1. Penguin Computing / IU Partnership HPC “cluster as a service” and Cloud Services
CASC Spring Meeting 2012
Craig A. Stewart
Executive Director, Pervasive Technology Institute
Associate Dean, Research Technologies
Matthew Jacobs
SVP Corporate Development
Penguincomputing.com

2. Please cite as: Stewart, C. A. and M. Jacobs. 2012
Please cite as: Stewart, C.A. and M. Jacobs “Penguin Computing / IU Partnership HPC ‘cluster as a service’ and Cloud Services.” Presentation. Presented at Coalition of Academic Scientific Computation, 29 February 2012, Arlington, VA. The image on slide 1 (title slide) and slides 3 – 7 © Penguin Computing Inc. all rights reserved; may not be reused without permission from Penguin Computing Inc. Other slides (except where explicitly noted) are copyright 2011 by the Trustees of Indiana University, and this content is released under the Creative Commons Attribution 3.0 Unported license (

3. What is POD Services On-demand HPC system
Compute, storage, low latency fabrics, GPU, non-virtualized
Robust software infrastructure
Full automation
User and administration space controls
Secure and seamless job migration
Extensible framework
Complete billing infrastructure
Services
Custom product design
Site and workflow integration
Managed services
Application support
HPC support expertise
Skilled HPC administrators
Leverage 13 yrs serving HPC market
Internet (150Mb, burstable to 1Gb)

4. Penguin HPC Cloud Services
Penguin Computing on Demand
True HPC in the cloud on a pay-as-you-go basis
Overflow, Targeted workload, Targeted user set
Post-Purchase Collocation
Collocation services provided by Penguin
Cost Reduction, Budget reallocation
Public-Private On-Demand Partnerships
Penguin-owned and operated PODs, hosted at academic or government facilities
Revenue sharing, Augment local resources, Self-sustaining growth
POD Hybrid
On-premise cluster designed to mean usage + POD
Save on initial capital outlay while sustaining high service level to users
OEM HPC Cloud
POD distribution to internal or external customers
Augment local resource, expertise, fund growth
HPC SaaS Platform
Hosting platform for SAAS providers
On-demand delivery platform for ISVs
Turnkey Managed Services
Remote managed services for penguin and non-Penguin clusters
Augment local expertise, reduce costs

5. Scyld HPC Cloud Management System
Created by POD Developers and Administrators
Create and Manage User and Group Hierarchies
Simultaneously Manage Multiple Collocated Clusters
Create Customer Facing Web Portals
Use Web Services to Integrate with Back-End Systems
Deploy HTML5 Based Cluster Management Tools
Securely Migrate User Workloads
Efficiently Schedule and Manage Cluster Resources
Create and Deploy Virtual Headnodes for User-Specific Clusters

6. 12 Million Commercial Jobs and Counting…
Current data centers: Salt Lake City, Indiana University, Mountain View
1,500 cores (AMD and Intel)
240 TB on-demand storage
Replaced in-house image analysis cluster with POD and co-located storage
Provides cloud analysis services on POD for world-wide bioinformatics customers
Replaced Amazon AWS cloud usage with PODTools workflow migration system
Nihon ESI provides crash analysis analyses to Honda R&D during Japan’s brown-outs

7. The POD Advantage Persistent, customized user environment
High-speed Intel and AMD compute nodes (physical)
Fast access to local storage (data guaranteed to be local)
Highly secure (https, shared key authentication, IP matching, VPN)
Billed by the fractional core hour
HPC expertise included (Penguin’s core business for many years)
Cluster software stack included
Troubleshooting included in support
Collocated storage options available
Highly dependable and dynamically scalable

8. Clouds look serene enough - But is ignorance bliss?
In the cloud, do you know:
Where your data are?
What laws prevail over the physical location of your data?
What license you really agreed to?
What is the security (electronic / physical) around your data?
And how exactly do you get to that cloud, or get things out of it?
How secure your provider is financially? (The fact that something seems unimaginable, like cloud provider such-and-such going out of business abruptly, does not mean it is impossible!)
Photo by

9. Penguin Computing & IU partner for “Cluster as a Service”
Just what it says: Cluster as a Service
Cluster physically located on IU’s campus, in IU’s Data Center
Available to anyone at a .edu or FFRDC (Federally Funded Research and Development Center)
To use it:
Go to podiu.penguincomputing.com
Fill out registration form
Verify via your
Get out your credit card
Go computing
This builds on Penguin’s experience - currently host Life Technologies' BioScope and LifeScope in the cloud (

10. We know where the data are … and they are secure

11. An example of NET+ Services / Campus Bridging
"We are seeing the early emergence of a meta-university — a transcendent, accessible, empowering, dynamic, communally constructed framework of open materials and platforms on which much of higher education worldwide can be constructed or enhanced.” Charles Vest, president emeritus of MIT, 2006
NET+ Goal: achieve economy of scale and retain reasonable measure of controlSee: Brad Wheeler and Shelton Waggener Above-Campus Services: Shaping the Promise of Cloud Computing for Higher Education. EDUCAUSE Review, vol. 44, no. 6 (November/December 2009):
Campus Bridging goal – make it all feel like it’s just a peripheral to your laptop (see pti.iu.edu/campusbridging)

12. IU POD – Innovation Through Partnership
True On-Demand HPC for Internet2
Creative Public/Private model to address HPC shortfall
Turning lost EC2 dollars into central IT expansion
Tiered channel strategy expansion to EDU sector
Program and discipline-specific enhancements under way
Objective third party resource for collaboration
EDU, Federal and Commercial

13. POD IU (Rockhopper) specifications
Server Information 
Architecture
Penguin Computing Altus 1804
TFLOPS
4.4
Clock Speed
2.1GHz
Nodes
11 compute; 2 login; 4 management; 3 servers
CPUs
4 x 2.1GHz 12-core AMD Opteron 6172 processors per compute node
Memory Type
Distributed and Shared
Total Memory
1408 GB
Memory per Node
128GB 1333MHz DDR3 ECC
Local Scratch Storage
6TB locally attached SATA2
Cluster Scratch
100TB Lustre
Further Details OS
CentOS 5
Network
QDR (40Gb/s) Infiniband, 1Gb/s ethernet
Job Management Software
SGE
Job Scheduling Software
Job Scheduling policy
Fair Share
Access
keybased ssh login to headnodes remote job control via Penguin's PODShell

14. Available applications at POD IU (Rockhopper)
Package name
Summary
COAMPS
Coupled ocean / atmosphere meoscale prediction system
Desmond
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters.
GAMESS
GAMESS is a program for ab initio molecular quantum chemistry.
Galaxy
Galaxy is an open, web-based platform for data intensive biomedical research.
GROMACS
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
HMMER
HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments.
Intel
compilers and libraries
LAMMPS
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
MM5
The PSU/NCAR mesoscale model (known as MM5) is a limited-area, nonhydrostatic, terrain-following sigma-coordinate model designed to simulate or predict mesoscale atmospheric circulation. The model is supported by several pre- and post-processing programs, which are referred to collectively as the MM5 modeling system.
mpiBLAST
mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST.
NAMD
NAMD is a parallel molecular dynamics code for large biomolecular systems.

15. Available applications at POD IU (Rockhopper)
Package name
Summary
NCBI-Blast
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
OpenAtom
OpenAtom is a highly scalable and portable parallel application for molecular dynamics simulations at the quantum level. It implements the Car-Parrinello ab-initio Molecular Dynamics (CPAIMD) method.
OpenFoam
The OpenFOAM®  (Open Field Operation and Manipulation) CFD Toolbox is a free, open source CFD software package produced by OpenCFD Ltd. It has a large user base across most areas of engineering and science, from both commercial and academic organisations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.
OpenMPI
Infinibad based Message Passing Interface - 2 (MPI-2) implementation
POP
POP is an ocean circulation model derived from earlier models of Bryan, Cox, Semtner and Chervin in which depth is used as the vertical coordinate. The model solves the three-dimensional primitive equations for fluid motions on the sphere under hydrostatic and Boussinesq approximations.
Portland Group
compilers R
R is a language and environment for statistical computing and graphics.
WRF
The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. It features multiple dynamical cores, a 3-dimensional variational (3DVAR) data assimilation system, and a software architecture allowing for computational parallelism and system extensibility.