Too slow for 1008 Ni atoms, 20 or more minutes per step

[yell... at gmail.com]

Dear  cp2k  users and developers, 

I am trying to run ab initio molecular dynamics on the system including 
1008 Ni atoms with PBE functional. The 1*24 mpi task is too slow, around 80 
steps per day on average; the 3*24 mpi task is slower, 38 steps per day on 
average.

Any help is highly appreciated.

 

Best regards,

 Huang


CP2K version 4.1

 SVN source code revision svn:17462

 cp2kflags: fftw3 parallel mpi2 scalapack

composer_xe_2015.2.164

Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz Haswell


# Step Nr. Time[fs] Kin.[a.u.] Temp[K] Pot.[a.u.] Cons Qty[a.u.] UsedTime[s]

 0 0.000000 9.566949152 2000.000000000 -170544.785566084 -170535.208832257 
0.000000000

 1 1.000000 9.646234174 2016.574776405 -170554.174550500 -170544.519479220 
13708.945765018

 2 2.000000 9.903391164 2070.334232377 -170556.710812560 -170546.798982374 
1826.637025118

 3 3.000000 10.258759808 2144.625134870 -170557.585906167 -170547.318873932 
748.965154886

 4 4.000000 10.622230399 2220.609774417 -170557.531726730 -170546.901213604 
856.725823164


&GLOBAL

  ! limit the runs to 5min

  ! WALLTIME 1000

  ! reduce the amount of IO

  IOLEVEL  LOW

  ! the project name is made part of most output files... useful to keep 
order 

  PROJECT Ni-1008-2k

  ! various runtypes (energy, geo_opt, etc.) available.

  RUN_TYPE MD             

&END GLOBAL


&FORCE_EVAL

  STRESS_TENSOR ANALYTICAL

  ! the electronic structure part of CP2K is named Quickstep

  METHOD Quickstep

  &DFT

    ! basis sets and pseudopotential files can be found in cp2k/data

    BASIS_SET_FILE_NAME BASIS_SET

    POTENTIAL_FILE_NAME GTH_POTENTIALS            


    ! Charge and multiplicity

    CHARGE 0

    MULTIPLICITY 1


    &MGRID

       ! PW cutoff ... depends on the element (basis) too small cutoffs 
lead to the eggbox effect.

       ! certain calculations (e.g. geometry optimization, vibrational 
frequencies,

       ! NPT and cell optimizations, need higher cutoffs)

       CUTOFF [Ry] 300 !500 

    &END


    &QS

       ! use the GPW method (i.e. pseudopotential based calculations with 
the Gaussian and Plane Waves scheme).

       METHOD GPW 

       ! default threshold for numerics ~ roughly numerical accuracy of the 
total energy per electron,

       ! sets reasonable values for all other thresholds.

       EPS_DEFAULT 1.0E-7 !10 

       ! used for MD, the method used to generate the initial guess.

       EXTRAPOLATION ASPC 

    &END


    &POISSON

       PERIODIC XYZ ! the default, gas phase systems should have 'NONE' and 
a wavelet solver

    &END


!    &PRINT

!       ! at the end of the SCF procedure generate cube files of the density

!       &E_DENSITY_CUBE OFF

!       &END E_DENSITY_CUBE

!       ! compute eigenvalues and homo-lumo gap each 20nd MD step

!       &MO_CUBES

!          ! compute 4 unoccupied orbital energies

!          NLUMO 4

!          NHOMO 4

!          ! but don't write the cube files

!          WRITE_CUBE .FALSE.

!          ! do this every 10th MD step.

!          &EACH

!            MD 20

!          &END

!       &END

!    &END


    ! use the OT METHOD for robust and efficient SCF, suitable for all 
non-metallic systems.

    &SCF                              

      SCF_GUESS ATOMIC ! can be used to RESTART an interrupted calculation

      MAX_SCF 50

      EPS_SCF 1.0E-4 ! accuracy of the SCF procedure typically 1.0E-6 - 
1.0E-7

      ! do not store the wfn during MD

      &PRINT

        &RESTART OFF

        &END

      &END

      

      &OT

        ! an accurate preconditioner suitable also for larger systems

        PRECONDITIONER FULL_SINGLE_INVERSE

        ! the most robust choice (DIIS might sometimes be faster, but not 
as stable).

        MINIMIZER DIIS

      &END OT

      &OUTER_SCF ! repeat the inner SCF cycle 10 times

        MAX_SCF 20

        EPS_SCF 1.0E-4 ! must match the above

      &END

    &END SCF


    ! specify the exchange and correlation treatment

    &XC

      ! use a PBE functional 

      &XC_FUNCTIONAL 

         &PBE

         &END

      &END XC_FUNCTIONAL

    &END XC

  &END DFT

 

  ! description of the system

  &SUBSYS

    &CELL 

      ! unit cells that are orthorhombic are more efficient with CP2K

      ABC [angstrom] 21.98167992 21.98167992 25.64529419

    &END CELL


    ! atom coordinates can be in the &COORD section,

    ! or provided as an external file.

    &TOPOLOGY

      COORD_FILE_NAME Ni-1008-2k.xyz

      COORD_FILE_FORMAT XYZ

    &END


    ! MOLOPT basis sets are fairly costly,

    ! but in the 'DZVP-MOLOPT-SR-GTH' available for all elements

    ! their contracted nature makes them suitable

    ! for condensed and gas phase systems alike.

    &KIND Ni                              

      BASIS_SET DZV-GTH-PADE        

      POTENTIAL GTH-PBE-q18             

    &END KIND

  &END SUBSYS

&END FORCE_EVAL


! how to propagate the system, selection via RUN_TYPE in the &GLOBAL section

&MOTION

! &GEO_OPT

!   OPTIMIZER LBFGS ! Good choice for 'small' systems (use LBFGS for large 
systems)

!   MAX_ITER  100

!   MAX_DR    [bohr] 0.003 ! adjust target as needed

!   &BFGS

!   &END

!  &END

 &MD

   ENSEMBLE NPT_I  ! sampling the canonical ensemble, accurate properties 
might need NVE

   TEMPERATURE [K] 2000

   TIMESTEP [fs] 1

   STEPS 1000000

   # GLE thermostat as generated at http://epfl-cosmo.github.io/gle4md 

   # GLE provides an effective NVT sampling.

   &BAROSTAT

       PRESSURE 1.0

   &END BAROSTAT

   &THERMOSTAT

      &NOSE

      &END NOSE

   &END THERMOSTAT

 &END MD

 &PRINT

   &TRAJECTORY

     &EACH

       MD 100

     &END EACH

   &END TRAJECTORY

   &VELOCITIES OFF

   &END VELOCITIES

   &FORCES OFF

   &END FORCES

   &RESTART_HISTORY

     &EACH

       MD 200

     &END EACH

   &END RESTART_HISTORY

   &RESTART

     BACKUP_COPIES 3

     &EACH

       MD 200

     &END EACH

   &END RESTART

  &END PRINT

&END
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