[gmx-developers] Thread affinity in log

Szilárd Páll pall.szilard at gmail.com
Mon Apr 25 22:08:32 CEST 2016 

On Mon, Apr 25, 2016 at 9:22 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> On Mon, Apr 25, 2016 at 8:56 PM Szilárd Páll <pall.szilard at gmail.com>
> wrote:
>
>> On Mon, Apr 25, 2016 at 8:46 PM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> On Mon, Apr 25, 2016 at 7:19 PM Szilárd Páll <pall.szilard at gmail.com>
>>> wrote:
>>>
>>>> Confirmed, we've ran into it last Friday and 5820 seemed to fix the
>>>> issue, but as the author of the change noted, it's is unclear what the
>>>> source of the crash is.
>>>>
>>>> BTW: we need to add a "-pin on" test to the verification matrix  to
>>>> make sure the thread pinning code gets tested. It can be post-submit too,
>>>> but we have none of those on the horizon so better add an otpion to the
>>>> current ones IMO.
>>>>
>>>
>>> Yes and no. Doing it that way
>>> * doesn't test the code any more than that it doesn't crash,
>>> * creates another degree of freedom of coverage for a matrix to manage,
>>> and
>>> * creates a situation where Jenkins could thrash if enough threads get
>>> pinned to a common core
>>>
>>> Much better is a unit test
>>>
>>
>> I partially agree, a unit test would be suitable to verify the
>> functionality of the pinning code in isolation from the "outer world".
>> However, it will not be able to control external conditions (e.g. affinity
>> set outside mdrun) - which I was going to mention bu it slipped my mind.
>>
>
> I'm not sure what case you're referring to. I don't think we can
> reasonably test that some external method has set affinity and that it
> doesnt work, in a way that a user or developer could act upon. We only have
> to test that when the user asks for pinning that it will work.
>

I am referring to the case where mdrun either backs off or overrides
affinities. We expect -pin on to work regardless of the original content of
the mask, right?

Lots of ways to influence affinity:
taskset 0x1 gmx mdrun ...
hwloc-bind core:0-3 gmx mdrun ...
GOMP_CPU_AFFINITY=0-4 gmx mdrun



> That -pin auto and -pin on have different behaviours under different
> combinations of inputs is its own standalone unit test that requires no
> external dependency - our job in such a unit test is to test that our logic
> does what we expect. It's a separate test that given the output of such
> logic that we can implement internal pinning - observing success there
> needs hardware capable of implementing pinning (or not).
>

Sure, I agree. That however won't test whether these give different results:

GOMP_CPU_AFFINITY=0-1 gmx mdrun -ntmpi 1 -ntomp 3 -pin on
GOMP_CPU_AFFINITY=0-1 gmx mdrun -ntmpi 1 -ntomp 3 -pin auto


> that puts a bunch of unpinned threads doing some simple computation and
>>> observes the expected behaviour of similar pinned threads.
>>>
>>
>> Why is doing computation relevant to testing stuff? Pinned or not,
>> threads will execute code correctly.
>>
>
> The relevant behaviour is that they don't migrate in practice. One can't
> test for that unless the conditions are such that the kernel might try to
> migrate them, because there's plenty of activity and lots of threads. Of
> course, on PowerPC that aspect of the test will automatically pass.
>

Well, if the OS reports that threads each have a distinct bit set in their
affinity mask, can't we consider that that a promise that migration won't
happen? I'm not deeply familiar with different aspects of affinity and
whether certain Linux settings may lead to silently ignored affinity masks.
Anyone else who knows, please pitch in!

Otherwise, if we want to get fancy about verifying that pinning works as
expected, there should certainly be ways to assess whether migration
happens in practice; for instance, could start two groups of threads, one
pinned one not (perhaps even under oversubscription) execute CPUID on the
pinned threads periodically and see if the core they reside on changes.
Can't provide a proof, but it should be decent evidence I think.

--
Szilárd


>
>
> Mark
>
>
>> That can run on every configuration because it can be a unit test that
>>> runs in milliseconds. Of course, we wrote this test before we changed the
>>> old working code, right?
>>>
>>
>>>
>>> Mark
>>>
>>>
>>>> --
>>>> Szilárd
>>>>
>>>> On Mon, Apr 25, 2016 at 7:07 PM, Vedran Miletić <rivanvx at gmail.com>
>>>> wrote:
>>>>
>>>>> Gladly. This one? https://gerrit.gromacs.org/#/c/5820/
>>>>>
>>>>> V.
>>>>>
>>>>> pon, 25. tra 2016. u 19:06 Mark Abraham <mark.j.abraham at gmail.com>
>>>>> napisao je:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Unsure offhand, but there's a fix in gerrit in this area if you want
>>>>>> to try that?
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>> On Mon, 25 Apr 2016 19:05 Vedran Miletić <rivanvx at gmail.com> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> since fa1360610d6fcf7eb263ce1181d9954074fd5151 "Make thread affinity
>>>>>>> failures always end up in log", I get crashes in mdrun when using tMPI on
>>>>>>> any simulation I tried (does not affect OpenMPI). I am seeing this on two
>>>>>>> machines using Fedora 23 and 24, GCC 5.3 and 6, respectively.
>>>>>>>
>>>>>>> Backtrace is
>>>>>>>
>>>>>>> #0 0x00007ffff78c966f in tMPI_Thread_getspecific (key=...) at
>>>>>>> /home/miletivn/workspace/gromacs/src/external/thread_mpi/src/pthreads.c:571
>>>>>>> #1 0x00007ffff78cff34 in tMPI_Reduce (sendbuf=0x7fffffffa4dc,
>>>>>>> recvbuf=0x7fffffffa4d8, count=1, datatype=0x7ffff7dd6660 <tmpi_int>,
>>>>>>> op=TMPI_LAND, root=0, comm=0x0) at
>>>>>>> /home/miletivn/workspace/gromacs/src/external/thread_mpi/src/reduce.c:247
>>>>>>> #2 0x00007ffff63038a5 in invalidWithinSimulation (cr=0x681bd0,
>>>>>>> invalidLocally=false) at
>>>>>>> /home/miletivn/workspace/gromacs/src/gromacs/mdrunutility/threadaffinity.cpp:73
>>>>>>> #3 0x00007ffff6303c0b in get_thread_affinity_layout (fplog=0x689410,
>>>>>>> cr=0x681bd0, hwinfo=0x680230, threads=8, pin_offset=0,
>>>>>>> pin_stride=0x7fffffffc634, localityOrder=0x7fffffffc638) at
>>>>>>> /home/miletivn/workspace/gromacs/src/gromacs/mdrunutility/threadaffinity.cpp:142
>>>>>>> ...
>>>>>>>
>>>>>>> Variable key looks like
>>>>>>>
>>>>>>> $1 = {initialized = {value = 0, padding = '\000' <repeats 59
>>>>>>> times>}, key = 0x0}
>>>>>>>
>>>>>>> So key is uninitialized. Any idea why?
>>>>>>>
>>>>>>> Regards,
>>>>>>> Vedran
>>>>>>>
>>>>>> --
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