[QE-users] memory problem
Neelam Swarnkar
neelamswarnkar35 at gmail.com
Tue Jul 7 09:58:03 CEST 2020
output file
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 Tue, Jul 7, 2020 at 1:27 PM Neelam Swarnkar <neelamswarnkar35 at gmail.com>
wrote:
> 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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