Re: [AMBER-Developers] Requirement to build serial before building parallel

From: Jason Swails <>
Date: Sat, 6 Mar 2010 10:33:28 -0500

On Sat, Mar 6, 2010 at 9:26 AM, case <> wrote:
> On Fri, Mar 05, 2010, Ross Walker wrote:
>> It is often VERY beneficial to just build sander.MPI and pmemd.MPI on
>> various machines without having to build the whole of AMBER Tools serial.
> I suppose we could have a flag like "-sander-pmemd-only" that would skip
> the test.  Right now I can't remember what part of the parallel compile
> needs might be on the amber11 side or the AmberTools side.  But

I know that pnetcdf needs yacc, but back when parallel ptraj was first
introduced, I could never get it installed on my Ubuntu system because
it could never find yacc. It also refused to use the yacc compiled in
the serial build. I could only fix it by installing byacc/bison from
aptitude. This is still a package that is listed on the "amber on
ubuntu" website as a package that should be installed beforehand. Is
there any reason not to list it as a prerequisite and not actually
include it in the release? Or perhaps give the user the option of
linking to the existing yacc in the parallel build? If this is the
only part of the serial build needed for parallel, then it would
remove the need for a serial build first. Probably not terribly

All the best,

> for the *general* user it seems better to flag problems like this early,
> rather than having a strange error pop up half-way through the build step.
> ....dac
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Sat Mar 06 2010 - 08:00:02 PST
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