[CP2K-user] [CP2K:12241] Running Cp2k in parallel using thread in a PC

[Pierre Cazade]

Hello,

Well , I assumed CP2K would do something similar. Considering that you 
are able to use Gromacs on your workstation without any issue, your 
system seems perfectly setup for CUDA. Let's then wait for a more 
experienced user to address this issue. I am also looking forward to it.

Regards,
Pierre

On 20/09/2019 16:54, Nikhil Maroli wrote:
> Hello,
>
> Im using GROMACS with GPU since 2014. Running Cp2k doest shows any 
> information about GPU. Im using ubuntu 16 LTS
>
> On Fri, Sep 20, 2019 at 9:17 PM Pierre Cazade 
> <pierre.a... at gmail.com <mailto:pierre.a... at gmail.com>> 
> wrote:
>
>     Hi Nikhil,
>
>     This is an excellent question. I did not try the GPU version of
>     CP2K yet. I am actually trying to compile it on the cluster that I
>     am using.
>
>     Normally, you only need to install CUDA libraries and set up the
>     environment variables properly. Then, the executable detects the
>     presence of the GPU automatically, provided you have installed the
>     driver from nvidia. At least, this is how gromacs behaves, for
>     example. Which linux distribution are you using?
>
>     If you use the GPU, avoid using too many threads. Ideally, one per
>     GPU.
>
>     Regards,
>     Pierre
>
>     PS: Regarding your previous post: rather than "mpirun -n 2", try
>     "mpirun -np 2". Finally, on a multiple node calculation on a
>     cluster, you can use "mpirun -np 8 -ppn 2". The "-np" tells mpirun
>     the total number of MPI threads requested and the "-ppn" tells how
>     many threads per node you want. In the present example, I am using
>     4 nodes and I want 2 MPI threads for each of them, so a total of
>     8. Of course, don't forget to set the OMP_NUM_TREADS as well.
>
>
>
>     On 20/09/2019 16:29, Nikhil Maroli wrote:
>>     Thank you very much for your reply.
>>     Could you please tell me how to use GPU in cp2k?
>>     I have installed all the libraries and compiled with cuda. I
>>     couldn't find any instructions to assign GPU for the calculations.
>>
>>     On Fri, Sep 20, 2019, 8:15 PM Pierre Cazade
>>     <pierre.a... at gmail.com
>>     <mailto:pierre.a... 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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>>
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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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>
>
>
> -- 
> Regards,
> Nikhil Maroli
>
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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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