Thanks, Francesco.
I'll give it a try
Sasha
Francesco Pietra wrote:
> 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.ucla.edu> wrote:
>
>
>> From: Sasha Buzko <obuzko.ucla.edu>
>> Subject: Re: AMBER: AMD Opteron: compiler recommendations?
>> To: amber.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.email.unc.edu> wrote:
>>
>>>
>>>
>>>> From: Robert Duke <rduke.email.unc.edu>
>>>> Subject: Re: AMBER: AMD Opteron: compiler
>>>>
>> recommendations?
>>
>>>> To: amber.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.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
>>>>
>>>>
>>>
>>>
>> ____________________________________________________________________________________
>>
>>> Be a better friend, newshound, and
>>> know-it-all with Yahoo! Mobile. Try it now.
>>>
>> http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
>>
>> -----------------------------------------------------------------------
>>
>>> The AMBER Mail Reflector
>>> To post, send mail to amber.scripps.edu
>>> To unsubscribe, send "unsubscribe amber" to
>>>
>> majordomo.scripps.edu
>>
>>>
>
>
> ____________________________________________________________________________________
> Be a better friend, newshound, and
> know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Apr 27 2008 - 06:08:18 PDT
