Hi George,
Once you have the compilers built for Mac OS X 10.6, installing Amber itself
is quite simple (all you need is a simple ./configure gnu, make serial, and
make serial in the amber11/AmberTools/src and amber11/src directories).
Luckily, building the compilers from macports or fink is a one-time
necessity, so from now on Amber11 should be quite easy to build.
Amber11 in parallel requires, once your system is properly set up, only for
you to type "./configure -mpi gnu" in the amber11/AmberTools/src directory
and then make parallel instead of make serial as described above. The only
additional thing you need is an MPI installation. You can either use
macports or fink to build the MPI, or you can build your own from source. I
would suggest building your own, since it's quite easy.
First thing to do is pick an MPI and download the source code. As has been
suggested many times before, I would suggest MPICH2 (you can download the
source code from
http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.2.1p1/mpich2-1.2.1p1.tar.gz
Untar the archive in a directory, then cd into that directory and type
"./configure --prefix=/usr; make; make install".
This will configure it to be put in /usr/bin and /usr/lib and /usr/include
for the binaries, libraries, and include files, respectively. This should
successfully overwrite the fortran-deficient MPI installation that comes
with xcode tools.
After you've done this, the 3 simple commands described above (and in the
Amber11 manual) should be sufficient to build a parallel version. However,
you have to make clean before you do this, since you don't want to use the
serial installation as a starting point.
Mengjuei has also set up a very helpful "amber on mac" weblog that you can
find here
http://amberonmac.blogspot.com/.
Good luck!
Jason
On Mon, May 31, 2010 at 5:09 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi folks,
>
> I've made a successful serial installation of AMBER11 on a quad core MAC
> (Intel Core i7). My installation was done pretty much on the lines suggested
> in the message of Erik Zuiderweg dated May 24.
>
> My question is whether there's a way to take this as a starting point for a
> parallel installation or does one need to recompile the program from
> scratch? If the former option is possible any suggestions on how to proceed
> from there would be most useful. I went through the mail archive but somehow
> I'm getting lost in the detail.
>
> Your help would be greatly appreciated
>
> George
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon May 31 2010 - 07:00:06 PDT
