Research Computing

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Research Computing

• Lecture 6
• BINF 5230
• Spring 2005

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GCG The University runs a Sun
Microsystems SunFire F6800 computer in support of
its major sequence analysis package. Access to
the Scientific Server - gcgserver.umdnj.edu
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Interfaces Three interfaces are available for the
Wisconsin .
Package

SeqLab the command-line interfaces come
with the Package SeqWeb is licensed separately.
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SeqLab interface GCG calculations in SHRP UMDNJ
Computer Account You must have an active umdnj
account Student ID Card access to Rm 927 You
have 24-7 access to computer lab/building. You
can use High Speed Internet access from home
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What is available to us?

• Computer Labs
• SHRP 9th FL
• SHRP 2nd FL
• UMDNJ
• Academic Computing Services (ACS)
• Campus Computer Labs

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Computer Labs have SGI workstations and
PCs Newark Campus Piscataway Campus
Each Campus has its own Server.
Our accounts are from Newark Campus Server
njmsa.umdnj.edu Login/Password Piscataway
Server rwja.umdnj.edu
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UMDNJ Unix Workstations

• SHRP 9th FL
• 
  3 SGIs
• 2 Suns
• 5 HPs

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UMDNJ Unix Workstations

• workstation names.umdnj.edu
• SHRP
• 9th Fl
• octane-1, octane-2, octane-3 SGI
• u60-1, u60-2 SUN
• xt1shrp-nwk,...,xt5shrp-nwk HP

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Unix 9th FL SSB Computer lab

• SGI PC PC
• Door
• Sun HP HP Sun
• SGI HP HP SGI
• HP

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Starting GCG from SHRP HPs

• On HP X-Windows workstations
• Log in at main log on screen
  (username, password)
• Once the terminal window opens,
  type the following
  echo
  DISPLAY and press Enter
• Screen for example, xt1shrp-nwk0
• Now type
  ssh X
  gcgserver.umdnj.edu press Enter
• Type
  export DISPLAY xt1shrp-nwk0

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Starting GCG from SHRP 9th Fl SGI

• On SGI workstations
• Log in at main log on screen
  (username, password)
• use username students
• Start iris-ansi terminal by clicking Desktop -
  Open Unix Shell.
• ssh X l xxxxx gcgserver.umdnj.edu
• xxxxx is your umdnj account
• Type echo DISPLAY response octane-10
• export DISPLAY octane-10
• octane-1 or octane-2.umdnj.edu0.0

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Starting GCG from SHRP 9th Fl Sun

• On Sun workstations
• Click Optins - Remote Login - Enter
  Host Name
• Use njmsa (.umdnj.edu) as host name
• Type ssh X gcgserver.umdnj.edu

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gcg
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XFree86 on PC
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SeqLab requires an X Windows display, such as an
X server running on a PC or Macintosh, an X
terminal, or a workstation that runs X Windows.
SeqLab's pull-down menus let you choose
programs
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When you select a program from a pull-down menu,
a separate window specific for that program
appears.
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Typical Scenario

Each program requires specific information to run
successfully. You answer questions with a YES or
NO or fill in a number or
letter from a menu or
simply press ltEntergt. Most programs have fewer
than six prompts. This
design allows you to concentrate on the analysis
that interests you without having to sift through
many program modifiers each time you run the
program.
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http//markchiang.no-ip.com/gcg/gcg.ppt
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Click Quick connect
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Click Quick connect
? Click