Research Computing
From Research Computing
Overview
Welcome to The Graduate Center’s Research Computing Web Site, maintained by the Research Computing group at the Graduate School and University Center (http://inside.gc.cuny.edu) of the City University of New York (http://www.cuny.edu). This site, organized as a wiki (http://www.wikipedia.org), provides information on computational research facilities and services available to The Graduate Center community and CUNY-wide.
The Graduate Center hosts parallel clusters for computationally intensive research and instructional use. An experimental grid is available for software evaluation and testing. For social scientists, The Graduate Center research computing group maintains computing facilities for statistical computation, such as the Survey Documentation and Analysis system for Census Data (http://cur.gc.cuny.edu) for the Center for Urban Research (http://web.gc.cuny.edu/cur/). For the Sociology department, the research computing group hosts the journal Situations (http://www.radicalimagination.com), using the Open Journal Systems (http://www.pkp.ubc.ca/ojs/) journal management and publishing system, developed by the Public Knowledge Project (http://www.pkp.ubc.ca/about/what.html) at the University of British Columbia (http://www.ubc.ca/). More specific information is available below and through the services page (http://research.gc.cuny.edu/index.php/Research_Computing:Services).
Where can I find...?
Visit the Services (http://research.gc.cuny.edu/wiki/index.php/Research_Computing:Services) page for information on our service offerings, including: hardware and software facilities, how to gain access, our projects, who we are (http://research.gc.cuny.edu/wiki/index.php/Research_Computing:About), and our policies and procedures. Documentation for users and system administrators is also available.
Information about CUNY's federation membership in the ICPSR and the ICPSR Summer Program in Quantitative Methods of Social Research is given below.
For current events and research computing technology fellowship opportunities, click here (http://research.gc.cuny.edu/wiki/index.php/Current_events).
If you don't find something that should be here, or if you find something that shouldn't be here, contact the Assistant Director for Research Computing (http://mailhide.recaptcha.net/d?k=01q5B1PJPOMuUdcyvLgRqGnw==&c=DtNMMNDZw6457tsk2ivk40OcITofyVEd3y4J7FoLomI=).
Citations
Our facilities should be cited in published research and technical reports as, "the computational facility at the CUNY Graduate Center." The following publications acknowledge the Graduate Center's parallel computational facilities.
Quinones, Monoradicals and Diradicals From 3- and 4-Mercaptocatechol, and 3,4-Bismercaptocatechol: A Computational Study of a Plausibly Biomimetic Reaction. A. Castillo, J. F. Liebman, A. Greer J. Sulfur Chem. 2008, 29, 461-474.
Computational Studies of the Tropone Natural Products, Thiotropocin, Tropodithietic acid, and Troposulfenin. Significance of Thiocarbonyl-enol Tautomerism. E. M. Greer, D. Aebisher, A. Greer, R. Bentley. J. Org. Chem. 2008, 73, 280-283.
Genetic Algorithms for Optical Character Recognition. Joseph Svitak. CUNY Graduate Center Doctoral Dissertation, 2007.
A Theoretical Study of Large Planar [N]Phenylenes.
Jerome M. Schulman* and Raymond L. Disch.
Phys. Chem. A; 2007; 111 (39), 10010 -10014
Calculation of trans-Hydrogen-Bond 13C-15N Three-Bond and Other Scalar J-Couplings in Cooperative Peptide Models. A Density Functional Theory Study. Pedro Salvador, Nadya Kobko, Robert Wieczorek, and J. J. Dannenberg. J. Am. Chem. Soc.; 2004; 126(43) pp 14190 - 14197 Abstract (http://pubs.acs.org/cgi-bin/abstract.cgi/jacsat/2004/126/i43/abs/ja0492788.html)
Comparison of Fully Optimized 
-and 3 10-Helices with Extended 
-Strands. An ONIOM Density Functional Theory Study.
Robert Wieczorek and J. J. Dannenberg. J. Am. Chem. Soc.; 2004; 126(43) pp 14198 - 14205 Abstract (http://pubs.acs.org/cgi-bin/abstract.cgi/jacsat/2004/126/i43/abs/ja048831i.html)
Time-resolved ring structure of circularly polarized beams backscattered from forward scattering media. Kevin G. Phillips, Min Xu, S. K. Gayen, and R. R. Alfano, City College of New York. Optics Express; Vol. 13, No. 20; October 03, 2005; pp 7954 - 7969 Abstract (http://www.opticsexpress.org/abstract.cfm?URI=OPEX-13-20-7954)
Regioselective (Biomimetic) Synthesis of a Pentasulfane from ortho-Benzoquinone
David Aebisher, Edyta M. Brzostowska, Adaickapillai Mahendran, and Alexander Greer
J. Org. Chem.; 2007; 72(8) pp 2951 - 2955 Abstract (http://pubs.acs.org/cgi-bin/abstract.cgi/joceah/2007/72/i08/abs/jo062677w.html)
Planar Chirality due to a Polysulfur Ring in Natural Pentathiepin Cytotoxins. Implications of Planar Chirality for Enantiospecific Biosynthesis and Toxicity
Brzostowska, E. M.; Paulynice, M.; Bentley, R.; Greer, A.
Chem. Res. Toxicol.; (Article); 2007; 20(7); 1046-1052. Abstract (http://pubs.acs.org/cgi-bin/abstract.cgi/crtoec/2007/20/i07/abs/tx7000465.html)
Through Hydrogen-Bond Vibrational Coupling in Hydrogen-Bonding Chains of 4-Pyridones with Implications for Peptide Amide I Absorptions: Density Functional Theory Compared with Transition Dipole Coupling
Chen, Y.-f.; Viswanathan, R.; Dannenberg, J. J.
J. Phys. Chem. B.; (Article); 2007; 111(28); 8329-8334. Abstract (http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/2007/111/i28/abs/jp072624y.html)
Research Computing Committee
The Research Computing Committee meets periodically to discuss CUNY parallel cluster and grid computing resources for faculty-sponsored research and instruction, and to set the direction for further development.
Next scheduled meeting
The next Research Computing Committee meeting will take place on Tuesday, June 17th from 3:00 – 4:30pm in room 8402.
Research Computing Committee Meeting Minutes
Click on the link above for the archive of RCC minutes.
Scheduled Maintenance
On Memorial Day the Graduate Center will be upgrading the network. The computational clusters will be unavailable Monday, May 26, 2008.
New: Cambridge Structural Database Web
The Cambridge 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. See the research computing IsoStar web documentation (http://research.gc.cuny.edu/wiki/index.php/Research_Computing:Services#CUNY_Graduate_Center_Cambridge_Structural_Database_and_IsoStar_Web) for further information.
New: High Performance Computing Course
CUNY HPC - Research Computing - Short Course - Jan 21-25
A training course on the use of high performance computing in research will be conducted during the week of 21 January at the CUNY Graduate Center in Room 6418 at 365 5th Avenue and 34th Street, New York, NY.
Topics covered will include the following: Use of the CUNY HPC systems;FORTRAN and C Review; HPC Systems Architecture; MPI; Alternative programming models such as OpenMP, UPC (unified parallel C) and CAF; Application Examples; Visualization; and the future of HPC.
The training course will include hands on exercises on he CUNY HPC systems. Prerequisites include prior experience in UNIX/LINUX and familiarity with either Fortran or C. To register for the course, please send an email and include your contact information to HPCHelp@mail.csi.cuny.edu. A confirming email will be sent back to you.
Inter-University Consortium for Political and Social Research
Federation Membership
CUNY has a federation membership (http://www.icpsr.org/membership/federation.html) in the Inter-University Consortium for Political and Social Research (http://www.icpsr.org). The CUNY Federation consists of all CUNY campuses, which are called member institutions; these are listed here (http://www.icpsr.umich.edu/membership/feds.html#fed290). Currently, CUNY's ICPSR membership is paid for by the Central Office of Library Services (http://libraries.cuny.edu/lib-abou.htm). CUNY benefits from federated membership as follows. Since the CUNY Federation has more than six members, the ICPSR discounts the membership fee of each member by 20%. There are trade-offs by comparison with individual memberships: orders for off-line data (e.g., data CDs) must go through the so-called Federation Hub (the CUNY Graduate Center). While the travel stipend for the popular ICPSR Summer Program in Quantitative Methods of Social Research (see below) is reduced (and must be administered through the Graduate Center for participants from the CUNY federation campuses), CUNY faculty and students can register for 1/2 of the non-member price.
Official Representatives
Each member institution of the CUNY Federation appoints an Official Representative to assist faculty and students with ICPSR data set access and to serve as the campus liaison to the ICPSR. For convenience, the list of CUNY Federation campuses and official representatives is shown here (http://www.icpsr.umich.edu/membership/ors.html).
ICPSR Direct
The Graduate Center participates in the ICPSR Direct program (http://webapp.icpsr.umich.edu/cocoon/ICPSR-FAQ/0104.xml). Any user of the Graduate Center computer network may download ICPSR data without going through an Official Representative. Other campuses of the CUNY Federation also participate in the ICPSR Direct program; these campuses are listed above.
First time users of ICPSR Direct must register with the ICPSR by creating an account with the MyData user registration and authentication (http://webapp.icpsr.umich.edu/cocoon/ICPSR-FAQ/0044.xml) system. During a data download attempt through the ICPSR's web site, the user will be prompted either to log in as a returning user or to create a new account through the ICPSR's MyData user registration system. The user's "username" in this system is the user's email address; if the password for an existing account is needed, it can be requested online and sent to the user's email address.
Important notes about ICPSR Direct access
- Access is restricted to authorized networks. To access ICPSR downloads, you must be logged on to a machine with an IP address within the range recognized by the ICPSR; this means either: you are logged into a machine on your campus network (excluding internal private networks); or you are remotely connected to your campus network through a Virtual Private Network (VPN), your campus provides remote access via VPN and allows internet access to the ICPSR through this connection; or your campus provides a proxy server for this purpose. Please inquire with your local network administrator or computer help-desk concerning VPN or proxy access. We'll attempt to answer your questions about which alternative applies to your situation.
- Proxy server may prevent downloads of large data sets. Downloading large data sets through the ICPSR Direct service may fail if they are sufficiently large (over 30 megabytes) due to limitations of the Graduate Center's proxy server, which performs a virus scan of each scans file accessed through the web. The workaround for this problem is to configure your browser connection settings not to use the proxy server.
When requesting assistance, tell us whether you were accessing data from off campus, or on campus. Try to include as much technical detail as you can, so that we can better assist you.
Ordering Data Sets
Some data sets are available on CD or other off-line media. Requests for these must go through the CUNY Graduate Center (the CUNY Federation Hub).
ICPSR Summer Program in Quantitative Methods of Social Research
Each summer, the Graduate Center allocates, to students and faculty from the CUNY member institutions, a stipend for travel to the ICPSR Summer Program in Quantitative Methods of Social Research (http://www.icpsr.umich.edu/training/summer/index.html), which is held in Ann Arbor Michigan, and other locations. In the summer of 2004, a total of $2500 was allocated to five Summer Program participants from the CUNY Federation. We thank the ICPSR Summer Program Director, Henry Heitowit, for his assistance. In 2005, there were three participants from CUNY.
Procedure for obtaining the ICPSR Summer Program travel stipend
If you are a Ph.D. student or faculty at one of the CUNY campuses (currently, every campus is a CUNY Federation member institution) and you would like to receive a portion of the Summer Program travel stipend, contact the Assistant Director for Research Computing. The deadline to apply for the travel stipend for the 2007 ICPSR Summer Program in Quantitative Methods of Social Research is Monday, May 14th, 2007. Please include your home campus, your Ph.D. program and a valid email address.
That's all there is to it--we'll add your name to the list. Note: you must register with the ICPSR Summer Program in time to receive the travel stipend. If you do not register in time (usually the last Friday of April), the ICPSR will notify us and ask if we would like to increase the allocation to the other participants. If we hear from the ICPSR that you did not attend (which can happen if you asked to be considered for the stipend but you did not register), we'll attempt to contact you; if you do not attend, we will ask the ICPSR to reallocate your portion of the stipend.
More on applying to the ICPSR Summer Program
You should register online (https://www.icpsr.umich.edu/cgi-bin/SUMMER/gensummerapp.prl). Completed applications should reach the Summer Program by Friday, April 27, 2007. There are a few exceptions: see the ICPSR applications and admissions procedures (http://www.icpsr.umich.edu/sumprog/tuition.html#admission) for further details.
icpsr-l email list
The Graduate Center hosts an email list (icpsr-l@gc.listserv.cuny.edu) for ICPSR related announcements. CUNY Federation Official Representatives are added to the list as a matter of policy; the list is also open to interested CUNY faculty and students.
Graduate Center faculty and students who wish to access ICPSR data sets or who would like further information should contact Florian Lengyel, Assistant Director for Research Computing, at flengyel@gc.cuny.edu.
Data sets available at the Graduate Center (coming soon)
Occasionally we receive CD-ROMS from the ICPSR.
ICPSR CD ROM datasets ICPSR datasets on CD ROM available from the Graduate Center to CUNY faculty and students.
For Research Computing Wiki contributors and administrators
Wiki Editing
Wiki Markup A no-frills crash course in the simplified wiki markup syntax.
The Wikipedia's How to edit a page (http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page) The definitive source for the wiki syntax connoisseur.
The Wikipedia's Manual of Style (http://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style) Mastery of wiki syntax leads to the larger question of style.
Wiki Configuration
Please see documentation on customizing the interface (http://meta.wikipedia.org/wiki/MediaWiki_i18n) and the User's Guide (http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide) for usage and configuration help.
