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17 October 2022
- 17:3317:33, 17 October 2022 diff hist −724 GAUSSIAN09 No edit summary current Tag: Visual edit
- 17:3217:32, 17 October 2022 diff hist +9,789 N GAUSSIAN09 Created page with "GAUSSIAN09 As a commercially license application, running Gaussian09 at the CUNY HPC Center comes with some restrictions 1. A Gaussian09 job can only run in parallel within a single-node at CUNY. 2. Gaussian09 users must comply with the licensing and citation requirements of Gaussian, Inc. The following citation must be included in publications that relied on Gaussian 09 computations at the CUNY HPC Center. Gaussian [03,09], Revision C.02, M. J. Frisch, G..."
- 17:3217:32, 17 October 2022 diff hist +2,589 N GAMESS-US Created page with "The program is installed on PENZIAS. Before run the program please load the proper module file: <pre> module load gamess-us </pre> Below is a simple test input file named '''test_1.inp''' for GAMESS: <pre> ! test_1 ! 1-A-1 CH2 RHF geometry optimization using GAMESS. ! ! Although internal coordinates are used (COORD=ZMAT), ! the optimization is done in Cartesian space (NZVAR=0). ! This run uses a criterion (OPTTOL) on the gradient ! which is tighter th..." current Tag: Visual edit: Switched
- 17:3117:31, 17 October 2022 diff hist +370 Data Transfers Table current Tag: Visual edit
- 17:2817:28, 17 October 2022 diff hist +1,370 N Data Transfers Created page with "The Center has deployed Data Transfer Nodes (DTN), which are servers dedicated to transfer data between remote sites and the DSMS (/global/u/<userid>), or between remote sites and the /scratch/<userid> on the designated HPC system on which the user has an account. DTNs are tuned to transfer data efficiently. There are three methods of transferring data between the CUNY HPC systems and the rest of the world: :• '''Globus Online''': The preferred method for large file..."
- 17:2817:28, 17 October 2022 diff hist +2,425 N BPP2 Created page with "At the CUNY HPC Center BPP2 is installed on Andy and Penzias. BPP2 is a serial code that takes its input from a simple text file provided on the command line. Below is an example SLURM script that will run the fence lizard test case provided with the distribution archive (/share/apps/bpp2/default/examples). To include all required environmental variables and the path to the BPP2 executable run the modules load command (the modules utility is discussed in detail above)..."
- 17:2717:27, 17 October 2022 diff hist +11,577 N BEAST Created page with "Currently, BEAST is installed on ANDY and PENZIAS at the CUNY HPC Center, BEAST is a serial program, but can also be run in parallel with the help of a companion library (BEAGLE) on systems with Graphics Processing Units (GPUs). PENZIAS supports GPU processing using NVIDIA Kepler GPUs and the BEAGLE 1.0 and 2.0 GPU libraries have been installed there for this purpose. (NOTE: GPU processing on ANDY has been eliminated as the FERMI GPUs their have reached end-of-life.) BE..."
- 17:2717:27, 17 October 2022 diff hist +2,204 N AUGUSTUS Created page with "Augustus is available on Karle, users must load the module by typing: <pre> module load augustus/[current-version] </pre> The current version can be found in /share/usr/augustus. More detailed information about AUGUSTUS capabilities along with data sets can be found on AUGUSTUS web page: <pre> http://bioinf.uni-greifswald.de/augustus/ </pre> When used in research the AUGUSTUS must be cited with appropriate paper from the following list: <pre> Oliver Keller, Martin K..." current
- 17:2717:27, 17 October 2022 diff hist +9,055 N Applications Environment/itasser Created page with "<h1><b>I-TASSER</b></h1> <br> __TOC__ <br> <font color=red><b>Description:</b></font color> <b><i>I-Tasser</i></b> is a platform for protein structure and function predictions. 3D models are built based on multiple-threading alignments by <strong>LOMETS</strong> and iterative template fragment assembly simulations; function inslights are derived by matching the 3D models with <strong>BioLiP</strong> protein function database. <font color=red><b>Additional Notes:</b></fo..." current
- 17:2417:24, 17 October 2022 diff hist +4,377 N Applications Environment/autodock Created page with "<h1><b>AUTODOCK</b></h1> <br> __TOC__ <br> <font color=red><b>Description:</b></font color> <b><i>AutoDock</i></b> is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. <font color=red><b>Additional Notes:</b></font color> Current distributions of <b><i>AutoDock</i></b> consist of two generations of software: <b><i>AutoDock 4</i></b> and <b><i>AutoDock Vina..." current
- 17:2317:23, 17 October 2022 diff hist +7,941 N Applications Environment/ADCIRC Created page with "= ADCIRC = ADCIRC is a system of programs for solving time-dependent, free-surface, circulation and transport problems in two and three dimensions. These programs utilize the finite element method in space allowing the use of highly flexible, unstructured grids. The ADCIRC distribution includes and integrates the METIS tool for unstructured grid generation. In addition, ADCIRC includes a distribution of SWAN to which it can be coupled to add a shore wave simulation mode..."
- 17:2317:23, 17 October 2022 diff hist +6,914 N ADCIRC Created page with "The CUNY HPC Center has installed version 50.79 on SALK (the Cray) and ANDY (the SGI) for general academic use. ADCIRC can be run in serial or MPI-parallel mode on either system. ADCIRC has demonstrated good scaling properties up to 512 cores on SALK and 64 cores on ANDY. A step-by-step walk through of running an ADCIRC test case in both serial and parallel mode follows. ==== Serial Execution ==== Create a directory where all the files needed to run the serial ADCIR..." current
- 17:0417:04, 17 October 2022 diff hist +3,058 N Forbidden Practices Created page with "In order to provide secure and efficient operation of the HPC Center resources for all users, certain practices are discouraged and/or forbidden on HPC Center systems. '''Allowing Someone Else to Login and Use Your Account:''' The CUNY IT security policy forbids this. Users are assumed to be responsible for all the usage and activities on account in their name. Providing access to another party undermines this assumption and puts the account owner at risk for the uns..." Tag: Visual edit: Switched
- 17:0317:03, 17 October 2022 diff hist −8,044 Contact Replaced content with "= Contact = For all problems and questions related to jobs please open ticket at https://hpchelp.csi.cuny.edu. If you have any questions about the CUNY HPCC, or in case of emergency please contact the CUNY HPCC Helpline at [mailto:HPCHelp@mail.csi.cuny.edu HPCHelp@csi.cuny.edu]" Tags: Replaced Visual edit: Switched
- 17:0317:03, 17 October 2022 diff hist +8,323 N Contact Created page with "<h1>Frequently Asked Questions</h1> <div class="noautonum">__TOC__</div> <br /> ===How do I get an account=== To gain access to the CUNY HPC Center, fill out the application form found on our website: https://hpcreg1.csi.cuny.edu/forms/requirements.php *Be sure to include your CUNY Email address in the form, and indicate the name and contact information of your CUNY supervisor. <br /> <br /> ===How do I login=== Use a ssh client to connect into the desired system...." Tag: Visual edit: Switched
- 17:0217:02, 17 October 2022 diff hist +8,323 N FAQs Created page with "<h1>Frequently Asked Questions</h1> <div class="noautonum">__TOC__</div> <br /> ===How do I get an account=== To gain access to the CUNY HPC Center, fill out the application form found on our website: https://hpcreg1.csi.cuny.edu/forms/requirements.php *Be sure to include your CUNY Email address in the form, and indicate the name and contact information of your CUNY supervisor. <br /> <br /> ===How do I login=== Use a ssh client to connect into the desired system...."
- 17:0217:02, 17 October 2022 diff hist +8,075 N Training & Workshops Created page with "The CUNY HPCC provides training course and organizes seminars on various HPC topics. The training courses are provided at no cost and may be held at any CUNY campus site, at the CUNY HPCC at College of Staten Island, or at the Graduate Center. The training course at the Graduate Center and its '''online''' version (during COVID-19) is course on parallel programming and use of HPC architectures. Therefore it covers various topics from basic SLURM scripting to basic..."
- 17:0217:02, 17 October 2022 diff hist +121,190 N Program Compilation Created page with "= Program Compilation and Job Submission = == Serial Program Compilation == The CUNY HPC Center supports four different compiler suites at this time; those from Cray, Intel, The Portland Group, and GNU. Basic serial programs in C, C++, and Fortran can be compiled with any of these offerings, although the Cray compilers are available only on SALK. Man pages (e.g. for Cray, man cc, for Intel, man icc; for PGI, man pgcc; for GNU, man gcc) and manuals exist for each co..."
- 17:0117:01, 17 October 2022 diff hist +143,878 N Applications Created page with "<div class="noautonum">__NOTOC__</div> '''This is an index of available applications sorted by their academic relevance, as well as alphabetically.''' For information about using modules to run your applications go to Using Modules To Run Your Applications. <div class= "mw-collapsible mw-collapsed"> == Computational Physics and Computational Chemistry == Applications in this section use classical mechanics, quantum mechanics and thermodynamics and are applied in..."
- 17:0117:01, 17 October 2022 diff hist +6,478 N Modules and Available Third Party Software Created page with "=Modules and available third party software= ==Modules== “Modules” makes it easier for users to run a standard or customized application and/or system environment. HPCC uses '''Lmod''' - an advanced module system that easily handles the MODULEPATH hierarchical problem common in UNIX based "modules" implementation. Application packages can be loaded and unloaded cleanly through the module system using modulefiles. This includes easily adding or removing directories to..."
- 17:0017:00, 17 October 2022 diff hist +1,364 Data Storage and Management System Table Tag: Visual edit
- 16:5416:54, 17 October 2022 diff hist +22,902 N Data Storage and Management System Created page with "=Data Storage and Management System (DSMS)= __TOC__ Key features of the '''DSMS''' system include: :• '''User''' home directories in a standard Unix file system called /global/u. :• Enhanced parallel scratch space on the HPC systems. :• '''Project''' directories in an Integrated Rule-Oriented Data-management System (iRODS) managed resource. Project directories exist in a “virtual file space” called '''cunyZone''' which contains a resource called '''Storage..."
- 16:5316:53, 17 October 2022 diff hist +14,811 N Running Jobs Created page with "__TOC__ ==Running jobs== In this section, we discuss the process for running jobs on a HPC system. Typically the process involves the following: :• Having input files within your <font face="courier">'''/scratch/<font color="red"><userid>'''</font color></font> directory on the HPC system you wish to use. :• Set up environment for the job. :• Creating a job submit script that identifies the input files, the application program you wish to use, the compute resour..."
- 16:5316:53, 17 October 2022 diff hist +5 File Transfers No edit summary Tag: Manual revert
- 16:5216:52, 17 October 2022 diff hist +37 File Transfers No edit summary Tags: Reverted Visual edit: Switched
- 16:5116:51, 17 October 2022 diff hist −42 File Transfers No edit summary Tags: Reverted Visual edit
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- 16:5016:50, 17 October 2022 diff hist +6 File Transfers No edit summary Tag: Visual edit: Switched
- 16:4816:48, 17 October 2022 diff hist 0 N File:Example File Transfer.png No edit summary current
- 16:3816:38, 17 October 2022 diff hist +1,698 N File Transfers Created page with " There are three methods of transferring data between the CUNY HPC systems and the rest of the world: :• '''Globus Online''': The preferred method for large files, with extra features for parallel data streams, auto-tuning and auto-fault recovery. Globus online is to transfer files between systems—between the CUNY HPC Center resources and XSEDE facilities, or even users’ desktops. A typical transfer rate ranges from 100 to 400 Mbps. : [https://cunyhpc.csi.cuny.e..."
- 16:3816:38, 17 October 2022 diff hist +4,841 N Basic Unix & Linux Commands Created page with "===UNIX Tutorial=== If you are unfamiliar with UNIX or Linux, an excellent online UNIX tutorial can be found in the "User's Guide to UNIX" from the Department of Electronic Engineering, University of Surrey, United Kingdom [http://www.ee.surrey.ac.uk/Teaching/Unix/unixintro.html]. Although that link is to a UNIX tutorial, the commands, at the user level, are essentially identical to those of Linux. === vi Usage === While other text editors exist, vi may be the most p..." current
- 16:3816:38, 17 October 2022 diff hist +6,278 N How to Login Created page with "<blockquote>''Notice: Users may not access CUNY computer resources without authorization or use it for purposes beyond the scope of authorization. This includes attempting to circumvent CUNY computer resource system protection facilities by hacking, cracking or similar activities, accessing or using another person's computer account, and allowing another person to access or use the user's account. CUNY computer resources may not be used to gain unauthorized access to an..."
- 16:3716:37, 17 October 2022 diff hist +63 MediaWiki:Sidebar No edit summary
- 16:3616:36, 17 October 2022 diff hist +9,761 N Administrative Information Created page with "__TOC__ ==How to get an account== ===User accounts=== CUNY faculty, research staff, collaborators at other universities, and public and private sector partners, and currently enrolled CUNY students (who MUST have a CUNY faculty sponsor) may receive authorization to use the CUNY HPC Center systems. Applications for accounts are accepted at any time. Undergraduate accounts are good for current semester only and must be renewed for each consecutive semester. Graduate stude..."
- 16:3516:35, 17 October 2022 diff hist +75 MediaWiki:Sidebar No edit summary
- 16:3316:33, 17 October 2022 diff hist −15 MediaWiki:Sidebar No edit summary
- 16:3216:32, 17 October 2022 diff hist +5 MediaWiki:Sidebar No edit summary
- 16:3016:30, 17 October 2022 diff hist +299 MediaWiki:Sidebar No edit summary
- 16:2716:27, 17 October 2022 diff hist +4 MediaWiki:Sidebar No edit summary
- 16:2616:26, 17 October 2022 diff hist +24 MediaWiki:Sidebar No edit summary
- 16:2616:26, 17 October 2022 diff hist −10 MediaWiki:Sidebar No edit summary
- 16:2516:25, 17 October 2022 diff hist +382 N MediaWiki:Sidebar Created page with " * navigation ** Overview of CUNYHPC ** Administrative Information ** User Manual ** How to Login ** Basic Unix & Linux Commands ** File Transfers ** Running Jobs ** Data Storage and Management System ** Modules and Available Third Party Software ** Applications ** Program Compilation ** Training & Workshops ** FAQS ** Contact ** Forbidden Practices * SEARCH * TOOLBOX * LANGUAGES"
- 16:0816:08, 17 October 2022 diff hist +297 Main Page →Partitions and jobs: Added Partitions table Tag: Visual edit
- 16:0516:05, 17 October 2022 diff hist +1 m Main Page No edit summary Tag: Visual edit
- 16:0416:04, 17 October 2022 diff hist +1,016 Main Page Cluster Table Tag: Visual edit
- 15:5015:50, 17 October 2022 diff hist +1 Main Page No edit summary Tag: Visual edit: Switched
- 15:4815:48, 17 October 2022 diff hist 0 N File:CUNY-HPCC-Logo.gif No edit summary current
- 15:4815:48, 17 October 2022 diff hist 0 N File:HPCC Chart.png No edit summary current
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- 14:5914:59, 17 October 2022 diff hist +11,369 Main Page No edit summary Tag: Visual edit: Switched
