NIH Computer Center |
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
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CP0=044625, | CP1=144625 |
CP0=044626, | CP1=144626 |
OS/390 Operating System
EOS (UNIX)
Unix System Hardware
Compaq AlphaServer GS60
Compaq/Digital AlphaServer GS140
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) 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.
DEC C
DEC C++
Apache HTTP server
Net8 (formerly SQL*Net)
Netscape Enterprise Server
EOS Oracle Hosting Services
Oracle Application Server (Middle Tier)
Hardware
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
Microsoft’s Content Management Server application in a shared Web environment
Co-Location serviceson-and off-sitefor 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 programdisaster recovery facilities and services for "critical"
applications that run on Titan and EOS
Search engine services for NIH Web sites using Google
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 In addition to the standard Unix tools for
software development, text formatting, and network
communications, software packages include:
Scientific Applications
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
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
MPI library, batch systems
Static analyzer, debugger, and performance analyzer tools
FIGARO: 2- and 3-d interactive graphics routines
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
ed and ex: line editors 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 literaturecontains 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.
http://helix.nih.gov/apps
http://biowulf.nih.gov/apps/
http://helix.nih.gov/webapps
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
ALW Application Software
Image processing
Other software
MEDX - medical imaging processing
Matlab
S-PLUS
WordPerfect - word processing
Gnu software and development tools
Internet Explorer - Web browser
Netscape - Web browser
PTR - problem reporting system for ALW
Sun Forte Developer/Workshop 6
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