Is someone willing to run the following calculation on his/hers system on more
than one node? If it works then I know the problem is not in my input file for
QE, but rather a memory, parallelization... problem in my script. This would
help me to narrow down the possible solutions I can try.
&control
calculation = 'relax'
restart_mode = 'from_scratch'
prefix = 'cti'
tstress = .false.
tprnfor = .true.
pseudo_dir = '../pseudo'
outdir = './TMP/'
wf_collect = .true.
verbosity='high'
nstep = 100
/
&SYSTEM
ibrav = 0
A = 10.2670500
nat = 79
ntyp = 4
ecutwfc = 60
ecutrho = 600
spline_ps = .true.
/
&electrons
electron_maxstep = 400
diagonalization = 'david'
conv_thr = 1.0d-8
diago_thr_init = 1e-4
mixing_mode = 'local-TF'
mixing_beta = 0.10
/
&ions
ion_dynamics = 'bfgs'
ion_positions = 'default'
/
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
K_POINTS automatic
3 3 1 1 1 0
ATOMIC_POSITIONS {angstrom}
Ti 0.4186429 0.0000000 1.0555597 0 0 0
Ti 0.4186429 3.7851500 1.0555597 0 0 0
Ti 13.4976069 0.0000000 8.2645045
Ti 13.4976069 3.7851500 8.2645045
Ti 11.9877668 3.7851500 4.6274892
Ti 11.9877668 0.0000000 4.6274892
Ti 6.8542418 1.8925750 4.6274892
Ti 6.8542418 5.6777250 4.6274892
Ti 5.5521679 1.8925750 1.0555597 0 0 0
Ti 5.5521679 5.6777250 1.0555597 0 0 0
Ti 8.3640819 5.6777250 8.2645045
Ti 8.3640819 1.8925750 8.2645045
Ti 8.4678023 1.8925750 1.9351998 0 0 0
Ti 8.4678023 5.6777250 1.9351998 0 0 0
Ti 11.1525460 1.8925750 8.8260622
Ti 11.1525460 5.6777250 8.8260622
Ti 9.7252141 5.6777250 5.4033466
Ti 9.7252141 1.8925750 5.4033466
Ti 4.5917059 0.0000000 5.4033889
Ti 4.5917059 3.7851500 5.4033889
Ti 3.3343024 0.0000000 1.9352631 0 0 0
Ti 3.3343024 3.7851500 1.9352631 0 0 0
Ti 6.0190191 3.7851500 8.8260833
Ti 6.0190191 0.0000000 8.8260833
O 8.8461469 0.0000000 1.7851414 0 0 0
O 8.8461469 3.7851500 1.7851414 0 0 0
O 3.7126116 1.8925750 1.7851414 0 0 0
O 3.7126116 5.6777250 1.7851414 0 0 0
O 11.6648815 0.0000000 9.0367308
O 11.6648815 3.7851500 9.0367308
O 10.1335967 3.7851500 5.3061929
O 10.1335967 0.0000000 5.3061929
O 5.0000903 1.8925750 5.3062141
O 5.0000903 5.6777250 5.3062141
O 6.5313733 5.6777250 9.0367731
O 6.5313733 1.8925750 9.0367731
O 6.4920242 1.8925750 2.6665971
O 6.4920242 5.6777250 2.6665971
O 9.5524047 1.8925750 9.6887500
O 9.5524047 5.6777250 9.6887500
O 7.9643783 5.6777250 6.2261554
O 7.9643783 1.8925750 6.2261554
O 2.8308616 0.0000000 6.2261765
O 2.8308616 3.7851500 6.2261765
O 1.3585262 0.0000000 2.6666393
O 1.3585262 3.7851500 2.6666393
O 4.4188778 3.7851500 9.6887712
O 4.4188778 0.0000000 9.6887712
O 6.4875556 0.0000000 4.7368663
O 6.4875556 3.7851500 4.7368663
O 5.1733648 0.0000000 1.2058080 0 0 0
O 5.1733648 3.7851500 1.2058080 0 0 0
O 10.3068917 1.8925750 1.2057869 0 0 0
O 10.3068917 5.6777250 1.2057869 0 0 0
O 7.9865405 3.7851500 8.2942713
O 7.9865405 0.0000000 8.2942713
O 13.1200655 1.8925750 8.2942713
O 13.1200655 5.6777250 8.2942713
O 11.6210871 5.6777250 4.7369085
O 11.6210871 1.8925750 4.7369085
O 8.6769466 1.8925750 3.8566351
O 8.6769466 5.6777250 3.8566351
O 7.3912657 1.8925750 0.3261679 0 0 0
O 7.3912657 5.6777250 0.3261679 0 0 0
O 10.2145938 5.6777250 7.3147541
O 10.2145938 1.8925750 7.3147541
O 3.5434486 0.0000000 3.8566773
O 3.5434486 3.7851500 3.8566773
O 2.2577304 0.0000000 0.3261679 0 0 0
O 2.2577304 3.7851500 0.3261679 0 0 0
O 5.0810874 3.7851500 7.3147752
O 5.0810874 0.0000000 7.3147752
C 11.8672904 1.1988342 12.0377009
H 10.8972048 1.5651949 12.4327181
H 12.6146411 1.4156404 12.8602406
H 11.7754366 0.0930383 12.0212237
C 12.1489342 1.7490971 10.6690556
H 12.2444435 2.8549331 10.7299854
H 13.1383125 1.3828863 10.3158727
CELL_PARAMETERS {alat}
1.0000000 0.0000000 0.0000000
0.0000000 0.7373394 0.0000000
0.8155077 0.0000000 2.0562083
Thanks in advance,
Laurens Siemons
________________________________
Van: [email protected] <[email protected]> namens Paolo
Giannozzi <[email protected]>
Verzonden: dinsdag 27 februari 2018 11:28
Aan: PWSCF Forum
Onderwerp: Re: [Pw_forum] Problems computing cholensky
On Mon, Feb 26, 2018 at 10:26 AM, Laurens Siemons
<[email protected]<mailto:[email protected]>> wrote:
Does anybody have a suggestion why it does work on 1 node with 20 cores, but
fails when I try to increase my nodes?
The final results do not depend upon the number of processors (modulo minor
numerical differences, within the convergence threshold) but intermediate
results may depend, due to a different starting point and to small numerical
differences. This may unfortunately lead some calculations that are "on the
brink" to fail. I have no evidence that this is related to a bug or to any
other easily solvable problem.
The "Cholesky" problem signals that the overlap matrix is not positive definite
(has a zero or negative eigenvalue). When it happens, it is invariably due
either to a badly wrong structure (not the case here) or to USPP/PAW with small
negative values of augmentation charges. It is a known problem and there is no
simple solution available.
Paolo
Thanks in advance,
Laurens Siemons
________________________________
Van: [email protected]<mailto:[email protected]>
<[email protected]<mailto:[email protected]>> namens Paolo
Giannozzi <[email protected]<mailto:[email protected]>>
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
<[email protected]<mailto:[email protected]>> 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, <[email protected]<mailto:[email protected]>>
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
<[email protected]<mailto:[email protected]>>:
> 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
[email protected]<mailto:[email protected]> - 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<tel:+39%200432%20558216>, fax
+39-0432-558222<tel:+39%200432%20558222>
_______________________________________________
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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<tel:+39%200432%20558216>, fax
+39-0432-558222<tel:+39%200432%20558222>
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