[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