[CP2K-user] [CP2K:16997] Running Cp2k in parallel using thread in a PC

[Matthew Graneri]

Hi Pierre,

I found this really valuable! Unfortunately, being very new to AIMD and 
very unfamiliar with computation in general, I was wondering if I might be 
able to get some advice? We have a HPC at my university where each node has 
34 processors, and ~750 GB RAM available for use. It runs on a slurm 
queuing system.

Until now, I've run all my jobs using: mpirun -np $SLURM_NTASKS cp2k.popt 
-I input.inp -o output.out
where $SLURM_NTASKS is whatever number of processors I've allocated to the 
job via the --ntasks=x flag.

So instead, I'm thinking it might be more appropriate to use the .psmp 
executable, but I'm not sure what the difference between the OpenMP and the 
MPI threads are, and what kind of ratios between the OMP and MPI threads 
would be most effective for speeding up an AIMD job, and how many threads 
of each type you can add before the parallelisation becomes less efficient.

Do you (or anyone else) have any advice on the matter? Is it better to have 
more OMP or MPI threads? And how many OMP threads per MPI thread would be 
appropriate? What kinds of ratios are most effective at speeding up 
calculations?

I would really appreciate any help I can get!

Regards,

Matthew
On Friday, September 20, 2019 at 10:45:55 PM UTC+8 pierre.an... at gmail.com 
wrote:

> Hello Nikhil,
>
> Withe command "mpirun -n 42 cp2k.pop -i inp.inp -o -out.out", you are 
> requesting 42 MPI threads and not 42 OpenMP threads. MPI usually relies on 
> replicated data which means that, for a poorly program software, it will 
> request a total amount of memory which the amount of memory required by a 
> scalar execution times the number of threads. This can very quickly become 
> problematic, in particular for QM calculations. OpenMP, however relies on 
> shared memory, the data is normally not replicated but shared between 
> threads and therefore, in an ideal scenario, the amount of memory needed 
> for 42 OpenMP threads is the same as a single one.
>
> This might explains why you calculation freezes. You are out of memory. On 
> your workstation, you should only use the executable "cp2k.ssmp" which is 
> the OpenMP version. Then you don't need the mpirun command:
>
> cp2k.ssmp -i inp.inp -o -out.out
>
> To control the number of OpenMP threads, set the env variable: 
> OMP_NUM_THREADS, e.g. in bash, export OMP_NUM_THREADS=48
>
> Now, if you need to balance between MPI and OpenMP, you should use the 
> executable named cp2k.psmp. Here is such an example:
>
> export OMP_NUM_THREADS=24
> mpirun -n 2 cp2k.psmp -i inp.inp -o -out.out
>
> In this example, I am requesting two MPI threads and each of them can use 
> up to 24 OpenMP threads.
>
> Hope this clarifies things for you.
>
> Regards,
> Pierre
>
>
> On 20/09/2019 14:09, Nikhil Maroli wrote:
>
> Dear all, 
>
> I have installed all the versions of CP2K in my workstation with 2 x 12 
> core processor, total thread=48
>
> I wanted to run cp2k in parallel using 42 threads, can anyone share the 
> commands that i can use.
>
> I have tried 
>
> mpirun -n 42 cp2k.pop -i inp.inp -o -out.out
>
> After this command there is a rise in memory to 100 % and the whole system 
> freezes. (i have 128GB ram).
>
> Any suggestion will be greatly appreciated,
>
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>
>
> -- 
> Dr Pierre Cazade, PhD
> AD3-023, Bernal Institute,
> University of Limerick,
> Plassey Park Road,
> Castletroy, co. Limerick,
> Ireland
>
>

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