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

[Mark Abraham]

FYI fix for better behaviour in 4.6 (which will migrate downstream in due
course).

Mark


On Fri, Jan 31, 2014 at 1:05 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

>
>
>
> 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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>> >>
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>
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