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

From: Yu Chen <>
Date: Thu, 1 Jul 2010 11:24:09 -0400

> I would also suggest using macports or fink to build gcc/gfortran 4.4. When
> you type gcc --version and gfortran --version, what do you get? Do you see
> anything that says "experimental" anywhere? In the past I've had problems
> using gfortran-4.5 from the hpc website, since it was an experimental build
> that had some bugs when it came to compiling amber. I believe gcc-4.5 was
> only recently released officially, and I'm not sure if the binaries on that
> site have caught up yet.

Thanks, and yes they do have (experimental) after the version number.
 I will try macports next if it failed again with included FFLAGS.

> Good luck!
> Jason
> On Thu, Jul 1, 2010 at 10:52 AM, case <> wrote:
>> On Thu, Jul 01, 2010, Yu Chen wrote:
>>> Thanks for quick replying and the patch. Seems the patch works, it got
>>> rid of the duplicated symbol problem, but now I have got undefined
>>> symbol problem as following, wondering if you have any thought about
>>> this. I am wondering if this is related to the "fno-underscoring"
>>> flag I have to pass to the MPICH compiling. For the gcc/gfortran
>>> 4.5.0. I followed Mengjuei Hsieh's amberonmac blog, and downloaded the
>>> pre-compiled package from Thanks in advance for your help!
>> If you haven't done so, I strongly recommend you compile your own version
>> of openmpi, rather than downloading some pre-compiled version. There
>> is a "configure_openmpi" script in $AMBERHOME/AmberTools/src that makes
>> sure
>> that all the flags are set correctly, etc. This is especially true if you
>> are giving different flags (like no_underscore) to MPI and to Amber -- that
>> sounds like a recipe for problems.
>> It takes a while for openmpi to compile, but you only have to do it once,
>> and then you are sure that it is compiled in the same way as Amber.
>> ....dac
>> _______________________________________________
>> AMBER mailing list
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list

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Received on Thu Jul 01 2010 - 08:30:05 PDT
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