Debian Science Project
Summary
Distributed computing
Debian Science - Pakete für »Distributed Computing«

Dieses Metapaket installiert »Debian Science«-Pakete, die für verschiedene Arten des verteilten Rechnens wie Grid-, Cloud-, Cluster- und Parallel- Computing nützlich sind.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Science to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Science mailing list

Links to other tasks

Debian Science Distributed computing packages

Official Debian packages with high relevance

Dmtcp
Checkpoint/Restart functionality for Linux processes
Maintainer: Paul Grosu
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DMTCP (Distributed MultiThreaded Checkpointing) is a tool to transparently checkpointing the state of an arbitrary group of applications including multi-threaded and distributed computations. It operates directly on the user binary executable, with no Linux kernel modules or other kernel mods.

Among the applications supported by DMTCP are Open MPI, MVAPICH2, MATLAB, R, Python, Perl, and many programming languages and shell scripting languages. It supports both TCP sockets and InfiniBand connections. With the use of TightVNC, it can also checkpoint and restart X-Window applications. The OpenGL library for 3D graphics is supported through a special plugin.

This package contains DMTCP binaries.

Please cite: Jason Ansel, Kapil Arya, and Gene Cooperman: DMTCP: Transparent Checkpointing for Cluster Computations and the Desktop (2009)
Environment-modules
Modulares System zur Behandlung von Umgebungsvariablen
Maintainer: Alastair McKinstry
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Das Paket Environment Modules ermöglicht die dynamische Modifikation einer Benutzerumgebung über »modulefiles«. Jedes »modulefile« enthält die Informationen, um die Shell für eine Anwendung zu konfigurieren. Sobald das Paket Environment Modules initialisiert wurde, kann die Umgebung dynamisch verändert werden. Dies geschieht mit dem Befehl module, der die »modulefiles« per Modul interpretiert. Typischerweise ändern oder setzen die »modulefiles« über den Befehl module Umgebungsvariablen wie PATH, MANPATH usw. »modulefiles« können von vielen Benutzern auf einem System gemeinsam genutzt werden. Benutzer könnten eine eigene Sammlung besitzen, um die gemeinsam genutzten »modulefiles« zu ergänzen oder zu ersetzen. Die Modules-Umgebung ist auf SGI/Crays und vielen Farmen von Arbeitsplatzrechnern verbreitet.

Globus-core
Globus Toolkit - Globus Core - Transitional Package
Maintainer: Mattias Ellert
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The Globus Toolkit is an open source software toolkit used for building Grid systems and applications. It is being developed by the Globus Alliance and many others all over the world. A growing number of projects and companies are using the Globus Toolkit to unlock the potential of grids for their cause.

The globus-core package is no longer needed with Globus Toolkit 6. This transitional package provides a dummy pkg-config file to fulfill dependencies during the transition. In can be removed when no longer needed.

Gridengine-client
Programme zur Verwaltung der »Grid Engine«-Warteschlangen
Maintainer: Debian HPC Team
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Die Software Grid Engine erleichtert die Verwaltung verteilter Ressourcen (distributed resource management, DRM). Weit mehr als nur einfache Werkzeuge zur Lastverteilung oder Mechanismen zur Batch-Planung, bietet DRM-Software typischerweise die folgenden Schlüsselfunktionen über große Gruppen verteilter Ressourcen:

  • Auf Richtlinien basierende Zuweisung verteilter Ressourcen (CPU-Zeit, Software-Lizenzen, usw.)
  • Planung von Batches & Verwaltung von Batch-Queues
  • Unterstützung vielfältiger Server-Hardware, Betriebssysteme und Architekturen
  • Lastausgleich & Ausführung von Aufträgen auf entfernten Rechnern
  • Detaillierte, kontenbezogene Statistiken und Auftragsprotokolle
  • Feinkörnige Verteilung nutzerspezifizierter Ressourcen
  • Unterbrechung/Wiederaufnahme/Verlagerung von Aufgaben
  • Statusinformationen von Aufgaben/Rechnern/Cluster
  • Wiederholter Aufruf des gleichen Kommandos mit unterschiedlichen Parametern (Job-Arrays)
  • Zusammenarbeit & Steuerung von parallelen Jobs

Dieses Paket enthält Benutzerprogramme zur Verwaltung der »Grid Engine«- Warteschlangen.

Gridengine-exec
Verwaltung verteilter Ressourcen - »Execution Server«
Maintainer: Debian HPC Team
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Die Software Grid Engine erleichtert die Verwaltung verteilter Ressourcen (distributed resource management, DRM). Weit mehr als nur einfache Werkzeuge zur Lastverteilung oder Mechanismen zur Batch-Planung, bietet DRM-Software typischerweise die folgenden Schlüsselfunktionen über große Gruppen verteilter Ressourcen:

  • Auf Richtlinien basierende Zuweisung verteilter Ressourcen (CPU-Zeit, Software-Lizenzen, usw.)
  • Planung von Batches & Verwaltung von Batch-Queues
  • Unterstützung vielfältiger Server-Hardware, Betriebssysteme und Architekturen
  • Lastausgleich & Ausführung von Aufträgen auf entfernten Rechnern
  • Detaillierte, kontenbezogene Statistiken und Auftragsprotokolle
  • Feinkörnige Verteilung nutzerspezifizierter Ressourcen
  • Unterbrechung/Wiederaufnahme/Verlagerung von Aufgaben
  • Statusinformationen von Aufgaben/Rechnern/Cluster
  • Wiederholter Aufruf des gleichen Kommandos mit unterschiedlichen Parametern (Job-Arrays)
  • Zusammenarbeit & Steuerung von parallelen Jobs

Dieses Paket enthält den »Grid Engine Execution Server«.

Gridengine-master
Distributed resource management - Master Server
Maintainer: Debian HPC Team
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Grid Engine is software that facilitates "distributed resource management" (DRM). Far more than just simple load-balancing tools or batch scheduling mechanisms, DRM software typically provides the following key features across large sets of distributed resources:

  • Policy based allocation of distributed resources (CPU time, software licenses, etc.)
  • Batch queuing & scheduling
  • Support diverse server hardware, OS and architectures
  • Load balancing & remote job execution
  • Detailed job accounting statistics
  • Fine-grained user specifiable resources
  • Suspend/resume/migrate jobs
  • Tools for reporting Job/Host/Cluster status
  • Job Arrays
  • Integration & control of parallel jobs

This package contains the Grid Engine master server.

Gridengine-qmon
Graphical utilities for Grid Engine queue management
Maintainer: Debian HPC Team
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Grid Engine is software that facilitates "distributed resource management" (DRM). Far more than just simple load-balancing tools or batch scheduling mechanisms, DRM software typically provides the following key features across large sets of distributed resources:

  • Policy based allocation of distributed resources (CPU time, software licenses, etc.)
  • Batch queuing & scheduling
  • Support diverse server hardware, OS and architectures
  • Load balancing & remote job execution
  • Detailed job accounting statistics
  • Fine-grained user specifiable resources
  • Suspend/resume/migrate jobs
  • Tools for reporting Job/Host/Cluster status
  • Job Arrays
  • Integration & control of parallel jobs

This package contains the graphical Grid Engine administration frontend.

Htcondor
distributed workload management system
Maintainer: HTCondor Developers
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Like other full-featured batch systems, HTCondor provides a job queueing mechanism, scheduling policy, priority scheme, resource monitoring, and resource management. Users submit their serial or parallel jobs to HTCondor; HTCondor places them into a queue. It chooses when and where to run the jobs based upon a policy, carefully monitors their progress, and ultimately informs the user upon completion.

Unlike more traditional batch queueing systems, HTCondor can also effectively harness wasted CPU power from otherwise idle desktop workstations. HTCondor does not require a shared file system across machines - if no shared file system is available, HTCondor can transfer the job's data files on behalf of the user.

This package can set up an appropriate initial configuration at install time for a machine intended either as a member of an existing HTCondor pool or as a "Personal" (single machine) HTCondor pool.

Please cite: Michael Litzkow, Miron Livny and Matt Mutka: Condor - A Hunter of Idle Workstations (eprint) Proceedings of the 8th International Conference of Distributed Computing Systems :104-111 (1988)
Ipython3
Erweiterte interaktive Python-3-Shell
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IPython kann als Ersatz zur Python-Standardshell oder, falls sie zusammen mit den wissenschaftlichen und numerischen Python-Werkzeugen genutzt wird, als vollständige Arbeitsumgebung für wissenschaftliches Rechnen (wie Matlab oder Mathematica) benutzt werden. Sie unterstützt dynamische Objektintrospektionen, nummerierte Eingabe-/Ausgabeprompts, ein Makrosystem, Protokollierung und Wiederherstellung von Sitzungen, vollständigen Shellzugriff auf das System, umfangreiche und farbige Traceback-Berichte, automatische Klammerung, automatische Anführungszeichen. Außerdem kann sie in andere Python-Programme integriert werden.

Dieses Paket enthält die eigentliche Terminal-Shell für Python 3.

The package is enhanced by the following packages: isympy3 python3-matplotlib python3-sympy
Mpich
Implementation of the MPI Message Passing Interface standard
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MPICH is a high-performance and widely portable implementation of the MPI-3.1 standard from the Argonne National Laboratory. It efficiently supports different computation and communication platforms including commodity clusters, SMPs, massively parallel systems, and high-speed networks. This release has all MPI 3.1 functions and features required by the standard with the exception of support for the "external32" portable I/O format and user-defined data representations for I/O.

This package includes the program binaries necessary to run MPICH programs.

Mpich2python
MPI-enhanced Python interpreter (MPICH2 based version)
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The package provides a python interpreter with MPI (Message Passing Interface, message-based parallel programming) support.

Nordugrid-arc-nox
ARC grid middleware
Maintainer: Anders Waananen
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The NorduGrid is a collaboration aiming at development, maintenance and support of the free Grid middleware, known as the Advanced Resource Connector (ARC).

The Advanced Resource Connector (ARC) brings computing resources together across institutional boundaries. This concept is commonly referred to as a "computational grid". Historically, grids address the organisation of distributed storage of data and parallel computation, but arbitrary services are thinkable.

Just like the web, ARC has its roots in the IT infrastructure that was erected to analyse the experiments for high energy physics at CERN. The first release, ARC-0.x, was dependent on Globus, the current release keeps that compatibility but can also be used independently.

With ARC-nox, formerly known as ARC-1, the user gains flexibility with additional services and more supported platforms. The service developer notices that even for persistent functionality across the two major versions, what has been a script on the server side once, that was repeatedly started and ran through, this has now become a service. Those are only started once and can then be queried, which is far more efficient, far more responsive, and is no longer stateless but can observe changes of values over time.

Openmpi-bin
Leistungsstarke Message-Passing-Bibliothek - Programmdateien
Maintainer: Alastair McKinstry
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Das Projekt Open MPI kombiniert Methoden und Ressourcen aus mehreren anderen Projekten (FT-MPI, LA-MPI, LAM/MPI und PACX-MPI), um die beste verfügbare MPI-Bibliothek (Message Passing Interface) zu verwirklichen. Als eine völlig neue, MPI-3.1-konforme Umsetzung bietet Open MPI Vorteile für System- und Software-Hersteller, Anwendungsentwickler und forschende Informatiker.

Merkmale:

  • vollständig konform zum MPI-3.1-Standard
  • Threadsicherheit und Nebenläufigkeit
  • dynamische Erzeugung von Prozessen
  • leistungsstark auf allen Plattformen
  • zuverlässige und schnelle Job-Verwaltung
  • tolerant gegenüber Netzwerk- und Prozessfehlern
  • unterstützt heterogene Netzwerke
  • eine einzelne Bibliothek unterstützt sämtliche Netzwerke
  • Instrumentierung zur Laufzeit
  • unterstützt viele Job-Scheduler
  • internationalsierte Fehlermeldungen
  • komponentenbasierter Entwurf, dokumentierte APIs

Dieses Paket enthält die Open-MPI-Dienstprogramme.

Openmpipython
MPI-enhanced Python interpreter (OpenMPI based version)
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The package provides a python interpreter with MPI (Message Passing Interface, message-based parallel programming) support.

Python3-scoop
Python3 library for concurrent parallel programming
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SCOOP (Scalable COncurrent Operations in Python) is a distributed task module allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.

This package contains the Python3 modules.

Official Debian packages with lower relevance

Coop-computing-tools
cooperative computing tools
Maintainer: Alastair McKinstry
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This is a collection of software that help users to share resources in a complex, heterogeneous, and unreliable computing environment. This includes:

  • Chirp: A personal filesystem and I/O protocol that allows unprivileged users to share space securely, efficiently, and conveniently. When combined with Parrot, Chirp allows users to create custom wide-area distributed filesystems.
  • Parrot: A transparent user-level virtual filesystem that allows any ordinary program to be attached to a remote storage device such as an FTP server or a Chirp server.
  • Makeflow: A workflow system for parallel and distributed computing that uses a language very similar to Make.
  • Work Queue: A system and API for building master-worker style programs that scale up to thousands of processors.
  • All Pairs: A computational abstraction for running very large Cartesian products.
  • Wavefront: A computational abstraction for running very large dynamic programming problems.
  • The Fault Tolerant Shell: A high-level programming language that allows users to combine the ease of shell scripting, the power of distributed programming, and the precision of compiled languages. Basically, parallel programming and exception handling for scripts.
Please cite: Douglas Thain, Christopher Moretti, and Jeffrey Hemmes: Chirp: A Practical Global Filesystem for Cluster and Grid Computing. (2009)
Hpcc
HPC Challenge benchmark
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The High Performance Computing (HPC) Challenge benchmark runs a suite of 7 tests that measure the performance of CPU, memory and network for HPC clusters. Amongst others, it includes the High-Performance LINPACK (HPL) benchmark, used by the Top500 ranking (http://www.top500.org/).

Octave-mpi
Octave toolbox for parallel computing using MPI
Maintainer: Debian Octave Group
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This package brings parallel computing capabilities to Octave by providing a convenient interface to MPI primitives. This is achieved using simple MPI Derived Datatypes.

This Octave add-on package is part of the Octave-Forge project.

Python3-mpi4py
bindings of the Message Passing Interface (MPI) standard
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buster2.0.0-3amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x
wheezy1.3+hg20120611-3amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc
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MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.

mpi4py is constructed on top of the MPI-1/MPI-2 specification and provides an object oriented interface which closely follows MPI-2 C++ bindings. It supports point-to-point (sends, receives) and collective (broadcasts, scatters, gathers) communications of any picklable Python object as well as optimized communications of Python object exposing the single-segment buffer interface (NumPy arrays, builtin bytes/string/array objects).

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Psom
pipeline system for Octave and Matlab
Responsible: NeuroDebian Team
License: MIT/Expat
Debian package not available
Language: Matlab/Octave

PSOM is a lightweight library to manage complex multi-stage data processing. A pipeline is a collection of jobs, i.e. Matlab or Octave code with a well identified set of options that are using files for inputs and outputs. To use PSOM, the only requirement is to generate a description of a pipeline in the form of a simple Matlab/Octave structure. PSOM then automatically offers the following services:

  • Run jobs in parallel using multiple CPUs or within a distributed computing environment.
  • Generate log files and keep track of the pipeline execution. These logs are detailed enough to fully reproduce the analysis.
  • Handle job failures: successful completion of jobs is checked and failed jobs can be restarted.
  • Handle updates of the pipeline: change options or add jobs and let PSOM figure out what to reprocess.
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