[gmx-developers] Slow PME with git master and gcc 4.3.3 & 4.3.4

[Roland Schulz]

Hi,

Two more things:
I can't reproduce Berk's measurement that 4.3.2 is fine. PME solve is as
slow for me compiled with 4.3.2 then with 4.3.4 (both 8.9s instead of 2.9s
for 4.4.2 for 20^3 grid on 8 threads). And this agrees with the bug report I
linked that the replacement is 4.2.x and 4.3.x are doing this replacement.
I'm running this on Xeon X5550.

I can't figure out so far whether the difference is in the function call
overhead or in the exp/expf function itself. The data is in (4 packed
floats) xmm registers and thus the call to exp/expf require
a cvtpd2ps/movss. That the expf is fast in a test program suggests it is the
data conversion. The profiling with hpctoolkit suggests it is the expf
function itself. I'm not sure whether my test program is not capturing the
problem correctly or whether I misread the hpctoolkit output. Or whether it
is some interplay of both (e.g. save/restore of registers).

If someone could run some profiling to verify my hpctoolkit results to test
what is the reason, this would help. As far as I know it has to be a
sampling based profiling: E.g. Apple Shark but not e.g. gprof/tau.

Roland

On Sat, May 15, 2010 at 4:30 AM, Alexey Shvetsov <alexxyum at gmail.com> wrote:

> Hi all!
>
> I made some tests with current git master and gcc-4.4.3 and gcc-4.5.0
> Seems gromacs compiled with gcc-4.5.0 is a little bit faster then gcc-4.4.3
> (~2-5%)
> I can do this tests with profiling if needed
>
> 2010/5/15 Roland Schulz <roland at utk.edu>
>
> Hi,
>>
>> it is caused by gcc using expf instead of exp.
>>
>> By changing pme.c in the two places where exp is called this way:
>> -                    tmp1[kx]  = exp(tmp1[kx]);
>> +                    double t = tmp1[kx];
>> +                    tmp1[kx]  = exp(t);
>>
>> gcc 4.3.4 is as fast as gcc 4.4.2.
>>
>> See also http://gcc.gnu.org/bugzilla/show_bug.cgi?id=35202
>> (The bug is not related to performance but it discusses the replacement
>> from exp->expf)
>>
>> But what I don't understand at all is why expf is so much slower (expf
>> 7-8x as slow in pme.c than exp (*)). A small test program which computes exp
>> on an array, compiled with gcc 4.3.4 is actually faster than with 4.4.2
>> (30%). Thus for the test-program the expf seams to be faster. Why expf is so
>> slow in pme.c is odd.
>>
>> *) Got that measurement form HPCToolkit. Shows performance line-by-line.
>> Thus it was easy to pin-point the cause.
>>
>> Roland
>>
>>
>> On Fri, May 14, 2010 at 10:43 AM, Berk Hess <hess at cbr.su.se> wrote:
>>
>>> Hi,
>>>
>>> The PME code in git master is a lot faster than the current 4.0.7
>>> release code.
>>> However, there seems to be a bug in gcc version 4.3.3 and 4.3.4 (4.3.2
>>> and 4.4.1 are fine)
>>> that make the pme_solve part 5 times (!) slower than with proper
>>> compiler versions.
>>> This is between 10% and 20% of the total mdrun performance.
>>> We are currently trying to figure out what triggers this issue and we
>>> are sending
>>> a bug report to the gcc mailing list.
>>>
>>> I someone has a hint, please reply.
>>>
>>> Berk
>>>
>>> --
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>>
>>
>>
>> --
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>> 865-241-1537, ORNL PO BOX 2008 MS6309
>>
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>
>
>
> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov
> Petersburg Nuclear Physics Institute, Russia
> Department of Molecular and Radiation Biophysics
> Gentoo Team Ru
> Gentoo Linux Dev
> mailto:alexxyum at gmail.com
> mailto:alexxy at gentoo.org
> mailto:alexxy at omrb.pnpi.spb.ru
>
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-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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