[QE-users] cp.x parallel run

Riccardo Bertossa rbertoss at sissa.it
Wed May 6 15:36:30 CEST 2020


Dear Zahra,

what command did you use to run the calculation? What error or 
unexpected behavior did you get?

Riccardo

Il 06/05/20 14:40, Zahra Nourbakhsh ha scritto:
> 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 
> <mailto: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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