Category Archives: Software

OIT Update: Apps.rutgers.edu & Apps.HPC.rutgers.edu Cloud Service Update

List of Software available on Apps.rutgers.edu and Apps.HPC.rutgers.edu:

Math & Science                  Desktop                         Programming

APBS 1.3.0                           Acrobat Reader *       CoqIDE 8.3

Avogadro 1.0.3                   Blender 2.7.0               Coq – Emacs

Cadabra 1.29                      Firefox *                           Eclipse IDE

Chemtool 1.6.13                Google Chrome *      GNU C/C++ 4.7

FSL 5.0                                 Google Earth 7.1.1   GNU Fortran 4.7

FSL View 4.0                       Gummi 0.6.3                 Google Android SDK *

Genome Workbench 2.4            Libre Office *       Meld 1.6

Gephi 0.8.1-1                      Pidgin IM 2.10             Netbeans IDE *

GNU Octave  3.6.2             Thunderbird *             Ox 7

Icarus Verilog 0.9.5            Pep8

Maple 18 – 100 user limit                Perl 5.14

Mathematica 10.0.0           PHP 5.3.28

Matlab 2014a                       Proof General 4.2

Maxima 5.27                          Python 2.7.3

NEURON 7.2

PSPP 0.7.9

Quantum GIS 2.4

R 3.1.1-3

RStudio 0.98.1025

Sage 5.10-1

SAS 9.4-1

SPSS 21 – 50 user limit

Stata MP2 13 (MP4 on Apps.HPC)

Weka 3.6.9

XDrawChem 2.0

*denotes packages that are regularly updated.

Likely updates by September include:

Sage Math

Thunderbird

Java

Android SDK/NDK

Netbeans

New users (any Rutgers user with a NetID) can access Apps and Apps.HPC resources by first selecting “activate services” via netid.rutgers.edu  Then just point your browser at apps.rutgers.edu and login. Getting started info is referenced on the apps.rutgers.edu  start up page.

Note that Stat Transfer has been deleted since licensing no longer supports servers.

To keep in touch with Apps updates, read Apps.blogs.rutgers.edu or join the Apps User Community by signing up at https://sakai.rutgers.edu/sitelogin.jsp?site=35fceac3-6829-4d99-b4c8-d28b54230f1e   For further information, please send email to oirt@rutgers.edu

Apps HPC Will Provide Accees to GPU Capability for Instruction – We are looking for folks to test the GPUs.

Apps.rutgers.edu will be debuting access to some GPU capability in April, but now we are looking for some users who would test this service and provide feedback before it is made generally available. Please send email to oirt@rutgers.edu indicatting your interest in testing this GPU capability.

Any Apps user will be able to submit assignments and basic research programs to the GPU cluster which is comprised of 500 core Tesla GPUs from Nvidia. There are 8 GPUs on a node. This system will allow users to submit parallelized code using Matlab, Mathematica, R, and other packages.

Apps.rutgers.edu Cloud Service Update(s)

2/27/14 – FSL 5.0 and FSL View have been added to Apps.rutgers.edu for more info refer to http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL for more info

1/20/14 – With the assistance of some folks who helped to test Apps.HPC.rutgers.edu, anyone can now use this new HPC Apps service. Read more about this capability below.

1/20/14 – As browsers no longer support Java applications, the older Java Login page will be less useful and associated descriptions in documentation (flagged with **JAVA) will be deleted.

Please note that webdrive (highlighted in the “Start up Document” at http://oirt.rutgers.edu/software/remotexserver/) is very easy to use for file transfers.

To keep in touch with Apps updates as they happen, join the Apps User Community by signing up at https://sakai.rutgers.edu/sitelogin.jsp?site=35fceac3-6829-4d99-b4c8-d28b54230f1e For further information, please send email to oirt@rutgers.edu

Apps Debuts HPC Capability for Instruction and Longer Running Jobs

Apps.rutgers.edu debuts HPC capability in support of instruction and some elementary research. Any Apps user can submit jobs to Apps.HPC.

One can test their code on Apps as usual. Then save their program and submit the job to Apps.HPC via the srun command from a terminal window. Note that Apps.rutgers.edu is prioritized for interactive use while Apps.HPC only prioritized to run HPC and longer running jobs.

Apps HPC system is a single node with 32 cores and 750 gig of memory. This system will allow users to submit longer running jobs as well as run parallelized code with Matlab, Mathematica, R, Stata MP4, and other packages.

Refer to https://oirt.rutgers.edu/software/remotexserver/ for basic info to get started. For further info, send email to oirt@rutgers.edu

Matlab Training November 15

Please join MathWorks at complimentary MATLAB seminars for educators, academic researchers, and students at Rutgers University:

Date: Friday, November 15, 2013
Location: Busch Campus Center – room 120ABC
Time: 9:30am – 11:00am
11:15am – 12:45pm

> > Register Here Now.

Our event features two technical sessions presented by a MathWorks engineer:

9:30am – 11:00am: Session 1: Data Analysis with MATLAB
Learn how to access data, use interactive tools, automate and capture your work and share your results.

11:15am – 12:45pm: Session 2: Parallel Computing with MATLAB
Learn how to solve and accelerate computationally and data-intensive problems using multicore processors, GPUs, and computer clusters and then generate readable and portable C and C++ code from your MATLAB algorithms using MATLAB Coder.

View complete session descriptions and register here.

Site Licensed Software Updates

Rutgers Community funded site licenses have been extended and include the following applications:

Software Category

  • Mathematical
  • Statistical
  • Chem&Bio Draw
  • Survey (SaaS)
  • Bibliographic (SaaS)
  • Qualitative Anal.
  • Bio Anal. (SaaS)
  • Measurement & Control
Package

Package

Package

General Highlights:

– ChemBioDraw site license has been upgraded to ChemBioOffice and includes ChemBioDraw, eNotebook, and more.
– Matlab site license now includes the Matlab Distributed Computing Server (MDCS) Toolbox (for 32 or less workers/nodes) and the OPC Toolbox.
– RefWorks site license now includes Flow. Flow incorporates the general bibliographic capabilities of RefWorks plus full text and annotation as well as improved processes for collecting references, collaboration, and ease of use.

Rutgers Biomedical and Health Sciences (RBHS) Community updates:

– ChemBioOffice, ChemDoodle, Matlab, Mathematica, Maple, Stata, Origin Pro, RefWorks & Flow, NVivo, LabVIEW, and Ingenuity IPA have been extended to include RBHS faculty, staff, and students.
– RBHS users do not yet have access to Qualtrics (cloud survey tool) and Stata (a statistical package).

Downloads and installation instructions are available via the software portal at http://software.rutgers.edu To keep up to date regarding a specific site license, sign up for its sakai listserv via the respective links listed with the software package either at the oirt.rutgers.edu/software site or on the software portal.

For further information, refer to http://oirt.rutgers.edu/software or send your queries to oirt@rutgers.edu

Apps.rutgers.edu Cloud Service Update – Summer 2013 Updates

– R updated to version 3.0.1-3 (summer 2013)

– SAS updated to version 9.2-3 (7/30)

– Stat Transfer updated to version 12 (7/30)

– Stata updated to version 13 (7/22)

– SPSS updated to version 21 (7/22)

– Maple updated to version 17 (6/10)

– Matlab updated to version 2013a (6/11)

– Sage updated to version 5.10-1 (6/27)

– RBHS users can now access Apps and all packages except Stata (they need to select activate services via netid.rutgers.edu)

To keep in touch with Apps updates as they happen, join the Apps User Community by signing up at https://sakai.rutgers.edu/sitelogin.jsp?site=35fceac3-6829-4d99-b4c8-d28b54230f1e For further information, please send email to oirt@rutgers.edu

Software Portal Update(s) – SAS JMP with Genomics Module

New software available from the software portal:

– SAS 9.3 and 9.4 now includes Enterprise Miner for Desktop and Text Minder for Desktop

– SAS/JMP 10 now includes Genomics v6

– SAS/JMP 11 is now available but Genomics v7 will not be released until the first quarter of 2014 at which time it will be add to the JMP 11 package

Note: Discover JMP 11 with a 30-day free trial at:
http://www.jmp.com/ads/adwords.shtml?gclid=CMST1oj75LkCFdGd4AodwBcA2w

For further information, go to http://software.rutgers.edu

Apps.rutgers.edu Cloud Service Updates

New and updated applications include:

– Gephi (http://gephi.org/), Graph Visualization Software, and Mallet (http://mallet.cs.umass.edu/), MAchine Learning for LanguagE Toolkit, have been added to Apps.rutgers.edu with Gephi being listed in the Education menu and Mallet being available from the command line.

– Filezilla (http://filezilla-project.org/) is a free sftp alternative that works with Windows or Macs and provides dialog boxes similar to that described in the Apps basic handout at http://oirt.rutgers.edu/software/remotexserver/

– Firefox has been upgraded to 16.0.2

– PHP was upgraded to 5.3.17

Let us know if you have other Open Source applications to recommend for Apps.rutgers.edu

To keep in touch with Apps updates as they happen, join the Apps User Community by signing up at
https://sakai.rutgers.edu/sitelogin.jsp?site=35fceac3-6829-4d99-b4c8-d28b54230f1e