[gmx-developers] Disabling Pthreads

[Gilles Gouaillardet]

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.

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*
>>
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>>
>>         *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
>