segmentation fault occurred

[AmirhTalebi]

Dear epw users

I am using the latest version of epw.x to calculate superconducting temperature of FeSe compound. I am getting this error every time that i run (I even tried "iverbosity = 2 " commented). this is the error:

"forrtl: severe (174): SIGSEGV, segmentation fault occurred"

along with my input files for scf and nscf and epw:


&control
calculation='scf',
prefix='FeSe',
pseudo_dir = '../pp/',
outdir='./',
tprnfor = .true.,
tstress = .true.,
etot_conv_thr = 1.0d-5
forc_conv_thr = 1.0d-4
/
&system
ibrav = 0,
nat= 4,
ntyp = 2,
ecutwfc = 40
ecutrho = 400
smearing = 'mp' ! methfessel-paxton
occupations = 'smearing'
degauss = 0.02
/
&electrons
mixing_mode = 'plain'
mixing_beta = 0.7
conv_thr = 1.0d-10
/
ATOMIC_SPECIES
Fe 55.845 Fe.upf
Se 78.96 Se.upf
CELL_PARAMETERS {angstrom}
3.689 0.000 0.000
0.000 3.689 0.000
0.000 0.000 5.854
ATOMIC_POSITIONS crystal
Fe 0.0 0.0 0.0
Fe 0.5 0.5 0.0
Se 0.0 0.5 0.7648
Se 0.5 0.0 0.2352
K_POINTS AUTOMATIC
12 12 10 0 0 0
________---------____________nscf______________-------------------

&control
calculation='nscf',
prefix='FeSe',
pseudo_dir = '../pp/',
outdir='./',
tprnfor = .true.,
tstress = .true.,
etot_conv_thr = 1.0d-5
forc_conv_thr = 1.0d-4
/
&system
ibrav = 0,
nat= 4,
ntyp = 2,
ecutwfc = 40
ecutrho = 400
smearing = 'mp' ! methfessel-paxton
occupations = 'smearing'
degauss = 0.02
/
&electrons
diagonalization = 'david'
mixing_mode = 'plain'
mixing_beta = 0.7
conv_thr = 1.0d-10
/
ATOMIC_SPECIES
Fe 55.845 Fe.upf
Se 78.96 Se.upf
CELL_PARAMETERS {angstrom}
3.689 0.000 0.000
0.000 3.689 0.000
0.000 0.000 5.854
ATOMIC_POSITIONS crystal
Fe 0.0 0.0 0.0
Fe 0.5 0.5 0.0
Se 0.0 0.5 0.7648
Se 0.5 0.0 0.2352
K_POINTS crystal
512
0.00000000 0.00000000 0.00000000 1.953125e-03
0.00000000 0.00000000 0.12500000 1.953125e-03
....
_________________________----------------------------------__________________________epw_______

&inputepw
prefix = 'FeSe',
amass(1) = 55.845 , ! iron
amass(2) = 78.96 ! Selenium
outdir = './'

ep_coupling = .true.
elph = .true.
laniso = .true. ! anistropic
kmaps = .false.
epbwrite = .true.
epbread = .false.

epwwrite = .true.
epwread = .false.

etf_mem = 1

nbndsub = 5,
nbndskip = 0

wannierize = .true.
num_iter = 500
dis_froz_max= 8.8
proj(1) = 'Fe:d'
proj(2) = 'Se:sp3'

! iverbosity = 2


eps_acustic = 2.0 ! Lowest boundary for the
ephwrite = .true. ! Writes .ephmat files used when wliasberg = .true.

fsthick = 0.4 ! eV
eptemp = 300 ! K
degaussw = 0.10 ! eV
nsmear = 1
delta_smear = 0.04 ! eV

degaussq = 0.5 ! meV
nqstep = 500

eliashberg = .true.

laniso = .true.
limag = .true.
lpade = .true.

conv_thr_iaxis = 1.0d-4

wscut = 1.0 ! eV Upper limit over frequency integration/summation in the Elisashberg eq

nstemp = 1
tempsmin = 15.00
tempsmax = 60.00

nsiter = 500

muc = 0.16

dvscf_dir = '../phonons/save'

nk1 = 8
nk2 = 8
nk3 = 8

nq1 = 4
nq2 = 4
nq3 = 4

mp_mesh_k = .true.
nkf1 = 24
nkf2 = 24
nkf3 = 24

nqf1 = 24
nqf2 = 24
nqf3 = 24
/
18 cartesian
0.000000000 0.000000000 0.000000000
....

I would be thankful if any body could help me or give me as suggestion.


Best regards,
Amir T

[hlee]

Dear Amir T:

If you are referring to the most-recent official version of EPW v5.3, there are several incompatible changes in EPW v5.3 compared with the previous versions; for instance, nbndskip is not an input anymore.
Please check carefully the Releases page at https://docs.epw-code.org/doc/Releases.html .

If you are not using EPW v5.3, please let me know which version of EPW you are using.

Additionally, please post the full output of EPW so that we can identify where the error occurs.

Sincerely,

H. Lee

[AmirhTalebi]

Dear Lee

Thank you very much for your reply.
I am using "Program EPW v.5.1.0" version for epw with "Program PWSCF v.6.4.1" version for quantum espresso installed on our cluster.
Please find below the output of epw calculation as I really couldn't upload my full output (with erorr : "Invalid file extension: epw.out").

_____________________________________________epw.out_________________________________________-----
...
...
k( 509) = ( 0.8750000 0.8750000 0.3150837), wk = 0.0039062
k( 510) = ( 0.8750000 0.8750000 0.3938546), wk = 0.0039062
k( 511) = ( 0.8750000 0.8750000 0.4726256), wk = 0.0039062
k( 512) = ( 0.8750000 0.8750000 0.5513965), wk = 0.0039062

PseudoPot. # 1 for Fe read from file:
../pp/Fe.upf
MD5 check sum: b1fb9d3cb1d156aba92c681262384fac
Pseudo is Norm-conserving + core correction, Zval = 16.0
Generated using ONCVPSP code by D. R. Hamann
Using radial grid of 1408 points, 6 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
l(5) = 2
l(6) = 2

PseudoPot. # 2 for Se read from file:
../pp/Se.upf
MD5 check sum: 134c4c62ae1a1890f780526fdd37a254
Pseudo is Norm-conserving + core correction, Zval = 16.0
Generated using ONCVPSP code by D. R. Hamann
Using radial grid of 1198 points, 6 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
l(5) = 2
l(6) = 2
EPW : 1.42s CPU 1.49s WALL

EPW : 5.36s CPU 5.45s WALL

No wavefunction gauge setting applied
-------------------------------------------------------------------
Wannierization on 8 x 8 x 8 electronic grid
-------------------------------------------------------------------

Spin CASE ( default = unpolarized )

Initializing Wannier90


Initial Wannier projections

( 0.00000 0.00000 0.00000) : l = 2 mr = 1
( 0.00000 0.00000 0.00000) : l = 2 mr = 2
( 0.00000 0.00000 0.00000) : l = 2 mr = 3
( 0.00000 0.00000 0.00000) : l = 2 mr = 4
( 0.00000 0.00000 0.00000) : l = 2 mr = 5

- Number of bands is ( 38)
- Number of total bands is ( 38)
- Number of excluded bands is ( 0)
- Number of wannier functions is ( 5)
- All guiding functions are given

Reading data about k-point neighbours

- All neighbours are found

AMN
k points = 512 in 112 pools
1 of 5 on ionode
2 of 5 on ionode
3 of 5 on ionode
4 of 5 on ionode
5 of 5 on ionode
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
epw.x 0000000007620D33 for__signal_handl Unknown Unknown
libpthread-2.17.s 00002AAAAB0C6630 Unknown Unknown Unknown
libiomp5.so 00002AAAAAE0C63B Unknown Unknown Unknown
libiomp5.so 00002AAAAAE08174 Unknown Unknown Unknown
libiomp5.so 00002AAAAAE094C5 Unknown Unknown Unknown
epw.x 000000000766119E for_dealloc_alloc Unknown Unknown
epw.x 00000000004BABA6 Unknown Unknown Unknown
epw.x 00000000004B0720 Unknown Unknown Unknown
epw.x 00000000004AD0A0 Unknown Unknown Unknown
epw.x 00000000004186EF Unknown Unknown Unknown
epw.x 0000000000417A12 Unknown Unknown Unknown
libc-2.17.so 00002AAAAD49C555 __libc_start_main Unknown Unknown
epw.x 0000000000417929 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
epw.x 0000000007620DD9 for__signal_handl Unknown Unknown
libpthread-2.17.s 00002AAAAB0C6630 Unknown Unknown Unknown
libiomp5.so 00002AAAAAE05DF7 Unknown Unknown Unknown
libiomp5.so 00002AAAAADFEA7F Unknown Unknown Unknown
libiomp5.so 00002AAAAADFE815 Unknown Unknown Unknown
libiomp5.so 00002AAAAAD840C8 Unknown Unknown Unknown
ld-2.17.so 00002AAAAAABB098 Unknown Unknown Unknown
libc-2.17.so 00002AAAAD4B3CE9 Unknown Unknown Unknown
libc-2.17.so 00002AAAAD4B3D37 Unknown Unknown Unknown
epw.x 0000000007613FA1 for__issue_diagno Unknown Unknown
epw.x 0000000007620D33 for__signal_handl Unknown Unknown
libpthread-2.17.s 00002AAAAB0C6630 Unknown Unknown Unknown
libiomp5.so 00002AAAAAE0C63B Unknown Unknown Unknown
libiomp5.so 00002AAAAAE08174 Unknown Unknown Unknown
libiomp5.so 00002AAAAAE094C5 Unknown Unknown Unknown
epw.x 000000000766119E for_dealloc_alloc Unknown Unknown
epw.x 00000000004BABA6 Unknown Unknown Unknown
epw.x 00000000004B0720 Unknown Unknown Unknown
epw.x 00000000004AD0A0 Unknown Unknown Unknown
epw.x 00000000004186EF Unknown Unknown Unknown
epw.x 0000000000417A12 Unknown Unknown Unknown
libc-2.17.so 00002AAAAD49C555 __libc_start_main Unknown Unknown
epw.x 0000000000417929 Unknown Unknown Unknown
srun: error: iris-053: task 111: Exited with exit code 174
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
epw.x 0000000007620D64 for__signal_handl Unknown Unknown
libpthread-2.17.s 00002AAAAB0C6630 Unknown Unknown Unknown
libmpi.so.12 00002AAAAC719D63 PMPIDI_CH3I_Progr Unknown Unknown
libmpi.so.12.0 00002AAAAC8811E0 Unknown Unknown Unknown
libmpi.so.12.0 00002AAAAC701CD8 Unknown Unknown Unknown
libmpi.so.12.0 00002AAAAC6F325D Unknown Unknown Unknown
libmpi.so.12 00002AAAAC6F723D MPI_Barrier Unknown Unknown
libmpifort.so.12. 00002AAAAC29272C pmpi_barrier Unknown Unknown
epw.x 0000000000D57FD5 Unknown Unknown Unknown
epw.x 0000000000D48DC5 Unknown Unknown Unknown
epw.x 00000000004BAC78 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
epw.x 0000000007620D64 for__signal_handl Unknown Unknown
libpthread-2.17.s 00002AAAAB0C6630 Unknown Unknown Unknown
libmpi.so.12 00002AAAAC719D19 PMPIDI_CH3I_Progr Unknown Unknown
libmpi.so.12.0 00002AAAAC880053 Unknown Unknown Unknown
libmpi.so.12.0 00002AAAAC6F3C34 Unknown Unknown Unknown
libmpi.so.12.0 00002AAAAC6F31FF Unknown Unknown Unknown
libmpi.so.12 00002AAAAC6F723D MPI_Barrier Unknown Unknown
libmpifort.so.12. 00002AAAAC29272C pmpi_barrier Unknown Unknown
epw.x 0000000000D57FD5 Unknown Unknown Unknown
epw.x 0000000000D48DC5 Unknown Unknown Unknown
epw.x 00000000004BAC78 Unknown Unknown Unknown
epw.x 00000000004B0720 Unknown Unknown Unknown
epw.x 00000000004AD0A0 Unknown Unknown Unknown
epw.x 00000000004186EF Unknown Unknown Unknown
epw.x 0000000000417A12 Unknown Unknown Unknown
libc-2.17.so 00002AAAAD49C555 __libc_start_main Unknown Unknown
epw.x 0000000000417929 Unknown Unknown Unknown
epw.x 00000000004B0720 Unknown Unknown Unknown
epw.x 00000000004AD0A0 Unknown Unknown Unknown
epw.x 00000000004186EF Unknown Unknown Unknown
epw.x 0000000000417A12 Unknown Unknown Unknown
libc-2.17.so 00002AAAAD49C555 __libc_start_main Unknown Unknown
epw.x 0000000000417929 Unknown Unknown Unknown
...

______________________________________________________________________

Thanks and kind regards,
Amir T.

[hlee]

Dear Amir T:

Code: Select all

proj(1) = 'Fe:d'
proj(2) = 'Se:sp3'

Since you chose the projections above and FeSe has 2 Fe and 2 Se, you should use "nbndsub = 18", not "nbndsub = 5".

Additionally, you don't need "ecutrho = 400" since you used norm-conserving pseudopotentials. However, this is not related to your error. Your error is due to the wrong value of nbndsub.

PseudoPot. # 1 for Fe read from file:
../pp/Fe.upf
MD5 check sum: b1fb9d3cb1d156aba92c681262384fac
Pseudo is Norm-conserving + core correction, Zval = 16.0
Generated using ONCVPSP code by D. R. Hamann
Using radial grid of 1408 points, 6 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
l(5) = 2
l(6) = 2

PseudoPot. # 2 for Se read from file:
../pp/Se.upf
MD5 check sum: 134c4c62ae1a1890f780526fdd37a254
Pseudo is Norm-conserving + core correction, Zval = 16.0
Generated using ONCVPSP code by D. R. Hamann
Using radial grid of 1198 points, 6 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
l(5) = 2
l(6) = 2

Sincerely,

H. Lee

[AmirhTalebi]

Dear H. Lee

Thanks a lot for your reply.
Now, i have got understood how to set the nbndsub, albeit after that I applied the changes and run it again, I got another error

__________________________________________epw_____________________________
....
k points = 512 in 112 pools
1 of 5 on ionode
2 of 5 on ionode
3 of 5 on ionode
4 of 5 on ionode
5 of 5 on ionode
MMN calculated

Running Wannier90
dis_windows: More states in the frozen window than target WFs
Error: examine the output/error file for details
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
slurmstepd: error: *** STEP 2001772.2 ON iris-122 CANCELLED AT 2020-08-30T13:29:32 ***
___________________________________________epw ______________________________________


i thought that it is related to "dis_froz_max" flag, so i decreased it but again the same problem came up.
I would be grateful if you could help me in this case.

Thank you
Amir T.

[hlee]

Dear Amir T:

As the error message says, in your case, the number of states in the frozen window is larger than that of target Wannier functions (WFs), leading to the error in the disentanglement step. Therefore, in order to solve this problem, you need to change the value of dis_froz_max so that the number of states in the frozen window is smaller than that of target WFs.

Since I don't know the details of your system such as all eigenvalues, etc., I can't suggest you the exact value of dis_froz_max; you need to try to find it yourself.
Please also check the output/error file of Wannier90 (*.wout/*.werr) for some hints.

Sincerely,

H. Lee