(from the back reference pages of Interface)
Enterprise Systems
Scientific Systems
Networks
ENTERPRISE SYSTEMS
The z/OS facility is an integrated multiprocessor complex, interconnected by shared disk storage. There is a single IBM z9 Business Class (BC) model 2096-M03 system, with 3 processors. The system has 8 gigabytes (GB) of memory and a complement of several hundred peripheral devices.
The peripheral devices include:
Sun 9990V Disk Storage System
3490E cartridge tape drives (36 track, 38,000 BPI)
STK 9310 (Powderhorn) ATL
Sun/STK SL8500 modular tape library system
STK VSM Virtual Storage Manager (virtual tapes)
STK 9840 ultra high performance magnetic tape drives
3900 laser printing subsystems
2105ES cut-sheet laser printers
4245 impact printers
3366 OSA-Express2 1000Base-T network interface cards
0863 Crypto Express2 cryptographic co-processor cards
Peripherals are available to all processors, providing non-idle redundancy and minimal disruption of service in the event of any subsystem or component failure.
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IBM z9 BC model 2096-M03
Serial Numbers
CP0=0077AED, CP1=0177AED, CP2=0277AED
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z/OS Operating System
The IBM z/OS 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, secure file transfer, executing TSO commands, and e-mail through a web interface.
Interactive Systems
CICS, ISPF, TSO, and NIH Extended WYLBUR
Databases
Model 204, DB2, and IMS
Language Processors
COBOL, VS FORTRAN, PL/I for MVS and VM, REXX, High Level Assembler, and C/C++
Graphics Systems
SAS/GRAPH
Scientific Statistical Systems
SAS, SPSS, and BMDP
Other
File management systems - VISION:Builder, IRS; BookManager online documentation system; Connect:Direct for advanced file exchange; VPS printing service; Interactive Output Facility (IOF) for controlling and examining batch jobs
Connectivity Products for Access to Titan
Full connectivity client software for tn3270 and ftp connections, including secure connections. Supported software includes QWS3270 Secure, web-based secure file transfer, WS_FTP Pro, and SSH.
Unix System Hardware
Servers
HP Servers
Multiple HP Servers—ranging in size from midrange to high-performance application servers, including HP AlphaServer, HP PA-RISC and HP Itanium technology.
Customized configurations are available depending on the requirements of the application.
Sun Servers
Single CPU/8 core Sun servers for midrange applications, including web servers
Other configurations are available depending on application requirements.
Storage
Hosted Unix systems will provide online storage for data as needed. Storage can be provided on SAN (storage attached networks) or locally attached storage, depending on the system, application, and storage required. Storage is provided in a RAID configuration for reliability.
Unix System Software Overview
Operating Systems
HP-UX
Sun Solaris
Database
Oracle on shared or dedicated Unix servers
Connectivity
FISMA-compliant highly available, secure connectivity, such as:
SSH
Connect:Direct
Middle Tier Application Servers
Oracle Application Server
Apache Server
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 with available fiber-connected SAN storage arrays. This facility provides a computing environment that has been proven suitable for mission-critical, enterprise-wide applications.
Windows Hardware
HP BL460C - Blade Server
Processors - Dual Intel Xeon Quad-core E5335 (2.00 GHz) standard
Memory - 4 GB (PC2-5300) standard - expandable to 32 GB
Storage - 2 Internal 146 GB SAS Drives with 128MB battery backed write cache standard
Direct attached storage blade available (730GB maximum size)
Network – Dual 1GB NIC (Teamed for redundancy)
HP BL685C Blade Server
Processors - Quad AMD Opteron Dual-core 8214 (2.2GHz) standard
Memory - 4 GB (PC2-5300) standard - expandable to 64 GB
Storage - 2 Internal 146 GB SAS Drives with 128MB battery backed write cache standard
Network – Dual 1GB NIC (Teamed for redundancy)
Other HP server configurations are available and supported upon request.
The Virtual Server service allows multiple operating system instances to pull resources from a pool of servers.
Windows Application Software
Windows operating systems including Server 2003 Standard, Enterprise and 64 bit Server 2003 Enterprise and Standard Edition
Major components of the Windows Server Suite
Supported applications include: Terminal Server, SQL Server 2005, Exchange, and IIS in our enterprise wide environment. We provide these services in virtualized, shared, and dedicated server environments.
ColdFusion in both a shared and dedicated web environment
Microsoft’s Content Management Server application in a shared web environment
Moss2007/SharePoint¾a web service for information sharing and document collaboration
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 32-processor Opteron 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.
An additional system, the NIH Biowulf Cluster (biowulf.nih.gov), offers computational capabilities for compute-intensive, large-memory, or swarms of independent jobs. Biowulf(biowulf.nih.gov) is a 6300+ processor Linux cluster, built by members of the Helix Systems staff, that runs the Linux operating system.
The main interactive system for scientific computing, helix.nih.gov, has 16 processors and 128 GB of memory.
The Biowulf cluster consists of over 2100 dual-processor or four-processor nodes, with at least 1 GB of memory and 20 GB of disk. Each node is connected to a fast Ethernet switch (100 MB/s). For applications that can take advantage of more memory or higher network speeds, some nodes contain as much as 8 GB of memory and others are connected to a gigabit speed low-latency network. An Altix 350 with 32 Itanium 2 processors and 96 GB of memory acts as a “fat node” of the cluster, and is reserved for applications that require large amounts of memory.
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: EMBOSS, Fasta, Blast, Wu-Blast, ClustalW, Pfsearch, HMMer, BLAT, MUMmer, RepeatMasker, MFOLD, Sequence Assembly/Mapping, Linkage and Phylogenetic Analysis programs
Systems Biology: The Biobase portfolio of databases including ExPlain for interpretation of microarray and ChIP-chip data, Transfac for signal transduction pathway data, TransPro for annotated transcription start sites, and TransCompel for composite gene regulatory elements.
Structural Biology: X-Plor, Quest, Gaussian, Charmm, GAMESS, NAMD, CNS, Gromacs, Prospect, Haddock, APBS, Rosetta
Molecular Modeling: AMBER, Charmm, Q-Chem, DOCK, Fdiscover, LOOK, Insight, NAOMI, Sybyl; other programs available on Helix through Mmignet
Mathematical/Graphical Analysis: Mathematica, MATLAB, S-PLUS, S, IMSL, xmgr, Xplot, GAUSS, Physica, R, BioConductor, SAS, Octave
Image Analysis: FSL, Analyze, AnalyzeAVW, AVS, IDL, GPHIGS, PHIGURE, AFNI, CTF
Molecular Graphics: Grasp, Molscript, Molauto, PovChem, Povscript, PovRay, Ribbons
Biological Databases
A large collection of nucleic and protein sequence databases are maintained in several formats on the Helix Systems, including Genbank, GenPept, NCBI’s nt and nr, Refseq, Swissprot/Trembl, and genome data. A comprehensive list with details and update status is available at: http://helixweb.nih.gov/helixdb.php.
Programming Language/Tools
C, FORTRAN 77, Fortran 90, Intel & Portland Group compilers, Lisp, gcc, C++, and other typical Unix tools like awk and perl
MPI library and PBS 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
IMAP: mail server for mail clients, pine, and Emacs rmail
SquirrelMail: web access to Helix e-mail
SSH: secure encrypted communications between two systems
WinSCP, Fugu, FileZilla, and scp: secure Internet file transfer utilities
X Window System: supports X-windows scientific applications such as S-PLUS, Mathematica, MATLAB, SeqLab
Netscape, mozilla, and lynx: web browsers
X-Win32: web browser plug-in that lets Windows PCs run the X Window System
Utilities
Editors: pico, nano, vi, jot, nedit, xedit, emacs, ed, ex
Image display and manipulation: imgworks, xv, convert, GIMP
http://helix.nih.gov/webapps
Scientific applications: EMBOSS-Lite (formerly GCG-Lite), Molecules To Go, UCSC Genome Browser mirror, ExPlain, Transfac, TransPath, TrxFacMiner, StrucTools, and other web interfaces to scientific tools
Proteomics: Mascot Mass Spectroscopy search engine
WHALES: automatic alert service for new sequences in the major nucleotide and protein databases
The Helix systems are restricted to NIH use.
NETWORKS
NIHnet
NIHnet is the NIH backbone network that interconnects the Institutes and Centers (ICs), local area networks (LANs), and the NIH Data 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 includes firewalls, intrusion detection systems (IDS), content filtering systems, and virus detectors.
Parachute provides dialup connectivity to the NIHnet. CIT also supports VPN for remote access to the NIHnet via 3rd party broadband providers.
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
(http://www.internet2.edu/network)
The Internet2 Network is the U.S. research and education network that provides members with high-capacity, low-latency connectivity that avoids the congestion of the Internet. The current network, fully redesigned and deployed in 2006 when it replaced Abilene, provides next-generation production services as well as a platform for the development of new networking ideas and protocols. NIHnet customers communicate with Universities, Labs, and other Federal research agencies through this “member-only” network.
Interface
About the NIH Data Center
