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The software list on this page is no longer current - please type "module avail" on the cluster for the current list, and see  Accessing software via Environment Modules for more information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

This page is retained from an earlier version of the HPC wiki only for reference.


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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