[gmx-developers] BlueGene

[Roland Schulz]

Hi,

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

Because this is a compile time problem it should as well not compile on
BlueGene/L with the special kernel enabled.
The Gromacs Wiki on BlueGene explained how to compile with the default
non-bonded kernel. Thus I'm expecting that people were running with the
default (non-instrinsic) kernel. I added an remark to the wiki that one
should compile with --enable-bluegene.

The configure had a bug too. The configure help said that the option is
colled --ennable-bluegene-asm but it was --enable-bluegene. This I also
commited.

Roland

On Thu, Jul 31, 2008 at 3:35 AM, <hessb at mpip-mainz.mpg.de> wrote:

> Hi,
>
> So there is really something wrong in the include statements?
> Is this only for bluegene/P, or probably also for bluegene/L?
> I know people who are running Gromacs on a bluegene/L and have
> not heard about these issues.
> Could you mail the fixes?
>
> Berk.
>
> > Hi,
> >
> > it was mostly wrong names in the #include statements.
> >
> > It works on BlueGene/P and is much faster than the C non-bonded kernel
> > (about 2x). With this intrinsic C kernel one gets 18% of peak. Because
> > BlueGene doesn't have SIMD commands specific for single precision (thus
> it
> > does only 2 at a time instead of 4) the performance difference to Opteron
> > is
> > greater than for double precision code. The performance difference to a
> > Barcelona 2.1Ghz core is 5.7x (at 20% peak).
> >
> > Roland
> >
> > On Wed, Jul 30, 2008 at 12:29 PM, Roland Schulz <roland at utk.edu> wrote:
> >
> >> Hi,
> >>
> >> it seems that the blugene non-bonded kernel in the CVS version is
> >> incomplete. E.g. the nb_kernel_bluegene_test_asm.h is missing as far as
> >> I
> >> can see. The gromacs wiki for bluegene explains how to get the kernel
> >> generated by mknb to work. Also on the mailinglist all the messages I
> >> found
> >> about BlueGene were about mknb and not abou the bluegene specifik
> >> kernel.
> >>
> >> Could it be that it is incomplete do one has to do somethng to generate
> >> these files?
> >>
> >> Roland
> >>
> >>
> >> On Wed, Jul 30, 2008 at 11:45 AM, Berk Hess
> >> <hessb at mpip-mainz.mpg.de>wrote:
> >>
> >>> Hi,
> >>>
> >>> Mathias Puetz from IBM wrote non-bonded kernels for BlueGene/L.
> >>> I don't know if these are also used for BlueGene/P.
> >>> If there are problems, he would be the person to contact.
> >>>
> >>> Berk.
> >>>
> >>>
> >>> Roland Schulz wrote:
> >>>
> >>>> Hi,
> >>>>
> >>>> has someone looked at the non-bonded kernels for BlueGene/P? Based on
> >>>> the
> >>>> assembler produced by the compiler, it does no SIMD, runs out of
> >>>> registers
> >>>> and does unnecessary rounding.
> >>>>
> >>>> Are there plans for a PPC450 assembler kernel?
> >>>>
> >>>> Roland
> >>>> This email was Anti Virus checked by Astaro Security Gateway.
> >>>> http://www.astaro.com
> >>>>
> ------------------------------------------------------------------------
> >>>>
> >>>> _______________________________________________
> >>>> gmx-developers mailing list
> >>>> gmx-developers at gromacs.org
> >>>> http://www.gromacs.org/mailman/listinfo/gmx-developers
> >>>> Please don't post (un)subscribe requests to the list. Use the www
> >>>> interface or send it to gmx-developers-request at gromacs.org.
> >>>>
> >>>
> >>> _______________________________________________
> >>> gmx-developers mailing list
> >>> gmx-developers at gromacs.org
> >>> http://www.gromacs.org/mailman/listinfo/gmx-developers
> >>> Please don't post (un)subscribe requests to the list. Use the www
> >>> interface or send it to gmx-developers-request at gromacs.org.
> >>>
> >>
> >>
> >
> > This email was Anti Virus checked by Astaro Security Gateway.
> > http://www.astaro.com
> >
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-developers
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-developers-request at gromacs.org.
>
>
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20080731/c5848b7a/attachment.html>