[gmx-developers] Wallcycle bug?

[Szilárd Páll]

On Tue, Sep 15, 2015 at 10:11 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> When verified, reviewed and merged, https://gerrit.gromacs.org/#/c/5094/ should
> resolve this for master branch.
>

Are you referring to the TSC synchronization issue? The change you liked
fixes #1823, a different issue.

--
Szilárd



>
> Mark
>
> On Tue, Sep 15, 2015 at 6:18 PM Szilárd Páll <pall.szilard at gmail.com>
> wrote:
>
>> On Tue, Sep 15, 2015 at 5:16 PM, Berk Hess <hess at kth.se> wrote:
>>
>>> Hi,
>>>
>>> We didn't realize that modern x86 cpus no longer synchronize clocks
>>> between cores.
>>
>>
>> Actually, having read up a bit more, the _opposite_ seems to be the case:
>> on older CPUs there could be a problem, but on newer ones the TSC should be:
>> - "constant", i.e. not affected by frequency scaling,
>> - "nonstop", i.e. unaffected by CPU ACPI states.
>> The "constant_tsc" and "nonstop_tsc" cpuid flags indicate whether these
>> are supported (most AMD and Nehalem+ on Intel).
>>
>> Intel seems to call both these cases "invariant TSC" (dev manual
>> section 17.14.1 [1]). Apparently a number sources claim [2,3] that
>>  invariant TSC implies that TSC is synchronized (or can be if the BIOS
>> syncs at boot) and the Intel docs seems to suggest this too by claiming
>> that the OS can use TSC for wall clock.
>>
>>
>> Based on this the issue you observed could only be caused by something
>> funny with your BIOS (or OS/kernel?). Thoughts?
>>
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>> [1]
>> http://www.intel.com/content/dam/www/public/us/en/documents/manuals/64-ia-32-architectures-software-developer-manual-325462.pdf
>>
>> [2] http://www.gossamer-threads.com/lists/xen/devel/185419
>>
>> [3]
>> https://software.intel.com/en-us/forums/intel-isa-extensions/topic/289368
>>
>> We should get the fix for this merged asap:
>>> https://gerrit.gromacs.org/#/c/5091/
>>>
>>> Cheers,
>>>
>>> Berk
>>>
>>> On 09/15/2015 05:06 PM, David van der Spoel wrote:
>>>
>>>> Hi,
>>>>
>>>> my patch stumbled over this issue in Jenkins:
>>>>
>>>> Program:     gmx mdrun, VERSION 5.2-dev-20150915-ef00eb4-local
>>>> Source file: src/gromacs/timing/wallcycle.cpp (line 398)
>>>> Function:    void subtract_cycles(wallcc_t *, int, int)
>>>>
>>>> Assertion failed:
>>>> Condition: wcc[ewc_main].c >= wcc[ewc_sub].c
>>>> Subcounter cannot have more ticks than parent
>>>>
>>>> For more information and tips for troubleshooting, please check the
>>>> GROMACS
>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>
>>>> Any clue? Or is this assertion just overly pedantic?
>>>>
>>>
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>
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