Cluster Documentation Project - User contributions [en]

CAE/CAD/EDA Modeling

2018-09-11T12:41:48Z

Deadline: added FreeCAD and OpenSCAD

* [http://sourceforge.net/projects/brlcad/ BRL-CAD] is a powerful cross-platform constructive solid geometry solid modeling system that includes an interactive geometry editor, ray-tracing for rendering & geometric analyses, network distributed framebuffer support, image & signal-processing tools.

* [http://www.salome-platform.org/ SALOME] is an open-source software that provides a generic platform for Pre- and Post-Processing for numerical simulation. It is based on an open and flexible architecture made of reusable components. SALOME can be used as standalone application for generation of CAD models, their preparation for numerical calculations and post-processing of the calculation results. SALOME can also be used as a platform for integration of the external third-party numerical codes to produce a new application for the full life-cycle management of CAD models.

* [http://www.code-aster.org/V2/spip.php?rubrique2 Code_Aster] is an Open Source software package for Civil and Structural Engineering finite element analysis and numeric simulation in structural mechanics originally developed as an in-house application by the French company EDF. This tool covers a large range of applications : 3D thermal analyses and mechanical analyses in linear and non-linear statics and dynamics, for machines, pressure vessels and civil engineering structures. Beyond the standard functionalities of a FEM software for solid mechanics, Code_Aster compiles specific research in various fields : fatigue, damage, fracture, contact, geomaterials, porous media, multi-physics coupling. It is widely used at EDF for the expertise and the maintenance of power plants and electrical networks.

* [http://kicad-pcb.org KiCad EDA] is a free software suite for electronic design automation (EDA). It facilitates the design of schematics for electronic circuits and their conversion to PCB designs. KiCad was originally developed by Jean-Pierre Charras. It features an integrated environment for schematic capture and PCB layout design. Tools exist within the package to create a bill of materials, artwork, Gerber files, and 3D views of the PCB and its components.

* [http://www.wings3d.com/ Wings 3D] is an advanced subdivision modeler that is both powerful and easy to use. Wings 3D offers a wide range of modeling tools, a customizable interface, support for lights and materials, and a built-in AutoUV mapping facility. There is no support in Wings for animation. Originally inspired by Nendo and Mirai from Izware, Wings 3D has been developed since 2001, when Björn Gustavsson (bjorng) and Dan Gudmundsson (dgud) first started the project. Richard Jones (optigon) maintained Wings and coded many new features between 2006 and 2011. Wings 3D is currently maintained by Dan and Richard with the help of the great community.

* [https://www.freecadweb.org FreeCAD] is a free and open-source (under the LGPLv2+ license) general-purpose parametric 3D CAD modeler and a building information modeling (BIM) software with finite-element-method (FEM) support. FreeCAD is aimed directly at mechanical engineering product design but also expands to a wider range of uses around engineering, such as architecture or electrical engineering. FreeCAD can be used interactively, or its functionality can be accessed and extended using the Python programming language and is currently in a beta stage of development.

* [http://www.openscad.org OpenSCAD] is a free software application for creating solid 3D CAD (computer-aided design) objects. It is a script-only based modeller that uses its own description language; parts can be previewed, but it cannot be interactively selected or modified by mouse in the 3D view. An OpenSCAD script specifies geometric primitives (such as spheres, boxes, cylinders, etc.) and defines how they are modified and combined (for instance by intersection, difference, envelope combination and Minkowski sums) to render a 3D model. As such, the program does constructive solid geometry (CSG). OpenSCAD is available for Windows, Linux and OS X.

CAE/CAD/EDA Modeling

2018-09-11T12:34:04Z

Deadline: added wings 3d

CAE/CAD Modeling

2018-09-11T12:30:08Z

Deadline: Deadline moved page CAE/CAD Modeling to CAE/CAD/EDA Modeling

#REDIRECT [[CAE/CAD/EDA Modeling]]

CAE/CAD/EDA Modeling

2018-09-11T12:30:07Z

Deadline: Deadline moved page CAE/CAD Modeling to CAE/CAD/EDA Modeling

Open/Freely Available Cluster Applications

2018-09-11T12:28:41Z

Deadline: added EDA

Below are the various categories of Cluster HPC applications. Please note, most of these applications are parallel (i.e. MPI applications).

You may also find other applications from [http://en.wikipedia.org/wiki/List_of_free_and_open_source_software_packages List of Free and Open Software Packages ]

* [[Aerospace]]
* [[Bioinformatics]]
* [[CAE/CAD/EDA Modeling]]
* [[Cosmology]]
* [[Computational Fluid Dynamics]]
* [[Database]]
* [[Electronic Structure/Quantum Chemistry]]
* [[Finite Element Analysis]]
* [[Molecular Modeling]]
* [[Oil and Gas]]
* [[Visualization/Rendering]]
* [[Weather Modeling]]

* [[Other]]

CAE/CAD/EDA Modeling

2018-09-11T12:27:53Z

Deadline: added kicad

Statcounter-project-id

2018-08-17T16:26:20Z

Deadline: Created page with "1303510"

1303510

Other

2017-08-05T16:24:30Z

Deadline: updated caos link

'''Genetic Algorithms'''

* [http://ftp.mcs.anl.gov/pub/pgapack/ PGAPack] (Parallel Genetic Algorithm Package) a general-purpose, data-structure-neutral, parallel genetic algorithm library developed at Argonne National Laboratory.
* [http://www.cisl.ucar.edu/css/staff/travis/mpikaia/ MPIKAIA] is a slightly modified version of the PIKAIA 1.2 code developed by Paul Charbonneau and Barry Knapp at the High Altitude Observatory. It uses MPI code to parallelize the "Full Generational Replacement" evolutionary strategy. This package comes with a sample fitness function, which you should replace with your own function/model after you successfully compile and run the sample code.
* [http://gpocl.sourceforge.net/ GPOLC] (Genetic Programming in OpenCL) is a parallel implementation of genetic programming targeted at heterogeneous devices, such as CPU and GPU. It is written in OpenCL, an open standard for portable parallel programming across many computing platforms.

'''Cellular Automata'''
* [https://staff.fnwi.uva.nl/c.u.grelck/caos.html CAOS] (Cells, Agents and Observers for Simulation) is a high-level domain-specific programming language for the definition of extended cellular automata and their parallel simulation on shared and distributed memory computing architectures.
* [http://code.google.com/p/reaction-diffusion/ Ready] is a program for exploring continuous cellular automata, including reaction-diffusion systems, on grids and arbitrary meshes. OpenCL is used as the computation engine, to take advantage of the many-core architectures on graphics cards and modern CPUs. OpenCL also allows rules to be written in a text format and compiled on the fly. Ready supports a compact XML-based file format so that images and rules can be shared easily.

'''Scientific Data Mining'''
* [http://www.nutonian.com/ Eureqa II] is a scientific data mining software package that searches for mathematical patterns hidden in your data. Free download for a single computer.

Programming Tools

2017-03-17T18:28:07Z

Deadline: added Linux performance page

==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/Code Conversion==

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.
*[http://people.nas.nasa.gov/~hjin/CAPO/ CAPO ] (Computer-Aided Parallelizer and Optimizer) automates the insertion of compiler directives to facilitate parallel processing on shared memory parallel (SMP) machines. While CAPO is currently integrated seamlessly into CAPTools (developed at the University of Greenwich, now marketed as ParaWise) CAPO is independently developed at NASA Ames Research Center as one of the components for the Legacy Code Modernization (LCM) project. The current version takes serial FORTRAN programs, performs interprocedual data dependence analysis, and generates OpenMP directives. Due to the widely support of the OpenMP standard, the generated OpenMP codes can potentially run on a wide range of SMP machines.

== 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.

==Profilers Analyzers==
*[http://www.mcs.anl.gov/research/projects/perfvis/software/viewers/index.htm Jumpshot] is a Java-based visualization tool for doing postmortem performance MPICH2 analysis.
*[http://mpip.sourceforge.net/ mpiP]is a lightweight profiling library for MPI applications. Because it only collects statistical information about MPI functions, mpiP generates considerably less overhead and much less data than tracing tools. All the information captured by mpiP is task-local. It only uses communication during report generation, typically at the end of the experiment, to merge results from all of the tasks into one output file.
*[http://www.openspeedshop.org/wp/ Open|SpeedShop] is explicitly designed with usability in mind and is for application developers and computer scientists. The base functionality include, Sampling Experiments, Support for Callstack Analysis, Hardware Performance Counters, MPI Profiling and Tracing,I/O Profiling and Tracing, and Floating Point Exception Analysis. In addition, Open|SpeedShop is designed to be modular and extensible. It supports several levels of plug-ins which allow users to add their own performance experiments.
*[http://developer.amd.com/tools/codeanalyst/pages/default.aspx AMD CodeAnalyst] Performance Analyzer helps software developers to improve the performance of applications, drivers and system software. Well-tuned software delivers a better end-user experience through shorter response time, increased throughput and better resource utilization.
*[http://ipm-hpc.sourceforge.net/ IPM] is a portable profiling infrastructure for parallel codes. It provides a low-overhead performance profile of the performance aspects and resource utilization in a parallel program. Communication, computation, and IO are the primary focus. While the design scope targets production computing in HPC centers, IPM has found use in application development, performance debugging and parallel computing education.
*[http://hpctoolkit.org/index.html HPCToolkit] is an integrated suite of tools for measurement and analysis of program performance on computers ranging from multicore desktop systems to the nation's largest supercomputers. By using statistical sampling of timers and hardware performance counters, HPCToolkit collects accurate measurements of a program's work, resource consumption, and inefficiency and attributes them to the full calling context in which they occur. HPCToolkit works with multilingual, fully optimized applications that are statically or dynamically linked. Since HPCToolkit uses sampling, measurement has low overhead (1-5%) and scales to large parallel systems. HPCToolkit's presentation tools enable rapid analysis of a program's execution costs, inefficiency, and scaling characteristics both within and across nodes of a parallel system. HPCToolkit supports measurement and analysis of serial codes, threaded codes (e.g. pthreads, OpenMP), MPI, and hybrid (MPI+threads) parallel codes.
*[http://www.brendangregg.com/linuxperf.html This Page ] provides a nice map of Linux performance "zones" in the kernel and the tools that are used to analyze them. Includes slide decks on Linux performance.

==Parallel Debuggers==
*[http://padb.pittman.org.uk/ Padb] is a Job Inspection Tool for examining and debugging parallel programs, primarily it simplifies the process of gathering stack traces on compute clusters however it also supports a wide range of other functions. Padb supports a number of parallel environments and it works out-of-the-box on the majority of clusters. It's an open source, non-interactive, command line, script-able tool intended for use by programmers and system administrators alike.

Essential HPC

2017-02-14T19:48:15Z

Deadline:

__NOTOC__
''Practical High Performance Concepts, Techniques, and Procedures''

This book will be based on CDP wiki content and is intended to help answer questions and get your HPC projects moving forward quickly. The book is expected to be available in the near future. A soft version will be available at no charge and a special limited edition hard copy will be printed "on demand." We are looking for sponsors for a SC 2017 version. (more details soon)

==Tentative Table of Contents==
[[File:E-HPC-cover2.png|right|alt=Book Cover|400x618px]]
=== Fundamental Concepts ===
*What is HPC and Why Does It Matter
*Introduction To Building Blocks
*Setting Expectations
*Parallel and Distributed Computing 101
*What Do I Need to Know As An Administrator?
*What Do I need to Know As A User?
===Taking The First Steps===
*It all Depends
*Understanding Costs
*Success Metrics
*Choosing Hardware
*Choosing Software
*Using A Cloud
===Techniques===
*Using an Open Approach To HPC
*Designing Your Solution
*Cluster Provisioning and Control
*Sharing The Resource
*Parallel Programming
===Procedures===
*Software Management
*File Systems
*Testing and Tuning
*Monitoring
===Next Steps===
*HPC Applications
*Other Resources

Funding The Cluster Documentation Project

2017-02-14T19:47:25Z

Deadline: /* Credible and Professional */

==A Unique and Effective Sponsorship Opportunity==

The Cluster Documentation Project (CDP) is seeking corporate and organizational sponsors to help fund additional content. 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, Hadoop and Big Data, software tools and applications, system design and procurement, and more. The project is expected to have a high impact on both users and vendors.

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.

===Wrap a Book Around Your Technology or Service===

Getting your message out to the HPC community and market is important. New and existing HPC users are constantly searching the Internet for up-to-date and accurate information, and the CDP is designed to be the first place users land when they are seeking cluster and HPC insights. You need to be there. In addition to contributing your technical value proposition, the CDP offers both banner ad and logo branding. We can also help you use the CDP to '''create professionally branded manuals, books, and documentation for your customers'''.

Understanding the full impact of an HPC product or service can require deep technical conversations. Companies often
produce high-level white papers to help explain new products and services. The CDP can be used to create short booklets or small books
that help potential customer fully understand your '''technological value proposition''' and give weight to your sales approach.

In order to kick-start the project, we will be releasing our first free book, entitled ''[[Essential HPC]]: Practical high performance concepts, techniques, and procedures.'' We are seeking sponsors for the 2017 edition Please contact [http://www.xandmarketing.com/contact.php Xand Marketing] for more details.

===Credible and Professional===

The principal editor of the CDP will be Douglas Eadline, a practitioner and chronicler of the Linux Cluster HPC revolution. Doug 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. Doug has written numerous articles in both print and web-based publications and was selected by AMD to write the short, but popular, book High Performance Computing for Dummies. He has also co-authored books on Big Data and Hadoop. A team of capable and experienced writers, editors, and artists has been assembled to work with Doug to create a professional resource for the entire community.

The project will be managed by [http://www.xandmarketing.com/ Xand Marketing] and Seagrove LLC, the publisher of [http://www.clustermonkey.net Cluster Monkey]. At this point in time, some basic information is already in place As mentioned, the project will also create books directly from the wiki content (print-on-demand and ebooks). At a minimum one new book will be professional produced each year. Most 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 Big Picture==

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. Continued support beyond the initial start-up period is expected to come from the production of CDP books and vendor sponsorships.

Beowulf Cluster History Project

2016-11-28T18:35:35Z

Deadline: Protected "Beowulf Cluster History Project" ([Edit=Allow only autoconfirmed users] (indefinite) [Move=Allow only autoconfirmed users] (indefinite))

==The Beowulf Cluster History Project ==

History links, pictures

Beowulf Cluster History Project

2016-11-28T18:32:13Z

Deadline: Initial creation

==The Beowulf Cluster History Project ==

History links, pictures

Main Page

2016-11-28T18:30:05Z

Deadline: added BCHP

__NOTOC__
== Cluster Documentation Project™ ==
[[File:cdp_logo_1.png|left|250x250px]]
Looking for Cluster Documentation? Jump right to [[Cluster Topics]].

Computational Clusters have grown from a back room curiosity to a driving force in the HPC community. The roll your own nature of cluster computing has also created a wide community of users, vendors, and applications. The Cluster Documentation Project (CDP) is an effort to help document best practices, tutorials, projects, benchmarks, products, and anything else that helps facilitate HPC cluster computing.

'''We plan on releasing our first book at in the near future ''' -- ''[[Essential HPC]]: Practical high performance concepts, techniques, and procedures''

'''VENDORS DON'T MISS A UNIQUE AND EFFECTIVE SPONSORSHIP OPPORTUNITY: [[Funding The Cluster Documentation Project]]'''

[[File:E-HPC-cover2.png|thumb|alt=Book Cover.|Contents [[Essential HPC]]]]

===Project Scope===

The word [http://en.wikipedia.org/wiki/Computer_cluster cluster] has many meanings. The Cluster Documentation Project is designed to document and professionally publish High Performance Computing (HPC) Cluster information. The focus will be on tutorial and how-to information rather than theoretical aspects of HPC. Currently there are [[Cluster Topics]] which is a compendium of current benchmarks, products, technologies, methods, best practices, etc. that will help those interested in clustering. When funded the project will enhance this resource.

See a recent [http://www.admin-magazine.com/HPC/Articles/Cluster-Documentation-Project/%28language%29/eng-US article] in HPC Admin magazine for more background.

[[Beowulf Cluster History Project]]

===Writers and Contributors===

Contributions are accepted from the community -- both users and vendors. All content is subject to approval by the editors and critical content will be created with paid experienced writers. If you are interested in contributing please join the [http://www.clustermonkey.net/mailman/listinfo/hpc-writers HPC Writers list]. All submitted content will be made available under a [http://creativecommons.org/licenses/by-nc-sa/2.5/ Creative Commons License].

===Questions===
If you have specific questions about clusters please visit our [[Cluster Questions]] section and enter your question.

If you have questions about this site, please contact [http://www.clustermonkey.net//component/option,com_contact/task,view/contact_id,1/Itemid,3/ Douglas Eadline] with any questions.

===History===
ClusterWorld magazine was the initial sponsor of a site called The Cluster Agenda. When ClusterWorld Magazine ceased publication the Agenda effort was stopped. Douglas Eadline, editor of ClusterWorld magazine, was the principle organizer of the Agenda effort and has decided with the help of Jeff Layton to preserve some of the content from the Agenda and morph the site into Cluster Tweaks. The original Agenda Working Committee was Jeff Layton, Glen Otero, Dan Stanzione, and Douglas Eadline.

Programming Tools

2016-09-05T18:14:27Z

Deadline: added CAPO

==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/Code Conversion==

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.
*[http://people.nas.nasa.gov/~hjin/CAPO/ CAPO ] (Computer-Aided Parallelizer and Optimizer) automates the insertion of compiler directives to facilitate parallel processing on shared memory parallel (SMP) machines. While CAPO is currently integrated seamlessly into CAPTools (developed at the University of Greenwich, now marketed as ParaWise) CAPO is independently developed at NASA Ames Research Center as one of the components for the Legacy Code Modernization (LCM) project. The current version takes serial FORTRAN programs, performs interprocedual data dependence analysis, and generates OpenMP directives. Due to the widely support of the OpenMP standard, the generated OpenMP codes can potentially run on a wide range of SMP machines.

== 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.

==Profilers Analyzers==
*[http://www.mcs.anl.gov/research/projects/perfvis/software/viewers/index.htm Jumpshot] is a Java-based visualization tool for doing postmortem performance MPICH2 analysis.
*[http://mpip.sourceforge.net/ mpiP]is a lightweight profiling library for MPI applications. Because it only collects statistical information about MPI functions, mpiP generates considerably less overhead and much less data than tracing tools. All the information captured by mpiP is task-local. It only uses communication during report generation, typically at the end of the experiment, to merge results from all of the tasks into one output file.
*[http://www.openspeedshop.org/wp/ Open|SpeedShop] is explicitly designed with usability in mind and is for application developers and computer scientists. The base functionality include, Sampling Experiments, Support for Callstack Analysis, Hardware Performance Counters, MPI Profiling and Tracing,I/O Profiling and Tracing, and Floating Point Exception Analysis. In addition, Open|SpeedShop is designed to be modular and extensible. It supports several levels of plug-ins which allow users to add their own performance experiments.
*[http://developer.amd.com/tools/codeanalyst/pages/default.aspx AMD CodeAnalyst] Performance Analyzer helps software developers to improve the performance of applications, drivers and system software. Well-tuned software delivers a better end-user experience through shorter response time, increased throughput and better resource utilization.
*[http://ipm-hpc.sourceforge.net/ IPM] is a portable profiling infrastructure for parallel codes. It provides a low-overhead performance profile of the performance aspects and resource utilization in a parallel program. Communication, computation, and IO are the primary focus. While the design scope targets production computing in HPC centers, IPM has found use in application development, performance debugging and parallel computing education.
*[http://hpctoolkit.org/index.html HPCToolkit] is an integrated suite of tools for measurement and analysis of program performance on computers ranging from multicore desktop systems to the nation's largest supercomputers. By using statistical sampling of timers and hardware performance counters, HPCToolkit collects accurate measurements of a program's work, resource consumption, and inefficiency and attributes them to the full calling context in which they occur. HPCToolkit works with multilingual, fully optimized applications that are statically or dynamically linked. Since HPCToolkit uses sampling, measurement has low overhead (1-5%) and scales to large parallel systems. HPCToolkit's presentation tools enable rapid analysis of a program's execution costs, inefficiency, and scaling characteristics both within and across nodes of a parallel system. HPCToolkit supports measurement and analysis of serial codes, threaded codes (e.g. pthreads, OpenMP), MPI, and hybrid (MPI+threads) parallel codes.

==Parallel Debuggers==
*[http://padb.pittman.org.uk/ Padb] is a Job Inspection Tool for examining and debugging parallel programs, primarily it simplifies the process of gathering stack traces on compute clusters however it also supports a wide range of other functions. Padb supports a number of parallel environments and it works out-of-the-box on the majority of clusters. It's an open source, non-interactive, command line, script-able tool intended for use by programmers and system administrators alike.

Funding The Cluster Documentation Project

2016-09-01T14:06:58Z

Deadline:

==A Unique and Effective Sponsorship Opportunity==

The Cluster Documentation Project (CDP) is seeking corporate and organizational sponsors to help fund additional content. 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, Hadoop and Big Data, software tools and applications, system design and procurement, and more. The project is expected to have a high impact on both users and vendors.

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.

===Wrap a Book Around Your Technology or Service===

Getting your message out to the HPC community and market is important. New and existing HPC users are constantly searching the Internet for up-to-date and accurate information, and the CDP is designed to be the first place users land when they are seeking cluster and HPC insights. You need to be there. In addition to contributing your technical value proposition, the CDP offers both banner ad and logo branding. We can also help you use the CDP to '''create professionally branded manuals, books, and documentation for your customers'''.

Understanding the full impact of an HPC product or service can require deep technical conversations. Companies often
produce high-level white papers to help explain new products and services. The CDP can be used to create short booklets or small books
that help potential customer fully understand your '''technological value proposition''' and give weight to your sales approach.

In order to kick-start the project, we will be releasing our first free book, entitled ''[[Essential HPC]]: Practical high performance concepts, techniques, and procedures.'' We are seeking sponsors for the 2017 edition Please contact [http://www.xandmarketing.com/contact.php Xand Marketing] for more details.

===Credible and Professional===

The principal editor of the CDP will be Douglas Eadline, a practitioner and chronicler of the Linux Cluster HPC revolution. Doug 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. Doug has written numerous articles in both print and web-based publications and was selected by AMD to write the short, but popular, book High Performance Computing for Dummies. He has also co-authored books on Big Data and Hadoop. A team of capable and experienced writers, editors, and artists has been assembled to work with Doug to create a professional resource for the entire community.

The project will be managed by [http://www.xandmarketing.com/ Xand Marketing] and Seagrove LLC, the publisher of [http://www.clustermonkey.net Cluster Monkey]. At this point in time, some basic information is already in place 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 Big Picture==

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. Continued support beyond the initial start-up period is expected to come from the production of CDP books and vendor sponsorships.

Essential HPC

2016-09-01T14:03:48Z

Deadline: updated dates

__NOTOC__
''Practical High Performance Concepts, Techniques, and Procedures''

This book will be based on CDP wiki content and is intended to help answer questions and get your HPC projects moving forward quickly. The book is expected to be available in the near future. A soft version will be available at no charge and a special limited edition hard copy will be printed "on demand." We are looking for sponsors for a SC 2016 version. (more details soon)

==Tentative Table of Contents==
[[File:E-HPC-cover2.png|right|alt=Book Cover|400x618px]]
=== Fundamental Concepts ===
*What is HPC and Why Does It Matter
*Introduction To Building Blocks
*Setting Expectations
*Parallel and Distributed Computing 101
*What Do I Need to Know As An Administrator?
*What Do I need to Know As A User?
===Taking The First Steps===
*It all Depends
*Understanding Costs
*Success Metrics
*Choosing Hardware
*Choosing Software
*Using A Cloud
===Techniques===
*Using an Open Approach To HPC
*Designing Your Solution
*Cluster Provisioning and Control
*Sharing The Resource
*Parallel Programming
===Procedures===
*Software Management
*File Systems
*Testing and Tuning
*Monitoring
===Next Steps===
*HPC Applications
*Other Resources

Main Page

2016-09-01T14:02:43Z

Deadline: change SC15 to the near future for release data

__NOTOC__
== Cluster Documentation Project™ ==
[[File:cdp_logo_1.png|left|250x250px]]
Looking for Cluster Documentation? Jump right to [[Cluster Topics]].

Computational Clusters have grown from a back room curiosity to a driving force in the HPC community. The roll your own nature of cluster computing has also created a wide community of users, vendors, and applications. The Cluster Documentation Project (CDP) is an effort to help document best practices, tutorials, projects, benchmarks, products, and anything else that helps facilitate HPC cluster computing.

'''We plan on releasing our first book at in the near future ''' -- ''[[Essential HPC]]: Practical high performance concepts, techniques, and procedures''

'''VENDORS DON'T MISS A UNIQUE AND EFFECTIVE SPONSORSHIP OPPORTUNITY: [[Funding The Cluster Documentation Project]]'''

[[File:E-HPC-cover2.png|thumb|alt=Book Cover.|Contents [[Essential HPC]]]]

===Project Scope===

The word [http://en.wikipedia.org/wiki/Computer_cluster cluster] has many meanings. The Cluster Documentation Project is designed to document and professionally publish High Performance Computing (HPC) Cluster information. The focus will be on tutorial and how-to information rather than theoretical aspects of HPC. Currently there are [[Cluster Topics]] which is a compendium of current benchmarks, products, technologies, methods, best practices, etc. that will help those interested in clustering. When funded the project will enhance this resource.

See a recent [http://www.admin-magazine.com/HPC/Articles/Cluster-Documentation-Project/%28language%29/eng-US article] in HPC Admin magazine for more background.

===Writers and Contributors===

Contributions are accepted from the community -- both users and vendors. All content is subject to approval by the editors and critical content will be created with paid experienced writers. If you are interested in contributing please join the [http://www.clustermonkey.net/mailman/listinfo/hpc-writers HPC Writers list]. All submitted content will be made available under a [http://creativecommons.org/licenses/by-nc-sa/2.5/ Creative Commons License].

===Questions===
If you have specific questions about clusters please visit our [[Cluster Questions]] section and enter your question.

If you have questions about this site, please contact [http://www.clustermonkey.net//component/option,com_contact/task,view/contact_id,1/Itemid,3/ Douglas Eadline] with any questions.

===History===
ClusterWorld magazine was the initial sponsor of a site called The Cluster Agenda. When ClusterWorld Magazine ceased publication the Agenda effort was stopped. Douglas Eadline, editor of ClusterWorld magazine, was the principle organizer of the Agenda effort and has decided with the help of Jeff Layton to preserve some of the content from the Agenda and morph the site into Cluster Tweaks. The original Agenda Working Committee was Jeff Layton, Glen Otero, Dan Stanzione, and Douglas Eadline.

Cluster Benchmarking Packages

2016-09-01T13:59:05Z

Deadline: added GPU tests

Here are some links to benchmarks:

'''Benchmark Suites'''
* [http://icl.cs.utk.edu/hpcc/ HPCC Challange Benchmark] - uses seven tests to measure several different performance parameters.
* [http://www.clustermonkey.net//content/view/38/27/ Beowulf Perforamnce Suite (BPS)] - Example results are [http://clustermonkey.net/download/kronos/bps-logs/ here].
* [http://www.nas.nasa.gov/Resources/Software/npb.html NASA Parallel Benchmarks] - One of the most, if not the most, widely used set of benchmarks for clusters.
* [https://software.intel.com/en-us/articles/intel-mpi-benchmarks/ Intel MPI Benchmarks] - freely available.
* [http://perfbase.tigris.org/ perfbase] - a set of front end tools using a PostgreSQL database as backend, which together form a system for the management and analysis of the output of tests and experiments.
* [http://liinwww.ira.uka.de/~skampi/ SKaMPI] - a suite of tests designed to measure the performance of MPI.
* [http://sourceforge.net/apps/trac/cbench/ Cbench] - a Perl-based scripting framework for building, running, and analyzing the output of various opensource codes
* [http://accc.riken.jp/HPC_e/himenobmt_e.html Himeno] Dr. Ryutaro Himeno, Director of the Advanced Center for Computing and Communication, has developedbenchmark to evaluate performance of incompressible fluid analysis code. This benchmark program takes measurements to proceed major loops in solving the Poisson's equation solution using the Jacobi iteration method. Being the code very simple and easy to compile and to execute, users can measure actual speed (in MFLOPS) immediately.
* [https://github.com/EPCCed ADEPT Benchmark] - a suite that addresses the power usage of parallel technologies. [http://www.adept-project.eu/ Adept] builds on the expertise of software developers from high-performance computing (HPC) to exploit parallelism for performance, and on the expertise of Embedded systems engineers in managing energy usage.

'''File Systems I/O'''

* [http://www.nus.edu.sg/comcen/svu/publications/hpc_nus/sep_2005/Performance.pdf GPFS vs. NFS evaluation]
* EXT3, EXT3, Reiser, JFS, XFS benchmarks [http://linuxgazette.net/102/piszcz.html Part 1] and [http://linuxgazette.net/122/piszcz.html Part 2]
* [http://www.clustermonkey.net/ Cluster Monkey] Series on Parallel File System Benchmarking
** [http://www.clustermonkey.net//content/view/62/28/ Benchmarking Parallel File Systems]
** [http://www.clustermonkey.net//content/view/87/32/ A Benchmark for Parallel File Systems]
** [http://www.clustermonkey.net//content/view/117/32/ Using the PIO Benchmark ]
* [http://stromberg.dnsalias.org/~strombrg/nfs-test.html nfs-test] is a program that tries a bunch of different rsizes, wsizes, protocols (tcp vs udp) and NFS versions to optimize performance
* [http://www.iozone.org IOZONE] Filesystem Benchmark
* [http://public.lanl.gov/jnunez/benchmarks/mpiiotest.htm MPI-IO Test] LANL's MPI-IO Test (The best test for MPI-IO codes)
* [http://www.llnl.gov/icc/lc/siop/downloads/download.html Livermore File System Tests] A collection of tests from Lawrence Livermore for testing parallel IO file systems. This include IOR (a great test for parallel file systems) and a bunch of metadata tests

'''Individual Codes for Benchmarks'''

These are codes that you can download (freely) and use for benchmarking. Some of them have benchmark results available and some don't.

* [http://www.gromacs.org/ Gromacs] - A great benchmark code. 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 and lipids that have a lot of complicated bonded interactions.\
* [http://hmmer.janelia.org/ HMMER] HMMER is used for profiling hidden Markov models (profile HMMs) to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.
* [http://gfs.sourceforge.net/ Gerris] - Gerris is an Open Source Free Software library for the solution of the partial differential equations describing fluid flow.
* [http://www.hlrs.de/people/resch/PROJECTS/PARACFD.html ParaCFD] While this is an old CFD benchmark, I think it is still useful. It contains both an OpenMP version and a MPI version.
* [http://www.mgnet.org/mgnet-codes.html MGNet] - A collection of Multi-Grid codes that you can use for benchmarking. There are no published results, but there are some MPI codes that you can use for benchmarks.

'''Network Benchmarks'''

These benchmarks can be used to test the networking aspects of cluster codes. Some of them can test the entire fabric and some test just a pair of nodes.
* [http://www.scl.ameslab.gov/netpipe/ NetPIPE] - One of the best network benchmarks. It tests a range of packet sizes and measures the time (bandwidth). It can use MPI as the message sending mechanism so it allows you to also test MPI implementations.
* [http://www.netperf.org/netperf/ Netperf] - Another good networking benchmark that is used frequently.

'''GPU Benchmarks/Tests'''
* [https://sourceforge.net/projects/cudagpumemtest CUDA GPU memtest] is a GPU memory test utility for NVIDIA and AMD GPUs using well established patterns from memtest86/memtest86+ as well as additional stress tests. The tests are designed to find hardware and soft errors. The code is written in CUDA and OpenCL.
* [https://github.com/ihaque/memtestCL MemtestCL] is a program to test the memory and logic of OpenCL-enabled GPUs, CPUs, and accelerators for errors. It is an OpenCL port of our CUDA- based tester for NVIDIA GPUs, MemtestG80.
* [https://launchpad.net/clamity Calamity] - is a testing framework that allows you test how your GPU is working, by running various tests. With its plugin system it can be expanded to test for more than just the core set.
* [https://github.com/Microway/gpu-burn GPU-Burn] thoroughly exercises the math units on NVIDIA GPUs. It is capable of stressing both the single-precision (32-bit) and double-precision (64-bit) math units of any GPU with CUDA support. Generally-speaking, this means any NVIDIA Tesla, Quadro or GeForce GPU released after 2010. During startup, all GPUs in the system are discovered and tests are run on each. As the tool runs, the status of each GPU is output (including number of passes, number of errors encountered, and current GPU temperatures).

Finite Element Analysis

2015-12-03T15:22:12Z

Deadline: added ASL

[http://en.wikipedia.org/wiki/Finite_element Finite Element] Analysis is a very computational intensive technique for solving a wide range of problems. This page will give you some suggestions for improving FEM performance of ISV codes such as [http://www.simulia.com/products/abaqus_fea.html Abaqus], [http://www.ansys.com/products/default.asp ANSYS], and [http://www.mscsoftware.com/products/nastran.cfm?Q=131&Z=457&Y=401 Nastran], as well as open-source codes such as [http://opensees.berkeley.edu/index.php OpenSees], [http://tahoe.ca.sandia.gov/ Tahoe], [http://www.oofem.org/en/oofem.html OOFEM], [http://www.calculix.de/ Calculix], [http://impact.sourceforge.net/ Impact], [http://www.csc.fi/english/pages/elmer Elmer], [http://cern49.cee.uiuc.edu/cfm/warp3d.html Warp3D], [http://mechsys.nongnu.org/index.shtml MechSysNG], [http://www.cimne.com/kratos/ Kratos], [http://sokocalo.engr.ucdavis.edu/~jeremic/PDD/ PDD], [http://adventure.sys.t.u-tokyo.ac.jp/ Adventure], [http://www.dealii.org/ deal.ii] [http://geofem.tokyo.rist.or.jp/ GeoFEM], [http://code.google.com/p/parafem/ ParaFEM] that are focused on solving solid mechanics problems with FEA techniques.

== Popular Open Source Packages ==

*[http://www.csc.fi/english/pages/elmer Elmer] is an open source multiphysical simulation software developed by CSC. Elmer development was started 1995 in collaboration with Finnish Universities, research institutes and industry. Elmer includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics, for example. These are described by partial differential equations which Elmer solves by the Finite Element Method (FEM).
*[http://impact.sourceforge.net/ Impact] is an open source finite element program suite which can be used to predict most dynamic events such as car crashes or metal sheet punch operations. They usually involve large deformations and high velocities. Simulations are made on a virtual three dimensional model which can be created with a pre-processor or with the built-in Fembic language. Results are viewed in a post-processor.
*[http://cern49.cee.uiuc.edu/cfm/warp3d.html WARP3D] is under continuing development as a research code for the solution of very large-scale, 3-D solid models subjected to static and dynamic loads. Specific features in the code oriented toward the investigation of fracture in metals include a robust finite strain formulation, a general J-integral computation facility (with inertia, thermal, face loading), interaction integrals for computation of linear-elastic fracture parameters, very general element extinction and node release facilities to model crack growth, nonlinear material models including viscoplastic and cyclic, cohesive elements and cohesive constitutive models, and the Gurson-Tvergaard dilatant plasticity model for void growth.
*[http://www.physics.drexel.edu/~olson/paramesh-doc/Users_manual/amr.html PARAMESH] is a package of Fortran 90 subroutines designed to provide an application developer with an easy route to extend an existing serial code which uses a logically cartesian structured mesh into a parallel code with adaptive mesh refinement(AMR). Alternatively, in its simplest use, and with minimal effort, it can operate as a domain decomposition tool for users who want to parallelize their serial codes, but who do not wish to use adaptivity. The package builds a hierarchy of sub-grids to cover the computational domain, with spatial resolution varying to satisfy the demands of the application. These sub-grid blocks form the nodes of a tree data-structure (quad-tree in 2D or oct-tree in 3D). Each grid block has a logically cartesian mesh.
*[http://mooseframework.org/ MOOSE ] or Multiphysics Object-Oriented Simulation Environment (MOOSE) is a finite-element, multiphysics framework primarily developed by Idaho National Laboratory. It provides a high-level interface to some of the most sophisticated nonlinear solver technology on the planet. MOOSE presents a straightforward API that aligns well with the real-world problems scientists and engineers need to tackle. Every detail about how an engineer interacts with MOOSE has been thought through, from the installation process through running your simulation on state of the art supercomputers, the MOOSE system will accelerate your research.
*[http://asl.org.il/ ASL] Advanced Simulation Library is a free and open source hardware accelerated multiphysics simulation software. Its computational engine is based, among others, on the Lattice Boltzmann Methods and is written in OpenCL which enable extraordinarily efficient deployment on a variety of massively parallel architectures, ranging from inexpensive FPGAs, DSPs and GPUs up to heterogeneous clusters and supercomputers. The engine is hidden entirely behind simple C++ classes, so that no OpenCL knowledge is required from application programmers. ASL can be utilized to model various coupled physical and chemical phenomena and employed in a multitude of fields: computational fluid dynamics, virtual sensing, industrial process data validation and reconciliation, image-guided surgery, computer-aided engineering, design space exploration, crystallography, etc..

== Non-FEM Solver tips ==
The following list of items are not related to the actual FEM solver itself. But since solvers range so widely, these tips are somewhat generic and may or may not help your specific applicaiton.

=== IO ===
FEM codes, for the most part, do a great deal of local IO. This is a result of several possibilities including the solver itself (an out-of-core solver) or retaining intermediate results to make post-processing, including stress recovery, much faster.

Based on some testing of commercial FEM codes, here are some tips for improving performance.

* Use RAID-0 for the local scratch space.
* If possible use EXT2 or XFS for the local IO

Cluster Benchmarking Packages

2015-10-07T21:12:51Z

Deadline: updated intel benchmarks url

Cluster Benchmarking Packages

2015-09-23T18:43:27Z

Deadline: removed cmbp

Here are some links to benchmarks:

'''Benchmark Suites'''
* [http://icl.cs.utk.edu/hpcc/ HPCC Challange Benchmark] - uses seven tests to measure several different performance parameters.
* [http://www.clustermonkey.net//content/view/38/27/ Beowulf Perforamnce Suite (BPS)] - Example results are [http://clustermonkey.net/download/kronos/bps-logs/ here].
* [http://www.nas.nasa.gov/Resources/Software/npb.html NASA Parallel Benchmarks] - One of the most, if not the most, widely used set of benchmarks for clusters.
* [http://www.intel.com/cd/software/products/asmo-na/eng/cluster/clustertoolkit/219848.htm Intel MPI Benchmarks] - freely available.
* [http://perfbase.tigris.org/ perfbase] - a set of front end tools using a PostgreSQL database as backend, which together form a system for the management and analysis of the output of tests and experiments.
* [http://liinwww.ira.uka.de/~skampi/ SKaMPI] - a suite of tests designed to measure the performance of MPI.
* [http://sourceforge.net/apps/trac/cbench/ Cbench] - a Perl-based scripting framework for building, running, and analyzing the output of various opensource codes
* [http://accc.riken.jp/HPC_e/himenobmt_e.html Himeno] Dr. Ryutaro Himeno, Director of the Advanced Center for Computing and Communication, has developedbenchmark to evaluate performance of incompressible fluid analysis code. This benchmark program takes measurements to proceed major loops in solving the Poisson's equation solution using the Jacobi iteration method. Being the code very simple and easy to compile and to execute, users can measure actual speed (in MFLOPS) immediately.
* [https://github.com/EPCCed ADEPT Benchmark] - a suite that addresses the power usage of parallel technologies. [http://www.adept-project.eu/ Adept] builds on the expertise of software developers from high-performance computing (HPC) to exploit parallelism for performance, and on the expertise of Embedded systems engineers in managing energy usage.

'''File Systems I/O'''

* [http://www.nus.edu.sg/comcen/svu/publications/hpc_nus/sep_2005/Performance.pdf GPFS vs. NFS evaluation]
* EXT3, EXT3, Reiser, JFS, XFS benchmarks [http://linuxgazette.net/102/piszcz.html Part 1] and [http://linuxgazette.net/122/piszcz.html Part 2]
* [http://www.clustermonkey.net/ Cluster Monkey] Series on Parallel File System Benchmarking
** [http://www.clustermonkey.net//content/view/62/28/ Benchmarking Parallel File Systems]
** [http://www.clustermonkey.net//content/view/87/32/ A Benchmark for Parallel File Systems]
** [http://www.clustermonkey.net//content/view/117/32/ Using the PIO Benchmark ]
* [http://stromberg.dnsalias.org/~strombrg/nfs-test.html nfs-test] is a program that tries a bunch of different rsizes, wsizes, protocols (tcp vs udp) and NFS versions to optimize performance
* [http://www.iozone.org IOZONE] Filesystem Benchmark
* [http://public.lanl.gov/jnunez/benchmarks/mpiiotest.htm MPI-IO Test] LANL's MPI-IO Test (The best test for MPI-IO codes)
* [http://www.llnl.gov/icc/lc/siop/downloads/download.html Livermore File System Tests] A collection of tests from Lawrence Livermore for testing parallel IO file systems. This include IOR (a great test for parallel file systems) and a bunch of metadata tests

'''Individual Codes for Benchmarks'''

These are codes that you can download (freely) and use for benchmarking. Some of them have benchmark results available and some don't.

* [http://www.gromacs.org/ Gromacs] - A great benchmark code. 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 and lipids that have a lot of complicated bonded interactions.\
* [http://hmmer.janelia.org/ HMMER] HMMER is used for profiling hidden Markov models (profile HMMs) to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.
* [http://gfs.sourceforge.net/ Gerris] - Gerris is an Open Source Free Software library for the solution of the partial differential equations describing fluid flow.
* [http://www.hlrs.de/people/resch/PROJECTS/PARACFD.html ParaCFD] While this is an old CFD benchmark, I think it is still useful. It contains both an OpenMP version and a MPI version.
* [http://www.mgnet.org/mgnet-codes.html MGNet] - A collection of Multi-Grid codes that you can use for benchmarking. There are no published results, but there are some MPI codes that you can use for benchmarks.

'''Network Benchmarks'''

These benchmarks can be used to test the networking aspects of cluster codes. Some of them can test the entire fabric and some test just a pair of nodes.
* [http://www.scl.ameslab.gov/netpipe/ NetPIPE] - One of the best network benchmarks. It tests a range of packet sizes and measures the time (bandwidth). It can use MPI as the message sending mechanism so it allows you to also test MPI implementations.
* [http://www.netperf.org/netperf/ Netperf] - Another good networking benchmark that is used frequently.

Cluster Benchmarking Packages

2015-09-23T18:41:53Z

Deadline: added ADEPT

Here are some links to benchmarks:

'''Benchmark Suites'''
* [http://icl.cs.utk.edu/hpcc/ HPCC Challange Benchmark] - uses seven tests to measure several different performance parameters.
* [http://www.clustermonkey.net//content/view/38/27/ Beowulf Perforamnce Suite (BPS)] - Example results are [http://clustermonkey.net/download/kronos/bps-logs/ here].
* [http://cmbp.clustermonkey.net/ Cluster Monkey Benchmark Project] - just started. It is based on the BPS.
* [http://www.nas.nasa.gov/Resources/Software/npb.html NASA Parallel Benchmarks] - One of the most, if not the most, widely used set of benchmarks for clusters.
* [http://www.intel.com/cd/software/products/asmo-na/eng/cluster/clustertoolkit/219848.htm Intel MPI Benchmarks] - freely available.
* [http://perfbase.tigris.org/ perfbase] - a set of front end tools using a PostgreSQL database as backend, which together form a system for the management and analysis of the output of tests and experiments.
* [http://liinwww.ira.uka.de/~skampi/ SKaMPI] - a suite of tests designed to measure the performance of MPI.
* [http://sourceforge.net/apps/trac/cbench/ Cbench] - a Perl-based scripting framework for building, running, and analyzing the output of various opensource codes
* [http://accc.riken.jp/HPC_e/himenobmt_e.html Himeno] Dr. Ryutaro Himeno, Director of the Advanced Center for Computing and Communication, has developedbenchmark to evaluate performance of incompressible fluid analysis code. This benchmark program takes measurements to proceed major loops in solving the Poisson's equation solution using the Jacobi iteration method. Being the code very simple and easy to compile and to execute, users can measure actual speed (in MFLOPS) immediately.
* [https://github.com/EPCCed ADEPT Benchmark] - a suite that addresses the power usage of parallel technologies. [http://www.adept-project.eu/ Adept] builds on the expertise of software developers from high-performance computing (HPC) to exploit parallelism for performance, and on the expertise of Embedded systems engineers in managing energy usage.

'''File Systems I/O'''

* [http://www.nus.edu.sg/comcen/svu/publications/hpc_nus/sep_2005/Performance.pdf GPFS vs. NFS evaluation]
* EXT3, EXT3, Reiser, JFS, XFS benchmarks [http://linuxgazette.net/102/piszcz.html Part 1] and [http://linuxgazette.net/122/piszcz.html Part 2]
* [http://www.clustermonkey.net/ Cluster Monkey] Series on Parallel File System Benchmarking
** [http://www.clustermonkey.net//content/view/62/28/ Benchmarking Parallel File Systems]
** [http://www.clustermonkey.net//content/view/87/32/ A Benchmark for Parallel File Systems]
** [http://www.clustermonkey.net//content/view/117/32/ Using the PIO Benchmark ]
* [http://stromberg.dnsalias.org/~strombrg/nfs-test.html nfs-test] is a program that tries a bunch of different rsizes, wsizes, protocols (tcp vs udp) and NFS versions to optimize performance
* [http://www.iozone.org IOZONE] Filesystem Benchmark
* [http://public.lanl.gov/jnunez/benchmarks/mpiiotest.htm MPI-IO Test] LANL's MPI-IO Test (The best test for MPI-IO codes)
* [http://www.llnl.gov/icc/lc/siop/downloads/download.html Livermore File System Tests] A collection of tests from Lawrence Livermore for testing parallel IO file systems. This include IOR (a great test for parallel file systems) and a bunch of metadata tests

'''Individual Codes for Benchmarks'''

These are codes that you can download (freely) and use for benchmarking. Some of them have benchmark results available and some don't.

* [http://www.gromacs.org/ Gromacs] - A great benchmark code. 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 and lipids that have a lot of complicated bonded interactions.\
* [http://hmmer.janelia.org/ HMMER] HMMER is used for profiling hidden Markov models (profile HMMs) to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.
* [http://gfs.sourceforge.net/ Gerris] - Gerris is an Open Source Free Software library for the solution of the partial differential equations describing fluid flow.
* [http://www.hlrs.de/people/resch/PROJECTS/PARACFD.html ParaCFD] While this is an old CFD benchmark, I think it is still useful. It contains both an OpenMP version and a MPI version.
* [http://www.mgnet.org/mgnet-codes.html MGNet] - A collection of Multi-Grid codes that you can use for benchmarking. There are no published results, but there are some MPI codes that you can use for benchmarks.

'''Network Benchmarks'''

These benchmarks can be used to test the networking aspects of cluster codes. Some of them can test the entire fabric and some test just a pair of nodes.
* [http://www.scl.ameslab.gov/netpipe/ NetPIPE] - One of the best network benchmarks. It tests a range of packet sizes and measures the time (bandwidth). It can use MPI as the message sending mechanism so it allows you to also test MPI implementations.
* [http://www.netperf.org/netperf/ Netperf] - Another good networking benchmark that is used frequently.

Finite Element Analysis

2015-08-04T00:36:55Z

Deadline: added MOOSE

[http://en.wikipedia.org/wiki/Finite_element Finite Element] Analysis is a very computational intensive technique for solving a wide range of problems. This page will give you some suggestions for improving FEM performance of ISV codes such as [http://www.simulia.com/products/abaqus_fea.html Abaqus], [http://www.ansys.com/products/default.asp ANSYS], and [http://www.mscsoftware.com/products/nastran.cfm?Q=131&Z=457&Y=401 Nastran], as well as open-source codes such as [http://opensees.berkeley.edu/index.php OpenSees], [http://tahoe.ca.sandia.gov/ Tahoe], [http://www.oofem.org/en/oofem.html OOFEM], [http://www.calculix.de/ Calculix], [http://impact.sourceforge.net/ Impact], [http://www.csc.fi/english/pages/elmer Elmer], [http://cern49.cee.uiuc.edu/cfm/warp3d.html Warp3D], [http://mechsys.nongnu.org/index.shtml MechSysNG], [http://www.cimne.com/kratos/ Kratos], [http://sokocalo.engr.ucdavis.edu/~jeremic/PDD/ PDD], [http://adventure.sys.t.u-tokyo.ac.jp/ Adventure], [http://www.dealii.org/ deal.ii] [http://geofem.tokyo.rist.or.jp/ GeoFEM], [http://code.google.com/p/parafem/ ParaFEM] that are focused on solving solid mechanics problems with FEA techniques.

== Popular Open Source Packages ==

*[http://www.csc.fi/english/pages/elmer Elmer] is an open source multiphysical simulation software developed by CSC. Elmer development was started 1995 in collaboration with Finnish Universities, research institutes and industry. Elmer includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics, for example. These are described by partial differential equations which Elmer solves by the Finite Element Method (FEM).
*[http://impact.sourceforge.net/ Impact] is an open source finite element program suite which can be used to predict most dynamic events such as car crashes or metal sheet punch operations. They usually involve large deformations and high velocities. Simulations are made on a virtual three dimensional model which can be created with a pre-processor or with the built-in Fembic language. Results are viewed in a post-processor.
*[http://cern49.cee.uiuc.edu/cfm/warp3d.html WARP3D] is under continuing development as a research code for the solution of very large-scale, 3-D solid models subjected to static and dynamic loads. Specific features in the code oriented toward the investigation of fracture in metals include a robust finite strain formulation, a general J-integral computation facility (with inertia, thermal, face loading), interaction integrals for computation of linear-elastic fracture parameters, very general element extinction and node release facilities to model crack growth, nonlinear material models including viscoplastic and cyclic, cohesive elements and cohesive constitutive models, and the Gurson-Tvergaard dilatant plasticity model for void growth.
*[http://www.physics.drexel.edu/~olson/paramesh-doc/Users_manual/amr.html PARAMESH] is a package of Fortran 90 subroutines designed to provide an application developer with an easy route to extend an existing serial code which uses a logically cartesian structured mesh into a parallel code with adaptive mesh refinement(AMR). Alternatively, in its simplest use, and with minimal effort, it can operate as a domain decomposition tool for users who want to parallelize their serial codes, but who do not wish to use adaptivity. The package builds a hierarchy of sub-grids to cover the computational domain, with spatial resolution varying to satisfy the demands of the application. These sub-grid blocks form the nodes of a tree data-structure (quad-tree in 2D or oct-tree in 3D). Each grid block has a logically cartesian mesh.
*[http://mooseframework.org/ MOOSE ] or Multiphysics Object-Oriented Simulation Environment (MOOSE) is a finite-element, multiphysics framework primarily developed by Idaho National Laboratory. It provides a high-level interface to some of the most sophisticated nonlinear solver technology on the planet. MOOSE presents a straightforward API that aligns well with the real-world problems scientists and engineers need to tackle. Every detail about how an engineer interacts with MOOSE has been thought through, from the installation process through running your simulation on state of the art supercomputers, the MOOSE system will accelerate your research.

== Non-FEM Solver tips ==
The following list of items are not related to the actual FEM solver itself. But since solvers range so widely, these tips are somewhat generic and may or may not help your specific applicaiton.

=== IO ===
FEM codes, for the most part, do a great deal of local IO. This is a result of several possibilities including the solver itself (an out-of-core solver) or retaining intermediate results to make post-processing, including stress recovery, much faster.

Based on some testing of commercial FEM codes, here are some tips for improving performance.

* Use RAID-0 for the local scratch space.
* If possible use EXT2 or XFS for the local IO

Main Page

2015-07-14T15:45:45Z

Deadline: added new link to sponsor page

__NOTOC__
== Cluster Documentation Project™ ==
[[File:cdp_logo_1.png|left|250x250px]]
Looking for Cluster Documentation? Jump right to [[Cluster Topics]].

Computational Clusters have grown from a back room curiosity to a driving force in the HPC community. The roll your own nature of cluster computing has also created a wide community of users, vendors, and applications. The Cluster Documentation Project (CDP) is an effort to help document best practices, tutorials, projects, benchmarks, products, and anything else that helps facilitate HPC cluster computing.

'''We plan on releasing our first book at SC15 ''' -- ''[[Essential HPC]]: Practical high performance concepts, techniques, and procedures''

'''VENDORS DON'T MISS A UNIQUE AND EFFECTIVE SPONSORSHIP OPPORTUNITY: [[Funding The Cluster Documentation Project]]'''

[[File:E-HPC-cover2.png|thumb|alt=Book Cover.|Contents [[Essential HPC]]]]

===Project Scope===

The word [http://en.wikipedia.org/wiki/Computer_cluster cluster] has many meanings. The Cluster Documentation Project is designed to document and professionally publish High Performance Computing (HPC) Cluster information. The focus will be on tutorial and how-to information rather than theoretical aspects of HPC. Currently there are [[Cluster Topics]] which is a compendium of current benchmarks, products, technologies, methods, best practices, etc. that will help those interested in clustering. When funded the project will enhance this resource.

See a recent [http://www.admin-magazine.com/HPC/Articles/Cluster-Documentation-Project/%28language%29/eng-US article] in HPC Admin magazine for more background.

===Writers and Contributors===

Contributions are accepted from the community -- both users and vendors. All content is subject to approval by the editors and critical content will be created with paid experienced writers. If you are interested in contributing please join the [http://www.clustermonkey.net/mailman/listinfo/hpc-writers HPC Writers list]. All submitted content will be made available under a [http://creativecommons.org/licenses/by-nc-sa/2.5/ Creative Commons License].

===Questions===
If you have specific questions about clusters please visit our [[Cluster Questions]] section and enter your question.

If you have questions about this site, please contact [http://www.clustermonkey.net//component/option,com_contact/task,view/contact_id,1/Itemid,3/ Douglas Eadline] with any questions.

===History===
ClusterWorld magazine was the initial sponsor of a site called The Cluster Agenda. When ClusterWorld Magazine ceased publication the Agenda effort was stopped. Douglas Eadline, editor of ClusterWorld magazine, was the principle organizer of the Agenda effort and has decided with the help of Jeff Layton to preserve some of the content from the Agenda and morph the site into Cluster Tweaks. The original Agenda Working Committee was Jeff Layton, Glen Otero, Dan Stanzione, and Douglas Eadline.

Funding The Cluster Documentation Project

2015-07-14T15:41:08Z

Deadline: reworked for direct vendor sponsorship

==A Unique and Effective Sponsorship Opportunity==

The Cluster Documentation Project (CDP) is seeking corporate and organizational sponsors to help fund additional content. 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, Hadoop and Big Data, software tools and applications, system design and procurement, and more. The project is expected to have a high impact on both users and vendors.

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.

===Wrap a Book Around Your Technology or Service===

Getting your message out to the HPC community and market is important. New and existing HPC users are constantly searching the Internet for up-to-date and accurate information, and the CDP is designed to be the first place users land when they are seeking cluster and HPC insights. You need to be there. In addition to contributing your technical value proposition, the CDP offers both banner ad and logo branding. We can also help you use the CDP to '''create professionally branded manuals, books, and documentation for your customers'''.

Understanding the full impact of an HPC product or service can require deep technical conversations. Companies often
produce high-level white papers to help explain new products and services. The CDP can be used to create short booklets or small books
that help potential customer fully understand your '''technological value proposition''' and give weight to your sales approach.

In order to kick-start the project, we will be releasing our first free book, entitled ''[[Essential HPC]]: Practical high performance concepts, techniques, and procedures.'' We are seeking sponsors for the 2015 edition (to be released at SC 2015 in Austin, TX.) Please contact [http://www.xandmarketing.com/contact.php Xand Marketing] fro more details.

===Credible and Professional===

The principal editor of the CDP will be Douglas Eadline, a practitioner and chronicler of the Linux Cluster HPC revolution. Doug 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. Doug has written numerous articles in both print and web-based publications and was selected by AMD to write the short, but popular, book High Performance Computing for Dummies. He has also co-authored books on Big Data and Hadoop. A team of capable and experienced writers, editors, and artists has been assembled to work with Doug to create a professional resource for the entire community.

The project will be managed by [http://www.xandmarketing.com/ Xand Marketing] and Seagrove LLC, the publisher of [http://www.clustermonkey.net Cluster Monkey]. At this point in time, some basic information is already in place 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 Big Picture==

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. Continued support beyond the initial start-up period is expected to come from the production of CDP books and vendor sponsorships.

Main Page

2015-07-14T14:47:04Z

Deadline:

__NOTOC__
== Cluster Documentation Project™ ==
[[File:cdp_logo_1.png|left|250x250px]]
Looking for Cluster Documentation? Jump right to [[Cluster Topics]].

Computational Clusters have grown from a back room curiosity to a driving force in the HPC community. The roll your own nature of cluster computing has also created a wide community of users, vendors, and applications. The Cluster Documentation Project (CDP) is an effort to help document best practices, tutorials, projects, benchmarks, products, and anything else that helps facilitate HPC cluster computing.

'''We plan on releasing our first book at SC15 ''' -- ''[[Essential HPC]]: Practical high performance concepts, techniques, and procedures''

[[File:E-HPC-cover2.png|thumb|alt=Book Cover.|Contents [[Essential HPC]]]]

===Project Scope===

The word [http://en.wikipedia.org/wiki/Computer_cluster cluster] has many meanings. The Cluster Documentation Project is designed to document and professionally publish High Performance Computing (HPC) Cluster information. The focus will be on tutorial and how-to information rather than theoretical aspects of HPC. Currently there are [[Cluster Topics]] which is a compendium of current benchmarks, products, technologies, methods, best practices, etc. that will help those interested in clustering. When funded the project will enhance this resource.

See a recent [http://www.admin-magazine.com/HPC/Articles/Cluster-Documentation-Project/%28language%29/eng-US article] in HPC Admin magazine for more background.

===Writers and Contributors===

Contributions are accepted from the community -- both users and vendors. All content is subject to approval by the editors and critical content will be created with paid experienced writers. If you are interested in contributing please join the [http://www.clustermonkey.net/mailman/listinfo/hpc-writers HPC Writers list]. All submitted content will be made available under a [http://creativecommons.org/licenses/by-nc-sa/2.5/ Creative Commons License].

===Questions===
If you have specific questions about clusters please visit our [[Cluster Questions]] section and enter your question.

If you have questions about this site, please contact [http://www.clustermonkey.net//component/option,com_contact/task,view/contact_id,1/Itemid,3/ Douglas Eadline] with any questions.

===History===
ClusterWorld magazine was the initial sponsor of a site called The Cluster Agenda. When ClusterWorld Magazine ceased publication the Agenda effort was stopped. Douglas Eadline, editor of ClusterWorld magazine, was the principle organizer of the Agenda effort and has decided with the help of Jeff Layton to preserve some of the content from the Agenda and morph the site into Cluster Tweaks. The original Agenda Working Committee was Jeff Layton, Glen Otero, Dan Stanzione, and Douglas Eadline.

Essential HPC

2015-07-14T14:44:24Z

Deadline: removed old funding stuff

__NOTOC__
''Practical High Performance Concepts, Techniques, and Procedures''

This book will be based on CDP wiki content and is intended to help answer questions and get your HPC projects moving forward quickly. The book is expected to be available in the fall of 2015. A soft version will be available at no charge and a special limited edition hard copy will be printed "on demand." We are looking for sponsors for a SC 2015 version. (more details soon)

==Tentative Table of Contents==
[[File:E-HPC-cover2.png|right|alt=Book Cover|400x618px]]
=== Fundamental Concepts ===
*What is HPC and Why Does It Matter
*Introduction To Building Blocks
*Setting Expectations
*Parallel and Distributed Computing 101
*What Do I Need to Know As An Administrator?
*What Do I need to Know As A User?
===Taking The First Steps===
*It all Depends
*Understanding Costs
*Success Metrics
*Choosing Hardware
*Choosing Software
*Using A Cloud
===Techniques===
*Using an Open Approach To HPC
*Designing Your Solution
*Cluster Provisioning and Control
*Sharing The Resource
*Parallel Programming
===Procedures===
*Software Management
*File Systems
*Testing and Tuning
*Monitoring
===Next Steps===
*HPC Applications
*Other Resources

Main Page

2015-07-14T14:40:48Z

Deadline: Take out indigogo stuff

__NOTOC__
== Cluster Documentation Project™ ==
[[File:cdp_logo_1.png|left|250x250px]]
Looking for Cluster Documentation? Jump right to [[Cluster Topics]].

Computational Clusters have grown from a back room curiosity to a driving force in the HPC community. The roll your own nature of cluster computing has also created a wide community of users, vendors, and applications. The Cluster Documentation Project (CDP) is an effort to help document best practices, tutorials, projects, benchmarks, products, and anything else that helps facilitate HPC cluster computing.

'''We plan on releasing our first book at SC15 ''' -- ''[[Essential HPC]]: Practical high performance concepts, techniques, and procedures''

[[File:E-HPC-cover2.png|thumb|alt=Book Cover.|Contents [[Essential HPC]]]]

===Project Scope===

The word [http://en.wikipedia.org/wiki/Computer_cluster cluster] has many meanings. The Cluster Documentation Project is designed to document and professionally publish High Performance Computing (HPC) Cluster information. The focus will be on tutorial and how-to information rather than theoretical aspects of HPC. Currently there are [[Cluster Topics]] which is a compendium of current benchmarks, products, technologies, methods, best practices, etc. that will help those interested in clustering. When funded the project will enhance this resource.\

See a recent [http://www.admin-magazine.com/HPC/Articles/Cluster-Documentation-Project/%28language%29/eng-US article] in HPC Admin magazine for more background.

===Writers and Contributors===

Contributions are accepted from the community -- both users and vendors. All content is subject to approval by the editors and critical content will be created with paid experienced writers. If you are interested in contributing please join the [http://www.clustermonkey.net/mailman/listinfo/hpc-writers HPC Writers list]. All submitted content will be made available under a [http://creativecommons.org/licenses/by-nc-sa/2.5/ Creative Commons License].

===Questions===
If you have specific questions about clusters please visit our [[Cluster Questions]] section and enter your question.

If you have questions about this site, please contact [http://www.clustermonkey.net//component/option,com_contact/task,view/contact_id,1/Itemid,3/ Douglas Eadline] with any questions.

===History===
ClusterWorld magazine was the initial sponsor of a site called The Cluster Agenda. When ClusterWorld Magazine ceased publication the Agenda effort was stopped. Douglas Eadline, editor of ClusterWorld magazine, was the principle organizer of the Agenda effort and has decided with the help of Jeff Layton to preserve some of the content from the Agenda and morph the site into Cluster Tweaks. The original Agenda Working Committee was Jeff Layton, Glen Otero, Dan Stanzione, and Douglas Eadline.

Computational Fluid Dynamics

2015-06-23T19:20:10Z

Deadline: added SU 2

* [http://gfs.sourceforge.net/index.html Gerris] - is an Open Source Free Software library for the solution of the partial differential equations describing fluid flow. The source code is available free of charge under the Free Software GPL license. Gerris is supported by NIWA (National Institute of Water and Atmospheric research) and by the Marsden Fund of the Royal Society of New Zealand. The code is written entirely in C and uses both the GLib Library and the GTS Library for geometrical functions and object-oriented programming.

* [http://www.opencfd.co.uk/openfoam/index.html#openfoam OpenFoam®] - The OpenFOAM® (Open Field Operation and Manipulation) CFD Toolbox can simulate anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics, electromagnetics and the pricing of financial options. OpenFOAM is produced by OpenCFD Ltd and is freely available and open source, licensed under the GNU General Public Licence. Domain decomposition parallelism is fundamental to the design of OpenFOAM and integrated at a low level so that solvers can generally be developed without the need for any ’parallel-specific’ coding.

* [https://computation.llnl.gov/casc/Overture/ Overture] Overture is an object-oriented code framework for solving partial differential equations in serial and parallel computing environments. It provides a portable, flexible software development environment for applications that involve the simulation of physical processes in complex moving geometry. It is implemented as a collection of C++ libraries that enable the use of finite difference and finite volume methods at a level that hides the details of the associated data structures, as well as the details of the parallel implementation.

* [http://code-saturne.org/cms/ Code_Saturne] solves the Navier-Stokes equations for 2D, 2D-axisymmetric and 3D flows, steady or unsteady, laminar or turbulent, incompressible or weakly dilatable, isothermal or not, with scalars transport if required. Several turbulence models are available, from Reynolds-Averaged models to Large-Eddy Simulation models. In addition, a number of specific physical models are also available as "modules": gas, coal and heavy-fuel oil combustion, semi-transparent radiative transfer, particle-tracking with Lagrangian modeling, Joule effect, electrics arcs, weakly compressible flows, atmospheric flows, rotor/stator interaction for hydraulic machines.

* [http://su2.stanford.edu/emails/su2_email_v4.html SU2] is a collection of C++ software tools for performing Partial Differential Equation (PDE) analysis and for solving PDE-constrained optimization problems, with special emphasis on Computational Fluid Dynamics (CFD) and aerodynamic shape design.

Basement Supercomputing Software Stack

2015-03-19T19:07:08Z

Deadline: /* DRAFT VERSION 5/10/12 */

=DRAFT VERSION 12/10/14=

== 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 ==

Bioinformatics

2015-02-19T14:13:50Z

Deadline: added GATK

* [http://www.mpiblast.org/ mpiBLAST] is a freely available, open-source, parallel implementation of [http://www.ncbi.nih.gov/blast/ NCBI BLAST]. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. mpiBLAST is also portable across many different platforms and operating systems. Lastly, a renewed focus and consolidation of the many codebases has positioned mpiBLAST to continue to be of high utility to the bioinformatics community.
* [http://mpihmmer.org/ MPI-HMMER] is an open source MPI implementation of the HMMER protein sequence analysis suite. The main search algorithms, hmmpfam and hmmsearch, have been ported to MPI in order to provide high throughput HMMER searches on modern computational clusters. MPI-HMMER has sophisticated I/O, a self-contained coordinator/worker model, and the easy inclusion of accelerated architectures (e.g. GP-GPUs).
* [https://www.broadinstitute.org/gatk/ GATK] (The Genome Analysis Toolkit) is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

Weather Modeling

2015-02-17T18:30:44Z

Deadline: added MOM

*[http://www.mmm.ucar.edu/mm5/mm5v3/wherev3.html MM5] The PSU/NCAR mesoscale model (known as MM5) is a limited-area, nonhydrostatic, terrain-following sigma-coordinate model designed to simulate or predict mesoscale atmospheric circulation. The model is supported by several pre- and post-processing programs, which are referred to collectively as the MM5 modeling system. The MM5 modeling system software is mostly written in Fortran, and has been developed at Penn State and NCAR as a community mesoscale model with contributions from users worldwide.
*[http://www.wrf-model.org/index.php WRF] The Weather Research and Forecasting (WRF) Model is a next-generation mesocale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. It features multiple dynamical cores, a 3-dimensional variational (3DVAR) data assimilation system, and a software architecture allowing for computational parallelism and system extensibility. WRF is suitable for a broad spectrum of applications across scales ranging from meters to thousands of kilometers.
*[http://climate.lanl.gov/Models/POP/ POP] (Parallel Ocean Program) is an ocean circulation model derived from earlier models of Bryan, Cox, Semtner and Chervin in which depth is used as the vertical coordinate. The model solves the three-dimensional primitive equations for fluid motions on the sphere under hydrostatic and Boussinesq approximations. Spatial derivatives are computed using finite-difference discretizations which are formulated to handle any generalized orthogonal grid on a sphere, including dipole and tripole grids which shift the North Pole singularity into land masses to avoid time step constraints due to grid convergence.
*[http://mom-ocean.org/web MOM] (The Modular Ocean Model) is a numerical ocean model based on the hydrostatic primitive equations. MOM development is led by scientists at NOAA/GFDL in collaboration with scientists worldwide. Version 5 of MOM (MOM5) is an open source project released under the GPL license.

Personal Clusters

2015-01-02T22:55:34Z

Deadline: added basement limulus

Commercial Personal Clusters

* [http://www.basement-supercomputing.com Limulus Systems]
There are several projects that my be of interest:

* [http://limulus.basement-supercomputing.com/ Limulus Project]
* [http://www.clustermonkey.net//content/view/273/33/ WhisperingWulf: A Silent Personal Cluster ]
* [http://www.clustermonkey.net//content/view/211/33/ Microwulf: Breaking the $100/GFLOP Barrier]
* [http://www.mini-itx.com/projects/cluster/ The "Mini-Cluster"]
* [http://antipastohw.blogspot.com/2010/09/how-to-make-beagleboard-elastic-r.html BeagleBoard Elastic R Beowulf Cluster in a Briefcase ]

Main System Software Page

2014-05-29T20:43:31Z

Deadline: Created page with "coming soon"

coming soon

Cluster Design

2014-05-12T15:46:18Z

Deadline: fixed CM links

Clusters are all about design. Indeed, clusters are about designing machines
around problems. When designing a cluster the following '''basic''' questions
may be helpful. If you need help with answers, try asking on the [http://www.beowulf.org/mailman/listinfo/beowulf Beowulf Mailing List] or submit a question to the [[Cluster Questions]] section.

'''Consider your budget'''
* Do you need help with software and support? If so, reserve some funds for this part of the project. While clusters can be easy to set up initially, continued operation can be time consuming.
* Do you plan on assembling the cluster yourself? If yes, at what level? Starting from motherboards, cases, memory, processors, etc. can be very time consuming. Buy quality parts.
* If you plan on using a vendor, provide them with a detailed specification and don't forget to run benchmarks.

'''How many and what type of processors do I need?'''
* This depends on your application. How well does you application scale. Have you tested it on a real cluster? If it is a common application, have other run it on a cluster?
*It also depends on how you want to arrange your processors. The introduction dual-core CPUs make this a more interesting question.

'''What Type of Interconnect?'''
*Again, this depends on your application. If you can use Gigabit Ethernet, then you can probably buy more nodes. If you need a faster interconnect, then you may have to sacrifice nodes for interconnects to stay in your budget. Benchmarking your code(s) is important.
* Remember Gigabit Ethernet performance will vary by chip-set, some are better than others.

'''What type of software?'''
* This depends on your needs. There are several preconfigured distributions, but which one is best depends upon your needs.

'''Do I need disk drives on my nodes?'''
* This decision also depends on on your needs. In some cases nodes can be run without hard drives, in others local swap or scratch space is needed.

'''What type of storage?'''
* do you need a parallel file system?
* Will a basic NFS setup be enough? Will it scale to the nodes you need?
* How do I construct a diskless cluster?
** Can I circumvent the local swap dilemma?

There are many other questions that need to be answered, but these should give you a start. The book below (freely available) is also a good place to start.

'''Books'''

* [http://www.phy.duke.edu/~rgb/Beowulf/beowulf_book.php Engineering a Beowulf-Style Compute Cluster by Robert G. Brown ] - A freely available book on building/designing Beowulf style clusters.

* See the Cluster Monkey [http://www.clustermonkey.net/Books/ Cluster Books Page ]

'''Tools'''

* [http://aggregate.org/CDR/ The Cluster Design Rules ] - A tool to help design a cluster tuned for an application

Cluster Concepts

2014-05-12T15:43:17Z

Deadline: fixed CM links

===Building Machines Around Problems ===

Cluster computing is a exciting technology. It allows users to design
a computing resource around a problem. In the past problems were often designed around large monolithic supercomputers. A typical supercomputer has a large amount of costly engineering and design that may or may not be needed for a specific application. Because the supercomputer comes in a "big box", the end user must pay for the cost of all the technology. Clusters built from commodity components allow the user to only buy what they needed at commodity prices. The use of clustered computing has redefined the price-to-performance curve for HPC (High Performance Computing).

A good working definition of a cluster was first given in the book '''How to Build a Beowulf: A Guide to the Implementation and Application of PC Clusters''' by
Thomas Sterling, John Salmon, Donald J. Becker and Daniel F. Savarese

''A Beowulf is a collection of personal computers (PCs) interconnected by widely available networking technology running one of several open-source Unix like operating systems.''

Cluster Monkey has a list of [http://www.clustermonkey.net/Books/ cluster books].

If you are new to the cluster community, you may find the [http://www.clustermonkey.net/Columns/Cluster-Newbie/ Getting Started with Clusters ] series on [http://www.clustermonkey.net/ Cluster Monkey] helpful.

Open/Freely Available Cluster Applications

2014-05-12T15:35:28Z

Deadline: added wikipedia link to free and open software

Below are the various categories of Cluster HPC applications. Please note, most of these applications are parallel (i.e. MPI applications).

You may also find other applications from [http://en.wikipedia.org/wiki/List_of_free_and_open_source_software_packages List of Free and Open Software Packages ]

* [[Aerospace]]
* [[Bioinformatics]]
* [[CAE/CAD Modeling]]
* [[Cosmology]]
* [[Computational Fluid Dynamics]]
* [[Database]]
* [[Electronic Structure/Quantum Chemistry]]
* [[Finite Element Analysis]]
* [[Molecular Modeling]]
* [[Oil and Gas]]
* [[Visualization/Rendering]]
* [[Weather Modeling]]

* [[Other]]

Basement Supercomputing Software Stack

2013-08-21T16:19:03Z

Deadline: moved Limulus Manual to Basement Supercomputing Software Stack: more general

=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 ==

Limulus Manual

2013-08-21T16:19:03Z

Deadline: moved Limulus Manual to Basement Supercomputing Software Stack: more general

#REDIRECT [[Basement Supercomputing Software Stack]]

Batch Schedulers

2013-07-18T14:09:03Z

Deadline: remove platform lava and added openlava

[http://gridengine.sunsource.net/ Sun Grid Engine ] - SGE is an openly available Batch Scheduler. The Grid Engine project is an open source community effort to facilitate the adoption of distributed computing solutions. Sponsored by Sun Microsystems and hosted by CollabNet, the Grid Engine project provides enabling distributed resource management software for wide ranging requirements from compute farms to grid computing. Current versions are 5.3 and 6.0.
* [http://gridengine.sunsource.net/howto/howto.html Grid Engine Howto's ] - A good set of howto documents including ''Tight Integration of Parallel Libraries'' (MPICH,MPICH2,LAM,PVM)
* [http://gridengine.sunsource.net/documentation.html Grid Engine Manuals ] - full documentation set.
* [http://wiki.gridengine.info/wiki/index.php/Main_Page Grid Engine Wiki ] - Links and discussion about Grid Engine

[http://www.clusterresources.com/pages/products/torque-resource-manager.php Torque] - TORQUE is an open source resource manager providing control over batch jobs and distributed compute nodes. It is a community effort based on the original *PBS project and, with more than 1,200 patches, has incorporated significant advances in the areas of scalability, fault tolerance, and feature extensions contributed by NCSA, OSC, USC , the U.S. Dept of Energy, Sandia, PNNL, U of Buffalo, TeraGrid, and many other leading edge HPC organizations

[http://slurm.schedmd.com/ SLURM] is an open-source workload manager designed for Linux clusters of all sizes. It provides three key functions. First it allocates exclusive and/or non-exclusive access to resources (computer nodes) to users for some duration of time so they can perform work. Second, it provides a framework for starting, executing, and monitoring work (typically a parallel job) on a set of allocated nodes. Finally, it arbitrates contention for resources by managing a queue of pending work.

[http://www.openlava.org/ openlava] is open-source software for distributed resource management. It is a fork of Platform Lava, which was positioned by Platform Computing as an entry-level workload management system. The not very well known fact is that Platform Lava is actually based on Platform LSF™ from version 4.2, and that this version of Platform LSF was in use at many companies who would be well characterized as "beyond entry-level" and certainly beyond the incorrectly advertised cluster size of 512 nodes. Scalable and robust, openlava is suitable for heavy duty production clusters, with hundreds of nodes, thousands of cores and jobs.

Batch Schedulers

2013-07-18T14:05:48Z

Deadline: added SLURM

[http://gridengine.sunsource.net/ Sun Grid Engine ] - SGE is an openly available Batch Scheduler. The Grid Engine project is an open source community effort to facilitate the adoption of distributed computing solutions. Sponsored by Sun Microsystems and hosted by CollabNet, the Grid Engine project provides enabling distributed resource management software for wide ranging requirements from compute farms to grid computing. Current versions are 5.3 and 6.0.
* [http://gridengine.sunsource.net/howto/howto.html Grid Engine Howto's ] - A good set of howto documents including ''Tight Integration of Parallel Libraries'' (MPICH,MPICH2,LAM,PVM)
* [http://gridengine.sunsource.net/documentation.html Grid Engine Manuals ] - full documentation set.
* [http://wiki.gridengine.info/wiki/index.php/Main_Page Grid Engine Wiki ] - Links and discussion about Grid Engine

[http://www.clusterresources.com/pages/products/torque-resource-manager.php Torque] - TORQUE is an open source resource manager providing control over batch jobs and distributed compute nodes. It is a community effort based on the original *PBS project and, with more than 1,200 patches, has incorporated significant advances in the areas of scalability, fault tolerance, and feature extensions contributed by NCSA, OSC, USC , the U.S. Dept of Energy, Sandia, PNNL, U of Buffalo, TeraGrid, and many other leading edge HPC organizations

[http://www.hpccommunity.org/index.php?pageid=lava Platform Lava] is an open source entry-level workload scheduler designed to meet a wide range of workload scheduling needs for clusters up to 512-nodes. Lava is available via the [http://www.hpccommunity.org/ HPCCommunity site] and is also included as a component of Platform Cluster Manager (PCM).

[http://slurm.schedmd.com/ SLURM] is an open-source workload manager designed for Linux clusters of all sizes. It provides three key functions. First it allocates exclusive and/or non-exclusive access to resources (computer nodes) to users for some duration of time so they can perform work. Second, it provides a framework for starting, executing, and monitoring work (typically a parallel job) on a set of allocated nodes. Finally, it arbitrates contention for resources by managing a queue of pending work.

Database

2013-07-16T22:18:34Z

Deadline: added MR-MPI

* [http://hadoop.apache.org/ Hadoop] is a free Java software framework that supports data intensive distributed applications. It enables applications to work with thousands of nodes and petabytes of data. Hadoop was inspired by Google's MapReduce and Google File System (GFS).
* [http://www.mongodb.org/display/DOCS/Home MongoDB] is a high-performance, open source, schema-free document-oriented database. MongoDB is written in C++. A key goal of MongoDB is to bridge the gap between key/value stores (which are fast and highly scalable) and traditional RDBMS systems (which are deep in functionality).
* [http://mapreduce.sandia.gov/ MapReduce-MPI Library] is a library, which is an open-source implementation of MapReduce written for distributed-memory parallel machines on top of standard MPI message passing.

Aerospace

2012-12-27T20:38:48Z

Deadline: added su2 and openvsp

* [http://su2.stanford.edu/ SU2] is the Stanford University Unstructured (SU2) suite is an open-source collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDE-constrained optimization problems. The toolset is designed with computational fluid dynamics and aerodynamic shape optimization in mind, but it is extensible (and has been extended) to treat arbitrary sets of governing equations such as electrodynamics, chemically reacting flows, and many others.

* [http://www.openvsp.org/ OpenVSP] is a parametric aircraft geometry tool. OpenVSP allows the user to create a 3D model of an aircraft defined by common engineering parameters. This model can be processed into formats suitable for engineering analysis. The predecessors to OpenVSP have been developed by J.R. Gloudemans and others for NASA since the early 1990's. On January 10 2012, OpenVSP was released as an open source project under the NASA Open Source Agreement (NOSA) version 1.3.

CAE/CAD/EDA Modeling

2012-12-27T15:47:59Z

Deadline:

Computational Fluid Dynamics

2012-12-27T15:46:56Z

Deadline: added Code_Saturne

CAE/CAD/EDA Modeling

2012-12-27T15:42:45Z

Deadline: added Code_Aster

Open/Freely Available Cluster Applications

2012-12-27T15:37:41Z

Deadline: change CAD to CAE/CAD Modeling

Below are the various categories of Cluster HPC applications. Please note, most of these applications are parallel (i.e. MPI applications)

* [[Aerospace]]
* [[Bioinformatics]]
* [[CAE/CAD Modeling]]
* [[Cosmology]]
* [[Computational Fluid Dynamics]]
* [[Database]]
* [[Electronic Structure/Quantum Chemistry]]
* [[Finite Element Analysis]]
* [[Molecular Modeling]]
* [[Oil and Gas]]
* [[Visualization/Rendering]]
* [[Weather Modeling]]

* [[Other]]

CAE/CAD/EDA Modeling

2012-12-27T15:36:14Z

Deadline: moved CAD Solid Modeling to CAE/CAD Modeling: Include CAE

CAD Solid Modeling

2012-12-27T15:36:14Z

Deadline: moved CAD Solid Modeling to CAE/CAD Modeling: Include CAE

#REDIRECT [[CAE/CAD Modeling]]