[QE-users] Turbo_eels.x crashing

Wed Oct 6 14:10:14 CEST 2021

Dear Elio,

The problem is due to the fact that you use k-points pools for the pw.x run but you don't use k-points pools for the turbo_eels.x run. Please note that the two calculations must be parallelized in exactly the same way. So try the following:

mpirun -np 64 pw.x -nk 2 < pwscf.in > pwscf.out

mpirun -np 64 turbo_eels.x -nk 2 < eels.in > eels.out

Other comments:

> wf_collect=.true.

This is no longer supported/need in the latest versions of QE

> occupations='fixed',

> smearing='mp'

Since the occupations are fixed, you don't need to specify smearing='mp'

> nbnd=55

There is not need to specify this: the turbo_eels.x code needs only occupied KS states and these are determined automatically by the pw.x code

> conv_thr=1.D-8

I would recommend to push it to 1.D-10 - 1.D-15

> Pd  106.42   Pd.rel-pbe-n-nc.UPF

> S   32.065   S.rel-pbe-n-nc.UPF

Norm-conserving pseudopotentials from the PSlibrary are not tested, as far as I know. So be careful when using these pseudopotentials. You can try to use fully-relativistic norm-conserving pseudopotentials from the PseudoDojo library.

HTH

Greetings,

Iurii

--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: Elio Physics <elio-physics at live.com>
Sent: Wednesday, October 6, 2021 4:52:50 AM
To: Iurii TIMROV; Quantum Espresso users Forum
Subject: Re: Turbo_eels.x crashing

Dear Dr. Iurii,

Once again , thanks for your quick reply.

>>>>>>>Which version of Quantum ESPRESSO do you use? Can you try the latest version (v6.8)?
QE-6.7MaX
>>>>>>Which compiler and libraries do you use?
F90 (mpif90 wrapper).
module load gcc-5.3.0 mpi/openmpi-3.0.0/gcc-5.3.0
module load lapack-3.7.1
>>>> Do you use norm-conserving or ultrasoft pseudopotentials?
Norm conserving with SOC

I have  shared  with you a folder with all input, output files and pseudopotentials.

Thank you for your help.

Regards

________________________________
From: Iurii TIMROV <iurii.timrov at epfl.ch>
Sent: Tuesday, October 5, 2021 6:16 AM
To: Elio Physics <elio-physics at live.com>; Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: Re: Turbo_eels.x crashing

  1.  Which version of Quantum ESPRESSO do you use? Can you try the latest version (v6.8)?
  2.  Which compiler and libraries do you use?
  3.  Do you use norm-conserving or ultrasoft pseudopotentials?
  4.  Can you share all your input and output files (with the right cutoff etc.) and the pseudopotentials via some shared folder (e.g. Google Drive)? I will try to reproduce your problem using QE v6.8 and investigate what is happening.

Greetings,
Iurii

--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: Elio Physics <elio-physics at live.com>
Sent: Monday, October 4, 2021 10:55:47 PM
To: Iurii TIMROV; Quantum ESPRESSO users Forum
Subject: Re: Turbo_eels.x crashing

After reproducing the examples in the TDFPPT directory (copied the exact same input files) , I realized that the source of the error is the spin orbit coupling flags. The program exited normally when the SOC was not included. However , when the SOC is considered, the code crashes and exits with the same error:

"Backtrace for this error:
--------------------------------------------------------------------------
A process has executed an operation involving a call to the
"fork()" system call to create a child process.  Open MPI is currently
operating in a condition that could result in memory corruption or
other system errors; your job may hang, crash, or produce silent
data corruption.  The use of fork() (or system() or other calls that
create child processes) is strongly discouraged.

4  0x40DD8C in lr_alloc_init_
#4  0x40DD8C in lr_alloc_init_
#4  0x40DD8C in lr_alloc_init_
#4  0x40DD8C in lr_alloc_init_
#5  0x404CFE in MAIN__ at lr_eels_main.f90:113
#5  0x404CFE in MAIN__ at lr_eels_main.f90:113
#4  0x40DD8C in lr_alloc_init_
#5  0x404CFE in MAIN__ at lr_eels_main.f90:113
#4  0x40DD8C in lr_alloc_init_
#5  0x404CFE in MAIN__ at lr_eels_main.f90:113
#5  0x404CFE in MAIN__ at lr_eels_main.f90:113
#5  0x404CFE in MAIN__ at lr_eels_main.f90:113
#4  0x40DD8C in lr_alloc_init_
#4  0x40DD8C in lr_alloc_init_
#5  0x404CFE in MAIN__ at lr_eels_main.f90:113
#5  0x404CFE in MAIN__ at lr_eels_main.f90:113
--------------------------------------------------------------------------
mpirun noticed that process rank 3 with PID 0 on node kcn159 exited on signal 11 (Segmentation fault)."

I tried to look if there was some additional flags in the scf input file, other than those for a usual scf calculation, but I could not find any. I do not really know what is going on.

Any clue would be highly appreciated.

Regards

________________________________
From: users <users-bounces at lists.quantum-espresso.org> on behalf of Elio Physics <elio-physics at live.com>
Sent: Monday, October 4, 2021 12:10 PM
To: Iurii TIMROV <iurii.timrov at epfl.ch>; Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] Turbo_eels.x crashing

The ecutwfc is not zero. It is 90Ry. It was incorrectly taken out while deleting some of the input.
I will try to reproduce the examples given in the TDFFPT directory. If these don't work, I will get back to you.

Thank you for your time.

________________________________
From: Iurii TIMROV <iurii.timrov at epfl.ch>
Sent: Monday, October 4, 2021 11:55 AM
To: Elio Physics <elio-physics at live.com>; Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: Re: Turbo_eels.x crashing

> ecutwfc=0

The kinetic-energy cutoff cannot be zero.

Try the QE input generator and then adjust the input to your needs (add noncolin=.true., lspinorb=.true. etc.):

https://www.materialscloud.org/work/tools/qeinputgenerator

HTH

Iurii

--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: Elio Physics <elio-physics at live.com>
Sent: Monday, October 4, 2021 3:29:17 PM
To: Iurii TIMROV; Quantum Espresso users Forum
Subject: Re: Turbo_eels.x crashing

Dear Dr. Timrov,

thanks for your reply.  The pw.x input is as follows:

&control
    prefix='pds2'
    calculation='scf',
    restart_mode='from_scratch',
    tstress=.true.,
    tprnfor=.true.,
    nstep=2000
     pseudo_dir = '/fefs1/physics/eamoujaes/PSEUDO-CREATED',
     wf_collect=.true.,
     outdir='/',
    etot_conv_thr=1.0D-5
    forc_conv_thr=2.5D-4

 /
  &system
   ibrav=4 ,A=4.376, C=18  nat=3, ntyp= 2, ecutwfc=0 , nbnd=55, occupations='smearing', noncolin=.true., lspinorb=.true., smearing='mp', degauss=0.005

/
 &electrons
    electron_maxstep=750
    conv_thr=1.D-8,
    mixing_beta=0.2D0,
    mixing_mode='plain',
    diago_david_ndim=2,

 /
&ions
   ion_dynamics ='bfgs'
/
 &cell
 cell_dynamics='bfgs'
 press=0.0
 cell_dofree='2Dxy'
/

ATOMIC_SPECIES
 Pd  106.42   Pd.rel-pbe-n-nc.UPF
 S   32.065   S.rel-pbe-n-nc.UPF

ATOMIC_POSITIONS crystal
.
.
.
K_POINTS {automatic}
10 10 1 0 0 0

________________________________
From: users <users-bounces at lists.quantum-espresso.org> on behalf of Iurii TIMROV via users <users at lists.quantum-espresso.org>
Sent: Monday, October 4, 2021 3:29 AM
To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] Turbo_eels.x crashing

Dear Elie,

Can you provide please your input file for the pw.x code?

Greetings,
Iurii

--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: users <users-bounces at lists.quantum-espresso.org> on behalf of Elio Physics <Elio-Physics at live.com>
Sent: Sunday, October 3, 2021 12:21:47 AM
To: Quantum Espresso users Forum
Subject: [QE-users] Turbo_eels.x crashing

Dear all,

I am trying to calculate the absorption spectrum using the turbo_eels.x toolset . My system is metallic and has noncollinear spin-orbit coupling switched on, which means I cannot use neither turbo_davidson nor turbo_lanczos. For that matter , my  turbo_eels input is :

&lr_input
prefix='pds'
outdir='/'
restart_step=50
restart=.false.
/
&lr_control
calculator='lanczos'
itermax=500
q1=0.001
q2=0.000
q3=0.000
/

The code starts by doing an nscf calculation but , right after that, it crashes. Looking at the error file, I found the following:

program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0  0x2B22A841FB97
#1  0x2B22A841ED90
#2  0x2B22A906091F
#3  0x2B22A90B1C76
#4  0x40DD8C in lr_alloc_init_
#4  0x40DD8C in lr_alloc_init_
#4  0x40DD8C in lr_alloc_init_
#5  0x404CFE in MAIN__ at lr_eels_main.f90:113
#5  0x404CFE in MAIN__ at lr_eels_main.f90:113
.
.
.
#5  0x404CFE in MAIN__ at lr_eels_main.f90:113
#0  0x2AC6091BCB97
#1  0x2AC6091BBD90
#5  0x404CFE in MAIN__ at lr_eels_main.f90:113
#2  0x2AC609DFD91F
#3  0x2AC609E4EC76
#4  0x40DD8C in lr_alloc_init_
#5  0x404CFE in MAIN__ at lr_eels_main.f90:113
#5  0x404CFE in MAIN__ at lr_eels_main.f90:113

Can anyone please let me know how to circumvent this error?

Thanks in advance

Elie Moujaes
Federal University of Rondonia
Portyo Velho
Brazil
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