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:
4A6996C2.5030308@cea.fr" type="cite">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
|
