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Running the example of Cr2_CNC.dat program is reporting errors
Date: 2018/05/09 14:25
Name: lucky   <3033467121@qq.com>

Hi
Recently, I calculated the example Cr2_CNC.dat of openmx3.8, Cr2.dat is in the folder of openmx3.8/work.
but the following error occurred. I used 10 cores to run the program.
The specific commands is mpirun.mpich -np 10 openmx3.8/source/openmx input.dat
I successfully installed OpenMX, and have done some calculations, I feel that there is no problem in my software,
I will give the total input.dat file and output.dat in next thread.
I do not know why happened to this mistake, I hope you can help me and give me some suggestions, thank you.

*******************************************************
SCF calculation at MD = 1
*******************************************************
.mpich
<MD= 1> Calculation of the overlap matrix
<MD= 1> Calculation of the nonlocal matrix
<MD= 1> Calculation of the VNA projector matrix

******************* MD= 1 SCF= 1 *******************
<Cluster> Solving the eigenvalue problem...
Assertion failed in file src/mpid/ch3/src/ch3u_buffer.c at line 77: FALSE
Assertion failed in file src/mpid/ch3/src/ch3u_buffer.c at line 77: FALSE
memcpy argument memory ranges overlap, dst_=0x60101c8 src_=0x60101c8 len_=32

internal ABORT - process 1
Assertion failed in file src/mpid/ch3/src/ch3u_buffer.c at line 77: FALSE
memcpy argument memory ranges overlap, dst_=0x41733a8 src_=0x41733a8 len_=24

internal ABORT - process 2
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Re: Running the example of Cr2_CNC.dat program is reporting errors ( No.1 )
Date: 2018/05/09 14:28
Name: lucky  <3033467121@qq.com>

Hi
The input file(Cr2_CNC.dat) is following as:

DATA.PATH /home/smc/package/openmx/openmx3.8/DFT_DATA13
System.CurrrentDirectory ./ # default=./
System.Name cr2_cnc
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (0-2)

Species.Number 1
<Definition.of.Atomic.Species
Cr Cr8.0-s2p2d1 Cr_CA13
Definition.of.Atomic.Species>

<Hubbard.U.values # eV
Cr 1s 0.0 2s 0.0 1p 0.0 1d 0.0
Hubbard.U.values>

Atoms.Number 2
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 Cr 0.00000 0.00000 0.00000 9.0 5.0 -20.0 0.0 -20.0 0.0 1 off
2 Cr 0.00000 2.00000 0.00000 9.0 5.0 20.0 0.0 20.0 0.0 1 off
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
#<Atoms.UnitVectors
# 10.0 0.0 0.0
# 0.0 10.0 0.0
# 0.0 0.0 10.0
#Atoms.UnitVectors>

scf.XcType LSDA-CA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization nc # On|Off|NC
scf.Hubbard.U off # On|Off , default=off
scf.Hubbard.Occupation dual # onsite|full|dual, default=dual
scf.SpinOrbit.Coupling on # On|Off, default=off
scf.Constraint.NC.Spin on # On|Off, default=off
scf.Constraint.NC.Spin.v 0.5 # default=0.0 (eV)
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 200.0 # default=150 (Ry)
scf.maxIter 200 # default=40
scf.EigenvalueSolver cluster # Recursion|Cluster|Band
scf.Kgrid 1 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diis # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.0010 # default=0.30
scf.Min.Mixing.Weight 0.0001 # default=0.001
scf.Max.Mixing.Weight 0.3000 # default=0.40
scf.Mixing.History 7 # default=5
scf.Mixing.StartPulay 15 # default=6
scf.criterion 1.0e-9 # default=1.0e-6 (Hartree)
scf.Electric.Field 0.0 0.0 0.0 # default=0 0 0 (GV/m)

scf.restart off # on|off, default=off

MD.Type nomd # Nomd|Opt|DIIS|NVE|NVT_VS|NVT_NH
MD.maxIter 1 # default=1
MD.TimeStep 1.0 # default=0.5 (fs)
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (Hartree/bohr)

MO.fileout off # on|off, default=off
num.HOMOs 1 # default=1
num.LUMOs 1 # default=1

Dos.fileout off # on|off, default=off
Dos.Erange -10.0 10.0 # default = -20 20
Dos.Kgrid 1 1 1 # default = Kgrid1 Kgrid2 Kgrid3

HS.fileout off # on|off, default=off



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Re: Running the example of Cr2_CNC.dat program is reporting errors ( No.2 )
Date: 2018/05/09 14:30
Name: lucky  <3033467121@qq.com>

Hi
The output file is following as:
The number of threads in each node for OpenMP parallelization is 1.


*******************************************************
*******************************************************
Welcome to OpenMX Ver. 3.8
Copyright (C), 2002-2014, T. Ozaki
OpenMX comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to
redistribute it under the constitution of the GNU-GPL.
*******************************************************
*******************************************************

<Set_Cluster_UnitCell> automatically determied UnitCell(Ang.)
<Set_Cluster_UnitCell> from atomic positions and Rc of PAOs (margin= 10.00%)
<Set_Cluster_UnitCell> 9.313520 0.000000 0.000000
<Set_Cluster_UnitCell> 0.000000 11.513520 0.000000
<Set_Cluster_UnitCell> 0.000000 0.000000 9.313520

widened unit cell to fit energy cutoff (Ang.)
A = 9.404267 0.000000 0.000000 (80)
B = 0.000000 11.520227 0.000000 (98)
C = 0.000000 0.000000 9.404267 (80)


<Input_std> Your input file was normally read.
<Input_std> The system includes 1 species and 2 atoms.

*******************************************************
PAO and VPS
*******************************************************

<SetPara_DFT> PAOs of species Cr were normally found.
<SetPara_DFT> VPSs of species Cr were normally found.
Cr_CA13.vps is j-dependent.

*******************************************************
Fourier transform of PAO and projectors of VNL
*******************************************************

<FT_PAO> Fourier transform of pseudo atomic orbitals
<FT_NLP> Fourier transform of non-local projectors
<FT_ProExpn_VNA> Fourier transform of VNA separable projectors
<FT_VNA> Fourier transform of VNA potentials
<FT_ProductPAO> Fourier transform of product of PAOs

*******************************************************
Allocation of atoms to proccesors at MD_iter= 1
*******************************************************

proc = 0 # of atoms= 1 estimated weight= 1.00000
proc = 1 # of atoms= 1 estimated weight= 1.00000
proc = 2 # of atoms= 0 estimated weight= 0.00000
proc = 3 # of atoms= 0 estimated weight= 0.00000
proc = 4 # of atoms= 0 estimated weight= 0.00000
proc = 5 # of atoms= 0 estimated weight= 0.00000
proc = 6 # of atoms= 0 estimated weight= 0.00000
proc = 7 # of atoms= 0 estimated weight= 0.00000
proc = 8 # of atoms= 0 estimated weight= 0.00000
proc = 9 # of atoms= 0 estimated weight= 0.00000




*******************************************************
Analysis of neighbors and setting of grids
*******************************************************

TFNAN= 2 Average FNAN= 1.00000
TSNAN= 0 Average SNAN= 0.00000
<truncation> CpyCell= 1 ct_AN= 1 FNAN SNAN 1 0
<truncation> CpyCell= 1 ct_AN= 2 FNAN SNAN 1 0
TFNAN= 2 Average FNAN= 1.00000
TSNAN= 0 Average SNAN= 0.00000
<truncation> CpyCell= 2 ct_AN= 1 FNAN SNAN 1 0
<truncation> CpyCell= 2 ct_AN= 2 FNAN SNAN 1 0
TFNAN= 2 Average FNAN= 1.00000
TSNAN= 0 Average SNAN= 0.00000
<truncation> CpyCell= 2 ct_AN= 1 FNAN SNAN 1 0
<truncation> CpyCell= 2 ct_AN= 2 FNAN SNAN 1 0
<Check_System> The system is molecule.
lattice vectors (bohr)
A = 17.771487323971, 0.000000000000, 0.000000000000
B = 0.000000000000, 21.770071971864, 0.000000000000
C = 0.000000000000, 0.000000000000, 17.771487323971
reciprocal lattice vectors (bohr^-1)
RA = 0.353554274476, 0.000000000000, 0.000000000000
RB = 0.000000000000, 0.288615734266, 0.000000000000
RC = 0.000000000000, 0.000000000000, 0.353554274476
Grid_Origin -8.774671866211 -8.884238201578 -8.774671866211
Cell_Volume = 6875.549562909530 (Bohr^3)
GridVol = 0.010962292033 (Bohr^3)
Grid_Origin -8.774671866211 -8.884238201578 -8.774671866211
Cell_Volume = 6875.549562909530 (Bohr^3)
GridVol = 0.010962292033 (Bohr^3)
<UCell_Box> Info. of cutoff energy and num. of grids
lattice vectors (bohr)
A = 17.771487323971, 0.000000000000, 0.000000000000
B = 0.000000000000, 21.770071971864, 0.000000000000
C = 0.000000000000, 0.000000000000, 17.771487323971
reciprocal lattice vectors (bohr^-1)
RA = 0.353554274476, 0.000000000000, 0.000000000000
RB = 0.000000000000, 0.288615734266, 0.000000000000
RC = 0.000000000000, 0.000000000000, 0.353554274476
Required cutoff energy (Ryd) for 3D-grids = 200.0000
Used cutoff energy (Ryd) for 3D-grids = 200.0010, 200.0010, 200.0010
Num. of grids of a-, b-, and c-axes = 80, 98, 80
Grid_Origin -8.774671866211 -8.884238201578 -8.774671866211
Cell_Volume = 6875.549562909530 (Bohr^3)
GridVol = 0.010962292033 (Bohr^3)
Cell vectors (bohr) of the grid cell (gtv)
gtv_a = 0.222143591550, 0.000000000000, 0.000000000000
gtv_b = 0.000000000000, 0.222143591550, 0.000000000000
gtv_c = 0.000000000000, 0.000000000000, 0.222143591550
|gtv_a| = 0.222143591550
|gtv_b| = 0.222143591550
|gtv_c| = 0.222143591550
Num. of grids overlapping with atom 1 = 195712
Num. of grids overlapping with atom 2 = 195712

*******************************************************
SCF calculation at MD = 1
*******************************************************

<MD= 1> Calculation of the overlap matrix
<MD= 1> Calculation of the nonlocal matrix
<MD= 1> Calculation of the VNA projector matrix

******************* MD= 1 SCF= 1 *******************
<Cluster> Solving the eigenvalue problem...
Assertion failed in file src/mpid/ch3/src/ch3u_buffer.c at line 77: FALSE
Assertion failed in file src/mpid/ch3/src/ch3u_buffer.c at line 77: FALSE
memcpy argument memory ranges overlap, dst_=0x60101c8 src_=0x60101c8 len_=32

internal ABORT - process 1
Assertion failed in file src/mpid/ch3/src/ch3u_buffer.c at line 77: FALSE
memcpy argument memory ranges overlap, dst_=0x41733a8 src_=0x41733a8 len_=24

internal ABORT - process 2
メンテ
Re: Running the example of Cr2_CNC.dat program is reporting errors ( No.3 )
Date: 2018/05/09 15:44
Name: Naoya Yamaguchi

Hi,

First, can you try it again without "mpirun.mpich" as follows?
openmx3.8/source/openmx Cr2_CNC.dat

If the calculation is normally finished, this problem is due to the MPI.

After that, please try it using 2 cores as follows, and check the behavior.
mpirun.mpich -np 10 openmx3.8/source/openmx Cr2_CNC.dat

Regards,
Naoya Yamaguchi
メンテ
Re: Running the example of Cr2_CNC.dat program is reporting errors ( No.4 )
Date: 2018/05/09 16:05
Name: lucky  <3033467121@qq.com>

Hi,Naoya Yamaguchi
Thank you for helping me again.

When I use one ,two and four cores ,the error still appeared.It is as follows:
*******************************************************
SCF calculation at MD = 1
*******************************************************

<MD= 1> Calculation of the overlap matrix
<MD= 1> Calculation of the nonlocal matrix
<MD= 1> Calculation of the VNA projector matrix

******************* MD= 1 SCF= 1 *******************
<Cluster> Solving the eigenvalue problem...
Assertion failed in file src/mpid/ch3/src/ch3u_buffer.c at line 77: FALSE
memcpy argument memory ranges overlap, dst_=0x6552190 src_=0x6552190 len_=208

internal ABORT - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor
メンテ
Re: Running the example of Cr2_CNC.dat program is reporting errors ( No.5 )
Date: 2018/05/09 17:16
Name: Naoya Yamaguchi

Hi,

I found that similar cases were reported previouslly:
http://www.openmx-square.org/forum/patio.cgi?mode=view&no=1019
http://www.openmx-square.org/forum/patio.cgi?mode=view&no=1968

And, from it and your trying, I guess that this problem may occur in the case of some environments (e.g. compilers; libraries). it may be solved modifying "Eigen_PHH.c" and "Eigen_PReHH.c" in OpenMX.
http://www.openmx-square.org/forum/patio.cgi?mode=view&no=2209
http://www.openmx-square.org/forum/patio.cgi?mode=view&no=2234

Or, you can avoid it using a different environment (e.g. Open MPI, instead of MPICH).

Regards,
Naoya Yamaguchi
メンテ
Re: Running the example of Cr2_CNC.dat program is reporting errors ( No.6 )
Date: 2018/05/09 20:46
Name: lucky  <3033467121@qq.com>

Dear Naoya Yamaguchi
I have solved this problem according your suggestions. Now the Cr2_CNC.dat is finished normally.
Thank you for taking your precious time to help me again.
Thanks to Kylin's solution.
Best wishes.
lucky.
メンテ

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