The DNA and Natural Algorithms Group:

All system-wide information should be here. Comments should be added for *where* it is, how one might start using it, etc. Should we restrict access to within Caltech? The system administrators for the Moore building (Dimitris Sakellariou, Naveed Neer-Ansari, and Michael Potter) are responsible for keeping our computer cluster purring along. Please email help@ee.caltech.edu if you notice anything broken. They also do software installs in a way that maintains all our machines in an equivalent state.

• Cluster set-up (note: other information can be found in /home/cluster_info)
  • Software is installed in /software/bin and /research/bin. These should be in your path. See this file for instructions on how to do this yourself, if you have "sudo" permission.
  • These web pages are in /home/www/html on centrosome (also linked from /research/public_html and /www on selected machines). Anyone in the group dnausers should be able to edit these files: in fact, it is your responsibility as a lab member to do so appropriately.
  • There is a CVS directory in /research/CVS. See Joseph Schaeffer's CVS help file (cvsdoc text file; cvsdoc.ps) for instructions on how to use CVS to coordinate research projects. Also see on-line help, e.g. CVShome.
  • Migrating to Red Hat Linux 8.0 in summer 2003, we are adopting the OpenMosix distributed cluster architecture -- which means processes can (and just do!) migrate around and use all the available CPU cycles. "top" now tells you all the processes running on the cluster; "openmosixview" is a more extensive GUI. More information can be found on the web site; try "man openmosix" for helpful commands controlling process migration (at the end of the man page).
• Email lists on the DNA cluster
  • announce@dna
    announcements such as interesting talks, group meetings, this includes "interested parties", Hideo's group, Niles' group, other people who request to be on the list, past members. Here is a list of people on announce.
  • lab@dna
    people who work in the lab now. lab policy, new instruments or orders. Here is a list of people on lab.
  • accounts@dna
    everyone who has an account on our cluster, including the system administrators. Here is a list of people on accounts.
  • sysadmin@dna
    This includes both the Moore building system administrators, as well as DNA lab people with sysadmin privileges. Here is a list of people on sysadmin.
  • webmaster@dna
    People mainting the website. List..
• Email lists around campus that you may want to subscribe to:
  • CNS-interest : to subscribe or unsubscribe, email Heather Hein at hhein@magica.systems.caltech.edu
  • the CS mailing list (cs-dept) to subscribe or unscribe, email Jeri Chittum at jeri@cs.caltech.edu
  • be-seminar -- Bioengineering seminar subjects and times
  • sysnet-seminar -- Computer science seminar subjects and times
  • biomail -- Biology department seminars, including biolunch
  • The last three lists can be joined using the Caltech mailing list server.
    To subscribe to Caltech mailing list "foo", send mail to majordomo@caltech.edu with body "subscribe foo".
    To unsubscribe from Caltech mailing list "foo", send mail to majordomo@caltech.edu with body "unsubscribe foo"
  • other lists?
  • Printers available
    • HP 4550 color laser printer: in the printer room on a network spooler, available on Linux as -Pcolor with continuations "d" for duplex, "d2" for duplex 2 pages/sheet, "2" for 2 pages/sheet single-sided, and "t" for transparencies. E.g. -Pcolord is the default. Print drivers: Windows NT4, Windows 2000, Windows XP, and MacOS.
    • Samsung 7050 B/W laser: in the library, on a network spooler, available on Linux as -Psamsunghid, samsunghi, samsungd, samsung, where "hi" is higher-resolution, "d" is duplex. The printer itself should always be set in "duplex long" mode.
    • Epson 777 color inkjet: on the SPEX computer only. (BTW: thank Hideo for this present!)
    • HP 990sce color inkjet: on AFM computer only (temporarily disconnected)
    • HP 630?? color inkjet: on AVIV computer only.
    • More printer information is here.
  • Accounts on other machines
  • For accounts on the CS & UGCS cluster, use this form, and enter that the justification is that you are in my lab, and mention that you should be in the "bio" group (for Unix).
  • Note that the CS cluster has a compute grid server.
  
  Nucleotide Machine Status
  • Necleotide1 - online
  • Necleotide2 - online
  • Necleotide3 - online
  • Necleotide4 - online
  • Necleotide5 - online
  • Necleotide6 - online
  • Necleotide7 - offline
  • Necleotide8 - online
  • Necleotide9 - online
  • Necleotide10 - offline
  • Necleotide11 - online
  • Necleotide12 - online
  • Necleotide13 - online
  • Necleotide14 - online
  • Necleotide15 - online - possible memory problems - swap_free: Bad swap offset entry
  • Necleotide16 - online

  Erik Winfree, 1/2/02

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