[CP2K-user] [CP2K:19390] Help with running cp2k in parallel with Slurm

[Ava Rajh]

Hi Matthias, 

Thank you for the reply

I tried both, first just with the srun command and as part of the #SBATCH 
file. 
If I run the "srun" command and specify the number of tasks I get the 
before mentioned multiple copies of the same program with 1 MPI rank each. 
The same happens if I run the command outside the container without the 
srun and specify the number of tasks with just: mpiexec -n 4 

and if I put the ntasks in the header of the batch file, then I just get 
one copy of the program with 1 MPI rank, no matter how many -ntasks are 
defined. 

Any idea about how to start my calculation would be very helpful, thank 
you. 
kind regards, Ava


On Wednesday, October 18, 2023 at 7:21:22 PM UTC+2 Krack Matthias wrote:

> Hi Ava
>
>  
>
> Do you run the “srun” command as part of a SLURM batch job file with a 
> #SBATCH header section or interactively?
>
> Your guess is right, the –ntasks flag defines the number of MPI ranks.
>
>  
>
> Best
>
>  
>
> Matthias
>
>  
>
> *From: *cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Ava 
> Rajh <ava.... at gmail.com>
> *Date: *Wednesday, 18 October 2023 at 14:17
> *To: *cp2k <cp... at googlegroups.com>
> *Subject: *[CP2K:19379] Help with running cp2k in parallel with Slurm
>
> Dear all, 
>
> I am trying to run cp2k on our HPC cluster and I am new in doing any kind 
> of parallel computing and work on a cluster, so I would appreciate if some 
> help and I apologize if I am missing something obvious. 
>
> I am trying to use Cp2k in combination with apptainer  and I followed 
> instructions at https://github.com/cp2k/cp2k/tree/master/tools/apptainer  
>
>  
>
> I have a .sif file in my work directory and if I work within it (Running 
> MPI within the container), everything works perfectly and I can set the 
> number of MPI threads. 
>
>  
>
> But when trying to run it through slurm, I can't seem to be able to set 
> the number of MPI processes per node. If i start a command like: 
>
> srun --ntasks=2 apptainer run -B $PWD cp2k-2023.2_mpich_generic_psmp.sif 
> cp2k -i H2O-32.in
>
> it just starts 2 instances of the program that run at the same time, and 
> for each, the total number of message passing processes is 1. I am able to 
> set and change the number of OpenMP threads though. 
>
> So my question would be first, am I wrongly assuming that --ntasks X 
> should correspond to the number of MPI threads? And if I am, how would I 
> set it. 
>
>  
>
> Please let me know if I need to provide any more information to diagnose 
> the issue. 
>
> Thank you very much for the help and kind regards, 
>
> Ava Rajh
>
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