The ABINIT Users Mailing List ( CLOSED )

[<Marc.TORRENT@cea.fr>]

Dear Xenophon,

I'm not sure that wfoptalg=1 was OK with PAW in one past version of Abinit.
It is an old "parallelisation over bands" that was implemented before the 
introduction of PAW.
More precisely:
It uses the Conjugate Gradient algorithm by blocks...
But, at the time of the implementation (as PAW didnt exist), the Conjugate 
Gradient solved a single eigenvalue problem (H.Psi= Eps.Psi); for PAW, the 
problem now is a generalized eigenvalue problem (H.Psi=Eps.S.Psi)... probably 
there is an issure with the treatment of this "S" overlap operator with 
wfoptalg=1.
But, as the wfoptalg=4/14 algorithm is much more efficient that the 
wfoptalg=1/11, we never worked on the latter with PAW.

By the way, did you test wfoptalg=11 ?
I suspect the issue is the same.


Marc Torrent


-------- Message d'origine--------
De: Xenophon Krokidis [mailto:Xenophon.Krokidis@scienomics.com]
Date: lun. 27/07/2009 17:32
À: forum@abinit.org
Objet : Re: [abinit-forum] PAW parallel calculation remains idle
 
Dear François,

let me summarize  the situation. I want to perform PAW type of calculation at 
one k-point (0.5 0.5 0.5). Below I list the trials I did and the observations.


*       PAW

        *       Parallel (wfoptalg 1; nbdblock 6): ABINIT stays idle.
        *       Paralle (wfoptalg 1; npband 6): ABINIT runs fine
                

        *       Parallel (wfoptalg 14; npband 6; paral_kgb 1, ... ): ABINIT 
runs fine

        *       Sequential : ABINIT runs fine.

        *       Norm-concerving pseudopotentials.

        *       Parallel (wfoptalg 1; nbdblock 6): ABINIT runs fine.

        *       Sequential : ABINIT runs fine

 So it seems that there is a problem when parallelization over bands is 
defined via the nbdblock keyword.

Xenophon

Xenophon Krokidis, PhD
Scienomics
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, 
        
        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>
 
<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>
 
<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>
 
<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>
 
<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>
 
<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>
 
<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>
 
<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

<<winmail.dat>>