Re: [QE-users] NEB unexpected crash
Dear Carlo, Thanks a lot! This should not happen because I'm using a queue batch system based on PBS. So normally if I close the terminal the jobs continue to run smoothly. Ciao, Mauro. Il giorno mar 21 set 2021 alle ore 10:31 Carlo Nervi ha scritto: > Dear Mauro, > sometimes the way in which remote shell behave could stop the child > processes. > If you are running programs over SSH and if the connection drops, the > session will be terminated, and all the executed processes will stop. > To avoid that you may use the *nohup *(No Hang Up) command. > > In my system, for example, I can avoid the stopping of the processes by > running normally my commands in background (&) and then exiting the shell. > This guarantee (according to my system settings) that the child processes > will be stopped. > HTH, > Carlo > > > Il giorno mar 21 set 2021 alle ore 09:47 Mauro Sgroi < > maurofrancesco.sg...@gmail.com> ha scritto: > >> Dear Paolo, >> all the 3 conditions you are reporting should not be the case. >> I'm going to investigate with our HPC manager. >> Best regards, >> Mauro. >> >> Il giorno mar 21 set 2021 alle ore 08:56 Paolo Giannozzi < >> p.gianno...@gmail.com> ha scritto: >> >>> On Mon, Sep 20, 2021 at 5:52 PM Mauro Sgroi < >>> maurofrancesco.sg...@gmail.com> wrote: >>> What does " Program stopped by user request" mean? >>> >>> it means one of the following cases: >>> - the time limit specified in input has been reached >>> - a file $prefix.EXIT or $prefix.save/EXIT or something like that has >>> been detected >>> - signal USR1 has been sent to the process (only if compiled with a >>> specific preprocessing option) >>> >>> Is there a way to fix this behaviour? >>> >>> there is nothing to be fixed: one should figure out which of the three >>> cases mentioned above has occurred >>> >>> Paolo >>> >>> Thanks a lot and best regards, Mauro Sgroi. ___ 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 >>> Phone +39-0432-558216, fax +39-0432-558222 >>> >>> ___ >>> 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 >> >> ___ >> 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 > > > > -- > > > Prof. Carlo Nervi carlo.ne...@unito.it Tel:+39 0116707507/8 > Fax: +39 0116707855 - Dipartimento di Chimica, via > P. Giuria 7, 10125 Torino, Italy.http://lem.ch.unito.it/ > > *ICCC2020 has been postponed at 2022* > > ICCC 2022 28 August - 2 September 2022, Rimini, Italy: http://www.iccc2020.com > International Conference on Coordination Chemistry (ICCC 2022) > > ___ > 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 ___ 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] NEB unexpected crash
Dear Mauro, sometimes the way in which remote shell behave could stop the child processes. If you are running programs over SSH and if the connection drops, the session will be terminated, and all the executed processes will stop. To avoid that you may use the *nohup *(No Hang Up) command. In my system, for example, I can avoid the stopping of the processes by running normally my commands in background (&) and then exiting the shell. This guarantee (according to my system settings) that the child processes will be stopped. HTH, Carlo Il giorno mar 21 set 2021 alle ore 09:47 Mauro Sgroi < maurofrancesco.sg...@gmail.com> ha scritto: > Dear Paolo, > all the 3 conditions you are reporting should not be the case. > I'm going to investigate with our HPC manager. > Best regards, > Mauro. > > Il giorno mar 21 set 2021 alle ore 08:56 Paolo Giannozzi < > p.gianno...@gmail.com> ha scritto: > >> On Mon, Sep 20, 2021 at 5:52 PM Mauro Sgroi < >> maurofrancesco.sg...@gmail.com> wrote: >> >>> >>> What does " Program stopped by user request" mean? >>> >> >> it means one of the following cases: >> - the time limit specified in input has been reached >> - a file $prefix.EXIT or $prefix.save/EXIT or something like that has >> been detected >> - signal USR1 has been sent to the process (only if compiled with a >> specific preprocessing option) >> >> Is there a way to fix this behaviour? >>> >> >> there is nothing to be fixed: one should figure out which of the three >> cases mentioned above has occurred >> >> Paolo >> >> >>> Thanks a lot and best regards, >>> Mauro Sgroi. >>> ___ >>> 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 >> Phone +39-0432-558216, fax +39-0432-558222 >> >> ___ >> 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 > > ___ > 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 -- Prof. Carlo Nervi carlo.ne...@unito.it Tel:+39 0116707507/8 Fax: +39 0116707855 - Dipartimento di Chimica, via P. Giuria 7, 10125 Torino, Italy.http://lem.ch.unito.it/ *ICCC2020 has been postponed at 2022* ICCC 2022 28 August - 2 September 2022, Rimini, Italy: http://www.iccc2020.com International Conference on Coordination Chemistry (ICCC 2022) ___ 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] NEB unexpected crash
Dear Paolo, all the 3 conditions you are reporting should not be the case. I'm going to investigate with our HPC manager. Best regards, Mauro. Il giorno mar 21 set 2021 alle ore 08:56 Paolo Giannozzi < p.gianno...@gmail.com> ha scritto: > On Mon, Sep 20, 2021 at 5:52 PM Mauro Sgroi < > maurofrancesco.sg...@gmail.com> wrote: > >> >> What does " Program stopped by user request" mean? >> > > it means one of the following cases: > - the time limit specified in input has been reached > - a file $prefix.EXIT or $prefix.save/EXIT or something like that has been > detected > - signal USR1 has been sent to the process (only if compiled with a > specific preprocessing option) > > Is there a way to fix this behaviour? >> > > there is nothing to be fixed: one should figure out which of the three > cases mentioned above has occurred > > Paolo > > >> Thanks a lot and best regards, >> Mauro Sgroi. >> ___ >> 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 > Phone +39-0432-558216, fax +39-0432-558222 > > ___ > 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 ___ 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] NEB unexpected crash
Dear Takahiro Chiba,
normally I don't set the max_seconds option expecting that the job runs
undefinitively.
The large number of steps is due to difficulties in convergence.
I'm going to verify if the problem is due to the batch queue system.
Best regards,
Mauro.
Il giorno mar 21 set 2021 alle ore 06:54 Takahiro Chiba <
takahiro_ch...@eis.hokudai.ac.jp> ha scritto:
> Dear Sgroi,
>
> Because "max_seconds" is not written in the "&control" section, I
> think this is related to your batch queue. Could you make sure that
> your job is not interrupted or paused by the batch queue?
>
> P.S.
> I am surprised to see your huge nstep_path. Is it intentional?
>
> ---Sender---
> Takahiro Chiba
> 1st-year student at grad. school of chem. sci. and eng., Hokkaido Univ.
> Expected graduation date: Mar. 2023
> takahiro_ch...@eis.hokudai.ac.jp
> -
>
> 2021年9月21日(火) 0:52 Mauro Sgroi :
> >
> > Dear QE users,
> > I'm writing to point out a strange behavior I'm facing using PWNEB.
> >
> > I'm trying to calculate the activation energy related to the movement of
> a Li-ion in NiO doped with one cobalt atom.
> >
> > My input is the following:
> > BEGIN
> > BEGIN_PATH_INPUT
> > &PATH
> > restart_mode = 'from_scratch'
> > string_method = 'neb'
> > nstep_path= 2500
> > ds= 1.D0
> > opt_scheme= "broyden"
> > num_of_images = 12
> > CI_scheme = "no-CI"
> > path_thr = 0.05D0
> > use_freezing = .true.
> > minimum_image = .true.
> > first_last_opt= .true.
> > opt_scheme='broyden'
> > /
> > END_PATH_INPUT
> > BEGIN_ENGINE_INPUT
> > &CONTROL
> > outdir = '/workhpc/FCA/FCA_CRF_STRUT/sgroi/tmp/modalis2/NEB_CO_no_CI'
> > prefix = 'R_3m_ODH_NEB_Co'
> > pseudo_dir = '/workhpc/FCA/FCA_CRF_STRUT/sgroi/DATABASE/ESPRESSO'
> > /
> > &SYSTEM
> > degauss = 1.0e-02
> > ecutrho = 3.25000e+02
> > ecutwfc = 5.0e+01
> > ibrav = 0
> > nat = 47
> > nspin = 2
> > ntyp = 4
> > occupations = "smearing"
> > smearing = "gaussian"
> > starting_magnetization(1) = 0.0e+00
> > starting_magnetization(2) = 0.5e-01
> > starting_magnetization(3) = 0.0e+00
> > starting_magnetization(4) = 0.0e-01
> > lda_plus_u = .true.
> > Hubbard_U(2) = 6.2
> > Hubbard_U(4) = 6.2
> > /
> > &ELECTRONS
> > conv_thr = 1.0e-07
> > electron_maxstep = 300
> > mixing_beta = 1.0e-01
> > startingpot = "atomic"
> > startingwfc = "atomic+random"
> > /
> > &IONS
> > /
> > ATOMIC_SPECIES
> > Li 6.94100 Li.pbe-sl-rrkjus_psl.1.0.0.UPF
> > Ni 58.69340 Ni.pbe-n-rrkjus_psl.1.0.0.UPF
> > O 15.99940 O.pbe-nl-rrkjus_psl.1.0.0.UPF
> > Co 58.93319 Co.pbe-n-rrkjus_psl.1.0.0.UPF
> > BEGIN_POSITIONS
> > FIRST_IMAGE
> > ATOMIC_POSITIONS {angstrom}
> > Ni -1.678337 2.906965-4.880813 0 0 0
> > Ni 2.517505-1.453482 0.001 1 1
> > Co 1.678337-2.906965 4.8808131 1 1
> > Ni 0.8459221.465179-4.802724 0 0 0
> > Ni 2.5175051.4534820.001 1 1
> > Ni 1.6918430.004.8027241 1 1
> > Ni 0.845922-1.465179 -4.802724 0 0 0
> > Ni 0.002.9069650.001 1 1
> > Co 0.000.000.001 1 1
> > Ni -0.845922 -1.465179 4.8027241 1 1
> > Ni -0.845922 1.4651794.8027241 1 1
> > Ni -1.691843 0.00-4.802724 0 0 0
> > O 1.7552230.00-5.980511 0 0 0
> > O 0.820882-1.421809 -1.166320 0 0 0
> > O 0.0867322.9069653.7156931 1 1
> > O -0.877611 1.520067-5.980511 0 0 0
> > O 0.8208821.421809-1.166320 0 0 0
> > O 0.000.003.9260371 1 1
> > O -0.877611 -1.520067 -5.980511 0 0 0
> > O -1.678337 2.906965-0.877278 0 0 0
> > O -1.641764 0.00-1.166320 0 0 0
> > O 2.4741401.5285943.7156931 1 1
> > O 2.474140-1.528594 3.7156931 1 1
> > O 1.678337-2.906965 -5.671852 0 0 0
> > O 2.560871-1.378371 -3.715693 0 0 0
> > O 1.678337-2.906965 0.8772781 1 1
> > O 0.8776111.5200675.9805110 0 0
> > O 0.000.00-3.926037 0 0 0
> > O 1.6417640.001.1663201 1 1
> > O 0.877611-1.520067
Re: [QE-users] NEB unexpected crash
On Mon, Sep 20, 2021 at 5:52 PM Mauro Sgroi wrote: > > What does " Program stopped by user request" mean? > it means one of the following cases: - the time limit specified in input has been reached - a file $prefix.EXIT or $prefix.save/EXIT or something like that has been detected - signal USR1 has been sent to the process (only if compiled with a specific preprocessing option) Is there a way to fix this behaviour? > there is nothing to be fixed: one should figure out which of the three cases mentioned above has occurred Paolo > Thanks a lot and best regards, > Mauro Sgroi. > ___ > 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 Phone +39-0432-558216, fax +39-0432-558222 ___ 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] NEB unexpected crash
Dear Sgroi,
Because "max_seconds" is not written in the "&control" section, I
think this is related to your batch queue. Could you make sure that
your job is not interrupted or paused by the batch queue?
P.S.
I am surprised to see your huge nstep_path. Is it intentional?
---Sender---
Takahiro Chiba
1st-year student at grad. school of chem. sci. and eng., Hokkaido Univ.
Expected graduation date: Mar. 2023
takahiro_ch...@eis.hokudai.ac.jp
-
2021年9月21日(火) 0:52 Mauro Sgroi :
>
> Dear QE users,
> I'm writing to point out a strange behavior I'm facing using PWNEB.
>
> I'm trying to calculate the activation energy related to the movement of a
> Li-ion in NiO doped with one cobalt atom.
>
> My input is the following:
> BEGIN
> BEGIN_PATH_INPUT
> &PATH
> restart_mode = 'from_scratch'
> string_method = 'neb'
> nstep_path= 2500
> ds= 1.D0
> opt_scheme= "broyden"
> num_of_images = 12
> CI_scheme = "no-CI"
> path_thr = 0.05D0
> use_freezing = .true.
> minimum_image = .true.
> first_last_opt= .true.
> opt_scheme='broyden'
> /
> END_PATH_INPUT
> BEGIN_ENGINE_INPUT
> &CONTROL
> outdir = '/workhpc/FCA/FCA_CRF_STRUT/sgroi/tmp/modalis2/NEB_CO_no_CI'
> prefix = 'R_3m_ODH_NEB_Co'
> pseudo_dir = '/workhpc/FCA/FCA_CRF_STRUT/sgroi/DATABASE/ESPRESSO'
> /
> &SYSTEM
> degauss = 1.0e-02
> ecutrho = 3.25000e+02
> ecutwfc = 5.0e+01
> ibrav = 0
> nat = 47
> nspin = 2
> ntyp = 4
> occupations = "smearing"
> smearing = "gaussian"
> starting_magnetization(1) = 0.0e+00
> starting_magnetization(2) = 0.5e-01
> starting_magnetization(3) = 0.0e+00
> starting_magnetization(4) = 0.0e-01
> lda_plus_u = .true.
> Hubbard_U(2) = 6.2
> Hubbard_U(4) = 6.2
> /
> &ELECTRONS
> conv_thr = 1.0e-07
> electron_maxstep = 300
> mixing_beta = 1.0e-01
> startingpot = "atomic"
> startingwfc = "atomic+random"
> /
> &IONS
> /
> ATOMIC_SPECIES
> Li 6.94100 Li.pbe-sl-rrkjus_psl.1.0.0.UPF
> Ni 58.69340 Ni.pbe-n-rrkjus_psl.1.0.0.UPF
> O 15.99940 O.pbe-nl-rrkjus_psl.1.0.0.UPF
> Co 58.93319 Co.pbe-n-rrkjus_psl.1.0.0.UPF
> BEGIN_POSITIONS
> FIRST_IMAGE
> ATOMIC_POSITIONS {angstrom}
> Ni -1.678337 2.906965-4.880813 0 0 0
> Ni 2.517505-1.453482 0.001 1 1
> Co 1.678337-2.906965 4.8808131 1 1
> Ni 0.8459221.465179-4.802724 0 0 0
> Ni 2.5175051.4534820.001 1 1
> Ni 1.6918430.004.8027241 1 1
> Ni 0.845922-1.465179 -4.802724 0 0 0
> Ni 0.002.9069650.001 1 1
> Co 0.000.000.001 1 1
> Ni -0.845922 -1.465179 4.8027241 1 1
> Ni -0.845922 1.4651794.8027241 1 1
> Ni -1.691843 0.00-4.802724 0 0 0
> O 1.7552230.00-5.980511 0 0 0
> O 0.820882-1.421809 -1.166320 0 0 0
> O 0.0867322.9069653.7156931 1 1
> O -0.877611 1.520067-5.980511 0 0 0
> O 0.8208821.421809-1.166320 0 0 0
> O 0.000.003.9260371 1 1
> O -0.877611 -1.520067 -5.980511 0 0 0
> O -1.678337 2.906965-0.877278 0 0 0
> O -1.641764 0.00-1.166320 0 0 0
> O 2.4741401.5285943.7156931 1 1
> O 2.474140-1.528594 3.7156931 1 1
> O 1.678337-2.906965 -5.671852 0 0 0
> O 2.560871-1.378371 -3.715693 0 0 0
> O 1.678337-2.906965 0.8772781 1 1
> O 0.8776111.5200675.9805110 0 0
> O 0.000.00-3.926037 0 0 0
> O 1.6417640.001.1663201 1 1
> O 0.877611-1.520067 5.9805110 0 0
> O -0.086732 2.906965-3.715693 0 0 0
> O -0.820882 1.4218091.1663201 1 1
> O -0.820882 -1.421809 1.1663201 1 1
> O -1.678337 2.9069655.6718520 0 0
> O -1.755223 0.005.9805110 0 0
> O 2.5608711.378371-3.715693 0 0 0
> Li 2.517505-1.453482 7.2400130 0 0
> Li 1.678337-2.906965 -2.350686 0 0 0
> Li 0.000.007.24001
