[QE-users] memory problem

Neelam Swarnkar neelamswarnkar35 at gmail.com
Tue Jul 7 09:57:09 CEST 2020


Dear Expert and all

Here i am sharing my input file
&control
    calculation = 'scf',
    prefix = 'Zn4Sb3_exc1',
    outdir = './tmp/'
    pseudo_dir = './'
    verbosity = 'low'

 /
 &system
    ibrav =  4,
    celldm(1)= 46.2264804,
    celldm(3)= 1.016106614,
    nat =  24,
    ntyp = 2,
    occupations='smearing', degauss=0.02,
    ecutwfc = 27,
    ecutrho = 136

 /
 &electrons
    mixing_beta = 0.6
 /

 ATOMIC_SPECIES
 Zn 60.00  Zn.pbe-dnl-kjpaw_psl.1.0.0.UPF
 Sb 102.00 Sb.pbe-n-kjpaw_psl.1.0.0.UPF


ATOMIC_POSITIONS {crystal}
 Zn   0.5000000000000000  0.8660250000000000  0.0161070000000001
 Zn   0.0000000000000000  0.8660250000000000  0.0161070000000001
 Zn   0.5080535000000000  0.0000000000000000  0.8660250000000000
 Zn   0.0080534999999999  0.0000000000000000  0.8660250000000000
 Zn   0.4330125000000000  0.0161070000000001  0.0000000000000000
 Zn   0.9330125000000000  0.0161070000000001  0.0000000000000000
 Zn   0.8169875000000000  0.5000000000000000  0.4838930000000000
 Zn   0.3169875000000000  0.5000000000000000  0.4838930000000000
 Zn   0.7419465000000001  0.6339750000000000  0.5000000000000000
 Zn   0.2419465000000000  0.6339750000000000  0.5000000000000000
 Zn   0.7500000000000000  0.4838930000000000  0.6339750000000000
 Zn   0.2500000000000000  0.4838930000000000  0.6339750000000000
 Sb   0.5000000000000000  0.1339750000000000  0.9838929999999999
 Sb   0.0000000000000000  0.1339750000000000  0.9838929999999999
 Sb   0.4919465000000000  0.0000000000000000  0.1339750000000000
 Sb   0.9919465000000000  0.0000000000000000  0.1339750000000000
 Sb   0.5669875000000000  0.9838929999999999  0.0000000000000000
 Sb   0.0669875000000000  0.9838929999999999  0.0000000000000000
 Sb   0.1830125000000000  0.5000000000000000  0.5161070000000000
 Sb   0.6830125000000000  0.5000000000000000  0.5161070000000000
 Sb   0.2580535000000000  0.3660250000000000  0.5000000000000000
 Sb   0.7580534999999999  0.3660250000000000  0.5000000000000000
 Sb   0.2500000000000000  0.5161070000000000  0.3660250000000000
 Sb   0.7500000000000000  0.5161070000000000  0.3660250000000000


K_POINTS (automatic)
 2 1 1 0 0 0

On Mon, Jul 6, 2020 at 5:49 PM Neelam Swarnkar <neelamswarnkar35 at gmail.com>
wrote:

> I am sharing my input and output files here. also the screenshot of error .
>
> input file
>
> &control
>     calculation = 'scf',
>     prefix = 'Zn4Sb3_exc1',
>     outdir = './tmp/'
>     pseudo_dir = './'
>     verbosity = 'low'
>
>  /
>  &system
>     ibrav =  4,
>     celldm(1)= 46.2264804,
>     celldm(3)= 1.016106614,
>     nat =  24,
>     ntyp = 2,
>     occupations='smearing', degauss=0.02,
>     ecutwfc = 27,
>     ecutrho = 136
>
>  /
>  &electrons
>     mixing_beta = 0.6
>  /
>
>  ATOMIC_SPECIES
>  Zn 60.00  Zn.pbe-dnl-kjpaw_psl.1.0.0.UPF
>  Sb 102.00 Sb.pbe-n-kjpaw_psl.1.0.0.UPF
>
>
> ATOMIC_POSITIONS {crystal}
>  Zn   0.5000000000000000  0.8660250000000000  0.0161070000000001
>  Zn   0.0000000000000000  0.8660250000000000  0.0161070000000001
>  Zn   0.5080535000000000  0.0000000000000000  0.8660250000000000
>  Zn   0.0080534999999999  0.0000000000000000  0.8660250000000000
>  Zn   0.4330125000000000  0.0161070000000001  0.0000000000000000
>  Zn   0.9330125000000000  0.0161070000000001  0.0000000000000000
>  Zn   0.8169875000000000  0.5000000000000000  0.4838930000000000
>  Zn   0.3169875000000000  0.5000000000000000  0.4838930000000000
>  Zn   0.7419465000000001  0.6339750000000000  0.5000000000000000
>  Zn   0.2419465000000000  0.6339750000000000  0.5000000000000000
>  Zn   0.7500000000000000  0.4838930000000000  0.6339750000000000
>  Zn   0.2500000000000000  0.4838930000000000  0.6339750000000000
>  Sb   0.5000000000000000  0.1339750000000000  0.9838929999999999
>  Sb   0.0000000000000000  0.1339750000000000  0.9838929999999999
>  Sb   0.4919465000000000  0.0000000000000000  0.1339750000000000
>  Sb   0.9919465000000000  0.0000000000000000  0.1339750000000000
>  Sb   0.5669875000000000  0.9838929999999999  0.0000000000000000
>  Sb   0.0669875000000000  0.9838929999999999  0.0000000000000000
>  Sb   0.1830125000000000  0.5000000000000000  0.5161070000000000
>  Sb   0.6830125000000000  0.5000000000000000  0.5161070000000000
>  Sb   0.2580535000000000  0.3660250000000000  0.5000000000000000
>  Sb   0.7580534999999999  0.3660250000000000  0.5000000000000000
>  Sb   0.2500000000000000  0.5161070000000000  0.3660250000000000
>  Sb   0.7500000000000000  0.5161070000000000  0.3660250000000000
>
>
> K_POINTS (automatic)
>  2 1 1 0 0 0
>
>
> output
> Program PWSCF v.6.3 starts on  6Jul2020 at 14:29:48
>
>      This program is part of the open-source Quantum ESPRESSO suite
>      for quantum simulation of materials; please cite
>          "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>          "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
>           URL http://www.quantum-espresso.org",
>      in publications or presentations arising from this work. More details
> at
>      http://www.quantum-espresso.org/quote
>
>      Parallel version (MPI), running on     1 processors
>
>      MPI processes distributed on     1 nodes
>      Waiting for input...
>      Reading input from standard input
>
>      Current dimensions of program PWSCF are:
>      Max number of different atomic species (ntypx) = 10
>      Max number of k-points (npk) =  40000
>      Max angular momentum in pseudopotentials (lmaxx) =  3
>                file Zn.pbe-dnl-kjpaw_psl.1.0.0.UPF: wavefunction(s)  4S 3D
> renormalized
>                file Sb.pbe-n-kjpaw_psl.1.0.0.UPF: wavefunction(s)  5S
> renormalized
>
>      Subspace diagonalization in iterative solution of the eigenvalue
> problem:
>      a serial algorithm will be used
>
>      Found symmetry operation: I + (  0.5000  0.0000  0.0000)
>      This is a supercell, fractional translations are disabled
>
>      G-vector sticks info
>      --------------------
>      sticks:   dense  smooth     PW     G-vecs:    dense   smooth      PW
>      Sum       20017   15937   4093              2328127  1647611  215359
>
>
>
>      bravais-lattice index     =            4
>      lattice parameter (alat)  =      46.2265  a.u.
>      unit-cell volume          =   86924.5388 (a.u.)^3
>      number of atoms/cell      =           24
>      number of atomic types    =            2
>      number of electrons       =       204.00
>      number of Kohn-Sham states=          122
>      kinetic-energy cutoff     =      27.0000  Ry
>      charge density cutoff     =     136.0000  Ry
>      convergence threshold     =      1.0E-06
>      mixing beta               =       0.6000
>      number of iterations used =            8  plain     mixing
>      Exchange-correlation      = SLA PW PBX PBC ( 1  4  3  4 0 0)
>
>      celldm(1)=  46.226480  celldm(2)=   0.000000  celldm(3)=   1.016107
>      celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=   0.000000
>
>      crystal axes: (cart. coord. in units of alat)
>                a(1) = (   1.000000   0.000000   0.000000 )
>                a(2) = (  -0.500000   0.866025   0.000000 )
>                a(3) = (   0.000000   0.000000   1.016107 )
>
>      reciprocal axes: (cart. coord. in units 2 pi/alat)
>                b(1) = (  1.000000  0.577350 -0.000000 )
>                b(2) = (  0.000000  1.154701  0.000000 )
>                b(3) = (  0.000000 -0.000000  0.984149 )
>
>
>      PseudoPot. # 1 for Zn read from file:
>      ./Zn.pbe-dnl-kjpaw_psl.1.0.0.UPF
>      MD5 check sum: 7217f78799bfc6aaa3738bf4cd09bafd
>      Pseudo is Projector augmented-wave + core cor, Zval = 12.0
>      Generated using "atomic" code by A. Dal Corso v.6.2.2
>      Shape of augmentation charge: PSQ
>      Using radial grid of 1201 points,  6 beta functions with:
>                 l(1) =   0
>                 l(2) =   0
>                 l(3) =   1
>                 l(4) =   1
>                 l(5) =   2
>                 l(6) =   2
>      Q(r) pseudized with 0 coefficients
>
>
>      PseudoPot. # 2 for Sb read from file:
>      ./Sb.pbe-n-kjpaw_psl.1.0.0.UPF
>      MD5 check sum: 8701ebd98ea0ddfeeee3c5089d2d8acc
>      Pseudo is Projector augmented-wave + core cor, Zval =  5.0
>      Generated using "atomic" code by A. Dal Corso v.6.2.2
>      Shape of augmentation charge: PSQ
>      Using radial grid of 1243 points,  6 beta functions with:
>                 l(1) =   0
>                 l(2) =   0
>                 l(3) =   1
>                 l(4) =   1
>                 l(5) =   2
>                 l(6) =   2
>      Q(r) pseudized with 0 coefficients
>
>
>      atomic species   valence    mass     pseudopotential
>         Zn            12.00    60.00000     Zn( 1.00)
>         Sb             5.00   102.00000     Sb( 1.00)
>
>      No symmetry found
>
>
>
>    Cartesian axes
>
>      site n.     atom                  positions (alat units)
>          1           Zn  tau(   1) = (   0.0669875   0.7499997   0.0163664
>  )
>          2           Zn  tau(   2) = (  -0.4330125   0.7499997   0.0163664
>  )
>          3           Zn  tau(   3) = (   0.5080535   0.0000000   0.8799737
>  )
>          4           Zn  tau(   4) = (   0.0080535   0.0000000   0.8799737
>  )
>          5           Zn  tau(   5) = (   0.4249590   0.0139491   0.0000000
>  )
>          6           Zn  tau(   6) = (   0.9249590   0.0139491   0.0000000
>  )
>          7           Zn  tau(   7) = (   0.5669875   0.4330127   0.4916869
>  )
>          8           Zn  tau(   8) = (   0.0669875   0.4330127   0.4916869
>  )
>          9           Zn  tau(   9) = (   0.4249590   0.5490385   0.5080533
>  )
>         10           Zn  tau(  10) = (  -0.0750410   0.5490385   0.5080533
>  )
>         11           Zn  tau(  11) = (   0.5080535   0.4190636   0.6441862
>  )
>         12           Zn  tau(  12) = (   0.0080535   0.4190636   0.6441862
>  )
>         13           Sb  tau(  13) = (   0.4330125   0.1160258   0.9997402
>  )
>         14           Sb  tau(  14) = (  -0.0669875   0.1160258   0.9997402
>  )
>         15           Sb  tau(  15) = (   0.4919465   0.0000000   0.1361329
>  )
>         16           Sb  tau(  16) = (   0.9919465   0.0000000   0.1361329
>  )
>         17           Sb  tau(  17) = (   0.0750410   0.8520763   0.0000000
>  )
>         18           Sb  tau(  18) = (  -0.4249590   0.8520763   0.0000000
>  )
>         19           Sb  tau(  19) = (  -0.0669875   0.4330127   0.5244197
>  )
>         20           Sb  tau(  20) = (   0.4330125   0.4330127   0.5244197
>  )
>         21           Sb  tau(  21) = (   0.0750410   0.3169869   0.5080533
>  )
>         22           Sb  tau(  22) = (   0.5750410   0.3169869   0.5080533
>  )
>         23           Sb  tau(  23) = (  -0.0080535   0.4469618   0.3719204
>  )
>         24           Sb  tau(  24) = (   0.4919465   0.4469618   0.3719204
>  )
>
>      number of k points=     4  gaussian smearing, width (Ry)=  0.0200
>                        cart. coord. in units 2pi/alat
>         k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   1.0000000
>         k(    2) = (  -0.5000000  -0.2886751   0.0000000), wk =   0.3333333
>         k(    3) = (   0.5000000  -0.2886751   0.0000000), wk =   0.3333333
>         k(    4) = (   0.0000000  -0.5773503   0.0000000), wk =   0.3333333
>
>      Dense  grid:  2328127 G-vectors     FFT dimensions: ( 180, 180, 180)
>
>      Smooth grid:  1647611 G-vectors     FFT dimensions: ( 160, 160, 160)
>
>      Estimated max dynamical RAM per process >      11.48 GB
>
>      Check: negative/imaginary core charge=   -0.000002    0.000000
>
>      Initial potential from superposition of free atoms
>      Check: negative starting charge=   -0.128417
>
>
> On Mon, Jul 6, 2020 at 3:39 PM Oleksandr Motornyi <
> oleksandr.motornyi at polytechnique.edu> wrote:
>
>> Dear Neelam
>>
>> Other than this, it would be useful if you could also show the in/output
>> files of your system. While it does not seem large the memory usage depends
>> on the atoms/pseudopotentials you are using, size of the vacuum (if any).
>>
>> Best
>>
>> Oleksandr
>> On 06/07/2020 11:52, Michal Krompiec wrote:
>>
>> Dear Neelam,
>> I am by no means an expert, but from my limited experience I can say that
>> 4GB of RAM is not a lot, to put it mildly - but at the same time, your
>> system isn't large. In this case, I wouldn't use any parallelization on
>> k-points (pw.x -npool 1) and make use of symmetry as much as possible
>> (correct ibrav instead of ibrav=0). You can save memory by reducing ecutwfc
>> (at the expense of accuracy) - so try choosing pseudopotentials which give
>> you desired accuracy at the lowest ecutwfc (use
>> https://www.materialscloud.org/discover/sssp to guide you).
>> Best,
>> Michal
>>
>> On Mon, 6 Jul 2020 at 10:27, Neelam Swarnkar <neelamswarnkar35 at gmail.com>
>> wrote:
>>
>>> Dear expert and all
>>>
>>> I am making the supercell of 2x1x1 total 24 no of atoms, and perform scf
>>> calculation .but there is memory related problem currently i am using 4gb
>>> RAM.
>>>
>>> What can i do to solve this problem?
>>>
>>> Thanks in advance
>>> Neelam
>>>
>>> _______________________________________________
>>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso
>>> )
>>> users mailing list users at lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>
>>
>> _______________________________________________
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
>> users mailing list users at lists.quantum-espresso.orghttps://lists.quantum-espresso.org/mailman/listinfo/users
>>
>> --
>> Oleksandr Motornyi
>> PhD, Data Scientist
>>
>> France
>>
>> _______________________________________________
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
>> users mailing list users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
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