Dear Siesta users,
I'm having a hard time trying to run SIESTA on my Debian-9 laptop.
I have:
GNU Fortran (Debian 6.3.0-18+deb9u1) 6.3.0 20170516
OpenMPI-2.0.2-2
libblas 3.7.0-2, liblapack 3.7.0-2
libscalapack-openmpi1 1.8.0-13
My arch.make is the following:
**********************************************************************
.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90 .c
SIESTA_ARCH = gfortran_openMPI
FPP = $(FC) -E -P -x c
FC = mpifort
FC_SERIAL = gfortran
FFLAGS = -O0 -g -fbacktrace -fcheck=all #-Wall
FFLAGS_DEBUG = -g -O0
PP = gcc -E -P -C
CC = gcc
CFLAGS = -O0 -g -Wall
AR = ar
RANLIB = ranlib
SYS = nag
LDFLAGS = -static-libgcc -ldl
BLASLAPACK_LIBS = -llapack -lblas \
-lscalapack-openmpi -lblacs-openmpi
-lblacsF77init-openmpi \
-lblacsCinit-openmpi \
-lpthread -lm
MPI_INTERFACE = libmpi_f90.a
MPI_INCLUDE = .
FPPFLAGS_MPI = -DMPI -DMPI_TIMING -D_DIAG_WORK
FPPFLAGS = $(DEFS_PREFIX) -DFC_HAVE_FLUSH -DFC_HAVE_ABORT $(FPPFLAGS_MPI)
INCFLAGS = $(MPI_INCLUDE)
LIBS = $(BLASLAPACK_LIBS) $(MPI_LIBS)
atom.o: atom.F
$(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS)
$(FPPFLAGS_fixed_F) $<
.c.o:
$(CC) -c $(CFLAGS) $(INCFLAGS) $(CPPFLAGS) $<
.F.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.F90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $<
.f.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $<
.f90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $<
**********************************************************************
The code compiles without errors.
If I run with Diag.ParallelOverK True, I can run on multiple cores, no
errors.
With Diag.ParallelOverK False, I can run `mpirun -np 1` without errors,
but if I try to use >=2 cores, it fails with:
**********************************************************************
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
#0 0x2ba6eb754d1d in ???
#1 0x2ba6eb753f7d in ???
#2 0x2ba6ec95405f in ???
#3 0x2ba70ec1cd8c in ???
#4 0x2ba6eab438a4 in ???
#5 0x2ba6eab44336 in ???
#6 0x563b3f1cfead in __m_diag_MOD_diag_c
at /home/fidanyan/soft/siesta-4.1/Src/diag.F90:709
#7 0x563b3f1d2ef9 in cdiag_
at /home/fidanyan/soft/siesta-4.1/Src/diag.F90:2253
#8 0x563b3ebc7c8d in diagk_
at /home/fidanyan/soft/siesta-4.1/Src/diagk.F:195
#9 0x563b3eb9d714 in __m_diagon_MOD_diagon
at /home/fidanyan/soft/siesta-4.1/Src/diagon.F:265
#10 0x563b3ed897cb in __m_compute_dm_MOD_compute_dm
at /home/fidanyan/soft/siesta-4.1/Src/compute_dm.F:172
#11 0x563b3edbfaa5 in __m_siesta_forces_MOD_siesta_forces
at /home/fidanyan/soft/siesta-4.1/Src/siesta_forces.F:315
#12 0x563b3f9a4005 in siesta
at /home/fidanyan/soft/siesta-4.1/Src/siesta.F:73
#13 0x563b3f9a408a in main
at /home/fidanyan/soft/siesta-4.1/Src/siesta.F:10
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node fenugreek exited
on signal 11 (Segmentation fault).
**********************************************************************
I ran it by
`mpirun -np 2 ~/soft/siesta-4.1/Obj-debug-O0/siesta control.fdf | tee
siesta.out`
The header of the broken calculation:
--------------------------------------------------------------------------------------------
Siesta Version : v4.1.5-1-g384057250
Architecture : gfortran_openMPI
Compiler version: GNU Fortran (Debian 6.3.0-18+deb9u1) 6.3.0 20170516
Compiler flags : mpifort -O0 -g -fbacktrace -fcheck=all
PP flags : -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DMPI -DMPI_TIMING
-D_DIAG_WORK
Libraries : -llapack -lblas -lscalapack-openmpi -lblacs-openmpi
-lblacsF77init-openmpi -lblacsCinit-openmpi -lpthread -lm
PARALLEL version
* Running on 2 nodes in parallel
--------------------------------------------------------------------------------------------
I also attach the fdf file and the full output with an error.
Do you have an idea what is wrong?
Sincerely,
Karen Fidanyan
PhD student
Max Planck Institute for the Structure and Dynamics of Matter
Hamburg, Germany
Siesta Version : v4.1.5-1-g384057250
Architecture : gfortran_openMPI
Compiler version: GNU Fortran (Debian 6.3.0-18+deb9u1) 6.3.0 20170516
Compiler flags : mpifort -O0 -g -fbacktrace -fcheck=all
PP flags : -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DMPI -DMPI_TIMING
-D_DIAG_WORK
Libraries : -llapack -lblas -lscalapack-openmpi -lblacs-openmpi
-lblacsF77init-openmpi -lblacsCinit-openmpi -lpthread -lm
PARALLEL version
* Running on 2 nodes in parallel
>> Start of run: 28-JUN-2021 18:42:45
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from control.fdf
reinit: -----------------------------------------------------------------------
reinit: System Name:
reinit: -----------------------------------------------------------------------
reinit: System Label: siesta
reinit: -----------------------------------------------------------------------
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 13 Label: Al
Species number: 2 Atomic number: 8 Label: O
Species number: 3 Atomic number: 1 Label: H
Ground state valence configuration: 3s02 3p01
Reading pseudopotential information in formatted form from Al.psf
Valence configuration for pseudopotential generation:
3s( 2.00) rc: 1.84
3p( 1.00) rc: 2.06
3d( 0.00) rc: 2.22
4f( 0.00) rc: 2.22
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 Al, 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 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>
===============================================================================
Al Z= 13 Mass= 26.980 Charge= 0.17977+309
Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=3
i=1 nzeta=2 polorb=0 (3s)
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=3
i=1 nzeta=2 polorb=1 (3p)
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
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 Al (Z = 13)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Valence charge for ps generation: 3.00000
read_vps: Pseudopotential includes a core correction:
read_vps: Pseudo-core for xc-correction
xc_check: Exchange-correlation functional:
xc_check: GGA Perdew, Burke & Ernzerhof 1996
V l=0 = -2*Zval/r beyond r= 2.3631
V l=1 = -2*Zval/r beyond r= 2.3631
V l=2 = -2*Zval/r beyond r= 2.3928
V l=3 = -2*Zval/r beyond r= 2.3928
All V_l potentials equal beyond r= 2.1923
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 2.3928
VLOCAL1: 99.0% of the norm of Vloc inside 9.031 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 20.583 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 2.61164
atom: Maximum radius for r*vlocal+2*Zval: 2.24783
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= 2.611638 el= -0.568159 Ekb= 4.040474 kbcos= 0.277596
l= 1 rc= 2.711441 el= -0.199904 Ekb= 1.392872 kbcos= 0.276298
l= 2 rc= 2.815058 el= 0.001961 Ekb= -1.480823 kbcos= -0.048555
l= 3 rc= 3.072491 el= 0.003052 Ekb= -0.466059 kbcos= -0.005740
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 3s
SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 5.669024
energy = -0.549483
kinetic = 0.432207
potential(screened) = -0.981690
potential(ionic) = -2.439369
izeta = 2
rmatch = 5.194051
splitnorm = 0.150000
energy = -0.487376
kinetic = 0.632137
potential(screened) = -1.119514
potential(ionic) = -2.628159
SPLIT: Orbitals with angular momentum L= 1
SPLIT: Basis orbitals for state 3p
SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 7.099496
energy = -0.179332
kinetic = 0.619035
potential(screened) = -0.798366
potential(ionic) = -2.139498
izeta = 2
rmatch = 5.885656
splitnorm = 0.150000
energy = -0.112919
kinetic = 0.879687
potential(screened) = -0.992605
potential(ionic) = -2.427065
POLgen: Perturbative polarization orbital with L= 2
POLgen: Polarization orbital for state 3p
izeta = 1
rc = 7.099496
energy = 0.332020
kinetic = 0.939799
potential(screened) = -0.607779
potential(ionic) = -1.859917
atom: Total number of Sankey-type orbitals: 13
atm_pop: Valence configuration (for local Pseudopot. screening):
3s( 2.00)
3p( 1.00)
Vna: chval, zval: 3.00000 3.00000
Vna: Cut-off radius for the neutral-atom potential: 7.099496
comcore: Pseudo-core radius Rcore= 3.395648
atom: _________________________________________________________________________
<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
i=1 nzeta=2 polorb=0 (2s)
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=2
i=1 nzeta=2 polorb=1 (2p)
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
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: ATM 3.2.2 Troullier-Martins
Valence charge for ps generation: 6.00000
read_vps: Pseudopotential includes a core correction:
read_vps: Pseudo-core for xc-correction
xc_check: Exchange-correlation functional:
xc_check: GGA Perdew, Burke & Ernzerhof 1996
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= 1.1278
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= 1.262145 el= -1.757696 Ekb= 9.224596 kbcos= 0.328556
l= 1 rc= 1.262145 el= -0.664256 Ekb= -7.912306 kbcos= -0.392969
l= 2 rc= 1.343567 el= 0.002031 Ekb= -1.926788 kbcos= -0.003514
l= 3 rc= 1.394919 el= 0.003153 Ekb= -0.739398 kbcos= -0.000358
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 = -1.740024
kinetic = 1.634553
potential(screened) = -3.374577
potential(ionic) = -11.335829
izeta = 2
rmatch = 2.510382
splitnorm = 0.150000
energy = -1.477377
kinetic = 2.490577
potential(screened) = -3.967954
potential(ionic) = -12.510092
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 = -0.646293
kinetic = 4.985707
potential(screened) = -5.632001
potential(ionic) = -13.399856
izeta = 2
rmatch = 2.541963
splitnorm = 0.150000
energy = -0.372935
kinetic = 7.381813
potential(screened) = -7.754748
potential(ionic) = -16.396628
POLgen: Perturbative polarization orbital with L= 2
POLgen: Polarization orbital for state 2p
izeta = 1
rc = 3.937239
energy = 2.424254
kinetic = 4.743947
potential(screened) = -2.319694
potential(ionic) = -8.626115
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
comcore: Pseudo-core radius Rcore= 1.377587
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
i=1 nzeta=2 polorb=1 (1s)
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
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
Valence charge for ps generation: 1.00000
xc_check: Exchange-correlation functional:
xc_check: GGA Perdew, Burke & Ernzerhof 1996
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= -0.477200 Ekb= -2.021939 kbcos= -0.344793
l= 1 rc= 1.434438 el= 0.001076 Ekb= -0.443447 kbcos= -0.022843
l= 2 rc= 1.470814 el= 0.002010 Ekb= -0.140543 kbcos= -0.002863
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 = 4.708991
energy = -0.457754
kinetic = 0.981121
potential(screened) = -1.438875
potential(ionic) = -1.967271
izeta = 2
rmatch = 3.759707
splitnorm = 0.150000
energy = -0.338992
kinetic = 1.585719
potential(screened) = -1.924710
potential(ionic) = -2.475126
POLgen: Perturbative polarization orbital with L= 1
POLgen: Polarization orbital for state 1s
izeta = 1
rc = 4.708991
energy = 0.764908
kinetic = 1.475831
potential(screened) = -0.710923
potential(ionic) = -1.203369
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: 4.708991
atom: _________________________________________________________________________
prinput: Basis input ----------------------------------------------------------
PAO.BasisType split
%block ChemicalSpeciesLabel
1 13 Al # Species index, atomic number, species label
2 8 O # Species index, atomic number, species label
3 1 H # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel
%block PAO.Basis # Define Basis set
Al 2 # Species label, number of l-shells
n=3 0 2 # n, l, Nzeta
5.669 5.194
1.000 1.000
n=3 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
7.099 5.886
1.000 1.000
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
4.709 3.760
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: 18.79317 13.53612 49.13290 2 1
siesta: 20.21349 14.70882 49.13290 3 2
siesta: 19.57990 11.87062 49.13290 3 3
siesta: 0.00000 0.00000 44.40510 1 4
siesta: System type = molecule
initatomlists: Number of atoms, orbitals, and projectors: 4 36 50
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: Spin configuration = none
redata: Number of spin components = 1
redata: Time-Reversal Symmetry = T
redata: Spin spiral = F
redata: Long output = T
redata: Number of Atomic Species = 3
redata: Charge density info will appear in .RHO file
redata: Write Mulliken Pop. = Atomic and Orbital charges
redata: Matel table size (NRTAB) = 1024
redata: Mesh Cutoff = 500.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Min. number of SCF Iter = 0
redata: Max. number of SCF Iter = 400
redata: SCF convergence failure will abort job
redata: SCF mix quantity = Hamiltonian
redata: Mix DM or H after convergence = F
redata: Recompute H after scf cycle = F
redata: Mix DM in first SCF step = T
redata: Write Pulay info on disk = F
redata: New DM Occupancy tolerance = 0.000000000001
redata: No kicks to SCF
redata: DM Mixing Weight for Kicks = 0.5000
redata: Require Harris convergence for SCF = F
redata: Harris energy tolerance for SCF = 0.000100 eV
redata: Require DM convergence for SCF = T
redata: DM tolerance for SCF = 0.000100
redata: Require EDM convergence for SCF = F
redata: EDM tolerance for SCF = 0.001000 eV
redata: Require H convergence for SCF = T
redata: Hamiltonian tolerance for SCF = 0.001000 eV
redata: Require (free) Energy convergence for SCF = F
redata: (free) 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 = Diagonalization
redata: Electronic Temperature = 580.2219 K
redata: Fix the spin of the system = F
redata: Dynamics option = CG coord. optimization
redata: Variable cell = F
redata: Use continuation files for CG = T
redata: Max atomic displ per move = 0.1058 Ang
redata: Maximum number of optimization moves = 100
redata: Force tolerance = 0.0050 eV/Ang
mix.SCF: Pulay mixing = Pulay
mix.SCF: Variant = stable
mix.SCF: History steps = 8
mix.SCF: Linear mixing weight = 0.005000
mix.SCF: Mixing weight = 0.005000
mix.SCF: SVD condition = 0.1000E-07
redata: ***********************************************************************
%block SCF.Mixers
Pulay
%endblock SCF.Mixers
%block SCF.Mixer.Pulay
# Mixing method
method pulay
variant stable
# Mixing options
weight 0.0050
weight.linear 0.0050
history 8
%endblock SCF.Mixer.Pulay
DM_history_depth set to one: no extrapolation allowed by default for geometry
relaxation
Size of DM history Fstack: 1
Total number of electrons: 11.000000
Total ionic charge: 11.000000
* ProcessorY, Blocksize: 1 19
* Orbital distribution balance (max,min): 19 17
k-point displ. along 1 input, could be: 0.00 0.50
k-point displ. along 2 input, could be: 0.00 0.50
Kpoints in: 4 . Kpoints trimmed: 4
siesta: k-point coordinates (Bohr**-1) and weights:
siesta: 1 0.000000 0.000000 0.000000 0.250000
siesta: 2 0.096276 -0.055585 0.000000 0.250000
siesta: 3 0.000000 0.111170 0.000000 0.250000
siesta: 4 0.096276 0.055585 0.000000 0.250000
siesta: k-grid: Number of k-points = 4
siesta: k-grid: Cutoff (effective) = 17.268 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid: 2 0 0 0.000
siesta: k-grid: 0 2 0 0.000
siesta: k-grid: 0 0 1 0.000
diag: Algorithm = D&C
diag: Parallel over k = F
diag: Use parallel 2D distribution = F
diag: Parallel block-size = 19
diag: Parallel distribution = 1 x 2
diag: Used triangular part = Lower
diag: Absolute tolerance = 0.100E-15
diag: Orthogonalization factor = 0.100E-05
diag: Memory factor = 1.5000
ts: **************************************************************
ts: Save H and S matrices = F
ts: Save DM and EDM matrices = F
ts: Only save the overlap matrix S = F
ts: **************************************************************
************************ Begin: TS CHECKS AND WARNINGS ************************
************************ End: TS CHECKS AND WARNINGS **************************
====================================
Begin CG opt. move = 0
====================================
outcoor: Atomic coordinates (Ang):
9.94491295 7.16300080 26.00000000 2 1 O
10.69651262 7.78357179 26.00000000 3 2 H
10.36123501 6.28165714 26.00000000 3 3 H
0.00000000 0.00000000 23.49815596 1 4 Al
outcell: Unit cell vectors (Ang):
17.267548 0.000000 0.000000
8.633774 14.954135 0.000000
0.000000 0.000000 60.000000
outcell: Cell vector modules (Ang) : 17.267548 17.267548 60.000000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 60.0000
outcell: Cell volume (Ang**3) : 15493.2741
<dSpData1D:S at geom step 0
<sparsity:sparsity for geom step 0
nrows_g=36 nrows=19 sparsity=.3372 nnzs=437, refcount: 7>
<dData1D:(new from dSpData1D) n=437, refcount: 1>
refcount: 1>
new_DM -- step: 1
Initializing Density Matrix...
Attempting to read DM from file... Failed...
DM filled with atomic data:
<dSpData2D:DM initialized from atoms
<sparsity:sparsity for geom step 0
nrows_g=36 nrows=19 sparsity=.3372 nnzs=437, refcount: 8>
<dData2D:DM n=437 m=1, refcount: 1>
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3
23
New grid distribution: 1
1 1: 108 1: 108 1: 203
2 1: 108 1: 108 204: 405
InitMesh: MESH = 216 x 216 x 810 = 37791360
InitMesh: (bp) = 108 x 108 x 405 = 4723920
InitMesh: Mesh cutoff (required, used) = 500.000 503.697 Ry
ExtMesh (bp) on 0 = 220 x 220 x 307 = 14858800
New grid distribution: 2
1 1: 108 1: 108 1: 167
2 1: 108 1: 108 168: 405
New grid distribution: 3
1 1: 108 1: 108 1: 165
2 1: 108 1: 108 166: 405
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 220 x 220 x 271 = 13116400
PhiOnMesh: Number of (b)points on node 0 = 1947888
PhiOnMesh: nlist on node 0 = 597163
cdiag-debug: jobz=V, algo= 1, Node= 0, work= 3135, rwork=
3566, iwork= 270
cdiag-debug: jobz=V, algo= 1, Node= 1, work= 3135, rwork=
3242, iwork= 270
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x2ace534f2d1d in ???
#1 0x2ace534f1f7d in ???
#2 0x2ace546f205f in ???
#3 0x2ace769c7d8c in ???
#4 0x2ace528e18a4 in ???
#5 0x2ace528e2336 in ???
#6 0x56186084cead in __m_diag_MOD_diag_c
at /home/fidanyan/soft/siesta-4.1/Src/diag.F90:709
#7 0x56186084fef9 in cdiag_
at /home/fidanyan/soft/siesta-4.1/Src/diag.F90:2253
#8 0x561860244c8d in diagk_
at /home/fidanyan/soft/siesta-4.1/Src/diagk.F:195
#9 0x56186021a714 in __m_diagon_MOD_diagon
at /home/fidanyan/soft/siesta-4.1/Src/diagon.F:265
#10 0x5618604067cb in __m_compute_dm_MOD_compute_dm
at /home/fidanyan/soft/siesta-4.1/Src/compute_dm.F:172
#11 0x56186043caa5 in __m_siesta_forces_MOD_siesta_forces
at /home/fidanyan/soft/siesta-4.1/Src/siesta_forces.F:315
#12 0x561861021005 in siesta
at /home/fidanyan/soft/siesta-4.1/Src/siesta.F:73
#13 0x56186102108a in main
at /home/fidanyan/soft/siesta-4.1/Src/siesta.F:10
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node fenugreek exited on
signal 11 (Segmentation fault).
--------------------------------------------------------------------------
# Syntax on
SystemLabel siesta
#NumberOfSpecies 3
#NumberOfAtoms 4
XC.functional GGA
XC.Authors PBE
Spin non-polarized
SlabDipoleCorrection T
MeshCutoff 500 Ry
ElectronicTemperature 50 meV
# ---------- SCF settings -----------
MaxSCFIterations 400
SCF.DM.Tolerance 1e-4
SolutionMethod diagon
Use.New.Diagk F
Diag.ELPA F
DM.MixingWeight 5e-3
SCF.Mixer.History 8
# -----------------------------------
MD.TypeOfRun cg
MD.NumCGsteps 100
MD.MaxForceTol 0.005 eV/Ang
MD.VariableCell F
Diag.Memory 1.5
%block kgridMonkhorstPack
2 0 0 0.0
0 2 0 0.0
0 0 1 0.0
%endblock kgridMonkhorstPack
UseSaveData T
DM.UseSaveDM T
LongOutput T
#Output variables
WriteCoordinates T
%block ChemicalSpeciesLabel
1 13 Al
2 8 O
3 1 H
%endblock ChemicalSpeciesLabel
LatticeConstant 1. Ang
%block LatticeVectors
17.267547596575 0.0 0.0
8.633773798288 14.954134879691 0.0
0.0 0.0 60.0
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
9.94491295 7.16300080 26.00000000 2 O
10.69651262 7.78357179 26.00000000 3 H
10.36123501 6.28165714 26.00000000 3 H
0.00000000 0.00000000 23.49815596 1 Al
%endblock AtomicCoordinatesAndAtomicSpecies
PAO.BasisType split
PAO.BasisSize DZP
--
SIESTA is supported by the Spanish Research Agency (AEI) and by the European
H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
