[CP2K:10738] Re: How to accelerate the calculation of pdos ?

Tianshu Jiang in Beijing jts2t... at gmail.com
Mon Sep 17 09:59:38 CEST 2018


Hi Krack,

Do you mean I should add a claim export OMP_NUM_THREADS=1  in my .bashrc or 
some else file ?

在 2018年9月16日星期日 UTC+8下午11:15:20,Matthias Krack写道:
>
> Hi
>
>  
>
> I suggest that you ask one of your sysadmins or an experienced user of 
> your cluster system how to launch a CP2K job properly using the desired 
> resources, especially if you did not understand my hints.
>
>  
>
> Matthias
>
>  
>
> *Von:* cp... at googlegroups.com <javascript:> <cp... at googlegroups.com 
> <javascript:>> *Im Auftrag von *Tianshu Jiang in Beijing
> *Gesendet:* Sonntag, 16. September 2018 08:58
> *An:* cp2k <cp... at googlegroups.com <javascript:>>
> *Betreff:* Re: [CP2K:10738] Re: How to accelerate the calculation of pdos 
> ?
>
>  
>
> Hi, Krack 
>
> Thanks for your patience ! 
>
> How should I use more cores to accelerate the calculation in cp2k 
> inputfile ? Should I add some more statement ?
>
> 在 2018年9月14日星期五 UTC+8下午3:27:21,Matthias Krack写道:
>
> Hi
>
>  
>
> As reported in the CP2K output headers
>
>  
>
> GLOBAL| Total number of message passing 
> processes                             1
>
> GLOBAL| Number of threads for this process                               
>     36
>
>  
>
> both runs were not MPI parallel and only OpenMP parallel using the same 
> resources, i.e. one MPI process and 36 OpenMP threads. Thus it is not 
> surprising that you observed no acceleration, since you used the same 
> resources. Moreover, the use of more than 8 threads per (MPI) process is 
> rarely beneficial for CP2K runs and will result rather in a slowdown than a 
> speedup. You have to launch the runs properly, e.g. using something like 
> “mpiexec –n 12 cp2k.popt” which depends, of course, on your installation. 
> If you are using a cp2k.psmp executable, then you should set in addition 
> “export OMP_NUM_THREADS=1”.
>
>  
>
> Matthias 
>
>  
>
> *From:* cp... at googlegroups.com <cp... at googlegroups.com> *On Behalf Of *Tianshu 
> Jiang in Beijing
> *Sent:* Freitag, 14. September 2018 03:50
> *To:* cp2k <cp... at googlegroups.com>
> *Subject:* [CP2K:10729] Re: How to accelerate the calculation of pdos ?
>
>  
>
> Hi Krack, thanks for your reply.
>
> In the attachment, bilayerIso.out is the file output by 1 core and 
> bilayerIsoPara.out is the file output by 12cores. 
>
> I have no idea where the problem is. 
>
> 在 2018年9月12日星期三 UTC+8下午7:58:50,Matthias Krack写道:
>
> Hi Tianshu Jiang
>
> without providing the CP2K output files of your 1-core and 12-cores runs, 
> it is quite unlikely that you will get any reasonable hint from someone in 
> this forum.
>
> Matthias
>
> On Wednesday, 12 September 2018 04:41:07 UTC+2, Tianshu Jiang in Beijing 
> wrote:
>
> Hi everyone in cp2k community,
>
>  
>
> I am using cp2k to calculate the pdos of graphene, but the time spent to 
> completing the calculation when I use 1 core and 12 cores is the same.
>
> The version I compile is Linux-x86-64-gfortran, and I use cp2k.psmp to 
> finish the job. 
>
> But from the *.out file I get that in both situation (1 core and 12 
> cores), the job finished after half an hour from beginning.
>
> My question is how can I accelerate the calculation using parallel 
> computing ?
>
>  
>
> The following is my inputfile. Thanks for your reply !
>
> &GLOBAL
>
>   PROJECT trilayerABCIso
>
>   RUN_TYPE ENERGY 
>
>   PRINT_LEVEL MEDIUM
>
> &END GLOBAL
>
>  
>
> &FORCE_EVAL
>
>   METHOD Quickstep
>
>   &DFT
>
>     BASIS_SET_FILE_NAME  BASIS_MOLOPT
>
>     POTENTIAL_FILE_NAME  POTENTIAL
>
>  
>
>     &POISSON
>
>       PERIODIC XYZ 
>
>     &END POISSON
>
>     &SCF
>
>       SCF_GUESS ATOMIC
>
>       EPS_SCF 1.0E-6
>
>       MAX_SCF 300 
>
>  
>
>       # The following settings help with convergence:
>
>       ADDED_MOS 100 
>
>       CHOLESKY INVERSE
>
>       &SMEAR ON
>
>         METHOD FERMI_DIRAC
>
>         ELECTRONIC_TEMPERATURE [K] 300 
>
>       &END SMEAR
>
>       &DIAGONALIZATION
>
>         ALGORITHM STANDARD
>
>         EPS_ADAPT 0.01
>
>       &END DIAGONALIZATION
>
>       &MIXING
>
>         METHOD BROYDEN_MIXING
>
>         ALPHA 0.2 
>
>         BETA 1.5
>
>         NBROYDEN 8
>
>       &END MIXING
>
>     &END SCF
>
>     &XC
>
>       &XC_FUNCTIONAL PBE
>
>       &END XC_FUNCTIONAL
>
>     &END XC
>
>     &PRINT
>
>       &PDOS
>
>         # print all projected DOS available:
>
>         NLUMO -1
>
>         # split the density by quantum number:
>
>         COMPONENTS
>
>       &END
>
>       &E_DENSITY_CUBE ON
>
>           STRIDE 1 1 1
>
>       &END E_DENSITY_CUBE
>
>     &END PRINT
>
>   &END DFT
>
>  
>
>   &SUBSYS
>
>     &CELL
>
>       # create a hexagonal unit cell:
>
>       ABC  [angstrom] 2.4612 2.4612 26.72
>
>       ALPHA_BETA_GAMMA 90. 90. 60.
>
>       SYMMETRY HEXAGONAL
>
>       PERIODIC XYZ
>
>       # and replicate this cell (see text):
>
>       MULTIPLE_UNIT_CELL 6 6 1
>
>     &END CELL
>
>     &TOPOLOGY
>
>       # also replicate the topology (see text):
>
>       MULTIPLE_UNIT_CELL 6 6 1
>
>     &END TOPOLOGY
>
>     &COORD
>
>       SCALED
>
>       # ABC stacked
>
>       C 1./3  1./3  0.
>
>       C 0.    3./3  0.
>
>       C 1./3  1./3  1./8
>
>       C 2./3  2./3  1./8
>
>       C 2./3  2./3  2./8
>
>       C 3./3  0.    2./8
>
>     &END
>
>     &KIND C
>
>       ELEMENT C
>
>       BASIS_SET TZVP-MOLOPT-GTH
>
>       POTENTIAL GTH-PADE-q4
>
>     &END KIND
>
>   &END SUBSYS
>
>  
>
> &END FORCE_EVAL
>
>  
>
>  
>
>  
>
>  
>
>  
>
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