[gmx-developers] mknb doesn't work on BlueGene with --enable-ppc-sqrt in single precision

[Mark Abraham]

Roland Schulz wrote:
> Hi,
> 
> on an email thread started by me on March 11 subject "Bluegene Kernel" (see
> below) Mathias said that the generic kernel should not be slower than the
> double hummer so this problem shouldn't matter.

Actually he said it the other way around, which will certainly be true :-)

> (Not saying that we shouldn't fix it just that is might not be important)

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.

Mark

> Roland
> 
> 
> ---------- Forwarded message ----------
> From: Erik Lindahl <lindahl at cbr.su.se>
> Date: Fri, Mar 13, 2009 at 8:58 AM
> Subject: Re: Bluegene Kernel
> To: Mathias PUETZ <mpuetz at de.ibm.com>
> Cc: Roland Schulz <roland at utk.edu>, "mark.abraham" <mark.abraham at anu.edu.au>,
> roland at rschulz.eu
> 
> 
> Hi,
> 
> With the new kernel structure in the head branch it will be quite fine to
> have separate kernel sets for
> 
> power4
> power5
> power6
> power7
> ...
> BG
> 
> As long as you
> 
> 1) Tell me exactly what options should we use for each architecture
> 2) Help test that it works :-)
> 
> 
> One question - since we now try to avoid generating kernels at build time
> (lots of reasons, coding simplicity being one of them), can you say in
> general whether xlf or xlc is faster?
> 
> Cheers,
> 
> Erik
> 
> 
> On Mar 13, 2009, at 1:28 PM, Mathias PUETZ wrote:
> 
>  Hi Roland,
>> each of the BlueGene "double hummer" kernels shouldn't be slower than the
>> generic ones,
>> so I think it's a more academic issue for the pair-force kernels. I had
>> checked the performance
>> of each kernel. I think the worst case was, that one or two double hummer
>> kernels ran 5% slower
>> than the generated ones.
>> However, enable-ppc-sqrt=1 also affects all other SQRT calculations in the
>> rest of the code,
>> that has not been specifically optimized, so you might get a minor
>> performance hit there,
>> if you can no longer specify --enable-ppc-sqrt=1.
>>
>> I don't quite understand, why PPC5 would be required regarding the SQRT
>> calculations.
>> FRSQRTE instructions is available since PPC4, but only Power6 (or higher)
>> and BlueGene offer enough
>> bits of precision to use just a single Newton-Raphson iteration to bring it
>> up to single precision.
>>
>> Viele Grüsse / Best regards,
>> Dr. Mathias Pütz
>>
>> IT Specialist for Application Performance
>>
>> Deep Computing - Strategic Growth Business
>> IBM Systems & Technology Group
>>
>> e-mail:  mpuetz at de.ibm.com
>> mobile: + 49-(0)160-7120602
>> fax:         + 49-(0)6131-84-6660
>>
>> Anschrift:
>>  IBM Deutschland GmbH
>>  Department B513
>>  Hechtsheimer Str. 2 / Building 12
>>  55131 Mainz
>>  Germany
>>
>> IBM Deutschland GmbH
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>> Geschäftsführung: Martin Jetter (Vorsitzender), Reinhard Reschke, Christoph
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>> Sitz der Gesellschaft: Stuttgart
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>>
>>
>>
>>
>>            Roland Schulz
>>            <roland at utk.edu>
>>            Sent by:                                                   To
>>            roland at rschulz.eu         "mark.abraham"
>>                                      <mark.abraham at anu.edu.au>, Mathias
>>                                      PUETZ/Germany/IBM at IBMDE
>>            03/11/2009 10:03                                           cc
>>            PM
>>                                                                  Subject
>>                                      Bluegene Kernel
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Hi Mark, Hi Matthias,
>>
>> I'm writing you because you have both edited the "Gromacs Bluegene"
>> wiki page and both recommend to use
>>              --enable-ppc-sqrt[=1] --enable-fortran --enable-bluegene
>>
>> I'm asking because the ppc-sqrt does not work on Bluegene anymore,
>> because Erik changed the single/double conversion so that it requires
>> PPC5. Should we add another option to the mknb to be PPC4 backward
>> compatible? Or is this not necssarry because Matthias' instrinsic
>> kernel is always faster?
>>
>> So my question:
>> Did you compare the performance of the intrinsic kernel with the
>> fortran and C kernel on Bluegene? Do you think the C/Fortran kernel
>> are thus needed on Bluegene? Or should we just change the compile
>> recommendation to not use -enable-ppc-sqrt so that it compiles again?
>> If the C/Fortran Kernel are not used anyhow this would not make a
>> difference, I think.
>>
>> Thanks
>> Roland
>>
>>
>> --
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>> 865-241-1537, ORNL PO BOX 2008 MS6309
>>
>>
>>
> ------------
> Erik Lindahl   <lindahl at cbr.su.se>  Backup: <erik.lindahl at gmail.com>
> Associate Professor, Computational Structural Biology
> Center for Biomembrane Research, Dept. Biochemistry & Biophysics
> Stockholm University, SE-106 91 Stockholm, Sweden
> Tel: +46(0)8164675  Mobile: +46(0)703844534  Fax: mail a PDF instead
> 
> 
> 
> 
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> 
> 
> 
> 
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