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

[Amadeu Sum]

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?

                         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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>