Cluster Documentation Project - New pages [en]

Limulus Manual

2012-05-11T00:30:18Z

Deadline: initial page

=DRAFT VERSION 5/10/12=

== Introduction ==
Welcome to the Limulus Documentation Page

More coming soon.

The [http://limulus.basement-supercomputing.com Limulus Project Page] has news, specifications, and benchmarks. These pages, as part of the Cluster Documentation Project will be software and hardware documentation.

== Hardware ==

== System Software ==

[[Main System Software Page]]
== Support ==

Cluster Documentation Project

2012-05-04T19:46:47Z

Deadline: added indiegogo link

==Background==

The Cluster Documentation Project (CDP) seeks [http://www.indiegogo.com/cluster-documentation-project?a=584398 start-up funding] to create an open community documentation resource that focuses on High Performance Computing (HPC) clusters. The content areas will cover a wide range of both hardware and software issues and is planned to include basic HPC fundamentals, parallel programming, HPC Cloud, GPU computing, software tools and applications, system design and procurement, and more. The project is expected to have a high impact on both users and vendors.

===What You Get And What We Need===

The project will focus on "how to" and essential background information. The resource will be created on-line as a wiki similar to Wikipedia and will be open and shareable to everyone. It will also be possible to create books directly from the wiki content. The entire wiki and any derived books will be available under a Creative Commons license. That is, readers are free to re-use, improve, and republish the information provided they keep the original author(s) attribution and do not charge for the content.

Community members can contribute content to the CDP. The project is seeking to raise $20,000 to support a design/managing editor, copy editors, writers, and graphic artists so the content can be produced and presented in a professional fashion. The more funds we raise the bigger and better the result! Total funds are expected to be used in the following proportions:

*Design/managing editor: 25%
*Copy editor: 20%
*Writers: 45%
*Graphics artists: 7%
*Web site 3%

The project will be managed by Seagrove LLC, the publisher of [http://www.clustermonkey.net Cluster Monkey]. At this point in time, some basic information is already in place at: [http://cdp.clustermonkey.net http://cdp.clustermonkey.net]. As mentioned, the project will also create books directly from the wiki content using the WikiBooks module. At a minimum one new book will be professional produced each year. Books will be freely available in Open Document Format (ODF - OpenOffice format), PDF, and as paper books using print on demand. The inaugural book will be entitled ''Essential HPC: Practical high performance concepts, techniques, and procedures'' and serve as an introduction to HPC.

===The Impact===

An open reservoir of documentation will help grow the community and market. HPC users and vendors are free to use any CDP content for their own projects and products as long as the license terms are maintained. A professional up-to-date documentation resource will bring HPC to new users and markets. Support beyond the initial start-up period is expected to come from the production of CDP books and vendor sponsorship.

===Experience===

The principal editor of the CDP is expected to be Douglas Eadline, a practitioner and chronicler of the Linux Cluster HPC revolution. He has worked with HPC systems since 1988 and is a co-author of the original Beowulf How-To document. Prior to starting and editing the popular Cluster Monkey web site in 2005, he served as Editor-in-chief for ClusterWorld Magazine. He has written numerous articles that have appeared in both print and web based publications and was selected by AMD to write the short, but popular, book ''High Performance Computing for Dummies''.

==Reward Levels==
{| class="wikitable"
| [[File:Blue-Supporter-200x200.png|left]]
|
===Supporter===
Contribution: $25.
Name placed in donors page in Wiki. Can use "Supporter" Badge on website.

===Platinum Supporter===
Contribution: $95.
Same as above and name placed on donor page in inaugural book and exclusive limited print edition of inaugural book.
|-
| [[File:Silver-Corp-Badge-2012-200x200.png|left]]
|
===Silver Corporate Sponsor===
Contribution: $500.
Six month banner advertisement on Wiki. Company/Organization name listed on Silver Corporate
Sponsor Page. Can display Silver Sponsor Badge for 6 months on company website and
collateral material. Single copy of limited print edition of inaugural book.

|-
| [[File:Gold-Corp-Badge-2012-200x200.png|left]]
|
===Gold Corporate Sponsor ===
Contribution: $1000
Twelve month banner advertisement on Wiki. Company/Organization name listed on Wiki Gold Corporate Sponsor Page with link. Name listed in Gold Corporate Sponsor Page of any book produced during 12
month term. Can display Gold Sponsor Badge for twelve months on company website and collateral material. Ten copies of limited print edition of inaugural book.
|-
| [[File:Platinum-Corp-Badge-200x200.png|left]]
|
===Platinum Founding Corporate Sponsor===
Contribution: $5000
Five year banner advertisement on Wiki. Company name and logo listed on Wiki in Platinum Founding Corporate Sponsor Page with link (does not expire). Name listed in Founding Corporate Sponsor Page of any book produced within five years. Can display Platinum Founding Sponsor Badge on company website or collateral material for five years. Twenty five copies of limited print edition of inaugural book.
|}

Programming Tools

2012-03-02T19:04:48Z

Deadline: added erlang, haskell, openmp, OpenACC

==Higher Level==
*[http://www.sagemath.org Sage] is a free open-source mathematics software system licensed under the GPL. It combines the power of many existing open-source packages into a common Python-based interface. The Sage Mission is to create a viable free open source alternative to Magma, Maple, Mathematica and Matlab.
*[http://numpy.scipy.org/ NumPy] is the fundamental package for scientific computing with Python. It contains among other things:
**a powerful N-dimensional array object
**sophisticated (broadcasting) functions
**tools for integrating C/C++ and Fortran code
**useful linear algebra, Fourier transform, and random number capabilities<br>Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. Numpy is licensed under the BSD license, enabling reuse with few restrictions.
*[http://www.r-project.org/ R] is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.
*[http://julialang.org/ Julia] is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library. The library, mostly written in Julia itself, also integrates mature, best-of-breed C and Fortran libraries for linear algebra, random number generation, FFTs, and string processing. More libraries continue to be added over time. Julia programs are organized around defining functions, and overloading them for different combinations of argument types (which can also be user-defined).
*[http://www.erlang.org/ Erlang] Erlang is a programming language used to build massively scalable soft real-time systems with requirements on high availability. Some of its uses are in telecoms, banking, e-commerce, computer telephony and instant messaging. Erlang's runtime system has built-in support for concurrency, distribution and fault tolerance.
*[http://www.haskell.org/haskellwiki/Haskell Haskell] is an advanced purely-functional programming language. An open-source product of more than twenty years of cutting-edge research, it allows rapid development of robust, concise, correct software. With strong support for integration with other languages, built-in concurrency and parallelism, debuggers, profilers, rich libraries and an active community, Haskell makes it easier to produce flexible, maintainable, high-quality software.

== Compiler Enhancements==

These enhancements are used with Fortran and C/C++ compilers.

*[http://openmp.org/wp/ OpenMP] is a standard for parallel programming on shared memory systems, continues to extend its reach beyond pure HPC to include embedded systems, multicore and real time systems. A new version is being developed that will include support for accelerators, error handling, thread affinity, tasking extensions and Fortran 2003. Note: OpenMP is not a cluster programming tool. It works for multi-core cluster nodes and is supported by virtually all compilers.
*[http://www.openacc-standard.org/ OpenACC] is an Application Program Interface (API) that describes a collection of compiler directives to specify loops and regions of code in standard C, C++ and Fortran to be offloaded from a host CPU to an attached accelerator (e.g. GPUs), providing portability across operating systems, host CPUs and accelerators.

== Lower Level Parallel Programming Libraries ==

These are programming libraries that can be used with Fortran, C/C++, and Java.

*[http://www.mcs.anl.gov/research/projects/mpich2/ MPICH2] is a freely available, portable implementation of MPI, the Standard for message-passing libraries.
*[http://mvapich.cse.ohio-state.edu/ MVAPICH2] enhanced MPICH2 version that delivers best performance, scalability and fault tolerance for high-end computing systems and servers using InfiniBand, 10GigE/iWARP and RoCE networking technologies.
*[http://www.open-mpi.org/ Open MPI] is a project combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI) in order to build the best MPI library available. Support runtime selection of interconnect.
*[http://www.jppf.org/ The Java Parallel Processing Framework] is a suite of software libraries and tools providing convenient ways to parallelize CPU-intensive processing. It is written in the Java programming language and is platform independent.
*[http://www.csm.ornl.gov/pvm/pvm_home.html PVM] (Parallel Virtual Machine) is a software package that permits a heterogeneous collection of Unix and/or Windows computers hooked together by a network to be used as a single large parallel computer.