[Fwd: Re: [ccp4bb]: Parallelization of ccp4 programs on linuxcluster ?]

[Michel Fodje <michel.fodje@mbfys.lu.se>]

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-----Forwarded Message-----

> From: Michel Fodje <michel.fodje@mbfys.lu.se>
> To: Paul Emsley <paule@chem.gla.ac.uk>
> Subject: Re: [ccp4bb]: Parallelization of ccp4 programs on linux cluster ?
> Date: 29 Aug 2002 10:31:30 +0200
> 
> There are several parallel implementations of the FFT routine.  Since
> many CCP4 programs do use FFT, it could be trivial to have these
> programs call the parallel FFT instead thus achieving widespread
> parallelization of most programs.  This is already possible with CNS on
> SGI by using SGI's parallel FFT routines.  
> 
> There is a GPL parallel FFT library called FFTW developed at MIT which
> is used in GROMACS 'The world's fastest molecular dynamics'. It performs
> quite well through  LAM-MPI (http://www.lam-mpi.org) or MPICH
> (http://www-unix.mcs.anl.gov/mpi/mpich/). 
> I'm not sure how the licensing is compatible with CCP4.  It is primarily
> a C-library but Fortran bindings exist. Converting a program which uses
> FFTW to be parallel is as easy as renaming the subroutine within the
> code.
> 
> /michel
> 
> On Wed, 2002-08-28 at 17:10, Paul Emsley wrote:
> > ***  For details on how to be removed from this list visit the  ***
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> > 
> > On Tue, 2002-08-27 at 05:36, Martin Laurberg wrote:
> > > ***  For details on how to be removed from this list visit the  ***
> > > ***          CCP4 home page http://www.ccp4.ac.uk         ***
> > > 
> > > Dear all,
> > > I have a small cluster of Linux Redhat7.3 openMosix machines
> > > and would like to take advantage of program parallelization.
> > > Has anyone had success on parallelizing parts of the ccp4
> > > suite under linux ?
> > > 
> > 
> > It is my understanding that this has considered by those involved - in
> > fact I may be so bold as to suggest that there is some enthusiasm for
> > the idea.  
> > 
> > It is much easier to implement parallelization at the shell-script
> > (ccp4i?) level rather than the fortran level - and this will be
> > attempted first (IIUC).
> > 
> > As you know, CCP4 software outputs files as the results of the
> > calculations. Thus there is a burden on the operating system to handle
> > some of the adminstrative load and (consistenly used) automount and
> > ssh (or a network queueing system) will be required (IIUC, you
> > understand).  You might like to voice your opinion on the
> > acceptability of this.
> > 
> > If you ask this question again in 6 months time, you may get a more
> > fully-rounded answer.
> > 
> > HTH somewhat, 
> > 
> > Paul.
> > 
> > 
> > 
> -- 
> _______________________________
> Michel N. Fodje
> Molecular Biophysics,
> Lund University, Sweden
> 
> phone: +46 46 222 45 13
> email: michel.fodje@mbfys.lu.se
> web:   http://www.mbfys.lu.se
> _______________________________
-- 
_______________________________
Michel N. Fodje
Molecular Biophysics,
Lund University, Sweden

phone: +46 46 222 45 13
email: michel.fodje@mbfys.lu.se
web:   http://www.mbfys.lu.se
_______________________________