[Smeagol-discuss] the reason of Segmentation fault！
Guangping Zhang
284107217 at qq.com
Fri Mar 12 08:16:19 GMT 2010
Dear smeagol users and developers:
Now I a have a problem with the smeagol in calculation.
The compilation is all right.Then I have some tests (Au capacitor test)in the code pakage,it is ok for thoes test.But for the test following ,the ifort version have a 'Segmentation fault' and the program aborted.
I compiled the smeagol using the following arch.make
----------BEGIN-smeagol arch.make using IFORT+MKL+MPICH------
SIESTA_ARCH=Intel-MKL-MPICH
EXEC=smeagolpara
SOURCE_DIR=/home/zgp/software/smeagol-1.3.7
#
# Intel fortran compiler for linux with mkl optimized blas and lapack
#
# Be sure to experiment with different optimization options.
# You have quite a number of combinations to try...
#
FC=mpif90
#
FFLAGS= -O2 -i-static
FFLAGS_DEBUG= -g
LDFLAGS=-Vaxlib
COMP_LIBS=
RANLIB=echo
#
NETCDF_LIBS=
NETCDF_INTERFACE=
DEFS_CDF=
#
MPI_INTERFACE= libmpi_f90.a
MPI_INCLUDE=/home/zgp/software/mpich-1.2.7/include
DEFS_MPI=-DMPI
#
BLAS= -L/home/zgp/intel/mkl/10.0.2.018/lib/em64t -lmkl_solver_lp64 -lmkl_intel_lp64 -lguide
BLACS= -L/home/zgp/intel/mkl/10.0.2.018/lib/em64t -lmkl_blacs_lp64
LAPACK= -L/home/zgp/intel/mkl/10.0.2.018/lib/em64t -lmkl_sequential -lmkl_core
SCALAPACK= -L/home/zgp/intel/mkl/10.0.2.018/lib/em64t -lmkl_scalapack_lp64
LIBS=$(SCALAPACK) $(BLACS) $(LAPACK) $(BLAS)
SYS=bsd
DEFS= $(DEFS_CDF) $(DEFS_MPI)
#
.F.o:
$(FC) -c $(FFLAGS) $(DEFS) $<
.f.o:
$(FC) -c $(FFLAGS) $<
.F90.o:
$(FC) -c $(FFLAGS) $(DEFS) $<
.f90.o:
$(FC) -c $(FFLAGS) $<
#
----------END-smeagol arch.make IFORT+MKL+MPICH----------
This is the 'Segmentation fault' :
++++++++++++BEGIN-THE ERROR +++++++++++++++
initatomlists: Number of atoms, orbitals, and projectors: 90 770 866
* ProcessorY, Blocksize: 1 8
siesta: System type = bulk
siesta: k-grid: Number of k-points = 8
siesta: k-grid: Cutoff = 15.067 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid: 4 0 0 0.500
siesta: k-grid: 0 4 0 0.500
siesta: k-grid: 0 0 1 0.000
siesta: overlap: rmaxh veclen direction
siesta: overlap: 22.0267 16.3487 1
siesta: overlap: rmaxh veclen direction
siesta: overlap: 22.0267 16.3487 2
siesta: overlap: rmaxh veclen direction
siesta: overlap: 22.0267 56.9464 3
superc: Internal auxiliary supercell: 3 x 3 x 1 = 9
superc: Number of atoms, orbitals, and projectors: 810 6930 7794
* Maximum dynamic memory allocated = 3 MB
siesta: ===============================
SMEAGOL Bias step = 0, V = 0.000 Ry
Begin CG move = 0
===============================
outcoor: Atomic coordinates (Ang):
0.83250000 1.44190000 -6.99380000 4 Au 1
0.83250000 4.32570000 -6.99380000 4 Au 2
0.83250000 7.20950000 -6.99380000 4 Au 3
3.32990000 0.00000000 -6.99380000 4 Au 4
3.32990000 2.88380000 -6.99380000 4 Au 5
3.32990000 5.76760000 -6.99380000 4 Au 6
5.82740000 -1.44190000 -6.99380000 4 Au 7
5.82740000 1.44190000 -6.99380000 4 Au 8
5.82740000 4.32570000 -6.99380000 4 Au 9
0.00000000 0.00000000 -4.63920000 4 Au 10
0.00000000 2.88380000 -4.63920000 4 Au 11
0.00000000 5.76760000 -4.63920000 4 Au 12
2.49740000 -1.44190000 -4.63920000 4 Au 13
2.49740000 1.44190000 -4.63920000 4 Au 14
2.49740000 4.32570000 -4.63920000 4 Au 15
4.99490000 -2.88380000 -4.63920000 4 Au 16
4.99490000 0.00000000 -4.63920000 4 Au 17
4.99490000 2.88380000 -4.63920000 4 Au 18
1.66500000 0.00000000 -2.28460000 4 Au 19
1.66500000 2.88380000 -2.28460000 4 Au 20
1.66500000 5.76760000 -2.28460000 4 Au 21
4.16240000 -1.44190000 -2.28460000 4 Au 22
4.16240000 1.44190000 -2.28460000 4 Au 23
4.16240000 4.32570000 -2.28460000 4 Au 24
6.65980000 -2.88380000 -2.28460000 4 Au 25
6.65980000 0.00000000 -2.28460000 4 Au 26
6.65980000 2.88380000 -2.28460000 4 Au 27
0.83250000 1.44190000 0.07000000 4 Au 28
0.83250000 4.32570000 0.07000000 4 Au 29
0.83250000 7.20950000 0.07000000 4 Au 30
3.32990000 0.00000000 0.07000000 4 Au 31
3.32990000 2.88380000 0.07000000 4 Au 32
3.32990000 5.76760000 0.07000000 4 Au 33
5.82740000 -1.44190000 0.07000000 4 Au 34
5.82740000 1.44190000 0.07000000 4 Au 35
5.82740000 4.32570000 0.07000000 4 Au 36
3.60229000 1.73127800 6.21232000 1 C 37
3.31983200 2.31488800 7.48368000 1 C 38
2.09598100 1.99500800 8.16095300 1 C 39
1.17988000 1.05528700 7.57906300 1 C 40
1.46310900 0.47028400 6.30704300 1 C 41
2.68636400 0.79215700 5.62978400 1 C 42
4.56082400 2.00638800 5.64455700 2 H 43
4.06091200 3.04492300 7.96250400 2 H 44
0.21879900 0.77886800 8.14161800 2 H 45
0.72005100 -0.26018200 5.83101200 2 H 46
2.26463700 3.52419400 9.54422300 2 H 47
0.77428000 2.66551800 9.60221500 2 H 48
4.02109600 0.08423600 4.22189900 2 H 49
2.49171200 -0.71019500 4.21664100 2 H 50
1.84035600 2.53197800 9.49871000 3 N 51
2.95818300 0.26242300 4.29261300 3 N 52
2.43833700 1.57610800 2.38599500 4 Au 53
2.57810400 1.32967400 11.40545900 4 Au 54
1.66500000 0.00000000 13.72250000 4 Au 55
1.66500000 2.88380000 13.72250000 4 Au 56
1.66500000 5.76760000 13.72250000 4 Au 57
4.16240000 -1.44190000 13.72250000 4 Au 58
4.16240000 1.44190000 13.72250000 4 Au 59
4.16240000 4.32570000 13.72250000 4 Au 60
6.65980000 -2.88380000 13.72250000 4 Au 61
6.65980000 0.00000000 13.72250000 4 Au 62
6.65980000 2.88380000 13.72250000 4 Au 63
0.83250000 1.44190000 16.07710000 4 Au 64
0.83250000 4.32570000 16.07710000 4 Au 65
0.83250000 7.20950000 16.07710000 4 Au 66
3.32990000 0.00000000 16.07710000 4 Au 67
3.32990000 2.88380000 16.07710000 4 Au 68
3.32990000 5.76760000 16.07710000 4 Au 69
5.82740000 -1.44190000 16.07710000 4 Au 70
5.82740000 1.44190000 16.07710000 4 Au 71
5.82740000 4.32570000 16.07710000 4 Au 72
0.00000000 0.00000000 18.43170000 4 Au 73
0.00000000 2.88380000 18.43170000 4 Au 74
0.00000000 5.76760000 18.43170000 4 Au 75
2.49740000 -1.44190000 18.43170000 4 Au 76
2.49740000 1.44190000 18.43170000 4 Au 77
2.49740000 4.32570000 18.43170000 4 Au 78
4.99490000 -2.88380000 18.43170000 4 Au 79
4.99490000 0.00000000 18.43170000 4 Au 80
4.99490000 2.88380000 18.43170000 4 Au 81
1.66500000 0.00000000 20.78630000 4 Au 82
1.66500000 2.88380000 20.78630000 4 Au 83
1.66500000 5.76760000 20.78630000 4 Au 84
4.16240000 -1.44190000 20.78630000 4 Au 85
4.16240000 1.44190000 20.78630000 4 Au 86
4.16240000 4.32570000 20.78630000 4 Au 87
6.65980000 -2.88380000 20.78630000 4 Au 88
6.65980000 0.00000000 20.78630000 4 Au 89
6.65980000 2.88380000 20.78630000 4 Au 90
superc: Internal auxiliary supercell: 3 x 3 x 1 = 9
superc: Number of atoms, orbitals, and projectors: 810 6930 7794
InitMesh: MESH = 50 x 50 x 200 = 500000
InitMesh: Mesh cutoff (required, used) = 120.000 121.738 Ry
* Maximum dynamic memory allocated = 449 MB
gensvd: Leads decimation
gensvd: Dim of H1 and S1 : 243
gensvd: Rank of H1: 45
gensvd: Rank of (H1,S1): 122
gensvd: Decimated states: 76
gensvd: Decimation from the left
gensvd: Leads decimation
gensvd: Dim of H1 and S1 : 243
gensvd: Rank of H1: 45
gensvd: Rank of (H1,S1): 122
gensvd: Decimated states: 76
gensvd: Decimation from the left
Segmentation fault
++++++++++++END-THE ERROR ++++++++++++++++++
But this test can be done successfully with the PGI-compiled verison smeagol.
The input file of the test is as follows:
++++++++++++BEGIN-test input++++++++++++++++++
# -----------------------------------------------------------------------------
SystemName scatter # Descriptive name of the system
SystemLabel scatter # Short name for naming files
# Output options
WriteCoorStep
WriteMullikenPop 1
SaveHS T
# Species and atoms
NumberOfSpecies 4
NumberOfAtoms 90
%block ChemicalSpeciesLabel
1 6 C
2 1 H
3 7 N
4 79 Au
%endblock ChemicalSpeciesLabel
# Basis
%block PAO.Basis # Define Basis set
C 2 # Species label, number of l-shells
n=2 0 1 # n, l, Nzeta
5.0
1.000
n=2 1 1 P 1 # n, l, Nzeta, Polarization, NzetaPol
8.0
1.000
N 2 # Species label, number of l-shells
n=2 0 1 # n, l, Nzeta
4.0
1.000
n=2 1 1 P 1 # n, l, Nzeta, Polarization, NzetaPol
7.0
1.000
H 1 # Species label, number of l-shells
n=1 0 1 P 1 # n, l, Nzeta, Polarization, NzetaPol
3.5
1.000
Au 2 # Species label, number of l-shells
n=6 0 1 P 1 # n, l, Nzeta, Polarization, NzetaPol
8.0
1.000
n=5 2 1 # n, l, Nzeta
5.8
1.000
%endblock PAO.Basis
%block Ps.lmax
Au 2
%endblock Ps.lmax
LatticeConstant 1.0 Ang
%block LatticeVectors
7.492316 -4.3256905 0.000000
0.000000 8.651381 0.000000
0.000000 0.000000 30.1347
%endblock LatticeVectors
# the larger KCutOff, the more K-point use
# KgridCutoff 6.72 Ang
# KgridCutoff 20.72 Ang
%block kgrid_Monkhorst_Pack
4 0 0 0.5
0 4 0 0.5
0 0 1 0.0
%endblock kgrid_Monkhorst_Pack
xc.functional GGA # Exchange-correlation functional
xc.authors PBE # Exchange-correlation version
SpinPolarized false # Logical parameters are: yes or no
MeshCutoff 120. Ry # Mesh cutoff. real space mesh
# SCF options
MaxSCFIterations 300 # Maximum number of SCF iter
DM.MixingWeight 0.02 # New DM amount for next SCF cycle
DM.Tolerance 1.d-3 # Tolerance in maximum difference
# between input and output DM
DM.UseSaveDM false # to use continuation files
DM.NumberPulay 5
SolutionMethod Diagon # OrderN or Diagon
ElectronicTemperature 25 meV # Temp. for Fermi smearing
# MD options
MD.TypeOfRun cg # Type of dynamics:
MD.VariableCell false
MD.NumCGsteps 0 # Number of CG steps for
# coordinate optimization
MD.MaxCGDispl 0.2 bohr # Maximum atomic displacement
# in one CG step (Bohr)
MD.MaxForceTol 0.08 eV/Ang # Tolerance in the maximum
# atomic force (Ry/Bohr)
MD.MaxStressTol 0.1 Gpa
# Atomic coordinates
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.832500 1.441900 -6.993800 4
0.832500 4.325700 -6.993800 4
0.832500 7.209500 -6.993800 4
3.329900 0.000000 -6.993800 4
3.329900 2.883800 -6.993800 4
3.329900 5.767600 -6.993800 4
5.827400 -1.441900 -6.993800 4
5.827400 1.441900 -6.993800 4
5.827400 4.325700 -6.993800 4
0.000000 0.000000 -4.639200 4
0.000000 2.883800 -4.639200 4
0.000000 5.767600 -4.639200 4
2.497400 -1.441900 -4.639200 4
2.497400 1.441900 -4.639200 4
2.497400 4.325700 -4.639200 4
4.994900 -2.883800 -4.639200 4
4.994900 0.000000 -4.639200 4
4.994900 2.883800 -4.639200 4
1.665000 0.000000 -2.284600 4
1.665000 2.883800 -2.284600 4
1.665000 5.767600 -2.284600 4
4.162400 -1.441900 -2.284600 4
4.162400 1.441900 -2.284600 4
4.162400 4.325700 -2.284600 4
6.659800 -2.883800 -2.284600 4
6.659800 0.000000 -2.284600 4
6.659800 2.883800 -2.284600 4
0.832500 1.441900 0.070000 4
0.832500 4.325700 0.070000 4
0.832500 7.209500 0.070000 4
3.329900 0.000000 0.070000 4
3.329900 2.883800 0.070000 4
3.329900 5.767600 0.070000 4
5.827400 -1.441900 0.070000 4
5.827400 1.441900 0.070000 4
5.827400 4.325700 0.070000 4
3.602290 1.731278 6.212320 1
3.319832 2.314888 7.483680 1
2.095981 1.995008 8.160953 1
1.179880 1.055287 7.579063 1
1.463109 0.470284 6.307043 1
2.686364 0.792157 5.629784 1
4.560824 2.006388 5.644557 2
4.060912 3.044923 7.962504 2
0.218799 0.778868 8.141618 2
0.720051 -0.260182 5.831012 2
2.264637 3.524194 9.544223 2
0.774280 2.665518 9.602215 2
4.021096 0.084236 4.221899 2
2.491712 -0.710195 4.216641 2
1.840356 2.531978 9.498710 3
2.958183 0.262423 4.292613 3
2.438337 1.576108 2.385995 4
2.578104 1.329674 11.405459 4
1.665000 0.000000 13.722500 4
1.665000 2.883800 13.722500 4
1.665000 5.767600 13.722500 4
4.162400 -1.441900 13.722500 4
4.162400 1.441900 13.722500 4
4.162400 4.325700 13.722500 4
6.659800 -2.883800 13.722500 4
6.659800 0.000000 13.722500 4
6.659800 2.883800 13.722500 4
0.832500 1.441900 16.077100 4
0.832500 4.325700 16.077100 4
0.832500 7.209500 16.077100 4
3.329900 0.000000 16.077100 4
3.329900 2.883800 16.077100 4
3.329900 5.767600 16.077100 4
5.827400 -1.441900 16.077100 4
5.827400 1.441900 16.077100 4
5.827400 4.325700 16.077100 4
0.000000 0.000000 18.431700 4
0.000000 2.883800 18.431700 4
0.000000 5.767600 18.431700 4
2.497400 -1.441900 18.431700 4
2.497400 1.441900 18.431700 4
2.497400 4.325700 18.431700 4
4.994900 -2.883800 18.431700 4
4.994900 0.000000 18.431700 4
4.994900 2.883800 18.431700 4
1.665000 0.000000 20.786300 4
1.665000 2.883800 20.786300 4
1.665000 5.767600 20.786300 4
4.162400 -1.441900 20.786300 4
4.162400 1.441900 20.786300 4
4.162400 4.325700 20.786300 4
6.659800 -2.883800 20.786300 4
6.659800 0.000000 20.786300 4
6.659800 2.883800 20.786300 4
%endblock AtomicCoordinatesAndAtomicSpecies
SaveHS F # Save the Hamiltonian and Overlap matrices
SaveRHO T # Save the valence pseudocharge density
SaveDeltaRHO F
WriteDenchar F # Write Denchar output
WriteDMT T
WriteDRHO T
WriteVT T
WriteEigenvalues T
WriteMullikenPop 1
EMTransport T
NEnergReal 100
NEnergImCircle 60
NEnergImLine 20
NPoles 5
VInitial 0.0 eV
VFinal 0.0 eV
NIVPoints 0
Delta 1.d-6
EnergLowestBound -100 eV
SpinConfLeads 0
NSlices 1
TrCoefficients T
NTransmPoints 1000
InitTransmRange -10.0 eV
FinalTransmRange 5.0 eV
HartreeLeadsBottom -4.55129433 eV
HartreeLeadsLeft -9.348400 Ang
HartreeLeadsRight 20.786300 Ang
SaveMemTranspK T
PeriodicTransp T
ParallelOverK T
TransmissionOverk T
SaveElectrostaticPotential T
#%block SaveBiasSteps
#0
#%endblock SaveBiasSteps
++++++++++++END-test input+++++++++++++++++++
By the way, IFORT is ifort-10.1.012,MKL is mkl-10.0.2.018 and MPI is mpich-1.2.7.
SO what is the reason?It is because there are too many atoms?So why PGI-compiled verison smeagol can do this job?
Can anyone help me out? It is really puzzling me!
THANKS IN ADVANCE@
------------------
BEST REGARDS!
Guangping Zhang
-----------------------------------
Atom and Melecular Physics
Physics and Electronics College
Shandong Normal University
Shandong,Jinan,China
------------------------------------
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