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Software

IT maintains a wide variety of software on the clusters it supports. There are several categories of software involved:

Category Description Examples
operating system (OS)Programs that collectively provide a working environment for computationRedHat Enterprise Linux (RHEL)
developmentPrograms that are used to create and refine other programsPortland Compiler Suite, GNU Debugger (gdb)
librariesReusable program fragments that provide additional functionality to programsOpenMPI, ScaLAPACK
applicationsIn HPC, a program that facilitates computation or data analysisMatlab, Gaussian

IT is solely responsible for maintaining the OS on the HPC systems. A number of development tools, libraries, and applications that are requested by multiple HPC users are also installed/compiled and managed by the IT HPC staff. This area of the site is dedicated to documentation associated with the latter three categories of software.

Availability

Each cluster has a unique complement of development tools, libraries, and applications. Visit the Clusters page and view the documentation for a specific cluster to determine what software is available.

Using software

Preparing the Linux environment for a particular software title usually involves modification of the PATH or LD_LIBRARY_PATH variables, setting additional variables in the environment, or even executing scripted commands. Often the documentation for installing such software suggests that the user edit his/her .bashrc or .bash_profile file so the changes are made automatically at login. On UD HPC clusters, these tasks are best accomplished using VALET, not by editing your login files.

When IT adds new software to a cluster or upgrades existing software titles the work necessary to configure the environment for that software is modeled in a VALET package file. Later, when a user issues the vpkg_require command to prepare his/her environment, VALET uses the package file to affect the necessary changes.

VALET commands

The following table provides a brief summary of the most often-used VALET commands. Additional information is available in the VALET software documentation. These commands are available in login shells and batch scripts (since they are run as login shells).

Command Description
vpkg_listList all available packages by their «package-id»
vpkg_versions «package-id»List the versions/variants of a specific package by their «version-id»
vpkg_require «versioned-package-id»Attempt to configure the environment to use the given software
vpkg_rollback «number or all»Roll back a number of package additions, use all for every package

A «versioned-package-id» is the combination of a package identifier (found using the vpkg_list command) with a version/variant identifier (via the vpkg_versions command). The two pieces are joined using a forward slash (/). For example, the commercial software “Matlab” has a «package-id» of matlab and the 2012 release has a «version-id» of r2012a, producing the «versioned-package-id» matlab/r2012a.

In the context of a «versioned-package-id», a blank «version-id» implies the default version of the package. If the 2012 release of Matlab were the default, then using matlab (or matlab/default) as the «versioned-package-id» would imply matlab/r2012a.

VALET environment changes apply to the shell in which the vpkg_require command is issued; the changes do not “stick” after exiting that shell (by logging-out, for example). Thus, one way to discard changes affected by a vpkg_require command is to just exit the shell. The vpkg_rollback command is a more graceful alternative and iteratively discards the changes produced by prior vpkg_require commands issued in the shell. To undo all changes, vpkg_require all can be used.

A script contains commands to be executed in a shell.

VALET source files

When sourced, the commands in the script are executed in the current shell and any changes to the environment with be in affect when done. You can put VALET commands in a sourced script.

In source files containing VALET commands, it is good idea to rollback all packages before the VALET commands.

vpkg_rollback all

When the script is done the environment may have been changed. Only source VALET scripts when you want the changes made by VALET to stay in affect.

VALET executable scripts

When executing a script, a new shell is started with all exported variables and functions. This shell does not have the VALET commands, unless it was executed as a login shell.

In an executable, non-login script containing VALET commands, the VALET functions must be setup. Put this source statement before the VALET commands:

source /etc/profile.d/valet.sh

When the script is done, or encounters an exit command, the new shell is terminated and the environment is back to the state it was in before execution.

Development

IT staff has created and hosted HPC workshops, which frequently are archived as a tutorials. The exacted steps to follow along on IT managed clusters may be different.

LaPlace Examples

Fortran Examples

Libraries

IT staff install commercial and open-source libraries that can be used in developing your own code. Use of some commercial libraries may require that your research group purchase a right-to-use license and provide of the appropriate license server information.

FFTW

LAPACK

Open MPI

Details by cluster

ScaLAPACK

Applications

IT staff install commercial and open-source applications that do not require you to develop your own code. Use of some commercial software may require that your research group purchase a right-to-use license and provide of the appropriate license server information.

Abaqus

Vendor documentation: Abaqus

ANSYS Fluent

ArcGIS

The Python shell embedded in ArcGIS 10.1 Server can be used on a Linux cluster to execute GIS tasks. This is a (relatively) undocumented feature, and the steps necessary to install and configure the package for this mode of operation proved difficult.

  • The installation procedure for ArcGIS: what worked, what did not work, and the solution we came up with. This document may be useful for other system administrators looking to get ArcGIS 10.1 Server to work in their Linux environment.

Gaussian

See Gaussian - Expanding the limits of computational chemistry

GROMACS

See GROMACS (GROningen MAchine for Chemical Simulations)

HPCC

HPCC version 1.4.2 a program to run a series of benchmarks, which comprises the High Performance Computing Challenge.

HPC Challenge Awards Competition at SC Conference

This program will read a file that contains the parameters needed to run the benchmarks. This then runs all be benchmarks and report the results using the appropriate metric - Floating point in Tflops (or Gflops), latency in usec, bandwidth in GBS.

Two benchmarks (HPL and DGEMM) use the ACML library for its BLAS. Version 5.2 of the ACML library has fftw wrappers, which you can use for the challenge.

Matlab

Matplotlib

Mpi4py

NAMD

OpenFOAM

ParaView

“ParaView is an open-source, multi-platform application designed to visualize data sets of varying sizes from small to very large.”

See ParaView Users Guide – Public Wiki

One of the main purposes of ParaView is to allow users to visualize large data sets thatreside on HPC clusters without first collecting and downloading the data to a single machine. The local workstation, which is good at visualization, may not have the memory or computing power for rending jobs that benefit from MPI on a cluster. The solution is a client server model

See Client-Server chapter of Users Guide

Python

R

“R is an integrated suite of software facilities for data manipulation, calculation and graphical display.”

See R manuals for documentation available on using R in various formats.

TAU - Tuning and Analysis Utilities

TAU Performance System® is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python. See TAU's documentation.

Tecplot

Tecplot 360 lets you quickly plot and animate your CFD data exactly the way you want it. You can analyze complex data, arrange multiple layouts, and communicate your results with professional images and animations. See Learn more about Tecplot 360.

VASP

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g., electronic structure calculations and quantum-mechanical molecular dynamics.

See VASP online manual.

software/start.txt · Last modified: 2017-04-25 09:37 by anita