AMBER Archive (2007)

Subject: RE: Re: AMBER: on PATH

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Thu Jun 28 2007 - 15:01:11 CDT

Dear Ross:

I should have better advised that the machine has indeed the X system and even
gnome, though it is used for QM computations, so that it is set to be launched
to give the console prompt. On rare occasions, the X system is called with
"startx" and after that, if needed, gnome is launched with "gnome-session".
When I carried out the compilation of amber9, no X had been called. Should you
need details about the X system on my machine, please ask (no nvidia modules
and no OpenGL installed).

To my excuse, I normally use that parallel machine with graphical output (ssh)
to the Athlon 32 bit single processor computer, where OpenGL is working, and
from where I am writing. In particular I do so with the NWChem/ECCE suite.
Calling X, with its unavoidable 32bit inside, to a 64bit system is slowing
down. I am already at the limit of possibilities for QM calculations with my
large molecules.

I thought urgent replying before examining the Makefile, as suggested by David
on another email. I'll do that. In particular I can't realize the advantage of
graphical xleap. It would be nice to have an arragement of amber9 where xleap
is startd only when X is started. May be installig xleap when X is activated
and then let it doormant when not needed? Is a support like gnome (and openGL)
also needed for xleap? I am already quite unhappy with the 32bit libraries that
I had to install for only the Intel compilers.

Is it possible to replace the service of graphical xleap with VMD? This is
installed on thei Athlon machine, together with a graphical MM package that I
use to build organic molecules and preliminarily minimizing it. It outpots also
pdb and sybyl files.

Thanks to all

francesco pietra

--- Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Hi Francesco,
>
> > After a long session it exited with Error 2
> >
> > Those errors that I can see on the screen comprise:
> >
> > WcActCB.c:1448: error: expected declaration specifiers before XEvent.
> > WcActCB.c:1448: error: expected declaration specifiers before
> > Cardinal.
> >
> >
> > WcActCB.c: In function WcDynamicActionACT:
> >
> > WcActCB.c:1450: error: expected declaration specifiers before Widget.
> >
> > WcActCB.c:1450: error: expected declaration specifiers before XEvent.
> >
> > WcActCB.c:1450: error: expected declaration specifiers before
> > Cardinal.
>
> At this point everything should have been built with the exception of xleap
> so you are good to run everything but can only use the non-graphical version
> of leap (tleap) to build the molecules. Normally problems with xleap come
> from not having the X11 development libraries installed but this would give
> a file not found error. I am not sure what the errors you are seeing are
> coming from and I'm not overly familiar with the way xleap works so I copied
> this email to Wei Zhang who is the xleap expert and will hopefully be able
> to help here.
>
> In the meantime you can run all the tests, everything should be good except
> the tests of xleap which should report that the executable is missing.
>
> > If relevant, I have seen during the process calling "gcc" and
> > "g++" (for
> > openmpi I have used intel for both fortran, C and C++).
>
> You don't need to worry here. Only sander and pmemd are 'parallel' using MPI
> and these are all fortran so the c/c++ compiler is irrelevant for compiling
> in parallel.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
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