AMBER Archive (2008)

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

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat May 17 2008 - 16:14:18 CDT

Here again (sorry) for the 3rd time, to say that config_amber.h seems to be correct as to mkl:

# Loader:
#------------------------------------------------------------------------------
LOAD= ifort $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADCC= gcc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADLIB= -L/opt/intel/mkl/10.0.1.014//lib/em64t -lvml -lmkl_lapack -lmkl -lguide -lpthread
LM= -lm
XHOME= /usr/X11R6
XLIBS= -L/usr/X11R6/lib64 -L/usr/X11R6/lib

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

> From: Francesco Pietra <chiendarret_at_yahoo.com>
> Subject: Fw: RE: AMBER: MKL libraries/Amber10
> To: "Amber" <amber_at_scripps.edu>
> Date: Saturday, May 17, 2008, 10:33 AM
> 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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