AMBER Archive (2008)

Subject: Fw: RE: AMBER: MKL libraries/Amber10

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat May 17 2008 - 12:33:10 CDT

Just to add that libmkl_intel.so is present in
 
/opt/intel/mkl/10.0.1.014/lib/32/

not in /64 or em64t, where there is libmkl.so

--- On Sat, 5/17/08, Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> From: Francesco Pietra <chiendarret_at_yahoo.com>
> Subject: RE: AMBER: MKL libraries/Amber10
> To: amber_at_scripps.edu
> Date: Saturday, May 17, 2008, 10:12 AM
> 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 |
> >
> > Note: Electronic Mail is not secure, has no guarantee
> of
> > delivery, may not be read every day, and should not be
> used
> > for urgent or sensitive issues.
> >
> >
> >
> >
> >
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