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User vs Centrally Supported Software

Hyak is provided as a basic hardware and software platform. Users are responsible for application support, including the installation and management of supporting software including libraries. Central support is limited to the packages listed on this page. Users are free to build and install whatever software they like in their shared scratch directories (e.g. /gscratch/esci/sw). Users may install and operate commercial software as well. Submit a help request to request flexlm license manager support if necessary.

System Software

Red Hat Enterprise Linux

Hyak runs Red Hat Enterprise Linux (RHEL) 6. Numerous development tools including the full GCC compiler suite (v4.1 and v4.4), lapack, blas, valgrind, as well as many other libraries and utilities are bundled with RHEL.

Environment Modules

Most of the production software is available via "modules" that must be "loaded" before the corresponding programs can be used. For instance,

makes R (3.2.0) available for the user. Loading a module executes certain setup tasks, typically configuring the environment and loading other modules, to make the particular program available for use. This is needed to allow compilation of applications and submission of jobs to the cluster by providing access to the required utilities. By default, the module command is loaded automatically during login to Hyak.

You can list the currently available modules with:

You can see a list of the currently loaded modules with:

and load and unload modules with:

show the content of a module:

VirtualBox

VirtualBox is a virtualization application that is available on Hyak nodes and you can run on your desktop as well. You can find out more about using our local installation on Hyak's VirtualBox page.

BLCR

Berkeley Labs Checkpoint and Restart allows some applications that do not have the feature builtin to be checkpointed and restarted.

Development Software

Intel Development Tools

The Intel compilers and tools installation can be found in /sw/intel. Below you will find links to support and documentation, as well as basic information for setting up your user environment to use the Intel development tools.

Support Information

There is no support for the compilers provided by UW-IT. Instead, users should read Intel's documentation and rely on Intel's standard support channels.

Product Information and Documentation

Find links to product information and documentation (http://software.intel.com/en-us/articles/intel-software-development-products-for-linux/).

A web tool that helps you to choose the proper command line arguments when using the Intel MKL (https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor).

Technical Support

Access Intel's knowledge base, user forums and premier support (http://software.intel.com/en-us/articles/intel-software-developer-support/).

Sample Compile Sessions

Below are two example sessions of how to use the Intel compilers to build a software package. In the examples, two versions of the HDF5 data format library are compiled, one serial with C++ support and one parallel without C++ support.

Compiling HDF5 Serial

Compiling HDF5 Parallel

Installed Products

Below is a list of the installed products as well as paths to the scripts that set up your environment to use them.

Product

Environment Module

C/C++ Compilers (Composer XE)

icc_<version>

Fortran Compilers (Composer XE)

icc_<version>

Debugger

Loaded with compiler environment

Integrated Performance Primitives

Loaded with compiler environment

Math Kernel Library

Loaded with compiler environment

MPI Library

icc_<version>-impi_<version>

Thread Building Blocks

Loaded with compiler environment

Trace Analyzer and Collector

itac_<version>

Advisor

advisor_<version>

Inspector

inspector_<version>

VTune™ Performance Analyzer

vtune_<version>

TotalView

Hyak has a 32 core license for the TotalView parallel debugger. You can use it by loading the totalview_<version> environment module. Links to documentation (http://www.roguewave.com/help-support/documentation/totalview).

Hyak_totalview_debugger

MPI Libraries

Please keep in mind that MPI behavior varies among implementations. If you encounter errors running with one version of MPI please consider trying your application with one of the other supported versions. For more information about submitting MPI jobs to the scheduler as well as sample job scripts, see the Hyak Job Scheduler page.

Intel MPI

Intel MPI is the recommended MPI library for all users. Only use Open MPI if your application does not support Intel MPI [See the above section on the Intel Development Tools. For more details about Intel MPI and job submission, see the Intel MPI page.

Open MPI

The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners. More information can be found on the Open MPI site (http://www.open-mpi.org/).

Compiler Supported

Environment Module

GCC

gcc_<version>-ompi_<version>

Intel

icc_<version>-ompi_<version>

For more details about Open MPI including job submission and debugging, see the Hyak Open MPI page.

MPICH2-MX

This MPI library is no longer recommended or supported. MPICH2-MX is a specialized version of MPICH2 distributed by Myricom. More information can be found on the Myricom site.

Compiler Supported

Environment Module

GCC

gcc_<version>-mpich2_mx_<version>

Intel

icc_<version>-mpich2_mx_<version>

For more details about MPICH2-MX and job submission, see the Hyak MPICH2-MX page.

Production Software

Open Source

  • R is a high-level language for statistics and data processing. Please refer to Hyak R programming for technical details.

Commercial Codes

Abaqus

Abaqus is a software suite for finite element analysis and computer-aided engineering. To use Abaqus on Hyak, run module load abaqus_<version>.

ANSYS

ANSYS is a software suite for finite element analysis and computer-aided engineering. You can find out more about using our local installation on Hyak's ANSYS page.

ANSYS EM

ANSYS EM is a software suite for electromagnetic, electronics, thermal & electromechanical simulation. You can find out more about using our local installation on Hyak's ANSYS EM page.

CFD-Post

CFD-Post is a computational fluid dynamics post-processor. To use CFD-Post on Hyak, run 'module load cfd-post_<version>'

CFX

CFX is a computational fluid dynamics package. You can find out more about using our local installation on Hyak's CFX page.

Fluent

Fluent is a computational fluid dynamics package. You can find out more about using our local installation on Hyak's Fluent page.

Mathematica

Mathematica is a computational software program used in scientific, engineering, and mathematical fields and other areas of technical computing. You can find out more about using our local installation on Hyak's Mathematica page. You can learn more about it at the vendor's web site.

MATLAB

MATLAB is a computational software program used in scientific, engineering, and mathematical fields and other areas of technical computing. You can find out more about using our local installation on Hyak's MATLAB page.

Premium Open Source Tools

Intel Python

Intel Python is based on Anaconda Python, but is a specially optimized version of Python intended for use on HPC systems like Hyak. You can find more information about it on the Intel site. To use Intel Python, run module load intel-python_<version>.

Anaconda Python

To use Anaconda Python, run module load anaconda_<version>. Please refer to the Anaconda Documentation or the Anaconda Mailing List if you encounter any problems.

Enthought Scientific Python

Enthought has rebranded their Python distribution as Canopy. To use this version, run module load canopy_<version> then run canopy --no-gui-setup. Install to the default location. Please refer to the Enthought Support Site for help if you encounter problems.

Microsoft R Open

The Microsoft R (formerly Revolution R) distribution provides many common packages compiled against the performance optimized Intel Math Kernel Library. Microsoft R is open source and licensed under the GPL v2. Full details are available on the vendor's web site. To use this R distribution, run module load msropen_<version> (old versions revolutionr_<version>).

Open Source Data Libaries

HDF5

HDF5 is a data storage library. Please see the HDF5 site for more information. To use this library, run module load hdf5_<version>-icc_<version>.

NetCDF

NetCDF is a data storage library. Please see the NetCDF site for more information. To use this library, run module load netcdf_<version>-icc_<version>.

Open Source Visualization Tools

ParaView

ParaView is an open-source, multi-platform data analysis and visualization application. More details and documentation can be found on the ParaView web site. To use ParaView on Hyak, run module load paraview_<version>.

VisIt

VisIt is an open source interactive parallel visualization and graphical analysis tool for viewing scientific data. Hyak has both serial and parallel editions of VisIt, to use run load module visit_<version> or visit_<version>-ompi_<version>.

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