[gmx-users] MPI and OpenMP threads

[Alexander Alexander]

Thanks for your response.

I hope you mean with "what has been used in parallel environment" this:

-------------------------------------------------------
hard resource_list:         h_rt=259000,h_vmem=6500M,h_stack=256M

env_list:                   PSM_RANKS_PER_CONTEXT=4

parallel environment:  smp range: 32

verify_suitable_queues:     1

scheduling info:            (Collecting of scheduler job information is
turned off)
-----------------------------------------------------------

Cheers,
Alex


On Tue, Feb 16, 2016 at 2:19 PM, Szilárd Páll <pall.szilard at gmail.com>
wrote:

> 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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