Dear siesta user I Install siesta 3.1 in parallel without any error . when I run the programme with one node it run successfully but when I increase the number of nodes the programmes terminated in the middle as shown below .I attached my arch .make file and h20.sh.e35125 file which showing the error which I cant conclude please help me out
Siesta Version: siesta-3.1
Architecture : x86_64-unknown-linux-gnu--unknown
Compiler flags: mpif90 -g -O2
PARALLEL version
* Running on 4 nodes in parallel
>> Start of run: 18-JAN-2014 18:17:31
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
************************** Dump of input data file
****************************
SystemName Water molecule
SystemLabel h2o
NumberOfAtoms 3
NumberOfSpecies 2
%block ChemicalSpeciesLabel
1 8 O # Species index, atomic number, species label
2 1 H
%endblock ChemicalSpeciesLabel
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1
0.757 0.586 0.000 2
-0.757 0.586 0.000 2
%endblock AtomicCoordinatesAndAtomicSpecies
************************** End of input data file
*****************************
reinit:
-----------------------------------------------------------------------
reinit: System Name: Water molecule
reinit:
-----------------------------------------------------------------------
reinit: System Label:
h2o
reinit:
-----------------------------------------------------------------------
initatom: Reading input for the pseudopotentials and atomic orbitals
----------
Species number: 1 Label: O Atomic number: 8
Species number: 2 Label: H Atomic number: 1
Ground state valence configuration: 2s02 2p04
Reading pseudopotential information in formatted form from O.psf
Valence configuration for pseudopotential generation:
2s( 2.00) rc: 1.14
2p( 4.00) rc: 1.14
3d( 0.00) rc: 1.14
4f( 0.00) rc: 1.14
Ground state valence configuration: 1s01
Reading pseudopotential information in formatted form from H.psf
Valence configuration for pseudopotential generation:
1s( 1.00) rc: 1.25
2p( 0.00) rc: 1.25
3d( 0.00) rc: 1.25
4f( 0.00) rc: 1.25
For O, 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.
For H, standard SIESTA heuristics set lmxkb to 2
(one more than the basis l, including polarization orbitals).
Use PS.lmax or PS.KBprojectors blocks to override.
<basis_specs>
===============================================================================
O Z= 8 Mass= 16.000 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 O (Z = 8)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Total valence charge: 6.00000
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.1278
V l=1 = -2*Zval/r beyond r= 1.1278
V l=2 = -2*Zval/r beyond r= 1.1278
V l=3 = -2*Zval/r beyond r= 1.1138
All V_l potentials equal beyond r= 1.1278
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.1278
VLOCAL1: 99.0% of the norm of Vloc inside 34.126 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 77.774 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.37759
atom: Maximum radius for r*vlocal+2*Zval: 1.18566
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= 1.294105 el= -1.742414 Ekb= 9.135903 kbcos= 0.326910
l= 1 rc= 1.294105 el= -0.676589 Ekb= -8.124878 kbcos= -0.395047
l= 2 rc= 1.448233 el= 0.002386 Ekb= -2.039267 kbcos= -0.003484
l= 3 rc= 1.561052 el= 0.003508 Ekb= -0.799141 kbcos= -0.000344
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 = 3.305093
energy = -1.723766
kinetic = 1.614911
potential(screened) = -3.338677
potential(ionic) = -11.304675
izeta = 2
rmatch = 2.510382
splitnorm = 0.150000
energy = -1.471299
kinetic = 2.446434
potential(screened) = -3.917732
potential(ionic) = -12.476133
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 = 3.937239
energy = -0.658841
kinetic = 5.005986
potential(screened) = -5.664827
potential(ionic) = -13.452360
izeta = 2
rmatch = 2.541963
splitnorm = 0.150000
energy = -0.367441
kinetic = 7.530509
potential(screened) = -7.897949
potential(ionic) = -16.611953
POLgen: Perturbative polarization orbital with L= 2
POLgen: Polarization orbital for state 2p
izeta = 1
rc = 3.937239
energy = 2.398520
kinetic = 4.716729
potential(screened) = -2.318209
potential(ionic) = -8.603170
atom: Total number of Sankey-type orbitals: 13
atm_pop: Valence configuration (for local Pseudopot. screening):
2s( 2.00)
2p( 4.00)
Vna: chval, zval: 6.00000 6.00000
Vna: Cut-off radius for the neutral-atom potential: 3.937239
atom:
_________________________________________________________________________
<basis_specs>
===============================================================================
H Z= 1 Mass= 1.0100 Charge= 0.17977+309
Lmxo=0 Lmxkb= 2 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=1
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
===============================================================================
</basis_specs>
atom: Called for H (Z = 1)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Total valence charge: 1.00000
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.2343
V l=1 = -2*Zval/r beyond r= 1.2189
V l=2 = -2*Zval/r beyond r= 1.2189
All V_l potentials equal beyond r= 1.2343
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.2343
VLOCAL1: 99.0% of the norm of Vloc inside 28.493 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 64.935 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.45251
atom: Maximum radius for r*vlocal+2*Zval: 1.21892
GHOST: No ghost state for L = 0
GHOST: No ghost state for L = 1
GHOST: No ghost state for L = 2
KBgen: Kleinman-Bylander projectors:
l= 0 rc= 1.364359 el= -0.467325 Ekb= -2.005361 kbcos= -0.336422
l= 1 rc= 1.434438 el= 0.001430 Ekb= -0.501708 kbcos= -0.021697
l= 2 rc= 1.470814 el= 0.002365 Ekb= -0.190555 kbcos= -0.002281
KBgen: Total number of Kleinman-Bylander projectors: 9
atom:
-------------------------------------------------------------------------
atom: SANKEY-TYPE ORBITALS:
atom: Selected multiple-zeta basis: split
SPLIT: Orbitals with angular momentum L= 0
SPLIT: Basis orbitals for state 1s
SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 4.828263
energy = -0.449375
kinetic = 0.929372
potential(screened) = -1.378747
potential(ionic) = -1.915047
izeta = 2
rmatch = 3.854947
splitnorm = 0.150000
energy = -0.336153
kinetic = 1.505294
potential(screened) = -1.841447
potential(ionic) = -2.413582
POLgen: Perturbative polarization orbital with L= 1
POLgen: Polarization orbital for state 1s
izeta = 1
rc = 4.828263
energy = 0.706972
kinetic = 1.396397
potential(screened) = -0.689424
potential(ionic) = -1.169792
atom: Total number of Sankey-type orbitals: 5
atm_pop: Valence configuration (for local Pseudopot. screening):
1s( 1.00)
Vna: chval, zval: 1.00000 1.00000
Vna: Cut-off radius for the neutral-atom potential: 4.828263
atom:
_________________________________________________________________________
prinput: Basis input
----------------------------------------------------------
PAO.BasisType split
%block ChemicalSpeciesLabel
1 8 O # Species index, atomic number, species
label
2 1 H # Species index, atomic number, species
label
%endblock ChemicalSpeciesLabel
%block PAO.Basis # Define Basis set
O 2 # Species label, number of
l-shells
n=2 0 2 # n, l, Nzeta
3.305 2.510
1.000 1.000
n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
3.937 2.542
1.000 1.000
H 1 # Species label, number of
l-shells
n=1 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
4.828 3.855
1.000 1.000
%endblock PAO.Basis
prinput:
----------------------------------------------------------------------
coor: Atomic-coordinates input format = Cartesian coordinates
coor: (in Angstroms)
siesta: Atomic coordinates (Bohr) and species
siesta: 0.00000 0.00000 0.00000 1 1
siesta: 1.43052 1.10738 0.00000 2 2
siesta: -1.43052 1.10738 0.00000 2 3
siesta: Automatic unit cell vectors (Ang):
siesta: 7.286412 0.000000 0.000000
siesta: 0.000000 5.746952 0.000000
siesta: 0.000000 0.000000 5.621012
siesta: System type = molecule
initatomlists: Number of atoms, orbitals, and projectors: 3 23 34
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 = 2
redata: Charge density info will appear in .RHO file
redata: Write Mulliken Pop. = NO
redata: Mesh Cutoff = 100.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Max. number of SCF Iter = 50
redata: Mixing is linear
redata: Mix DM in first SCF step ? = F
redata: Write Pulay info on disk? = F
redata: Discard 1st Pulay DM after kick = F
redata: New DM Mixing Weight = 0.2500
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) = F
redata: Use continuation files for DM = F
redata: Neglect nonoverlap interactions = F
redata: Method of Calculation = Diagonalization
redata: Divide and Conquer = T
redata: Electronic Temperature = 0.0019 Ry
redata: Fix the spin of the system = F
redata: Dynamics option = Verlet MD run
redata: Initial MD time step = 1
redata: Final MD time step = 1
redata: Length of MD time step = 1.0000 fs
redata: Initial Temperature of MD run = 0.0000 K
redata: Perform a MD quench = F
redata:
***********************************************************************
Total number of electrons: 8.000000
Total ionic charge: 8.000000
* ProcessorY, Blocksize: 2 6
Kpoints in: 1 . Kpoints trimmed: 1
siesta: k-grid: Number of k-points = 1
siesta: k-grid: Cutoff (effective) = 2.811 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid: 1 0 0 0.000
siesta: k-grid: 0 1 0 0.000
siesta: k-grid: 0 0 1 0.000
* Maximum dynamic memory allocated = 2 MB
siesta: ==============================
Begin MD step = 1
==============================
outcell: Unit cell vectors (Ang):
7.286412 0.000000 0.000000
0.000000 5.746952 0.000000
0.000000 0.000000 5.621012
outcell: Cell vector modules (Ang) : 7.286412 5.746952 5.621012
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 235.3780
New_DM. Step: 1
Initializing Density Matrix...
InitMesh: MESH = 48 x 36 x 36 = 62208
InitMesh: Mesh cutoff (required, used) = 100.000 108.450 Ry
* Maximum dynamic memory allocated = 3 MB
arch.make
Description: Binary data
h20.sh.e35124
Description: Binary data
