[Pw_forum] Problems computing cholensky
Laurens Siemons
laurenssiemons at hotmail.be
Mon Feb 26 10:26:14 CET 2018
Hi,
Thanks all for the response. I tried to run Will DeBenedetti's script for his anatase (001) slab and the calculation runs without an error (on 4 nodes and 20 cores per node). I don't understand though why his script does run and mine does not. Does anybody has an idea about this?
I also tried to add 'ndiag=1' for some of my scripts like Mostafa Youssef suggested, but unfortunately without succes.
Somebody at my departement suggested to try and run it on 1 node with 20 cores. For some reason this does work. This will probably not be enough power to complete the calculation, but I don't get the error 'problems computing cholensky'. Does anybody have a suggestion why it does work on 1 node with 20 cores, but fails when I try to increase my nodes? (except when I try to run Will's script)
Thanks in advance,
Laurens Siemons
________________________________
Van: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> namens Paolo Giannozzi <p.giannozzi at gmail.com>
Verzonden: zondag 25 februari 2018 8:33
Aan: PWSCF Forum
Onderwerp: Re: [Pw_forum] Problems computing cholensky
You can use cell_parameters together with A or celldm(1).
On Sat, Feb 24, 2018 at 8:53 PM, Manu Hegde <mhegde at uwaterloo.ca<mailto:mhegde at uwaterloo.ca>> wrote:
Hi,
I do not know much about your system but looking quickly into the crystal structure there is something that might be causing problem. Looks like you have set ibrav=0, in that case you have to use card cell_parameters. A=xx not required. Also double check ypur system with xcrysden before starting the calculations.
Manu
(SFU)
On Fri, Feb 23, 2018 at 10:19 AM, <elchatz at auth.gr<mailto:elchatz at auth.gr>> wrote:
Hello Laurens Siemons,
Although I am not one of the experts, I had the same problem in one of
the scf runs I was doing for a GW calculation. Because of the high
number of bands and ecutwfc that I needed to use and in order to get
any results, I had to run the simulation on 100 cores. The strange
thing for me also was that the first one I tried run, but then nothing
again. After a few weeks of trying I was notified by our cluster
services that I should not use more than 60 cores as the I/O
operations that are done by QE were too high and the disk could not
cope. I gave up GW since then, but if there is a solution to this
problem, I would like to hear it too :S
Eleni
Quoting Laurens Siemons <laurenssiemons at hotmail.be<mailto:laurenssiemons at hotmail.be>>:
> Dear all,
>
>
> I'm a master student chemistry and I'm using QE (v. 6.1) for a relax
> calculation of a rutile 101 slab with a vacuum above it.
>
> I'm getting the famous error:
>
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error in routine cdiaghg (161):
> problems computing cholesky
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> I've read almost every related topic on the forum that I could find
> and I tried a lot already to overcome this, like:
> - changing values for ecutwfc and ecutrho
> - changing mixing_beta
> - changing functionals
> - Tried to run the calcualtion with other input files (anatase 101, 001...)
> - Changed diagonalization to 'cg' (In this case it calculates some
> itterations but then crashes with the error: 'Error in routine
> c_bands (1): >> too many bands are not converged')
>
> Nothing seems to help and I'm out of options... I even tried to run
> a calculation of my predecessor (that has succeeded in the past) but
> this also failed (he used an older version of QE though...).
>
> I'm postig my input file at the end here and I really hope somebody
> can help me.
>
> Kind Regards,
> Laurens Siemons
>
> &CONTROL
> calculation = 'relax'
> restart_mode = "from_scratch",
> prefix = "testen",
> pseudo_dir =
> '/data/antwerpen/204/vsc20442/pseudo/pslibrary.1.0.0/wc/PSEUDOPOTENTIALS'
> outdir = '/data/antwerpen/204/vsc20442'
> nstep = 100
> /
> &SYSTEM
> ibrav = 0
> A = 4.59631
> nat = 36
> ntyp = 2
> ecutwfc = 60
> ecutrho = 600
> /
> &ELECTRONS
> electron_maxstep = 300
> mixing_beta = 0.10
> conv_thr = 1.0d-8
> mixing_mode = 'local-TF'
> diago_thr_init = 1e-4
> /
> &IONS
> ion_dynamics = 'bfgs'
> ion_positions = 'default'
> /
> CELL_PARAMETERS {alat}
> 1.000000000000000 0.000000000000000 0.640859733133753
> 0.000000000000000 2.000000000000000 0.000000000000000
> 0.000000000000000 0.000000000000000 3.845158398802518
> ATOMIC_SPECIES
> O 15.99900 O.wc-n-kjpaw_psl.1.0.0.UPF
> Ti 47.86700 Ti.wc-spn-kjpaw_psl.1.0.0.UPF
> ATOMIC_POSITIONS {crystal}
> Ti -0.000000000000000 -0.000000000000000 0.075000000000000 0 0 0
> Ti -0.000000000000000 -0.000000000000000 0.408333333333333
> Ti -0.000000000000000 0.500000000000000 0.241666666666667
> Ti -0.000000000000000 -0.000000000000000 0.241666666666667
> Ti -0.000000000000000 0.500000000000000 0.075000000000000 0 0 0
> Ti -0.000000000000000 0.500000000000000 0.408333333333333
> Ti 0.500000000000000 0.250000000000000 0.075000000000000 0 0 0
> Ti 0.500000000000000 0.250000000000000 0.408333333333333
> Ti 0.500000000000000 0.750000000000000 0.241666666666667
> Ti 0.500000000000000 0.250000000000000 0.241666666666667
> Ti 0.500000000000000 0.750000000000000 0.075000000000000 0 0 0
> Ti 0.500000000000000 0.750000000000000 0.408333333333333
> O 0.304303000000000 0.152151500000000 0.024282833333333 0 0 0
> O 0.304303000000000 0.152151500000000 0.357616166666667
> O 0.304303000000000 0.652151500000000 0.190949500000000
> O 0.304303000000000 0.152151500000000 0.190949500000000
> O 0.304303000000000 0.652151500000000 0.024282833333333 0 0 0
> O 0.304303000000000 0.652151500000000 0.357616166666667
> O 0.695697000000000 0.347848500000000 0.459050500000000
> O 0.695697000000000 0.347848500000000 0.292383833333333
> O 0.695697000000000 0.847848500000000 0.125717166666667 0 0 0
> O 0.695697000000000 0.347848500000000 0.125717166666667 0 0 0
> O 0.695697000000000 0.847848500000000 0.459050500000000
> O 0.695697000000000 0.847848500000000 0.292383833333333
> O 0.804303000000000 0.097848500000000 0.024282833333333 0 0 0
> O 0.804303000000000 0.097848500000000 0.357616166666667
> O 0.804303000000000 0.597848500000000 0.190949500000000
> O 0.804303000000000 0.097848500000000 0.190949500000000
> O 0.804303000000000 0.597848500000000 0.024282833333333 0 0 0
> O 0.804303000000000 0.597848500000000 0.357616166666667
> O 0.195697000000000 0.402151500000000 0.125717166666667 0 0 0
> O 0.195697000000000 0.402151500000000 0.459050500000000
> O 0.195697000000000 0.902151500000000 0.292383833333333
> O 0.195697000000000 0.402151500000000 0.292383833333333
> O 0.195697000000000 0.902151500000000 0.125717166666667 0 0 0
> O 0.195697000000000 0.902151500000000 0.459050500000000
> K_POINTS {automatic}
> 4 4 6 1 1 1
--
Dr. Eleni Chatzikyriakou
Computational Physics lab
Aristotle University of Thessaloniki
elchatz at auth.gr<mailto:elchatz at auth.gr> - tel:+30 2310 998109<tel:%2B30%202310%20998109>
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--
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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