[gmx-developers] random123 library portability issues

[Alexey Shvetsov]

Roland Schulz писал 01-07-2014 09:01:
> 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

It should work on android. Also if needed i can give ssh access with pub 
key to armv7a platform.
Sure i post issue to redmine with new trace

>> 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] [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
>>>> 
>>>> --
>>>> Gromacs Developers mailing list
>>>> 
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
>> [2] [2]
>>>> before posting!
>>>> 
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> [3] [3]
>> 
>>>> 
>>>> * For (un)subscribe requests visit
>>>> 
>>> 
>> 
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>> [4]
>>>> [4] or send a mail to gmx-developers-request at gromacs.org.
>>> 
>>> --
>>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov [5] [5]
>> 
>>> 865-241-1537 [6], ORNL PO BOX 2008 MS6309
>>> 
>>> Links:
>>> ------
>>> [1] http://goo.gl/YdKofG [1]
>>> [2]
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List [2]
>>> [3] http://www.gromacs.org/Support/Mailing_Lists [3]
>>> [4]
>>> 
>> 
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>> [4]
>>> [5] http://cmb.ornl.gov [5]
>> 
>> --
>> 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 [5]
> 865-241-1537, ORNL PO BOX 2008 MS6309
> 
> Links:
> ------
> [1] http://goo.gl/YdKofG
> [2] http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
> [3] http://www.gromacs.org/Support/Mailing_Lists
> [4] 
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
> [5] http://cmb.ornl.gov
> [6] tel:865-241-1537

-- 
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