[CP2K:10742] Re: How to accelerate the calculation of pdos ?
Krack Matthias (PSI)
matthia... at psi.ch
Mon Sep 17 15:29:31 UTC 2018
Yes, you may set that environment variable in your .bashrc file or each time when you launch a CP2K job (which would overwrite the actual definition in .bashrc). As you like. Finally, check the CP2K output file, if it has had the desired effect.
From: cp... at googlegroups.com <cp... at googlegroups.com> On Behalf Of Tianshu Jiang in Beijing
Sent: Montag, 17. September 2018 10:00
To: cp2k <cp... at googlegroups.com>
Subject: Re: [CP2K:10742] Re: How to accelerate the calculation of pdos ?
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<mailto:cp... at googlegroups.com> <cp... at googlegroups.com<mailto:cp... at googlegroups.com>> On Behalf Of Tianshu Jiang in Beijing
Sent: Freitag, 14. September 2018 03:50
To: cp2k <cp... at googlegroups.com<mailto: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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