[gmx-developers] Thread affinity in log
Mark Abraham
mark.j.abraham at gmail.com
Mon Apr 25 23:44:25 CEST 2016
Hi,
On Mon, Apr 25, 2016 at 10:08 PM Szilárd Páll <pall.szilard at gmail.com>
wrote:
> 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
>
Sure, but what behaviour is there for us to test? We can test that if we
detect external affinity setting that we do nothing unless -pin on, but
that's just trivial logic. I think we have no need to try to set the
external condition and observe that the API permits us to detect the
conditions that were set up for the test binary. (Though that could change
if there was evidence that stuff didn't work - I'm just aware of none.)
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
>
The essential difference there is that if external affinity is set, we
should respond differently considering the setting of -pin. IIRC the
implementation difference there is that we honor the user's strange request
with -pin auto, but perhaps over-ride it with something better when -pin
on. But it's enough to test our logic if we provide synthetic results from
querying the OpenMP and/or hardware APIs - and we can get much better
coverage of our code paths more easily if we do it that way.
>> 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?
>
Such a test is merely that if someone has arranged to call the API
function, that some visible setting results. We could just as easily call
the query function after the set function and give an error if they don't
match. Basically, finding out that running either
hwloc -something ./affinity-test
or that our own API call to set affinities leads to no bit being set isn't
an observation we can do anything about, except report a bug upstream. I
think we should be worrying about getting our own unit tests in place,
before considering testing infrastructure common to lots of projects. :-)
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.
>
Sure. That was my original suggestion. The most important behaviour that we
can test is that ostensibly pinned threads do not observe different CPUID
values in practice in a realistic scenario. There might even already be
code somewhere else that we can re-use.
I think the added value of such end-to-end tests (relative to their
test-harness complexity) that
gmx mdrun -pin on
actually leads to internally pinned threads, and that
gmx mdrun -pin auto
may or may not lead to internally pinned threads, is too low to be worth
it, if we have in place unit tests that show
* the command-line option parsing works (done AFAIK),
* that given various synthetic detection results that our combined logic
works as we expect, and
* that given a decision to implement internal pinning, that it will work.
Mark
Mark
> --
> 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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>>>>>>>
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>>>>>>
>>>>>>
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>>>>>
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>>>>
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