The ABINIT Users Mailing List ( CLOSED )

[BOTTIN Francois <francois.bottin@cea.fr>]

Dear Xenophon,

Xenophon Krokidis a écrit :
> Dear Francois,
>
> I followed Emannuel's and your recommendations and I still get 
> problems. I summarize below:
> Using the input (see below) I get a message saying that only Gamma 
> points should work and that I need to give istwfk 1. 
If you set shiftk 0 0 0 in your input file, as Emmanuel said, you should 
have the Gamma point (kpt 0 0 0).
So, the code should detect and echo istwfk 2.
> Giving this option allows the calculation to run however in output it 
> is reported that all 30 bands are treated by node 0. So the question 
> is am I running parallel on bands or FFT ?
Yes. At the top level of ABINIT, these are the plane waves coefficients 
which are distributed over the processors.
More deeper within the code, the distribution switch between this one 
and a band distribution.
For more informations see the article,
F. Bottin, S. Leroux, A. Knyazev and G. Zerah, /Large scale ab initio 
calculations based on three levels of parallelization/, Comput. Mat. 
Science *42*, 329 (2008)
or the presentations at the 3rd and 4th ABINIT Workshop.
> Moreover, reading the 
> http://www.abinit.org/documentation/helpfiles/for-v5.8/input_variables/varpar.html#paral_kgb 
> I found the following (which makes me think that in PAW case kgb 
> parallelization doesn't work, is this correct ?):
>
> The keywords wfoptalg 
> <http://www.abinit.org/documentation/helpfiles/for-v5.8/input_variables/vardev.html#wfoptalg>=4, 
> nloalg 
> <http://www.abinit.org/documentation/helpfiles/for-v5.8/input_variables/vardev.html#nloalg>=4, 
> fftalg 
> <http://www.abinit.org/documentation/helpfiles/for-v5.8/input_variables/vardev.html#fftalg>=401, 
> intxc 
> <http://www.abinit.org/documentation/helpfiles/for-v5.8/input_variables/vardev.html#intxc>=0, 
> and fft_opt_lob 
> <http://www.abinit.org/documentation/helpfiles/for-v5.8/input_variables/varpar.html#fft_opt_lob>=2 
> have to be used for a band/FFT/k-point parallelisation. Spin-polarized 
> ( nsppol 
> <http://www.abinit.org/documentation/helpfiles/for-v5.8/input_variables/varbas.html#nsppol>=2 
> or nspden 
> <http://www.abinit.org/documentation/helpfiles/for-v5.8/input_variables/varbas.html#nspden>=2) 
> as well as PAW method calculations are now allowed in production in 
> the framework of band/FFT/k-point parallelisation.
No. "... are NOW allowed in ....".
The PAW/spin polarized calculations with bandfft parallelization are in 
production and should work.

Regards,
Francois

NB: What's going on wfoptalg=1 in parallel? I don't find any test in 
parallel for this case. Only sequential one (v3/t41).
Dear Xenophon, does your calculation work with wfoptalg=1 nbdbock=6 in 
sequential?
> Best regards, Xenophon
>
>
> # pALA-paw
>  paral_kgb 1
>  npband 6
>  wfoptalg 14
> # keywords for kgb parallelization
>  nloalg 4
>  fftalg 401
>  intxc 0
>  fft_opt_lob 2
>  strprecon 0.1
>  acell 4.601012 7.043279 6.411174 Angstr
>  angdeg 89.847876 89.911537 62.696451
>  chkprim 0
>  ecut 15 Hartree
>  ecutsm 0.5 Hartree
>  pawecutdg 45 Hartree
>  ionmov 2
>  ntime 200
>  tolmxf 0.00005
>  kptrlen 20.0
>  nkpt 0
>  kptopt 1
>  ngkpt 1 1 1
>
>
> Xenophon Krokidis, PhD
> *Scienomics* <www.scienomics.com>
> T: + 33 (0)1 40 07 56 60
> F: + 33 (0)1 71 19 75 83
> M: + 33 (0)6 76 68 06 47
>
>
>
> BOTTIN Francois wrote:
> > Dear Xenophon,
> >
> > In fact, you use the band-only parallelization drived by wfoptalg=1 
> > and nbdblock=6.
> > What Emmanuel suggests is to use the triple parallelization 
> > (wfoptalg=14, npband=6).
> > Note that, in this case, you also need paral_kgb=1 and a few others 
> > input variables (see the email of Emmanuel).
> > But perhaps, you need a feature which is not available in the second 
> > parallelization scheme!
> >
> > Moreover, by using the second scheme, if your calculation works fine, 
> > this will give
> > indications concerning the problem.
> >
> > Regards,
> > Francois
> >
> > Xenophon Krokidis a écrit :
> > > Dear Emmanuel,
> > >
> > > thank you for the response. Please find here some more precisions.
> > >
> > > a) The system I simulating is a beta sheet structure of polyalanine 
> > > (polymer chain not an isolated molecule) therefore there are 
> > > periodic boundary conditions. The 0.5 0.5 0.5 k-points gives 
> > > excellent result compared to Gamma.
> > > b) The same input but with FHI potentials (Norm concerving not PAW 
> > > ones) works.
> > > c) The parallelization I want to use is only on bands.
> > > d) The same input (with PAW) one one core runs and easily on one 
> > > core (the parallel one doesn't run)
> > > e)  I am using ABINIT 5.8.3
> > >
> > > Thank you for your kind support.
> > >
> > > Xenophon
> > >
> > > Xenophon Krokidis, PhD
> > > *Scienomics* <www.scienomics.com>
> > > T: + 33 (0)1 40 07 56 60
> > > F: + 33 (0)1 71 19 75 83
> > > M: + 33 (0)6 76 68 06 47
> > >
> > >
> > >
> > > Emmanuel Arras wrote:
> > > > Hi,
> > > > First there is a tab after nband, and abinit doesn't like that.
> > > >
> > > > Then I'm guessing the computation is to heavy to be performed on 
> > > > only one core, and that is why nothing happens. Indeed, you are 
> > > > talking about parallel calculation, and since you don't have any 
> > > > k-points I guess you are talking band / fft parallelisation. In 
> > > > that case you must put /paral_kgb 1/ to activate band 
> > > > parallelisation (since abinit 5.6 I'd say, but I'm not sure). You 
> > > > must then specify npband, npfft, npkpt (see 
> > > > http://www.abinit.org/documentation/helpfiles/for-v5.8/input_variables/varpar.html#paral_kgb) 
> > > >
> > > >
> > > >
> > > > Two pther things :
> > > > - I guess you are computing a molecule, and I guess you want to 
> > > > compute only the gamma point, so you should had /shiftk 0 0 0/ 
> > > > because default is 0.5 0.5 0.5
> > > > - if you want to perform the computation for the isolated molecule, 
> > > > i'd say your box is to small, and you don't need /optcell/, but 
> > > > that may not be your aim.
> > > >
> > > >
> > > > Emmanuel ARRAS
> > > >
> > > >
> > > >
> > > > xenophon.krokidis@scienomics.com a écrit :
> > > > > Dear All,
> > > > >
> > > > > I am trying to perform a PAW calculation with the setup given 
> > > > > below. However,
> > > > > there is no any SCF step printed out and the calculation seems to 
> > > > > run (several
> > > > > wfoptalg values were tried such as 1, 11). Any ideas ?
> > > > >
> > > > > Thank you in advance for the kind help. Xenophon
> > > > >
> > > > >  nbdblock 6
> > > > >  wfoptalg=1
> > > > >  strprecon 0.1
> > > > >  acell 5.0557 6.9684 6.1975 Angstr
> > > > >  angdeg 90.1725 89.9883 55.884
> > > > >  chkprim 0
> > > > >  ecut 15 Hartree
> > > > >  ecutsm 0.5 Hartree
> > > > >  pawecutdg 45 Hartree
> > > > >  ionmov 2
> > > > >  ntime 200
> > > > >  tolmxf 0.00005
> > > > >  nkpt 0
> > > > >  kptopt 1
> > > > >  ngkpt 1 1 1
> > > > >  nstep 50
> > > > >  ixc 11
> > > > >  nband    30
> > > > >  nsppol 1
> > > > >  natom 20
> > > > >  nsym 1
> > > > >  symrel 1 0 0  0 1 0  0 0 1
> > > > >  ntypat 4
> > > > >  occopt 1
> > > > >  strtarget 0 0 0 0 0 0
> > > > >  dilatmx 1.1
> > > > >  optcell 2
> > > > >  prtden 1
> > > > >  toldff 0.000001
> > > > >  typat 1 2 2 1 2 2 2 2 3 3 4 4 4 4 4 4 4 4 4 4
> > > > >  xred 0.514506 0.517578 0.337544
> > > > >  0.354529 0.65856 0.149121
> > > > >  0.543363 0.523401 0.948735
> > > > >  0.429453 0.418779 0.837167
> > > > >  0.589942 0.278259 0.647364
> > > > >  0.401054 0.412616 0.448164
> > > > >  0.321035 0.887354 0.165817
> > > > >  0.625195 0.0490203 0.661742
> > > > >  0.792921 0.505765 0.898215
> > > > >  0.152579 0.428644 0.397331
> > > > >  0.722061 0.497055 0.381453
> > > > >  0.220395 0.441001 0.880055
> > > > >  0.819528 0.25585 0.644386
> > > > >  0.554285 0.85897 0.171695
> > > > >  0.192376 0.999226 0.0304452
> > > > >  0.191765 0.978743 0.310754
> > > > >  0.753587 0.958288 0.80614
> > > > >  0.392761 0.076104 0.666813
> > > > >  0.756119 0.937023 0.526133
> > > > >  0.124522 0.681636 0.145734
> > > > >  znucl 7 6 8 1
> > > > >
> > > > >   
> > > >
> > > > --
> > > > Emmanuel ARRAS
> > > > L_Sim (Laboratoire de Simulation Atomistique)
> > > > SP2M / INAC
> > > > CEA Grenoble
> > > > tel : 00 33 (0)4 387 86862
> > > >   


--
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Francois Bottin                    tel: 01 69 26 41 73
CEA/DIF                            fax: 01 69 26 70 77
BP 12 Bruyeres-le-Chatel         email: Francois.Bottin@cea.fr
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