[gmx-users] Opteron: compile with 32-bit SSE

[David van der Spoel]

On Fri, 2004-09-10 at 03:27, Amadeu Sum wrote:
> Dear Choon-Peng,
> 
> Thank you for your comments. I had already done exactly what David and
> you suggested, and now I am facing also the same problem as you, that
> is, we have a specific interconnect for the Opteron cluster and it has
> to be compiled with specific libraries only available in the Opteron.
> 
> Anyone else with this dilemma? Or will we have to wait until the
> adjusting Erik is doing for the 64-bit version?

I think it is actually unrelated to 64 bit extensions. It should be
possible to use SSE even if you compile in 64 bit. The only problem I
can think of is the use of 64 bit integers iso 32 bit.

I'll try to compile on an AMD64 OS, and report back later.
> 
>                          Amadeu
> 
> 
> On Fri, 10 Sep 2004 08:44:56 +0800, Chng Choon Peng
> <cpchng at bii.a-star.edu.sg> wrote:
> > Dear Amadeu,
> > 
> >   I'm also facing this problem and followed the suggestion from David to
> > compile GROMACS on a Pentium system and then transfer the binary across.
> > It worked for me and I would like to share my experiences.
> > 
> > For GCC (I used default 2.96), you have to compile with the additional flags
> > "--without-x" and "--without-xml". When compiling on the Opteron (yes, no
> > SSE/SSE2), I have to include these 2 flags as well.
> > You can just use the default set of flags.
> > 
> > For Intel C Compilers:
> > export CFLAGS="-O3 -static -static-libcxa"
> > And I believe you have to compile FFTw 2.1.x in static mode as well.
> > 
> > In general, ICC compiled SSE code performs better than GCC.
> > And of course with SSE/SSE2, performance is better than without.
> > I collected some benchmark numbers on my homepage that might be of
> > reference:
> > http://web.bii.a-star.edu.sg/~cpchng/Gromacs_benchmarks.html
> > 
> > I used bold to highlight the best performance for single-precision GROMACS
> > across platforms and purple for double-precision.
> > The Opteron 2.2GHz we have is the best platform in almost all gmx
> > benchmarks.
> > 
> > However, I still wish for the compilation problem with SSE to be resolved,
> > as we will be using an interconnect that does not exist on the Pentium
> > cluster. So, will not be able to compile an optimal parallel version for the
> > Opterons.
> > 
> > cheers,
> > Choon-Peng
> > --
> > Mr. Choon-Peng CHNG
> > Research Associate
> > Computational Biology Group
> > BioInformatics Institute, BMSI, A*STAR
> > 30 Biopolis Street
> > #07-01 Matrix Building
> > Singapore 138671
> > Tel (O): +65 64788301 Fax (O): +65 64789047
> > www.bii.a-star.edu.sg/~cpchng
> > 
> > 
> > 
> > 
> > On 9/10/04 5:09 AM, "David" <spoel at xray.bmc.uu.se> wrote:
> > 
> > > On Thu, 2004-09-09 at 22:26, Amadeu Sum wrote:
> > >> I would like to ask the help from those who are using Gromacs in the
> > >> Opteron system.
> > >>
> > >> I have read many of the posting related to the performance issue and
> > >> it seems that Gromacs compiled in 32-bit with SSE works better in the
> > >> Opteron.  Can anyone point out what are the options/flags they are
> > >> using to get Gromacs to compile in an Opteron system in 32-bit with
> > >> SSE? I can get it to compile in 32-bit, but I have been unable to get
> > >> SSE. I am specifying:
> > >> CPFLAGS = -O6 -fomit -fomit-frame-pointer -finline-functions -Wall
> > >> -Who-unused -malign-double -funroll-all-loops -m32 -msse -msse2
> > >> -mfpmath=sse
> > >>
> > >> I have also tried explicitly specifying "--enable-x86-asm" and
> > >> "--disable-cpu-optimization" in configure, but that has not helped.
> > >>
> > >> I am using gcc v3.2.3
> > >>
> > > Do you have a normal pentium somewhere?
> > > Then your best bet is to compile there with the intel compilers---
> > >
> > >> Thanks in advance,
> > >>
> > >>                          Amadeu
> > >> _______________________________________________
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> > 
> >
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