AMBER Archive (2008)

Subject: Re: AMBER: AMD Opteron: compiler recommendations?

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Apr 26 2008 - 15:56:13 CDT

Hi:
can't remember if I set something special, probably not. At any event, the config.h follows
francesco
===========================================================================

#------------------------------------------------------------------------------
# Main AMBER source root directory
#------------------------------------------------------------------------------
AMBER_SRC=/usr/local/amber9/src

#------------------------------------------------------------------------------
# AMBERBUILDFLAGS provides a hook into the build process for installers;
# for example, to build debug versions of the amber programs
# make -e AMBERBUILDFLAGS="-DDEBUG -g"
#------------------------------------------------------------------------------
AMBERBUILDFLAGS=

#------------------------------------------------------------------------------
# LOCALFLAGS is intended for program specific modifications to the
# Fortran build process and may be modified by the program's local makefile
#------------------------------------------------------------------------------
LOCALFLAGS=

#------------------------------------------------------------------------------
# Availability and method of delivery of math and optional libraries
#------------------------------------------------------------------------------
USE_BLASLIB=$(SOURCE_COMPILED)
USE_LAPACKLIB=$(SOURCE_COMPILED)
USE_LMODLIB=$(LMOD_UNAVAILABLE)

#------------------------------------------------------------------------------
# C compiler
#------------------------------------------------------------------------------
CC= gcc
CPLUSPLUS=g++
CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2
CPPFLAGS= $(AMBERBUILDFLAGS)

#------------------------------------------------------------------------------
# Fortran preprocessing and compiler.
# FPPFLAGS holds the main Fortran options, such as whether MPI is used.
#------------------------------------------------------------------------------
FPPFLAGS= -I/usr/local/include -P -DMPI $(AMBERBUILDFLAGS)
FPP= cpp -traditional $(FPPFLAGS)
FC= ifort
FFLAGS= -w95 -mp1 -O0 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FOPTFLAGS= -w95 -mp1 -ip -O3 -tpp7 -axWP $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -FR

#------------------------------------------------------------------------------
# Loader:
#------------------------------------------------------------------------------
LOAD= ifort $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADCC= gcc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADLIB= -L/usr/local/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil
LM= -lm
LOADPTRAJ= ifort -nofor_main $(LOCALFLAGS) $(AMBERBUILDFLAGS)
XHOME= /usr/X11R6
XLIBS= -L/usr/X11R6/lib64 -L/usr/X11R6/lib

#------------------------------------------------------------------------------
# Other stuff:
#------------------------------------------------------------------------------
.SUFFIXES: .f90
EMPTY=
AR=ar rv $(EMPTY)
M4=m4
RANLIB=ranlib
SFX=
NETCDF=
NETCDFLIB=
MODULEDIR=-I
MAKEDEPEND=$(AMBER_SRC)/../bin/amber_makedepend
SLKO=skipDFTB

# default rules for Fortran and C compilation:

.f.o: $<
        $(FPP) $< > _$<
        $(FC) -c $(FFLAGS) -o $@ _$<

.c.o:
        $(CC) -c $(CFLAGS) $(CPPFLAGS) -o $@ $<

__________________-

--- On Sat, 4/26/08, Sasha Buzko <obuzko_at_ucla.edu> wrote:

> From: Sasha Buzko <obuzko_at_ucla.edu>
> Subject: Re: AMBER: AMD Opteron: compiler recommendations?
> To: amber_at_scripps.edu
> Date: Saturday, April 26, 2008, 1:31 PM
> Francesco,
> sure, if you used compilation options that differed from
> the generic
> installation instructions, it would be useful to try if you
> get a chance
> to post them.
>
> Thank you
>
> Sasha
>
>
> Francesco Pietra wrote:
> > There must be the comparison you are looking for on
> the Amber archives. I remember that a comparison of Intel
> with other compilers for dual-opteron was posted, and Intel
> was scored very high. As Intel is free for non commercial
> use, I choose Intel for Amber and OpenMPI and found Amber
> running very fast. As I am no expert, I guess I have no
> particular settings. On request I can show my settings for
> a NUMA system of 8 logical opterons. Tell me what you want,
> unless some other guy can provide the settings far better
> than I can.
> > francesco
> >
> >
> > --- On Fri, 4/25/08, Robert Duke
> <rduke_at_email.unc.edu> wrote:
> >
> >
> >> From: Robert Duke <rduke_at_email.unc.edu>
> >> Subject: Re: AMBER: AMD Opteron: compiler
> recommendations?
> >> To: amber_at_scripps.edu
> >> Date: Friday, April 25, 2008, 3:04 PM
> >> The pathscale compilers are pretty good for
> opterons; the
> >> pgi compilers are used for cray machines running
> opterons,
> >> so they must not be too bad on performance either,
> though
> >> there has been grief with pgi from time to time
> (in
> >> fairness, they have tried to fix their problems,
> so I
> >> should give them credit for responding to the past
> >> problems). With intel, it may be a specific
> switches
> >> problem; I last tried running them on opterons a
> couple of
> >> years ago. I preferred pathscale for the opteron,
> but
> >> there was not a 30% performance differential at
> that point
> >> in time (things could have changed). It is
> completely
> >> possible that my default ifort settings for the
> opteron are
> >> no longer the best choice (sorry, I just
> didn't get
> >> around to trying this combination in the current
> release
> >> cycle).
> >> Regards - Bob Duke
> >> ----- Original Message -----
> >> From: Sasha Buzko
> >> To: amber_at_scripps.edu
> >> Sent: Friday, April 25, 2008 5:54 PM
> >> Subject: AMBER: AMD Opteron: compiler
> recommendations?
> >>
> >>
> >> Hi all,
> >> I've compiled sander.MPI and pmemd using
> Intel
> >> compilers and tested them with no apparent errors
> on AMD
> >> processors. However, the executables seem to be
> >> considerably faster on Intel chips (while the
> hardware is a
> >> bit better in that case, it shouldn't account
> for a 30%
> >> performance increase).
> >>
> >> Has anyone had any experience with comparing
> performance
> >> of binaries built using different compilers on AMD
> >> hardware? For instance, how do Pathscale compilers
> compare
> >> to Intel on Opterons? I've read reports about
> the evil
> >> Intel intentionally under-optimizing code on
> non-Intel
> >> chips, but hope it's not the issue here :).
> >>
> >> Any recommendations and/or benchmark results
> would be
> >> very much appreciated.
> >>
> >> Thanks in advance
> >>
> >> Sasha
> >>
> >
> >
> >
> ____________________________________________________________________________________
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