[gmx-developers] random123 library portability issues

[Roland Schulz]

On Tue, Jul 1, 2014 at 12:47 AM, Alexey Shvetsov <alexxy at omrb.pnpi.spb.ru>
wrote:

> Roland Schulz писал 01-07-2014 03:59:
> > HI Alexey ,
> >
> > On Fri, May 30, 2014 at 6:52 AM, Alexey Shvetsov
> > <alexxy at omrb.pnpi.spb.ru> wrote:
> >
> >> Hi!
> >>
> >> I tryed to build 5.0 branch on ARM board (dual core cortex-a7). It
> >> builds (if
> >> i define arm as allowed arch in features/gccfeatures.h) but some
> >> regression
> >> tests fails.
> >
> > What compiler did you use? Which tests fail?
>
> Hi!
>
> I tryed with gcc-4.8.2. Spc and methanol test failed with SIGBUS
>
> There were 2 notes
> Reading file
>
> /home/alexxy/Develop/gromacs_build/none/src/programs/mdrun/tests/Testing/Temporary/CanWrite_Trajectories_ThatDifferInNstxout_0.tpr,
> VERSION 5.0-beta2-dev-20140211-9a31310 (single precision)
> Changing nstlist from 10 to 25, rlist from 1.022 to 1.076
>
> Using 1 MPI thread
> starting mdrun 'spc-and-methanol'
> 6 steps,      0.0 ps.
> Bus error
>

Could you post a backtrace to redmine?

BTW: Has anyone tried to compile & run Gromacs on Android? That way I would
have test hardware ;-).

Roland


>
>
> I'll rebuild current master with gcc-4.9 to check if there are same
> issue.
>
> >
> > Roland
> >
> >> В письме от 30 мая 2014 12:43:29
> >> пользователь Szilárd Páll написал:
> >>
> >>> Hi,
> >>>
> >>> A few days ago I did some sanity checks by compiling and
> >>> regressiontesting the 5.0 branch on ARM. This exercise made me
> >> realize
> >>> that the recently included Random123 library is now the single
> >> most
> >>> limiting factor when it comes to portability. In fact, as it is
> >> not
> >>> optional, v5.0 is ATM practically limited to x86* and Powerpc64
> >> (BGQ)
> >>> architectures -- based on the docs (see http://goo.gl/YdKofG [1])
> >>> Random123 has not been tested (let alone optimized) on anything
> >> else.
> >>> Additionally, note that the code won't even compile on
> >> non-supported
> >>> architectures, so in its current state GROMACS 5.0 won't compile
> >> on
> >>> anything else but x86* and PPC64, e.g. with gcc compilation will
> >> be
> >>> aborted by the "#error" in features/gccfeatures.h:38. Removing
> >> these
> >>> sanity checks does let the code compile on ARM and
> >> regressiontests do
> >>> pass, though.
> >>>
> >>> I've exchanged a couple of emails with the developers and they
> >> suggest
> >>> that in practice Threefry should work on ARM (and perhaps other
> >>> architectures too), but testing/validation is definitely
> >> necessary.
> >>> Performance is not optimized on unsupported architectures, I
> >> assume,
> >>> so some optimization may not hurt too - especially if there are
> >> cases
> >>> where we generate many PRNGs per step (BTW has the potential
> >> overhead
> >>> been assessed?).
> >>>
> >>> Cheers,
> >>> --
> >>> Szilárd
> >>
> >> --
> >> Best Regards,
> >> Alexey 'Alexxy' Shvetsov, PhD
> >> Department of Molecular and Radiation Biophysics
> >> FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
> >> Leningrad region, Gatchina, Russia
> >> mailto:alexxyum at gmail.com
> >> mailto:alexxy at omrb.pnpi.spb.ru
> >>
> >> --
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> > --
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> >
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> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov, PhD
> Department of Molecular and Radiation Biophysics
> FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
> Leningrad region, Gatchina, Russia
> mailto:alexxyum at gmail.com
> mailto:alexxy at omrb.pnpi.spb.ru
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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