[QE-users] users Digest, Vol 153, Issue 2
Nawaf A
iamnawafa at gmail.com
Fri Apr 3 13:34:28 CEST 2020
Respected Sir,
How much computational power is sufficient? (for 47 atoms, HSE).
( The maximum I employed is 2.4 GHz 120 core. I tried in high memory node
with 1.5 TB RAM & 80 core also )
Thank You
Nawaf A
MSc Energy Science student
IIT Bombay
On Thu, Apr 2, 2020 at 3:30 PM <users-request at lists.quantum-espresso.org>
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> Today's Topics:
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> 1. Re: misbehaving pp.x for plot_num 3 (Paolo Giannozzi)
> 2. Videos of the "Virtual Edition" Wannier90 School online on
> Materials Cloud Learn (Giovanni Pizzi)
> 3. Problem using hse calculation (Nawaf A)
> 4. Re: Problem using hse calculation (Lorenzo Paulatto)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 1 Apr 2020 14:24:12 +0200
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] misbehaving pp.x for plot_num 3
> Message-ID:
> <
> CAPMgbCukq17LvjAiMuEehZwQw9k8JHJ28yGwd708nnL7bQiyAQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On Wed, Apr 1, 2020 at 8:27 AM <pdelugas at sissa.it> wrote:
>
> Maybe the manual is not very clear.
> >
>
> or maybe it is clear but wrong: for plot_num=3, it says
>
> emax upper boundary of energy grid (in eV).
> If not specified, LDOS is computed just for energy
> emin
>
> Paolo
>
> The ldos is always computed from emin to emax. If you specify values for
> > emin or emax, the program will use them; otherwise it assumes the lowest
> > and highest computed levels as emin and emax.
> > Hope it helps
> > Pietro
> >
> >
> >
> >
> >
> > Il 1 apr 2020 6:17 AM, Christoph Wolf <wolf.christoph at qns.science> ha
> > scritto:
> >
> > Dear all,
> >
> > I think pp.x does not follow the rule printed in the manual in the latest
> > version 6.5. The manual says that if emax is not specified the LDOS will
> > only be integrated for emin, however in my test it still calculates it
> for
> > other energies as well:
> >
> > &inputpp
> > prefix = "agmgofe",
> > outdir = "./tmp",
> > plot_num=3,
> > filplot = "wf.dat"
> > * emin = -.8283*
> > degauss_ldos = 0.1 ! in eV !
> > /
> >
> >
> > output:
> >
> > Calling punch_plot, plot_num = 3
> >
> > Energy = -0.82830 eV, broadening = 0.10000eV
> > Writing data to file wf.dat001
> >
> > Calling punch_plot, plot_num = 3
> >
> > Energy = -0.72830 eV, broadening = 0.10000eV
> > Writing data to file wf.dat002
> >
> > Calling punch_plot, plot_num = 3
> >
> > Energy = -0.62830 eV, broadening = 0.10000eV
> > Writing data to file wf.dat003
> >
> > Calling punch_plot, plot_num = 3
> >
> > Energy = -0.52830 eV, broadening = 0.10000eV
> > Writing data to file wf.dat004
> >
> > Calling punch_plot, plot_num = 3
> >
> > Energy = -0.42830 eV, broadening = 0.10000eV
> > Writing data to file wf.dat005
> >
> > Calling punch_plot, plot_num = 3
> >
> > Energy = -0.32830 eV, broadening = 0.10000eV
> > Writing data to file wf.dat006
> >
> > Calling punch_plot, plot_num = 3
> >
> > Energy = -0.22830 eV, broadening = 0.10000eV
> > Writing data to file wf.dat007
> >
> > ...
> >
> > until it reaches Ef. Seems like emax also defaults to Ef
> >
> > to avoid this behavior emax has to be set to the same as emin.
> >
> > Best,
> > Chris
> > --
> > Postdoctoral Researcher
> > Center for Quantum Nanoscience, Institute for Basic Science
> > Ewha Womans University, Seoul, South Korea
> >
> >
> > _______________________________________________
> > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso
> )
> > users mailing list users at 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 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
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> ------------------------------
>
> Message: 2
> Date: Wed, 1 Apr 2020 17:30:21 +0000
> From: Giovanni Pizzi <giovanni.pizzi at epfl.ch>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: [QE-users] Videos of the "Virtual Edition" Wannier90 School
> online on Materials Cloud Learn
> Message-ID: <D7895950-CA88-47CF-A662-C2CBF2250A19 at epfl.ch>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
>
> We are glad to inform you that the video recordings of the first "Virtual
> Edition? of the Wannier90 School [1] are now all available in the Learn
> section of Materials Cloud, at this link:
>
>
> https://www.materialscloud.org/learn/sections/C8ad91/wannier90-v3-0-school-virtual-edition-2020
>
> Beside the videos, the Learn section also includes:
> - the slides of the presentations;
> - the list of all questions asked during the presentations, with detailed
> replies by the speakers;
> - all tutorial hands-on materials.
>
> In particular, the tutorial was run on the "Quantum Mobile" Virtual
> Machine<https://www.materialscloud.org/work/quantum-mobile> that made it
> very easy for all 30+ participants to quickly get started with the various
> codes presented (Quantum ESPRESSO, Wannier90, WannierTools, AiiDA, EPW,
> ...) with almost zero setup time.
>
> As an additional benefit, anybody can download again the Quantum Mobile
> [2] and run the same tutorials, even if they could not attend the event.
>
> We believe that these virtual events can be very effective and can become
> a model for the future, even when travel restrictions will be lifted, with
> the additional advantages of allowing a broader and more diverse audience,
> and of reducing our carbon footprint, under the slogan "less carbon, more
> silicon"!
>
> Best regards,
> Giovanni Pizzi, on behalf of all event organisers
>
> [1] http://www.wannier.org/events/school-2020-virtual-edition/
> [2] The tutorial was run using version 20.03.1:
> https://github.com/marvel-nccr/quantum-mobile/releases/tag/20.03.1
>
> PS: sorry if you received this message multiple times, but we felt this
> could be relevant also to the Quantum ESPRESSO community
>
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> ------------------------------
>
> Message: 3
> Date: Thu, 2 Apr 2020 11:01:58 +0530
> From: Nawaf A <iamnawafa at gmail.com>
> To: users at lists.quantum-espresso.org
> Subject: [QE-users] Problem using hse calculation
> Message-ID:
> <CALk+9Mv_j1-vqVDzqTJHZ7yByXEPjv0XH=cMq9KKxa+m=
> ev-xQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear QE developers and users .
>
> while trying to do hse calculation ( 47 atoms ) the calculation is not
> terminating , it converges but ace calculation is not terminating.
> This is how the output file ends
>
> the Fermi energy is 7.5626 ev
>
> ! total energy = -7271.48782233 Ry
> Harris-Foulkes estimate = -7271.48803855 Ry
> estimated scf accuracy < 0.00023200 Ry
>
> convergence has been achieved in 11 iterations
>
> Using ACE for calculation of exact exchange
>
> EXX grid: 48141 G-vectors FFT dimensions: ( 45, 45, 45)
> Application 969344 exit codes: 1, 139
> Application 969344 resources: utime ~410607s, stime ~626186s, Rss ~43360,
> inblocks ~1310, outblocks ~0
>
> -----------------------------------------------------------------------------------------------------
>
> 18) perftools-base/7.0.0
> 19) PrgEnv-intel/6.0.4
> 20) intel/18.0.1.163
> 21) craype-network-aries
> 22) craype/2.5.13
> 23) cray-mpich/7.7.0
> 24) craype-hugepages2M
> 25) pbs/default
> cray-mpich/7.7.0 requires craype/1.00 or later
> 16.0.4(103):ERROR:105: Unable to locate a modulefile for
> 'craype-x86-skylake'
> 16.0.4(104):ERROR:105: Unable to locate a modulefile for
> 'craype-hugepages2M'
> Currently Loaded Modulefiles:
> 1) modules/3.2.10.6
> 2) alps/6.5.30-6.0.5.1_5.1__g60cce32.ari
> 3) nodestat/2.3.78-6.0.5.0_8.13__gbe57af8.ari
> 4) sdb/3.3.751-6.0.5.0_20.25__gb936019.ari
> 5) udreg/2.3.2-6.0.5.0_13.12__ga14955a.ari
> 6) ugni/6.0.14-6.0.5.0_16.9__g19583bb.ari
> 7) gni-headers/5.0.12-6.0.5.0_2.15__g2ef1ebc.ari
> 8) dmapp/7.1.1-6.0.5.0_49.8__g1125556.ari
> 9) xpmem/2.2.4-6.0.5.1_8.6__g35d5e73.ari
> 10) llm/21.3.467-6.0.5.0_25.1__g4c6f300.ari
> 11) nodehealth/5.5.7-6.0.5.0_9.8__g7732908.ari
> 12) system-config/3.5.2545-6.0.5.0_5.1__g8a8b20f.ari
> 13) sysadm/2.4.125-6.0.5.0_16.13__g98e00a9.ari
> 14) Base-opts/2.4.123-6.0.5.0_11.2__g6460790.ari
> 15) rca/2.2.16-6.0.5.0_15.34__g5e09e6d.ari
> 16) craype-network-aries
> 17) craype-hugepages2M
> 18) pbs/default
> 19) PrgEnv-intel/6.0.4
> 20) cray-fftw/3.3.6.2
> 21) intel/16.0.4.258
> 22) /home/apps/qe/6.2.0/modulefiles/int/16.0.4
> =>> PBS: job killed: walltime 345616 exceeded limit 345600
> aprun: Apid 969344: Caught signal Terminated, sending to application
> forrtl: error (78): process killed (SIGTERM)
> Image PC Routine Line Source
>
> libintlc.so.5 00002AAAB1EA579D Unknown Unknown Unknown
> libintlc.so.5 00002AAAB1EA3637 Unknown Unknown Unknown
> pw.x 0000000020C32DA4 Unknown Unknown Unknown
> pw.x 0000000020C32BB6 Unknown Unknown Unknown
> pw.x 0000000020B9F659 Unknown Unknown Unknown
> pw.x 0000000020BA677E Unknown Unknown Unknown
> Unknown 00002AAAB7168B10 Unknown Unknown Unknown
> libpthread.so.0 00002AAAB7165785 Unknown Unknown Unknown
> forrtl: error (78): process killed (SIGTERM)
>
> This is how the file listing modules terminates , the walltime is 96 hours.
> I have attatched my input file . I have tried smaller parameters and
> smearing instead of tetrahedron , still the same error.
>
> Thank You.
> Nawaf A
> MSc Energy Science student
> IIT Bombay
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> ------------------------------
>
> Message: 4
> Date: Thu, 2 Apr 2020 09:18:53 +0200
> From: Lorenzo Paulatto <paulatz at gmail.com>
> To: users at lists.quantum-espresso.org
> Subject: Re: [QE-users] Problem using hse calculation
> Message-ID: <366f1acf-188e-2029-5f58-85e1535ecd30 at gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Hello Nawaf,
> the HSE calculation has to do a self-consistency on the wavefunctions
> that starts from a standard local-density PBE calculation. Note that the
> HSE calculation, even when using the ACE algorithm, is orders of
> magnitude longer than the PBE one.
>
> It is the PBe calculation that converges in your case, the HSE one is
> too heavy for your computer, it cannot even reach the first step when it
> is killed (after 4 days).
>
> regards
>
>
> >
> > while trying to do hse calculation ( 47 atoms ) the calculation is not
> > terminating , it converges but ace calculation is not terminating.
> > This is how the output file ends
> >
> > ? ? the Fermi energy is ? ? 7.5626 ev
> >
> > ! ? ?total energy ? ? ? ? ? ? ?= ? -7271.48782233 Ry
> > ? ? ?Harris-Foulkes estimate ? = ? -7271.48803855 Ry
> > ? ? ?estimated scf accuracy ? ?< ? ? ? 0.00023200 Ry
> >
> > ? ? ?convergence has been achieved in ?11 iterations
> >
> > ? ? ?Using ACE for calculation of exact exchange
> >
> > ? ? ?EXX grid: ? ?48141 G-vectors ? ? FFT dimensions: ( ?45, ?45, ?45)
> > Application 969344 exit codes: 1, 139
> > Application 969344 resources: utime ~410607s, stime ~626186s, Rss
> > ~43360, inblocks ~1310, outblocks ~0
> >
> -----------------------------------------------------------------------------------------------------
> >
> > ?18) perftools-base/7.0.0
> > ?19) PrgEnv-intel/6.0.4
> > ?20) intel/18.0.1.163 <http://18.0.1.163>
> > ?21) craype-network-aries
> > ?22) craype/2.5.13
> > ?23) cray-mpich/7.7.0
> > ?24) craype-hugepages2M
> > ?25) pbs/default
> > cray-mpich/7.7.0 requires craype/1.00 or later
> > 16.0.4(103):ERROR:105: Unable to locate a modulefile for
> > 'craype-x86-skylake'
> > 16.0.4(104):ERROR:105: Unable to locate a modulefile for
> > 'craype-hugepages2M'
> > Currently Loaded Modulefiles:
> > ? 1) modules/3.2.10.6 <http://3.2.10.6>
> > ? 2) alps/6.5.30-6.0.5.1_5.1__g60cce32.ari
> > ? 3) nodestat/2.3.78-6.0.5.0_8.13__gbe57af8.ari
> > ? 4) sdb/3.3.751-6.0.5.0_20.25__gb936019.ari
> > ? 5) udreg/2.3.2-6.0.5.0_13.12__ga14955a.ari
> > ? 6) ugni/6.0.14-6.0.5.0_16.9__g19583bb.ari
> > ? 7) gni-headers/5.0.12-6.0.5.0_2.15__g2ef1ebc.ari
> > ? 8) dmapp/7.1.1-6.0.5.0_49.8__g1125556.ari
> > ? 9) xpmem/2.2.4-6.0.5.1_8.6__g35d5e73.ari
> > ?10) llm/21.3.467-6.0.5.0_25.1__g4c6f300.ari
> > ?11) nodehealth/5.5.7-6.0.5.0_9.8__g7732908.ari
> > ?12) system-config/3.5.2545-6.0.5.0_5.1__g8a8b20f.ari
> > ?13) sysadm/2.4.125-6.0.5.0_16.13__g98e00a9.ari
> > ?14) Base-opts/2.4.123-6.0.5.0_11.2__g6460790.ari
> > ?15) rca/2.2.16-6.0.5.0_15.34__g5e09e6d.ari
> > ?16) craype-network-aries
> > ?17) craype-hugepages2M
> > ?18) pbs/default
> > ?19) PrgEnv-intel/6.0.4
> > ?20) cray-fftw/3.3.6.2 <http://3.3.6.2>
> > ?21) intel/16.0.4.258
> > ?22) /home/apps/qe/6.2.0/modulefiles/int/16.0.4
> > =>> PBS: job killed: walltime 345616 exceeded limit 345600
> > aprun: Apid 969344: Caught signal Terminated, sending to application
> > forrtl: error (78): process killed (SIGTERM)
> > Image ? ? ? ? ? ? ?PC ? ? ? ? ? ? ? ?Routine ? ? ? ? ? ?Line ? ? ?
> ?Source
> > libintlc.so.5 ? ? ?00002AAAB1EA579D ?Unknown ? ? ? ? ? ? ? Unknown
> ?Unknown
> > libintlc.so.5 ? ? ?00002AAAB1EA3637 ?Unknown ? ? ? ? ? ? ? Unknown
> ?Unknown
> > pw.x ? ? ? ? ? ? ? 0000000020C32DA4 ?Unknown ? ? ? ? ? ? ? Unknown
> ?Unknown
> > pw.x ? ? ? ? ? ? ? 0000000020C32BB6 ?Unknown ? ? ? ? ? ? ? Unknown
> ?Unknown
> > pw.x ? ? ? ? ? ? ? 0000000020B9F659 ?Unknown ? ? ? ? ? ? ? Unknown
> ?Unknown
> > pw.x ? ? ? ? ? ? ? 0000000020BA677E ?Unknown ? ? ? ? ? ? ? Unknown
> ?Unknown
> > Unknown ? ? ? ? ? ?00002AAAB7168B10 ?Unknown ? ? ? ? ? ? ? Unknown
> ?Unknown
> > libpthread.so.0 ? ?00002AAAB7165785 ?Unknown ? ? ? ? ? ? ? Unknown
> ?Unknown
> > forrtl: error (78): process killed (SIGTERM)
> >
> > This is how the file listing modules terminates , the walltime is 96
> > hours. I have attatched my input file . I have tried smaller parameters
> > and smearing instead of tetrahedron , still the same error.
> >
> > Thank You.
> > Nawaf A
> > MSc Energy Science student
> > IIT Bombay
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso
> )
> > users mailing list users at lists.quantum-espresso.org
> > https://lists.quantum-espresso.org/mailman/listinfo/users
> >
>
> --
> Lorenzo Paulatto - Paris
>
>
> ------------------------------
>
> Subject: Digest Footer
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> ------------------------------
>
> End of users Digest, Vol 153, Issue 2
> *************************************
>
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