[gmx-users] Is version 5.0 generating portable binaries?

[Mark Abraham]

On Fri, Jan 31, 2014 at 11:54 AM, Szilárd Páll <pall.szilard at gmail.com>wrote:

> Note that both Opteron 2354 K10/Barcelona (http://goo.gl/6hyfO) and
> the Xeon 53xx / Clovertown (http://goo.gl/6hyfO) are quite old and
> none of them supports SSE4.1. Hence, pick SSE2 and build distributable
> binaries (AFAIK Clovertown does not support the rdtscp instructions).
>

Sure, old machines need SSE2 - I didn't check.


> Also note that GROMACS does not have a "portability problem" - it's a
> tradeoff between avoiding code complexity, performance and
> portability. For obvious reasons, we pick the first two. We seem to
> have a documentation problem though, I can't find the
> GMX_DISTRIBUTABLE_BUILD option anywhere on the website.
>

There was no in-repo install guide when Roland implemented the feature, and
nobody who actually uses GMX_DISTRIBUTABLE_BUILD has thought to add it
since.

Mark


>
> Cheers,
> --
> Szilárd
>
>
> On Fri, Jan 31, 2014 at 8:53 AM, Erik Lindahl
> <erik.lindahl at scilifelab.se> wrote:
> > Hi Raffaella,
> >
> > First: You absolutely shouldn't remove all acceleration in cases like
> this - that would hit your performance by ~50%. Instead, you can pick the
> greatest common divisor, which is SSE4.1.
> >
> > Second, the segfault happens because we use a timing instruction. You
> can disable this by using the Cmake argument
> >
> > cmake  -DGMX_DISTRIBUTABLE_BUILD ...
> >
> > Which creates a binary that will work on most x86 machines.
> >
> >
> > This will be more automated in 5.0, but by not using AVX_128_FMA on your
> new AMD nodes you will lose ~30% performance compared to what is possible,
> so you might want to consider installing at least two mdrun binaries
> (renamed to, say, mdrun_intel and mdrun_amd).
> >
> > Cheers,
> >
> > Erik
> >
> >
> > On 30 Jan 2014, at 23:35, Raffaella D'Auria <rdauria at ucla.edu> wrote:
> >
> >> Hello All,
> >>
> >> I have just performed a fresh installation of gromacs version 4.6.5 on
> a heterogeneous linux cluster (running centos 6.4) . After the installation
> I see that the binaries, for say mdrun,  work on all the machines with
> hardware similar to the one on which they were installed (namely AMD
> processor such as: Quad-Core AMD Opteron Processor 2354) but produce an
> "illegal instruction (core dumped)" when run on nodes with intel processors
> (such as: Intel Xeon CPU E5335  @ 2.00GHz).
> >>
> >> As suggested in the documentation (
> http://www.gromacs.org/Documentation/Acceleration_and_parallelization#CPU_acceleration.3a_SSE.2c_AVX.2c_etc)
> I have tried to compile with GMX_CPU_ACCELERATION set to "none" (I have
> also turned down the optimization levels) with always the same result
> (illegal instruction) across different hardware.
> >>
> >> Is this expected behavior? If so will the binaries of version 5.* have
> the same portability problem?
> >>
> >> One more thing the situation described above occurs with both the gnu
> 4.4.7 compiler and the intel 13.1.1.
> >>
> >> Any feedback would be greatly appreciated.
> >>
> >> Thanks,
> >>
> >> Raffaella.
> >>
> >> --
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