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<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">Dear David,<br>
</span></p>
<p class="MsoNormal" style=""> here are the VERY preliminary results.
I've run d.dppc as I have downloaded it from the gromacs site.<br>
</p>
<p class="MsoNormal" style="">Please do not consider these numbers as
significant for any comparisions between processors/architecture. This
is NOT optimized.<br>
</p>
<p class="MsoNormal" style="">I think that it should be possible to
improve performance by changing compilation options (expecially in fftw
and gromacs).<br>
For the time being I just wanted to check if the code compiled and run
successfully.<br>
</p>
<p class="MsoNormal" style="">Are there any news on the new assembly
loops for the Opteron?<br>
I read a message mentioning that gromacs 4 will know of the k8
architecture.<br>
</p>
<p class="MsoNormal" style="">What do you think of creating a page on
the gromacs site with the best optimization flags for the major
processors? I guess that most users have tried this, but it is quite
complex and time-consuming. I'm thinking of something like a Wiki.</p>
<p class="MsoNormal" style="">It would also be great to have a place
where people could share protocols for the most common simulations.this
would make it easier to learn (for novices) and to compare (for experts)<br>
</p>
<p class="MsoNormal" style="">Pier<br>
</p>
<p class="MsoNormal" style=""><br>
</p>
<p class="MsoNormal" style=""><br>
</p>
<p class="MsoNormal" style="">System: Opteron quad processor <br>
vendor_id : AuthenticAMD<br>
cpu family : 15<br>
model : 5<br>
model name : AMD Opteron(tm) Processor 846<br>
stepping : 8<br>
cpu MHz : 1993.080<br>
cache size : 1024 KB<br>
fpu : yes<br>
fpu_exception : yes<br>
cpuid level : 1<br>
wp : yes<br>
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge
mca cmov<br>
pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext lm 3dnowext 3dnow<br>
bogomips : 3948.54<br>
TLB size : 1088 4K pages<br>
clflush size : 64<br>
cache_alignment : 64<br>
address sizes : 40 bits physical, 48 bits virtual<br>
power management: ts ttp<br>
</p>
<p class="MsoNormal" style="">OS: Suse Prof. 9.1 64 bit version<br>
<br>
</p>
<p class="MsoNormal" style=""><br>
</p>
<p class="MsoNormal" style="">All tests run with mdrun -np 4 -shuffle
-sort<br>
</p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><br>
LAM 7.0.6<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">gcc<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">fftw
(no_386_hacks)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">4 CPU<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">Reading specs
from
/usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/specs<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">Configured with:
../configure --enable-threads=posix
--prefix=/usr --with-local-prefix=/usr/local --infodir=/usr/share/info
--mandir=/usr/share/man --enable-languages=c,c++,f77,objc,java,ada
--disable-checking --libdir=/usr/lib64 --enable-libgcj
--with-gxx-include-dir=/usr/include/g++ --with-slibdir=/lib64
--with-system-zlib --enable-shared --enable-__cxa_atexit
x86_64-suse-linux<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">Thread model:
posix<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">gcc version 3.3.3
(SuSE Linux)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">_________________<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">mpirun -ssi rpi
usysv -v C <o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>NODE (s)<span style=""> </span>Real (s)<span style=""> </span>(%)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>Time:<span style=""> </span>1413.000<span style=""> </span>1413.000<span
style=""> </span>100.0<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>23:33<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>(Mnbf/s)<span style=""> </span>(GFlops) (ps/NODE
hour) (NODE hour/ns)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">Performance:<span
style="">
</span>82.451<span style=""> </span>2.973<span style=""> </span>25.478<span
style=""> </span>39.250<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--><!--[endif]-->
<!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">_______________________<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">mpirun -ssi rpi
sysv -v C <o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>NODE (s)<span style=""> </span>Real (s)<span style=""> </span>(%)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>Time:<span style=""> </span>1412.000<span style=""> </span>1412.000<span
style="">
</span>100.0<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span><span style=""> </span>23:32<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>(Mnbf/s)<span style=""> </span>(GFlops) (ps/NODE
hour) (NODE hour/ns)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">Performance:<span
style=""> </span>82.509<span style=""> </span>2.975<span
style=""> </span>25.496<span style=""> </span>39.222<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@<o:p></o:p><br>
With a different setup for usysv (short message size)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><span style=""> </span>mpirun
-ssi rpi usysv<span style=""> </span>-v C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span></span><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">NODE
(s)<span style=""> </span>Real (s)<span style=""> </span>(%)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>Time:<span style=""> </span>1427.000<span style=""> </span>1427.000<span
style="">
</span>100.0<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>23:47<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>(Mnbf/s)<span style=""> </span>(GFlops) (ps/NODE
hour) (NODE hour/ns)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">Performance:<span
style=""> </span>81.642<span style=""> </span>2.944<span
style=""> </span>25.228<span style=""> </span>39.639<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<div
style="border-style: none none solid; border-color: -moz-use-text-color -moz-use-text-color windowtext; border-width: medium medium 1.5pt; padding: 0cm 0cm 1pt;">
<p class="MsoNormal" style="border: medium none ; padding: 0cm;"><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
</div>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">PGI
– Benchmarks <o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">uname
-m = x86_64<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">uname -r =
2.6.5-7.75-smp<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">uname -s = Linux<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="FR"
style="font-size: 10pt; font-family: "Courier New";">uname -v = #1 SMP
Mon Jun 14 10:44:37 UTC 2004<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="FR"
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="DE"
style="font-size: 10pt; font-family: "Courier New";">/usr/bin/uname -p
= unknown<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="DE"
style="font-size: 10pt; font-family: "Courier New";">/bin/uname -X<span
style="">
</span>= unknown<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="DE"
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="DE"
style="font-size: 10pt; font-family: "Courier New";">/bin/arch<span
style="">
</span>= x86_64<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="DE"
style="font-size: 10pt; font-family: "Courier New";">/usr/bin/arch -k<span
style="">
</span>= unknown<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">/usr/convex/getsysinfo
= unknown<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">hostinfo<span
style=""> </span>= unknown<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">/bin/machine<span
style=""> </span>= unknown<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">/usr/bin/oslevel<span
style=""> </span>= unknown<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">/bin/universe<span
style=""> </span>= unknown<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="DE"
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="DE"
style="font-size: 10pt; font-family: "Courier New";">/usr/pgi/linux86-64/5.1/bin/pgcc
-V<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">pgcc 5.1-6<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">Copyright
1989-2000, The Portland Group, Inc.<span style=""> </span>All Rights
Reserved.<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">Copyright
2000-2003, STMicroelectronics, Inc.<span style=""> </span>All Rights
Reserved.<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">PGI COMPILER
(using -tp=k8-64)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">LAM
7.0.6<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">Fftw<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">4
CPU<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>NODE (s)<span style=""> </span>Real (s)<span style=""> </span>(%)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>Time:<span style=""> </span>1753.000<span style=""> </span><span
style=""> </span>1753.000<span style=""> </span>100.0<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>29:13<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>(Mnbf/s)<span style=""> </span>(GFlops) (ps/NODE
hour) (NODE hour/ns)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">Performance:<span
style=""> </span>66.459<span style=""> </span>2.397<span
style=""> </span>20.536<span style=""> </span>48.694<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">_______________________<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">mpirun
-ssi rpi usysv<span style=""> </span>-v C<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span></span><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";">NODE
(s)<span style=""> </span>Real (s)<span style=""> </span>(%)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>Time:<span style=""> </span>1745.000<span style="">
</span>1745.000<span style=""> </span>100.0<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>29:05<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span lang="EN-GB"
style="font-size: 10pt; font-family: "Courier New";"><span style="">
</span>(Mnbf/s)<span style=""> </span>(GFlops) (ps/NODE
hour) (NODE hour/ns)<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";">Performance:<span
style=""> </span>66.764<span style=""> </span>2.408<span
style=""> </span>20.630<span style=""> </span>48.472<o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span
style="font-size: 10pt; font-family: "Courier New";"><!--[if !supportEmptyParas]--> <!--[endif]--><o:p></o:p></span></p>
<pre class="moz-signature" cols="72">--
Pierfrancesco Zuccato
HPC Architect
EXADRON, a division of Eurotech Spa
Via Jacopo Linussio, 1
33020 AMARO (UD) - ITALY
Phone: +39 0433 940 54
Fax: +39 0433 485 499
<a class="moz-txt-link-freetext" href="http://www.exadron.com">http://www.exadron.com</a> </pre>
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