I fixed it in the release branch (thus it will be in 4.0.6). <br><br>How is one supposed to change the kernels in the head branch? Is there some script to generate the generic kernels? The output of mknb -fortran --ppc_invsqrt is different than what is in nb_kernel_power6. So changing something in nb_kernel_power6 requires to change each file?<br>
<br>Roland<br><br><br><div class="gmail_quote">On Wed, Sep 2, 2009 at 8:08 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">Roland Schulz wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
on an email thread started by me on March 11 subject "Bluegene Kernel" (see<br>
below) Mathias said that the generic kernel should not be slower than the<br>
double hummer so this problem shouldn't matter.<br>
</blockquote>
<br></div>
Actually he said it the other way around, which will certainly be true :-)<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
(Not saying that we shouldn't fix it just that is might not be important)<br>
</blockquote>
<br></div>
Sure - as it stands, configuration fails in the given case, and this should be fixed correctly so that correct non-optimized kernels are available in all cases.<br><font color="#888888">
<br>
Mark<br>
<br>
</font><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
Roland<br>
<br>
<br>
---------- Forwarded message ----------<br>
From: Erik Lindahl <<a href="mailto:lindahl@cbr.su.se" target="_blank">lindahl@cbr.su.se</a>><br>
Date: Fri, Mar 13, 2009 at 8:58 AM<br>
Subject: Re: Bluegene Kernel<br>
To: Mathias PUETZ <<a href="mailto:mpuetz@de.ibm.com" target="_blank">mpuetz@de.ibm.com</a>><br>
Cc: Roland Schulz <<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>>, "mark.abraham" <<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>>,<br>
roland@rschulz.eu<br>
<br>
<br>
Hi,<br>
<br>
With the new kernel structure in the head branch it will be quite fine to<br>
have separate kernel sets for<br>
<br>
power4<br>
power5<br>
power6<br>
power7<br>
...<br>
BG<br>
<br>
As long as you<br>
<br>
1) Tell me exactly what options should we use for each architecture<br>
2) Help test that it works :-)<br>
<br>
<br>
One question - since we now try to avoid generating kernels at build time<br>
(lots of reasons, coding simplicity being one of them), can you say in<br>
general whether xlf or xlc is faster?<br>
<br>
Cheers,<br>
<br>
Erik<br>
<br>
<br>
On Mar 13, 2009, at 1:28 PM, Mathias PUETZ wrote:<br>
<br>
Hi Roland,<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
each of the BlueGene "double hummer" kernels shouldn't be slower than the<br>
generic ones,<br>
so I think it's a more academic issue for the pair-force kernels. I had<br>
checked the performance<br>
of each kernel. I think the worst case was, that one or two double hummer<br>
kernels ran 5% slower<br>
than the generated ones.<br>
However, enable-ppc-sqrt=1 also affects all other SQRT calculations in the<br>
rest of the code,<br>
that has not been specifically optimized, so you might get a minor<br>
performance hit there,<br>
if you can no longer specify --enable-ppc-sqrt=1.<br>
<br>
I don't quite understand, why PPC5 would be required regarding the SQRT<br>
calculations.<br>
FRSQRTE instructions is available since PPC4, but only Power6 (or higher)<br>
and BlueGene offer enough<br>
bits of precision to use just a single Newton-Raphson iteration to bring it<br>
up to single precision.<br>
<br>
Viele Grüsse / Best regards,<br>
Dr. Mathias Pütz<br>
<br>
IT Specialist for Application Performance<br>
<br>
Deep Computing - Strategic Growth Business<br>
IBM Systems & Technology Group<br>
<br>
e-mail: <a href="mailto:mpuetz@de.ibm.com" target="_blank">mpuetz@de.ibm.com</a><br>
mobile: + 49-(0)160-7120602<br>
fax: + 49-(0)6131-84-6660<br>
<br>
Anschrift:<br>
IBM Deutschland GmbH<br>
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Vorsitzender des Aufsichtsrats: Erich Clementi<br>
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<br>
<br>
<br>
Roland Schulz<br>
<<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>><br>
Sent by: To<br>
roland@rschulz.eu "mark.abraham"<br>
<<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>>, Mathias<br>
PUETZ/Germany/IBM@IBMDE<br>
03/11/2009 10:03 cc<br>
PM<br>
Subject<br>
Bluegene Kernel<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
Hi Mark, Hi Matthias,<br>
<br>
I'm writing you because you have both edited the "Gromacs Bluegene"<br>
wiki page and both recommend to use<br>
--enable-ppc-sqrt[=1] --enable-fortran --enable-bluegene<br>
<br>
I'm asking because the ppc-sqrt does not work on Bluegene anymore,<br>
because Erik changed the single/double conversion so that it requires<br>
PPC5. Should we add another option to the mknb to be PPC4 backward<br>
compatible? Or is this not necssarry because Matthias' instrinsic<br>
kernel is always faster?<br>
<br>
So my question:<br>
Did you compare the performance of the intrinsic kernel with the<br>
fortran and C kernel on Bluegene? Do you think the C/Fortran kernel<br>
are thus needed on Bluegene? Or should we just change the compile<br>
recommendation to not use -enable-ppc-sqrt so that it compiles again?<br>
If the C/Fortran Kernel are not used anyhow this would not make a<br>
difference, I think.<br>
<br>
Thanks<br>
Roland<br>
<br>
<br>
--<br>
ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>
865-241-1537, ORNL PO BOX 2008 MS6309<br>
<br>
<br>
<br>
</blockquote>
------------<br>
Erik Lindahl <<a href="mailto:lindahl@cbr.su.se" target="_blank">lindahl@cbr.su.se</a>> Backup: <<a href="mailto:erik.lindahl@gmail.com" target="_blank">erik.lindahl@gmail.com</a>><br>
Associate Professor, Computational Structural Biology<br>
Center for Biomembrane Research, Dept. Biochemistry & Biophysics<br>
Stockholm University, SE-106 91 Stockholm, Sweden<br>
Tel: +46(0)8164675 Mobile: +46(0)703844534 Fax: mail a PDF instead<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
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<br>
<br>
<br></div></div>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>