S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology StarCluster Justin Riley Software Tools for Academics and Researchers Office of Educational Innovation and Technology Massachusetts Institute of Technology 77 Massachusetts Ave. Cambridge, MA HPC on Amazon's Elastic Compute Cloud (

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology Outline About STAR Overview of Amazon Web Services (AWS) Elastic Compute Cloud (EC2) Hardware Motivations Behind StarCluster About StarCluster StarCluster Features StarCluster Advantages StarCluster Live Demo EC2 Performance Materials Science Research Case Study

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology About STAR What's your biggest problem bringing your research into the classroom?

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology Elastic Compute Cloud (EC2) Features: Amazon EC2 allows you to dynamically allocate and terminate Linux “virtual” machines with a variety of hardware configurations Pay only for what you use (i.e. machine hours and data transfer) Ability to capture software configurations into Amazon Machine Images (AMI) for later use. AMI's can be used to launch multiple machines with identical software configurations. Overview of

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology Elastic Block Storage (EBS) Features: EBS volumes are highly available, highly reliable volumes that can be attached to a running Amazon EC2 machine and are exposed as standard block devices Allows you to create point-in-time snapshots of your data. Pay per month based on allocation as well as per 1 million I/O requests ($0.10/GB allocated/month and $0.10/million I/O requests) 1GB-1TB limit per EBS volume Overview of

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology Elatic Compute Cloud Hardware InstanceArchCPURAMStorageI/O PerformanceCost/hr Small32bit GHz1.7GB160GBModerate$0.10/hr Large64bit GHz dual-core 7.5GB860GBHigh$0.40/hr Extra Large64bit GHz quad-core 15GB1.690TBHigh$0.80/hr InstanceArchCPURAMStorageI/O PerformanceCost/hr Medium32bit GHz dual-core 1.7GB350GBModerate$0.20/hr Extra Large64bit GHz quad-core(ht) 7GB1.690TBHigh$0.80/hr Standard Instances High CPU Instances One EC2 Compute Unit provides the equivalent CPU capacity of a GHz 2007 Opteron or 2007 Xeon processor.

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology Motivations Behind StarCluster StarHPC - an on demand compute cluster for parallel programming with both OpenMP and OpenMPI technologies. It provides a virtual desktop environment, hosted on EC2, configured with all the necessary tools for programming in OpenMP/OpenMPI. StarMolsim - a web application used to run materials modeling research software. It enables the user to run various simulations on a distributed compute cluster and retrieve the results, all from a web browser.

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology HPC in the Classroom Constantinos Evangelinos,PhD Researcher in Earth, Atmospheric, and Planetary Sciences. Nicola Marzari, PhD Associate Professor in Computational Materials Science Markus Buehler, PhD Assistant Professor in Civil and Environmental Engineering Materials Modeling Parallel Programming

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology StarHPC Use case: students have direct access to a HPC cluster to actively develop parallel programs using the Message Passing Interface (MPI) StarHPC was used for 2 weeks in an Independent Activities Period (IAP) course for parallel programming using OpenMP and OpenMPI. Result: Creating a 4-node cluster for two weeks came out to about $25 per student using Amazon EC2. SSH/VNC Virtual Desktop Environment EC2 OpenMPI Cluster User

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology StarMolsim Use case: students log in to a web application as a proxy to the computing resources. The web application handles communicating with the cluster to submit jobs, retrieve the results, etc. Result: Amazon EC2 was used to replace a traditional 9-node HPC cluster for an entire semester. The cost for using the 9 node EC2 cluster for the semester was around $3,000-$4,000. User EC2 Cluster Web Server hosting GenePattern from the Broad Institute of MIT and Harvard

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology About StarCluster StarCluster is a utility for creating and managing general purpose compute clusters hosted on Amazon's Elastic Compute Cloud (EC2). StarCluster makes it easy for a user to create their own compute cluster on EC2 and pay only for what they use. Software included in the virtual machine: OpenMPI NFS'd /home directory Sun Grid Engine Scipy/Numpy/IPython Compilers for installing your own custom software Ubuntu Linux OS with apt-get for installing additional OS software StarCluster Dependencies: Registered and fully configured EC2 account. Python 2.4+ Paramiko library for Python

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology StarCluster Features Simple configuration with sensible defaults One command to create and configure a n-node cluster on EC2 Utilizes Amazon's Elastic Block Storage to store and snapshot your applications and data. Easily recreate identical working environments 32bit/64bit Ubuntu 9.04 public AMI's

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology StarCluster Features Automatic Configuration of : o Sun Grid Engine with Parallel Environment (PE) o OpenMPI with SGE PE Support o NFS shares (e.g. /home and /opt) o Passwordless SSH o ~147GB local scratch space on /scratch for each node

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology StarCluster Advantages Portable, launch a cluster from virtually anywhere! Supplements existing resources when needed Easily store your applications and data in the cloud via EBS. Simply upload your applications/data to /home and your data will be available each time you launch StarCluster. Easy to install additional OS software. Just launch the AMI, use the package manager to install additional software, and rebundle the AMI to create your own customized version of StarCluster Easily package results of computational experiment for reproducible research

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology StarCluster Live Demo

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology EC2 Performance Summary: Message Passing – extremely poor in comparison to local HPC resources. Embarrassingly Parallel – much better, but still under performs compared to local HPC resources. Walker, E. (2008, October) benchmarking Amazon EC2 for high-performance scientific computing. Retrieved from

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology Materials Science Case Study 54 relaxation calculations, 25 and 32 atoms (C,N,O,H), standard convergence criterion (Espresso with MKL 10 and gfortran/gcc 4.3.3) Worst : 53% Best : 57% Worst : 58% Best : 69%

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology Getting Started with StarCluster Point your web browser to

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology AWS Funding Opportunities... Teaching Grants for educators using AWS in courses (plus access to selected course content resources) Research Grants for academic researchers using AWS in their work Project Grants for student organizations pursuing entrepreneurial endeavors; Tutorials for students that want to use AWS for self-directed learning Solutions for university administrators looking to use cloud computing to be more efficient and cost-effective in the university's IT Infrastructure The AWS in Education program offers: Learn more about AWS in Education programs:

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology Acknowledgements Professor Buehler (MIT) Professor Marzari (MIT) Constantinos Evangelinos (MIT) Nicolas Poilvert Nicolas Pinto (MIT) Amazon Web Services

S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology Thanks for coming! Any questions?