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

[Chn]

Hi,
The keyword NPROC_REP has a default value of {1}, it should be only one 
output *-r.out file in a job. So can I explain that I got six files just 
because I used six threads..? Is it normal in a parallel job..?
regards,
chn

在 2019年9月29日星期日 UTC+8上午3:08:34，Ari Paavo Seitsonen写道：
>
> Hello,
>
>   Maybe you received the six files because of this:
>
> <<
>
> NPROC_REP {Integer} 
>
> *Specify the number of processors to be used per replica environment (for 
> parallel runs). In case of mode selective calculations more than one 
> replica will start a block Davidson algorithm to track more than only one 
> frequency*  [Edit on GitHub 
> <https://github.com/cp2k/cp2k/blob/master/src/motion/input_cp2k_vib.F#L83>] 
>
>
> This keyword cannot be repeated and it expects precisely one integer. 
>
> Default value: 1>>
>
>
> https://manual.cp2k.org/trunk/CP2K_INPUT/VIBRATIONAL_ANALYSIS.html#list_NPROC_REP
>
>     Greetings from Paris,
>
>        apsi
>
> Le sam. 28 sept. 2019 à 14:14, Pierre-André Cazade <pie... at gmail.com 
> <javascript:>> a écrit :
>
>> 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 
>>
>> Get Outlook for iOS <https://aka.ms/o0ukef>
>>  
>> ------------------------------
>> *From:* c... at googlegroups.com <javascript:> on behalf of Chn <
>> ch... at gmail.com <javascript:>>
>> *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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>
>
> -- 
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>   Ari Paavo Seitsonen / Ar... at iki.fi <javascript:> / 
> http://www.iki.fi/~apsi/
>     Ecole Normale Supérieure (ENS), Département de Chimie, Paris
>     Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935
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