Dear Dr. iurii, Reducing the number of nodes and /or the k-points does not help. Commenting out the 'noncolin' and 'lspinorb' flags solves the issue, no matter what the number of Kpoints and ecut values used.
Regards ________________________________ From: Iurii TIMROV <iurii.tim...@epfl.ch> Sent: Wednesday, October 6, 2021 11:54 AM To: Elio Physics <elio-phys...@live.com>; Iurii TIMROV <iurii.tim...@epfl.ch>; Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org> Subject: Re: Turbo_eels.x crashing 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 Actually this is no longer needed. So the problem is somewhere else. Your example works for me with ifort (IFORT) 19.1.3.304 20200925 on my workstation with 8 cores. In your files (PAl-turbo-eels.e1813454) it is written: "Program received signal SIGSEGV: Segmentation fault - invalid memory reference." "#4 0x40DD8C in lr_alloc_init_" The subroutine "lr_alloc_init" allocates arrays and it seems that the code crashes at this stage. > 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 Can you try with SOC but by lowering the cutoff down to e.g. 50 Ry and reducing the k-mesh down to 6x6x1? Maybe there is not enough RAM in your case when SOC is included? Do you manage to run example 16, which includes SOC and uses NC PP? 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-boun...@lists.quantum-espresso.org> on behalf of Iurii TIMROV via users <users@lists.quantum-espresso.org> Sent: Wednesday, October 6, 2021 2:10:14 PM To: Elio Physics; Quantum ESPRESSO users Forum Subject: Re: [QE-users] Turbo_eels.x crashing 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-phys...@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.tim...@epfl.ch> Sent: Tuesday, October 5, 2021 6:16 AM To: Elio Physics <elio-phys...@live.com>; Quantum ESPRESSO users Forum <users@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-phys...@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-boun...@lists.quantum-espresso.org> on behalf of Elio Physics <elio-phys...@live.com> Sent: Monday, October 4, 2021 12:10 PM To: Iurii TIMROV <iurii.tim...@epfl.ch>; Quantum ESPRESSO users Forum <users@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.tim...@epfl.ch> Sent: Monday, October 4, 2021 11:55 AM To: Elio Physics <elio-phys...@live.com>; Quantum ESPRESSO users Forum <users@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-phys...@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-boun...@lists.quantum-espresso.org> on behalf of Iurii TIMROV via users <users@lists.quantum-espresso.org> Sent: Monday, October 4, 2021 3:29 AM To: Quantum Espresso users Forum <users@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-boun...@lists.quantum-espresso.org> on behalf of Elio Physics <elio-phys...@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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