[gmx-developers] Disabling Pthreads

[Berk Hess]

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***
>>>
>>>         **
>>>
>>>         HUAWEI TECHNOLOGIES Duesseldorf GmbH
>>>         Hansaallee 205, 40549 Dusseldorf, Germany, *www.huawei.com*
>>>         <http://www.huawei.com/>
>>>         Registered Office: Düsseldorf, Register Court Düsseldorf, HRB
>>>         56063,
>>>         Managing Director: Li Peng, Li Jian, Shi Yanli**
>>>
>>>         Sitz der Gesellschaft: Düsseldorf, Amtsgericht Düsseldorf,
>>>         HRB 56063,
>>>         Geschäftsführer: Li Peng, Li Jian, Shi Yanli
>>>
>>> *-----------------------------------------------------------------------------------------------*
>>>
>>>         *This e-mail and its attachments contain confidential
>>>         information from HUAWEI, which is intended only for the
>>>         person or entity whose address is listed above. Any use of
>>>         the information contained herein in any way (including, but
>>>         not limited to, total or partial disclosure, reproduction, or
>>>         dissemination) by persons other than the intended
>>>         recipient(s) is prohibited. If you receive this e-mail in
>>>         error, please notify the sender by phone or email immediately
>>>         and delete it!*
>>>
>>>
>>
>>         --         Gromacs Developers mailing list
>>
>>         * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
>> <http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List>
>>         before posting!
>>
>>         * Can't post? Read
>>         http://www.gromacs.org/Support/Mailing_Lists
>>         <http://www.gromacs.org/Support/Mailing_Lists>
>>
>>         * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>> <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers>
>>         or send a mail to gmx-developers-request at gromacs.org
>>         <mailto:gmx-developers-request at gromacs.org>.
>>
>>     --     Gromacs Developers mailing list
>>
>>     * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
>> <http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List>
>>     before posting!
>>
>>     * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>     <http://www.gromacs.org/Support/Mailing_Lists>
>>
>>     * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
>> <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers>
>>     or send a mail to gmx-developers-request at gromacs.org
>>     <mailto:gmx-developers-request at gromacs.org>.
>>
>>
>>
>> -- 
>> 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
>>