[gmx-users] MPI and OpenMP threads

[Szilárd Páll]

On Tue, Feb 16, 2016 at 1:49 PM, Alexander Alexander
<alexanderwien2k at gmail.com> wrote:
> Dear Gromacs user,
>
> Gromacs works fine for me with the below first group of parallel
> environment and threads but it crashed with the second group complaining
> that:
>
> libgomp: Thread creation failed: Resource temporarily unavailable
> Thread creation failed: Resource temporarily unavailable

What exactly are you using in that "parallel environment"? The error
is somewhere in there, so without some details about it it's hard to
tell. My guess is that (assuming you're using MPI) your MPI
environment is screwed up or misbehaving in some way.

BTW, you don't need MPI if you want to run on that one node with 64 cores!

--
Szilárd

>
> Works fine  :-)
> ----------------------------------
> #$ -pe smp 16
>
> gmx mdrun -deffnm nvt -s nvt.tpr -ntomp 4 -ntmpi 4
> ------------------------------------
> #$ -pe smp 6
>
> gmx mdrun -deffnm nvt -s nvt.tpr -ntomp 2 -ntmpi 3
> --------------------------------------
>
>
> Crashed  :-(
> ------------------------------------
> #$ -pe smp 32
>
> gmx mdrun -deffnm nvt -s nvt.tpr -ntomp 4 -ntmpi 8
> -------------------------------------
> #$ -pe smp 32
>
> gmx mdrun -deffnm nvt -s nvt.tpr -ntomp 2 -ntmpi 16
> -------------------------------------
> #$ -pe orte_sl32* 64
>
> gmx mdrun -deffnm nvt -s nvt.tpr -ntomp 32 -ntmpi 2
> ---------------------------------------
>
> Here is the properties of the machine which I am using for Gromacs:
>
> Running on 1 node with total 64 cores, 64 logical cores
> Hardware detected:
>   CPU info:
>     Vendor: AuthenticAMD
>     Brand:  AMD Opteron(TM) Processor 6276
>     SIMD instructions most likely to fit this hardware: AVX_128_FMA
>     SIMD instructions selected at GROMACS compile time: AVX_128_FMA
>
>
> Any body knows what is the reason please?
>
> Best regards,
> Alex
> --
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