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

From: Yu Chen <>
Date: Thu, 1 Jul 2010 11:37:46 -0400

>> 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.

Sorry for the misunderstanding. I DO compiled MPICH2 myself, the gcc/gfortran package is downloaded from, although I could have done if from Macports too (maybe try it next).

The passing flags do remind me that I didn't pass the no_underscoring to Amber, so I just tried that (I put the no_underscoring in config.h on FFLAGS ... line), but it seems the compiler didn't pick it up, the flag still not included when compiling. I did the ./configure -mpi gnu first, then edit the config.h file, then make clean ; make parallel.

Thanks in advance.

> 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
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Received on Thu Jul 01 2010 - 09:00:03 PDT
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