[QE-users] unefficient parallelization of scf calculation
Thomas Brumme
thomas.brumme at uni-leipzig.de
Wed Apr 10 12:18:51 CEST 2019
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
> #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
>
>
> _______________________________________________
> users mailing list
> users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
--
Dr. rer. nat. Thomas Brumme
Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry
Leipzig University
Phillipp-Rosenthal-Strasse 31
04103 Leipzig
Tel: +49 (0)341 97 36456
email: thomas.brumme at uni-leipzig.de
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