[QE-users] unefficient parallelization of scf calculation
JULIEN, CLAUDE, PIERRE BARBAUD
julien_barbaud at sjtu.edu.cn
Fri Apr 12 11:30:17 CEST 2019
Well actually, this remark may be much closer to solve my problem than you might think !
I tried to run the simulation again on the cluster without the assume_isolated=’2D’ flag, and the parallelization was efficient this time. It seemed to scale well with growing number of procs. So thank you very much for this suggestion.
However, this raised other questions that I was not able to find an answer to:
* Where does the information about the need to center the system come from? I could not find track of it in the INPUT_PW documentation. I only quickly glanced over the paper mentioned as reference in the ‘2D’ flag, but I don’t suppose that such technical details would be explained there ( as I imagine that it is more relevant to the particular coding implementation in quantum espresso than the general method described in the article)
* I tried to correct the assume_isolated, but I might have misunderstood how to center the system. I just took the atom with “highest z” zh and the one with “lowest z” zl, and made sure to shift the whole so that the average (zh+zl)/2=0. This did not work. However, this particular example being made of a slab and a 2d layer over it, this means, among others, that the slab itself is not centered, and I am unsure whether this is the correct way to do it
Best,
Julien
From: Thomas Brumme [mailto:thomas.brumme at uni-leipzig.de]
Sent: mercredi 10 avril 2019 18:19
To: Quantum Espresso users Forum; Julien Barbaud
Subject: Re: [QE-users] unefficient parallelization of scf calculation
Dear Julien,
I can't give any valuable input for your question regarding the parallelization, but I think your
input is wrong. Using assume_isolated needs the system to be centered around z=0.
Regards
Thomas
On 4/10/19 11:36 AM, Julien Barbaud wrote:
I am starting to use a hpc cluster of my university, but I am very green on parallel computation.
I have made a first test (test #1) on a very small-scale simulation (relaxation of a GO sheet with 19 atoms, with respect to the gamma point). The calculation took 3m20s to run on 1 proc on my personal computer. On the cluster with 4 proc and default parallel options, it took 1m5s, and on 8 proc it took 44s. This seems like a reasonable behavior, and at least shows that raising the number of procs does reduce computation time in this case (with obvious limitations if too many procs for the job).
However I tried with another test, a bit bigger (test #2). This example is a scf calculation with 120 atoms (still with respect to the gamma point). In this case, the parallelization brings absolutely no improvement. In fact, although the outfile confirms that the code is running on N procs, it has similar performances as if it was running on 1 proc (sometimes even worse actually, but probably not in a significant manner, as the times are fluctuating a bit from 1 run to another)
I tried to run this same input file on my personal computer both on 1 and 2 cores. Turns out that it takes 10376s to run 10 iterations on 1 core, while it takes 6777s on two cores, so it seems that the parallelization is doing ok on my computer.
I have tried to run with different number of cores on the hpc, and different parallelization options (like for instance –nb 4), but nothing seems to improve the time
Basically, I am stuck with those 2 seemingly conflicting facts:
* Parallelization seems to have no particular problem on the hpc cluster because test #1 gives good results
* Parallelization seems to have no particular problem with the particular input file #2 because it seems to scale reasonably with proc number on my individual computer
However, combining both and running this file in parallel on the hpc cluster ends up not working correctly…
I included below the input file and output file of test #2. I also included as well as the slurm script that I use to submit the calculation to the job manager, in case it helps (test2.scf.slurm.txt)
Any suggestion on what is going wrong would be very welcome.
Julien
----------------------------------test2.in---------------------------------------
&CONTROL
title = '# Quantum Espresso PWSCF output snapshot # 0'
pseudo_dir = '/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/' ,
prefix='bonding_scf'
calculation = 'scf'
outdir='./outslurm'
/
&SYSTEM
nat= 120
ntyp= 7
ibrav= 0
ecutwfc= 50, ecutrho=400,
occupations='smearing', smearing='mv', degauss=1.0d-3
assume_isolated='2D'
/
&ELECTRONS
mixing_beta = 0.5
conv_thr = 1.0d-7
electron_maxstep=1
/
&IONS
/
&CELL
/
ATOMIC_SPECIES
C 12.011 C.pbesol-n-kjpaw_psl.1.0.0.UPF
N 14.007 N.pbesol-n-kjpaw_psl.0.1.UPF
H 1.008 H.pbesol-kjpaw_psl.0.1.UPF
Pb 207.2 Pb.pbesol-dn-kjpaw_psl.1.0.0.UPF
I 126.9 I.pbesol-n-kjpaw_psl.1.0.0.UPF
O 15.999 O.pbesol-n-kjpaw_psl.1.0.0.UPF
Cl 35.450 Cl.pbesol-n-kjpaw_psl.1.0.0.UPF
CELL_PARAMETERS angstrom
6.40743642 0.00000000 0.00000000
0.00000000 12.53119000 0.00000000
0.00000000 0.00000000 39.01263233
ATOMIC_POSITIONS angstrom
C 3.20373698 3.26295456 22.67510117
N 4.36830205 2.66824164 22.67510117
N 2.03914607 2.66824164 22.67510117
H 3.20373076 4.35970913 22.67510117
H 5.20200492 3.26227865 22.67510117
H 4.49794030 1.65118734 22.67510117
H 1.90952027 1.65118734 22.67510117
H 1.20545622 3.26227865 22.67510117
Pb 6.40746106 6.04808537 19.50631617
I 3.20373108 6.16571088 19.50631617
I 6.40746051 2.89948619 19.50631617
I 0.00000101 5.76270558 22.67510117
C 3.20373698 9.52854956 22.67510117
N 4.36830205 8.93383664 22.67510117
N 2.03914607 8.93383664 22.67510117
H 3.20373076 10.62530413 22.67510117
H 5.20200492 9.52787365 22.67510117
H 4.49794030 7.91678234 22.67510117
H 1.90952027 7.91678234 22.67510117
H 1.20545622 9.52787365 22.67510117
Pb 6.40746106 12.31368037 19.50631617
I 3.20373108 12.43130588 19.50631617
I 6.40746051 9.16508119 19.50631617
I 0.00000101 12.02830057 22.67510117
C 3.20373698 3.26295456 29.01264528
N 4.36830205 2.66824164 29.01264528
N 2.03914607 2.66824164 29.01264528
H 3.20373076 4.35970913 29.01264528
H 5.20200492 3.26227865 29.01264528
H 4.49794030 1.65118734 29.01264528
H 1.90952027 1.65118734 29.01264528
H 1.20545622 3.26227865 29.01264528
Pb 6.40746106 6.04808537 25.84386028
I 3.20373108 6.16571088 25.84386028
I 6.40746051 2.89948619 25.84386028
I 0.00000101 5.76270558 29.01264528
C 3.20373698 9.52854956 29.01264528
N 4.36830205 8.93383664 29.01264528
N 2.03914607 8.93383664 29.01264528
H 3.20373076 10.62530413 29.01264528
H 5.20200492 9.52787365 29.01264528
H 4.49794030 7.91678234 29.01264528
H 1.90952027 7.91678234 29.01264528
H 1.20545622 9.52787365 29.01264528
Pb 6.40746106 12.31368037 25.84386028
I 3.20373108 12.43130588 25.84386028
I 6.40746051 9.16508119 25.84386028
I 0.00000101 12.02830057 29.01264528
C 3.20373698 3.26295456 35.35018939
N 4.36830205 2.66824164 35.35018939
N 2.03914607 2.66824164 35.35018939
H 3.20373076 4.35970913 35.35018939
H 5.20200492 3.26227865 35.35018939
H 4.49794030 1.65118734 35.35018939
H 1.90952027 1.65118734 35.35018939
H 1.20545622 3.26227865 35.35018939
Pb 6.40746106 6.04808537 32.18140439
I 3.20373108 6.16571088 32.18140439
I 6.40746051 2.89948619 32.18140439
I 0.00000101 5.76270558 35.35018939
C 3.20373698 9.52854956 35.35018939
N 4.36830205 8.93383664 35.35018939
N 2.03914607 8.93383664 35.35018939
H 3.20373076 10.62530413 35.35018939
H 5.20200492 9.52787365 35.35018939
H 4.49794030 7.91678234 35.35018939
H 1.90952027 7.91678234 35.35018939
H 1.20545622 9.52787365 35.35018939
Pb 6.40746106 12.31368037 32.18140439
I 3.20373108 12.43130588 32.18140439
I 6.40746051 9.16508119 32.18140439
I 0.00000101 12.02830057 35.35018939
C -2.65922562 1.02746622 13.15267801
C -1.57082020 2.76789659 14.15213700
C -1.55249267 1.43382279 13.92545145
C -2.76678501 3.43396657 13.80880118
C -0.51572401 0.59007742 14.27042957
C 0.45127539 2.57771266 15.36479250
C 0.54032636 1.13871696 14.89500427
C -0.61858466 3.46111062 14.87552012
C 1.75850840 0.45260751 14.42517077
C 2.51877126 2.72823145 14.25997933
C 2.54527275 1.46853929 13.80948684
C 1.69149484 3.42061251 15.24764489
C -2.84434923 4.73311498 13.75015587
C -1.79251576 6.80155604 13.82062727
C -1.71556103 5.46156288 14.02089871
C -2.79591766 7.89012407 13.91075998
C -0.67171524 4.85078215 14.72657807
C 0.42299842 7.09269756 14.52980725
C 0.31418038 5.75006370 15.32008815
C -0.54822530 7.37927093 13.62065670
C 1.58501883 4.93901110 15.15192558
C 1.95672818 6.38683569 12.97082740
C 2.39800998 5.48893963 14.08928384
C 2.19010582 7.82391704 13.36789777
C -2.58931431 9.73216977 11.12323260
C -1.53736385 11.49261513 12.63531287
C -1.43991415 10.25590370 11.85590265
C -2.46212319 12.58463568 12.27360914
C -0.60003148 9.34961386 12.41523759
C 0.61521796 10.90977347 13.68739727
C 0.56702168 9.72454135 13.05961564
C -0.57311928 11.74387481 13.77090253
C 1.73778864 8.96596466 12.44952664
C 2.44039831 11.26999757 12.43362532
C 2.66220529 10.00525725 12.01318349
C 1.83430055 11.66382030 13.76046404
Cl -0.00001799 6.04797424 17.07363791
Cl 1.25165378 8.40223027 10.76754187
O -1.79125675 11.13196776 14.04477237
O 2.87346590 12.19705486 11.50562577
O 2.66595523 5.77705032 15.51329335
O 1.68196546 5.86106544 11.91469705
O 2.44111071 11.89613785 15.06748010
O 3.89019144 8.86144083 14.58391140
O -2.48663871 8.96018517 10.18744705
O -0.74483722 7.99628057 12.39035840
O 1.51084248 7.88917390 14.66305294
O 1.28942315 2.85893197 16.48674549
K_POINTS gamma
-----------------------------------------------------test2.out--------------------------------------------
Program PWSCF v.6.3 starts on 10Apr2019 at 15:35:34
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 8 processors
MPI processes distributed on 1 nodes
R & G space division: proc/nbgrp/npool/nimage = 8
Reading input from /lustre/home/acct-mseyxd/mseyxd/QE/GO-Cl/FAPBI3_bonding/scf/1x2x3_matching/bonding.scf.in
Warning: card &IONS ignored
Warning: card / ignored
Warning: card &CELL ignored
Warning: card / ignored
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 C.pbesol-n-kjpaw_psl.1.0.0.UPF: wavefunction(s) 2S 2P renormalized
file N.pbesol-n-kjpaw_psl.0.1.UPF: wavefunction(s) 2P renormalized
file H.pbesol-kjpaw_psl.0.1.UPF: wavefunction(s) 1S renormalized
file Pb.pbesol-dn-kjpaw_psl.1.0.0.UPF: wavefunction(s) 6S 6P 5D renormalized
file I.pbesol-n-kjpaw_psl.1.0.0.UPF: wavefunction(s) 5S renormalized
file O.pbesol-n-kjpaw_psl.1.0.0.UPF: wavefunction(s) 2S 2P renormalized
file Cl.pbesol-n-kjpaw_psl.1.0.0.UPF: wavefunction(s) 3S 3P renormalized
gamma-point specific algorithms are used
Subspace diagonalization in iterative solution of the eigenvalue problem:
a serial algorithm will be used
Parallelization info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Min 1140 570 141 356988 126222 15758
Max 1142 572 142 357012 126236 15798
Sum 9123 4565 1135 2856023 1009807 126259
Title:
# Quantum Espresso PWSCF output snapshot # 0
bravais-lattice index = 0
lattice parameter (alat) = 12.1083 a.u.
unit-cell volume = 21138.7101 (a.u.)^3
number of atoms/cell = 120
number of atomic types = 7
number of electrons = 542.00
number of Kohn-Sham states= 325
kinetic-energy cutoff = 50.0000 Ry
charge density cutoff = 400.0000 Ry
convergence threshold = 1.0E-07
mixing beta = 0.5000
number of iterations used = 8 plain mixing
Exchange-correlation = SLA PW PSX PSC ( 1 4 10 8 0 0)
celldm(1)= 12.108300 celldm(2)= 0.000000 celldm(3)= 0.000000
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) = ( 0.000000 1.955726 0.000000 )
a(3) = ( 0.000000 0.000000 6.088649 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( 1.000000 0.000000 0.000000 )
b(2) = ( 0.000000 0.511319 0.000000 )
b(3) = ( 0.000000 0.000000 0.164240 )
PseudoPot. # 1 for C read from file:
/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/C.pbesol-n-kjpaw_psl.1.0.0.UPF
MD5 check sum: f9b2fe17d1f478429498b05d17159f9e
Pseudo is Projector augmented-wave + core cor, Zval = 4.0
Generated using "atomic" code by A. Dal Corso v.6.3
Shape of augmentation charge: PSQ
Using radial grid of 1073 points, 4 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
Q(r) pseudized with 0 coefficients
PseudoPot. # 2 for N read from file:
/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/N.pbesol-n-kjpaw_psl.0.1.UPF
MD5 check sum: 15bd223d5d75e9eda893d0f4e6bdad1b
Pseudo is Projector augmented-wave + core cor, Zval = 5.0
Generated using "atomic" code by A. Dal Corso v.6.3
Shape of augmentation charge: PSQ
Using radial grid of 1085 points, 4 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
Q(r) pseudized with 0 coefficients
PseudoPot. # 3 for H read from file:
/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/H.pbesol-kjpaw_psl.0.1.UPF
MD5 check sum: 27a6b98f1514c59d399e798f1258b8b7
Pseudo is Projector augmented-wave, Zval = 1.0
Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9415
Shape of augmentation charge: PSQ
Using radial grid of 929 points, 2 beta functions with:
l(1) = 0
l(2) = 0
Q(r) pseudized with 0 coefficients
PseudoPot. # 4 for Pb read from file:
/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/Pb.pbesol-dn-kjpaw_psl.1.0.0.UPF
MD5 check sum: 56da3be0db09ba43f309b470f7bff7d1
Pseudo is Projector augmented-wave + core cor, Zval = 14.0
Generated using "atomic" code by A. Dal Corso v.6.3
Shape of augmentation charge: PSQ
Using radial grid of 1281 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. # 5 for I read from file:
/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/I.pbesol-n-kjpaw_psl.1.0.0.UPF
MD5 check sum: 6038403ff9b03366b27f71806436e734
Pseudo is Projector augmented-wave + core cor, Zval = 7.0
Generated using "atomic" code by A. Dal Corso v.6.3
Shape of augmentation charge: PSQ
Using radial grid of 1247 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. # 6 for O read from file:
/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/O.pbesol-n-kjpaw_psl.1.0.0.UPF
MD5 check sum: cb766521a97cf798d01896eaf7ac9a0a
Pseudo is Projector augmented-wave + core cor, Zval = 6.0
Generated using "atomic" code by A. Dal Corso v.6.3
Shape of augmentation charge: PSQ
Using radial grid of 1095 points, 4 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
Q(r) pseudized with 0 coefficients
PseudoPot. # 7 for Cl read from file:
/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/Cl.pbesol-n-kjpaw_psl.1.0.0.UPF
MD5 check sum: 939a64fc035742408689cdf8470f8314
Pseudo is Projector augmented-wave + core cor, Zval = 7.0
Generated using "atomic" code by A. Dal Corso v.6.3
Shape of augmentation charge: PSQ
Using radial grid of 1157 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
C 4.00 12.01100 C ( 1.00)
N 5.00 14.00700 N ( 1.00)
H 1.00 1.00800 H ( 1.00)
Pb 14.00 207.20000 Pb( 1.00)
I 7.00 126.90000 I ( 1.00)
O 6.00 15.99900 O ( 1.00)
Cl 7.00 35.45000 Cl( 1.00)
No symmetry found
Cartesian axes
site n. atom positions (alat units)
1 C tau( 1) = ( 0.5000029 0.5092449 3.5388726 )
2 N tau( 2) = ( 0.6817550 0.4164289 3.5388726 )
3 N tau( 3) = ( 0.3182468 0.4164289 3.5388726 )
4 H tau( 4) = ( 0.5000020 0.6804140 3.5388726 )
5 H tau( 5) = ( 0.8118699 0.5091394 3.5388726 )
6 H tau( 6) = ( 0.7019875 0.2576986 3.5388726 )
7 H tau( 7) = ( 0.2980163 0.2576986 3.5388726 )
8 H tau( 8) = ( 0.1881339 0.5091394 3.5388726 )
9 Pb tau( 9) = ( 1.0000038 0.9439166 3.0443246 )
10 I tau( 10) = ( 0.5000020 0.9622742 3.0443246 )
11 I tau( 11) = ( 1.0000038 0.4525189 3.0443246 )
12 I tau( 12) = ( 0.0000002 0.8993777 3.5388726 )
13 C tau( 13) = ( 0.5000029 1.4871079 3.5388726 )
14 N tau( 14) = ( 0.6817550 1.3942919 3.5388726 )
15 N tau( 15) = ( 0.3182468 1.3942919 3.5388726 )
16 H tau( 16) = ( 0.5000020 1.6582770 3.5388726 )
17 H tau( 17) = ( 0.8118699 1.4870024 3.5388726 )
18 H tau( 18) = ( 0.7019875 1.2355616 3.5388726 )
19 H tau( 19) = ( 0.2980163 1.2355616 3.5388726 )
20 H tau( 20) = ( 0.1881339 1.4870024 3.5388726 )
21 Pb tau( 21) = ( 1.0000038 1.9217796 3.0443246 )
22 I tau( 22) = ( 0.5000020 1.9401372 3.0443246 )
23 I tau( 23) = ( 1.0000038 1.4303819 3.0443246 )
24 I tau( 24) = ( 0.0000002 1.8772407 3.5388726 )
25 C tau( 25) = ( 0.5000029 0.5092449 4.5279646 )
26 N tau( 26) = ( 0.6817550 0.4164289 4.5279646 )
27 N tau( 27) = ( 0.3182468 0.4164289 4.5279646 )
28 H tau( 28) = ( 0.5000020 0.6804140 4.5279646 )
29 H tau( 29) = ( 0.8118699 0.5091394 4.5279646 )
30 H tau( 30) = ( 0.7019875 0.2576986 4.5279646 )
31 H tau( 31) = ( 0.2980163 0.2576986 4.5279646 )
32 H tau( 32) = ( 0.1881339 0.5091394 4.5279646 )
33 Pb tau( 33) = ( 1.0000038 0.9439166 4.0334166 )
34 I tau( 34) = ( 0.5000020 0.9622742 4.0334166 )
35 I tau( 35) = ( 1.0000038 0.4525189 4.0334166 )
36 I tau( 36) = ( 0.0000002 0.8993777 4.5279646 )
37 C tau( 37) = ( 0.5000029 1.4871079 4.5279646 )
38 N tau( 38) = ( 0.6817550 1.3942919 4.5279646 )
39 N tau( 39) = ( 0.3182468 1.3942919 4.5279646 )
40 H tau( 40) = ( 0.5000020 1.6582770 4.5279646 )
41 H tau( 41) = ( 0.8118699 1.4870024 4.5279646 )
42 H tau( 42) = ( 0.7019875 1.2355616 4.5279646 )
43 H tau( 43) = ( 0.2980163 1.2355616 4.5279646 )
44 H tau( 44) = ( 0.1881339 1.4870024 4.5279646 )
45 Pb tau( 45) = ( 1.0000038 1.9217796 4.0334166 )
46 I tau( 46) = ( 0.5000020 1.9401372 4.0334166 )
47 I tau( 47) = ( 1.0000038 1.4303819 4.0334166 )
48 I tau( 48) = ( 0.0000002 1.8772407 4.5279646 )
49 C tau( 49) = ( 0.5000029 0.5092449 5.5170566 )
50 N tau( 50) = ( 0.6817550 0.4164289 5.5170566 )
51 N tau( 51) = ( 0.3182468 0.4164289 5.5170566 )
52 H tau( 52) = ( 0.5000020 0.6804140 5.5170566 )
53 H tau( 53) = ( 0.8118699 0.5091394 5.5170566 )
54 H tau( 54) = ( 0.7019875 0.2576986 5.5170566 )
55 H tau( 55) = ( 0.2980163 0.2576986 5.5170566 )
56 H tau( 56) = ( 0.1881339 0.5091394 5.5170566 )
57 Pb tau( 57) = ( 1.0000038 0.9439166 5.0225086 )
58 I tau( 58) = ( 0.5000020 0.9622742 5.0225086 )
59 I tau( 59) = ( 1.0000038 0.4525189 5.0225086 )
60 I tau( 60) = ( 0.0000002 0.8993777 5.5170566 )
61 C tau( 61) = ( 0.5000029 1.4871079 5.5170566 )
62 N tau( 62) = ( 0.6817550 1.3942919 5.5170566 )
63 N tau( 63) = ( 0.3182468 1.3942919 5.5170566 )
64 H tau( 64) = ( 0.5000020 1.6582770 5.5170566 )
65 H tau( 65) = ( 0.8118699 1.4870024 5.5170566 )
66 H tau( 66) = ( 0.7019875 1.2355616 5.5170566 )
67 H tau( 67) = ( 0.2980163 1.2355616 5.5170566 )
68 H tau( 68) = ( 0.1881339 1.4870024 5.5170566 )
69 Pb tau( 69) = ( 1.0000038 1.9217796 5.0225086 )
70 I tau( 70) = ( 0.5000020 1.9401372 5.0225086 )
71 I tau( 71) = ( 1.0000038 1.4303819 5.0225086 )
72 I tau( 72) = ( 0.0000002 1.8772407 5.5170566 )
73 C tau( 73) = ( -0.4150218 0.1603553 2.0527208 )
74 C tau( 74) = ( -0.2451558 0.4319819 2.2087050 )
75 C tau( 75) = ( -0.2422954 0.2237748 2.1733265 )
76 C tau( 76) = ( -0.4318084 0.5359346 2.1551211 )
77 C tau( 77) = ( -0.0804884 0.0920926 2.2271668 )
78 C tau( 78) = ( 0.0704299 0.4023002 2.3979625 )
79 C tau( 79) = ( 0.0843280 0.1777180 2.3246433 )
80 C tau( 80) = ( -0.0965417 0.5401709 2.3216025 )
81 C tau( 81) = ( 0.2744480 0.0706378 2.2513170 )
82 C tau( 82) = ( 0.3931012 0.4257914 2.2255358 )
83 C tau( 83) = ( 0.3972373 0.2291930 2.1552281 )
84 C tau( 84) = ( 0.2639893 0.5338504 2.3796795 )
85 C tau( 85) = ( -0.4439138 0.7386909 2.1459684 )
86 C tau( 86) = ( -0.2797555 1.0615097 2.1569667 )
87 C tau( 87) = ( -0.2677453 0.8523788 2.1882228 )
88 C tau( 88) = ( -0.4363551 1.2314011 2.1710336 )
89 C tau( 89) = ( -0.1048337 0.7570551 2.2983573 )
90 C tau( 90) = ( 0.0660168 1.1069478 2.2676475 )
91 C tau( 91) = ( 0.0490337 0.8974047 2.3909856 )
92 C tau( 92) = ( -0.0855608 1.1516729 2.1257576 )
93 C tau( 93) = ( 0.2473718 0.7708248 2.3647407 )
94 C tau( 94) = ( 0.3053839 0.9967849 2.0243396 )
95 C tau( 95) = ( 0.3742542 0.8566514 2.1988956 )
96 C tau( 96) = ( 0.3418069 1.2210682 2.0863099 )
97 C tau( 97) = ( -0.4041108 1.5188867 1.7359880 )
98 C tau( 98) = ( -0.2399343 1.7936370 1.9719763 )
99 C tau( 99) = ( -0.2247255 1.6006251 1.8503348 )
100 C tau( 100) = ( -0.3842603 1.9640672 1.9155257 )
101 C tau( 101) = ( -0.0936461 1.4591817 1.9376295 )
102 C tau( 102) = ( 0.0960162 1.7026737 2.1361737 )
103 C tau( 103) = ( 0.0884943 1.5176961 2.0381967 )
104 C tau( 104) = ( -0.0894460 1.8328508 2.1492063 )
105 C tau( 105) = ( 0.2712143 1.3993061 1.9429809 )
106 C tau( 106) = ( 0.3808697 1.7588934 1.9404992 )
107 C tau( 107) = ( 0.4154868 1.5615071 1.8748814 )
108 C tau( 108) = ( 0.2862768 1.8203568 2.1475771 )
109 Cl tau( 109) = ( -0.0000028 0.9438992 2.6646597 )
110 Cl tau( 110) = ( 0.1953439 1.3113248 1.6804758 )
111 O tau( 111) = ( -0.2795590 1.7373513 2.1919488 )
112 O tau( 112) = ( 0.4484580 1.9035780 1.7956676 )
113 O tau( 113) = ( 0.4160721 0.9016165 2.4211389 )
114 O tau( 114) = ( 0.2625021 0.9147286 1.8595108 )
115 O tau( 115) = ( 0.3809809 1.8566143 2.3515614 )
116 O tau( 116) = ( 0.6071370 1.3829932 2.2760915 )
117 O tau( 117) = ( -0.3880864 1.3984041 1.5899412 )
118 O tau( 118) = ( -0.1162457 1.2479688 1.9337466 )
119 O tau( 119) = ( 0.2357952 1.2312528 2.2884430 )
120 O tau( 120) = ( 0.2012385 0.4461897 2.5730642 )
number of k points= 1 Marzari-Vanderbilt smearing, width (Ry)= 0.0010
cart. coord. in units 2pi/alat
k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 2.0000000
Dense grid: 1428012 G-vectors FFT dimensions: ( 80, 160, 480)
Smooth grid: 504904 G-vectors FFT dimensions: ( 60, 108, 360)
Estimated max dynamical RAM per process > 965.66 MB
Estimated total dynamical RAM > 7.54 GB
----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D
The code is running with the 2D cutoff
Please refer to:
Sohier, T., Calandra, M., & Mauri, F. (2017),
Density functional perturbation theory for gated two-dimensional heterostructures:
Theoretical developments and application to flexural phonons in graphene.
Physical Review B, 96(7), 75448. https://doi.org/10.1103/PhysRevB.96.075448
----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D
Check: negative/imaginary core charge= -0.000002 0.000000
Initial potential from superposition of free atoms
Check: negative starting charge= -0.001132
starting charge 541.98383, renormalised to 542.00000
negative rho (up, down): 1.132E-03 0.000E+00
Starting wfcs are 420 randomized atomic wfcs
Checking if some PAW data can be deallocated...
total cpu time spent up to now is 125.6 secs
Self-consistent Calculation
iteration # 1 ecut= 50.00 Ry beta= 0.50
Davidson diagonalization with overlap
c_bands: 3 eigenvalues not converged
ethr = 1.00E-02, avg # of iterations = 40.0
negative rho (up, down): 1.031E-05 0.000E+00
total cpu time spent up to now is 2094.5 secs
total energy = 82142.85683667 Ry
Harris-Foulkes estimate = -53335.51769720 Ry
estimated scf accuracy < 111068.31785845 Ry
End of self-consistent calculation
convergence NOT achieved after 1 iterations: stopping
Writing output data file bonding_scf.save/
init_run : 119.18s CPU 120.33s WALL ( 1 calls)
electrons : 1961.71s CPU 1969.12s WALL ( 1 calls)
Called by init_run:
wfcinit : 52.26s CPU 52.44s WALL ( 1 calls)
potinit : 19.26s CPU 19.33s WALL ( 1 calls)
hinit0 : 36.63s CPU 36.68s WALL ( 1 calls)
Called by electrons:
c_bands : 1919.78s CPU 1923.97s WALL ( 1 calls)
sum_band : 28.22s CPU 30.08s WALL ( 1 calls)
v_of_rho : 2.26s CPU 2.35s WALL ( 2 calls)
newd : 20.58s CPU 22.50s WALL ( 2 calls)
PAW_pot : 4.00s CPU 4.00s WALL ( 2 calls)
mix_rho : 0.23s CPU 0.24s WALL ( 1 calls)
Called by c_bands:
init_us_2 : 0.22s CPU 0.27s WALL ( 3 calls)
regterg : 1919.41s CPU 1923.60s WALL ( 2 calls)
Called by sum_band:
sum_band:bec : 0.00s CPU 0.00s WALL ( 1 calls)
addusdens : 16.57s CPU 17.94s WALL ( 1 calls)
Called by *egterg:
h_psi : 680.38s CPU 682.69s WALL ( 43 calls)
s_psi : 259.57s CPU 259.75s WALL ( 43 calls)
g_psi : 0.93s CPU 0.94s WALL ( 40 calls)
rdiaghg : 52.76s CPU 52.86s WALL ( 41 calls)
Called by h_psi:
h_psi:pot : 679.62s CPU 681.90s WALL ( 43 calls)
h_psi:calbec : 255.27s CPU 255.54s WALL ( 43 calls)
vloc_psi : 164.42s CPU 166.01s WALL ( 43 calls)
add_vuspsi : 259.93s CPU 260.35s WALL ( 43 calls)
General routines
calbec : 263.20s CPU 263.88s WALL ( 44 calls)
fft : 2.33s CPU 2.43s WALL ( 23 calls)
ffts : 0.09s CPU 0.09s WALL ( 3 calls)
fftw : 128.50s CPU 130.07s WALL ( 10237 calls)
interpolate : 0.25s CPU 0.26s WALL ( 2 calls)
davcio : 0.00s CPU 0.10s WALL ( 3 calls)
Parallel routines
fft_scatt_xy : 23.50s CPU 23.55s WALL ( 10263 calls)
fft_scatt_yz : 10.98s CPU 12.22s WALL ( 10263 calls)
PWSCF : 34m45.53s CPU 34m55.12s WALL
This run was terminated on: 16:10:30 10Apr2019
=------------------------------------------------------------------------------=
JOB DONE.
=------------------------------------------------------------------------------=
-----------------------------------------------------SLURM command-------------------------------------
#!/bin/bash
#SBATCH --job-name=QE_GO-Cl_bonding_scf
#SBATCH --partition=cpu
#SBATCH --mail-type=end
#SBATCH --mail-user=julien_barbaud at sjtu.edu.cn <mailto:--mail-user=julien_barbaud at sjtu.edu.cn>
#SBATCH --output=bonding.scf.slurm.out
#SBATCH --error=bonding.scf.slurm.err
#SBATCH -p cpu
#SBATCH -n 8
#SBATCH --ntasks-per-node=8
ulimit -l unlimited
ulimit -s unlimited
INPUT=$HOME/QE/GO-Cl/FAPBI3_bonding/scf/1x2x3_matching/bonding.scf.in
EXEC=$HOME/QE/qe-6.3/bin/pw.x
srun --mpi=pmi2 $EXEC -in $INPUT
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--
Dr. rer. nat. Thomas Brumme
Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
Leipzig University
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email: thomas.brumme at uni-leipzig.de <mailto:thomas.brumme at uni-leipzig.de>
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