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Available Software

NYU HPC provides a range of third party and open source software for general use. To see the list of available software on a cluster, please use the Modules command. The resulting output lists the name of the software/compiler used to create the binary and version number:

$ module avail -t

The software list on this page is no longer current - please type "module avail" on the cluster for the current list, and see  Accessing software via Environment Modules for more information

Available Software on Clusters

Note

Always, run the command module avail from the terminal to view the up to date available software.

General List

The table below lists the software that is currently available from NYU HPC services in alphabetical order.  We also encourage researchers to use the "module avail" command to get a list of all software and version numbers available in real time.

Available Software

Descriptions

amber10/intel-mvapich
amber11/intel-mvapich

Amber is a package of molecular mechanics simulation.

fftw/gnu/2.1.5
fftw/gnu/3.1.2

Fastest Fourier Transform in the West (FFTW), a collection of discrete Fourier transform routines available publicly. Compiled with a GNU compiler. 

fftw/intel/2.1.5
fftw/intel/3.2.2

Fastest Fourier Transform in the West (FFTW), a collection of discrete Fourier transform routines available publicly. Compiled with a Intel compiler. 

gaussian/intel/G03-D01
gaussian/intel/G03-E01
gaussian/intel/G09-B01

Gaussian is a quantum mechanic electronic structure package. This software is capable of handling proteins and large molecules using semi-empirical, ab initio molecular orbital (MO), density functional. Compiled with the Intel compiler.

gaussview/5.0.9

GaussView is an advanced and powerful graphical interface available for Gaussian.

gsl/intel/1.12
gsl/intel/1.13

The GNU Scientific Library (GSL) is a collection of routines written in C for numerical computing. Compiled with the Intel compiler.

intel-c/cce/11.1.046

Intel C compiler.

intel-fortran/fce/11.1.046

Intel Fortran compiler.

mathematica/7.0
mathematica/8.0

Mathematica is a general computing environment with organizing algorithmic, visualization, and user interface capabilities. The many mathematical algorithms included in Mathematica make computation easy and fast.

matlab/2009a
matlab/2009b
matlab/2010b

Matlab is a technical computing environment for high performance numeric computation and visualization. Matlab integrates numerical analysis, matrix computation, signal processing, and graphics in an easy to use environment without using traditional programming. Typical uses include general purpose numeric computation, algorithm prototyping, and special purpose problem solving with matrix formulations that arise in disciplines such as control theory, statistics, and digital signal processing.

molden/gnu/4.7

Molden is a package for displaying molecular density. It supports a number of other programs via the Molden format. This version has been compiled with the GNU compiler.

mpiexec84/mpiexec84

MPI executable file used to start executable binary file that has been compiled with MVAPICH 1.1.

mvapich/gnu/1.1.0

Ohio State University's MVAPICH MPI wrapper. This version has been compiled with a GNU compiler.

mvapich/intel/1.1.0

Ohio State University's MVAPICH MPI wrapper. This version has been compiled with a Intel compiler.

NAG Library

Numerical Algorithms Group Library. The NAG Library is a comprehensive collection of numerical and statistical algorithms. It has over 1600 tested routines that can be used to add mathematical and statistical functionality to your applications.

ncview/intel/1.93g

A visual browser uses ncview to look at NetCDF (Network Common Data Form) files; view simple movies of the data, view along various dimensions; see actual data values, change color maps, invert the data, etc.

neuron/intel/7.1

For empirically-based simulations of neurons and networks of neurons.

netcdf/intel/3.6.3
netcdf/intel/4.1.1

NetCDF (Network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This version has been compiled with the Intel compiler.

openmpi/gnu/1.2.8

Open MPI compiled with a GNU compiler.

openmpi/intel/1.3.3

Open MPI compiled with an Intel compiler.

R/intel/ 2.9.2

R is a highly extensible language and environment that provides a wide variety of statistical (linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering) and graphical techniques. It is a GNU project which is similar to the S language and environment.

stata/11 (on USQ only)

Stata is a complete, integrated statistical package that provides everything you need for data analysis, data management, and graphics. For help with Stata, contact the Data Services

tinker/intel/4.2
tinker/intel/5.0

TINKER is a molecular modeling software for molecular mechanics and dynamics, with some special features for biopolymers. Includes a variety of algorithms such as an implementation of atomic multipole-based electrostatics with explicit dipole polarizability. This version of TINKER was compiled with an Intel compiler.

totalview/8.8.0-2

Totalview is a source code and memory debugger for C, C++ and Fortran applications. 

vmd/1.8.7

VMD  (Visual Molecular Dynamics) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Compilers

There are several Fortran, C, and C++ compilers available on our systems.

Compiler Type

Name

Source

Documentation

Cluster availability

C Compilers

c99

Standard C

man c99

usq, bowery, cardiac

 

gcc

GNU C

man gcc

usq, bowery, cardiac

 

icc

Intel C

man icc

usq, bowery, cardiac

C++ Compilers

g++

GNU C++

man g++

usq, bowery, cardiac

 

icpc

Intel C++

man icpc

usq, bowery, cardiac

Fortran Compilers

gfortran

GNU Fortran95

man gfortran

usq, bowery, cardiac

 

ifort

Intel Fortran

man ifort

usq, bowery, cardiac

 MPI Wrappers

mpif77

MPI Fortran77

man mpif77

usq, bowery, cardiac

 

mpif90

MPI Fortran90

man mpif90

usq, bowery, cardiac

 

mpicc

MPI C

man mpicc

usq, bowery, cardiac

 

mpiCC

MPI C++

man mpiCC

usq, bowery, cardiac

Useful Information

Other compiler versions can be loaded using the modules.

Handy Hint

Add this line before loading any modules in your batch script to declare where the "module" program is located.
 
For batch scripts in sh/bash

For batch scripts in csh/tcsh

Note

For online manuals and guides, please see our Finding documentation section.

 

Loading Software

Environment Modules

   

Software usually needs specific settings of environmental variables. NYU HPC uses an open source software package called "Environment Modules," (or Modules for short) which allows you to add various path definitions to your shell environment. Default compilers, applications and libraries can be set by individual or combinations of Modules commands. Modules are not applications, rather they simply add the location of applications to your environment. So you can load "modules" to set up the environment which is necessary for the software.

You can list the available Modules using the command module avail.

The content may vary on different clusters. If you would like to run the "vmd" program, for example, you need to first find "vmd" in this list (vmd/1.8.7) and type,

$ module load vmd/1.8.7

The "module load" command loads all the configuration information for the specific software.

Then you will be able to execute "vmd" by simply typing vmd.

In case the module did not load or a different module was loaded by mistake, the which command will return an error:

$ which vmd
/usr/bin/which: no vmd

Note

Some modules might depend on other modules.

For example, you will encounter an error message like shown below if you try to load Amber 11 directly;

$ module load amber11/intel-mvapich
amber11/intel-mvapich(16):ERROR:151: Module 'amber11/intel-mvapich' depends on one of the module(s) 'intel/11.1.046'
amber11/intel-mvapich(16):ERROR:102: Tcl command execution failed: prereq intel/11.1.046

In this case, you have to load the intel (Intel C/C++ compiler) first.

The correct method to do so is to as follows:

$ module load intel/11.1.046 (as well as loading all the other prerequisite modules)

THEN

$ module load amber11/intel-mvapich

Version Changes

NYU HPC sends out notifications on a regular basis about software version upgrades. Such notifications include version number upgrade, module and path changes, as well as new features and bug fixes related to the new version.

Requesting Additional Software

High performance computing is a fast changing field and requires researchers to keep up with the latest developments. Experimentation is part of this process.

NYU HPC maintains a wide variety of software. Despite these efforts we cannot cover all available software. If you require additional software installations we will do our best to accommodate you. Email these requests to hpc@nyu.edu. Depending on the level of difficulty please allow for up to five working days for installation.

Software Available at NYU

For generic software offered by ITS, such as scp, ssh and vpn clients, please see http://www.nyu.edu/its/software

For a complete list of all research software, including non-HPC software, please see http://www.nyu.edu/its/research/software

   

 

 

PBS Script Generator
An interactive tool that generates PBS script based on user's input. Check this page for more details.
Front-Line HPC Consulting
HPC consultations are available once a week, Monday 1-3 PM. Appointments are required. Please make an appointment at hpc@nyu.edu.

 

 

 

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