thanks a lot, I fought a bit, but finally it worked
best
Andrea
On Thu, 29 Mar 2007 12:36:01 -0400
"Robert Duke" <rduke.email.unc.edu> wrote:
> Undoubtedly, but I have never had access to a machine with scali. You may
> want to look at how it is being done in sander and see if that gives you
> some clues as to what is required in pmemd. I presume it is mostly a matter
> of picking up the headers and libraries correctly. Try doing a fake
> configure of mpich (ie., run the pmemd configure command, and act like you
> have mpich instead of scali), and then do the following to the config.h for
> pmemd (in the pmemd subdir):
> 1) remove -DSLOW_NONBLOCKING_MPI from the MPI_DEFINES = line
> 2) for the MPI_LIBS line, change -lmpich to -lfmpi -lmpi
>
> Please let me know how this works.
>
> Regards - Bob Duke
>
> ----- Original Message -----
> From: "Andrea Bortolato" <andrea.bortolato.1.unipd.it>
> To: <amber.scripps.edu>
> Sent: Thursday, March 29, 2007 12:17 PM
> Subject: AMBER: is possible to compile pmemd using scali MPI?
>
>
> > Dear all,
> >
> > I installed successfully amber serial and parallel in our cluster with
> > scali MPI.
> >
> > however I cannot compile pmemd: is possible to compile it using scali MPI?
> >
> > Thank you very much and best regards
> > Andrea
> >
> > ---------------------------------------
> > Andrea Bortolato, Ph.D. Student
> >
> > Molecular Modeling Section
> > Department of Pharmaceutical Sciences
> > University of Padova,
> > Via Marzolo, 5
> > 35131 Padova - ITALY
> > Phone: +39-049-8275801
> > Fax: +39-049-8275801
> > e-mail:andrea.bortolato.1.unipd.it
> > Webpage URL http://mms.dsfarm.unipd.it
> > ----------------------------------------
> > -----------------------------------------------------------------------
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> >
>
>
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---------------------------------------
Andrea Bortolato, Ph.D. Student
Molecular Modeling Section
Department of Pharmaceutical Sciences
University of Padova,
Via Marzolo, 5
35131 Padova - ITALY
Phone: +39-049-8275801
Fax: +39-049-8275366 or +39-049-8275704
e-mail:andrea.bortolato.1.unipd.it
Webpage URL
http://mms.dsfarm.unipd.it
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Received on Sun Apr 01 2007 - 06:07:45 PDT
