[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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