[gmx-developers] Disabling Pthreads
Berk Hess
hess at kth.se
Wed Nov 11 08:47:38 CET 2020
Hi,
Then there is a strange bug somewhere.
Are you using real MPI or thread-MPI. Do you know where this happens?
Are you running with OpenMP support?
Cheers,
Berk
On 2020-11-11 08:26, Gilles Gouaillardet wrote:
> Berk,
>
>
> There is a total of 52 cores, and my observation is that each MPI task
> does spawn 52 threads.
>
> So the worst case scenario is 48 MPI tasks each spawning 52 threads,
> so a total of 48 * 52 threads on a single node
>
>
> Cheers,
>
>
> Gilles
>
> On 11/11/2020 4:23 PM, Berk Hess wrote:
>> On 2020-11-11 03:37, Gilles Gouaillardet wrote:
>>> Erik and all,
>>>
>>>
>>> I am kind of facing the exact opposite issue on an other ARM processor:
>>>
>>> High end A64fx (Fugaku/FX1000) have 48 cores plus 2 or 4 assistant
>>> cores.
>>>
>>> A job is put in a cgroup of 48 cores (e.g. no assistant cores)
>>>
>>> Worst case scenario, a flat mpi run (48 tasks) will spawn 48 * 52
>>> cores to spin up all the cores.
>> What do you mean with 48 * 52 cores? There are only 52 cores. Gromacs
>> will by default not spawn more threads in total then there are cores.
>> If you ask for 48 MPI ranks with a real MPI library Gromacs will not
>> spawn any additional threads. With thread-mpi it will spawn 48 or 52
>> total.
>>
>> Cheers,
>>
>> Berk
>>>
>>> 1) GROMACS is not cgroup aware and hence consider there are 52 (or
>>> 50) cores per node (this is a very minor issue)
>>>
>>> 2) spawning such a high number of threads caused some crashes (weird
>>> stack traces, I did not spend much time investigating)
>>>
>>> 3) in the case of A64fx, all cores are up and running, ready to
>>> crunch, and do not require any special tricks.
>>>
>>>
>>> At this stage, I think the easiest path to address this on A64fx is
>>> to add yet an other cmake option to
>>>
>>> unconditionally skip the spin up phase.
>>>
>>> This could be improved by adding a command line option, or an
>>> environment variable, to change the default behavior
>>>
>>> (default behavior should be a cmake option imho)
>>>
>>>
>>> Any thoughts on how to best move forward?
>>>
>>>
>>> Cheers,
>>>
>>>
>>> Gilles
>>>
>>> On 11/11/2020 6:08 AM, Erik Lindahl wrote:
>>>> We might be able to work around the last aspect, but it will likely
>>>> take a couple of weeks until I can lay hands on a new ARM-based
>>>> Macbook.
>>>>
>>>> Long story made short: The advanced power-saving features on ARM
>>>> mean some cores are not visible until they are used, so we created
>>>> a small hack where we "spin up" the CPU by exercising all cores.
>>>>
>>>> We might anyway need to do something different with the new type of
>>>> big.LITTLE cores where we have 4+4 or 8+4 cores, but I can't even
>>>> start to work on that until I have suitable hardware. The good news
>>>> is that such hardware was announced a couple of hours ago, with
>>>> availability next week ;-)
>>>>
>>>> Cheers,
>>>>
>>>> Erik
>>>>
>>>> On Tue, Nov 10, 2020 at 9:45 PM Mark Abraham
>>>> <mark.j.abraham at gmail.com <mailto:mark.j.abraham at gmail.com>> wrote:
>>>>
>>>> No, the use of std::thread in eg hardware detection also requires
>>>> a lower level threading implementation.
>>>>
>>>> Mark
>>>>
>>>> On Tue, Nov 10, 2020, 20:41 Berk Hess <hess at kth.se
>>>> <mailto:hess at kth.se>> wrote:
>>>>
>>>> Hi,
>>>>
>>>> Turning off GMX_THREAD_MPI in cmake should remove the
>>>> dependency on pthreads.
>>>>
>>>> Cheers,
>>>>
>>>> Berk
>>>>
>>>> On 2020-11-10 18:06, Guido Giuntoli wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> Is there any way to disable the “Pthreads” dependency during
>>>>> the configuration/compilation of GROMACS?
>>>>>
>>>>> *Best regards | Mit freundlichen Grüßen*
>>>>>
>>>>> **
>>>>>
>>>>> *Guido Giuntoli***
>>>>>
>>>>> **
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>>>> --
>>>> Erik Lindahl <erik.lindahl at dbb.su.se <mailto:erik.lindahl at dbb.su.se>>
>>>> Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
>>>> University
>>>> Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
>>>>
>>
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