[QE-users] problem in cp.x parallel calculation version 6.4 and 6.3

Zahra Nourbakhsh z.nourbakhsh at gmail.com
Thu May 7 13:22:17 CEST 2020


Dear Paulo,

Thank you very much for your reply. I want to do BOMD so I used
electron_dynamics = 'cg'. What is wrong about it?

Yours sincerely,
Zahra


On Thu, May 7, 2020 at 12:01 PM Zahra Nourbakhsh <z.nourbakhsh at gmail.com>
wrote:

> Dear Lorenzo
>
> Yes, I know many people use cp.x parallel but as I mentioned this problem
> occurs for me when I use version 6.4 and 6.3; for qe-6.1, I don't have this
> problem and I don't know about other versions.
>
> Here are some lines of my BOMD calculations using
>
> srun -n 16 cp.x <in
>
> and
>
> srun -n 32 cp.x <in
>
>
> for 16 cores:
>
>   nfi     ekinc              temph  tempp     etot                 enthal
>               econs                econt              vnhh    xnhh0   vnhp
>    xnhp0
>
>        nfi   tempp            E -T.S-mu.nbsp         +K_p #Iter
> Step     1       0   -550.100617   -550.100617   -550.100617    42
> Step     2       0   -550.100617   -550.100617   -550.100617     6
> Step     3       0   -550.100617   -550.100617   -550.100617     6
>
>    MAIN:          EKINC   (thr)          DETOT   (thr)       MAXFORCE
> (thr)
>    MAIN:   0.000000D+00  0.1D-05  0.484306D-10  0.1D-07  0.000000D+00
>  0.1D+11
>    MAIN: convergence achieved for system relaxation
>
>  * Physical Quantities at step:     4
>      Pressure of Nuclei (GPa)             0.00000      4
>      Pressure Total (GPa)            -3.80754      4
> NOTE: eigenvalues are not computed without ortho
>
>
>                 total energy =     -550.10061707572 Hartree a.u.
>               kinetic energy =      405.35380 Hartree a.u.
>         electrostatic energy =     -595.48960 Hartree a.u.
>                          esr =        1.06694 Hartree a.u.
>                        eself =      625.54150 Hartree a.u.
>       pseudopotential energy =     -286.39030 Hartree a.u.
>   n-l pseudopotential energy =       61.79974 Hartree a.u.
>  exchange-correlation energy =     -135.37426 Hartree a.u.
>            average potential =        0.00000 Hartree a.u.
> .
> .
> .
>
> ----------------------------------------------------------------------------------------------------
> for 32 core:
>
>   nfi     ekinc              temph  tempp     etot                 enthal
>               econs                econt              vnhh    xnhh0   vnhp
>    xnhp0
>
>        nfi   tempp            E -T.S-mu.nbsp         +K_p #Iter
> Step     1       0   -523.513474   -523.513474   -523.513474    42
> Step     2       0   -525.555463   -525.555463   -525.555463    21
> Step     3       0   -527.873907   -527.873907   -527.873907    20
> Step     4       0   -529.108725   -529.108725   -529.108725    20
> Step     5       0   -529.707861   -529.707861   -529.707861    20
> Step     6       0   -530.035707   -530.035707   -530.035707    20
> Step     7       0   -530.220064   -530.220064   -530.220064    20
> and it continues up to Step 50 while I have run cp.x for BO system where
> ion_velocity=0 and electron_dynamics = 'cg'.
>
>
> and if I run the program on higher cores, for example, srun -n 64 cp.x
>
>
>         nfi   tempp            E -T.S-mu.nbsp         +K_p #Iter
> Step     1       0   -439.090690   -439.090690   -439.090690    46
> Step     2       0           NaN           NaN           NaN   100
> Step     3       0           NaN           NaN           NaN   100
>
>
>
> *my input file is as follow*
>
> &control
>     title = ' Water 32 molecules ',
>     calculation = 'cp',
>     restart_mode = 'from_scratch', ! 'restart',
>     ndr = 50,
>     ndw = 50,
> !    nstep  = 100,
> !    iprint = 10,
> !    isave  = 100,
>     tstress = .TRUE.,
>     tprnfor = .TRUE.,
> !    dt    = 3.0d0,
>     etot_conv_thr = 1.d-8,
>     prefix = 'h2o',
>     pseudo_dir='/u/nzahra/pseudo',
>     outdir='/ptmp/nzahra/water/bo/scan/32/blyp',
> /
>  &system
>     ibrav = 14,
>     celldm(1) = 18.65,
>     celldm(2) = 1.0,
>     celldm(3) = 1.0,
>     celldm(4) = 0.0,
>     celldm(5) = 0.0,
>     celldm(6) = 0.0,
>     nat = 96,
>     ntyp = 2,
>     nbnd = 128,
>     ecutwfc = 70.0,
> input_dft='BLYP'
>  /
>  &electrons
>     electron_dynamics = 'cg',
> !    electron_velocities = 'zero',
> /
>  &ions
>    ion_dynamics = 'none',
>    ion_velocities = 'zero',
>    ion_radius(1) = 0.8d0,
>    ion_radius(2) = 0.5d0,
>  /
> &cell
>     cell_dynamics = 'none',
>  /
> ATOMIC_SPECIES
>  O  16.0d0    O.blyp-mt.UPF
>  H  1.0079d0  H.blyp-vbc.UPF
> ATOMIC_POSITIONS (crystal)
> O        0.378966142   0.399351787   0.153232022
> O        0.674080975   0.071652846   0.096431003
> O        0.502725138   0.249767593   0.960543532
> O        0.870124149   0.014393000   0.900181919
> O        0.370188926   0.134633533   0.543797631
> O        0.890478795   0.251227789   0.734444338
> O        0.942635278   0.708667766   0.077711606
> O        0.525930248   0.628961766   0.190669923
> O        0.824014650   0.270393021   0.220728713
> O        0.759518359   0.515784572   0.070294996
> O        0.623729416   0.669186389   0.445331655
> O        0.680125097   0.418204412   0.825978850
> O        0.996082615   0.864590486   0.308543405
> O        0.770361333   0.914797185   0.470010581
> O        0.945419200   0.594216294   0.657975197
> O        0.067635795   0.453586124   0.286217145
> O       -0.035358869   0.169241966   0.480014817
> O        0.779742615   0.439946163   0.474919680
> O        0.645018862   0.163367314   0.499583173
> O        0.305792605   0.499856745   0.608241857
> O        0.130443525   0.393912011   0.788840284
> O        0.229230973   0.237679258   0.336167096
> O        0.285232159   0.176280147   0.808692313
> O        0.475886585   0.903937356   0.211739054
> O        0.173759156   0.531282254   0.024620567
> O        0.209963773   0.999982487   0.194716580
> O        0.121031392   0.668269158   0.455966686
> O        0.284992985   0.749172203   0.852530295
> O        0.539738019   0.637507450   0.704744940
> O        0.363201790   0.862178393   0.486282852
> O        0.778560789   0.808717073   0.723047518
> O        0.145671119   0.973743672   0.921717439
> H        0.426295336   0.340207686   0.086508715
> H        0.341110554   0.340071056   0.223999914
> H        0.901742783   0.187895961   0.406332781
> H        0.614247468   0.002591432   0.137160396
> H        0.737402864   0.029853334   0.031561454
> H        0.562667835   0.181611878   1.003775164
> H        0.564472433   0.307913217   0.906055245
> H        0.870911680   0.095248333   0.841283158
> H        0.361495596   0.035370667   0.530609224
> H        0.341028286   0.151696206   0.638151234
> H        0.722481104   0.002887488   0.473461397
> H        0.905090080   0.219954239   0.640293326
> H        0.954076861   0.766015557   0.158801634
> H        0.610163252   0.596939823   0.147107980
> H        0.466232471   0.548685433   0.185384792
> H        0.765821036   0.195960162   0.185901401
> H        0.912890221   0.253846698   0.182869659
> H        0.785503768   0.438364362   0.126964918
> H        0.831590067   0.586920501   0.079653737
> H        0.685923292   0.590588094   0.448446869
> H        0.574485302   0.655736601   0.358925659
> H        0.750458474   0.361169500   0.783295312
> H        0.720257953   0.455946686   0.910136383
> H        1.038756633   0.795539302   0.367591617
> H        0.919030853   0.899810647   0.361832880
> H        0.836130766   0.940160626   0.842150509
> H        0.705435215   0.844189019   0.443076318
> H        0.888087349   0.668069262   0.695421637
> H        0.126921868   0.376078035   0.307926241
> H        0.088965741   0.478032540   0.192394629
> H        0.053662315   0.190925279   0.443309179
> H        0.844720849   0.472080648   0.542930479
> H        0.833371218   0.414408856   0.396199674
> H        0.547079627   0.164405051   0.517471345
> H        0.676341327   0.256807216   0.498799966
> H        0.261012491   0.567734272   0.551837812
> H        0.385073439   0.545908944   0.646744137
> H        0.190247229   0.440084410   0.720831264
> H        0.183107423   0.307801224   0.803750912
> H       -0.026090029   0.302102511   0.754164090
> H        0.282273377   0.209449298   0.418128934
> H        0.222760066   0.154169627   0.279980690
> H        0.235413166   0.097779415   0.848240164
> H        0.365798276   0.193666507   0.865859469
> H        0.381805142   0.932319112   0.194456804
> H        0.482699112   0.808034933   0.185394178
> H        0.030863614   0.666924190   0.062015985
> H        0.252956198   0.485820135   0.067028091
> H        0.185028596   0.993855524   0.097525880
> H        0.134140048   0.954300465   0.242452683
> H        0.060467045   0.649466748   0.533895806
> H        0.104799632   0.590923687   0.392958285
> H        0.263687068   0.672221596   0.911020950
> H        0.369208033   0.727116113   0.806274112
> H        0.591365151   0.557840346   0.736279678
> H        0.560587315   0.649238296   0.606795414
> H        0.153193921   0.477570557   0.941851144
> H        0.281022580   0.809008014   0.474911677
> H        0.406393144   0.864434913   0.396869127
> H        0.688858471   0.767344468   0.733825538
> H        0.776549080   0.853385230   0.632459869
> H       -0.012423931   0.546193409   0.732603372
> H        0.185208669   0.887687972   0.889096725
> H        0.046119603   0.973148479   0.910544721
>
>
>
>
>
> Yours sincerely,
> Zahra Nourbakhsh
>
>
> On Thu, May 7, 2020 at 1:23 AM Zahra Nourbakhsh <z.nourbakhsh at gmail.com>
> wrote:
>
>> Dear experts,
>>
>> I have just started BOMD calculations using the QE package.
>>
>> I found that for QE version 6.3.0 and 6.4.1, the cp.x command does not
>> work properly when I run it parallel and increase/decrease the number of
>> cores. I have run the same input from scratch, but the results are core
>> dependent!
>>
>> But this issue does not exist for version 6.1.0 and using this version,
>> my results are the same for any numbers of cores.
>>
>> I have asked our cluster supporting team about this issue but they
>> believe that it comes from QE. Does anyone have any suggestions?
>>
>> Yours sincerely,
>> Zara
>>
>
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