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

From: case <>
Date: Thu, 1 Jul 2010 10:52:30 -0400

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.


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Received on Thu Jul 01 2010 - 08:00:06 PDT
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