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

Pierre-André Cazade pierre.a... at gmail.com
Mon Sep 30 14:34:57 UTC 2019
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Hi,

I find it strange the error you get. CP2K OMP+MPI works fine for me. Just 
for the sake of validation, could you try :

export OMP_NUM_THREADS=X

mpirun -np Y cp2k.psmp -i input > output

rather than

 mpirun -np Y cp2k.psmp -i input -o output

Just to check.

Regards,
Pierre

On Monday, September 30, 2019 at 4:38:32 AM UTC+1, Chn wrote:
>
> 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> 
>> 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 on behalf of Chn <ch... 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,
>>>> -- 
>>>> You received this message because you are subscribed to the Google 
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>>>> To unsubscribe from this group and stop receiving emails from it, send 
>>>> an email to c... at googlegroups.com.
>>>> To view this discussion on the web visit 
>>>> https://groups.google.com/d/msgid/cp2k/39284c57-f6eb-463e-81a6-3a123596a9f2%40googlegroups.com 
>>>> <https://groups.google.com/d/msgid/cp2k/39284c57-f6eb-463e-81a6-3a123596a9f2%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>> .
>>>>
>>>>
>>>> -- 
>>>> Dr Pierre Cazade, PhD
>>>> AD3-023, Bernal Institute,
>>>> University of Limerick,
>>>> Plassey Park Road,
>>>> Castletroy, co. Limerick,
>>>> Ireland
>>>>
>>>> -- 
>>> You received this message because you are subscribed to the Google 
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>>> .
>>>
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>>> <https://groups.google.com/d/msgid/cp2k/AM6PR10MB26968C27CCEC14903050632EAE800%40AM6PR10MB2696.EURPRD10.PROD.OUTLOOK.COM?utm_medium=email&utm_source=footer>
>>> .
>>>
>>
>>
>> -- 
>>
>> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>>   Ari Paavo Seitsonen / Ar... at iki.fi / 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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