Molecular Science Computing Facility: Glossary

MSCF Glossary

Images, names, terms, and acronyms you may encounter in and around the MSCF web site.

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ADF: Amsterdam Density Functional package for first-principle relativistic electronic structure calculations via density-functional theory (DFT) and Slater-type orbital (STO) basis functions
AMBER: Amber refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain and are used in NWChem); and a suite of programs distributed by the University of California, San Francisco (UCSF) some of which (version 7) are licensed and available on MPP2.
CARS: Computer Access Request System - [restricted access] Online system for users and their hosts to request general computer access at Pacific Northwest National Laboratory.
CaNS: Computing and Networking Services organization - develops, maintains, and operates the EMSL's computing infrastructure; advances research in electronic collaboration, information, and instrumentation. Collaborates with the MSCF.
Ecce: Extensible Computational Chemistry Environment - Ecce is pronounced etch'-ay.
EMSL: William R. Wiley Environmental Molecular Sciences Laboratory - a national scientific user facility, operated by the Department of Energy's Pacific Northwest National Laboratory (PNNL) for the DOE Office of Biological and Environmental Research. The EMSL is the realization of former PNNL director Bill Wiley's dream to establish a "center for molecular science research" at PNNL.
GAMESS: The General Atomic and Molecular Electronic Structure System (GAMESS) for performing a variety of ab initio molecular orbital (MO) calculations
Global Arrays: Parallel Software Development Tools provide the high-performance, efficient, and portable computing libraries and tools that enable programs like NWChem to run on a wide variety of parallel computing systems with leading-edge performance and scalability.
Grand Challenge: A type of proposal to use the MSCF Resources. These are complex problems in science and engineering with broad scientific and environmental or economic impacts whose solution can be advanced by applying high-performance computing techniques and resources. Grand Challenge proposals can run several years and often are comprised of several research groups from various institutions. (See Pilot Project)
GOLD: Allocation manager for users of the MSCF parallel computers used to distribute and monitor processor time.
GVL: Graphics & Visualization Laboratory - MSCF lab facilities, tools, and expertise for visualizing complex data sets (EMSL 1101).
HPCC: High Performance Computing Center - EMSL 1117 (Computer Operations Center) and EMSL 1119 (Production Computer Laboratory) where MSCF's principal computing hardware resides.
IOPS: Integrated Operations System - [restricted access] An online tool for implementing the Environment, Safety, and Health program of a facility. IOPS is the online system used to request accounts on EMSL compute resources.
LSF: Load-sharing facility for scheduling compute jobs to run on MPP2. To submit a job to the MPP2 queue, use the 'bsub' command.
LUSTRE: The globally mounted shared file system on mpp2. It is visible from all nodes, including the login nodes.
Maya: Maya is a 3-D animation and rendering software that can be used for scientific visualization, simulation, video special effects and concept engineering.
MOLPRO: An advanced ab initio quantum chemistry software package that allows high-level electron correlation calculations
MPP2: Massively Parallel Processing system 2 consisting of 1976 1.5GHz Intel® Itanium®-2 processors with 6.9TByes of RAM, 450TBytes of aggregate disk, and 53TBytes of global disk using Lustre.
MS3: The Molecular Science Software Suite (MS3) is a comprehensive, integrated set of tools that enables scientists to understand complex chemical systems at the molecular level by coupling the power of advanced computational chemistry techniques with existing and rapidly evolving high-performance, massively parallel computing systems.
MSCF: Molecular Science Computing Facility - EMSL's advanced computing capability, maintained and operated in collaboration with Computing and Networking Services .
NWChem: The NorthWest Chemistry (NWChem ) molecular modeling and computational chemistry software developed by the High Performance Computational Chemistry group in EMSL.
NWfs: A disk farm for storing large amount of data. (Replaces SAM and NWArchive)
ParSoft: Parallel Software Development Tools provide the high-performance, efficient, and portable computing libraries and tools that enable programs like NWChem to run on a wide variety of parallel computing systems with leading-edge performance and scalability.
Pilot Project: A type of proposal to use the MSCF Resources. This is a non-Grand Challenge project, restricted to no more than 75,000 processor hours over a period of 1 year or less. (See Grand Challenge)
PNNL: Pacific Northwest National Laboratory - the multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. Pacific Northwest operates EMSL for DOE.
Point-of-Contact: EMSL Staff Member you have contacted about a proposal to use MSCF resources and who will be notified when you submit your proposal. The Point-of-Contact may be either an EMSL collaborator or Erich Vorpagel (MSCF Visualization and User Services group).
RMS: Resource management system used by LSF to dispatch compute jobs on MPP2. Use the 'prun' command to run a parallel job on MPP2.
TotalView: A parallel and multithreaded application debugger that allows you to analyze your program flow, find bugs, and test and monitor program variables.
Vampir: A Gui driven profiling tool for MPI jobs. It may be tailored for profiling other parts of user codes.

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MSCF Glossary

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