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Research and Cluster Computing at SDSU

Research and Cluster Computing at SDSU. Summer, 2014 Division of Technology and Security University Networking and Research Computing (UNRC) Brian.Moore@sdstate.edu. 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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  1. Research and Cluster Computingat SDSU Summer, 2014 Division of Technology and Security University Networking and Research Computing (UNRC) Brian.Moore@sdstate.edu

  2. About UNRC Some information is available athttp://wiki.sdstate.edu/User:UNRC/UNRC(not all is up-to-date). Mailing list UNRC_RESEARCHCOMUTING@lists.sdstate.edu 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.

  3. SDSU Research Computing Support People—implementation Admin Building Rms. 119/117 Brian Moore x4679, SAD 117 Brian.Moore@SDSTATE.EDU user support, research computing, applications Alan Carter x5395, SAD 119 Alan.Carter@SDSTATE.EDU sysadmin SMP systems, SAS support Bryan Riegerx5799, SAD 117 Bryan.Rieger@SDSTATE.EDU sysadmin cluster, ANSYS, COMSOL support People—leadership/policies Mike Adelaine VP of Technology & Security Kevin Brandt Manager of UNRC Ryan KnutsenAssistant VP, Security

  4. 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.

  5. 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

  6. 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)

  7. 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

  8. 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 supportdesk@sdstate.edu ] 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 Bryan.Rieger@sdstate.edu.

  9. 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)

  10. Why Linux Command Line? DEC VAX 11/780 circa mid 1980s http://www.st-andrews.ac.uk/itsnew/newsletter/2005/01/historicalvax.html

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

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