**one problem when running the calculation** |
- Date: 2010/04/04 20:43
- Name:
**yang**
<yangzw1985@163.com>
- The first error as follows:
[yang@yang work]$ mpirun -np 4 openmx Methane.dat The number of threads in each node for OpenMP parallelization is 1. ******************************************************* ******************************************************* Welcome to OpenMX Ver. 3.5 Copyright (C), 2002-2009, 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. ******************************************************* ******************************************************* ******************************************************* read the input file and initializing ******************************************************* <Set_Cluster_UnitCell> automatically determied UnitCell(Ang.) <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_TM.vps is l-dependent. <SetPara_DFT> VPSs of species C were normally found. C_TM_PCC.vps is l-dependent. ******************************************************* Fourier transform of PAO and projectors of VNL ******************************************************* Num. of grids overlapping with atom 2 = 11349 Num. of grids overlapping with atom 3 = 11349 Num. of grids overlapping with atom 4 = 11349 Num. of grids overlapping with atom 5 = 11349 ******************************************************* 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: 0 memcpy argument memory ranges overlap, dst_=0x1b967e50 src_=0x1b967e50 len_=16 internal ABORT - process 0 Assertion failed in file ch3u_buffer.c at line 77: 0 memcpy argument memory ranges overlap, dst_=0x1c2ceab0 src_=0x1c2ceab0 len_=24 internal ABORT - process 1 Assertion failed in file ch3u_buffer.c at line 77: 0 memcpy argument memory ranges overlap, dst_=0xf33b418 src_=0xf33b418 len_=24 internal ABORT - process 2 Assertion failed in file ch3u_buffer.c at line 77: 0 memcpy argument memory ranges overlap, dst_=0x2ad97f0 src_=0x2ad97f0 len_=24 internal ABORT - process 3 rank 0 in job 3 yang_53304 caused collective abort of all ranks exit status of rank 0: return code 1
The second error as follows:
[yang@yang work]$ openmx Methane.dat The number of threads in each node for OpenMP parallelization is 1. ******************************************************* ******************************************************* Welcome to OpenMX Ver. 3.5 Copyright (C), 2002-2009, 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. ******************************************************* ******************************************************* ******************************************************* read the input file and initializing ******************************************************* <Set_Cluster_UnitCell> automatically determied UnitCell(Ang.) <Set_Cluster_UnitCell> from atomic positions and Rc of PAOs (margin= 10.00%) <Set_Cluster_UnitCell> 6.614718 0.000000 0.000000 <Set_Cluster_UnitCell> 0.000000 6.041246 0.000000 <Set_Cluster_UnitCell> 0.000000 0.000000 6.614718 widened unit cell to fit energy cutoff (Ang.) A = 6.829220 0.000000 0.000000 (45) B = 0.000000 6.070418 0.000000 (40) C = 0.000000 0.000000 6.829220 (45) <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_TM.vps is l-dependent. <SetPara_DFT> VPSs of species C were normally found. C_TM_PCC.vps is l-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= 5 estimated weight= 5.00000 ******************************************************* Truncation and setting of grids ******************************************************* <truncation> Logically truncation of the whole system TFNAN= 20 Average FNAN= 4.00000 TSNAN= 0 Average SNAN= 0.00000 < |gtv_a| = 0.286785665539 |gtv_b| = 0.286785665539 |gtv_c| = 0.286785665539 Num. of grids overlapping with atom 1 = 16144 Num. of grids overlapping with atom 2 = 11349 Num. of grids overlapping with atom 3 = 11349 Num. of grids overlapping with atom 4 = 11349 Num. of grids overlapping with atom 5 = 11349 ******************************************************* 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: 0 memcpy argument memory ranges overlap, dst_=0x168dd730 src_=0x168dd730 len_=64 internal ABORT - process 0
As we can see, if i use the commend: mpirun -np 4 openmx Methane.dat , and the error is the first.
if i use :openmx Methane.dat, the error is the second.
Can anyone tell me how to solve the problem?
Thank you!
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