[gmx-developers] Wallcycle bug?

[Mark Abraham]

Hi,

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

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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