The ABINIT Users Mailing List ( CLOSED )

[Xenophon Krokidis <Xenophon.Krokidis@scienomics.com>]

Title: Signature text

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. 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 ?

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=4, nloalg=4, fftalg=401, intxc=0, and fft_opt_lob=2 have to be used for a band/FFT/k-point parallelisation. Spin-polarized ( nsppol=2 or nspden=2) as well as PAW method calculations are now allowed in production in the framework of band/FFT/k-point parallelisation.

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
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:

4A6980E9.2030203@cea.fr" type="cite">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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