MPI error in cluster SCF eigenvaluesolver (OpenMX3.7) |
- Date: 2014/05/26 23:24
- Name: Jae Nyeong Kim
<algetnya@postech.ac.kr>
- Dear Professor,
I have compiled OpenMx with the following option with out error.
MKLROOT=/opt/intel/Compiler/11.1/059
CC = mpicc -O3 -xHOST -openmp -ip -no-prec-div -mkl=parallel -I$(MKLROOT)/mkl/include/fftw -shared-intel
FC = mpif90 -O3 -xHOST -openmp -ip -no-prec-div -mkl=parallel -I$(MKLROOT)/mkl/include/fftw -shared-intel
LIB = -L$(MKLROOT)/lib/intel64 -lifcore -limf
However, in the test calculation. I have error message like
./openmx Methane.dat
The number of threads in each node for OpenMP parallelization is 1.
*******************************************************
*******************************************************
Welcome to OpenMX Ver. 3.7.8
Copyright (C), 2002-2013, 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.
*******************************************************
*******************************************************
<Input_std> Your input file was normally read.
<Input_std> The system includes 2 species and 5 atoms.
*******************************************************
PAO and VPS
*******************************************************
<SetPara_DFT> PAOs of species H were normally found.
<SetPara_DFT> PAOs of species C were normally found.
<SetPara_DFT> VPSs of species H were normally found.
H_PBE13.vps is j-dependent.
In case of scf.SpinOrbit.Coupling=off,
j-dependent pseudo potentials are averaged by j-degeneracy,
which corresponds to a scalar relativistic treatment.
<SetPara_DFT> VPSs of species C were normally found.
C_PBE13.vps is j-dependent.
In case of scf.SpinOrbit.Coupling=off,
j-dependent pseudo potentials are averaged by j-degeneracy,
which corresponds to a scalar relativistic treatment.
*******************************************************
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= 5 estimated weight= 5.00000
*******************************************************
Analysis of neigbors and setting of grids
*******************************************************
TFNAN= 20 Average FNAN= 4.00000
TSNAN= 0 Average SNAN= 0.00000
<truncation> CpyCell= 1 ct_AN= 1 FNAN SNAN 4 0
<truncation> CpyCell= 1 ct_AN= 2 FNAN SNAN 4 0
<truncation> CpyCell= 1 ct_AN= 3 FNAN SNAN 4 0
<truncation> CpyCell= 1 ct_AN= 4 FNAN SNAN 4 0
<truncation> CpyCell= 1 ct_AN= 5 FNAN SNAN 4 0
TFNAN= 20 Average FNAN= 4.00000
TSNAN= 0 Average SNAN= 0.00000
<truncation> CpyCell= 2 ct_AN= 1 FNAN SNAN 4 0
<truncation> CpyCell= 2 ct_AN= 2 FNAN SNAN 4 0
<truncation> CpyCell= 2 ct_AN= 3 FNAN SNAN 4 0
<truncation> CpyCell= 2 ct_AN= 4 FNAN SNAN 4 0
<truncation> CpyCell= 2 ct_AN= 5 FNAN SNAN 4 0
TFNAN= 20 Average FNAN= 4.00000
TSNAN= 0 Average SNAN= 0.00000
<truncation> CpyCell= 2 ct_AN= 1 FNAN SNAN 4 0
<truncation> CpyCell= 2 ct_AN= 2 FNAN SNAN 4 0
<truncation> CpyCell= 2 ct_AN= 3 FNAN SNAN 4 0
<truncation> CpyCell= 2 ct_AN= 4 FNAN SNAN 4 0
<truncation> CpyCell= 2 ct_AN= 5 FNAN SNAN 4 0
<Check_System> The system is molecule.
lattice vectors (bohr)
A = 18.897259885789, 0.000000000000, 0.000000000000
B = 0.000000000000, 18.897259885789, 0.000000000000
C = 0.000000000000, 0.000000000000, 18.897259885789
reciprocal lattice vectors (bohr^-1)
RA = 0.332491871581, 0.000000000000, 0.000000000000
RB = 0.000000000000, 0.332491871581, 0.000000000000
RB = 0.000000000000, 0.000000000000, 0.332491871581
Grid_Origin -9.300995100037 -9.300995100037 -9.300995100037
Cell_Volume = 6748.333037104149 (Bohr^3)
GridVol = 0.025742847584 (Bohr^3)
Grid_Origin -9.300995100037 -9.300995100037 -9.300995100037
Cell_Volume = 6748.333037104149 (Bohr^3)
GridVol = 0.025742847584 (Bohr^3)
<UCell_Box> Info. of cutoff energy and num. of grids
lattice vectors (bohr)
A = 18.897259885789, 0.000000000000, 0.000000000000
B = 0.000000000000, 18.897259885789, 0.000000000000
C = 0.000000000000, 0.000000000000, 18.897259885789
reciprocal lattice vectors (bohr^-1)
RA = 0.332491871581, 0.000000000000, 0.000000000000
RB = 0.000000000000, 0.332491871581, 0.000000000000
RB = 0.000000000000, 0.000000000000, 0.332491871581
Required cutoff energy (Ryd) for 3D-grids = 120.0000
Used cutoff energy (Ryd) for 3D-grids = 113.2041, 113.2041, 113.2041
Num. of grids of a-, b-, and c-axes = 64, 64, 64
Grid_Origin -9.300995100037 -9.300995100037 -9.300995100037
Cell_Volume = 6748.333037104149 (Bohr^3)
GridVol = 0.025742847584 (Bohr^3)
Cell vectors (bohr) of the grid cell (gtv)
gtv_a = 0.295269685715, 0.000000000000, 0.000000000000
gtv_b = 0.000000000000, 0.295269685715, 0.000000000000
gtv_c = 0.000000000000, 0.000000000000, 0.295269685715
|gtv_a| = 0.295269685715
|gtv_b| = 0.295269685715
|gtv_c| = 0.295269685715
Num. of grids overlapping with atom 1 = 20336
Num. of grids overlapping with atom 2 = 20346
Num. of grids overlapping with atom 3 = 20346
Num. of grids overlapping with atom 4 = 20346
Num. of grids overlapping with atom 5 = 20346
*******************************************************
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 ch3u_buffer.c at line 77: FALSE
memcpy argument memory ranges overlap, dst_=0x251bc50 src_=0x251bc50 len_=512
internal ABORT - process 0
As I searched the internet and got to know that this is error from MPI. (I could not understand meaning fully)
Could I know how to fix this?
I am using mpich2-1.4.1p1 version and mkl library 11.1/059 version.
I also have openmpi, but I think that mkl library is compiled with mpich2.
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Re: MPI error in cluster SCF eigenvaluesolver (OpenMX3.7)