ITC Research Computing Support Overview of Research Hardware, Software, Support,

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ITC Research Computing SupportOverview of
Research Hardware, Software, Support, Data
Storage

• By Tim F. Jost Tolson, Manager
• Research Computing Support Center
• Phone [phone] F Fax [phone]
• E-Mail Res-Consult_at_Virginia.EDU
• http//www.itc.Virginia.edu/researchers
• Welcome Help yourself to the snacks
• and drinks. Please sign-in
• and get a handout feedback form

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ITC Research Computing SupportKathy Gerber, Ed
Hall, Katherine Holcomb, Nancy Kechner,
Tim F. Jost Tolson

• This talk is designed to give you an introduction
  into the range of hardware, software, support,
  and data storage options available from ITC to
  enable and enhance your research and scholarly
  endeavors.
• Please feel free to ask questions at any time
  during the presentation.

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ITC Computing Support

• ITCWeb web resource for help, information, etc.
  at www.itc.virginia.edu
• Researchers Portal specific to needs of
  researchers, see www.itc.virginia.edu/researchers
  
• Specific services, software, etc. listed under
  this portal at www.itc.virginia.edu/researchers/se
  rvices.html
• Instructional Technology Group (www.itc.virginia.e
  du/instructors)
• Includes Digital Media Lab provides equipment and
  support for digitizing and editing images, sound,
  and video. Offices in Clemons Library adjacent to
  the RMC.

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ITC Computing Support continued

• ITC Training (www.itc.virginia.edu/training)
• Computer workshops and training ranging from 2
  hour courses to multiple week courses and from
  Introduction to Word to Perl and ASP classes.
  Many available for free, others for small fee.
  ITC Training classes are handled by the Division
  of Training, please call 243-5998. ITC offers
  Byte-Size seminars. Have CBT and Videos, etc.
  Complete list of courses at http//www.itc.virgi
  nia.edu/training/courses/courses.html
• DCI Program (www.itc.virginia.edu/dci)
• Program for purchasing PC and Mac computers that
  standardizes software builds, available models,
  etc. Voluntary program. Also available for
  personal purchases of Dell or Apple computers.
• Off-Grounds Access
• SSH Tunnelling using SecureCRT
• http//www.itc.virginia.edu/research/unix/ssh_tun
  neling/
• Virtual Private Network (VPN) http//www.itc.virg
  inia.edu/desktop/pki/vpn/
• Proxy server access available http//www.itc.virg
  inia.edu/desktop/proxy/

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ITC Computing Support continued

• Software Availability (www.itc.virginia.edu/licens
  es)
• Provides list of all software generally available
  about which ITC knows both that licensed by ITC
  and by other departments.
• Provides links and information about U.Va.'s
  Microsoft Select contract, which provides all
  Microsoft software at greatly reduced prices.
  From Word to C compilers and Windows XP.
• http//www.itc.virginia.edu/licenses/selectmain.ht
  m
• Provides information and tips about how to get
  good deals on software purchases.
• http//www.itc.virginia.edu/licenses/savvyshop.htm
  l
• Software Central (www.itc.virginia.edu/central)
• Provides web download area for software available
  to U.Va. faculty, staff, and students such as
  SecureCRT, Mulberry (emailer) Norton AntiVirus
  that dont require authenticated use or restrict
  number of UVa users.

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ITC Academic Computing Health Sciences (ACHS)
www.itc.virginia.edu/achs

• Technical consulting for the applications and
  hardware supported by ITC-ACHS to specialized
  consulting in areas such as molecular biology,
  health informatics, and data visualization.
• Public computing laboratories for medical
  research and a teaching lab facility, including
  slide scanning high-resolution color printing
  (fee)
• 42 node dual CPU HPC cluster, half Intel CPU
  nodes and half Apple G4 nodes with gigabit
  Ethernet interconnect. Five terabytes of disk
  storage local to cluster.
• Program to provide intensive support for selected
  faculty projects for a defined period of time
• Website provides links to grant submission
  templates
• Located on the third floor of Hospital West (also
  known as the Multistory Building), around the
  corner from the elevators. Tom Spraggins,
  Manager
• Open 830 AM to 500 PM. Telephone [phone]
  or e-mail ITC-ACHS_at_Virginia.edu.

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Other Research Support

• Alderman Library (www.lib.virginia.edu)
• Digital Research Instructional Services
  Geospatial and Statistical Data Center (GeoStat)
  and Electronic Text Center (Etext) on 3rd floor
  of Alderman, 982-2630, www.lib.virginia.edu/ecente
  rs.html /)
• See Yellow Handout for details of their services
• Science Engineering Library (SEL) Digital Lab
  (http//www.lib.virginia.edu/science/sedi/
• Supports digital content creation and the
  development of a complementary public digital
  workspace .

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Other Research Support (continued)

• Office of the Vice President for Research and
  Graduate Studies
• http//www.virginia.edu/vprgs/
• Office of Research and Public Service
  http//www.virginia.edu/researchandpublicservice/
  
• Office of Sponsored Programs conducts an annual
  seminar in the Fall focusing on key components of
  doing research at U.Va. Details at
  www.virginia.edu/sponpgm or call Ms. Carole
  Wagonhurst at 924-6346

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Other Research Support (continued)

• ITC Advisory Committees
• www.itc.virginia.edu/oit/org/committees
• Southeastern Universities Research Association
  (SURA) www.sura.org
• Consortium of over 60 universities across the US,
  predominately in southeast.
• Promotes initiatives in nuclear physics,
  information technologies, and coastal research.
• Mid-Atlantic Terascale Partnership (MATP)
  www.midatlantic-terascale.org
• Consortium of research institutions in Virginia,
  Maryland, and Washington formed to support
  research activities that require next-generation
  high-performance network connectivity.

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Student Research

• Robert J. Huskey Graduate Research Exhibition
• Forum for graduate students to publicize their
  research and be rewarded for superior research.
  All GSAS students eligible. (www.student.virginia
  .edu/gsasc/exhibition)
• Undergraduate Research Network (URN)
• Collaborative effort dedicated to fostering
  undergraduate research community, guiding
  students to initiate independent projects.
  (www.student.virginia.edu/research)

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ITC Research Computing Support

• Research Computing Support Center (RCSC)
• 244 Wilson Hall - Phone [phone], Fax
  243-8769
• Hours 900 to 500 PM Monday thru Friday,
  walk-in
• 4 full-time staff 3 with Ph.D., and student
  consultants
• 3 PCs, 3 Apple G4 or G5 (dual CPU, 2GB), 2 Sun
  workstations, 3 Linux workstations (1 with dual
  CPU Xeon, 2GB). Color and B/W printers.
• Software distribution for ITC site licensed
  packages.
• http//web.virginia.edu/rescomp/software.html
• Researchers Portal specific to needs of
  researchers, see www.itc.virginia.edu/researchers
  
• Specific services, software, etc. listed under
  this portal at www.itc.virginia.edu/researchers/se
  rvices.html

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Research Computing Resources Available to U.Va.
Researcherswww.itc.virginia.edu/research/services
.html

• Software
• Statistical SPSS, SAS, Minitab, S-PLUS, Stata,
  Amos, Lisrel/Prelis
• Scientific ESRI-ArcGIS, IDL, LabView, Maple,
  Mathematica, Matlab, PGI and Intel Compilers
• http//web.virginia.edu/rescomp/software.html

• Hardware
• 3 HPC Linux Clusters
• IBM p640 Model B80 SMP computer
• Sun SGI Clusters
• NPACI/NSCA Resources
• Disk Storage
• blue.unix

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Classes and Workshops

• ITC Training Courseshttp//www.itc.virginia.edu/
  training/student/programming.htm
• Research Computing Support
• We can teach Intro to Unix and have taught
  Introductions to the HPC Linux Cluster and
  Introduction to MPI (Message Passing Interface)
  used for parallel computing.
• We can also teach introductions on any of our
  software packages. Can be tailored in length and
  content to fit your class or labs needs.
• Most of our packages have built-in tutorials
  and/or we have course notes on-line. You can
  come to the RCSC and work on these at your own
  pace with staff present to assist your learning.

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HPC Computing Resources

• Aspen AMD Linux cluster
• 48 compute nodes, with dual Athlon processors and
  1GB of memory in each node and Gigabit Ethernet
  interconnect between nodes. 1 TB of storage local
  to cluster. Use PBSPro commands to submit jobs.
• Login to aspen.itc.virginia.edu
• Links to the Home Directory, HSM, and existing
  disk resources on researchers workstations
• Various serial and parallel computing tools
  (e.g., HPF, C, MPICH, Matlab, Mathematica,
  S-PLUS )
• Intended for serial (single node, single CPU)
  jobs.
• Tutorial and Getting Started Tips
  athttp//www.itc.virginia.edu/research/linux-clu
  ster/aspen/
• See usage status http//aspen.itc.virginia.edu/
  ganglia

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HPC Computing Resources(continued)

• Birch Xeon Linux cluster
• 32 compute nodes, with dual Xeon processors (2.4
  GHz 512Kb OD Cache) and 2 GB of memory in each
  node and Myrinet and Gigabit Ethernet
  interconnect among nodes. 1 TB of storage local
  to cluster. Use PBSPro commands to submit jobs.
• Login to birch.itc
• Links to the Home Directory, HSM, and existing
  disk resources on researchers workstations
• Various serial and parallel computing tools
  (e.g., HPF, C, MPICH, Matlab, Mathematica)
  including Intel and gcc compilers.
• Intended for parallel (multiple nodes or multiple
  CPUs) jobs
• Tutorial and Getting Started Tips
  athttp//www.itc.virginia.edu/research/linux-clu
  sters/birch/
• See usage status at http//birch.itc.virginia.e
  du/ganglia

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HPC Computing Resources(continued)

• Cedar AMD 64-bit CPU Linux cluster
• 125 compute nodes, with dual Operteron 244
  processors (1.8 GHz 1MB OD Cache) and 2 GB of
  memory in each node and Gigabit Ethernet
  interconnect among nodes. 1Terabye of storage
  local to cluster. Use PBSPro commands to submit
  jobs.
• Login to cedar.itc
• Links to the Home Directory, HSM, and existing
  disk resources on researchers workstations
• Various serial and parallel computing tools
  (e.g., HPF, C, MPICH, Matlab, Mathematica)
  including Intel and gcc compilers.
• Intended for both parallel (multiple nodes or
  multiple CPUs) and serial jobs, with slight
  priority to parallel jobs.
• First year of Condo-Cluster model where
  researchers can purchase nodes for their use that
  we maintain.
• Tutorial and Getting Started Tips
  athttp//www.itc.virginia.edu/research/linux-clu
  sters/cedar/
• Information on nodes running, system load, usage,
  etc. http//cedar.itc.virginia.edu/ganglia

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HPC Linux Cluster Hands-on Training

• Tuesday 9/27 and Thursday 9/28 3 - 5PM
• In Brown Science and Engineering Library's
  Electronic Classroom in Clark Hall
• Registration required http//www.itc.virginia.ed
  u/research/linux-clusters/hpc-register.html
• Teach new users of the Linux clusters how to log
  on, navigate the filesystem, create Makefiles,
  compile codes, and submit (run) jobs to the
  cluster via the PBS batch queueing system.

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HPC Computing Resources (continued)

• IBM p640 Model B80 SMP computer
• Symmetric Multi-Processor (SMP) computer
• Four 450 MHz Power3 II processor
• 12 GB of total memory, available to any CPU.
• Running AIX operating system Uses PBSPro
  commands to submit jobs.
• Log into athena.itc
• Various serial and parallel computing tools
  (e.g., HPF, C, MPICH, Matlab, Mathematica,
  S-PLUS )
• Tutorial and Getting Started Tips
  athttp//www.itc.virginia.edu/research/ibm/smp/

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Unix Lab Sun Workstations For interactive
(console) and remote login

• E225 Thornton has 8 Sun Workstations (sun-1 to
  sun-8.unixlab) Model Ultra 60s.
• http//www.itc.virginia.edu/research/unixlabhw.htm
  l
• No time limits
• 450Mhz UltraII CPUs with 512MB

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SGI Sun Clusters for remote login, batch jobs
only

• teak.itc.virginia.edu 2 sets of two SGI O200
  servers with 4 CPUs of 180Mhz R10000 CPUs and
  1.6 to 2 GB memory and high-speed interconnect
  between the 2 SGIs within a set. Uses PBSPro to
  submit jobs.
• oak.itc.virginia.edu 8 Sun Netras
  UltraSPARC-IIIi 1GHz processors with 2 GB of RAM
  per node. Uses PBSPro to submit jobs.

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Thinking of getting your own Linux Cluster?

• ITC purchasing another medium size Linux cluster
  this year.
• Second year of a program that allows researchers
  to purchase nodes in a Linux Cluster that ITC
  would house and maintain for a three-year period.
  
• Benefits include free system administration,
  timely security updates, 24x7 monitoring, and the
  ability to use more nodes than purchased during
  periods of non-peak demand.
• Details of the program
• http//www.itc.virginia.edu/research/itc-clusters/
  cluster-purchase.html
• Interested? Please contact Tim Tolson at
  243-6592 or TTolson_at_Virginia.EDU to discuss this
  exciting opportunity.

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National SuperComputer Centershttp//www.itc.virg
inia.edu/research/npaci.html

• NPACI - National Partnership for Advanced
  Computational Infrastructure. http//www.npaci.edu
  /
• NCSA - National Center for Supercomputing
  Applications http//www.ncsa.edu/
• NPACI National Partnership for Advanced
  Computational Infrastructre. NCSA National
  Center for Supercomputing Applications NERSC
  National Energy Research Scientific Computing
  Center - (DoE funded research only)
  http//www.nersc.gov/
• US researchers are eligible to apply for time on
  NCSA/NPACI machines.
• If application is successful time is free. Small
  allocations for 10,000 hours are relatively easy
  to get.
• BlueHorizon 1152 IBM Power3 CPUs configured in
  144 nodes with 8 CPUs and 4GB per nodes based at
  San Diego. http//www.npaci.edu/BlueHorizon/
• TeraScale Computing System 2728 1GHz Alpha CPUs
  configured in 682 nodes http//www.psc.edu/machin
  es/tcs/
• Distributed Terascale Facility a 13.6 Teraflop
  Linux Cluster http//www.npaci.edu/teragrid/ind
  ex.html

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Storage Facilities at U.Va.

• Home Directory Service
• /tmp and /bigtmp
• /longtmp
• HSM
• Other ITC supported Storage Options

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Home Directory Servicehttp//www.itc.virginia.edu
/homedir

• Quotas are in place, but have been raised
  substantially.
• Backed-up multiple times per day using Snapshot
  facility
• http//www.itc.virginia.edu/unixsys/homedir/snapsh
  ot.html
• Default file-system on blue.unix, all research
  HPC clusters and Unix Lab workstations.
• Web interface now available www.homedir.virginia.
  edu
• The home directory service can be mapped to your
  PC, Mac, or Linux computer so you can access your
  files directly from your office or from home!
• http//www.itc.virginia.edu/unixsys/homedir/hdlo
  ginwin.html
• http//www.itc.virignia.edu/unixsys/homdir/hdlog
  inmac.html
• http//www.itc.virignia.edu/unixsys/homdir/hdlog
  inlinux.html

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/tmp and /bigtmp

• www.itc.virginia.edu/research/filestorage.html
  
• Used for short time data storage time limit of
  24-72 hours for files before they are deleted.
• Can be accessed from blue.unix, HPC Sun, SGI
  clusters and Unix Lab workstations.
• No quota, however /bigtmp is only 2GB and is
  scrubbed every 48-72 hours.

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/longtmp

• www.itc.virginia.edu/research/filestorage.html
• Two week limit on files in longtmp although in
  general users get longer.
• longtmp has a total space of 64 GB.
• Users request their required space by sending an
  e-mail to Res-Consult_at_Virginia.EDU
• longtmp can be accessed from blue.unix, Unix lab
  any of our research HPC clusters, PCs, or Macs
• longtmp can also be mapped to your PC.
• www.itc.virginia.edu/research/hsm.htmlmaps

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HSM-Hierarchical Storage Management System

• Large Tape system with a hard disk cache
• To use a file from the tape system it is
  necessary to insure that the file is moved to the
  disk cache. Use the command
• /common/uva/bin/hsmread filename

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HSMwww.itc.virginia.edu/research/hsm.html

• Large Tape library multiple Terabytes of space.
• Should be used to archive files that are not used
  regularly.
• Although it is a tape-system, files are accessed
  in exactly the same way as any other disk based
  file-system .
• HSM can be mapped to your PC for direct access.
• www.itc.virginia.edu/research/hsm.htmlmaps
• Multiple copies of files are kept for data
  integrity, but there is NO backup made!
• Request space by e-mailing Res-Consult_at_Virginia.e
  du
• Students usually have their space allocated
  within their supervisors directory space unless
  special request to do otherwise.
• Initial allocations are for 5GB with up to 20GB
  or more available upon on request.

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blue.unix

• www.itc.virginia.edu/desktop/unix/cluster/hom
  e.html
• Cluster of sixteen IBM RS/6000 machines running
  AIX 4.3
• Will be come cluster of three IBM RS/6000s,
  64-bit architecture running AIX 5.3 this fall gt
  called blue.itc
• General purpose Unix cluster
• CPU limit of one hour for jobs

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Other ITC supported Storage Options

• Departmental file-systems can be exported to ITC
  machines users can then access their
  directories on their departmental machines
  directly from ITC computers.
• ACHS can provide up to 8 GB of temporary data
  storage (2 weeks).
• ITC Unix Systems (www.itc.virginia.edu/unixsys)
• Departments can also buy additional disk wedges
  the cost is 36 for a 250MB wedge per year.
  Pricing to be revised this fall. More likely to
  be per Gigabyte (GB)
• http//www.itc.virginia.edu/unixsys/storage.htmli
  ndwedge

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Research Computing Support Groupwww.itc.virginia.
edu/researchers/services.html

• Guide you to the appropriate resources to run a
  long running or memory intensive program
• Recommend software for computer simulations
• Provide computer workshops on supported software
  packages
• Assist you in using Latex to write a journal or
  conference submission
• Help with survey design and planning
• Assist with data and statistical analysis, data
  management, data and file sharing with colleagues.

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Research Computing Support Groupwww.itc.virginia.
edu/researchers/services.html

• Help you to replicate a statistical analysis
  described in a journal article
• We distribute over 20 statistical, mathematical,
  scientific visualization and other academic
  software packages for use at U.Va. (most are
  available for free).
• http//web.virginia.edu/rescomp/software.html
• And much, much more please contact us, if we
  can't help we'll try to find someone who can.
  Phone [phone] or E-Mail Res-Consult_at_Virginia.
  EDU

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Thank you for coming to our
ITC Research Computing Support Colloquium in
244 Wilson Hall 243-8800 Res-Consult_at_Virgini
a.EDU http//www.itc.virginia.edu/research/tal
ks Presented by theITC Research Computing
Support Group Kathy Gerber, Ed
Hall, Katherine Holcomb, Nancy Kechner,
Tim F. Jost Tolson

• ----------------------
• UPCOMING COLLOQUIA
• Missing Values Analysis Imputation, Wed., Oct.
  5, at 330 PM
• "A Picture Says a Thousand Words Displaying
  Quantitative Data Information Effectively,
  Wed., October 19, at 330 PM.
• ICPSR Social Science Data for Teaching
  Research, Wed., November 2, at 330
• ----------------------
• Please take a minute to complete the feedback
  form and leave it on the counter as you exit.
  Thank you.

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HPC Linux Cluster Hands-on Training

• Tuesday 9/27 and Thursday 9/28 3 - 5PM
• In Brown Science and Engineering Library's
  Electronic Classroom in Clark Hall
• Registration required http//www.itc.virginia.ed
  u/research/linux-clusters/hpc-register.html
• Teach new users of the Linux clusters how to log
  on, navigate the filesystem, create Makefiles,
  compile codes, and submit (run) jobs to the
  cluster via the PBS batch queueing system.