 Re: Segmentation Fault for openMX MPI version 3.0 ( No.1 ) |
- Date: 2006/09/29 10:57
- Name: jessK
Hi,
It is hard to say without any information (input file, output file). There are a lot of factors which could cause such error. Try to run your using serial version of openmx. If it is OK, so there is a problem with your MPI envronment.
JK
|
| Re: Segmentation Fault for openMX MPI version 3.0 ( No.2 ) |
- Date: 2006/09/29 11:48
- Name: KC <kianchau@gmail.com>
- Hi jessK,
The serial program runs okay. We suspect is some memory error that we do not know how to resolve.
The input file and output file is as follows:
======================= INPUT FILE ======================================
#
# File Name
#
System.CurrrentDirectory ./ # default=./
System.Name si8
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (1-3)
#
# restart using a restart file, *.rst
#
scf.restart off # on|off,default=off
#
# Definition of Atomic Species
#
Species.Number 1
<Definition.of.Atomic.Species
Si Si6.0-s2p2d1 Si_LDA
Definition.of.Atomic.Species>
#
# Atoms
#
Atoms.Number 8
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates # Unit=Ang.
1 Si 0.300000000000 0.000000000000 0.000000000000 2.0 2.0
2 Si 0.000000000000 2.715000000000 2.715000000000 2.0 2.0
3 Si 2.715000000000 0.000000000000 2.715000000000 2.0 2.0
4 Si 2.715000000000 2.715000000000 0.000000000000 2.0 2.0
5 Si 1.357500000000 1.357500000000 1.357500000000 2.0 2.0
6 Si 1.357500000000 4.072500000000 4.072500000000 2.0 2.0
7 Si 4.072500000000 1.357500000000 4.072500000000 2.0 2.0
8 Si 4.072500000000 4.072500000000 1.357500000000 2.0 2.0
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors # unit=Ang.
5.430000000000 0.000000000000 0.000000000000
0.000000000000 5.430000000000 0.000000000000
0.000000000000 0.000000000000 5.430000000000
Atoms.UnitVectors>
#
# SCF or Electronic System
#
scf.XcType LDA # LDA|LSDA-CA|LSDA-PW
scf.SpinPolarization off # On|Off
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 100.0 # default=150 (Ry)
scf.maxIter 100 # default=40
scf.EigenvalueSolver band # Recursion|Cluster|Band
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 4 4 4 # means 4x4x4
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay
scf.Init.Mixing.Weight 0.010 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.200 # default=0.40
scf.Mixing.History 6 # default=5
scf.Mixing.StartPulay 12 # default=6
scf.criterion 1.0e-8 # default=1.0e-6 (Hartree)
#
# 1D FFT
#
1DFFT.NumGridK 900 # default=900
1DFFT.NumGridR 900 # default=900
1DFFT.EnergyCutoff 3600.0 # default=3DFFT.EnergyCutoff*3.0 (Ry)
#
# Orbital Optimization
#
orbitalOpt.Method off # Off|Unrestricted|Restricted
orbitalOpt.InitCoes Symmetrical # Symmetrical|Free
orbitalOpt.initPrefactor 0.1 # default=0.1
orbitalOpt.scf.maxIter 15 # default=12
orbitalOpt.MD.maxIter 4 # default=5
orbitalOpt.per.MDIter 4 # default=1000000
orbitalOpt.criterion 1.0e-4 # default=1.0e-4 (Hartree/borh)^2
#
# output of contracted orbitals
#
CntOrb.fileout off # on|off, default=off
Num.CntOrb.Atoms 1 # default=1
<Atoms.Cont.Orbitals
1
Atoms.Cont.Orbitals>
#
# SCF Order-N
#
orderN.HoppingRanges 8.389 # default=5.0 (Ang)
orderN.NumHoppings 2 # default=2
orderN.KrylovH.order 800 # default=400
#
# MD or Geometry Optimization
#
MD.Type diis # Nomd|Constant_Energy_MD|Opt
MD.Opt.DIIS.History 4
MD.Opt.StartDIIS 5 # default=5
MD.maxIter 100 # default=1
MD.TimeStep 0.5 # default=0.5 (fs)
MD.Opt.criterion 1.0e-6 # default=1.0e-4 (Hartree/bohr)
#
# Band dispersion
#
# if <Band.KPath.UnitCell does not exist,
# the reciprical lattice vector is employed.
Band.dispersion off # on|off, default=off
Band.Nkpath 5
<Band.kpath
15 0.0 0.0 0.0 1.0 0.0 0.0 g X
15 1.0 0.0 0.0 1.0 0.5 0.0 X W
15 1.0 0.5 0.0 0.5 0.5 0.5 W L
15 0.5 0.5 0.5 0.0 0.0 0.0 L g
15 0.0 0.0 0.0 1.0 1.0 0.0 g X
Band.kpath>
#
# MO output
#
MO.fileout off # on|off
num.HOMOs 1 # default=1
num.LUMOs 1 # default=1
MO.Nkpoint 2 # default=1
<MO.kpoint
0.0 0.0 0.0
0.3 0.0 0.0
MO.kpoint>
#
# DOS and PDOS
#
Dos.fileout off # on|off, default=off
Dos.Erange -20.0 20.0 # default = -20 20
Dos.Kgrid 12 12 12 # default = Kgrid1 Kgrid2 Kgrid3
========================================END===================
 |
| Re: Segmentation Fault for openMX MPI version 3.0 ( No.3 ) |
- Date: 2006/09/29 11:51
- Name: KC <kianchau@gmail.com>
- The output file error occures here:
*******************************************************
Computational times (s) at MD = 8
*******************************************************
Set_OLP_Kin = 2.06381
Set_Nonlocal = 7.18251
Set_Hamiltonian = 4.93897
Poisson = 0.09348
diagonalization = 22.76009
Mixing_DM = 0.03620
Force = 5.01993
Total_Energy = 0.55234
*******************************************************
MD or geometry opt. at MD = 8
*******************************************************
<DIIS2> |Maximum force| (Hartree/Bohr) = 0.026205738600 tuned_dt= 0.120945
<DIIS2> Criterion (Hartree/Bohr) = 0.000001000000
<DIIS2> DIIS matrix
<DIIS2> 1.000000 1.000000
<DIIS2> 1.000000 0.000000
M_GDIIS_HISTORY= 4 diis_iter= 1
<DIIS2> diis alpha=1.000000 -1.000000
<DIIS2> |tilde{R}|=1.517086E-01
<DIIS2> mixing= 0.100000000000
<DIIS2> diff_x= 0.013103 , dE= 0.006854
<DIIS2> atomnum= 8
1 Si XYZ(ang) Fxyz(a.u.)= 0.1579 -0.0000 -0.0000 0.0262 -0.0001 -0.0001
2 Si XYZ(ang) Fxyz(a.u.)= -0.0160 2.7148 2.7148 0.0022 0.0001 0.0001
3 Si XYZ(ang) Fxyz(a.u.)= 2.7328 0.0001 2.7152 -0.0057 -0.0001 -0.0001
4 Si XYZ(ang) Fxyz(a.u.)= 2.7328 2.7152 0.0001 -0.0057 -0.0001 -0.0001
5 Si XYZ(ang) Fxyz(a.u.)= 1.3894 1.3853 1.3853 -0.0037 -0.0026 -0.0026
6 Si XYZ(ang) Fxyz(a.u.)= 1.3892 4.0447 4.0447 -0.0037 0.0026 0.0026
7 Si XYZ(ang) Fxyz(a.u.)= 4.1021 1.3360 4.0941 -0.0047 0.0040 -0.0041
8 Si XYZ(ang) Fxyz(a.u.)= 4.1021 4.0941 1.3360 -0.0047 -0.0041 0.0040
<Steepest_Descent> |Maximum force| (Hartree/Bohr) = 0.026205738600
<Steepest_Descent> Criterion (Hartree/Bohr) = 0.000001000000
atom= 1, XYZ(ang) Fxyz(a.u.)= 0.1579 -0.0000 -0.0000 0.0262 -0.0001 -0.0001
atom= 2, XYZ(ang) Fxyz(a.u.)= -0.0160 2.7148 2.7148 0.0022 0.0001 0.0001
atom= 3, XYZ(ang) Fxyz(a.u.)= 2.7328 0.0001 2.7152 -0.0057 -0.0001 -0.0001
atom= 4, XYZ(ang) Fxyz(a.u.)= 2.7328 2.7152 0.0001 -0.0057 -0.0001 -0.0001
atom= 5, XYZ(ang) Fxyz(a.u.)= 1.3894 1.3853 1.3853 -0.0037 -0.0026 -0.0026
atom= 6, XYZ(ang) Fxyz(a.u.)= 1.3892 4.0447 4.0447 -0.0037 0.0026 0.0026
atom= 7, XYZ(ang) Fxyz(a.u.)= 4.1021 1.3360 4.0941 -0.0047 0.0040 -0.0041
atom= 8, XYZ(ang) Fxyz(a.u.)= 4.1021 4.0941 1.3360 -0.0047 -0.0041 0.0040
--- mpimon --- Aborting run after process-3 terminated abnormally Childprocess 31074 got signal SIGSEGV(11): segmentation violation ---
0.035u 0.093s 7:06.28 0.0% 0+0k 0+0io 0pf+0w
|
| Re: Segmentation Fault for openMX MPI version 3.0 ( No.4 ) |
- Date: 2006/09/29 14:31
- Name: T.Ozaki
- Hi,
Have you checked the thread entitled by
"Bugs in MD_pac.c of OpenMX Ver. 3.0" ?
If you have and still have the problem,
let us know.
Regards,
TO
|
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Segmentation Fault for openMX MPI version 3.0