Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 2 Jul 2010 10:19:51 -0400

Hello,

It's just a series of perl scripts. I don't remember where I found the
source code, but I'll attach it here.

All the best,
Jason

On Fri, Jul 2, 2010 at 9:50 AM, Yu Chen <chen.hhmi.umbc.edu> wrote:

> > I'll pitch in with something you can try, but no guarantee it will work.
> > Because no_underscoring is a flag built into mpif90, you did NOT have to
> add
> > it to FFLAGS or FOPTFLAGS, since it was part of the compiler. Also,
> > according to Professor Case, this does bad things for amber due to the
> > Fortran/C 'hybridization' of sorts. Therefore, my suspicion is that the
> > presence of no_underscoring in mpif90 is what was causing your errors in
> the
> > first place. What you can probably do is use your MPICH2 build that has
> the
> > no_underscoring in place, but rather than using "mpif90" as your fortran
> > compiler, use what is returned by "mpif90 -show" without the
> no_underscoring
> > flag. It's a hack, but probably the only way (if it works) to avoid
> > installing 2 MPICH2's.
>
> I didn't know it's built into the compiler, then I don't know why it's
> still needed when I compile the other program. I think it's better to just
> install 2 MPICH2s.
>
> > The other option, of course, is to install 2 MPICH2's, just keep them
> > separate so you don't get any stepping on toes. mpi-selector is a nifty
> > little tool that helps organize multiple MPIs on a single cluster or
> > machine. It's what I have running on my machine so I can keep MPICH2 and
> > OpenMPI running for both the intel and gnu compilers easily. It takes a
> > little bit of setup, but it's pretty convenient when you have it up and
> > working.
>
> The mpi-selector sounds a very good idea. But when I googled
> "mpi-selector", I only found RPM packages. Do you know if there is a OS X
> package? I didn't even find the source code to compile. I will do more
> search to see if I can find something.
>
> Thanks!
> Chen
>
> >
> > Good luck!
> > Jason
> >
> > On Thu, Jul 1, 2010 at 5:58 PM, case <case.biomaps.rutgers.edu> wrote:
> >
> >> On Thu, Jul 01, 2010, Yu Chen wrote:
> >>>
> >>> I added "-fno-underscoring" at the end of "FFLAGS .." and "FOPTFLAGS
> ..."
> >> lines.
> >>
> >> I don't know where the idea of "no_underscoring" came from, but I'm
> pretty
> >> sure it will do bad things to Amber. Amber has both Fortran and C code,
> >> and
> >> assumes in many places that the fortran compiler will add an extra
> >> underscore,
> >> as is the usual practice for Unix/Linux compilers. If you turn this
> off,
> >> you should be prepared for lots of grunt work changing the code. I
> would
> >> strongly recommend not trying to use this flag.
> >>
> >>>
> >>>> I still recommend using the configure_openmpi script. There should be
> >> no
> >>>> need to manually edit the config.h file.
> >>
> >> Above I guess is a dead horse, I guess. I've attached a
> "configure_mpich2"
> >> script which should do the same thing for MPICH2 that configure_openmpi
> >> does
> >> for OpenMPI: provide an installation of MPI where you don't have to add
> or
> >> subtract flags, or edit config.h files, and which should work under most
> >> circumstances.
> >>
> >> ....dac
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032



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Received on Fri Jul 02 2010 - 07:30:06 PDT
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