AMBER Archive (2009)
Subject: Re: [AMBER] Installation on MacOSX
From: Alan (alanwilter_at_gmail.com)
Date: Tue Dec 15 2009 - 04:26:48 CST
Hi David W! I always follow anything you wright about Amber on Mac and best
Xmas gift would Ambertools 1.3. And thanks for your offlist emails with
I didn't check today, but did Intel finally release its compilers to work
with Snow Leopard? There were serious issues about it.
Your recipe AFAIR is for 32 bits only right?
And do you still see this with intel MKL (excerpt from another email):
"I got the absolute values identical to 1rrb_vac_distcovarmat_evecs.dat.save
except for the sign where with MKL they were inverted (like a matrix
multiplied by -1), e.g.:
< 0.00237 -0.00485 0.00133 0.00259 -0.00563 0.00178
> -0.00237 0.00485 -0.00133 -0.00259 0.00563 -0.00178
On Mon, Dec 14, 2009 at 20:01, David Watson <dewatson_at_olemiss.edu> wrote:
> On Dec 14, 2009, at 12:59 PM, Freedman, Tanya wrote:
> > Hi,
> > I have used amber before, but I'm a beginner when it comes to installing
> this type of package. I haven't yet been able to find very simple,
> step-by-step guidelines for getting Amber installed and running on MacOSX.
> Can anyone give me these instructions in the simplest, most cookbook terms
> > Thanks for your help!
> 1) Get XCode 3 from Apple or install an older version from your OS
> installation media
> 2) Get a fortran compiler and install it. I would recommend gfortran for
> price, intel fortran for speed.
> gfortran: http://hpc.sourceforge.net/
> or intel:
> http://www.programmers.com/PPI_US/PartnerCenter/partners.aspx?name=intel(you may find it at other vendors)
> or absoft: http://www.absoft.com/
> 3) unpack your amber tarball and learn how to use "sudo" from the
> command-line, as you will likely want to install Amber to /usr/local/amber
> or some such directory where you will need root permissions.
> 4) Download the latest and greatest AmberTools (you may want to wait a week
> or two) and install that package using the installation instructions. You
> don't need to use MKL or intel fortran for these, and it's probably best to
> avoid them if at all possible. Make sure that you export AMBERHOME
> appropriately (read the instructions!) in your .bash_profile, then log out
> and back into a Terminal session.
> 5) Follow the instructions to build Amber in serial, but go ahead and use
> MKL if you have the intel compilers.
> You will have to edit your .bash_profile to export MKL_HOME. Also, make
> note of
> as that note is your best friend.
> 6) If you want to use all cores on a modern system, then you will want to
> get a working installation of mpi.
> I would recommend mpich2, but you are going to have to download the source
> and compile it to support your fortran compiler. Install this to
> /opt/mpich2, then set up your .bash_profile to export MPI_HOME=/opt/mpich2
> before you attempt to install parallel. Please read the Installer guide and
> User guide for mpich2 if you run into problems with this one. And before you
> attempt to compile amber parallel, be sure that you can run
> /opt/mpich2/bin/mpirun -np 2 hostname
> without errors (e.g. you will see your computer's name printed on two
> separate lines.)
> 7) If you've gotten to this point, you may want to compile pmemd, but this
> requires mojo and I'm not going to explain it in anymore detail unless you
> get to this point and write me back personally.
> Some important notes:
> a) You will want to be familiar with the bash shell, so pick up a book on
> that if you aren't a console guru.
> b) Your choice of fortran compiler can make simulations go faster, but
> newer intel compilers with MKL can cause weird problems on a few of the
> c) At no point in time should you fail to read the instructions. Memorize
> them, recite them in prayer to your deity (if applicable), and if you are
> persistent, you will be rewarded.
> I hope that's enough to get you pointed in the right direction.
> I have configuration files available upon request for compiling 64 bit
> versions of sander (serial and parallel) and pmemd with intel fortran.
> I can't provide support for them, should you wish to use them, because you
> will likely have a different MKL path than I do.
> AMBER mailing list
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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