Psi-k - Ab initio (from electronic structure) calculation of complex processes in materials


Software solutions for data exchange and code gluing

The official workshop web-page, including the programme and some of the presentations


From: Xavier Gonze []
Sent: 14 September 2002 18:38
To:
Cc: Hinsen
Subject: CECAM Tutorial

Dear Walter,

Please, find herewith, a proposal for a joint CECAM - Ψk - SIMU tutorial, that Konrad Hinsen and myself would like to organize. It actually originates from the Free Software project for Atomic-Scale Simulations (www.fsatom.org).

With best wishes,
Xavier


NB : Thanks again for the help in the organisation of the ABINIT developer workshop! I received recently the administrative information from the ESF, and the ESF logo is now mentioned (as well as the Ψk network) at the bottom of the main Web page of the workshop: www.abinit.org/workshop/


Proposal for a CECAM - Ψk - SIMU joint Tutorial

1) Title (tentative): Software solutions for data exchange and code gluing.

Location: Lyon
Dates : three days in May or June 2003 (should be synchronized with a CECAM workshop dealing with component architectures)

Purpose: In this tutorial, we aim to teach the software tools and standards that have recently emerged in view of the exchange of data (formatted and unformatted) and gluing of codes :
(1) Python, as scripting langage, its interfaces with C and FORTRAN ;
(2) XML, as the leading standard for formatted data exchange
(3) netCDF, as an emerging standard for unformatted data exchange

Organizers :
X. Gonze
Université Catholique de Louvain
1, place Croix du Sud
B-1348 Louvain-la-Neuve
Belgium

K. Hinsen
Centre de Biophysique Moleculaire (CNRS)
Rue Charles Sadron
F-45071 Orleans Cedex 2
France


2) Scientific content

Recent discussions, related to the future I3 initiative linked to Ψk, as well as to the CECAM workshop on "Open Source Software for Microscopic Simulations", June 19-21, 2002, or to GRIDS, have made clear that one challenge for the coming years is the ability to establish standards for accessing codes, transferring data between codes, testing codes against each other, and become able to "glue" them (this being facilitated by the Free Software concept).

In the present tutorial, we would like to teach three "software solutions" that have recently emerged, to face this challenge : Python, XML and netCDF.

Python is now the de facto "scripting langage" standard in the computational physics community. XML (eXtended Markup Language) is an extension of HTML, allowing to set-up self-descripting documents, readable by humans and machines. netCDF allows unformatted files to be portable accross platforms. It is not our aim to cover all possible solutions to the above-mentioned challenges (e.g PERL, Tcl, or HDF), but these three have proven suitable for atomic-scale simulations, in the framework of leading projects like CAMPOS (www.fysik.dtu.dk/campos), MMTK (http://starship.python.net/crew/hinsen/MMTK), and GROMACS (www.gromacs.org), while other software projects like ABINIT (www.abinit.org) and PWSCF (www.pwscf.org - in the DEMOCRITOS context), among others, have made clear their interest for these.

Program of the tutorial.
Lectures in the morning, hands-on training in the afternoon.

1st day
-------
2h Python basics
1h Interface : Python/C or FORTRAN
1h XML basics
Afternoon Training with Python, and interfaces with C and FORTRAN

2nd day
-------
2h Python : object oriented
(+ an application to GUI and Tk)
1h Interface : Python/XML
1h Interface : XML + C or FORTRAN
Afternoon Training with XML + interfaces

3rd day
-------
1h Python : numerical
1h netCDF basics
1h Interface : netCDF/Python
1h Interface : netCDF/C or FORTRAN
Afternoon Training with netCDF + interfaces

3) List of lecturers

4) Number of participants: around 20,
Most of the participants should be PhD students, postdoc or young permanent scientists, involved in code development. It is assumed that the attendants have a good knowledge of C or FORTRAN.

5) Tutorial: this is a tutorial

6) Budget:

The expenses of invited lecturers and half of the participants should be taken care of by CECAM and SIMU. We apply thus for the coverage of expenses of the remaining 10 young researchers : three days/nights (3x75 Euros=225 Euros) average travel expenses (175 Euros). This makes an average 400 Euros per attendant.

*** We apply for 4000 Euros ***

7) Other funding:

As mentioned earlier, this should be a CECAM tutorial, also sponsored by SIMU. They should cover the expenses of the remaining 16 attendees and instructors.

8) The workshop should be held at CECAM, in Lyon.