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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Re: one problem when running the calculation