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

• 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

• Available to anyone at a .edu or FFRDC
• Applications available to support research in
– Mesoscale Atmospheric Prediction
– Genomics
– Quantum Chemistry
– Molecular Dynamics
– Etc.

• 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

Package Name
COAMPS
Desmond
GAMESS
Galaxy
GROMACS
Summary
Coupled ocean / atmosphere meoscale prediction system
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 is a program for ab initio molecular quantum chemistry.
Galaxy is an open, web-based platform for data intensive biomedical research.
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.

Package Name
HMMER
Intel
LAMMPS
MM5
Summary
HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments.
compilers and libraries
LAMMPS is a classical molecular dynamics code, and an acronym for
Large-scale Atomic/Molecular Massively Parallel Simulator.
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.

Package Name Summary 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.
NCBI-Blast
OpenAtom
OpenFoam
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 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.
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.

Package Name
OpenMPI
POP
Portland Group
R
WRF
Summary
Infinibad based Message Passing Interface - 2 (MPI-2) implementation
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.
compilers
R is a language and environment for statistical computing and graphics.
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.

• 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.

• 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

• 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/2022/15432
• 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/).
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