Re: [AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5

From: David A Case <>
Date: Wed, 1 Aug 2012 10:08:29 -0400

On Wed, Aug 01, 2012, Prabu Manoharan wrote:
> I am successful in installing both openmpi and mpich2 (as per the
> procedure given in the ambertools manual)

It was not the intent to have people install both MPI versions. I think you
will get the one that was installed last, but I'm not sure we have tested for

I would be better to say what you actually did. Just saying "per the
procedure in the manual" leaves a lot of uncertainty.

> applecluster:amber12 admin$ make install
> cd AmberTools/src && make install
> Starting installation of AmberTools12 MPI at Wed Aug 1 17:33:45 IST 2012.
> (cd etc && make parallel)
> mpif90 -DBINTRAJ -DMPI -o numprocs numprocs.F90
> ld: warning: -macosx_version_min not specificed, assuming 10.6
> ld: warning: could not create compact unwind for _main: register 3
> saved somewhere other that in frame
> ld: warning: could not create compact unwind for _MAIN__: register 6
> saved somewhere other that in frame
> ld: warning: ignoring file
> /opt/local/lib/gcc46/gcc/i386-apple-darwin9/4.6.3//libgcc.a, file was
> built for archive which is not the architecture being linked (x86_64)

We don't know which mpif90 you are running. Could you provide the output from
"which mpif90"? It looks like your MPI installation cannot be used to compile
any fortran programs.

> (cd sff && make libsff_mpi )
> mpicc -c -Dflex -O3 -mtune=native -msse -mfpmath=sse -DBINTRAJ -DHASGZ
> -I/Volumes/data/common/amber12/include -o binpos.o binpos.c
> icc: command line error: invalid argument for option '-mtune'

Here you are accessing an mpicc that uses the Intel compilers, but you
said earlier in your post that you were using the gnu compilers. You have
to be consistent; this is also the reason I wanted to know exactly how you
installed your MPI. It would help to know the output of the following

which mpicc
icc --version
mpicc --show (or mpicc -show)

Jason is correct that you can probably install MPI from macports. But we
would certainly like to figure out why the scripts we provide are not working.

Finally, since you say you are new to Amber: be sure you really need the
parallel capability before investing a lot of time in getting it to work.

...good luck....dac

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Received on Wed Aug 01 2012 - 07:30:02 PDT
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