Plant and Animal Genome XXI

Rockhopper: Penguin on
Demand at Indiana University
Barbara Hallock
[email protected]
Plant and Animal Genome XXI
© Trustees of Indiana University
Released under Creative Commons 3.0
unported license; license terms on last slide.
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
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.
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
Rockhopper Applications
Package Name
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
GAMESS is a program for ab initio molecular quantum
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.
Rockhopper Applications cont.
Package Name
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
Rockhopper Applications cont.
Package Name
mpiBLAST is a freely available, open-source, parallel implementation of NCBI
NAMD is a parallel molecular dynamics code for large biomolecular systems.
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.
Rockhopper Applications cont.
Package Name
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
Portland Group
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.
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.
Acknowledgments & Disclaimer
• This material is based upon work supported by
the National Science Foundation under
Grants No. ACI-0338618l, OCI-0451237, OCI0535258, 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
License Terms
Please cite as: Hallock, B. H. Rockhopper Penguin on Demand at IU.
(Presentation) Plant and Animal Genome XXI (San Diego, January
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