[QE-users] unefficient parallelization of scf calculation

Julien Barbaud julien_barbaud at sjtu.edu.cn
Wed Apr 10 11:36:23 CEST 2019


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

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