[QE-users] cp.x parallel run

Zahra Nourbakhsh z.nourbakhsh at gmail.com
Wed May 6 14:40:29 CEST 2020


Dear Riccardo,

Thank you for your answer. my input is as follows which is almost same as
qe example


&control
    title = ' Water 64 molecules ',
    calculation = 'cp',
    restart_mode = 'reset_counters' !'from_scratch', ! 'restart',
    ndr = 52,
    ndw = 52,
    nstep  = 40000,
    iprint = 1,
    isave  = 50,
    tstress = .TRUE.,
    tprnfor = .TRUE.,
    dt    = 30.0d0,
    etot_conv_thr = 1.d-8,
    prefix = 'h2o',
    pseudo_dir='/u/nzahra/pseudo',
    outdir='/ptmp/nzahra/water/bo/scan/nve/',
/
 &system
    ibrav = 14,
    celldm(1) = 23.4976, ! 18.65,
    celldm(2) = 1.0,
    celldm(3) = 1.0,
    celldm(4) = 0.0,
    celldm(5) = 0.0,
    celldm(6) = 0.0,
    nat = 192,
    ntyp = 2,
    nbnd = 256,
    ecutwfc = 70.0,
 /
 &electrons
!     emass = 100.d0,
!    emass_cutoff = 2.5d0,
!    orthogonalization = 'ortho',
!    ortho_eps = 5.d-8,
!    ortho_max = 25,
    electron_dynamics = 'cg',
!    electron_velocities = 'zero',
/
 &ions
   ion_dynamics = 'verlet',
   ion_velocities = 'zero',
   ion_radius(1) = 0.8d0,
   ion_radius(2) = 0.5d0,
 /
&cell
    cell_dynamics = 'none',
 /
ATOMIC_SPECIES
 O  16.0d0   O.SCAN.UPF
 H  1.0079d0 H.SCAN.UPF
ATOMIC_POSITIONS (angstrom)
    O    3.1085973690    3.1085973690    0.0000000000
    O    0.0000000000    0.0000000000    0.0000000000
    O    3.1085973690    0.0000000000    3.1085973690
    O    0.0000000000    3.1085973690    3.1085973690
    O    4.6628960530    4.6628960530    1.5542986840
    O    1.5542986840    1.5542986840    1.5542986840
    O    4.6628960530    1.5542986840    4.6628960530
    O    1.5542986840    4.6628960530    4.6628960530
    H    3.6526019090    3.6526019090    0.5440045400
    H    0.5440045400    0.5440045400    0.5440045400
    H    3.6526019090    0.5440045400    3.6526019090
    H    0.5440045400    3.6526019090    3.6526019090
    H    3.6526019090    2.5645928290   -0.5440045400
    H    0.5440045400   -0.5440045400   -0.5440045400
    H    3.6526019090   -0.5440045400    2.5645928290
    H    0.5440045400    2.5645928290    2.5645928290
    H    5.2069005930    4.1188915140    2.0983032240
    H    2.0983032240    1.0102941450    2.0983032240
    H    5.2069005930    1.0102941450    5.2069005930
    H    2.0983032240    4.1188915140    5.2069005930
    H    5.2069005930    5.2069005930    1.0102941450
    H    2.0983032240    2.0983032240    1.0102941450
    H    5.2069005930    2.0983032240    4.1188915140
    H    2.0983032240    5.2069005930    4.1188915140
    O    3.1085973690    3.1085973690    6.2171947380
    O    0.0000000000    0.0000000000    6.2171947380
    O    3.1085973690    0.0000000000    9.3257921070
    O    0.0000000000    3.1085973690    9.3257921070
    O    4.6628960530    4.6628960530    7.7714934220
    O    1.5542986840    1.5542986840    7.7714934220
    O    4.6628960530    1.5542986840   10.8800907910
    O    1.5542986840    4.6628960530   10.8800907910
    H    3.6526019090    3.6526019090    6.7611992780
    H    0.5440045400    0.5440045400    6.7611992780
    H    3.6526019090    0.5440045400    9.8697966470
    H    0.5440045400    3.6526019090    9.8697966470
    H    3.6526019090    2.5645928290    5.6731901980
    H    0.5440045400   -0.5440045400    5.6731901980
    H    3.6526019090   -0.5440045400    8.7817875670
    H    0.5440045400    2.5645928290    8.7817875670
    H    5.2069005930    4.1188915140    8.3154979620
    H    2.0983032240    1.0102941450    8.3154979620
    H    5.2069005930    1.0102941450   11.4240953310
    H    2.0983032240    4.1188915140   11.4240953310
    H    5.2069005930    5.2069005930    7.2274888830
    H    2.0983032240    2.0983032240    7.2274888830
    H    5.2069005930    2.0983032240   10.3360862520
    H    2.0983032240    5.2069005930   10.3360862520
    O    3.1085973690    9.3257921070    0.0000000000
    O    0.0000000000    6.2171947380    0.0000000000
    O    3.1085973690    6.2171947380    3.1085973690
    O    0.0000000000    9.3257921070    3.1085973690
    O    4.6628960530   10.8800907910    1.5542986840
    O    1.5542986840    7.7714934220    1.5542986840
    O    4.6628960530    7.7714934220    4.6628960530
    O    1.5542986840   10.8800907910    4.6628960530
    H    3.6526019090    9.8697966470    0.5440045400
    H    0.5440045400    6.7611992780    0.5440045400
    H    3.6526019090    6.7611992780    3.6526019090
    H    0.5440045400    9.8697966470    3.6526019090
    H    3.6526019090    8.7817875670   -0.5440045400
    H    0.5440045400    5.6731901980   -0.5440045400
    H    3.6526019090    5.6731901980    2.5645928290
    H    0.5440045400    8.7817875670    2.5645928290
    H    5.2069005930   10.3360862520    2.0983032240
    H    2.0983032240    7.2274888830    2.0983032240
    H    5.2069005930    7.2274888830    5.2069005930
    H    2.0983032240   10.3360862520    5.2069005930
    H    5.2069005930   11.4240953310    1.0102941450
    H    2.0983032240    8.3154979620    1.0102941450
    H    5.2069005930    8.3154979620    4.1188915140
    H    2.0983032240   11.4240953310    4.1188915140
    O    3.1085973690    9.3257921070    6.2171947380
    O    0.0000000000    6.2171947380    6.2171947380
    O    3.1085973690    6.2171947380    9.3257921070
    O    0.0000000000    9.3257921070    9.3257921070
    O    4.6628960530   10.8800907910    7.7714934220
    O    1.5542986840    7.7714934220    7.7714934220
    O    4.6628960530    7.7714934220   10.8800907910
    O    1.5542986840   10.8800907910   10.8800907910
    H    3.6526019090    9.8697966470    6.7611992780
    H    0.5440045400    6.7611992780    6.7611992780
    H    3.6526019090    6.7611992780    9.8697966470
    H    0.5440045400    9.8697966470    9.8697966470
    H    3.6526019090    8.7817875670    5.6731901980
    H    0.5440045400    5.6731901980    5.6731901980
    H    3.6526019090    5.6731901980    8.7817875670
    H    0.5440045400    8.7817875670    8.7817875670
    H    5.2069005930   10.3360862520    8.3154979620
    H    2.0983032240    7.2274888830    8.3154979620
    H    5.2069005930    7.2274888830   11.4240953310
    H    2.0983032240   10.3360862520   11.4240953310
    H    5.2069005930   11.4240953310    7.2274888830
    H    2.0983032240    8.3154979620    7.2274888830
    H    5.2069005930    8.3154979620   10.3360862520
    H    2.0983032240   11.4240953310   10.3360862520
    O    9.3257921070    3.1085973690    0.0000000000
    O    6.2171947380    0.0000000000    0.0000000000
    O    9.3257921070    0.0000000000    3.1085973690
    O    6.2171947380    3.1085973690    3.1085973690
    O   10.8800907910    4.6628960530    1.5542986840
    O    7.7714934220    1.5542986840    1.5542986840
    O   10.8800907910    1.5542986840    4.6628960530
    O    7.7714934220    4.6628960530    4.6628960530
    H    9.8697966470    3.6526019090    0.5440045400
    H    6.7611992780    0.5440045400    0.5440045400
    H    9.8697966470    0.5440045400    3.6526019090
    H    6.7611992780    3.6526019090    3.6526019090
    H    9.8697966470    2.5645928290   -0.5440045400
    H    6.7611992780   -0.5440045400   -0.5440045400
    H    9.8697966470   -0.5440045400    2.5645928290
    H    6.7611992780    2.5645928290    2.5645928290
    H   11.4240953310    4.1188915140    2.0983032240
    H    8.3154979620    1.0102941450    2.0983032240
    H   11.4240953310    1.0102941450    5.2069005930
    H    8.3154979620    4.1188915140    5.2069005930
    H   11.4240953310    5.2069005930    1.0102941450
    H    8.3154979620    2.0983032240    1.0102941450
    H   11.4240953310    2.0983032240    4.1188915140
    H    8.3154979620    5.2069005930    4.1188915140
    O    9.3257921070    3.1085973690    6.2171947380
    O    6.2171947380    0.0000000000    6.2171947380
    O    9.3257921070    0.0000000000    9.3257921070
    O    6.2171947380    3.1085973690    9.3257921070
    O   10.8800907910    4.6628960530    7.7714934220
    O    7.7714934220    1.5542986840    7.7714934220
    O   10.8800907910    1.5542986840   10.8800907910
    O    7.7714934220    4.6628960530   10.8800907910
    H    9.8697966470    3.6526019090    6.7611992780
    H    6.7611992780    0.5440045400    6.7611992780
    H    9.8697966470    0.5440045400    9.8697966470
    H    6.7611992780    3.6526019090    9.8697966470
    H    9.8697966470    2.5645928290    5.6731901980
    H    6.7611992780   -0.5440045400    5.6731901980
    H    9.8697966470   -0.5440045400    8.7817875670
    H    6.7611992780    2.5645928290    8.7817875670
    H   11.4240953310    4.1188915140    8.3154979620
    H    8.3154979620    1.0102941450    8.3154979620
    H   11.4240953310    1.0102941450   11.4240953310
    H    8.3154979620    4.1188915140   11.4240953310
    H   11.4240953310    5.2069005930    7.2274888830
    H    8.3154979620    2.0983032240    7.2274888830
    H   11.4240953310    2.0983032240   10.3360862520
    H    8.3154979620    5.2069005930   10.3360862520
    O    9.3257921070    9.3257921070    0.0000000000
    O    6.2171947380    6.2171947380    0.0000000000
    O    9.3257921070    6.2171947380    3.1085973690
    O    6.2171947380    9.3257921070    3.1085973690
    O   10.8800907910   10.8800907910    1.5542986840
    O    7.7714934220    7.7714934220    1.5542986840
    O   10.8800907910    7.7714934220    4.6628960530
    O    7.7714934220   10.8800907910    4.6628960530
    H    9.8697966470    9.8697966470    0.5440045400
    H    6.7611992780    6.7611992780    0.5440045400
    H    9.8697966470    6.7611992780    3.6526019090
    H    6.7611992780    9.8697966470    3.6526019090
    H    9.8697966470    8.7817875670   -0.5440045400
    H    6.7611992780    5.6731901980   -0.5440045400
    H    9.8697966470    5.6731901980    2.5645928290
    H    6.7611992780    8.7817875670    2.5645928290
    H   11.4240953310   10.3360862520    2.0983032240
    H    8.3154979620    7.2274888830    2.0983032240
    H   11.4240953310    7.2274888830    5.2069005930
    H    8.3154979620   10.3360862520    5.2069005930
    H   11.4240953310   11.4240953310    1.0102941450
    H    8.3154979620    8.3154979620    1.0102941450
    H   11.4240953310    8.3154979620    4.1188915140
    H    8.3154979620   11.4240953310    4.1188915140
    O    9.3257921070    9.3257921070    6.2171947380
    O    6.2171947380    6.2171947380    6.2171947380
    O    9.3257921070    6.2171947380    9.3257921070
    O    6.2171947380    9.3257921070    9.3257921070
    O   10.8800907910   10.8800907910    7.7714934220
    O    7.7714934220    7.7714934220    7.7714934220
    O   10.8800907910    7.7714934220   10.8800907910
    O    7.7714934220   10.8800907910   10.8800907910
    H    9.8697966470    9.8697966470    6.7611992780
    H    6.7611992780    6.7611992780    6.7611992780
    H    9.8697966470    6.7611992780    9.8697966470
    H    6.7611992780    9.8697966470    9.8697966470
    H    9.8697966470    8.7817875670    5.6731901980
    H    6.7611992780    5.6731901980    5.6731901980
    H    9.8697966470    5.6731901980    8.7817875670
    H    6.7611992780    8.7817875670    8.7817875670
    H   11.4240953310   10.3360862520    8.3154979620
    H    8.3154979620    7.2274888830    8.3154979620
    H   11.4240953310    7.2274888830   11.4240953310
    H    8.3154979620   10.3360862520   11.4240953310
    H   11.4240953310   11.4240953310    7.2274888830
    H    8.3154979620    8.3154979620    7.2274888830
    H   11.4240953310    8.3154979620   10.3360862520
    H    8.3154979620   11.4240953310   10.3360862520



Yours sincerely,
Zara


On Wed, May 6, 2020 at 1:13 PM Riccardo Bertossa <rbertoss at sissa.it> wrote:

> I always do cp calculation with any number of mpi processes without any
> issue! What is your input? How do you run the calculation? Did you follow
> the user's guide?
>
>
> all the best,
>
>
> Riccardo Bertossa, PhD student at SISSA
> Il 06/05/20 12:09, Zahra Nourbakhsh ha scritto:
>
> Dear all,
>
> I would like to do molecular-dynamics calculations using cp.x command, but
> I have faced with a strange issue. I found that in cp.x calculations, the
> number of requested cores has to be equal to the number of system molecules!
>
> For example, if I have 32 (or 64) H2O molecules, I have to run cp.x with
> "-n 32 (or -n 64)". But for other qe commands, such as pw.x, I can do
> parallel calculations on as many nodes/cores as I want/need.
>
> I would like to know that is this a usual feature of cp calculations? If
> so, does anyone know if it exists in all md packages like cp2k?
> Is there any way for me to solve this problem in qe package?
>
> Yours sincerely,
> Zara
>
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