AMBER Archive (2008)

Subject: RE: AMBER: MKL libraries/Amber10

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat May 17 2008 - 12:12:06 CDT

Hi Ross:
With the attached config_amber.h, Amber10 compiled serial with all tests PASSED (except dftb as I had not inserted the parameter files). I exported and sourced MKL_HOME in my .bashrc as indicated below, however I missed to add libmkl in the config.h. Examining the matter back, that occurred because it was not clear to me how to add to the config.h the two lines indicated below

/opt/intel/mkl...

(the path corresponds to my installation of mkl).

In fact, trying to compile dock for mkl I got the error: cannot find libmkl_intel.so

Much indebted for plainly explaining how (and in place of?) inserting the two lines. Apologiers for my lower than low level in compiling. Is the double "//" correct in those two lines?

Thanks a lot
francesco

--- On Fri, 5/16/08, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> From: Ross Walker <ross_at_rosswalker.co.uk>
> Subject: RE: AMBER: MKL libraries/Amber10
> To: amber_at_scripps.edu
> Date: Friday, May 16, 2008, 11:25 AM
> Hi Francesco,
>
> > Before performing tests, may I ask why during the
> compilation both g++ and
> > g77 were used. In particular about g77, should I have
> indicated ifort as
> > compiler (as I'll do for Amber10 and openmpi)? I
> was unable to see an
> > option for ifort in place of g77 for the above
> compilation.
>
> Ambertools always uses g77 for the Fortran compiler. There
> is no performance sensitive code in there that would
> benefit from ifort so in short don't worry about it. If
> it all compiled correctly and the tests pass you are good to
> go.
>
> > When all that is in order, I understand to unpack
> Amber10.tar.bz2 into
> > /usr/local/amber10
> > and proceed to compile.
>
> Yes and here you would benefit from specifying ifort since
> this is for the compilation of the MD engine code which is
> more computationally intensive.
>
> > Incidentally (which I forgot to mention in my original
> post), are MKL
> > libraries of help even for a NUMA-type machine with
> dual-opterons?
>
> Yes they can although it depends very much on the type of
> simulation you are running. QMMM runs (especially if you
> specify diag_routine=0 in &qmmm) can benefit enormously
> from MKL. GB runs can also benefit quite a bit. For regular
> classical PME MD simulations the difference is much
> smaller, on the order of 5 to 10% or so but if you have MKL
> available you might as well use it.
>
> Good luck,
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on
> request |
>
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