Research Computing
From Research Computing
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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://www.gc.cuny.edu) of the City University of New York (http://www.cuny.edu).
The CUNY Graduate Center provides high-performance computational research facilities and associated support services to doctoral student and faculty researchers across the breadth of the City University of New York.
The Graduate Center hosts parallel computer clusters locally for computationally intensive research and instructional use, and in March 2008 joined the New York State Grid (NYSGrid) (http://www.nysgrid.org) and the Open Science Grid (http://www.opensciencegrid.org) to provide users with access to a highly advanced technological infrastructure supported by major public and private universities and colleges across the state.
Current users of the Graduate Center’s research computing resources include 45 CUNY doctoral faculty researchers in eight disciplines (biochemistry, biology, chemistry, computer science, engineering, finance, mathematics, and physics) from 7 CUNY campuses and over 100 doctoral student users from 8 CUNY campuses. A sampling reveals faculty and student research activities including artificial intelligence, combinatorial models of evolutionary processes, computational chemistry, computational linguistics, computational number theory, computational algebraic geometry, group theory, molecular dynamics, genetic algorithms for phylogenetic analysis, neural networks, photonics, fire dynamics, protein folding and molecular recognition, quantal density functional theory, spatial statistics and traffic simulation.
GC-specific resources
The Graduate Center’s research computing operation began in 1999 with the development of a parallel-Linux cluster. This system was expanded in 2000 to include dedicated research and instructional clusters providing high-end computational support to science and social science doctoral programs, particularly those that were campus-based. As of October 2009, the local research computing resources at the Graduate Center consist of 62 compute nodes, including 27 Intel Q9550 2.83 GHz quad-core compute nodes, equipped with 8 gigabytes of RAM and 500-gigabyte hard drives; 30 Intel E6600 2.4 GHz dual-core compute nodes, equipped with 8 gigabytes of RAM and 250-gigabyte hard drives; and Intel L5240 2.5 GHz dual processor quad core, with 64 gigabytes of RAM and 1 terabyte hard drives. Four terabytes of storage is available for user files.
Application software maintained by the research computing group includes:
* Gaussian 03 and Gaussian 09 (ab initio computational chemistry); * NAMD (NAnoscale Molecular Dynamics); * GAMESS (General Atomic and Molecular Electronic Structure System); * Parallel Mathematica; * Sage (an open source symbolic computation package); * NIST Fire Dynamics Simulator; * Emergent neural network simulator; * LEDA libraries (combinatorial computing); and * CPLEX (linear programming). * MATLAB
The Portland group C, C++, FORTRAN 77 and FORTRAN 90 compilers and the OpenMPI message passing libraries are available for parallel programming development, in addition to the standard GNU/Linux compilers and libraries. For social scientists, the computing resources for statistical computation include the Survey Documentation and Analysis system for Census Data for the Center for Urban Research and the R programming environment for statistical computing.
NYSGrid and the Open Science Grid
In March 2008, the Graduate Center became the twenty-first institution state-wide – and the first CUNY campus – to join the New York State Grid (NYSGrid) (http://www.nysgrid.org). NYSGrid was formed in 2006 when member institutions united to facilitate information and technology exchange, to develop an advanced technological infrastructure across the state, and to provide access to computational and data resources on a statewide grid basis. NYSGrid itself is a "virtual organization" within the Open Science Grid (http://www.opensciencegrid.org), a national, distributed computing grid for data-intensive research, supported by the National Science Foundation (http://www.nsf.gov) and the U.S. Department of Energy's Office of Science. These resources provide CUNY researchers with extraordinary access to high-performance computing facilities.
Research Computing Fellows
The CUNY Graduate Center currently supports three doctoral student Research Computing Fellowship recipients, who assist with the operation, management and design of the grid and with specialized applications. The Research Computing Fellows also fulfill critical roles as technical liaisons between the research computing resources and faculty and student grid users at the various campus sites. Research groups and departments may recommend their doctoral students for these fellowships as they become available. Resarch Computing fellows have gone on to apply their experiences at the Graduate Center in such work environments as Standard & Poor’s, Platform Computing and Google. Contact the Assistant Director for Research Computing (mailto:flengyel@gc.cuny.edu) for further information.
Note: starting to the 2009-2010 academic year, the Research Computing Technology Fellowship, which was sponsored through the Office of Academic Affairs from 2002 until 2009, became a Graduate Assistant A (GAA) appointment and was renamed the Research Computing Fellowship. See this link for details (http://research.gc.cuny.edu/wiki/index.php/Current_events#Research_Computing_Fellowships).
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." A bar graph illustrating the number of publications per year that cite the facilities is shown below.
The following publications acknowledge the Graduate Center's parallel computational facilities.
Singlet Oxygen Chemistry in Water. 2. Photoexcited Sensitizer Quenching by O2 at the Water-Porous Glass Interface Jovan Giaimuccio, Matibur Zamadar, David Aebisher, Gerald J. Meyer and Alexander Greer
J. Phys. Chem. B, 2008, 112 (49), pp 15646-15650 Abstract (http://pubs.acs.org/doi/abs/10.1021/jp807556x)
Analyses of Haplotype Inference Algorithms Sean Cleary and Katherine St. John. Far East Journal of Mathematical Sciences, 28:2, p 257-495, 2008. PDF (http://comet.lehman.cuny.edu/stjohn/research/farEast08.pdf)
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.
A Density Functional Theory Study of Vibrational Coupling in the Amide I Band of β-Sheet Models Raji Viswanathan and J. J. Dannenberg. J. Phys. Chem. B, 2008, 112 (16), pp 5199–5208. Abstract (http://pubs.acs.org/doi/abs/10.1021/jp8001004)
Amide I Vibrational Frequencies of α-Helical Peptides Based upon ONIOM and Density Functional Theory (DFT) Studies Robert Wieczorek and J. J. Dannenberg. J. Phys. Chem. B, 2008, 112 (4), pp 1320–1328
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
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)
Approximating Subtree Distances Between Phylogenies Maria Luisa Bonet, Katherine St. John, Ruchi Mahindru, and Nina Amenta. Journal of Computational Biology, 13(8): p 1419-1434, 2006. PDF (http://comet.lehman.cuny.edu/stjohn/research/jcb06.pdf)
Enthalpies of Hydrogen-Bonds in α-Helical Peptides. An ONIOM DFT/AM1 Study Robert Wieczorek and J. J. Dannenberg.
J. Am. Chem. Soc., 2005, 127 (42), pp 14534–14535
Abstract (http://pubs.acs.org/doi/abs/10.1021/ja053839t)
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)
Completely Geometrically Optimized DFT/ONIOM Triple-Helical Collagen-like Structures Containing the ProProGly, ProProAla, ProProDAla, and ProProDSer Triads Midas (I-Hsien) Tsai, Yujia Xu, and J. J. Dannenberg. J. Am. Chem. Soc., 2005, 127 (41), pp 14130–14131. Abstract (http://pubs.acs.org/doi/abs/10.1021/ja053768y)
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)
Dependence upon Basis Sets of trans Hydrogen-Bond 13C−15N 3-Bond and Other Scalar J-Couplings in Amide Dimers Used as Peptide Models. A Density Functional Theory Study Pedro Salvador and J. J. Dannenberg. J. Phys. Chem. B, 2004, 108 (39), pp 15370–15375. Abstract (http://pubs.acs.org/doi/abs/10.1021/jp0480955)
Molecular Orbital Calculations on the Protonation of Hydrogen-Bonded Formamide Chains. Implications for Peptides Sandy Moisan and J. J. Dannenberg. J. Phys. Chem. B, 2003, 107 (46), pp 12842–12846. Abstract (http://pubs.acs.org/doi/abs/10.1021/jp035791g)
Phenyl-Bridging in the 2-Phenylethyl Radical. A Molecular Orbital Study
Amparo Asensio‡ and J. J. Dannenberg. J. Org. Chem., 2001, 66 (18), pp 5996–5999. Abstract (http://pubs.acs.org/doi/abs/10.1021/jo0017483)
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
To be determined.
Research Computing Committee Meeting Minutes
Click on the link above for the archive of RCC minutes.
HPC facilities around CUNY
College of Staten Island HPC facility (http://www.csi.cuny.edu/cunyhpc/application.html)
Wildebeest cluster at CCNY (http://comet.lehman.cuny.edu/stjohn/research/wildebeest.html)
Scheduled Maintenance
Memorial Day software upgrades May 25, 2009
Note: the cur server was affected by a routine up2date. New SELinux rules interfered with the MySQL database, causing web sites to report database connection errors. This problem has been addressed.
Friday February 27, 2009 from 5PM to 9PM
- upgrade of the cluster network from 100mb/sec to 1Gb/sec.
- modification of the SGE port configuration
ALL JOBS WILL BE TERMINATED. We will do this as gracefully
as we can, by issuing a qdel -u all command at 5PM Friday
February 27, 2009. Graceful shutdowns will allow checkpointed jobs,
such as G03 geometry optimizations, to be resubmitted after the upgrade.
From now until next Friday, we recommend that users not run any new non-checkpointed jobs (such as frequency jobs) that are likely to terminate after Friday Feb 27th at 5PM--start jobs running longer than one week after the upgrade.
The following servers will be inaccessible during the upgrade:
- cunygrid.gc.cuny.edu
- neptune.gc.cuny.edu
- monad.gc.cuny.edu
- grid.gc.cuny.edu
We will send period reminders about the network upgrade. Other upgrades are planned in the future.
Inter-University Consortium for Political and Social Research
Click on the link above for information on the ICPSR. Dr Brian Schwartz is now the Official Representative.
Cyber Attack Pattern Recognition
Click on the link above for slides and other material.
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.
