[QE-users] Fail in drawing fat band
Dear all I am using DFTtoolbox to draw fat band for Ni3SiTe8. However, I am puzzled. The crystral structure is obtained from experiment, so I omit the procedure of doing structure relax. Than I submit the commands one by one srun -n 128 pw.x scf.out srun -n 128 pw.x bands.out srun -n 1 bands.x pp.bands.out (Nb3SiTe8_bands.dat Nb3SiTe8_bands.dat.gnu Nb3SiTe8_bands.dat.rap is obtained after this step while Nb3SiTe8_bands.dat.rap is an empty file) srun -n 2 projwfc.x projwfc.out (Nb3SiTe8_proj.dat.projwfc_up is obtained after this step) After that, I used the code provided by DFTtoolbox to draw my fatband plot. I used the postproc.py file given in the webside DFTtoolbox/build/lib/DFTtoolbox/postproc.py at master · pipidog/DFTtoolbox · GitHub I haven't made any change to the code. I changed some parameter of the file qe_pp.py this is my code (Nb3SiTe8_proj.dat.projwfc_up is the file I obtained in the fouth step) import postproc import os # Parameter run_task=[1,2,3,4] wkdir=os.path.dirname(os.path.realpath(Nb3SiTe8_proj.dat.projwfc_up)) # band_read & fatband_read Ef=8.65 #band_plot kdiv=[15,7,5,15,13,9,5,10,9,1] klabel=['$\Gamma$','X','W','K','$\Gamma$','L','U','W','L','K'] Ebound=[-5,5] #fatband_plot state_grp=[['1:1/2/a/a'],['2:2/1/a/a']] # Main pp=postproc(wkdir) for task in run_task: if task==1: #'band_read': pp.band_read(Ef=Ef,bandfile='pw.bands.out') elif task==2: #'band_plot': pp.band_plot(kdiv=kdiv,klabel=klabel,Ebound=Ebound) elif task==3: #'fatband_read': pp.fatband_read(Ef=Ef,projout='projwfc.fat.out',projprefix='fatband') elif task==4: #'fatband_plot': pp.fatband_plot(state_grp=state_grp,kdiv=kdiv,klabel=klabel,Ebound=Ebound) elif task==5: #pdos_read: pp.pdos_read(Ef=Ef) elif task==6: pp.pdos_plot(state_grp=state_grp,Ebound=Ebound) However, the fatband haven't been draw. I only obtained another python file postproc.cpython-37.pyc what's wrong? Where should I change? Or what should I write to obtain the fatband plot? Could you please help me? Thank you very much! Zongyi Wang ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] [SPAM] error with parallel execution
Dear, dedevelopers and subscribers. I'm Jerry from Peking University. I configure by option ./configure and make by option make all. After that I run PW/examples/example01 (by option ./run_example) succesfully. and when I use the input file this example (al.scf.david.in) (by option pw.x scf.out). I run it successfully. and when I use the input file this example (al.scf.david.in) (by option mpirun -np 1 pw.x scf.out). I run it successfully. The problem occurs when I run it (by option mpirun -np 2 pw.x scf.out). I get a write_line error. So I don't know what happened with my mpi parallel execution. I will attach my files here. Including config.log configure.msg and scf.out -- Failed to register memory region (MR): Hostname: wm1-login01 Address: 98769000 Length: 4194304 Error:Cannot allocate memory -- -- Open MPI has detected that there are UD-capable Verbs devices on your system, but none of them were able to be setup properly. This may indicate a problem on this system. You job will continue, but Open MPI will ignore the "ud" oob component in this run. Hostname: wm1-login01 -- from test_input_xml: input file not opened or empty application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for write_line failure : Bad file descriptor forrtl: error (78): process killed (SIGTERM) Image PCRoutineLineSource pw.x 01001F1E Unknown Unknown Unknown libpthread-2.17.s 7FA56F8AC5F0 Unknown Unknown Unknown libc-2.17.so 7FA56F2C1D37 getrusage Unknown Unknown pw.x 00F26E5D Unknown Unknown Unknown pw.x 00F26BFB Unknown Unknown Unknown pw.x 00E34EFF Unknown Unknown Unknown pw.x 00A1AA18 Unknown Unknown Unknown pw.x 008319ED Unknown Unknown Unknown pw.x 007ACAAB Unknown Unknown Unknown pw.x 007ABE7A Unknown Unknown Unknown pw.x 0086C4B4 Unknown Unknown Unknown pw.x 0069C6FF Unknown Unknown Unknown pw.x 0069ADB1 Unknown Unknown Unknown pw.x 00699427 Unknown Unknown Unknown pw.x 0040D0AA Unknown Unknown Unknown pw.x 0040A3ED Unknown Unknown Unknown pw.x 0057E9AE Unknown Unknown Unknown pw.x 004074DF Unknown Unknown Unknown pw.x 0040735E Unknown Unknown Unknown libc-2.17.so 7FA56F1EF505 __libc_start_main Unknown Unknown pw.x 00407269 Unknown Unknown Unknown forrtl: error (78): process killed (SIGTERM) Image PCRoutineLineSource pw.x 01001F1E Unknown Unknown Unknown libpthread-2.17.s 7F6443BBF5F0 Unknown Unknown Unknown libpthread-2.17.s 7F6443BBE69E write Unknown Unknown pw.x 01018835 Unknown Unknown Unknown pw.x 0101970E Unknown Unknown Unknown pw.x 01057D2E Unknown Unknown Unknown pw.x 00535DA9 Unknown Unknown Unknown pw.x 00536AF6 Unknown Unknown Unknown pw.x 00412300 Unknown Unknown Unknown pw.x 0040A3ED Unknown Unknown Unknown pw.x 0057E9AE Unknown Unknown Unknown pw.x 004074DF Unknown Unknown Unknown pw.x 0040735E Unknown Unknown Unknown libc-2.17.so 7F6443502505 __libc_start_main Unknown Unknown pw.x 00407269 Unknown Unknown Unknown forrtl: error (78): process killed (SIGTERM) Image PCRoutineLineSource pw.x 01001F1E Unknown Unknown Unknown libpthread-2.17.s 7FDAD78995F0 Unknown Unknown Unknown libmkl_avx2.so 7FDAD4258B23 Unknown Unknown Unknown
[QE-users] A strange error when using GPU accelerated ph.x
Dear developers and users, I tried to run GPU version of QE for electron phonon coupling calculation on an a100 card. The structure relaxation and self-consistent calculation are successful. However, when I did phonon calculation, my job crashed with a strange error: ## [m005:65520:0:65520] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xfffc) /fs08/home/js_luqing/src/qe-7.2/PHonon/PH/phq_setup.f90: [ phq_setup_() ] ... 322 ! nat_todo, atomo, comp_irr 323 324 DO irr=0,nirr == 325 comp_irr(irr)=comp_irr_iq(irr,current_iq) 326 IF (elph .AND. irr0) comp_elph(irr)=comp_irr(irr) 327 ENDDO 328 ! backtrace (tid: 65520) 0 0x004a2780 phq_setup_() /fs08/home/js_luqing/src/qe-7.2/PHonon/PH/phq_setup.f90:325 1 0x004700e1 initialize_ph_() /fs08/home/js_luqing/src/qe-7.2/PHonon/PH/initialize_ph.f90:79 2 0x0041a811 do_phonon_() /fs08/home/js_luqing/src/qe-7.2/PHonon/PH/do_phonon.f90:100 3 0x00413d25 MAIN_() /fs08/home/js_luqing/src/qe-7.2/PHonon/PH/phonon.f90:78 4 0x00413c71 main() ???:0 5 0x00022555 __libc_start_main() ???:0 6 0x0040cd8d _start() ???:0 = [m005:65520] *** Process received signal *** [m005:65520] Signal: Segmentation fault (11) [m005:65520] Signal code: (-6) [m005:65520] Failing at address: 0x6a8fff0 [m005:65520] [ 0] /lib64/libpthread.so.0(+0xf630)[0x2ac4edf09630] [m005:65520] [ 1] /fs08/home/js_luqing/src/qe-7.2/bin/ph.x[0x4a2780] [m005:65520] [ 2] /fs08/home/js_luqing/src/qe-7.2/bin/ph.x[0x4700e1] [m005:65520] [ 3] /fs08/home/js_luqing/src/qe-7.2/bin/ph.x[0x41a811] [m005:65520] [ 4] /fs08/home/js_luqing/src/qe-7.2/bin/ph.x[0x413d25] [m005:65520] [ 5] /fs08/home/js_luqing/src/qe-7.2/bin/ph.x[0x413c71] [m005:65520] [ 6] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2ac4ee9e7555] [m005:65520] [ 7] /fs08/home/js_luqing/src/qe-7.2/bin/ph.x[0x40cd8d] [m005:65520] *** End of error message *** -- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -- -- mpirun noticed that process rank 0 with PID 0 on node m005 exited on signal 11 (Segmentation fault). # I am not an expert of coding, but it seems like the line 325 wasn't recognized, which is fairly strange. I don't know how to solve this problem, and I am glad if anyone can help me. Yours, Qing Lu lq1998 1148330...@qq.com ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Difference between data file saved inside outdir
hdf5 files are in portable format, one per k-point, independent upon the number of processors and the kind of parallelization. prefix.wfc* files are in nonportable binary format, one per processor, depend upon the number of processors and the kind of parallelization. For reasons that is too long to explain, calculations that use SCF wavefunctions read then from "portable" format and re-write them to "non-portable" format. It's a little bit dumb and actually unnecessary in most cases. Paolo On 28/03/2024 08:04, Abdul Muhaymin via users wrote: Hello all, After a spin-polarized scf calculation, I have several files such as wfcup#.hdf5, wfcdw#hdf5 etc in in outdir/prefix.save. The number of the files are equal to the 2*number of k points. However, after nscf calculation, I am getting more data files in the outdir (not in outdir/prefix.save). I have N number of prefix.wfc* files where N is the number of processor I used. What is the difference between these two type of files? Are they both wavefunction? If I delete them, will there be any problem? Sincerely, Abdul Muhaymin, Graduate student, Bilkent University, Ankara. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216 ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] [SPAM] GPU for QE
Dear users and developers, How can i add GPU in this input/slurm? Or i need plugin for QE? Bes regards, -- Vorobyev Stepan ITMO university , Infochemistry science centre TiO2101.slurm Description: Binary data calculation = 'relax' etot_conv_thr = 6.00d-05 forc_conv_thr = 1.00d-04 outdir = './out/' prefix = 'aiida' pseudo_dir = './pseudo/' tprnfor = .true. tstress = .true. verbosity = 'high' tprnfor = .true. tstress = .true. verbosity = 'high' tefield = .true. dipfield = .true. wf_collect = .true. !max_seconds = 64800 / degauss = 0.02 ecutrho = 5.00d+02 ecutwfc = 5.00d+01 ibrav = 0 nat = 384 !nosym = .true. !nspin = 2 ntyp = 2 occupations = 'smearing' smearing = 'gaussian' vdw_corr = 'DFT-D3' edir= 3 emaxpos = 0.85 eopreg = 0.0304432958 eamp= 0.0 / !conv_thr = 1.20d-09 electron_maxstep = 300 mixing_beta = 4.00d-01 / / / ATOMIC_SPECIES O 15.9994 O.pbesol-n-kjpaw_psl.0.1.UPF Ti 47.867 ti_pbesol_v1.4.uspp.F.UPF ATOMIC_POSITIONS crystal O 0.0876560.9284370.000 0 0 O 0.0876560.4284370.000 0 0 O 0.3376560.9284370.000 0 0 O 0.3376560.4284370.000 0 0 O 0.5876560.9284370.000 0 0 O 0.5876560.4284370.000 0 0 O 0.8376560.9284370.000 0 0 O 0.8376560.4284370.000 0 0 O 0.9626560.1784380.000 0 0 O 0.9626560.6784380.000 0 0 O 0.2126560.1784380.000 0 0 O 0.2126560.6784380.000 0 0 O 0.4626560.1784380.000 0 0 O 0.4626560.6784380.000 0 0 O 0.7126560.1784380.000 0 0 O 0.7126560.6784380.000 0 0 Ti 0.0876560.3419790.0221450 0 0 Ti 0.0876560.8419790.0221450 0 0 Ti 0.3376560.3419790.0221450 0 0 Ti 0.3376560.8419790.0221450 0 0 Ti 0.5876560.3419790.0221450 0 0 Ti 0.5876560.8419790.0221450 0 0 Ti 0.8376560.3419790.0221450 0 0 Ti 0.8376560.8419790.0221450 0 0 Ti 0.9626560.0919790.0221450 0 0 Ti 0.9626560.5919790.0221450 0 0 Ti 0.2126560.0919790.0221450 0 0 Ti 0.2126560.5919790.0221450 0 0 Ti 0.4626560.0919790.0221450 0 0 Ti 0.4626560.5919790.0221450 0 0 Ti 0.7126560.0919790.0221450 0 0 Ti 0.7126560.5919790.0221450 0 0 O 0.0876560.0742710.0266800 0 0 O 0.0876560.5742710.0266800 0 0 O 0.3376560.0742710.0266800 0 0 O 0.3376560.5742710.0266800 0 0 O 0.5876560.0742710.0266800 0 0 O 0.5876560.5742710.0266800 0 0 O 0.8376560.0742710.0266800 0 0 O 0.8376560.5742710.0266800 0 0 O 0.9626560.3242710.0266800 0 0 O 0.9626560.8242710.0266800 0 0 O 0.2126560.3242710.0266800 0 0 O 0.2126560.8242710.0266800 0 0 O 0.4626560.3242710.0266800 0 0 O 0.4626560.8242710.0266800 0 0 O 0.7126560.3242710.0266800 0 0 O 0.7126560.8242710.0266800 0 0 O 0.9626560.0055210.0442890 0 0 O 0.9626560.5055210.0442890 0 0 O 0.2126560.0055210.0442890 0 0 O 0.2126560.5055210.0442890 0 0 O
Re: [QE-users] lambda.x: at line 61 of file lambda.f90
On 19/04/2024 10:21, Dawid Ciszewski wrote: At line 61 of file lambda.f90 (unit = 5, file = 'stdin') Fortran runtime error: End of file look at line 61 of file lambda.f90: it reads the first line of the input. You are not reading the input file. Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216 ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] lambda.x: at line 61 of file lambda.f90
For completeness, I use QE version 7.2. niedz., 14 kwi 2024 o 14:30 Dawid Ciszewski napisał(a): > Hello QE users and developers, > > I tried to run lambda.x to calculate Tc for my graphene layer, but I got the > following error: > > > Error termination. Backtrace: > At line 61 of file lambda.f90 (unit = 5, file = 'stdin') > Fortran runtime error: End of file > > Error termination. Backtrace: > -- > Primary job terminated normally, but 1 process returned > a non-zero exit code. Per user-direction, the job has been aborted. > -- > At line 61 of file lambda.f90 (unit = 5, file = 'stdin') > Fortran runtime error: End of file > > Error termination. Backtrace: > #0 0x7f6ba9a23860 in ??? > #1 0x7f6ba9a243b9 in ??? > #2 0x7f6ba9a2507f in ??? > #3 0x7f6ba9c5780b in ??? > #4 0x7f6ba9c50d64 in ??? > #5 0x7f6ba9c518f9 in ??? > #6 0x402615 in elph > at /scientific/qe-7.2/PHonon/PH/lambda.f90:61 > #7 0x40246c in main > at /scientific/qe-7.2/PHonon/PH/lambda.f90:187 > At line 61 of file lambda.f90 (unit = 5, file = 'stdin') > Fortran runtime error: End of file > > > This is the content of my lamdba.in file: > > 45 0.121 0 > 7 > 0.0 0.0 0.0 1 > 0.0 0.192450090 0.0 6 > 0.0 0.384900179 0.0 6 > 0.0 -0.577350269 0.0 3 > 0.16667 0.288675135 0.0 6 > 0.16667 0.481125224 0.0 12 > 0.3 0.577350269 0.0 2 > elph_dir/elph.inp_lambda.1 > elph_dir/elph.inp_lambda.2 > elph_dir/elph.inp_lambda.3 > elph_dir/elph.inp_lambda.4 > elph_dir/elph.inp_lambda.5 > elph_dir/elph.inp_lambda.6 > elph_dir/elph.inp_lambda.7 > 0.20 > > > I have elph.inp files in a separate folder - elph_dir. I would be very > grateful for any hints on how to resolve this problem. I searched for similar > subjects in the archive but none of the solutions worked in my case. > > > With kind regards, > > Dawid Ciszewski > > Phd Student > > University of Warsaw, Center of New Technologies > > Email: d.ciszew...@cent.uw.edu.pl > > ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] QE 7.2 error required attribute rank not found
Can't reproduce
Paolo
On 12/04/2024 09:43, Sol Loja via users wrote:
Dear QE Users Forum,
I am encountering the following error after running a nscf calculation
on QE 7.2:
%%
task # 0
from qes_read: matrixType : error # 10
required attribute rank not found, can't read further, stopping
%%
Please advise me on how to address this. Below is the input file:
ibrav=1,
celldm(1)=15,
nat=3,
ntyp=2,
ecutwfc=44.099,
ecutrho=440.99,
/
conv_thr=1.0d-6,
mixing_beta=0.7,
/
ion_dynamics = 'bfgs',
/
ATOMIC_SPECIES
C 12.011 C.pbe-n-kjpaw_psl.1.0.0.UPF
O 15.999 O.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
C 7.50 7.50 7.50 0
0 0
O 8.6736893489 7.5000297668 7.5000297668
O 6.3262902178 7.4999803011 7.4999803011
K_POINTS {gamma}
Best regards,
Sol Loja
___
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effects that the Russian military offensive has on their
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___
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users mailing list users@lists.quantum-espresso.org
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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users@lists.quantum-espresso.org
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Re: [QE-users] [SPAM] about relax-structure issue
On 18/04/2024 15:14, 孙昊冉 wrote:
Dear Professors and Experts:
When I use pw.x to relax a cell structure. I meet a question that "= Bad
termination of one of your application processes =rank 0 pid... running
at ... =exit status: 3." I wonder that what is the exactly meaning of
exit status: 3.
it means that the ionic optimization has not converged (see the header
of PW/src/run_pwscf.f90). You should look at the output for more information
Paolo
Many Thanks
The input file is list as follows:
calculation='vc-relax'
disk_io='low'
prefix='***'
restart_mode='from_scratch'
verbosity='high'
tprnfor=.true.
tstress=.true.
pseudo_dir = '~/qe-6.8/pseudo'
forc_conv_thr=1.0d-5
outdir='./tmp'
/
ibrav= 0,
nat= 40,
ntyp= 2,
occupations = 'smearing', smearing = 'gauss', degauss = 1.0d-2,
ecutwfc = 160,
ecutrho = 800,
/
conv_thr = 1.0d-8
mixing_beta = 0.7d0
diagonalization = 'cg'
/
ion_dynamics='bfgs'
/
press_conv_thr=0.1
/
ATOMIC_SPECIES
***
CELL_PARAMETERS (angstrom)
***
ATOMIC_POSITIONS (crystal)
***
K_POINTS {automatic}
***
Dr Haoran
Xinjiang University, Urumqi
18/4/2024
___
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people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users@lists.quantum-espresso.org
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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users@lists.quantum-espresso.org
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