HI developers and users,
I am following the steps in the recent EPW tutorial for transport properties.
I am getting this kind of error (corrupted size vs. prev_size) (Please see the output and input files below. Can you please suggest how may I get rid of such error?
I was suggested to do the following:
The error you are getting is an internal memory chunk error (nor really an error in EPW) indicating that the code tried to write out-of-bound. Can you provide more information such as how many bands are there in the disentanglement window because this error has occurred at the wannierization step? Also, your nscf output. Try a run without bands_skipped and see if it works.
I tried running without bands_skipped but got the same error. Also, I do not know how may I check how many bands in disentanglement window? Can you please suggest to me how may I fix this error?
I am attaching the output files here.
Thank you
Best
RIjan
Input files are:
##################################################### NSCF ###############
&CONTROL
calculation = 'nscf'
pseudo_dir = '/lustre/scratch4/turquoise/rkarkee/pseudo_pbe'
outdir = './'
prefix = 'scf'
wf_collect=.true.
nstep=200
/
&SYSTEM
ecutwfc = 70,
ibrav = 0,
nat = 12,
ntyp = 2,
lspinorb=.true.
noncolin = .true.
vdw_corr='Grimme-D2'
nbnd=200
/
&ELECTRONS
conv_thr = 1.00000e-10
electron_maxstep = 200
mixing_beta = 0.2
diagonalization = "david"
/
&IONS
ion_dynamics='fire'
/
&CELL
!cell_dofree= '2Dxy'
press_conv_thr=0.01
/
ATOMIC_SPECIES
Hf 178.49 Hf.upf
Te 127.60 Te.upf
CELL_PARAMETERS (angstrom)
1.986290526 7.133125762 0.000000000
-1.986290526 7.133125762 0.000000000
0.000000000 0.000000000 13.590793271
ATOMIC_POSITIONS (crystal)
Hf 0.8185156643 0.8185156643 0.7500000000
Hf 0.1814843357 0.1814843357 0.2500000000
Te 0.7081381988 0.7081381988 0.5663333564
Te 0.2918618012 0.2918618012 0.0663333564
Te 0.7081381988 0.7081381988 0.9336666436
Te 0.2918618012 0.2918618012 0.4336666436
Te 0.4351577475 0.4351577475 0.8531097652
Te 0.5648422525 0.5648422525 0.3531097652
Te 0.4351577475 0.4351577475 0.6468902348
Te 0.5648422525 0.5648422525 0.1468902348
Te 0.1625555034 0.1625555034 0.7500000000
Te 0.8374444966 0.8374444966 0.2500000000
K_POINTS crystal
32
0.00000000 0.00000000 0.00000000 3.125000e-02
0.00000000 0.00000000 0.50000000 3.125000e-02
0.00000000 0.25000000 0.00000000 3.125000e-02
0.00000000 0.25000000 0.50000000 3.125000e-02
0.00000000 0.50000000 0.00000000 3.125000e-02
0.00000000 0.50000000 0.50000000 3.125000e-02
0.00000000 0.75000000 0.00000000 3.125000e-02
0.00000000 0.75000000 0.50000000 3.125000e-02
0.25000000 0.00000000 0.00000000 3.125000e-02
0.25000000 0.00000000 0.50000000 3.125000e-02
0.25000000 0.25000000 0.00000000 3.125000e-02
0.25000000 0.25000000 0.50000000 3.125000e-02
0.25000000 0.50000000 0.00000000 3.125000e-02
0.25000000 0.50000000 0.50000000 3.125000e-02
0.25000000 0.75000000 0.00000000 3.125000e-02
0.25000000 0.75000000 0.50000000 3.125000e-02
0.50000000 0.00000000 0.00000000 3.125000e-02
0.50000000 0.00000000 0.50000000 3.125000e-02
0.50000000 0.25000000 0.00000000 3.125000e-02
0.50000000 0.25000000 0.50000000 3.125000e-02
0.50000000 0.50000000 0.00000000 3.125000e-02
0.50000000 0.50000000 0.50000000 3.125000e-02
0.50000000 0.75000000 0.00000000 3.125000e-02
0.50000000 0.75000000 0.50000000 3.125000e-02
0.75000000 0.00000000 0.00000000 3.125000e-02
0.75000000 0.00000000 0.50000000 3.125000e-02
0.75000000 0.25000000 0.00000000 3.125000e-02
0.75000000 0.25000000 0.50000000 3.125000e-02
0.75000000 0.50000000 0.00000000 3.125000e-02
0.75000000 0.50000000 0.50000000 3.125000e-02
0.75000000 0.75000000 0.00000000 3.125000e-02
0.75000000 0.75000000 0.50000000 3.125000e-02
~
################################################################# Ph calculation
&inputph
recover=.true.
tr2_ph=1.0d-15,
prefix='scf',
amass(1)=178.49,
amass(2)= 127.60,
outdir='./',
fildyn='HfTe5.dyn.xml',
fildvscf='dvscf',
ldisp=.true.
epsil=.true.
nq1=4,
nq2=4,
nq3=2,
nmix_ph=12
/
################################################################### epw1.inp #####################
&inputepw
prefix='scf'
outdir='./'
elph=.true.
epbwrite=.true.
epbread=.false.
epwwrite=.true.
epwread=.false.
etf_mem=1
lpolar=.true.
vme='dipole'
nbndsub=3
bands_skipped='exclude_bands=1-178, 190-200'
wannierize=.true.
num_iter=50000
iprint=2
dis_win_max=12
dis_win_min=-1
proj(1)='Te:p'
proj(2)='Hf:d'
wdata(1)='bands_plot = .true.'
wdata(2)='begin kpoint_path'
wdata(3)=' X 0.5 0.0 0.0 G 0.0 0.0 0.0 '
wdata(4)=' G 0.0 0.0 0.0 X 0.5 0.0 0.0 '
wdata(5)=' Y 0.0 0.5 0.0 G 0.0 0.0 0.0 '
wdata(6)=' G 0.0 0.0 0.0 Y 0.0 0.5 0.0 '
wdata(7)=' Z 0.0 0.0 0.5 G 0.0 0.0 0.0 '
wdata(8)=' G 0.0 0.0 0.0 Z 0.0 0.0 0.5 '
wdata(9)='end kpoint_path'
wdata(10)='bands_plot_format = gnuplot'
wdata(11)='guiding_centres=.true.'
wdata(12)='dis_num_iter =5000'
wdata(13)='num_print_cycles =10'
wdata(14)='dis_mix_ratio =1.0'
wdata(15)='conv_tol=1E-12'
wdata(16)='use_ws_distance =T'
fsthick =100
degaussw=0.001
dvscf_dir='./save'
band_plot=.true.
filkf='./XGYGZ.txt'
filqf='./XGYGZ.txt'
nk1=4
nk2=4
nk3=2
nq1=4
nq2=4
nq3=2
/
##################################################################################### epw1.out
-sh//yy+` +yy +yy -+h+-oyy
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`.-.` `yh+ -oyyyo. `/syys: oys `.`
`/+ssys+-` `sh+ ` oys` .:osyo`
-yh- ./syyooyo` .sys+/oyo--yh/
`yy+ .-:-. `-/+/:` -sh-
/yh. oys
``..---hho---------` .---------..` `.-----.` -hd+---.
`./osmNMMMMMMMMMMMMMMMs. +NNMMMMMMMMNNmh+. yNMMMMMNm- oNMMMMMNmo++:`
+sy--/sdMMMhyyyyyyyNMMh- .oyNMMmyyyyyhNMMm+` -yMMMdyyo:` .oyyNMMNhs+syy`
-yy/ /MMM+.`-+/``mMMy- `mMMh:`````.dMMN:` `MMMy-`-dhhy```mMMy:``+hs
-yy+` /MMMo:-mMM+`-oo/. mMMh: `dMMN/` dMMm:`dMMMMy..MMMo-.+yo`
.sys`/MMMMNNMMMs- mMMmyooooymMMNo: oMMM/sMMMMMM++MMN//oh:
`sh+/MMMhyyMMMs- `-` mMMMMMMMMMNmy+-` -MMMhMMMsmMMmdMMd/yy+
`-/+++oyy-/MMM+.`/hh/.`mNm:` mMMd+/////:-.` NMMMMMd/:NMMMMMy:/yyo/:.`
+os+//:-..-oMMMo:--:::-/MMMo. .-mMMd+---` hMMMMN+. oMMMMMo. `-+osyso:`
syo `mNMMMMMNNNNNNNNMMMo.oNNMMMMMNNNN:` +MMMMs:` dMMMN/` ``:syo
/yh` :syyyyyyyyyyyyyyyy+.`+syyyyyyyyo:` .oyys:` .oyys:` +yh
-yh- ```````````````` ````````` `` `` oys
-+h/------------------------::::::::://////++++++++++++++++++++++///////::::/yd:
shdddddddddddddddddddddddddddddhhhhhhhhyyyyyssssssssssssssssyyyyyyyhhhhhhhddddh`
S. Ponce, E. R. Margine, C. Verdi, and F. Giustino,
Comput. Phys. Commun. 209, 116 (2016)
Program EPW v.5.7 starts on 16Jul2023 at 11:53:28
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);
"P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
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 32 processors
MPI processes distributed on 1 nodes
K-points division: npool = 32
500985 MiB available memory on the printing compute node when the environment starts
Waiting for input...
Reading input from standard input
Title line not specified: using 'default'.
WARNING: The specified dis_win_min is ignored.
You should instead use bands_skipped = 'exclude_bands = ...'
to control the lower bound of band manifold.
No temperature supplied. Setting temps(:) to 300 K.
Reading xml data from directory:
./scf.save/
IMPORTANT: XC functional enforced from input :
Exchange-correlation= PBE
( 1 4 3 4 0 0 0)
Any further DFT definition will be discarded
Please, verify this is what you really want
G-vector sticks info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Sum 2245 2245 657 205449 205449 32301
Using Slab Decomposition
Reading collected, re-writing distributed wavefunctions
default
bravais-lattice index = 0
lattice parameter (a_0) = 13.9925 a.u.
unit-cell volume = 2598.9268 (a.u.)^3
number of atoms/cell = 12
number of atomic types = 2
kinetic-energy cut-off = 70.0000 Ry
charge density cut-off = 280.0000 Ry
Exchange-correlation= PBE
( 1 4 3 4 0 0 0)
Non magnetic calculation with spin-orbit
celldm(1)= 13.99250 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 a_0)
a(1) = ( 0.2683 0.9633 0.0000 )
a(2) = ( -0.2683 0.9633 0.0000 )
a(3) = ( 0.0000 0.0000 1.8355 )
reciprocal axes: (cart. coord. in units 2 pi/a_0)
b(1) = ( 1.8639 0.5190 -0.0000 )
b(2) = ( -1.8639 0.5190 0.0000 )
b(3) = ( 0.0000 -0.0000 0.5448 )
Atoms inside the unit cell:
Cartesian axes
site n. atom mass positions (a_0 units)
1 Hf 178.4900 tau( 1) = ( -0.00000 1.57703 1.37661 )
2 Hf 178.4900 tau( 2) = ( 0.00000 0.34967 0.45887 )
3 Te 127.6000 tau( 3) = ( -0.00000 1.36437 1.03949 )
4 Te 127.6000 tau( 4) = ( 0.00000 0.56233 0.12175 )
5 Te 127.6000 tau( 5) = ( -0.00000 1.36437 1.71372 )
6 Te 127.6000 tau( 6) = ( 0.00000 0.56233 0.79598 )
7 Te 127.6000 tau( 7) = ( -0.00000 0.83842 1.56586 )
8 Te 127.6000 tau( 8) = ( -0.00000 1.08828 0.64812 )
9 Te 127.6000 tau( 9) = ( -0.00000 0.83842 1.18735 )
10 Te 127.6000 tau(10) = ( -0.00000 1.08828 0.26961 )
11 Te 127.6000 tau(11) = ( 0.00000 0.31320 1.37661 )
12 Te 127.6000 tau(12) = ( -0.00000 1.61350 0.45887 )
9 Sym.Ops. (with q -> -q+G )
G cutoff = 1388.6385 ( 205449 G-vectors) FFT grid: ( 75, 75,144)
number of k points= 32
cart. coord. in units 2pi/a_0
k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0312500
k( 2) = ( 0.0000000 0.0000000 0.2724092), wk = 0.0312500
k( 3) = ( -0.4659763 0.1297558 0.0000000), wk = 0.0312500
k( 4) = ( -0.4659763 0.1297558 0.2724092), wk = 0.0312500
k( 5) = ( -0.9319526 0.2595116 0.0000000), wk = 0.0312500
k( 6) = ( -0.9319526 0.2595116 0.2724092), wk = 0.0312500
k( 7) = ( -1.3979289 0.3892673 0.0000000), wk = 0.0312500
k( 8) = ( -1.3979289 0.3892673 0.2724092), wk = 0.0312500
k( 9) = ( 0.4659763 0.1297558 0.0000000), wk = 0.0312500
k( 10) = ( 0.4659763 0.1297558 0.2724092), wk = 0.0312500
k( 11) = ( 0.0000000 0.2595116 0.0000000), wk = 0.0312500
k( 12) = ( 0.0000000 0.2595116 0.2724092), wk = 0.0312500
k( 13) = ( -0.4659763 0.3892673 0.0000000), wk = 0.0312500
k( 14) = ( -0.4659763 0.3892673 0.2724092), wk = 0.0312500
k( 15) = ( -0.9319526 0.5190231 0.0000000), wk = 0.0312500
k( 16) = ( -0.9319526 0.5190231 0.2724092), wk = 0.0312500
k( 17) = ( 0.9319526 0.2595116 0.0000000), wk = 0.0312500
k( 18) = ( 0.9319526 0.2595116 0.2724092), wk = 0.0312500
k( 19) = ( 0.4659763 0.3892673 0.0000000), wk = 0.0312500
k( 20) = ( 0.4659763 0.3892673 0.2724092), wk = 0.0312500
k( 21) = ( 0.0000000 0.5190231 0.0000000), wk = 0.0312500
k( 22) = ( 0.0000000 0.5190231 0.2724092), wk = 0.0312500
k( 23) = ( -0.4659763 0.6487789 0.0000000), wk = 0.0312500
k( 24) = ( -0.4659763 0.6487789 0.2724092), wk = 0.0312500
k( 25) = ( 1.3979289 0.3892673 0.0000000), wk = 0.0312500
k( 26) = ( 1.3979289 0.3892673 0.2724092), wk = 0.0312500
k( 27) = ( 0.9319526 0.5190231 0.0000000), wk = 0.0312500
k( 28) = ( 0.9319526 0.5190231 0.2724092), wk = 0.0312500
k( 29) = ( 0.4659763 0.6487789 0.0000000), wk = 0.0312500
k( 30) = ( 0.4659763 0.6487789 0.2724092), wk = 0.0312500
k( 31) = ( 0.0000000 0.7785347 0.0000000), wk = 0.0312500
k( 32) = ( 0.0000000 0.7785347 0.2724092), wk = 0.0312500
PseudoPot. # 1 for Hf read from file:
/lustre/scratch4/turquoise/rkarkee/pseudo_pbe/Hf.upf
MD5 check sum: bde2e012f831674a856dc5e85ca34ee8
Pseudo is Norm-conserving + core correction, Zval = 12.0
Generated using ONCVPSP code by D. R. Hamann
Using radial grid of 1716 points, 14 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
l(5) = 1
l(6) = 1
l(7) = 2
l(8) = 2
l(9) = 2
l(10) = 2
l(11) = 3
l(12) = 3
l(13) = 3
l(14) = 3
PseudoPot. # 2 for Te read from file:
/lustre/scratch4/turquoise/rkarkee/pseudo_pbe/Te.upf
MD5 check sum: d198e370297ac1d7edee156d0fe975c4
Pseudo is Norm-conserving + core correction, Zval = 16.0
Generated using ONCVPSP code by D. R. Hamann
Using radial grid of 1324 points, 10 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
l(5) = 1
l(6) = 1
l(7) = 2
l(8) = 2
l(9) = 2
l(10) = 2
EPW : 2.58s CPU 4.63s WALL
EPW : 4.87s CPU 6.93s WALL
-------------------------------------------------------------------
Wannierization on 4 x 4 x 2 electronic grid
-------------------------------------------------------------------
Spin CASE ( non-collinear )
Initializing Wannier90
Initial Wannier projections
( 0.70814 0.70814 0.56633) : l = 1 mr = 1
( 0.70814 0.70814 0.56633) : l = 1 mr = 1
( 0.70814 0.70814 0.56633) : l = 1 mr = 2
- Number of bands is ( 11)
- Number of total bands is (200)
- Number of excluded bands is (189)
- Number of wannier functions is ( 3)
- All guiding functions are given
Reading data about k-point neighbours
- All neighbours are found
AMN
k points = 32 in 32 pools
1 of 1 on ionode
corrupted size vs. prev_size
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
corrupted size vs. prev_size
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
corrupted size vs. prev_size
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
corrupted size vs. prev_size
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
corrupted size vs. prev_size
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
corrupted size vs. prev_size
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
corrupted size vs. prev_size
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
corrupted size vs. prev_size
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
corrupted size vs. prev_size
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
corrupted size vs. prev_size
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
corrupted size vs. prev_size
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 0x7f03d5c70d6f in ???
#1 0x7f03d5c70cdb in ???
#2 0x7f03d5c72374 in ???
#3 0x7f03d5cb6b06 in ???
#4 0x7f03d5cbeb89 in ???
#5 0x7f03d5cbf455 in ???
#6 0x7f03d5cc099a in ???
#7 0x5a11bb in ???
#8 0x5a8074 in ???
#9 0x420e5e in ???
How to fix corrupted size vs. prev_size error?
Moderator: stiwari
Re: How to fix corrupted size vs. prev_size error?
Hi,
Looking at the input, it seems you provided an initial project of: proj(1)='Te:p' and proj(2)='Hf:d'. Note that this needs to match the number of Wannier functions you give the code (nbndsub). With these projections, 10 Te, and 2 Hf, I believe that gives a total of 80 electrons (40 orbitals), but you only gave it 3 Wannier functions.
You can either increase nbndsub to match the Wannerization (set nbndsub=40), or you can change the projection. One way to test is to simply replace your projection by proj(1)='random' and see if the problem goes away, or you can provide the explicit Wannier centers. I'd suggest check the Wannier90 user guide: https://wannier.org/support/. Note that you could also try auto projection in Wannier90, see: https://docs.epw-code.org/doc/Inputs.ht ... rojections.
That being said, I suspect that in your case it may be very difficult to achieve good Wannierization using only 3 Wannier functions. You may want to play around this and increase it if necessary.
Best!
Xiao
Looking at the input, it seems you provided an initial project of: proj(1)='Te:p' and proj(2)='Hf:d'. Note that this needs to match the number of Wannier functions you give the code (nbndsub). With these projections, 10 Te, and 2 Hf, I believe that gives a total of 80 electrons (40 orbitals), but you only gave it 3 Wannier functions.
You can either increase nbndsub to match the Wannerization (set nbndsub=40), or you can change the projection. One way to test is to simply replace your projection by proj(1)='random' and see if the problem goes away, or you can provide the explicit Wannier centers. I'd suggest check the Wannier90 user guide: https://wannier.org/support/. Note that you could also try auto projection in Wannier90, see: https://docs.epw-code.org/doc/Inputs.ht ... rojections.
That being said, I suspect that in your case it may be very difficult to achieve good Wannierization using only 3 Wannier functions. You may want to play around this and increase it if necessary.
Best!
Xiao