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Hardware and Software


Enterprise Systems

TITAN SYSTEM (OS/390)

OS/390 System Hardware

The OS/390 facility is an integrated multiprocessor complex, interconnected by shared disk storage. There are two IBM 9672 model R44 systems, each with 2 processors. Each system has two gigabytes (GB) of memory and a complement of several hundred peripheral devices.

The peripheral devices include:

HDS 9960 Disk Storage Subsystem
3480 cartridge tape drives (18 track, 38,000 BPI)
3490E cartridge tape drives (36 track, 38,000 BPI)
3422 tape drives (6250/1600 BPI)
STK 9310 (Powderhorn) ATL
STK 9490 (Timberline) cartridge tape drives (36 track, 38,000 BPI)
Wolfcreek ATL
STK virtual tape storage subsystem (VTSS)
STK 9840 ultra high performance magnetic tape drives
3900 laser printing subsystems
3160 cut-sheet laser printers
4245 impact printers
OSA-2 (Open System Adapter) Fast Ethernet
5665 NCR Comten communications controllers

Peripherals are available to all processors, providing non-idle redundancy and minimal disruption of service in the event of any subsystem or component failure.

IBM 9672-RB6 Serial Numbers
CP0=044625, CP1=144625
CP0=044626, CP1=144626
   

OS/390 System Software

OS/390 Operating System

The IBM OS/390 Operating System uses job control language as the user interface and the Job Entry Subsystem Version 2 (JES2). SILK Web Facilities Customized, public, and secure servers are available for general use. SILK provides online services that include: directory and account information, management functions, RACF processing, data set listing, batch job submission, and e-mail through a Web interface. Interactive Systems CICS, ISPF, TSO, and NIH Extended WYLBUR Databases ADABAS, Model 204, DB2, and IMS Language Processors COBOL/370, VS FORTRAN, PL/I for OS and VM, REXX, High Level Assembler Graphics Systems SAS/GRAPH Scientific Statistical Systems SAS, SPSS Other File management systems - VISION:Builder, IRS; BookManager online documentation system; CONNECT:Direct for advanced file exchange; VPS printing service Connectivity Products for Access to the OS/390 System Terminal emulation and full connectivity client software for telnet and dialup connections. Supported software packages include QWS3270 PLUS, WQS3270 Secure, and WS_FTP Pro.
EOS (UNIX)

Unix System Hardware

Compaq AlphaServer GS60

4 CPUs (500 MHz EV6)
4 GB RAM

Compaq/Digital AlphaServer GS140

10 CPUs (440 MHz+)
8 GB RAM

Compaq/Digital AlphaServers: 1000s, 1200s, and a 4100

Sun Enterprise 250 and 420-R servers

Unix System Software

Tru64 UNIX Operating System

Sun Solaris Operating System

Installed Software (commercial)

DEC COBOL
DEC C
DEC C++
Apache HTTP server
Net8 (formerly SQL*Net)
Netscape Enterprise Server
EOS Oracle Hosting Services Oracle Database Server
Oracle Application Server (Middle Tier)
Database Hosting Oracle Database and Middle Tier instances on shared or dedicated Unix Servers WINDOWS SERVER SERVICES

Windows Server operating systems applications can be hosted on a series of servers that are carefully managed and monitored by CIT on a 7x24 basis. These are HP Enterprise class servers and storage arrays. This facility provides a computing environment that has been proven suitable for mission-critical, enterprise-wide applications.

Hardware

HP DL380G3
Dual - Intel Pentium 4 3.2 GHz Processors
1GB RAM expandable to 4 GB
Storage: 4 - 6 Internal Drives - 18.2, or 36GB standard - large storage arrays available
Size: 3U

HP BL20P
Dual - Intel Pentium 4 3.2 GHz Processors
1GB RAM expandable to 4 GB
Storage: 2 Internal Drives - 18.2, standard upgradeable to 146 GB - large storage arrays available

HP BL40P
Quad - Intel Pentium 4 2.8 GHz Processors
2GB SDRAM expandable to 12 GB
Storage: 2 Internal Drives - 18.2 GB standard upgradeable up to 146 GB - large storage arrays available

Other HP server configurations available and supported upon request. Contact the Back Office Support Branch.

Software

Windows operating systems including Server 2003

Major components of the Microsoft Server Suite

Supported applications include: Terminal Server, SQL Server 2000, Exchange, and IIS in our enterprise wide environment. We provide these services in both a shared and dedicated server environment. ColdFusion in both a shared and dedicated Web environment

Microsoft’s Content Management Server application in a shared Web environment

OTHER SERVICES

Co-Location services—on-and off-site—for customer-owned servers

Central Email Service (CES) —e-mail services for the NIH community

NBARS, an OS/390-based service using TSM software, providing backup and recovery for distributed data

Disaster recovery program—disaster recovery facilities and services for "critical" applications that run on Titan and EOS

Search engine services for NIH Web sites using Google


Helix Systems

http://helix.nih.gov

The NIH Helix Systems manage high-performance computing systems for the NIH intramural scientific community. The staff provides training, documentation and consulting for the resources on these systems. The front-end SGI Origin 2400 system (with the network name helix.nih.gov) is used for many scientific applications as well as general purpose tasks, such as reading mail, transferring files and Web browsing.

Additional systems offer special computational capabilities that enable compute-intensive scientific applications to run faster or more efficiently. An SGI Origin 3400 (nimbus.nih.gov) augments helix by running specific scientific applications or user programs that require long execution times. The SGI systems run the IRIX operating system. The NIH Biowulf Cluster (biowulf.nih.gov) is a Beowulf parallel processing system that currently has over 2000 processors. Biowulf was built by members of the Helix Systems staff and runs the Redhat Linux operating system.

Helix Systems Hardware

The front-end SGI Origin 2400 system (helix) consists of 8 processors based on the MIPS R12000 chip. Each CPU has shared access to 6 GB of memory.

The back-end SGI Origin 3400 (nimbus) consists of 32 processors based on the MIPS R14000 chip. Each CPU has shared access to 16 GB of memory and 20 GB of swap space.

The Biowulf cluster consists of over 900 dual-processor 866 MHz, 1.4 GHz, 1.8 GHz, and 2.8 GHz nodes, most with 1 GB of memory and 8 GB of disk. Each node is connected to a fast Ethernet switch (100 Mb/s). For applications that can take advantage of more memory and higher network speeds, some nodes contain as much as 4 GB of memory and others are connected to a gigabit speed network.  

Helix Systems Software
http://helix.nih.gov/apps
http://biowulf.nih.gov/apps/

In addition to the standard Unix tools for software development, text formatting, and network communications, software packages include:

Scientific Applications

BioInformatics: GCG, Fasta, Blast, ClustalW, BoxShade, Pfsearch, HMMer, BLAT, MUMmer, RepeatMasker

Structural Biology: X-Plor, Quest, Gaussian, Charmm, GAMESS, NAMD, CNS

Molecular Modeling: AMBER, Charmm, DOCK, Fdiscover, LOOK, Insight, NAOMI, Sybyl; available on helix through MMIGNET

Mathematical/Graphical Analysis: Mathematica, MATLAB, S-PLUS, IMSL, xmgr, Xplot, GAUSS, Physica

Image Analysis: Analyze, AnalyzeAVW, AVS, IDL, xv, imgworks, convert, GIMP, GPHIGS, PHIGURE

Molecular Graphics: Grasp, Molscript, Molauto, PovChem, Povscript, PovRay, Ribbons

Biological Databases

GenBank: nucleic acid sequences

PIR: protein sequences

Genpept: protein translations from Genbank

SwissProt: curated and highly annotated protein sequence database

Human & Mouse Genome Assemblies: chromosome sequences and annotation

PDB: protein structures

Cambridge Structural Database: small organic and organometallic molecules

Programming Language/Tools C, FORTRAN 77, Fortran 90, Lisp, gcc, C++, and other typical Unix tools like awk and perl

MPI library, batch systems

Static analyzer, debugger, and performance analyzer tools

Subroutine Libraries IMSL: mathematical and statistical routines

FIGARO: 2- and 3-d interactive graphics routines

Network Services

mail, pine, and Emacs rmail: e-mail readers

SquirrelMail: Web access to Helix e-mail

ssh: secure encrypted communications between two systems

ftp: Internet file transfer utility

X Window System: supports X-windows scientific applications such as S-PLUS, Mathematica, MATLAB, SeqLab.

netscape and lynx: Web browsers

tin, rn, xrn: newsgroup reader

WebTermX: Web browser plug-in that lets Windows PCs run the X Window System

eXodus: X Windows System for Macintosh

Editors pico, vi, jot, nedit, xedit, and GNU Emacs: full-screen editors

ed and ex: line editors

Web-based Services
http://helix.nih.gov/webapps Xwindows: Graphics applications run on helix can be displayed on a desktop Mac or PC

Scientific applications: GCG-Lite, Molecules R Us, SeqWeb, UCSC Genome Browser mirror, and other Web interfaces to scientific tools

Literature Searching: Web of Science, a citation-oriented database of scientific literature—contains the Science Citation Index Expanded and the Social Science Citation Index Expanded

Proteomics: Mascot Mass-Spectroscopy search engine

Porpoise: automatic alert service for new scientific literature that searches the weekly updates of the Web of Science

WHALES: automatic alert service for new sequences in the major nucleotide and protein databases

NIH Directory and Email Forwarding Service

The Helix systems are restricted to NIH use.


Advanced Laboratory Workstation (ALW) System

http://www.alw.nih.gov

The Advanced Laboratory Workstation (ALW) System is a general-purpose, open, distributed computing system. All Advanced Laboratory Workstations are interconnected by the NIH campus-wide network, which they use to share resources and access services. The AFS file system provides distributed file services.

ALW System Hardware

Client workstations

Sun UltraSPARC and SunBlade
File Servers 3 servers with combined storage of over 500 GB

ALW Application Software

Image processing

Analyze - medical image processing
MEDX - medical imaging processing

Mathematics packages Mathematica
Matlab
Molecular modeling software Refer to http://cmm.info.nih.gov/modeling Statistical packages R
S-PLUS
Office automation applications StarOffice - integrated spreadsheet, word processing, and graphics
WordPerfect - word processing
Operating System Sun Solaris 7, 8

Other software

Emacs - text editor
Gnu software and development tools
Internet Explorer - Web browser
Netscape - Web browser
PTR - problem reporting system for ALW
Sun Forte Developer/Workshop 6


Networks

NIHnet
NIHnet is the NIH backbone network that interconnects the Institutes and Centers (ICs), local area networks (LANs), and the NIH Computer Center with the Internet, Internet2, HHS operating divisions, and other government agencies. It controls access between the ICs and between NIH and the outside world. Information carried by NIHnet includes biomedical, clinical, and administrative data. NIHnet is a wide area network (WAN) comprised of a physical infrastructure of cable, optical fiber, routers and switches; network management control systems, servers, and workstations. This infrastructure supports the NIHnet operation; wireless access points; and security control systems which include firewalls, intrusion detection systems (IDS), content filtering systems, and virus detectors.

Internet
The Internet is a worldwide system of computer networks that allows computers from one network to connect to resources on other networks. The most widely used features of the Internet are the World Wide Web and electronic mail. NIHnet maintains physically and logically diverse connections to the Internet in order to ensure high availability.

Internet2 and Abilene
Internet2 is a consortium led by over 200 universities in partnership with industry and government to develop and deploy advanced network applications and technologies. The Abilene network, created by Internet2, is a high performance backbone network that interconnects the NIHnet with universities and research centers at speeds which exceed the capability of the Internet.

Interface    NIH Computer Center


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page last updated 8/30/04

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