If the virtualenv command is not available, try the following set of commands,
wget --no-check-certificate https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.11.tar.gz tar xzf virtualenv-1.11.tar.gz python virtualenv-1.11/virtualenv.py --system-site-packages $HOME/ExTASY-tools/ source $HOME/ExTASY-tools/bin/activate
Step 1 : Create the virtualenv,
If your shell is BASH,
If your shell is CSH,
Setuptools might not get installed with virtualenv and hence using pip would fail. Please look at https://pypi.python.org/pypi/setuptools for installation instructions.
To install the Ensemble MD Toolkit Python modules in the virtual environment, run:
pip install radical.ensemblemd
You can check the version of Ensemble MD Toolkit with the ensemblemd-version command-line tool.
If your shell is CSH you would need to do,
This will reset the PATH variable to also point to the packages which were just installed.
Installation is complete !
2.2. Preparing the Environment¶
ExTASY is developed using Ensemble MD Toolkit which is a client-side library and relies on a set of external software packages. One of these packages is radical.pilot, an HPC cluster resource access and management library. It can access HPC clusters remotely via SSH and GSISSH, but it requires (a) a MongoDB server and (b) a properly set-up SSH environment.
For the purposes of the examples in this guide, we provide access to a mongodb url (mongodb://extasy:firstname.lastname@example.org/radicalpilot). This is for trying out these examples only and is periodically purged. We recommend setting up your own mongodb instances for production simulations/experiments.
2.2.1. MongoDB Server¶
The MongoDB server is used to store and retrieve operational data during the execution of an Ensemble MD Toolkit application. The MongoDB server must be reachable on port 27017 from both, the host that runs the Ensemble MD Toolkit application and the host that executes the MD tasks, i.e., the HPC cluster (see blue arrows in the figure above). In our experience, a small VM instance (e.g., Amazon AWS) works exceptionally well for this.
If you want to run your application on your laptop or private workstation, but run your MD tasks on a remote HPC cluster, installing MongoDB on your laptop or workstation won’t work. Your laptop or workstations usually does not have a public IP address and is hidden behind a masked and firewalled home or office network. This means that the components running on the HPC cluster will not be able to access the MongoDB server.
A MongoDB server can support more than one user. In an environment where multiple users use Ensemble MD Toolkit applications, a single MongoDB server for all users / hosts is usually sufficient.
22.214.171.124. Install your own MongoDB¶
Once you have identified a host that can serve as the new home for MongoDB, installation is straight forward. You can either install the MongoDB server package that is provided by most Linux distributions, or follow the installation instructions on the MongoDB website:
2.2.2. HPC Cluster Access¶
In order to execute MD tasks on a remote HPC cluster, you need to set-up password-less SSH login for that host. This can either be achieved via an ssh-agent that stores your SSH key’s password (e.g., default on OS X) or by setting up password-less SSH keys.
126.96.36.199. Password-less SSH with ssh-agent¶
An ssh-agent asks you for your key’s password the first time you use it and then stores it for you so that you don’t have to enter it again. On OS X (>= 10.5), an ssh-agent is running by default. On other Linux operating systems you might have to install or launch it manually.
You can test whether an ssh-agent is running by default on your system if you
log-in via SSH into the remote host twice. The first time, the ssh-agent
should ask you for a password, the second time, it shouldn’t. You can use the
ssh-add command to list all keys that are currently managed by your
%> ssh-add -l 4096 c3:d6:4b:fb:ce:45:b7:f0:2e:05:b1:81:87:24:7f:3f /Users/enmdtk/.ssh/rsa_work (RSA)
For more information on this topic, please refer to this article:
188.8.131.52. Password-less SSH keys¶
Using password-less SSH keys is really not encouraged. Some sites might even have a policy in place prohibiting the use of password-less SSH keys. Use ssh-agent if possible.
These instructions were taken from http://www.linuxproblem.org/art_9.html
Follow these instructions to create and set-up a public-private key pair that doesn’t have a password.
user_a on host
workstation, generate a pair of keys.
Do not enter a passphrase:
user_a@workstation:~> ssh-keygen -t rsa Generating public/private rsa key pair. Enter file in which to save the key (/home/a/.ssh/id_rsa): Created directory '/home/a/.ssh'. Enter passphrase (empty for no passphrase): Enter same passphrase again: Your identification has been saved in /home/a/.ssh/id_rsa. Your public key has been saved in /home/a/.ssh/id_rsa.pub. The key fingerprint is: 3e:4f:05:79:3a:9f:96:7c:3b:ad:e9:58:37:bc:37:e4 a@A
Now use ssh to create a directory ~/.ssh as
(The directory may already exist, which is fine):
user_a@workstation:~> ssh user_b@cluster mkdir -p .ssh user_b@cluster's password:
usera_a‘s new public key to
user_b‘s password one last time:
user_a@workstation:~> cat .ssh/id_rsa.pub | ssh user_b@cluster 'cat >> .ssh/authorized_keys' user_b@cluster's password:
From now on you can log into
user_a without a password:
user_a@workstation:~> ssh user_b@cluster
Depending on your version of SSH you might also have to do the following changes:
- Put the public key in
.ssh/authorized_keys2(note the 2)
- Change the permissions of .ssh to 700
- Change the permissions of .ssh/authorized_keys2 to 640