UVA Research Computing

Research Computing

Creating innovative solutions for researchers

/tag/software

  • Rivanna HPC Software

    Overview Research Computing at UVA offers a variety of standard software packages for all Rivanna users. We also install requested software based on the needs of the high-performance computing (HPC) community as a whole. Software used by a single group should be installed by that group’s members, ideally on leased storage controlled by the group. Departments with a set of widely-used software packages may install them to the lsp_apps space. The Research Computing group also provides limited assistance for individual installations. For help installing research software on your PC, please contact Research Software Support at res-consult@virginia.edu. Software Modules and Containers Software on Rivanna is accessed via environment modules or containers.
  • Compilers on Rivanna

    Rivanna offers multiple compiler bundles for C, C++, and Fortran. Different compilers have different strengths and weaknesses and different error messaging and debugging features, so users should be willing to try another one when appropriate. The modules system manages the compiler environment and ensures that only compatible libraries are available for loading. Many users of compiled languages are working with codes that can employ MPI for multinode parallel runs. MPI users should first understand how their chosen compiler works, then see the MPI instructions at our parallel programming page. Compiled languages can be more difficult to debug, and the assistance of a good debugger can be essential.
  • Machine Learning on Rivanna

    Overview Many machine learning packages can utilize general purpose graphics processing units (GPGPUs). If supported by the respective machine learning framework or application, code execution can be manyfold, often orders of magnitude, faster on GPU nodes compared to nodes without GPU devices. Rivanna has several nodes that are equipped with GPU devices. These nodes are available in the GPU partition. Access to a GPU node and its GPU device(s) requires specific SLURM directives or command line options as described in the Jobs using a GPU Node section. Applications Several machine learning software packages are installed on Rivanna. The most commonly used ones are:
  • Message Passing Interface (MPI) on Rivanna

    Overview MPI stands for Message Passing Interface. The MPI standard is defined by the Message Passing Interface Forum. The standard defines the interface for a set of functions that can be used to pass messages between processes on the same computer or on different computers. MPI can be used to program shared memory or distributed memory computers. There is a large number of implementations of MPI from various computer vendors and academic groups. MPI is supported on the Rivanna cluster. MPI On Rivanna MPI is a standard that describes the behavior of a library. It is intended to be used with compiled languages (C/C++/Fortran).
  • Rivanna Software List

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  • Software Containers

    Overview Containers bundle an application, the libraries and other executables it may need, and even the data used with the application into portable, self-contained files called images. Containers simplify installation and management of software with complex dependencies and can also be used to package workflows. Singularity is a container application targeted to multi-user, high-performance computing systems. It interoperates well with SLURM and with the Lmod modules system. Singularity can be used to create and run its own containers, or it can import Docker containers. Creating Singularity Containers To create your own image from scratch, you must have root privileges on some computer running Linux (any version).
  • Software Modules

    The lmod modules system on Rivanna enables users to easily set their environments for selected software and to choose versions if appropriate. The lmod system is hierarchical; not every module is available in every environment. We provide a core environment which contains most of the software installed by Research Computing staff, but software that requires a compiler or MPI is not in that environment and a compiler must first be loaded. View All Modules   Basic Commands List all available software in the core environment: module avail Use “module spider” to find all possible modules. module spider module spider hdf5 If a version is specified to spider, it will indicate how to load that version.
  • Bowtie2 on Ivy Linux VM

    Bowtie2 is a memory-efficient tool for aligning short sequences to long reference genomes. It indexes the genome using FM Index, which is based on Burrows-Wheeler Transform algorithm, to keep its memory footprint small. Bowtie2 supports gapped, local and paired-end alignment modes. Alignment to a known reference using Bowtie2 is often an essential first step in a myriad of NGS analyses workflows. Bowtie2 Usage Alignment using bowtie2 is a 2-step process - indexing the reference genome, followed by aligning the sequence data. Create indexes of your reference genome of interest stored in reference.fasta file: bowtie2-build [option(s)] <reference.fasta> <bt2-index-basename> This will create new files with the provided basename and extensions .
  • Bowtie2 on Ivy Windows VM

    Bowtie2 is a memory-efficient tool for aligning short sequences to long reference genomes. It indexes the genome using FM Index, which is based on Burrows-Wheeler Transform algorithm, to keep its memory footprint small. Bowtie2 supports gapped, local and paired-end alignment modes. Alignment to a known reference using Bowtie2 is often an essential first step in a myriad of NGS analyses workflows. Bowtie2 Usage Alignment using bowtie2 is a 2-step process - indexing the reference genome, followed by aligning the sequence data. Create indexes of your reference genome of interest stored in reference.fasta file: bowtie2-build [option(s)] <reference.fasta> <bt2-index-basename> This will create new files with the provided basename and extensions .
  • HISAT2 on Ivy Linux VM

    * Please note that HISAT2 requires approval prior to installation on the VM HISAT2 is a fast and sensitive tool for aligning short reads against the general human population (as well as single reference genome). It indexes the genome using a Hierarchical Graph FM Index (HGFM) strategy, i.e. a large set of small indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp). HISAT2 Usage: Alignment using HISAT2 is a 2-step process - indexing the reference genome, followed by aligning the sequence data. Create indexes of your reference genome of interest stored in reference.
  • HISAT2 on Ivy Windows VM

    * Please note that HISAT2 requires approval prior to installation on the VM HISAT2 is a fast and sensitive tool for aligning short reads against the general human population (as well as single reference genome). It indexes the genome using a Hierarchical Graph FM Index (HGFM) strategy, i.e. a large set of small indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp). HISAT2 Usage: Alignment using HISAT2 is a 2-step process - indexing the reference genome, followed by aligning the sequence data. Create indexes of your reference genome of interest stored in reference.
  • UVa Licensed SPSS on Ivy Windows VM

    SPSS Overview SPSS (or Statistical Package for Social Sciences), was initially developed as a social survey project but later on has grown to encompass statistical applications in almost all disciplines. Different industries use SPSS for their data analysis work. Its features include database management, reporting, graphing, among many others. SPSS Usage SPSS is available only on the Windows VM at the moment. To run SPSS go to: Start Menu > All Programs > IBM SPSS Statistics Licensing We have a limited number of SPSS licenses available, which are provided on a first-come-first-serve basis. As a consequence, availability of SPSS on your VM is not always guaranteed once a VM request is submitted.
  • cTAKES on Ivy Linux VMs

    cTAKES Overview cTAKES or The clinical Text Analysis and Knowledge Extraction System, is a Mayo Clinic developed Natural Language Processing (NLP) tool used to extract information out of clinical records. It is open-source, and built on the Apache Unstructured Information Management Architecture. cTAKES is modular, expandable, for a number of generic use cases, and contains excellent best practice notes. cTAKES Usage cTAKES components Some of cTAKES components are listed below: Sentence boundary detection (OpenNLP technology) *Tokenization (rule-based) Morphologic normalization (NLM’s LVG) POS tagging (OpenNLP technology) Shallow parsing (OpenNLP technology) Named Entity Recognition Negation and context identification (both based on NegEx) cTAKES Named Entities cTAKES contains the following Named Entities:
  • cTAKES on Ivy Windows VMs

    cTAKES Overview cTAKES or The clinical Text Analysis and Knowledge Extraction System, is a Mayo Clinic developed Natural Language Processing (NLP) tool used to extract information out of clinical records. It is open-source, and built on the Apache Unstructured Information Management Architecture. cTAKES is modular, expandable, for a number of generic use cases, and contains excellent best practice notes. cTAKES Usage cTAKES components Some of cTAKES components are listed below: Sentence boundary detection (OpenNLP technology) *Tokenization (rule-based) Morphologic normalization (NLM’s LVG) POS tagging (OpenNLP technology) Shallow parsing (OpenNLP technology) Named Entity Recognition Negation and context identification (both based on NegEx) cTAKES Named Entities cTAKES contains the following Named Entities:
  • User Licensed Stata on Ivy Linux VMs

    Stata Overview Stata is a graphical data analysis tool developed by StataCorp, and is short for Statiscs and Data. It is used in various disciplines, including biomedicine, economics, epidemiology, among others. It is capable of performing statistical analysis, simulations, regression, and data management. Besides the standard version Stata also ships with the MP version (multi=processing), and SE for large databases. NB Users requesting an installation of Stata would be required to bring their own license. Please consult with us before requesting an installation. You may also request a Stata license from the UVa Software Gateway
  • User Licensed Stata on Ivy Windows VMs

    Stata Overview Stata is a graphical data analysis tool developed by StataCorp, and is short for Statiscs and Data. It is used in various disciplines, including biomedicine, economics, epidemiology, among others. It is capable of performing statistical analysis, simulations, regression, and data management. Besides the standard version Stata also ships with the MP version (multi=processing), and SE for large databases. NB Users requesting an installation of Stata would be required to bring their own license. Please consult with us before requesting an installation. You may also request a Stata license from the UVa Software Gateway
  • UVa Licensed IDL on Ivy Linux VMs

    IDL Overview IDL, short for Interactive Data Language, is an interactive shell based data analysis programming language. Used vastly in medical imaging, it can quickly create visualizations and graphs of large data sets in a few easy steps due to its vector nature. FORTRAN users would be familiar with the IDL syntax. IDL is not to be confused with Java IDL or Microsoft IDL. Basic IDL Usage To start IDL, open a terminal window and type idl. This will start the interactive shell. Variables in IDL To initialize variables in IDL, type: <variable_name> = <variable_value> e.g. x = 3 and hit Enter/Return
  • UVa Licensed IDL on Ivy Windows VMs

    IDL Overview IDL, short for Interactive Data Language, is an interactive shell based data analysis programming language. Used vastly in medical imaging, it can quickly create visualizations and graphs of large data sets in a few easy steps due to its vector nature. FORTRAN users would be familiar with the IDL syntax. IDL is not to be confused with Java IDL or Microsoft IDL. Licensing We have a limited number of IDL Licenses available, which are provided on a first-come-first-serve basis. As a consequence, availability of IDL on your VM is not always guaranteed once a VM request is submitted.
  • UVa Licensed MATLAB on Ivy Linux Virtual Machines

    MATLAB Overview MATLAB is a high-performance language for technical computing. It integrates computation, visualization, and programming environment. MATLAB stands for MATrix LABoratory. MATLAB was made to provide easy access to matrix software developed by the LINPACK (linear system package) and EISPACK (Eigen system package) projects. MATLAB includes a programming language environment with built-in editing and debugging tools, and supports object-oriented programming. Programming in MATLAB MATLAB has many advantages compared to conventional computer languages (e.g., C, FORTRAN) for solving technical problems. MATLAB is an interactive system whose basic data element is an array, and almost all problems can be solved in MATLAB using that one data element.
  • UVa Licensed MATLAB on Ivy Windows Virtual Machines

    MATLAB Overview MATLAB is a high-performance language for technical computing. It integrates computation, visualization, and programming environment. MATLAB stands for MATrix LABoratory. MATLAB was made to provide easy access to matrix software developed by the LINPACK (linear system package) and EISPACK (Eigen system package) projects. MATLAB includes a programming language environment with built-in editing and debugging tools, and supports object-oriented programming. Programming in MATLAB MATLAB has many advantages compared to conventional computer languages (e.g., C, FORTRAN) for solving technical problems. MATLAB is an interactive system whose basic data element is an array, and almost all problems can be solved in MATLAB using that one data element.
  • UVa Licensed SAS on the Ivy Linux VM

    SAS Overview SAS is a command-driven software package used for statistical analysis and data visualization. It is available in . It is one of the most widely used statistical software packages in both industry and academia. You may use it if you have a large number of statistical algorithms. It is not limited to an industry, and could be used in both scientific and non-scientific contexts. We only offer the Teaching & Research version at the moment. Common Usage For this example we will use a common scenario from SAS Clinical Standards Toolkit, which is used for supporting clinical research activiites.
  • UVa Licensed SAS on the Ivy Windows VM

    SAS Overview SAS is a command-driven software package used for statistical analysis and data visualization. It is available in . It is one of the most widely used statistical software packages in both industry and academia. You may use it if you have a large number of statistical algorithms. It is not limited to an industry, and could be used in both scientific and non-scientific contexts. We only offer the Teaching & Research version at the moment. Common Usage For this example we will use a common scenario from SAS Clinical Standards Toolkit, which is used for supporting clinical research activiites.
  • Image Processing Software on Ivy Linux VM

    Pre-approved packages The following software packages are pre-approved for image processing on an Ivy Linux VM KNIME KNIME is open source analytics platform for data mining and pipelining. KNIME’s Image Processing Plugin allows users to perform common image processing techniques such as registration, segmentation, and feature extraction. KNIME is compatible with over 120 image file types and can be used alongside ImageJ. ImageJ ImageJ is a Java-based image processing program developed at the NIH. ImageJ can be used interactively through a graphical user interface or automatically with Java. OpenCV OpenCV is an open source library for computer vision applications.
  • Image Processing Software on Ivy Windows VM

    Pre-approved packages The following software packages are pre-approved for image processing on an Ivy Windows VM Axiovision Axiovision is software for microscopy image processing and analysis. Axiovision is highly configurableto meet the needs of your individual workflows. KNIME KNIME is open source analytics platform for data mining and pipelining. KNIME’s Image Processing Plugin allows users to perform common image processing techniques such as registration, segmentation, and feature extraction. KNIME is compatible with over 120 image file types and can be used alongside ImageJ. ImageJ ImageJ is a Java-based image processing program developed at the NIH. ImageJ can be used interactively through a graphical user interface or automatically with Java.
  • LibreOffice On Ivy Linux VM

    LibreOffice Overview Our Linux VMs come prepackaged with the open source alternative to Microsoft Office®, called LibreOffice. As of last writing, version 5 is installed, including the specific software suites mentioned below. LibreOffice is compatible with all Microsoft Office formats, and can be connected to services like Google Drive or DropBox. It is available under the Mozilla Public License. LibreOffice is full GUI software and would require you to RDP into your VM or use a graphical tool such as FastX in order to render it. LibreOffice Writer LibreOffice Writer is the word processor component of LibreOffice. It can save documents in .
  • Preinstalled Java SDK on Ivy Linux VM

    Java SDK Overview Ivy Linux VMs are installed with Java SDK 1.8. Java is a popular Object Oriented programming language and is used in a multitude of scenarios. It is available under the GNU General Public License for all users. The SDK consists of a large number of tools such as javac that help in application development. Running Java commands from the Command Line Open a Command Line Terminal and enter java followed by the desired command. E.g. to find the version of the SDK java -version Running your code To compile java code, first cd to the location of your .
  • Sumatra PDF on Ivy Windows VM

    Sumatra PDF Overview Sumatra PDF is an open source software to view PDF files in Windows. It could be used to view PDF documents stored within the Ivy VM. As of the latest version, Sumatra supports multiple formats including PDF, EPUB, MOBI, and XPS. Running Sumatra PDF From the Start menu, go to All Programs and search for Sumatra PDF. Click on the icon to run it. More Information For more information, visit the Sumatra PDF official website.
  • Preinstalled R on Ivy Linux VM

    R Overview R is an open source programming language, used by Data Miners, Scientists, Data Analysts, and Statisticians. It is available under the GNU GPL V2 license from the Comprehensive R Archive Network R can be used for many statistical, modeling, and graphical solutions. It is very Object Oriented in nature and is easily extensible. Running the command line R console Type R at the terminal to launch the R console. Installing packages Our Linux VMs come equipped with R preinstalled. Most major R packages are also installed and further could be installed from CRAN using (from within the R console)
  • Preinstalled Python 2 and Python 3 with Anaconda on Ivy Linux VM

    Anaconda Our VMs have python 2 and 3 available as part of the Anaconda distribution. Anaconda comes installed with many packages best suited for scientific computing, data processing, and data analysis, while making deployment very simple. Its package manager conda installs and updates python packages and dependencies, keeping different package versions isolated on a project-by-project basis. Anaconda is available as open source under the New BSD license. It also ships with pip, the common python package manager. Installing packages Packages could be installed via pip or conda package managers Installing packages on a Linux VM A) Using conda Open the bash terminal, and type:
  • Preinstalled Python 2 and Python 3 with Anaconda on Ivy Windows VM

    Anaconda Our VMs have python 2 and 3 available as part of the Anaconda distribution. Anaconda comes installed with many packages best suited for scientific computing, data processing, and data analysis, while making deployment very simple. Its package manager conda installs and updates python packages and dependencies, keeping different package versions isolated on a project-by-project basis. Anaconda is available as open source under the New BSD license. It also ships with pip, the common python package manager. Installing packages Packages could be installed via pip or conda package managers Installing packages on a Windows VM A) Using conda From the Start menu, open a new Command Prompt (or Anaconda prompt) window, and type:
  • Preinstalled Office 2016 on Ivy Windows VM

    Microsoft Office Overview The Ivy Windows VMs are installed with Microsoft Office 2016. Features such as OneDrive are not available since Ivy is not connected to the public internet. Therefore in order to load documents in and out of the VM, you would have to use the Globus DTN. Softwares available The following software are available for use on the Ivy Windows VM: Word 2016 Excel 2016 PowerPoint 2016 Access 2016 OneNote 2016 Outlook 2016 Publisher 2016 Running Office All Office software could be accessed from the Start menu using Start > All Programs More Information For more Information about Microsoft Office, please visit its official website.