ITC Research Computing Support December 7, 2005

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ITC Research Computing SupportDecember 7, 2005

• Research Computing Support Center
• 244 Wilson Hall
• Phone [phone] F Fax [phone]
• E-Mail Res-Consult_at_Virginia.EDU
• http//www.itc.virginia.edu/researchers
• By Tim F. Jost Tolson,
• Manager, ITC-RCS Phone [phone]
• Email TfjTolson_at_Virginia.EDU

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ITC Research Computing Support

• This talk is designed to give you an introduction
  into the range of hardware, software, support and
  data storage options available from ITC/RCS 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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Other Research Support

• University Library (www.lib.virginia.edu)
• Electronic Centers in Alderman (www.lib.virginia.e
  du/ecenters.html)
• Geospatial and Statistical Data Center (GeoStat)
  on 3rd floor of Alderman, 982-2630,
  (fisher.lib.virginia.edu)
• Geostat supports a wide range of academic and
  scholarly activities through access to extensive
  collections of numeric and geospatial data files
  computing facilities and software for data
  manipulation, research, and instruction and a
  suite of Internet-accessible data extraction
  tools.
• 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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ITC Computing Support

• 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 Research Computing Support

• Research Computing Support Center (RCSC)
• 244 Wilson Hall - Phone [phone], Fax
  243-8769
• Hours 900 to 500 PM Monday through Friday,
  walk-in
• 4 full-time staff 3 with Ph.D., 4 student
  consultants
• 3 PCs, 3 Apple G4 or G5 (dual CPU, 2GB), SGI
  workstation, 2 Sun workstations, 2 Linux
  workstations (1 with dual CPU Xeon, 2GB). Color
  and B/W printers.
• Software distribution for ITC site licensed
  packages.
• https//www.web.virginia.edu/rescomp/ldb/swdb.asp
• 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
• Unix lab Cluster
• 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 Terabyte(TB) of
  storage local to cluster. Login to aspen.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,
  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/
• Information on nodes running, system load, usage,
  etc. http//lc0.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 Terabyte (TB) of
  storage local to cluster. 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
  ster/birch/
• Information on nodes running, system load, usage,
  etc. http//lc1.itc.virginia.edu/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. 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
  ster/cedar/
• Information on nodes running, system load, usage,
  etc. http//lc1.itc.virginia.edu/ganglia

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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
• Log into mplogin.itc and use PBSPro commands to
  submit jobs.
• 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
• Unix lab CPU usage page

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SGI Sun Clusters for remote login only

• 2 SGI O200 servers with 4 CPUs of 180Mhz R10000
  CPUs and 1.6 to 2 GB memory. Will soon be
  available under batch queue management system
  (PBS).
• 6 Sun Netras with 500Mhz Ultra IIe CPUs and 1GB
  (named orange1.unix to orange6.unix)

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Thinking of getting your own Linux Cluster?

• ITC purchasing another Linux cluster this year
  using Condo-Cluster model. (Cedar is last
  years condo cluster purchase.)
• Which 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 www.itc.virginia.edu/resea
  rch/itc-clusters/
• Interested? Next purchase window is NOW.
  Ordering in late January/February. 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

• Currently faculty, staff and students get 1
  Gigabyte (GB) by default! (Expanded September 1.)
• 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, Unix lab and
  HPC clusters
• Web interface 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 hours for files before they are deleted.
• Can be accessed from blue.unix, HPC clusters and
  Unix lab.
• No quota, however /bigtmp is only 2GB.

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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 14GB.
• Users request their required space by sending an
  e-mail to res-consult.
• longtmp can be accessed from blue.unix, Unix lab
  and HPC clusters.
• 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
• General purpose Unix cluster
• CPU limit of one hour for jobs
• Limited memory
• Being upgraded this winter to new hardware and
  only 3 nodes. IBM RS/6000s model p520, AIX 5.3
• 5 times faster than current blue.unix nodes.
  (waiting on fix from IBM on login issues.)

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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
  rates pending approval are about 35-45 per GB
  per year. 100 GB about 2,500-3,000/year.
  Includes daily backups, sys admin, restores, etc.
• 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).
• https//www.web.virginia.edu/rescomp/ldb/swdb.asp
• 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.ED
  U

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Upcoming Research Computing Colloquia

• at the ITC Research Computing Support Center,
• 244 Wilson Hall from 330 PM to 445 PM
• We give colloquia 2-3 times per month during fall
  and spring semester on variety of topics.
• The notes from these talks and previous ones are
  available on-line at http//www.itc.virginia.edu/
  research/talks

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ITC Research Computing Support

• Research Computing Support Center
• 244 Wilson Hall
• Phone [phone] F Fax [phone]
• E-Mail Res-Consult_at_Virginia.EDU
• http//www.itc.virginia.edu/researchers
• Thank you for your interest.
• Tim F. Jost Tolson
• 243-6592 tfjtolson_at_Virginia.EDU