[Pw_forum] How to deal with the error (bad termination exit code: 9) in phonon calculation?

Paolo Giannozzi p.giannozzi at gmail.com
Thu May 28 11:02:32 CEST 2015


Error 9 = SIGKILL = some serious error. See the FAQ for "Segmentation
fault", it's nmore or less the same

Paolo

On Thu, May 28, 2015 at 9:44 AM, liyincumt at gmail.com <liyincumt at gmail.com>
wrote:

> Dear QE developers,
>
> I am trying to calculate the IR spectrum of a compound. First, I run
> ‘relax’ calculation and got a successful convergence. After that, I started
> a phonon calculation. I always got the error (bad termination exit code:
> 9). What does this “9” mean? How could I deal with it?
>
> Thanks a lot in advance!
>
>
> Below are my input files.
>
>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
>
> &CONTROL
>
>                        title = 'data_7107445-arginine' ,
>
>                  calculation = 'relax' ,
>
>                       outdir = '/home/calc/pwscf_calc' ,
>
>                       wfcdir = '/home/calc/pwscf_calc' ,
>
>                   pseudo_dir = '/home/calc/espresso-5.1.1/pseudo/' ,
>
>                       prefix = 'data_7107445-arginine' ,
>
>                etot_conv_thr = 5.0d-7 ,
>
>                forc_conv_thr = 5.0d-4 ,
>
>  /
>
>  &SYSTEM
>
>                        ibrav = -12,
>
>                    celldm(1) = 18.437112,
>
>                    celldm(2) = 1.64229,
>
>                    celldm(3) = 0.571978,
>
>                    celldm(5) = -0.1391731,
>
>                          nat = 52,
>
>                         ntyp = 4,
>
>                      ecutwfc = 60 ,
>
>                      ecutrho = 600 ,
>
>  /
>
>  &ELECTRONS
>
>                     conv_thr = 1.0d-8 ,
>
>                  mixing_beta = 0.7 ,
>
>              diagonalization = 'david' ,
>
>  /
>
>  &IONS
>
>                 ion_dynamics = 'bfgs' ,
>
>  /
>
> ATOMIC_SPECIES
>
>     H    1.00794  H.pbe-rrkjus.UPF
>
>     C   12.01070  C.pbe-rrkjus.UPF
>
>     N   14.00670  N.pbe-rrkjus.UPF
>
>     O   15.99940  O.pbe-rrkjus.UPF
>
> ATOMIC_POSITIONS alat
>
>     O      0.006300000    0.868200000   -0.013020000
>
>     O      0.227050000    0.848140000    0.009000000
>
>     C      0.113660000    0.830180000    0.075430000
>
>     N     -0.033250000    0.760590000    0.333950000
>
>     H     -0.054180000    0.815120000    0.399610000
>
>     H     -0.037610000    0.717490000    0.457260000
>
>     H      0.174350000    0.773830000    0.406070000
>
>     C      0.106340000    0.762260000    0.263410000
>
>     H      0.213720000    0.684400000    0.060870000
>
>     H      0.164840000    0.638380000    0.288880000
>
>     C      0.137820000    0.678170000    0.157380000
>
>     H     -0.057580000    0.626040000    0.098650000
>
>     H     -0.031440000    0.691400000   -0.106990000
>
>     C      0.009770000    0.646120000   -0.002820000
>
>     C      0.050230000    0.574960000   -0.158890000
>
>     H      0.112570000    0.595930000   -0.268380000
>
>     H      0.097240000    0.531350000   -0.055010000
>
>     N     -0.075080000    0.540090000   -0.301670000
>
>     H     -0.166460000    0.552870000   -0.257220000
>
>     C     -0.064600000    0.493230000   -0.493500000
>
>     N      0.058320000    0.475550000   -0.553220000
>
>     H      0.142080000    0.497130000   -0.455420000
>
>     H      0.065820000    0.440830000   -0.695370000
>
>     N     -0.177240000    0.464120000   -0.625370000
>
>     H     -0.268580000    0.477200000   -0.581240000
>
>     H     -0.169570000    0.429410000   -0.767470000
>
>     O      0.463600000   -0.043890000    0.555130000
>
>     O      0.676180000   -0.009900000    0.529510000
>
>     C      0.549490000   -0.001970000    0.458450000
>
>     N      0.351640000    0.045210000    0.173950000
>
>     H      0.337800000   -0.009980000    0.098730000
>
>     H      0.317190000    0.088270000    0.055990000
>
>     H      0.551850000    0.048920000    0.119150000
>
>     C      0.499980000    0.058530000    0.254810000
>
>     H      0.616920000    0.152610000    0.434850000
>
>     H      0.513740000    0.185840000    0.206620000
>
>     C      0.523500000    0.147600000    0.345010000
>
>     H      0.326790000    0.177670000    0.413310000
>
>     H      0.412360000    0.124580000    0.626920000
>
>     C      0.417650000    0.169790000    0.510300000
>
>     C      0.461390000    0.250030000    0.645100000
>
>     H      0.550340000    0.241340000    0.747570000
>
>     H      0.470870000    0.294590000    0.528260000
>
>     N      0.356090000    0.273940000    0.797270000
>
>     H      0.266500000    0.245270000    0.778340000
>
>     C      0.384690000    0.331760000    0.966840000
>
>     N      0.285130000    0.362190000    1.078710000
>
>     H      0.189970000    0.342050000    1.036490000
>
>     H      0.306350000    0.404930000    1.204040000
>
>     N      0.512780000    0.359050000    1.024210000
>
>     H      0.586910000    0.336560000    0.941400000
>
>     H      0.533710000    0.401790000    1.149600000
>
> K_POINTS automatic
>
>   1 1 2   0 0 0
>
>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
>
> normal modes for 7107445-arginine
>
>  &inputph
>
>   recover=.true.,
>
>   prefix='data_7107445-arginine',
>
>   epsil=.true.,
>
>   fildyn='dmat.arginine',
>
>   tr2_ph=1.0d-14,
>
>   amass(1)=1.00794,
>
>   amass(2)=12.01070,
>
>   amass(3)=14.00670,
>
>   amass(4)=15.99940,
>
>   outdir='/home/calc/pwscf_calc/relax/60-1,1,2'
>
>  /
>
> 0.0   0.0 0.0
>
>
>
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
>
>
>
>    .....
>
>      Atomic displacements:
>
>      There are 156 irreducible representations
>
>
>
>      Representation     1      1 modes -A  To be done
>
>
>
>      Representation     2      1 modes -A  To be done
>
>
>
>      Representation     3      1 modes -A  To be done
>
>
>
>      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
>
>
>
>      Representation    38      1 modes -A  To be done
>
>
>
>      Representation    39      1 modes -A  To be done
>
>
>
>      Representation    40      1 modes -A  To be done
>
>
>
>      Representation    41      1 modes -A  To be done
>
>
>
>      Representation    42      1 modes -A  To be done
>
>
>
>      Representation    43      1 modes -A  To be done
>
>
>
>      Representation    44      1 modes -A  To be done
>
>
>
>      Representation    45      1 modes -A  To be done
>
>
>
>      Representation    46      1 modes -A  To be done
>
>
>
>      Representation    47      1 modes -A  To be done
>
>
>
>      Representation    48      1 modes -A  To be done
>
>
>
>      Representation    49      1 modes -A  To be done
>
>
>
>      Representation    50      1 modes -A  To be done
>
>
>
>      Representation    51      1 modes -A  To be done
>
>
>
>      Representation    52      1 modes -A  To be done
>
>
>
>      Representation    53      1 modes -A  To be done
>
>
>
>      Representation    54      1 modes -A  To be done
>
>
>
>      Representation    55      1 modes -A  To be done
>
>
>
>      Representation    56      1 modes -A  To be done
>
>
>
>      Representation    57      1 modes -A  To be done
>
>
>
>      Representation    58      1 modes -A  To be done
>
>
>
>      Representation    59      1 modes -A  To be done
>
>
>
>      Representation    60      1 modes -A  To be done
>
>
>
>      Representation    61      1 modes -A  To be done
>
>
>
>      Representation    62      1 modes -A  To be done
>
>
>
>      Representation    63      1 modes -A  To be done
>
>
>
>      Representation    64      1 modes -A  To be done
>
>
>
>      Representation    65      1 modes -A  To be done
>
>
>
>      Representation    66      1 modes -A  To be done
>
>
>
>      Representation    67      1 modes -A  To be done
>
>
>
>      Representation    68      1 modes -A  To be done
>
>
>
>      Representation    69      1 modes -A  To be done
>
>
>
>      Representation    70      1 modes -A  To be done
>
>
>
>      Representation    71      1 modes -A  To be done
>
>
>
>      Representation    72      1 modes -A  To be done
>
>
>
>      Representation    73      1 modes -A  To be done
>
>
>
>      Representation    74      1 modes -A  To be done
>
>
>
>      Representation    75      1 modes -A  To be done
>
>
>
>      Representation    76      1 modes -A  To be done
>
>
>
>      Representation    77      1 modes -A  To be done
>
>
>
>      Representation    78      1 modes -A  To be done
>
>
>
>      Representation    79      1 modes -A  To be done
>
>
>
>      Representation    80      1 modes -A  To be done
>
>
>
>      Representation    81      1 modes -A  To be done
>
>
>
>      Representation    82      1 modes -A  To be done
>
>
>
>      Representation    83      1 modes -A  To be done
>
>
>
>      Representation    84      1 modes -A  To be done
>
>
>
>      Representation    85      1 modes -A  To be done
>
>
>
>      Representation    86      1 modes -A  To be done
>
>
>
>      Representation    87      1 modes -A  To be done
>
>
>
>      Representation    88      1 modes -A  To be done
>
>
>
>      Representation    89      1 modes -A  To be done
>
>
>
>      Representation    90      1 modes -A  To be done
>
>
>
>      Representation    91      1 modes -A  To be done
>
>
>
>      Representation    92      1 modes -A  To be done
>
>
>
>      Representation    93      1 modes -A  To be done
>
>
>
>      Representation    94      1 modes -A  To be done
>
>
>
>      Representation    95      1 modes -A  To be done
>
>
>
>      Representation    96      1 modes -A  To be done
>
>
>
>      Representation    97      1 modes -A  To be done
>
>
>
>      Representation    98      1 modes -A  To be done
>
>
>
>      Representation    99      1 modes -A  To be done
>
>
>
>      Representation   100      1 modes -A  To be done
>
>
>
>      Representation   101      1 modes -A  To be done
>
>
>
>      Representation   102      1 modes -A  To be done
>
>
>
>      Representation   103      1 modes -A  To be done
>
>
>
>      Representation   104      1 modes -A  To be done
>
>
>
>      Representation   105      1 modes -A  To be done
>
>
>
>      Representation   106      1 modes -A  To be done
>
>
>
>      Representation   107      1 modes -A  To be done
>
>
>
>      Representation   108      1 modes -A  To be done
>
>
>
>      Representation   109      1 modes -A  To be done
>
>
>
>      Representation   110      1 modes -A  To be done
>
>
>
>      Representation   111      1 modes -A  To be done
>
>
>
>      Representation   112      1 modes -A  To be done
>
>
>
>      Representation   113      1 modes -A  To be done
>
>
>
>      Representation   114      1 modes -A  To be done
>
>
>
>      Representation   115      1 modes -A  To be done
>
>
>
>      Representation   116      1 modes -A  To be done
>
>
>
>      Representation   117      1 modes -A  To be done
>
>
>
>      Representation   118      1 modes -A  To be done
>
>
>
>      Representation   119      1 modes -A  To be done
>
>
>
>      Representation   120      1 modes -A  To be done
>
>
>
>      Representation   121      1 modes -A  To be done
>
>
>
>      Representation   122      1 modes -A  To be done
>
>
>
>      Representation   123      1 modes -A  To be done
>
>
>
>      Representation   124      1 modes -A  To be done
>
>
>
>      Representation   125      1 modes -A  To be done
>
>
>
>      Representation   126      1 modes -A  To be done
>
>
>
>      Representation   127      1 modes -A  To be done
>
>
>
>      Representation   128      1 modes -A  To be done
>
>
>
>      Representation   129      1 modes -A  To be done
>
>
>
>      Representation   130      1 modes -A  To be done
>
>
>
>      Representation   131      1 modes -A  To be done
>
>
>
>      Representation   132      1 modes -A  To be done
>
>
>
>      Representation   133      1 modes -A  To be done
>
>
>
>      Representation   134      1 modes -A  To be done
>
>
>
>      Representation   135      1 modes -A  To be done
>
>
>
>      Representation   136      1 modes -A  To be done
>
>
>
>      Representation   137      1 modes -A  To be done
>
>
>
>      Representation   138      1 modes -A  To be done
>
>
>
>      Representation   139      1 modes -A  To be done
>
>
>
>      Representation   140      1 modes -A  To be done
>
>
>
>      Representation   141      1 modes -A  To be done
>
>
>
>      Representation   142      1 modes -A  To be done
>
>
>
>      Representation   143      1 modes -A  To be done
>
>
>
>      Representation   144      1 modes -A  To be done
>
>
>
>      Representation   145      1 modes -A  To be done
>
>
>
>      Representation   146      1 modes -A  To be done
>
>
>
>      Representation   147      1 modes -A  To be done
>
>
>
>      Representation   148      1 modes -A  To be done
>
>
>
>      Representation   149      1 modes -A  To be done
>
>
>
>      Representation   150      1 modes -A  To be done
>
>
>
>      Representation   151      1 modes -A  To be done
>
>
>
>      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
>
>
>
>
>
>
>
>
> ===================================================================================
>
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>
> =   EXIT CODE: 9
>
> =   CLEANING UP REMAINING PROCESSES
>
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>
>
> ===================================================================================
>
> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)
>
> This typically refers to a problem with your application.
>
> Please see the FAQ page for debugging suggestions
>
>
> ------------------------------
> Dr. Yin Li
> Department of Biophysics,Medical School, University of Pecs,
> No.12 Szigeti Street, Pecs, H-7624, HUNGARY
> Phone: +36-72-535271/36271
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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