Hpcc2-head1 Cluster
v 4.4.0 (Flintstone)
Hpcc2-head1 Cluster |
v 4.4.0 (Flintstone) |
Cluster Database (SSL) | (read-only)
Kickstart Graph
landscape
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Roll Users Guide
Installed Rolls
Rocks Users Guide | Reference Guide
See the Platform OCS site for more information. For the latest update information and hotfixes, please vist the Platform OCS hotfix web site.
Please Register with Platform Computing.
This product includes software developed by the Rocks Cluster Group at the San Diego Supercomputer Center and its contributors.
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All members of the MUSC Research Community are encouraged to make use of the CBRC computer cluster. Prospective users of the CBRC Cluster must have a current MUSC NetID and must fill out this page. Such basic accounts will allow access to existing schedulers (LAVA, PBS), middleware (LAM MPI.OPENMPI) and currently installed software http://cbrc.musc.edu/homepage/InstallationLog.html . Users will be able to login to the head node only. Tasking compute nodes will have to be through scheduler software. Basic users will NOT be allowed to install new applications or to customize existing applications. User access to this research facility will be limited by the operators of the cluster whenever any one user or group begins to limit reasonable access by others. Proposals for customizing existing software for the CBRC cluster will be reviewed by the Administrator for the cluster Proposals for adding new software for the CBRC cluster will be reviewed by the CBRC Advisory Committee and the Systems Administrator for the cluster. Generally software proposals will be expected to be a part of a project proposal. All proposals for use of the CBRC cluster will be reviewed by the CBRC Advisory Committee. Basic users whose projects become excessive will be required to submit a formal proposal for review. All proposals for use of the CBRC cluster should address the following issues: 1. The CBRC cluster is a parallel computer system. Potential CBRC Projects must demonstrate a need for the power of parallel computing and the software they request to be installed must be able to utilize such power. Does the project need parallel computing? 2. CBRC use is controlled via scheduler software such as PBS-Pro and SGE Has the software been used with scheduler software before? 3. Proposals should provide estimates of the magnitude of the computational power needed. Saturation of the resource due numbers of projects or size of individual projects will trigger limiting restrictions. What is the project’s size? 4. Software installation is facilitated when ROLL packages are available (http://www.rocksclusters.org/wordpress/). Preference will be granted to software available in ROLLs. Software NOT available as a ROLL will be considered but will require a customized installation and will trigger committee scrutiny. Is the requested software currently distributed as a roll? 5. Installation of software that creates conflicts with previously installed software will be denied or delayed until the conflicts can be fully resolved. Will the software conflict with current software?
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High Performance Computing -- Getting Started Workshop
February 15-17 (Tue, Wed, Thu), 2011 | |
TUESDAY, Feb. 15 Colbert Education Center and Library Room 438 |
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8:30-10:00 MUSC Library Room 438 |
Introduction to Linux Galen Collier,
Basic introduction to the Linux operating environment, intended for anyone who needs the Linux skills necessary for using the Palmetto cluster.Topics covered will include user accounts, permissions, the BASH shell, navigation, useful commands, manipulating files and folders, text editors, installing and running programs. |
10:30-12:30 MUSC Library Room 438 |
Introduction to the Palmetto Cluster Galen Collier,
Introduction to accessing and using Clemson's Palmetto cluster for running computational jobs.Topics covered will include system architecture, getting an account, SSH clients, customizing your user environment, useful commands, the PBS batch queuing system, job scripts, submitting a serial job, interactive jobs, submitting parallel jobs. |
Break for Lunch (2 hours) |
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2:30-4:00 MUSC Library Room 438 |
Introduction to Parallel Computing Galen Collier,
Basic introduction to parallel computing, including a quick tutorial on writing parallel code using the Message Passing Interface (MPI). Participants with very limited programming experience are welcome. The Palmetto cluster will be used for all activities. Topics covered will include parallel computing and programming concepts, parallel computer architecture, data vs. task parallelism, the MPI interface, and an example of modifying serial code to run in parallel will be demonstrated. |
WEDNESDAY,Feb. 16 Colbert Education Center and Library Room 438 |
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8:30-10:00 MUSC Library Room 438 |
Introduction to Linux Galen Collier,
Basic introduction to the Linux operating environment, intended for anyone who needs the Linux skills necessary for using the Palmetto cluster.Topics covered will include user accounts, permissions, the BASH shell, navigation, useful commands, manipulating files and folders, text editors, installing and running programs. |
10:30-12:30 MUSC Library Room 438 |
Introduction to the Palmetto Cluster Galen Collier,
Introduction to accessing and using Clemson's Palmetto cluster for running computational jobs.Topics covered will include system architecture, getting an account, SSH clients, customizing your user environment, useful commands, the PBS batch queuing system, job scripts, submitting a serial job, interactive jobs, submitting parallel jobs. |
Break for Lunch (2 hours) |
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2:30-4:00 MUSC Library Room 438 |
Introduction to Parallel Computing Galen Collier,
Basic introduction to parallel computing, including a quick tutorial on writing parallel code using the Message Passing Interface (MPI). Participants with very limited programming experience are welcome. The Palmetto cluster will be used for all activities. Topics covered will include parallel computing and programming concepts, parallel computer architecture, data vs. task parallelism, the MPI interface, and an example of modifying serial code to run in parallel will be demonstrated. |
THURSDAY,Feb. 17 9:00 AM Start Presentations Ashley River Tower (ART) Auditorium Room 1119 Session Chair Dr. Bhanu Rekepalli NICS |
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9:00-9:30 |
Computing resources at Clemson that you can use: Palmetto Cluster and HUBZero collaborative software
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9:30-10:00 |
Bhanu Rekepalli NICS University of Tennessee Knoxville Research collaborations and Scientific Program Development Stages on Kraken Supercomputer The informatics fields are seeing an exponential growth in the size of data sets, and thus the problem size is the single-most pressing grand challenge of informatics. Data analysis becomes increasingly difficult and sometimes prohibitive because existing computational tools and resources are poorly suited for analysis of such large datasets. Thus the solution is to speed up development of sensitive data mining tools along with highly scalable informatics tools organized in robust, massively parallel computation infrastructures such as supercomputers. This talk will introduce various developmental stages of the most popular and widely used informatics applications on NSF-funded National Institute for Computational Sciences (NICS) supercomputer "Kraken" (the fastest academic supercomputer in the world), located in Oak Ridge National Laboratory. Participants will be introduced to various resources available at NICS for the scientific community to enhance their research. I will talk about a research collaboration project with a faculty member at MUSC and show the progress and benefits that can be attained through such collaborations. |
10:00-10:30 |
Supporting biophysical studies with molecular dynamics simulations
Brendan M. Duggan Medical University of South Carolina
Biophysical characterization of biological molecules enables insights into chemical mechanisms, signaling pathways and enables rational drug design. However, most biophysical techniques produce a global view of the molecule in question. NMR is the obvious exception but the atomic detail it provides is in the form of rates, order parameters and populations. Molecular dynamics (MD) simulations can be used to supplement biophysical measurements by providing descriptions of motions and interactions in atomic detail. We are using MD simulations to support several of our biophysical projects. The simulations have helped us identify a critical stabilizing interaction in anticoagulants we are developing, and are helping us to understand the behavior of a critical protein in the progression of HIV infection. |
10:30-11:00 |
George Rudolph, Citadel Parallel Simulation of Electromagnetic Effects in Aircraft Design Modern aircraft include complex electronic systems that provide many essential functions such as communications, navigation, and control. In the design of a new aircraft, a substantial engineering investment is made to ensure that the systems do not interfere with each other and, even more importantly, do not pose a risk to the safety of flight. Dr. Thomas Jerse has working simulation code in Fortran currently in use by Boeing. The existing code is based on implementing the PEEC (Partial-Element Equivalent Circuit Method) algorithm devised by A.E. Ruehli of IBM labs, which has proven robust and successful for three decades. Part of this solution requires an indefinite admittance matrix (IAM) that embodies electric and magnetic couplings between all the elements in the circuit. Producing the IAM matrix requires two large matrix inversions, with a correspondingly large increase in the number of linear operations that must be performed when we increase the size of the matrix. We propose to extend the quality and accuracy of the existing simulation by parallelizing the simulation using Fortran with MPI.
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11:00-11:30 |
Galen Collier, Clemson University
Evaluating Molecular Dynamics Force Fields for Simulations of Peptide-Surface Interactions: An Example of the Role of HPC in Biological and Materials Engineering
This presentation will include a brief overview of a biomolecular simulation research project, including special attention to the use of HPC resources. Project background: A shortcoming of the application of molecular dynamics (MD) in studying protein adsorption to material surfaces is that the most widely used MD force fields (i.e., equations and parameter sets used for calculating structural and energetic properties) have been designed and validated for simulations of solvated molecular systems in the absence of solid surfaces. To address this shortcoming of an otherwise extremely powerful research tool, an initial evaluation of the applicability of existing simulation methods and MD force fields to model systems of structured peptides interacting with functionalized material surfaces was warranted. This work encompasses an initial evaluation of simulation methods and a comparison of force fields. Analyses of simulated water, ions, and model peptides were completed in order to evaluate the selected simulation methods, and those methods were used for a comparison of force field performance in representing peptide structural characteristics in a simulated material-solution interfacial environment. |
11:30-12:00 |
Jacek Jakowski NICS University of Tennessee Knoxville Modeling nano-scale carbon materials A primary tool for theoretical studies of condensed matter, material science and nano-chemistry are direct molecular dynamics methods in which electrons are treated quantum mechanically. Constant quest for a more advanced technologies, specialized materials and new, better sources of energy puts always increasing demand on computational power. To fulfill this increasing demand one needs to turn into new parallel architectures, parallel applications and new algorithms. I will review our studies on modeling nano-scale carbon materials via molecular dynamics.
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12:00-12:30 |
Yuri Karl Peterson, PhD – SCCP PBS High-Throughput Computational Drug Discovery Access to computational power has increased to the point that it is feasible to explore large amounts of chemical space. Multiple techniques including QSAR modeling, pharmacophore modeling, and docking all provide utility while having inherent limitations. Additionally, the content and quality of the probe databases creates an additional layer of complexity. Practical examples of multiple aspects of high-throughput primary drug screening using high-performance computing will be presented.
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12:30-1:00 |
Jonathan Yantis Network Engineer MUSC OCIO-IS High Performance Networking in South Carolina This presentation will provide an introduction to high performance research networks in South Carolina and how to utilize those resources. Participants will get an update on the South Carolina Light Rail and the SCGigapop, and their relationships with Internet2, the National Lambda Rail and the Energy Sciences Network. Participants will also learn how to achieve maximum network performance to transfer large data sets off-campus (http://fasterdata.es.net), and how to work with OCIO-IS to provide network solutions for collaborative research projects.
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Break for Lunch (1.5 hours) |
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Consultation Time: Room 405 Colbert Education Center and Library. Schedule an appointment for you or your group to meet with HPC staff members (administration and computational scientists) to discuss research, training, the Palmetto cluster, TeraGrid resources, the HUBzero platform, or whatever interests you. contact Starr Hazard to schedule a session |
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2:30-3:30 Room 405 Colbert Education Center and Library |
Jill Gemmill, Executive Director Cyberinfrastructure Technology Integration, Clemson University How Campus IT can help advance research computing: a conversation The use of Information Technology is ubiquitous, including all areas of university research. Research faculty depend on a robust, varied, and distributed IT infrastructure to get their work done, and are typically aware of this need only when “things aren’t working”. There are common themes describing what researchers need in the way of IT support and contributions that IT staff can make to research; however, organization, reporting lines, and funding vary from one organization to another. Clemson is evolving a model for supporting research needs by leveraging investments in traditional IT and also by leveraging existing staff expertise.
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