sysadmin

Software (mostly free software) useful for system and network administrators
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 02/08/12
  • Minor correction: 02/08/12

Stratuslab : complete IaaS cloud distribution

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: v2.0 - 25 June 2012
  • License(s): Other - Apache-2, AGPL
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): StratusLab Collaboration (CNRS, UCM, GRNET, SixSq, TID, et TCD)
  • Contact designer(s): support@stratuslab.eu
  • Laboratory, service: Universidad Complutense de Madrid (Madrid, Spain), GRNET (Athens, Greece), SixSq (Geneva, Switzerland), Telefónica I+D (Madrid, Spain), Trinity College Dublin (Dublin, Irland)

 

General software features

logo stratuslab
The distribution contains all of the necessary for deploying an Infrastructure-as-a-Service (IaaS) cloud: network, storage, and virtual machine management. Moreover, it provides innovative features like the Marketplace that facilitates sharing of virtual appliances, service management that allows deployment and autoscaling of multi-machine services, and support for multi-cloud scenarios. The distribution supports multiple operating systems (CentOS 6.2, Fedora16, and OpenSuSE 12.1) and is ideal for both public and private cloud deployments. The StratusLab client, written in Python, provides a simple command line interface to access to StratusLab cloud infrastructures from GNU/Linux, Mac OS X, and Windows machines.

Source code for the distribution can be found on GitHub.

Context in which the software is used

StratusLab is used at LAL to provide one of the StratusLab reference cloud infrastructures, a public cloud open to anyone for non-commercial use. The other StratusLab reference cloud is operated by GRNET in Greece. LAL also operates a second, private cloud infrastructure for deployment of laboratory services; existing services are gradually being migrated to this cloud infrastructure.

CNRS/IBCP operates a StratusLab cloud to support bioinformatics research and services. This public cloud infrastructure is available to users of the ReNaBi network. A portal, customized for bioinformatics users, facilitates use of the IBCP cloud and simplifies access to relevant virtual appliances and databases.

There are also commercial deployments of the StratusLab cloud distribution that support software engineering processes (such as deployment of ESA's SCOS-2000 platform) and scientific use (like the Atos Helix Nebula cloud infrastructure).

Publications related to the software

All of the related publications of the project are available from :

The chapter of the book "European Research Activities in Cloud Computing" contains a general description of the StratusLab project and its cloud distribution.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 20/03/12
  • Minor correction: 20/03/12

HINTS : network on demand diagnostic tool

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.

 

General software features

HINTS is a tool that provides quick network troubleshooting between two "probes", which are usually installed in remote geographical locations.
Although HINTS was primarily designed to diagnose potential network problems between two nodes of a grid, it is completely usable in a classical context, between two standard sites not involved in a grid infrastructure.

Historically, HINTS was born as part of the european project Enabling Grids for E-sciencE - EGEE, and continues today its evolution within the European Grid Infrastructure - EGI. HINTS is developed and maintained by CNRS, partner of France Grilles, the French National Grid Initiative and GARR, partner of the Italian Grid Initiative.

HINTS allows a user, from a centralized web interface, to initiate basic network tests between two specific agents (probes) previously deployed within local networks one want to qualify the link.

The qualification of the network between two probes is done through the following traditional system tools:

  • Ping
  • Traceroute,
  • Nmap,
  • DNS Resolution,
  • Iperf.

The main benefits of HINTS are:

  • A user may (subject to accreditation) test the quality of the network between its site and another site without involving an administrator of that other site,
  • All tests are symmetric (made in both directions between the selected probes),
  • Direct access to the probes (and thus access to the various diagnostic tools) is not possible, everything is done only via a centralized interface,
  • Fine and flexible user management (certification, delegation of rights),
  • The probes are based on those proposed by the well known PerfSONAR project.
Context in which the software is used

HINTS becomes useful when a user wants to diagnose the network between two sites without involving a network administrator and above all without disturbing the network administrator at the remote site.

If HINTS highlights some dysfunction between these two sites, network administrators will then not be disturbed for nothing.

If HINTS finds no problem, then the problems faced by users are likely not due to the network and is the reason to be searched elsewhere (application layers).

Today, HINTS is available in Scientific Linux 6.x RPM format.

Publications related to the software

  • Presentation at the EGI Technical forum, Lyon, September 2011
  • Poster for the EGI Community Forum, Munich, March 2012
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 16/08/10
  • Minor correction: 01/06/11
  • Index card author: Bruno Bzeznik (Projet CIMENT de l'Université Joseph Fourier)
  • Theme leader : Geneviève Romier (Institut des Grilles et du Cloud)

CiGri : lightweight computing grid

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 1.3 - Aout 2009
  • License(s): GPL - v2
  • Status: validated (according to PLUME), stable release, under development
  • Support: maintained, ongoing development
  • Designer(s): Bruno Bzeznik, Nicolas Capit, Olivier Richard, Elton Nicoletti Mathias, Yiannis Georgiou, and various contributors (internships, google summer of code)
  • Contact designer(s): Bruno.Bzeznik@imag.fr
  • Laboratory, service: CIMENT (University of Grenoble Computing center)

 

General software features

The CiGri software allows to set up a grid center to exploit a pre-existing set of super-computers. It is specialised on the management of "bag-of-tasks" jobs. It gathers the unused computing resources from an intranet infrastructure and makes it available for large set of tasks.

More information (in French) at fiche logiciel Fiche Plume.

Context in which the software is used

CiGri software is used at the computing center at Joseph Fourier University of Grenoble (CIMENT) since 2002.

Publications related to the software
  • Yiannis Georgiou, Olivier Richard, et Nicolas Capit.
    Evaluations of the lightweight grid cigri upon the grid5000 platform. In E-SCIENCE '07: Proceedings of the Third IEEE International Conference on e-Science and Grid Computing, pages 279-286, Washington, DC, USA, 2007. IEEE Computer Society.
  • Yiannis Georgiou, Nicolas Capit, Bruno Bzeznik, et Olivier Richard.
    Simple, fault tolerant, lightweight grid computing approach for bag-of-tasks applications. 3rd EGEE User Forum, 2008.
    http://indico.cern.ch/contributionDisplay.py?contr....
  • Yvan Calas, Nicolas Capit, et Estelle Gabarron.
    Cigri : Expériences autour de l’exploitation d’une grille légère. JRES, 2005.
    http://2005.jres.org/paper/90.pdf.
  • F. Dupros, F. Boulahya, J. Vairon, P. Lombard, N. Capit, et J-F. Méhaut.
    Iggi, a computing framework for large scale parametric simulations: Application to uncertainty analysis with toughreact. TOUGH Symposium, 2006.
    http://esd.lbl.gov/TOUGHsymposium/pdf/Dupros_IGGI.pdf.
  • J. Aoun, V. Breton, L. Desbat, B. Bzeznik, M. Leabadand, et J. Dimastromatteo.
    Validation of the Small Animal Biospace Gamma Imager Model Using GATE Monte Carlo Simulations on the Grid. In J. Montagnat S. D. Olabarriaga, D. Lingrand, editor, Proceedings of MICCAI-Grid Workshop Medical imaging on grids: achievements and perspectives, MICCAI-Grid Workshop, New York États-Unis d'Amérique, 2008.
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 31/03/10
  • Minor correction: 16/09/10

ChemAzTech : chemical product library & management software

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 0.6a - 07-30-2010
  • License(s): GPL
  • Status: beta release, under development
  • Support: maintained, ongoing development
  • Designer(s): Rémy Dernat (CNRS, IBMM). Contributions are wellcome.
  • Contact designer(s): remy(_dot_)dernat(_at_)univ-montp1(_dot_)fr
  • Laboratory, service:

 

General software features

Chemical product library & management software

This software includes lots of features. Main objective is to involve a maximum of people around a single interface, avalaible from a browser. It's a freely OpenSource and powerfull tool based on existing OpenSource chemical softwares.
You can download and see documentation and sources on sourceforge : http://chemaztech.sourceforge.net

Main features :

  •  Manage chemical products (with structures, place of storage, references, experiment number...).
  •  Draw, édit structures with JChemPaint.
  •  See your molecules 3D with JMol, in 2D with JChemPaint (java) or with the python librairy OASA (SVG pictures)
  •   Search by sub-structures with MyChem.
  •  Automated threatment for mol properties, with Smiles codes, Inchi with MyChem.
  •   Import molecules from a single MOL file, or CDX (ChemDraw)** or all a database from a SDF file (eg : from ISIS/Base) **
  •   Extract CSV, export as PDF or XLS(X)...
  •  Manage storage and accounting.
  •  Manage users and groups and a visibility level for products

** These softwares are not OpenSource but are very usefull in chemistry.

Other softwares used by ChemAzTech are OpenSource, under GPL or LGPL for JMol and
JChemPaint (JChemPaint is associated to Chemistry Development Kit (CDK)).
Thus, I can use them as building blocks for ChemAzTech, without forgetting OpenBabel, which is an important component of MyChem and which I use to convert files CDX and the MOL into MOL2 for 3D visualization .

On plume : OpenBabel

Context in which the software is used

First of all, this software needs a LAMP (Linux Apache MySQL PHP) server with OpenBabel and MyChem. Then you will have to install java and python (+ OASA library). It's a powerfull software for the management of chemical products, but as you can see, you need a lot a lot of features on your server to install it.

It's a beta software. Use it at your own risks.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 11/12/09
  • Minor correction: 11/12/09

Qolyester : test platform for the routing protocol QOLSR

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 20090302 - 2 mars 2009
  • License(s): GPL
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Equipe QOLSR
  • Contact designer(s): qolsr @ lri.fr
  • Laboratory, service:

 

General software features

Qolyester is the main in-the-field testbed for QOLSR over wireless Ad-Hoc networks.
It computes the best path with respect several metrics like capacity, delay, jitter, cost, loss probability, etc.
The goal of the current version is to be fully RFC 3626 compliant but without any QoS feature for the moment.

Context in which the software is used

This C++ software is at the heart of the QOLSR project, that is combining QoS with protocols OLSR, with the aim of dealing with metrics such as capacity, delay, jitter, cost in routing consideration with particular interest in IEEE 802.11-style MAC protocols due to their popular deployment in realistic wireless systems.

The major problems are the:

  • Interferences: flows that traverse the same geographical vicinity contend for the same wireless channel capacity;
  • Buffer size: After the saturation point the ad hoc network performance decreases;
  • Mac queuing time and service time based on the IEEE 802.11 binary exponential backoff algorithm;
  • Mobility.
Publications related to the software
  • An Efficient Source-Based Heuristic for Multicasting Multimedia Information, H. Badis, GESTS Transactions on Computer Science and Engineering, vol. 38, no. 1, 2007.
  • A complete and efficient quality of service model for mobile ad Hoc networks, H. Badis, GESTS Transactions on Computer Science and Engineering, vol. 36, no. 1: 427-442, 2007.
  • CEQMM: A Complete and Effecient Quality of Service Model for MANETs, H. Badis and K. Al Agha, The Third ACM International Workshop on Performance Evaluation of Wireless Ad Hoc PE-WASUN, Spain, October 2006.
  • Hakim Badis, Khaldoun Al Agha, "Quality of Service for Ad hoc Optimized Link State Routing Protocol (QOLSR)", October 2006.
  • Hakim Badis, Khaldoun Al Agha, "Quality of Service for Ad hoc Optimized Link State Routing Protocol (QOLSR)", March 2006.

Other publications are available on http://qolsr.lri.fr/papers/ and http://igm.univ-mlv.fr/~badis/#hakim-pap.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 17/04/09
  • Minor correction: 16/12/09

IPv6 CARE : IPv6 compliance testing

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System:
  • Current version: 2.2 - 9 March 2009
  • License(s): Other - Apache Licence (open source without copyleft)
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Etienne Dublé
  • Contact designer(s): etienne.duble _at_ urec.cnrs.fr
  • Laboratory, service: EGEE Project

 

General software features

IPv6 CARE, “IPv6 Compliance Automatic Runtime Experiment”, is a Linux tool able to diagnose the IPv6 compliance of programs at run time.

Mainly, it detects non IPv6 compliant function calls performed by the running program, for example gethostbyname().

For each problem detected, it generates :

  • a description of the problem
  • a tip explaining how to avoid this problem
  • the function calls stack, which is useful in order to know where the calls were performed in the source code

Moreover it generates a log file of all network related function calls.

IPv6 CARE works with all programs linked to the standard shared library (libc), which means:

  • Programs compiled (C/C++, …) in a standard way (that is, not statically compiled).
  • Programs written in some "Interpreted" language (Java, Perl, Python,…) if the interpreter or the virtual machine is compiled in a standard way (see limits below).
Usage example:
This shows how to test the IPv6 compliance of the telnet program:

$ ipv6_care check -v telnet localhost 7777
IPV6 CARE detected: getaddrinfo() with [ ai_family=AF_UNSPEC ai_socktype=SOCK_STREAM nodename=localhost servname=7777 ]
IPV6 CARE detected: getnameinfo() with [ sa.ip=127.0.0.1 sa.port=7777 ]
Trying 127.0.0.1…
IPV6 CARE detected: socket() with [ domain=AF_INET type=SOCK_STREAM protocol=ip ]
IPV6 CARE detected: connect() with [ socket=3 address.ip=127.0.0.1 address.port=7777 ]
IPV6 CARE detected: getnameinfo() with [ sa.ip=::1 sa.port=7777 ]
Trying ::1…
IPV6 CARE detected: close() with [ fd=3 ]
IPV6 CARE detected: socket() with [ domain=AF_INET6 type=SOCK_STREAM protocol=ip ]
IPV6 CARE detected: connect() with [ socket=3 address.ip=::1 address.port=7777 ]
telnet: Unable to connect to remote host: Connection refused
IPV6 CARE detected: close() with [ fd=3 ]
——————————————————————————————————————————————————————————
IPv6 diagnosis for ‘telnet localhost 7777’ was generated in: /tmp/ipv6_diagnosis/telnet/by_pid/pid_16537
——————————————————————————————————————————————————————————
$

The generated messages show that telnet has an IPv6 compliant behavior (mainly because it uses getaddrinfo).
For more information, we can check the details of the diagnosis in the directory indicated.

Interoperability:
Until now IPv6 CARE has only been tested on Linux systems.

It should also work on other UNIX-like systems if they allow dynamic loading of shared libraries (defined by the environment variable LD_PRELOAD) and if they have the program “addr2line”.

Limits:

In the case of "interpreted" langages (in the sense that they are not compiled into machine code), the tool interacts between the interpreter and the standard library (libc). For this reason IPv6 CARE diagnoses the behavior of the interpreter and not directly the script's behavior, which makes the diagnosis harder to be understood. Please refer to the documentation for further information on this issue.

Durability indicators:
IPv6 CARE is open source software and it is published on the sourceforge server in order to extend its audience and to allow a continuation of the development, even after the end of the EGEE project.


Downloads statistics:

http://sourceforge.net/project/stats/detail.php?gr...

Help and documentation
Forum: http://sourceforge.net/forum/forum.php?forum_id=89...
User guide: https://sourceforge.net/project/showfiles.php?grou...
Wikipedia article (in french) : http://fr.wikipedia.org/wiki/IPv6_CARE
Article explaining how to use IPv6 CARE (french, early version) : http://www.g6.asso.fr/blog/?p=33
Examples of IPv6 compliance reports using IPv6 CARE: https://edms.cern.ch/document/980424, https://edms.cern.ch/document/980820.

Contribution:
For contributions to IPv6 CARE please contact the author of this card.

Context in which the software is used

I developped this program for the EGEE project, in order to ease the IPV6 compliance tests of the middleware (gLite).

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