[QE-users] ph.x can not run

Timrov Iurii iurii.timrov at epfl.ch
Thu Dec 19 10:10:48 CET 2019


Dear Shaofeng Wang,


You are trying to perform a phonon calculation with the +U correction for a large system containing 93 atoms and using only 12 cores. I think that the code crashes because you do not have enough RAM. Please note that using PHonon+U for such a large system will be very very tough. Probably a better solution is to use Phonopy on top of DFT+U with supercells.


HTH


Iurii


--
Dr. Iurii Timrov
Postdoctoral Researcher
STI - IMX - THEOS and NCCR - MARVEL
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: users <users-bounces at lists.quantum-espresso.org> on behalf of wangshaofeng at iae.ac.cn <wangshaofeng at iae.ac.cn>
Sent: Thursday, December 19, 2019 9:04:06 AM
To: users
Subject: [QE-users] ph.x can not run

Dear expert,

I am calculating a dynamical matrix using ph.x. But it can not run. The error is shown as follow. Please give me some suggestion.

Thanks in advance.


     Program PHONON v.6.4.1 starts on 19Dec2019 at  0:32: 7

     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    12 processors

     MPI processes distributed on     1 nodes
     R & G space division:  proc/nbgrp/npool/nimage =      12

     Reading data from directory:
     ./tmp/mm.save/

     IMPORTANT: XC functional enforced from input :
     Exchange-correlation      = PBE ( 1  4  3  4 0 0)
     Any further DFT definition will be discarded
     Please, verify this is what you really want


     Parallelization info
     --------------------
     sticks:   dense  smooth     PW     G-vecs:    dense   smooth      PW
     Min        1012    1012    253               123568   123568   15453
     Max        1013    1013    255               123573   123573   15454
     Sum       12155   12155   3047              1482853  1482853  185445

     Generating pointlists ...
     new r_m :   0.7846 (alat units)  1.4827 (a.u.) for type    1
     new r_m :   0.7645 (alat units)  1.4447 (a.u.) for type    2
     new r_m :   0.3978 (alat units)  0.7518 (a.u.) for type    3
     new r_m :   0.3978 (alat units)  0.7518 (a.u.) for type    4
     new r_m :   0.6791 (alat units)  1.2833 (a.u.) for type    5

     Phonon calculation with DFPT+U; please cite
     A. Floris et al., Phys. Rev. B 84, 161102(R) (2011)
     in publications or presentations arising from this work.

     Calculation of q =    0.0000000   0.0000000   0.0000000

     ir calculation for HAsO4 adsorbed on goethite 110 in mm

     bravais-lattice index     =            0
     lattice parameter (alat)  =       1.8897  a.u.
     unit-cell volume          =   15341.5236 (a.u.)^3
     number of atoms/cell      =           93
     number of atomic types    =            5
     kinetic-energy cut-off    =      80.0000  Ry
     charge density cut-off    =     320.0000  Ry
     convergence threshold     =      1.0E-14
     beta                      =       0.7000
     number of iterations used =            4
     Exchange-correlation      = PBE ( 1  4  3  4 0 0)
      Hubbard parameters:
      U ( 1)     =  3.30000000
      U ( 2)     =  3.30000000


     celldm(1)=    1.88973  celldm(2)=    0.00000  celldm(3)=    0.00000
     celldm(4)=    0.00000  celldm(5)=    0.00000  celldm(6)=    0.00000

     crystal axes: (cart. coord. in units of alat)
               a(1) = ( 12.2147  0.0000  0.0000 )
               a(2) = (  0.0000 10.9482  0.0000 )
               a(3) = (  0.0000  0.0000 17.0000 )

     reciprocal axes: (cart. coord. in units 2 pi/alat)
               b(1) = (  0.0819  0.0000  0.0000 )
               b(2) = (  0.0000  0.0913  0.0000 )
               b(3) = (  0.0000  0.0000  0.0588 )


     Atoms inside the unit cell:

     Cartesian axes

     site n.  atom      mass           positions (alat units)
        1     H    1.0079   tau(    1) = (    1.12234    8.47343    5.06647  )
        2     H    1.0079   tau(    2) = (    2.57322    4.33959    4.43826  )
        3     H    1.0079   tau(    3) = (    2.54507    7.97823    1.08413  )
        4     H    1.0079   tau(    4) = (    0.95358    1.24139    1.69003  )
        5     H    1.0079   tau(    5) = (    1.50731   10.59710    0.32301  )
        6     H    1.0079   tau(    6) = (    2.56223    3.22337    0.49951  )
        7     H    1.0079   tau(    7) = (    3.02013    5.97989    5.95020  )
        8     H    1.0079   tau(    8) = (    1.11657    0.87403    5.71145  )
        9     H    1.0079   tau(    9) = (    4.38886    8.47398    4.96420  )
       10     H    1.0079   tau(   10) = (    5.63348    4.31121    4.41727  )
       11     H    1.0079   tau(   11) = (    5.69880    8.18447    0.95789  )
       12     H    1.0079   tau(   12) = (    4.15616    1.23787    1.64230  )
       13     H    1.0079   tau(   13) = (    3.68335   -0.41718    0.21817  )
       14     H    1.0079   tau(   14) = (    5.64184    3.24716    0.45592  )
       15     H    1.0079   tau(   15) = (    4.10690    0.79699    5.64323  )
       16     H    1.0079   tau(   16) = (    6.43988    8.36404    5.50599  )
       17     H    1.0079   tau(   17) = (    8.66013    4.34551    4.49757  )
       18     H    1.0079   tau(   18) = (    8.85525    8.05569    1.22272  )
       19     H    1.0079   tau(   19) = (    7.26703    1.15835    1.76365  )
       20     H    1.0079   tau(   20) = (    6.63268   10.58622    0.51057  )
       21     H    1.0079   tau(   21) = (    8.75040    3.21518    0.52301  )
       22     H    1.0079   tau(   22) = (    9.72366    5.80098    5.56701  )
       23     H    1.0079   tau(   23) = (    7.10488    0.78989    5.70570  )
       24     H    1.0079   tau(   24) = (   10.23777    8.35790    5.27171  )
       25     H    1.0079   tau(   25) = (   11.76575    4.38250    4.47156  )
       26     H    1.0079   tau(   26) = (   11.62271    8.09061    1.18360  )
       27     H    1.0079   tau(   27) = (   10.18874    1.30508    1.76682  )
       28     H    1.0079   tau(   28) = (    8.94148   10.64086    0.75306  )
       29     H    1.0079   tau(   29) = (   11.71830    3.36945    0.45177  )
       30     H    1.0079   tau(   30) = (    0.53865    5.83961    5.50125  )
       31     H    1.0079   tau(   31) = (   10.24451    0.97374    5.83049  )
       32     H    1.0079   tau(   32) = (    7.76150    5.93123    6.61613  )
       33     H    1.0079   tau(   33) = (   10.58477   10.52031    0.29869  )
       34     O   15.9994   tau(   34) = (    1.07970    5.96897    2.69764  )
       35     O   15.9994   tau(   35) = (    1.08047    8.23500    4.13181  )
       36     O   15.9994   tau(   36) = (    2.57127    4.06456    0.97787  )
       37     O   15.9994   tau(   37) = (    2.41326    5.85133    5.17613  )
       38     O   15.9994   tau(   38) = (    2.59340    3.69364    3.66020  )
       39     O   15.9994   tau(   39) = (    2.58204   10.68168    3.32289  )
       40     O   15.9994   tau(   40) = (    2.56568    8.43746    1.93298  )
       41     O   15.9994   tau(   41) = (    0.76649   10.71240    0.93256  )
       42     O   15.9994   tau(   42) = (    1.09538    1.60609    5.08133  )
       43     O   15.9994   tau(   43) = (    1.02834    1.96111    2.39319  )
       44     O   15.9994   tau(   44) = (    4.09676    5.94986    2.63985  )
       45     O   15.9994   tau(   45) = (    4.11694    8.22747    4.05302  )
       46     O   15.9994   tau(   46) = (    5.65578    4.05676    0.98560  )
       47     O   15.9994   tau(   47) = (    5.63807    5.86834    5.01668  )
       48     O   15.9994   tau(   48) = (    5.63368    3.66565    3.65320  )
       49     O   15.9994   tau(   49) = (    5.63465   10.65243    3.40622  )
       50     O   15.9994   tau(   50) = (    5.66353    8.39987    1.89772  )
       51     O   15.9994   tau(   51) = (    4.34139   10.73471    0.89449  )
       52     O   15.9994   tau(   52) = (    4.10121    1.56122    5.04985  )
       53     O   15.9994   tau(   53) = (    4.11790    1.94898    2.35943  )
       54     O   15.9994   tau(   54) = (    7.21411    5.89705    2.66423  )
       55     O   15.9994   tau(   55) = (    7.13646    8.15204    4.11161  )
       56     O   15.9994   tau(   56) = (    8.72176    4.04364    1.02172  )
       57     O   15.9994   tau(   57) = (    8.78367    5.83656    5.29801  )
       58     O   15.9994   tau(   58) = (    8.67150    3.68995    3.73244  )
       59     O   15.9994   tau(   59) = (    8.72059   10.67245    3.55138  )
       60     O   15.9994   tau(   60) = (    8.80388    8.38018    2.12945  )
       61     O   15.9994   tau(   61) = (    7.43493   10.65255    1.05441  )
       62     O   15.9994   tau(   62) = (    7.13020    1.56820    5.13020  )
       63     O   15.9994   tau(   63) = (    7.20308    1.91500    2.43533  )
       64     O   15.9994   tau(   64) = (   10.20696    5.95565    2.79882  )
       65     O   15.9994   tau(   65) = (   10.23983    8.19229    4.32056  )
       66     O   15.9994   tau(   66) = (   11.72531    4.14105    1.03415  )
       67     O   15.9994   tau(   67) = (   11.81076    5.86418    5.20360  )
       68     O   15.9994   tau(   68) = (   11.76207    3.71350    3.70846  )
       69     O   15.9994   tau(   69) = (   11.74205   10.69418    3.46463  )
       70     O   15.9994   tau(   70) = (   11.68976    8.40735    2.09243  )
       71     O   15.9994   tau(   71) = (    9.94885   10.73384    0.99701  )
       72     O   15.9994   tau(   72) = (   10.23921    1.65723    5.14798  )
       73     O   15.9994   tau(   73) = (   10.21802    1.98128    2.48378  )
       74     O   15.9994   tau(   74) = (    7.07132    6.02056    7.35698  )
       75     O   15.9994   tau(   75) = (    4.18092    6.27139    7.40096  )
       76     O   15.9994   tau(   76) = (    5.78137    8.30347    6.29357  )
       77     Fe  55.8450   tau(   77) = (    1.04682    9.72347    2.62366  )
       78     Fe1 55.8450   tau(   78) = (    2.59389    1.58652    3.72700  )
       79     Fe  55.8450   tau(   79) = (    2.62040    6.85509    3.57379  )
       80     Fe1 55.8450   tau(   80) = (    1.06022    4.14433    2.31704  )
       81     Fe  55.8450   tau(   81) = (    4.12951    9.71811    2.57959  )
       82     Fe1 55.8450   tau(   82) = (    5.63719    1.56412    3.76487  )
       83     Fe  55.8450   tau(   83) = (    5.68508    6.88647    3.34371  )
       84     Fe1 55.8450   tau(   84) = (    4.11193    4.12217    2.28869  )
       85     Fe  55.8450   tau(   85) = (    7.18919    9.62711    2.81373  )
       86     Fe1 55.8450   tau(   86) = (    8.68351    1.60418    3.88113  )
       87     Fe  55.8450   tau(   87) = (    8.61599    6.87184    3.64706  )
       88     Fe1 55.8450   tau(   88) = (    7.17773    4.07472    2.31155  )
       89     Fe  55.8450   tau(   89) = (   10.22216    9.67442    2.93407  )
       90     Fe1 55.8450   tau(   90) = (   11.75990    1.62587    3.82921  )
       91     Fe  55.8450   tau(   91) = (   11.76012    6.83408    3.56016  )
       92     Fe1 55.8450   tau(   92) = (   10.21322    4.15058    2.37869  )
       93     As  74.9216   tau(   93) = (    5.59227    6.55758    6.60320  )

     Computing dynamical matrix for
                    q = (   0.0000000   0.0000000   0.0000000 )

      2 Sym.Ops. (with q -> -q+G )


     G cutoff =   28.9460  ( 123573 G-vectors)     FFT grid: (135,120,192)
     number of k points=     2
                       cart. coord. in units 2pi/alat
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   1.0000000
        k(    2) = (   0.0000000   0.0000000   0.0000000), wk =   1.0000000

     PseudoPot. # 1 for Fe read from file:
     ../pseudo/ncpp/Fe_00PBE_OP.ncpp
     MD5 check sum: 7dd2af9bf891824878553aaa4b1a5245
     Pseudo is Norm-conserving, Zval = 16.0
     Generated by old ld1 code (numerical format)
     Using radial grid of 1160 points,  2 beta functions with:
                l(1) =   1
                l(2) =   2

     PseudoPot. # 2 for Fe read from file:
     ../pseudo/ncpp/Fe_00PBE_OP.ncpp
     MD5 check sum: 7dd2af9bf891824878553aaa4b1a5245
     Pseudo is Norm-conserving, Zval = 16.0
     Generated by old ld1 code (numerical format)
     Using radial grid of 1160 points,  2 beta functions with:
                l(1) =   1
                l(2) =   2

     PseudoPot. # 3 for O  read from file:
     ../pseudo/ncpp/O_00PBE_OP.ncpp
     MD5 check sum: 2e5ae166b87ab36fb9ab3e3b2efbba94
     Pseudo is Norm-conserving, Zval =  6.0
     Generated by old ld1 code (numerical format)
     Using radial grid of 1130 points,  1 beta functions with:
                l(1) =   1

     PseudoPot. # 4 for H  read from file:
     ../pseudo/ncpp/H_00PBE_OP.ncpp
     MD5 check sum: e8e81ce5ac2edd34d10201b0089f8ee4
     Pseudo is Norm-conserving, Zval =  1.0
     Generated by old ld1 code (numerical format)
     Using radial grid of 1076 points,  0 beta functions with:

     PseudoPot. # 5 for As read from file:
     ../pseudo/ncpp/As_ONCV_PBE-1.2.upf
     MD5 check sum: f455bf46e89b39f2ebbcf20cc3d72839
     Pseudo is Norm-conserving, Zval =  5.0
     Generated using ONCVPSP code by D. R. Hamann
     Using radial grid of 1358 points,  6 beta functions with:
                l(1) =   0
                l(2) =   0
                l(3) =   1
                l(4) =   1
                l(5) =   2
                l(6) =   2

     Mode symmetry, C_1 (1)     point group:

     k=gamma and q=gamma tricks are used


     Atomic displacements:
     There are 279 irreducible representations

     Representation     1      1 modes - Calculated using asr

     Representation     2      1 modes - Calculated using asr

     Representation     3      1 modes - Calculated using asr

     Representation     4      1 modes -A  To be done

     Representation     5      1 modes -A  To be done

     Representation     6      1 modes -A  To be done

     Representation     7      1 modes -A  To be done

     Representation     8      1 modes -A  To be done

     Representation     9      1 modes -A  To be done

     Representation    10      1 modes -A  To be done

     Representation    11      1 modes -A  To be done

     Representation    12      1 modes -A  To be done

     Representation    13      1 modes -A  To be done

     Representation    14      1 modes -A  To be done

     Representation    15      1 modes -A  To be done

     Representation    16      1 modes -A  To be done

     Representation    17      1 modes -A  To be done

     Representation    18      1 modes -A  To be done

     Representation    19      1 modes -A  To be done

     Representation    20      1 modes -A  To be done

     Representation    21      1 modes -A  To be done

     Representation    22      1 modes -A  To be done

     Representation    23      1 modes -A  To be done

     Representation    24      1 modes -A  To be done

     Representation    25      1 modes -A  To be done

     Representation    26      1 modes -A  To be done

     Representation    27      1 modes -A  To be done

     Representation    28      1 modes -A  To be done

     Representation    29      1 modes -A  To be done

     Representation    30      1 modes -A  To be done

     Representation    31      1 modes -A  To be done

     Representation    32      1 modes -A  To be done

     Representation    33      1 modes -A  To be done

     Representation    34      1 modes -A  To be done

     Representation    35      1 modes -A  To be done

     Representation    36      1 modes -A  To be done

     Representation    37      1 modes -A  To be done

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     Representation   152      1 modes -A  To be done

     Representation   153      1 modes -A  To be done

     Representation   154      1 modes -A  To be done

     Representation   155      1 modes -A  To be done

     Representation   156      1 modes -A  To be done

     Representation   157      1 modes -A  To be done

     Representation   158      1 modes -A  To be done

     Representation   159      1 modes -A  To be done

     Representation   160      1 modes -A  To be done

     Representation   161      1 modes -A  To be done

     Representation   162      1 modes -A  To be done

     Representation   163      1 modes -A  To be done

     Representation   164      1 modes -A  To be done

     Representation   165      1 modes -A  To be done

     Representation   166      1 modes -A  To be done

     Representation   167      1 modes -A  To be done

     Representation   168      1 modes -A  To be done

     Representation   169      1 modes -A  To be done

     Representation   170      1 modes -A  To be done

     Representation   171      1 modes -A  To be done

     Representation   172      1 modes -A  To be done

     Representation   173      1 modes -A  To be done

     Representation   174      1 modes -A  To be done

     Representation   175      1 modes -A  To be done

     Representation   176      1 modes -A  To be done

     Representation   177      1 modes -A  To be done

     Representation   178      1 modes -A  To be done

     Representation   179      1 modes -A  To be done

     Representation   180      1 modes -A  To be done

     Representation   181      1 modes -A  To be done

     Representation   182      1 modes -A  To be done

     Representation   183      1 modes -A  To be done

     Representation   184      1 modes -A  To be done

     Representation   185      1 modes -A  To be done

     Representation   186      1 modes -A  To be done

     Representation   187      1 modes -A  To be done

     Representation   188      1 modes -A  To be done

     Representation   189      1 modes -A  To be done

     Representation   190      1 modes -A  To be done

     Representation   191      1 modes -A  To be done

     Representation   192      1 modes -A  To be done

     Representation   193      1 modes -A  To be done

     Representation   194      1 modes -A  To be done

     Representation   195      1 modes -A  To be done

     Representation   196      1 modes -A  To be done

     Representation   197      1 modes -A  To be done

     Representation   198      1 modes -A  To be done

     Representation   199      1 modes -A  To be done

     Representation   200      1 modes -A  To be done

     Representation   201      1 modes -A  To be done

     Representation   202      1 modes -A  To be done

     Representation   203      1 modes -A  To be done

     Representation   204      1 modes -A  To be done

     Representation   205      1 modes -A  To be done

     Representation   206      1 modes -A  To be done

     Representation   207      1 modes -A  To be done

     Representation   208      1 modes -A  To be done

     Representation   209      1 modes -A  To be done

     Representation   210      1 modes -A  To be done

     Representation   211      1 modes -A  To be done

     Representation   212      1 modes -A  To be done

     Representation   213      1 modes -A  To be done

     Representation   214      1 modes -A  To be done

     Representation   215      1 modes -A  To be done

     Representation   216      1 modes -A  To be done

     Representation   217      1 modes -A  To be done

     Representation   218      1 modes -A  To be done

     Representation   219      1 modes -A  To be done

     Representation   220      1 modes -A  To be done

     Representation   221      1 modes -A  To be done

     Representation   222      1 modes -A  To be done

     Representation   223      1 modes -A  To be done

     Representation   224      1 modes -A  To be done

     Representation   225      1 modes -A  To be done

     Representation   226      1 modes -A  To be done

     Representation   227      1 modes -A  To be done

     Representation   228      1 modes -A  To be done

     Representation   229      1 modes -A  To be done

     Representation   230      1 modes -A  To be done

     Representation   231      1 modes -A  To be done

     Representation   232      1 modes -A  To be done

     Representation   233      1 modes -A  To be done

     Representation   234      1 modes -A  To be done

     Representation   235      1 modes -A  To be done

     Representation   236      1 modes -A  To be done

     Representation   237      1 modes -A  To be done

     Representation   238      1 modes -A  To be done

     Representation   239      1 modes -A  To be done

     Representation   240      1 modes -A  To be done

     Representation   241      1 modes -A  To be done

     Representation   242      1 modes -A  To be done

     Representation   243      1 modes -A  To be done

     Representation   244      1 modes -A  To be done

     Representation   245      1 modes -A  To be done

     Representation   246      1 modes -A  To be done

     Representation   247      1 modes -A  To be done

     Representation   248      1 modes -A  To be done

     Representation   249      1 modes -A  To be done

     Representation   250      1 modes -A  To be done

     Representation   251      1 modes -A  To be done

     Representation   252      1 modes -A  To be done

     Representation   253      1 modes -A  To be done

     Representation   254      1 modes -A  To be done

     Representation   255      1 modes -A  To be done

     Representation   256      1 modes -A  To be done

     Representation   257      1 modes -A  To be done

     Representation   258      1 modes -A  To be done

     Representation   259      1 modes -A  To be done

     Representation   260      1 modes -A  To be done

     Representation   261      1 modes -A  To be done

     Representation   262      1 modes -A  To be done

     Representation   263      1 modes -A  To be done

     Representation   264      1 modes -A  To be done

     Representation   265      1 modes -A  To be done

     Representation   266      1 modes -A  To be done

     Representation   267      1 modes -A  To be done

     Representation   268      1 modes -A  To be done

     Representation   269      1 modes -A  To be done

     Representation   270      1 modes -A  To be done

     Representation   271      1 modes -A  To be done

     Representation   272      1 modes -A  To be done

     Representation   273      1 modes -A  To be done

     Representation   274      1 modes -A  To be done

     Representation   275      1 modes -A  To be done

     Representation   276      1 modes -A  To be done

     Representation   277      1 modes -A  To be done

     Representation   278      1 modes -A  To be done

     Representation   279      1 modes -A  To be done



     Atomic wfc used for the DFT+U projector are NOT orthogonalized

     Calculating the dnsbare matrix...
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[57415,1],2]
  Exit code:    174
--------------------------------------------------------------------------


________________________________
Shaofeng Wang
Ph.D
Email: wangshaofeng at iae.ac.cn
Key Laboratory of Pollution Ecology and Environmental Engineering
Institute of Applied Ecology
Chinese Academy of Sciences
China

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