[CP2K-user] [CP2K:12283] Running Cp2k in parallel using thread in a PC

[Pierre-André Cazade]

Hi Nikhil,

As you are using a mix of MPI and OpenMP, you have to use the executable with the extension psmp.

You can find a table describing all the executables in the section 3 of the “how to compile” page:

https://www.cp2k.org/howto:compile

Yet, it does not explain why your calculation behaved as if there were 6 independent calculations.

Please try the same calculation with the psmp executable and let me know how it goes.

Regards,
Pierre

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________________________________
From: cp... at googlegroups.com on behalf of Chn <chen... at gmail.com>
Sent: Saturday, September 28, 2019 3:03 a.m.
To: cp2k
Subject: Re: [CP2K:12283] Running Cp2k in parallel using thread in a PC

Hi Pierre,
I tried to combine openMP with MPI as you mentioned above when I do vibrational analysis. I required 6 MPI threads and got 6 output files named as *-r-number.out, however in each file it printed that:
 GLOBAL| Total number of message passing processes                             1
 GLOBAL| Number of threads for this process                                  1
 GLOBAL| This output is from process                                       0
also I used 'top' command and found that only 6 cores were busy.
I use 2 x 24 core processor, and set:
export OMP_NUM_THREADS=8
mpirun -n 6 /lib/CP2K/cp2k/exe/local/cp2k.popt -i project.inp -o output.out
Any suggestion will be greatly appreciated..



在 2019年9月20日星期五 UTC+8下午10:45:55，Pierre Cazade写道：
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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