[gmx-developers] BlueGene

Thu Jul 31 16:31:42 CEST 2008

On Thu, 31 Jul 2008, Roland Schulz wrote:

RS> Hi,
RS> 
RS> I already commited them to CVS. This timing is after fixing the include
RS> statements. Without the intrinsic (the default) non-bonded kernel I get only
RS> .3Gflop/s (/2 of with).

roland,

have you compared to the fortran kernel? last time i compiled gmx on
a bg/l the fortran kernel was significantly faster than the c kernel.

i also remember having to make a few adjustments that i posted here,
but didn't show up in the cvs. we've stopped using gmx on the bg/l
(too depressingly slow) since, so i didn't care much anymore.

i'm certain, i have the scripts and patches somewhere stashed away.
so if you are curious, give me a holler and i'll start digging.

cheers,
   axel.

RS> 
RS> Because this is a compile time problem it should as well not compile on
RS> BlueGene/L with the special kernel enabled.
RS> The Gromacs Wiki on BlueGene explained how to compile with the default
RS> non-bonded kernel. Thus I'm expecting that people were running with the
RS> default (non-instrinsic) kernel. I added an remark to the wiki that one
RS> should compile with --enable-bluegene.
RS> 
RS> The configure had a bug too. The configure help said that the option is
RS> colled --ennable-bluegene-asm but it was --enable-bluegene. This I also
RS> commited.
RS> 
RS> Roland
RS> 
RS> On Thu, Jul 31, 2008 at 3:35 AM, <hessb at mpip-mainz.mpg.de> wrote:
RS> 
RS> > Hi,
RS> >
RS> > So there is really something wrong in the include statements?
RS> > Is this only for bluegene/P, or probably also for bluegene/L?
RS> > I know people who are running Gromacs on a bluegene/L and have
RS> > not heard about these issues.
RS> > Could you mail the fixes?
RS> >
RS> > Berk.
RS> >
RS> > > Hi,
RS> > >
RS> > > it was mostly wrong names in the #include statements.
RS> > >
RS> > > It works on BlueGene/P and is much faster than the C non-bonded kernel
RS> > > (about 2x). With this intrinsic C kernel one gets 18% of peak. Because
RS> > > BlueGene doesn't have SIMD commands specific for single precision (thus
RS> > it
RS> > > does only 2 at a time instead of 4) the performance difference to Opteron
RS> > > is
RS> > > greater than for double precision code. The performance difference to a
RS> > > Barcelona 2.1Ghz core is 5.7x (at 20% peak).
RS> > >
RS> > > Roland
RS> > >
RS> > > On Wed, Jul 30, 2008 at 12:29 PM, Roland Schulz <roland at utk.edu> wrote:
RS> > >
RS> > >> Hi,
RS> > >>
RS> > >> it seems that the blugene non-bonded kernel in the CVS version is
RS> > >> incomplete. E.g. the nb_kernel_bluegene_test_asm.h is missing as far as
RS> > >> I
RS> > >> can see. The gromacs wiki for bluegene explains how to get the kernel
RS> > >> generated by mknb to work. Also on the mailinglist all the messages I
RS> > >> found
RS> > >> about BlueGene were about mknb and not abou the bluegene specifik
RS> > >> kernel.
RS> > >>
RS> > >> Could it be that it is incomplete do one has to do somethng to generate
RS> > >> these files?
RS> > >>
RS> > >> Roland
RS> > >>
RS> > >>
RS> > >> On Wed, Jul 30, 2008 at 11:45 AM, Berk Hess
RS> > >> <hessb at mpip-mainz.mpg.de>wrote:
RS> > >>
RS> > >>> Hi,
RS> > >>>
RS> > >>> Mathias Puetz from IBM wrote non-bonded kernels for BlueGene/L.
RS> > >>> I don't know if these are also used for BlueGene/P.
RS> > >>> If there are problems, he would be the person to contact.
RS> > >>>
RS> > >>> Berk.
RS> > >>>
RS> > >>>
RS> > >>> Roland Schulz wrote:
RS> > >>>
RS> > >>>> Hi,
RS> > >>>>
RS> > >>>> has someone looked at the non-bonded kernels for BlueGene/P? Based on
RS> > >>>> the
RS> > >>>> assembler produced by the compiler, it does no SIMD, runs out of
RS> > >>>> registers
RS> > >>>> and does unnecessary rounding.
RS> > >>>>
RS> > >>>> Are there plans for a PPC450 assembler kernel?
RS> > >>>>
RS> > >>>> Roland
RS> > >>>> This email was Anti Virus checked by Astaro Security Gateway.
RS> > >>>> http://www.astaro.com
RS> > >>>>
RS> > ------------------------------------------------------------------------
RS> > >>>>
RS> > >>>> _______________________________________________
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RS> > >>>>
RS> > >>>
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RS> > >>>
RS> > >>
RS> > >>
RS> > >
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RS> > >
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RS> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
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