1. © Trustees of Indiana University Released under Creative Commons 3.0 unported license; license terms on last slide. Rockhopper: Penguin on Demand at Indiana University Barbara Hallock bahalloc@iu.edu Plant and Animal Genome XXI

2. Rockhopper: What is it? A real (not virtual) HPC cluster Located in Indiana University’s secure Data Center facility Managed by Penguin on Demand Core hours and storage available for a nominal fee

3. Rockhopper: Who is it for? Available to anyone at a.edu or FFRDC Applications available to support research in – Mesoscale Atmospheric Prediction – Genomics – Quantum Chemistry – Molecular Dynamics – Etc.

4. Rockhopper: Why? XSEDE-allocated projects that have run out of allocation but still need to complete further computational work Projects that might need to “scale” up to XSEDE in the future – XSEDE-standardized interface means less time learning to compute and more time doing research

5. Rockhopper Applications Package NameSummary COAMPSCoupled 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.

6. Rockhopper Applications cont. Package NameSummary 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.

7. Rockhopper Applications cont. Package NameSummary mpiBLAST mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST. NAMDNAMD is a parallel molecular dynamics code for large biomolecular systems. 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.

8. Rockhopper Applications cont. Package NameSummary 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.

9. Added Benefit: For genomics researchers completing analysis on Rockhopper, consulting and support services from the National Center for Genome Analysis Support (NCGAS) are provided at no additional charge thanks to a grant from the NSF.

10. Acknowledgments & Disclaimer This material is based upon work supported by the National Science Foundation under Grants No. ACI-0338618l, OCI-0451237, OCI- 0535258, and OCI-0504075. This work was supported in part by the Lilly Endowment, Inc. and the Indiana University Pervasive Technology Institute Any opinions presented here are those of the presenter(s) and do not necessarily represent the opinions of the National Science Foundation or any other funding agencies

11. License Terms Please cite as: Hallock, B. H. Rockhopper Penguin on Demand at IU. (Presentation) Plant and Animal Genome XXI (San Diego, January 2013). http://hdl.handle.net/2022/15432http://hdl.handle.net/2022/15432 Items indicated with a © are under copyright and used here with permission. Such items may not be reused without permission from the holder of copyright except where license terms noted on a slide permit reuse. Except where otherwise noted, contents of this presentation are copyright 2013 by the Trustees of Indiana University. This document is released under the Creative Commons Attribution 3.0 Unported license (http://creativecommons.org/licenses/by/3.0/). This license includes the following terms: You are free to share – to copy, distribute and transmit the work and to remix – to adapt the work under the following conditions: attribution – you must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). For any reuse or distribution, you must make clear to others the license terms of this work.