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

From: Prabu Manoharan <>
Date: Thu, 2 Aug 2012 18:18:32 +0530


I am giving the details of the installation procedure which I followed
to install Amber12 and Ambertools.

In the first step I created a directory named amber12 under

Then I extracted the amber12 and amber12 tools software to the amber12
directory using below commands.

tar xvfj AmberTools12.tar.bz2
tar xvfj Amber12.tar.bz2

Then I set the amber environment variable

export AMBERHOME=/Volumes/data/common/amber12

Then I downloaded and applyed the patches as below

./ --update-tree

Then I ran the configure script inside the AMBERHOME directory by
choosing the gnu compiler as below

./configure gnu

make install

All the above steps went fine.

make test

 In the make test step one test experienced error was found related
to amber12 installation and also 2 file comparison failures in
amber12tools installation. I think this is because of the rounding
off differences.

In the next step for the parallel installation, first I tried to
install mpich2 using macports by giving the below command.

sudo port install mpich2 +gcc44

But after a overnight of time the installation was not complete.
It was not moving from one step called configure. so i cancelled it.

Then first i downloaded the openmpi version 1.5.4 and extracted inside
the $AMBERHOME/AmberTools/src directory and ran the configure_openmpi
script with compiler option as gnu as below

cd $AMBERHOME/AmberTools/src
./configure_openmpi gnu

Then I went to AMBERHOME directory and ran the configure script as below


./configure -mpi gnu

This step went fine without any error. I also added the below line to
the bashrc file.


In the next step (make install), it throw the error.

make install

Then the parallel installation was not successful.

Then I followed the same procedure as openmpi for the mpich2 (V 1.4.1)
 installation and configuration. The mpich2 installation went fine
without error. But the ./configure -mpi gnu step ended with error.

The error outputs from the mpich2 configuration step was posted in
the AMBER mailing list.

For your information I have also other mpich installations in the
below directories. which is been used by other applications.


May be the older version of installation may cause the problem.

As suggested in your previous mail to me i also ran the below commands
and the output also given here.

applecluster:~ admin$ which mpif90
applecluster:~ admin$ which mpicc
applecluster:~ admin$ icc --version
icc (ICC) 11.0 20090318
Copyright (C) 1985-2009 Intel Corporation. All rights reserved.

applecluster:~ admin$ mpicc -show
-L/common/mpich/ch_p4/lib -lpmpich -lmpich -lpmpich -lmpich



On Wed, Aug 1, 2012 at 7:38 PM, David A Case <> wrote:
> 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
> conflicts.
> 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
> commands:
> 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
> _______________________________________________
> AMBER mailing list

M. Prabu
AMBER mailing list
Received on Thu Aug 02 2012 - 06:00:04 PDT
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