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Here is a list of all 64-bit applications currently installed on the research cluster. It is policy to retain only the two most recent versions.
Platform Computing, Inc.'s LSF (Load Sharing Facility) software is a distributed load sharing and batch queuing suite of applications that can dispatch user requests to compute nodes in accordance with a Tufts-defined policy. It manages, monitors, and analyzes resources and load on the cluster. Platform LSF is layered in a way that allows it to sits on top of and extend the operating system services, speaking to the competing needs of resource management on the cluster. LSF commands must be used to submit batch jobs and assign interactive jobs to processors. bsub and lsrun are the usual command tools for this. It's important to note that cluster compute nodes are the only targets under LSF control. Jobs are not submitted to computers outside of the cluster. For more information about LSF command usage and job submission, you can read the man pages (example: type man lsrun at the cluster prompt). Most commands begin with the letter 'b' such as: bsub, bkill, lsrun, and bjobs.
Ansys is a suite of finite element based applications that provide real-world simulations of structural, thermal, electromagnetic and fluid-flow behavior of 3-D product. All Ansys products integrate with CAD environments. Ansys's Polyflow is now available. This is normally access via the WorkBench interface.
Fluent is a Computational Fluid Dynamics (CFD) software package commonly used in engineering education for research in fluid mechanics. ANSYS purchased Fluent recently and has incorporated Fluent functionality into Ansys on an ongoing basis. The Ansys WorkBench product is how you access this functionality. Note Fluent 2d and 3d and Icepak products are available outside of WorkBench.
Abaqus
Abaqus is a suite of applications used by many in the engineering community for the analysis of multi-body dynamics problems that aid the medical, automotive, aerospace, defense, and manufacturing community.
FE-Safe
The Abaqus add-on product FE-Safe is a highly effective tool for Ansys
Ansys is a suite of finite element based applications that provide real-world simulations of structural, thermal, electromagnetic and fluid-flow behavior of 3-D product. All Ansys products integrate with CAD environments. Ansys's Polyflow is now available. This is normally access via the WorkBench interface.
Fluent is a Computational Fluid Dynamics (CFD) software package commonly used in engineering education for research in fluid mechanics. ANSYS purchased Fluent recently and has incorporated Fluent functionality into Ansys on an ongoing basis. The Ansys WorkBench product is how you access this functionality. Note Fluent 2d and 3d and Icepak products are available outside of WorkBench.
Abaqus
Abaqus is a suite of applications used by many in the engineering community for the analysis of multi-body dynamics problems that aid the medical, automotive, aerospace, defense, and manufacturing community.
Comsol is specifically designed to easily couple transport phenomena, including computational fluid dynamics (CFD) as well as mass and energy transport to chemical-reaction kinetics and process-related modeling. Licensed Modules include: MultiPhysics, Chemical Engineering, Acoustics, Structural Mechanics, Script.
Desmond
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems.
FE-Safe
The Abaqus add-on product FE-Safe is a highly effective tool for fatigue analysis of Finite Element models.Matlab
MATLAB is a high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numerical computation. Using MATLAB, you can solve technical computing problems faster than with traditional programming languages, such as C, C++, and Fortran. Extensive documentation and tutorials are provided within Matlab. The following Matlab toolboxes are licensed, however for an up to date list, type ver within Matlab's command line:
MATLAB, Simulink,Control System,Curve Fitting,Distributed Computing,Financial,Fuzzy Logic,Image Processing,MATLAB Compiler,Neural Network,Optimization,Partial Differential Equation,Real-Time Workshop,Signal Processing,Simulink Control Design,Simulink 3D Animation,Spline,Statistics,Symbolic Math,System Identification,Virtual Reality,Wavelet Toolbox,Bioinformatics,Simbiology
The MATLAB Compiler Runtime (MCR) is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components without using MATLAB licensing. This is useful for running a large number of jobs that might exceed the license counts.
Comsol is specifically designed to easily couple transport phenomena, including computational fluid dynamics (CFD) as well as mass and energy transport to chemical-reaction kinetics and process-related modeling. Licensed Modules include: MultiPhysics, Chemical Engineering, Acoustics, Structural Mechanics, Script.
Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.
Stata SE is an integrated statistical package for Windows, Macintosh, and Unix platforms. More than just a statistical package, Stata is also a full data-management system with complete statistical and graphical capabilities. It features both X-window and text user interfaces.
RATS
RATS(Regression Analysis of Time Series) is a leading econometrics and time-series analysis software package.
R is a widely available object oriented statistical package. The current list of installed packages, to numerous to list, can be found in directory
/opt/shared/R/2.15.0-rhel6/lib64/R/library/.
This represents an augmented base installation suitable for most routine tasks, however not all available packages as found on the R web site are installed. If some other R package is needed, please make a software installation request as outlined above. However, for many people use of RStudio will allow for local installations in your home directory. Extensive user documentation and tutorials are available on the R web site. There are many texts as well, here is nice example
Note BioConductor and many genetics related R packages are installed as well.
RStudio
RStudio is a free and open source integrated development environment(IDE) for R.
Gromacs
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
Desmond
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems.
PetSc
PetSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for parallelism. Note, another useful link to visit. PetSc has a complex build environment that allows one to include various applications. We encourage interested users to build the suite of interest in their home directory. Installation instructions for a particular set of applications can be found here GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
Platform Computing, Inc.'s LSF (Load Sharing Facility) software is a distributed load sharing and batch queuing suite of applications that can dispatch user requests to compute nodes in accordance with a Tufts-defined policy. It manages, monitors, and analyzes resources and load on the cluster. Platform LSF is layered in a way that allows it to sits on top of and extend the operating system services, speaking to the competing needs of resource management on the cluster. LSF commands must be used to submit batch jobs and assign interactive jobs to processors. bsub and lsrun are the usual command tools for this. It's important to note that cluster compute nodes are the only targets under LSF control. Jobs are not submitted to computers outside of the cluster. For more information about LSF command usage and job submission, you can read the man pages (example: type man lsrun at the cluster prompt). Most commands begin with the letter 'b' such as: bsub, bkill, lsrun, and bjobs.
MATLAB is a high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numerical computation. Using MATLAB, you can solve technical computing problems faster than with traditional programming languages, such as C, C++, and Fortran. Extensive documentation and tutorials are provided within Matlab. The following Matlab toolboxes are licensed, however for an up to date list, type ver within Matlab's command line:
MATLAB, Simulink,Control System,Curve Fitting,Distributed Computing,Financial,Fuzzy Logic,Image Processing,MATLAB Compiler,Neural Network,Optimization,Partial Differential Equation,Real-Time Workshop,Signal Processing,Simulink Control Design,Simulink 3D Animation,Spline,Statistics,Symbolic Math,System Identification,Virtual Reality,Wavelet Toolbox,Bioinformatics,Simbiology
The MATLAB Compiler Runtime (MCR) is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components without using MATLAB licensing. This is useful for running a large number of jobs that might exceed the license counts.
PetSc
PetSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for parallelism. Note, another useful link to visit. PetSc has a complex build environment that allows one to include various applications. We encourage interested users to build the suite of interest in their home directory. Installation instructions for a particular set of applications can be found here
RATS
RATS(Regression Analysis of Time Series) is a leading econometrics and time-series analysis software package.
R is a widely available object oriented statistical package. The current list of installed packages, to numerous to list, can be found in directory
/opt/shared/R/2.15.0-rhel6/lib64/R/library/.
This represents an augmented base installation suitable for most routine tasks, however not all available packages as found on the R web site are installed. If some other R package is needed, please make a software installation request as outlined above. However, for many people use of RStudio will allow for local installations in your home directory. Extensive user documentation and tutorials are available on the R web site. There are many texts as well, here is nice example
Note BioConductor and many genetics related R packages are installed as well.
RStudio
RStudio is a free and open source integrated development environment(IDE) for R.
Stata SE is an integrated statistical package for Windows, Macintosh, and Unix platforms. More than just a statistical package, Stata is also a full data-management system with complete statistical and graphical capabilities. It features both X-window and text user interfaces.
SAS
Sas is general purpose statistics package. Installed is the Education Analytical Suite of programs. These include:
• Base SAS
• SAS Bridge for ESRI
• SAS Enterprise Guide
• SAS Integration Technologies
• SAS/ACCESS
• SAS/AF
• SAS/ASSIST
• SAS/CONNECT
• SAS/EIS
• SAS/ETS
• SAS/FSP
• SAS/GRAPH
• SAS/IML
• SAS/INSIGHT
• SAS/LAB
• SAS/OR
• SAS/QC
• SAS/SECURE 168-bit
• SAS/SHARE
• SAS/STAT
SAS Enterprise Guide
SAS/Genetics
Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.
Namd
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
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