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

From: Jason Swails <>
Date: Thu, 1 Jul 2010 23:55:20 -0400


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.

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

Good luck!

On Thu, Jul 1, 2010 at 5:58 PM, case <> 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

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Jul 01 2010 - 21:00:03 PDT
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