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

From: Yu Chen <>
Date: Thu, 1 Jul 2010 17:16:04 -0400

>> 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).
> This is a little confusing, since you mentioned openmpi(?) in the previous
> email. We also don't know what flags you used to compile the MPI.

No, I didn't use OpenMPI, I used MPICH2. The output of "mpif90 -show" is:
gfortran -fno-underscoring -O -L/opt/mx/lib64 -L/opt/mx/lib -I/common2/SL_upgrade/mpich2-mx/include -I/common2/SL_upgrade/mpich2-mx/include -L/common2/SL_upgrade/mpich2-mx/lib -L/common2/SL_upgrade/mpich2-mx/lib -lmpichf90 -lmpichf90 -lpmpich -lmpich -lopa -lmyriexpress

>> 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
> It's not clear exactly what you did to config.h, whether you are literally
> using "no_underscoring" (which is not correct), etc.

I added "-fno-underscoring" at the end of "FFLAGS .." and "FOPTFLAGS ..." lines. I found out that I have to add to both config.h, one in Amber's src dir and the other in AmberTools src dir. And the flags finally shown in the output of make parallel, yet, it still gave the same undefined symbol messages. I do think the problem is with "-fno-underscoring", which is required by another program (CYANA). Since I recompiled MPICH2 without the "-fno-underscoring" flag, and use that MPI successfully compiled everything in Amber, didn't even need the 'rand2.patch' you sent early. Here is the "mpif90 -show" output:

gfortran -L/opt/mx/lib64 -L/opt/mx/lib -I/common2/SL_upgrade/mpich2-mx-underscore/include -I/common2/SL_upgrade/mpich2-mx-underscore/include -L/common2/SL_upgrade/mpich2-mx-underscore/lib -L/common2/SL_upgrade/mpich2-mx-underscore/lib -lmpichf90 -lmpichf90 -lpmpich -lmpich -lopa -lmyriexpress

I guess I will have to find a way to make two programs both working. Probably install two MPICH2, and launch different one according to the program.
I will try macports installation later too.

Thanks for all the helps.

> I still recommend using the configure_openmpi script. There should be no
> need to manually edit the config.h file.
> ...dac
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Thu Jul 01 2010 - 15:00:05 PDT
Custom Search