Dear siesta users!
I have a problem with my calculations using OrderN method, I hope you will
help me.
I tried to make relaxation of a big carbon structure with 530 atoms.
My problem is I can't run this calculation using big number of processors.
When I tried 16 nodes it worked fine, but 16 modes is not enough for such
calculations because the lack of memory.
Here is my output file.
Siesta Version: siesta-3.0-b
Architecture : intel-mkl
Compiler flags: mpif90 -w -mp -O3 -DGRID_DP
PARALLEL version
* Running on 32 nodes in parallel
>> Start of run: 14-MAY-2012 9:43:09
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
************************** Dump of input data file
****************************
SystemName diamond
SystemLabel diamond
NumberOfSpecies 1
NumberOfAtoms 530
%block ChemicalSpeciesLabel
1 6 Ctm2
%endblock ChemicalSpeciesLabel
LatticeConstant 1 Ang
%block LatticeVectors
14.26400 0.000000 0.000000
0.000000 14.26400 0.000000
0.000000 0.000000 14.26400
%endblock LatticeVectors
%block GeometryConstraints
stress 4 5 6
%endblock GeometryConstraints
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
-4.89756 -5.84157 -5.87831 1
-5.10333 -6.0651 -2.56257 1
...
-1.05884 -11.9085 -11.9433 1
-4.3804 -11.6846 -2.13475 1
-0.0827804 -1.86345 -11.9853 1
%endblock AtomicCoordinatesAndAtomicSpecies
#kgrid_cutoff 12 Ang
XC.functional LDA
XC.authors PZ
SaveRho F
MeshCutoff 175.0 Ry
MaxSCFIterations 200
SolutionMethod ordern
SpinPolarized F
ON.eta -3.6 eV
DM.MixingWeight 0.1
DM.NumberPulay 8
MD.VariableCell T
MD.TypeOfRun cg
MD.NumCGsteps 99
WriteXML F
WriteCoorXmol T
WriteCoorStep T
WriteForces T
WriteMDXmol T
UseSaveData T
************************** End of input data file
*****************************
reinit:
-----------------------------------------------------------------------
reinit: System Name: diamond
reinit:
-----------------------------------------------------------------------
reinit: System Label: diamond
reinit:
-----------------------------------------------------------------------
initatom: Reading input for the pseudopotentials and atomic orbitals
----------
Species number: 1 Label: Ctm2 Atomic number: 6
Ground state valence configuration: 2s02 2p02
Reading pseudopotential information in formatted form from Ctm2.psf
Valence configuration for pseudopotential generation:
2s( 2.00) rc: 1.25
2p( 2.00) rc: 1.25
3d( 0.00) rc: 1.25
4f( 0.00) rc: 1.25
For Ctm2, standard SIESTA heuristics set lmxkb to 3
(one more than the basis l, including polarization orbitals).
Use PS.lmax or PS.KBprojectors blocks to override.
<basis_specs>
===============================================================================
Ctm2 Z= 6 Mass= 12.010 Charge= 0.17977+309
Lmxo=1 Lmxkb=3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=2
n=1 nzeta=2 polorb=0
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=2
n=1 nzeta=2 polorb=1
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
L=2 Nkbl=1 erefs: 0.17977+309
L=3 Nkbl=1 erefs: 0.17977+309
===============================================================================
</basis_specs>
atom: Called for Ctm2 (Z = 6)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Total valence charge: 4.00000
read_vps: Pseudopotential includes a core correction:
read_vps: Pseudo-core for xc-correction
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
xc_check: WARNING: Pseudopotential generated with GGA Perdew, Burke &
Ernzerhof 1996 functional
V l=0 = -2*Zval/r beyond r= 1.2942
V l=1 = -2*Zval/r beyond r= 1.2942
V l=2 = -2*Zval/r beyond r= 1.2942
V l=3 = -2*Zval/r beyond r= 1.2942
All V_l potentials equal beyond r= 1.2311
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.2942
VLOCAL1: 99.0% of the norm of Vloc inside 28.641 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 65.273 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.48507
atom: Maximum radius for r*vlocal+2*Zval: 1.27815
GHOST: No ghost state for L = 0
GHOST: No ghost state for L = 1
GHOST: No ghost state for L = 2
GHOST: No ghost state for L = 3
KBgen: Kleinman-Bylander projectors:
l= 0 rc= 1.395070 el= -0.993346 Ekb= 7.951876 kbcos= 0.278490
l= 1 rc= 1.412623 el= -0.377750 Ekb= -4.662111 kbcos= -0.274382
l= 2 rc= 1.641300 el= 0.002326 Ekb= -1.205690 kbcos= -0.005065
l= 3 rc= 1.747182 el= 0.003420 Ekb= -0.463594 kbcos= -0.000519
KBgen: Total number of Kleinman-Bylander projectors: 16
atom:
-------------------------------------------------------------------------
atom: SANKEY-TYPE ORBITALS:
atom: Selected multiple-zeta basis: split
SPLIT: Orbitals with angular momentum L= 0
SPLIT: Basis orbitals for state 2s
SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 4.191849
energy = -0.974966
kinetic = 0.916257
potential(screened) = -1.891223
potential(ionic) = -5.488584
izeta = 2
rmatch = 3.431921
splitnorm = 0.150000
energy = -0.839329
kinetic = 1.376842
potential(screened) = -2.216171
potential(ionic) = -6.042859
SPLIT: Orbitals with angular momentum L= 1
SPLIT: Basis orbitals for state 2p
SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 4.993604
energy = -0.359316
kinetic = 2.509128
potential(screened) = -2.868444
potential(ionic) = -6.342029
izeta = 2
rmatch = 3.563077
splitnorm = 0.150000
energy = -0.204841
kinetic = 3.776860
potential(screened) = -3.981700
potential(ionic) = -7.838036
POLgen: Perturbative polarization orbital with L= 2
POLgen: Polarization orbital for state 2p
izeta = 1
rc = 4.993604
energy = 1.224104
kinetic = 2.486024
potential(screened) = -1.261920
potential(ionic) = -4.160402
atom: Total number of Sankey-type orbitals: 13
atm_pop: Valence configuration (for local Pseudopot. screening):
2s( 2.00)
2p( 2.00)
Vna: chval, zval: 4.00000 4.00000
Vna: Cut-off radius for the neutral-atom potential: 4.993604
comcore: Pseudo-core radius Rcore= 1.791422
atom:
_________________________________________________________________________
prinput: Basis input
----------------------------------------------------------
PAO.BasisType split
%block ChemicalSpeciesLabel
1 6 Ctm2 # Species index, atomic number, species
label
%endblock ChemicalSpeciesLabel
%block PAO.Basis # Define Basis set
Ctm2 2 # Species label, number of
l-shells
n=2 0 2 # n, l, Nzeta
4.192 3.432
1.000 1.000
n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
4.994 3.563
1.000 1.000
%endblock PAO.Basis
prinput:
----------------------------------------------------------------------
coor: Atomic-coordinates input format = Cartesian coordinates
coor: (in Angstroms)
siesta: WARNING: XV file not found
siesta: Atomic coordinates (Bohr) and species
siesta: -9.25505 -11.03897 -11.10840 1 1
siesta: -9.64390 -11.46138 -4.84256 1 2
...
siesta: -8.27776 -22.08070 -4.03409 1 529
siesta: -0.15643 -3.52141 -22.64894 1 530
siesta: System type = bulk
initatomlists: Number of atoms, orbitals, and projectors: 530 6890 8480
siesta: ******************** Simulation parameters
****************************
siesta:
siesta: The following are some of the parameters of the simulation.
siesta: A complete list of the parameters used, including default values,
siesta: can be found in file out.fdf
siesta:
redata: Non-Collinear-spin run = F
redata: SpinPolarized (Up/Down) run = F
redata: Number of spin components = 1
redata: Long output = F
redata: Number of Atomic Species = 1
redata: Charge density info will appear in .RHO file
redata: Write Mulliken Pop. = NO
redata: Mesh Cutoff = 175.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Max. number of SCF Iter = 200
redata: Performing Pulay mixing using = 8 iterations
redata: Mix DM in first SCF step ? = F
redata: Write Pulay info on disk? = F
redata: New DM Mixing Weight = 0.1000
redata: New DM Occupancy tolerance = 0.000000000001
redata: No kicks to SCF
redata: DM Mixing Weight for Kicks = 0.5000
redata: DM Tolerance for SCF = 0.000100
redata: Require Energy convergence for SCF = F
redata: DM Energy tolerance for SCF = 0.000100 eV
redata: Require Harris convergence for SCF = F
redata: DM Harris energy tolerance for SCF = 0.000100 eV
redata: Using Saved Data (generic) = T
redata: Use continuation files for DM = T
redata: Neglect nonoverlap interactions = F
redata: Method of Calculation = Order-N
redata: Fix the spin of the system = F
redata: Maximum number of iterations = 1000
redata: Relative tolerance = 0.10D-07
redata: Eta (Fermi level parameter) = -0.2646 Ry
redata: Radius of LWFs = 9.5000 Bohr
redata: Use continuation files for LWF = T
redata: Method to build LWFs = kim
redata: Dynamics option = CG coord. optimization
redata: Variable cell = T
redata: Use continuation files for CG = T
redata: Max atomic displ per move = 0.2000 Bohr
redata: Maximum number of CG moves = 99
redata: Force tolerance = 0.0016 Ry/Bohr
redata: Stress tolerance = 1.0000 GPa
redata:
***********************************************************************
Total number of electrons: 2120.000000
Total ionic charge: 2120.000000
* Spatial decomposition: Cutoff = 5.3910
Spatial decomposition data :
Cutoff = 2.8528 Angstroms
Spatial decomposition cells (containing atoms) :
Ncells Cell min Cell length
x : 5 0.0000 26.9551
y : 5 0.0000 26.9551
z : 5 0.0000 26.9551
--------------------------------------------------------------------------------
Cell No. of atoms Atom No. x y z
--------------------------------------------------------------------------------
1 3 136 6.1206 7.6685 7.5461
356 7.7377 5.8988 9.1685
409 7.7407 9.2319 5.7149
--------------------------------------------------------------------------------
2 5 54 11.0436 9.2554 9.1626
152 12.7218 7.6009 7.5377
303 11.1218 5.9328 5.8689
320 14.2893 5.9341 9.2702
375 14.3607 9.2659 5.8674
--------------------------------------------------------------------------------
...
--------------------------------------------------------------------------------
123 4 9 17.1237 29.6483 29.6840
481 20.7196 29.3756 28.5874
506 19.3352 30.9581 30.9146
517 21.5013 27.8825 30.7666
--------------------------------------------------------------------------------
124 3 473 23.9226 28.7994 31.9252
525 22.4925 31.3485 27.5596
528 24.9541 31.4063 31.3406
--------------------------------------------------------------------------------
125 4 448 32.0980 29.2465 28.8353
488 27.5598 31.5617 31.7552
490 30.6054 29.3665 31.4876
492 30.4968 31.4872 28.1263
--------------------------------------------------------------------------------
Cells per Processor = 0 12
Cells per Processor = 1 8
Cells per Processor = 2 12
Cells per Processor = 3 8
Cells per Processor = 4 6
Cells per Processor = 5 4
Cells per Processor = 6 0
Cells per Processor = 7 0
Cells per Processor = 8 12
Cells per Processor = 9 8
Cells per Processor = 10 12
Cells per Processor = 11 8
Cells per Processor = 12 6
Cells per Processor = 13 4
Cells per Processor = 14 0
Cells per Processor = 15 0
Cells per Processor = 16 6
Cells per Processor = 17 4
Cells per Processor = 18 6
Cells per Processor = 19 4
Cells per Processor = 20 3
Cells per Processor = 21 2
Cells per Processor = 22 0
Cells per Processor = 23 0
Cells per Processor = 24 0
Cells per Processor = 25 0
Cells per Processor = 26 0
Cells per Processor = 27 0
Cells per Processor = 28 0
Cells per Processor = 29 0
Cells per Processor = 30 0
Cells per Processor = 31 0
Warning: Bad load balancing: no cells allocated to node 6
Try specifying a number of nodes that is
an exact factor of the number of cells: 125
ERROR STOP from Node: 0
Also, I tried to use 125 nodes, as wrote in error message, resuts was the
same.
If anybody knows how I can fix this problem, it would be very kind of you
if you can help me
Thanks!
*--*
*Sincerely yours,*
*Alexander G. Kvashnin *
*=====================================================
Second year of master degree study
Moscow Institute of Physics and Technology http://mipt.ru/*
*141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia*
*
* *Junior research scientist
Technological Institute for Superhard
and Novel Carbon Materials http://www.ntcstm.troitsk.ru/
142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia
=====================================================* *
*
