OSC is refreshing the software stack for Oakley and Ruby on February 22, 2017 (during the scheduled downtime). During the software refresh, some default versions are updated to be more up-to-date and some older versions are removed. Information about the old and new default versions, as well as all available versions of each software package will be included on the corresponding OSC software webpage. See https://www.osc.edu/supercomputing/software-list.
A hadoop cluster can be launched within the HPC environment, but managed by the PBS job scheduler using Myhadoop framework developed by San Diego Supercomputer Center. (Please see http://www.sdsc.edu/~allans/MyHadoop.pdf)
This documentation is to discuss how to run STAR-CCM+ to STAR-CCM+ Coupling simulation in batch job at OSC. The following example demonstrates the process of using STAR-CCM+ version 11.02.010 on Owens. Depending on the version of STAR-CCM+ and cluster you work on, there mighe be some differences from the example. Feel free to contact OSC Help if you have any questions.
Darshan is a lightweight "scalable HPC I/O characterization tool
Availability and Restrictions
The following versions of Darshan are available on OSC clusters:
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
Caffe is "
From their README:
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.
Bowtie2 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.