**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.
| |