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

Vijay Amirtharaj A vijayamirtharajit at gmail.com
Thu May 28 11:39:22 CEST 2015


Hi Dr.Yin,

By seeing this message, we can't identy the issue. "YOUR APPLICATION
TERMINATED WITH THE EXIT STRING: Killed (signal 9)" may be this error
message printed by job scheduler.

So,do not run your job in baground, the output will print on your screen.
If there is any problem. That will print on your scree. You can solve the
problem. I do like that.

Thanks,
Vijay Amirtharaj A

System Administrator.
JNCASR,Jakkur,
Bangalore-64, India.

Vijay Amirtharaj A

On Thu, May 28, 2015 at 2:32 PM, Paolo Giannozzi <p.giannozzi at gmail.com>
wrote:

> 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
>>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20150528/9614683c/attachment.html>


More information about the users mailing list