Research Computing:Services
From Research Computing
Intro
This page links to other pages which describe our hardware and software facilities, how to gain access, research computing projects, who we are, and our policies and procedures.
How to gain access
How to apply for a computational cluster account
How to obtain a Research Computing Wiki account
Getting Help
"Who you gonna call? Ghostbusters!"
If you are new to the computational cluster
If you're new to the computational cluster, see the sections on the computational cluster (http://research.gc.cuny.edu/wiki/index.php/Research_Computing:Services#Computational_Clusters) and the section on SUN Grid Engine Documentation (http://research.gc.cuny.edu/wiki/index.php/Research_Computing:Services#SUN_Grid_Engine_Documentation) for information on submitting and monitoring jobs using the SGE job manager.
If you are new to Linux
We can suggest a few online tutorials. The Quick Linux Tutorial (http://www.fsid.cvut.cz/cz/U201/LINUX.HTML) covers basic commands for interacting with a Linux System. A more comprehensive series of tutorials is available from Dr. Bob's Lowfat Linux (http://lowfatlinux.com/) site.
If something isn't working
If an online trouble isn't covered online, write to the Assistant Director for Research Computing (mailto:flengyel@gc.cuny.edu). If a trouble cannot be resolved immediately, we may create a trouble ticket and assign the task of resolving it to a member of our group. How to report a trouble
Projects
Our projects include development and support of high-performance computational clusters and grids, and open source LAMP technology web sites.
The CUNY Grid Project
The CUNY Grid has been upgraded to the Globus Toolkit 4.0.5 (http://www.globus.org) on m248.gc.cuny.edu and on wildebeest.ccny.cuny.edu. We currently have gridftp, Reliable file transfer, GRAM and the SGE job manager adapters installed. Coming soon: the gridway (http://www.gridway.org) multi-cluster scheduler.
LAMP Web Sites
LAMP (http://www.onlamp.com/) is an acronym for Linux (http://www.linux.org/) Apache (http://www.apache.org/) MySQL (http://www.mysql.com/) PHP (http://www.php.net/)/PERL (http://www.perl.org/)/Python (http://www.python.org/). Research computing implemented the Graduate Center's first LAMP (http://www.onlamp.com/) web sites in April, 2005 CE (http://www.radix.net/~dglenn/defs/ce.html). LAMP technology is an open source alternative to proprietary operating systems and applications.
CUR Center for Urban Research
Research computing provides administration and assistance for several Center for Urban Research sites.
Online Analysis of Census Data
Survey Documentation and Analysis of Census Data (http://cur.gc.cuny.edu) The site currently has the NYC Public Urban Microdata Survey for the year 2000 census. US Census data coming soon!
Urban Research Wiki
Urban Research (http://urbanresearch.gc.cuny.edu)
OASIS NYC
Oasis NYC (http://oasisnyc.gc.cuny.edu) Maintained by the CUNY Mapping Service
Research Computing Wiki
Research Computing Web (http://research.gc.cuny.edu). The site you are viewing is implemented with the open source code wiki engine MediaWiki (http://wikipedia.sourceforge.net/).
New Media Lab sites.
Moodle
Moodle: open source course management (http://moodle.gc.cuny.edu) Moodle (http://www.moodle.org) is a popular open source alternative to course management systems such as Blackboard.
Center for Media and Learning
Sites from the Center for Media and Learning and the New Media Lab are running on now running on the Graduate Center's LAMP servers; previously these were hosted at CIS 57th Street. The sites are:
Virtual New York (http://www.vny.cuny.edu/)
The American Social History Project (http://ashp.cuny.edu)
The New Media Lab (http://nml.cuny.edu)
The Lost Museum (http://lostmuseum.cuny.edu)
The Forever Free Project (http://www.foreverfreeproject.org)
CUNY Wired (http://cunywired.cuny.edu)
Thanks to Andre Pitanga of the New Media Lab for transferring the sites.
Online Journals
The following sites are implemented with the Open Journal Systems (http://www.pkp.ubc.ca/ojs/) journal management and publishing system. We are grateful to Patrick Inglis of the CUNY Graduate Center Ph.D. Program in Sociology, and to John Willinsky and Alec Smecher of Open Journal Systems for technical assistance.
Situations
Situations: Project of the Radical Imagination (http://www.radicalimagination.com) has been online since April 2005.
Music in Gotham
Music in Gotham : A Century of Composing in America: 1820-1920 (http://ojs.gc.cuny.edu/index.php/MusicInGotham) is expected to go online during the Fall 2005 semester.
Performance and Spiritual Movements
Performance and Spiritual Movements (http://ojs.gc.cuny.edu/index.php/PerformanceAndSpiritualMovements) Coming soon. For further information see the Performance and Spiritual Movements web page (http://www.newmedialab.cuny.edu/PSM/index.html).
LLJournal
LLJournal (http://lljournal.gc.cuny.edu) LL is an online journal dedicated to the promotion of research related to the Hispanic and Luso-Brazilian worlds. Our publication seeks to be a multidisciplinary forum highlighting quality contributions in all relevant fields of study.
Aurora
Aurora (http://aurora.gc.cuny.edu) is the online graduate journal of philosophy at the Graduate Center of the City University of New York. The aim of the journal is to publish high quality papers by philosophers starting their career. In so doing, the journal promotes serious academic work within the international postgraduate community. Aurora welcomes work by postgraduate students in any area of philosophy, in an analytic style, broadly construed. Papers submitted will be reviewed by faculty members of the Graduate Center.
Your online open access journal here
For information on hosting and managing your online academic journal under the Graduate Center's OJS system (http://ojs.gc.cuny.edu), contact the Vice President for Information Technology and External Programs or the Assistant Director for Research Computing at the CUNY Graduate Center.
GC Research Computing: ridding the world of copyright monopolists, one open access journal at a time. Free The Journals (http://www.dklevine.com/general/intellectual/oajournals.htm)!
Interactive Technology Certificate Program
The Graduate Center's Interactive Technology Certificate Program has four LAMP sites: The blogs are implemented in Wordpress; the wiki uses Mediawiki.
ITCP blog (http://itcp.gc.cuny.edu)
ITCP blog for CORE 1 course (http://itcp.gc.cuny.edu/core1)
ITCP blog for CORE 2 course (http://itcp.gc.cuny.edu/core2)
ITCP Wiki (http://itcp.gc.cuny.edu/wiki)
The ITCP sites are currently under development.
Math Wiki
The Mathematics Wiki (http://mathwiki.gc.cuny.edu) is live. Local SELinux policy modifications were needed for Wikitex.
Project Stretch
Research computing supports three sites for Project Stretch:
Project Stretch Moodle (http://stretchmoodle.gc.cuny.edu) An implementation of Moodle, an Open Source course management system, for Project Stretch.
Project Stretch Wiki (http://stretchwiki.gc.cuny.edu) A Wikipedia style wiki for Project Stretch.
Project Stretch Blog (http://stretchmoodle.gc.cuny.edu/blog) A Wordpress (http://www.wordpress.org) Blog for Project STretch.
Research Computing Request Tracker
In February 2006, Research Computing implemented a professional ticketing system on an old 500 MHz DELL 2450 using the freely available open source software Request Tracker v 3.4.5 (http://www.bestpractical.com/rt/), Apache 1.13.34 with mod_perl version 1.29, MySQL version 4.024. and PERL 5.8.7; all running under the free Debian 3.1 Linux operating system (stable release "Sarge"). In April 2008, the Request Tracker was upgraded to version 3.6 and moved to a Red Hat Enterprise Linux server.
Women's Studies CUNY-wide
Women's Studies Blog (http://womenstudies-cunywide.gc.cuny.edu/) Events of the women’s centers and programs of the City University of New York.
The Graduate Center User Support Wiki
GC user support (http://support.gc.cuny.edu) This wiki provides technical support articles for Students, Faculty and Staff at The Graduate Center, CUNY.
Spanish Ph.D. Program Wiki and blog
Hlbll wiki (http://hlbll.gc.cuny.edu)
Hlbll blog (http://hlbll.gc.cuny.edu/blog)
Open Source Statistics
Research computing supports the open source statistical computing environment R (see the R Project (http://www.r-project.org/) website). To facilitate the import into the R system of SPSS syntax files for data in text format, we have available PSPP (http://www.gnu.org/software/pspp/) version 0.4.0, an open source clone of SPSS. Although PSPP provides a limited subset of the full SPSS functionality, it enables the conversion of an SPSS syntax file with text data to SPSS binary format, which can then be imported into R using the foreign library. This software is available on monad.gc.cuny.edu.
For further details on importing SPSS syntax data into R under Linux, please see the following link. The example illustrates the process with a dataset obtained from the ICPSR (http://www.icpsr.org).
Importing SPSS syntax data files into R under Linux using PSPP
Science and the Arts Blog
Science and the Arts Blog (http://sciart.gc.cuny.edu) Science & the Arts presents programs in theatre, art, music, dance and film that bridge the worlds of art and science. Since 2001, The Graduate Center's Science and the Arts program has presented over 85 public events, ranging from conferences and concerts to science demonstrations on the streets of New York.
Doctoral Students Council Wiki
The CUNY Doctoral Students Council blog is available at http://www.cunydsc.org
CUNY Graduate Center Cambridge Structural Database and IsoStar Web
The Cambrdige Structural Database IsoStar system is now available on the web to authorized users at http://isostar.gc.cuny.edu. SSH access to the X Windows program Mogul is also enabled. Please contact the Assistant Director for Research Computing at the CUNY Graduate Center for an account and for assistance. If you already have a cluster account, you may use this to access the IsoStar web.
IsoStar Users
IsoStar users should download the IsoStar client software for local installation from http://isostar.gc.cuny.edu. Install the IsoStar client for your operating system only. Windows users should download the install program and run it. MIME file type associations (for the chemical/x-isostar MIME filetype) will work automatically with Microsoft Internet Explorer 7 and Firefox under Windows. Linux users will have to configure their browsers to recognize the ISTR MIME type so that the run_isostar program will be invoked when an ISTR file is downloaded from IsoStar; see below.
Running the Linux IsoStar Client under Firefox
Unzip the file isostar_client.tar.gz in a convenient location (in this example, /home/mydir). When you download an istar file from an IsoStar web page, your Firefox will prompt you to ask how to handle ISTR (chemical/x-isostar MIME type) files. Firefox will open a dialog box prompting you to tell it what to do with ISTR files. Select Open with and Browse to /home/mydir/isostar/bin/run_isostar. Also, check "Do this automatically for files like this from now on."
Mogul, Mercury and ConQuest Users
Use an SSH client with X-windows tunneling enabled. For example, from the Linux command line, use the command
ssh -X yourusername@isostar.gc.cuny.edu
to gain access. Windows users will need an SSH client with X-Windows tunneling enabled, as well as an X-Windows emulation program. First-time users will be prompted for the site number and the confirmation number; these numbers are displayed in the ssh login screen. The Cambridge Structural Database is installed under /usr/local/cambridge on the isostar.gc.cuny.edu machine. Your path on that machine includes the CSD binaries.
Computational Clusters
The CUNY Graduate Center supports three parallel LINUX clusters for use by the Graduate Center community: a research cluster for faculty and faculty sponsored research; an instructional cluster for classroom use; and an experimental grid, used to test software for the research and instructional clusters and for the CUNY Grid Project.
Software
Operating systems: 64-bit compute nodes: Open SuSE10. All compute nodes will be migrated to this OS
File servers: Red Hat Enterprise Linux 5 AS Hat (some compute nodes and file server);
LINUX 9.0 (monad.gc.cuny.edu) to be upgraded Spring 2008
Software development: Portland Group Cluster Development Kit (CDK), versions 6.2-1, 7.0 and 7.0-3. This includes C, C++ and FORTRAN compilers.
Computational chemistry: Gaussian 03 (http://www.gaussian.com) version d.02
X-windows emulation: Starnet XWin32 X-emulation software and SSH, SFTP clients for classroom use
Job submission and control software: Sun Microsystems Sun Grid Engine version 6.0u10. The research and instructional clusters run under the control of a single queue master. The SGE instation uses a reduced NFS usage design, in which the configuration directory $SGE_ROOT/default/common is exported to all hosts.
Grid middleware: Globus Toolkit version 4.0.5. The City College of New York, and the College of Staten Island have SGE clusters connected to ours via a PIX 501 firewall/VPN concentrators.
Special purpose libraries: MPI-CH, LAPACK Libraries, BLAS Libraries, FFW, VLISP and others.
Research cluster: monad.gc.cuny.edu
Doctoral faculty and faculty sponsored doctoral students may use this cluster for their research.
Job submission host
Dell Poweredge 4400 Server with dual 731 MHz Pentium 3 CPUs, 1 gigabyte of RAM, and 50 gigabytes RAID storage. There is an attached NAS with an additional 50 gigabytes of storage.
Execution Hosts
30 Dual 933 MHz Pentium 3 Dell 1550’s, with 1 gigabyte of RAM and 20 gigabytes of disk storage. These are interconnected by a 100/Mb/s Ethernet switch.
30 Core Duo E6600 processors (dual core) with 8GB memory, Intel DG965RYCK motherboards, and 250GB SATA hard drives.
9 Pentium 4 2.6 GHZ CPU, 533 MHz Bus, Intel 875P Chipset motherboard, an 80 gigabyte hard drive and two 512 megabyte PC3200, DDR 400 memory modules for a total of 1 gigabytes of RAM.
The P4 and E6600 systems have internal gigabit NICS and are interconnected to a pair of 24 port gigabit switches; the gigabit switches are connected to the 100/Mb/s Ethernet switch as well.
Instructional cluster
Graduate Center instructors may request access to the Linux cluster for their courses. Pentium III nodes are allocated from the research cluster as needed for instruction.
External cluster: wildebeest.cuny.edu
Dual Pentium(tm) Pro @ 1666.761 MHz , Memory 3669504k with 20G HD, runnnig Linux 2.4.20-6smp kernel
Research Computing Policies
Operational Policies Our policy is to go public with our policies.
Research Computing policy on guest system administrators
Account policy (http://research.gc.cuny.edu/wiki/index.php/Account_policy)
SUN Grid Engine Documentation
Submitting MPICH jobs to the Sun Grid Engine
MPICH software installations and programming hacks
Submitting single-threaded Gaussian 03 jobs to the Sun Grid Engine
Instructional cluster: submitting gaussian jobs with gsub
Submitting parallel Gaussian 03/Linda jobs to the Sun Grid Engine
Submitting array jobs to the Sun Grid Engine
System Documentation
SGE mpich parallel execution environment (SGE 5.3p6)
SGE gauss parallel execution environment for Gaussian 03 with Linda (SGE 5.3p6)
SGE queue configuration This is updated and simplified to reflect the upgrade to SGE version 6.07u.
Globus 2.4 configuration Retained for details on configuration of the certificate authority (though this is better covered in the globus 4.x documentation).
Parallel Gaussian, util.so and LD_LIBRARY_PATH
Ganglia installation and configuration
System Administration Notes
Some of our adventures in system administration are recorded here (not including confidential system details).
Amanda configuration notes for the Spectra Logic 2K
A step by step tutorial on AMANDA (http://fedoranews.org/ghenry/amanda/) Note the step on editing /etc/xinetd/amanda.
Amanda cheat sheet (http://www.mast.queensu.ca/~mastop/service.catalogue/backup/cheat-sheet.html) This will be adapted for our site.
Notes on Disaster Recovery A work in progress.
Brute force SSH attacks (http://www.whitedust.net/article/27/Recent%20SSH%20Brute-Force%20Attacks/) Article on a common attack on Linux systems.
Unlocking a Digital UNIX account Worth a small fortune in consulting fees.
Software RAID for RDHCP server
Load balancing by bonding interfaces
Triple boot Knoppix CentOS Windows
Research Computing Committee
Minutes of the Feb 7 2005 Meeting of the Research Computing Committee
Tech Fellows
External Links
Who we are
See About Research Computing (http://research.gc.cuny.edu/wiki/index.php/Research_Computing:About).
