Spark Documentation

Apache Spark is an open source cluster-computing framework originally developed in the AMPLab at University of California, Berkeley but was later donated to the Apache Software Foundation where it remains today. In contrast to Hadoop's disk-based analytics paradigm, Spark has multi-stage in-memory analytics. Spark can run programs upto 100x faster than Hadoop’s MapReduce in memory or 10x faster on disk. Spark support applications written in python, java, scala and R


From WARP3D's webpage:

WARP3D is under continuing development as a research code for the solution of large-scale, 3-Dsolid models subjected to static and dynamic loads. The capabilities of the code focus on 
fatigue & fracture analyses primarily in metals. WARP3D runs on laptops-to-supercomputers and can analyze models with several million nodes and elements. 

Availability and Restrictions


The following versions of WARP3D are available on OSC clusters:


R is a language and environment for statistical computing and graphics. It is similar to the S language and environment developed at Bell Laboratories (formerly AT&T, now Lucent Technologies). R provides a wide variety of statistical and graphical techniques and is highly extensible.


Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.


Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command-line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language.

Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, integrating ordinary functions, manipulating polynomials, and integrating ordinary differential and differential-algebraic equations. It is easily extensible and customizable via user-defined functions written in Octave's own language, or using dynamically loaded modules written in C++, C, Fortran, or other languages.


Allinea software analyzes how HPC software runs. It consists of two applications, Allinea Performance Reports and Allinea MAP: 

  • Allinea Performance Reports: simple tool to generate a single-page HTML or plain text report that presents overall performance characteristics of HPC applications.
  • Allinea MAP: HPC application profiler with easy-to-use GUI environment.

Availability & Restrictions


The following versions of Allinea are available on OSC clusters:


BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

Availability and Restrictions

The following versions of BamTools are available on OSC clusters:


STAR: Spliced Transcripts Alignment to a Reference.

Availability and Restrictions

The following versions of STAR are available on OSC clusters:


miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs. The tool reports known and hundreds of novel microRNAs with high accuracy in seven species representing the major animal clades. The low consumption of time and memory combined with user-friendly interactive graphic output makes miRDeep2 accessible for straightforward application in current reasearch.

Availability and Restrictions

The following versions of miRDeep2 are available on OSC clusters:


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