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

Chng Choon Peng cpchng at bii.a-star.edu.sg
Fri Sep 10 02:44:56 CEST 2004

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

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

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

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

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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