Question regarding a Segmentation Fault with elphbolt on an HPC cluster

[balabala12s]

Dear Dr. Protik,

I hope this email finds you well.

I am a user of the elphbolt software. First, I would like to thank you and your team for developing this powerful and useful tool.

I am writing to report an issue I’ve encountered while running elphbolt on an HPC cluster. The same calculation runs successfully on a standalone server, but it fails with a segmentation fault on the cluster.

Here are the details of the problem:
WARNING: There was an error initializing an OpenFabrics device.

Local host: hpc2021
Local device: mlx5_0

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| \ \ _|_|/|/ | /| / _/||___/ |
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| A solver for the coupled electron-phonon Boltzmann transport equations. |
| Copyright 2020 elphbolt contributors. |
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| This is 'free as in freedom'[] software, distributed under the GPLv3. |
| [] https://www.gnu.org/philosophy/free-sw.en.html |
+-------------------------------------------------------------------------+

Number of coarray images = 1

---

______________________________________________________Setting up crystal...
Material: Cubic Si
Dominant isotopic masses (DIB) will be used.
Si mass = 0.27976928E+02 u
Lattice vectors [nm]:
-0.27010011E+00 0.00000000E+00 0.27010011E+00
0.00000000E+00 0.27010011E+00 0.27010011E+00
-0.27010011E+00 0.27010011E+00 0.00000000E+00
Primitive cell volume = 0.39409804E-01 nm^3
Reciprocal lattice vectors [1/nm]:
-0.11631216E+02 -0.11631216E+02 0.11631216E+02
0.11631216E+02 0.11631216E+02 0.11631216E+02
-0.11631216E+02 0.11631216E+02 -0.11631216E+02
Brillouin zone volume = 0.15943204E+03 1/nm^3
Crystal temperature = 300.00 K

---

____________________________________________Reading numerics information...
cp: cannot stat '/home/u3012863/app/3/elphbolt/examples/Si/input/_batches': No such file or directory
cp: cannot stat '/home/u3012863/app/3/elphbolt/examples/Si/input/T0.300E+03/_batches': No such file or directory
q-mesh = 6 6 6
k-mesh = 24 24 24
Fermi window thickness (each side of reference energy) = 0.40000000E+00 eV
Working directory = /home/u3012863/app/3/elphbolt/examples/Si/input
T-dependent working directory = /home/u3012863/app/3/elphbolt/examples/Si/input/T0.300E+03
Data dump directory = ./scratch/
T-dependent data dump directory = ./scratch/T0.300E+03
e-ph directory = ./scratch/g2
Use Wannier ifcs: F
ph-ph directory = ./scratch/V2
Reuse e-ph matrix elements: F
Number of batches: 1
Restart from old batch processing records: F
Reuse ph-e matrix elements: F
Reuse ph-ph matrix elements: F
Reuse ph-ph transition probabilities: F
Calculate ph-ph transition probabilities on-the-fly: F
Calculate ph-e interaction: T
Calculate ph-e transition probabilities on-the-fly: F
Calculate 1st Born ph-isotope interaction: F
Calculate ph-isotope interaction via T-matrix: F
Include ph-substitution interaction: F
Include ph-boundary interaction: F
Include 4-ph interaction: F
Include ph-thin-film interaction: F
Include ph-defect interaction using the T-matrix: F
Include el-charged impurity interaction: F
Include el-el interaction: F
Include el-boundary interaction: F
Solve bulk-BTE: T
Solve nano-BTE: F
Include drag: T
Use tetrahedron method: F
Plot quantities along path: F
Maximum number of BTE/Migdal-Eliashberg equations iterations = 50
BTE/Migdal-Eliashberg equations convergence threshold = 0.10000000E-03
B-field is on: F

---

______________________________________________________Analyzing symmetry...
Crystal symmetry group = Fd-3m
Spacegroup number = 227
Number of crystal symmetries (without time-reversal) = 48
..............
| Timing info: Initialization 0.24534845E-04 hr
..............

---

______________________________________________________Setting up Wannier...
Wannier data from EPW will be read.
Reading Wannier rep. Hamiltonian...
Reading Wannier rep. dynamical matrix...
Reading Wannier rep. e-ph vertex and distributing...
Reading Wannier cells and multiplicities...
..............
| Timing info: Wannier 0.76359137E-02 hr
..............

---

____________________________________________________Setting up electrons...
Spin degeneracy = 2
Number of Wannier electronic bands = 8
Number of transport active electronic bands = 2
Lowest and highest transport active electronic bands = 5 6
Reference electron energy = 0.67003500E+01 eV
System is metallic: F
Lowest conduction band index = 5
Energy unrestricted calculation:

Calculating FBZ...
Calculating IBZ and IBZ -> FBZ mappings...
Number of FBZ wave vectors = 13824
Number IBZ wave vectors = 413
Calculating IBZ energies...
Mapping out FBZ energies...
Calculating carrier concentrations...
Transport energy window restricted calculation:

Calculating Fermi window restricted FBZ blocks...
Sorting FBZ blocks index list...
Calcutating FBZ blocks quantities...
Calculating IBZ blocks...
Number of FBZ wave vectors = 501
Number IBZ wave vectors = 25
Calcutating IBZ blocks quantities...
Number of energy restricted FBZ blocks states = 546
Calculating FBZ -> IBZ mappings...
Number of energy restricted IBZ blocks states = 29
Calculating electron mesh triangles...
Electron calculations summary:

Chemical potential = 0.67003500E+01 eV
Band resolved carrier concentration (+/- = hole/electron):
Band: 5, concentration: -0.23778557E+20 cm^-3
Band: 6, concentration: -0.56521819E+17 cm^-3
Absolute total electron concentration = 0.23835079E+20 cm^-3
Absolute total hole concentration = 0.00000000E+00 cm^-3
Ionization of donor impurity = 0.00000000E+00
Ionization of acceptor impurity = 0.00000000E+00
Donor impurity concentration = 0.00000000E+00 cm^-3
Acceptor impurity concentration = 0.00000000E+00 cm^-3
..............
| Timing info: Electrons 0.95655315E-03 hr
..............

---

______________________________________________________Setting up phonons...
Reading espresso format 2nd order force constants...
Number of pairs read in = 36
q-mesh used in IFC2 calculation = 6 6 6
Precomputing q-independent quantities related to dynamical matrix...
Calculating phonon FBZ quantities...
Calculating IBZ and IBZ -> FBZ mappings...
Number of FBZ wave vectors = 216
Number IBZ wave vectors = 16
Calculating phonon mesh triangles...
Reading ShengBTE format third order force constants...
Number of triplets read in = 4646
..............
| Timing info: Phonons 0.11638282E-03 hr
..............

---

___________________________________________Calculating density of states...
Calculating electron density of states...
Calculating Thomas-Fermi screening wave vector...
Thomas-Fermi screening wave vector = 0.34539993E+01 1/nm
Calculating phonon density of states and (if needed) isotope/substitution scattering...
..............
| Timing info: Density of states and one-particle scattering rates 0.25003418E-04 hr
..............

---

________________________________________________Calculating interactions...
Calculating g(Re,Rp) -> g(Re,q) for all IBZ q...
#q = 16
#q/image <= 16
Calculating g(Re,q) -> |g(k,q)|^2 for all IBZ phonons...
Processing batch 1 of 1
batch # = 1
#states = 96
#states/image <= 96
..............
| Timing info: IBZ q e-ph interactions 0.12605939E-01 hr
..............
Calculating ph-e transition probabilities for all IBZ phonons...
Processing batch 1 of 1
batch # = 1
#states = 96
#states/image <= 96
..............
| Timing info: IBZ ph-e transition probilities 0.61617972E-04 hr
..............
Calculating g(Re,Rp) -> g(k,Rp) for all IBZ k...
Current shape of gwann = 8 8 1957 6 279

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x154f756ac5af in ???
#1 0x53536f in ???
#2 0x4a452f in ???
#3 0x404f9b in ???
#4 0x40568d in ???
#5 0x154f756987e4 in ???
#6 0x4029bd in ???
#7 0xffffffffffffffff in ???
Segmentation fault (core dumped)

How can I slove this problem. Thanks for your assistance.

Regards,
Lei

[balabala12s]

Dear Dr. Protik,

I have sloved this problem. Thank you.

Best regards,
Lei