[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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