Rockhopper

Pervasive Technology Institute: UITS Research Technologies Division

Rockhopper (rockhopper.uits.iu.edu) is Penguin Computing's Penguin-On-Demand (POD) supercomputing cloud appliance hosted by Indiana University.

Rockhopper is a collaborative effort between Penguin Computing, IU, the University of Virginia, the University of California Berkeley, and the University of Michigan to provide supercomputing cloud services in a secure US facility. Researchers at US institutions of higher education and federally-funded research centers can purchase computing time from Penguin Computing, and receive access via high-speed national research networks operated by IU.

To gain access to POD, fill out and submit the registration form. For user and support information, see the POD wiki.

System Specifications

Primary Use
Penguin on Demand beowulf computing.

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		SGE
Job Scheduling policy		FIFO
Access		keybased ssh login to headnodes remote job control via Penguin's PODShell

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.
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.