Research and cluster computing at sdsu
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Research and Cluster Computing at SDSU. Summer, 2014 Division of Technology and Security University Networking and Research Computing (UNRC) [email protected] About UNRC. Some information is available at http://wiki.sdstate.edu/User:UNRC/UNRC (not all is up-to-date).

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Research and Cluster Computing at SDSU

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Research and cluster computing at sdsu

Research and Cluster Computingat SDSU

Summer, 2014

Division of Technology and Security

University Networking and Research Computing (UNRC)

[email protected]


About unrc

About UNRC

Some information is available athttp://wiki.sdstate.edu/User:UNRC/UNRC(not all is up-to-date).

Mailing list [email protected]

New users should be automatically added. Each message has an unsubscribe link. Go to http://lists.sdstate.edu/scripts to view list, re-subscribe, etc.


Sdsu research computing support

SDSU Research Computing Support

People—implementation Admin Building Rms. 119/117

Brian Moore x4679, SAD 117 [email protected]

user support, research computing, applications

Alan Carter x5395, SAD 119 [email protected]

sysadmin SMP systems, SAS support

Bryan Riegerx5799, SAD 117 [email protected]

sysadmin cluster, ANSYS, COMSOL support

People—leadership/policies

Mike Adelaine VP of Technology & Security

Kevin Brandt Manager of UNRC

Ryan KnutsenAssistant VP, Security


Main research cluster bigjack

Main research cluster: “bigjack”

  • bigjack

    • IBM IdataPlex, IBM DX350 M3 nodes, 71 nodes

    • Each node: 12 cores, two hex-core Intel Xeon X5670 (Westmere), 2.93 GHz

    • 48 GB RAM on each node (a few with 96 GB)

    • Infiniband – high speed low latency interconnect – to each node, as well as gigabit ethernet

    • Nine nodes have dual GPU: Nvidia Tesla 2090 series

    • SLES 11.1 operating system

    • SAN storage allows flexible deployment of large partitions to head node

      Three nodes for interactive use:

      bigjack—for submission to nodes via Moab/PBS scheduler

      kojack—for visualization

      flapjack—general interactive use and GPU development/compile

      All three interactive nodes share same credentials and storage.


Also available special project smp servers

Also available: special project SMP servers

  • silvertip

    • IBM x3755, 24 cores, four hex-core AMD 8435, 2.6 GHz

    • 128GB RAM, OpenSUSE

  • silvertip2 and silvertip3

    • IBM x3755 M3's, 64 cores, four 16 core AMD 6282SE,2.6GHz

    • 512 GB RAM, OpenSUSE/SLES

  • yeti

    • HP Z820 workstation, 16 cores, two 8 core Intel Xeon E5-2690, 2.90 GHz

    • 256 GB RAM, SLED 11.2

    • Main use is CLC Genomics Workbench

  • sasquatch

    • HP Z820 workstation, 16 cores, two 8 core Intel Xeon E5-2690, 2.90 GHz

    • Two Nvidia Tesla 2050 GPUs

    • 128 GB RAM, SLED 11.2

    • GPU development, Virtual Machines


Some software examples main theme all linux unix

Some software examplesmain theme—all Linux/UNIX

  • ANSYS

  • BLAST (and related)

  • CLC Workbench

  • COMSOL

  • Gaussian

  • MATLAB

  • MERLIN

  • NAMD

  • NWCHEM

  • PETSc

  • R

  • SAS

  • SPSS

  • CPMD

  • ESRI

  • ERDAS

  • Compilers (gcc/gfortran, pgi, IBM XL)


Getting connected logged on

Getting connected, logged on

  • Access software—Windows

    • PuTTY (http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html)

    • WinSCP (http://winscp.net)

    • VNC (http://www.realvnc.com/download/viewer/)

  • Mac: Terminal App and FileZilla (or similar)

  • Linux: Terminal and file manager, Nautilus (or similar)

  • All UNRC servers are behind campus firewall—no direct incoming network connections from outside allowed


Getting connected logging in

Getting connected, logging in

~5 min; make a few attempts; Connect to SDSUFacStaff wireless

[For wireless laptop general connection issues, you can bring laptop to Support Desk, 131 Admin. Building (SAD), or call 688-6776, or email [email protected] ]

In your terminal program (PuTTY, Mac Terminal) first connect to

flapjack (or bigjack.jacks.local). General use/GPU

Server account/login/password questions on cluster systems: contact me or Bryan Rieger, x5799 [email protected]


Change your password

Change your password

  • passwdon the command lineFirst prompts you for old passwordthen prompts for a new oneconfirmation

  • USE STRONG PASSWORDS!Several characters (8 at least)Include a numberUpper and lower case both usedSpecial characters

  • Note: UNIX is case sensitive! (test is not same as Test)


Why linux command line

Why Linux Command Line?

DEC VAX 11/780 circa mid 1980s

http://www.st-andrews.ac.uk/itsnew/newsletter/2005/01/historicalvax.html


Research and cluster computing at sdsu

https://www.tacc.utexas.edu/user-services/training/course-materials


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