problem with 'Automatic Running Test" |
- Date: 2012/10/05 18:32
- Name: Surender
<surenderkumar1987@gmail.com>
- =======================================================================================
I compiled the MPI version of openmx with
CC = mpicc -O3 -Dnoomp
LIB = -L/usr/local/lib -lfftw3 -llapack -lblas -lgfortran
it compiled with out any errors and I got the executable 'openmx' in source/ directory. Then I thought of running the Automatic test just to check whether all the funtionalities of OpenMX have been successfully installed or not. First I try to run SERIALLY
../source/openmx -runtest
and I get the following error
========================================================================================
../source/openmx -runtest
The number of threads in each node for OpenMP parallelization is 1.
*******************************************************
*******************************************************
Welcome to OpenMX Ver. 3.6
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.
*******************************************************
*******************************************************
OpenMX is now in the mode to check whether OpenMX runs normally
on your machine or not by comparing the stored *.out and
generated *.out
14 dat files are found in the directory 'input_example'.
*******************************************************
*******************************************************
Welcome to OpenMX Ver. 3.6
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.
*******************************************************
*******************************************************
<Input_std> Your input file was normally read.
<Input_std> The system includes 2 species and 12 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_CA11.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_CA11.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= 12 estimated weight= 0.36000
*******************************************************
Truncation and setting of grids
*******************************************************
<truncation> Logically truncation of the whole system
TFNAN= 132 Average FNAN= 11.00000
TSNAN= 0 Average SNAN= 0.00000
<logical truncation> myid= 0 CpyCell= 1 ct_AN= 1 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 1 ct_AN= 2 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 1 ct_AN= 3 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 1 ct_AN= 4 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 1 ct_AN= 5 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 1 ct_AN= 6 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 1 ct_AN= 7 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 1 ct_AN= 8 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 1 ct_AN= 9 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 1 ct_AN= 10 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 1 ct_AN= 11 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 1 ct_AN= 12 FNAN SNAN 11 0
TFNAN= 132 Average FNAN= 11.00000
TSNAN= 0 Average SNAN= 0.00000
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 1 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 2 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 3 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 4 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 5 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 6 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 7 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 8 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 9 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 10 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 11 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 12 FNAN SNAN 11 0
TFNAN= 132 Average FNAN= 11.00000
TSNAN= 0 Average SNAN= 0.00000
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 1 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 2 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 3 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 4 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 5 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 6 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 7 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 8 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 9 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 10 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 11 FNAN SNAN 11 0
<logical truncation> myid= 0 CpyCell= 2 ct_AN= 12 FNAN SNAN 11 0
<Check_System> The system is molecule.
lattice vectors (bohr)
A = 24.566437851526, 0.000000000000, 0.000000000000
B = 0.000000000000, 24.566437851526, 0.000000000000
C = 0.000000000000, 0.000000000000, 13.228081920052
reciprocal lattice vectors (bohr^-1)
RA = 0.255762978139, 0.000000000000, 0.000000000000
RB = 0.000000000000, 0.255762978139, 0.000000000000
RB = 0.000000000000, 0.000000000000, 0.474988387973
UCell_Box: Cutoff=205.140502(112) 205.140502(112) 231.028704(64)
UCell_Box: (tuned) Cutoff=205.140502(112) 205.140502(112) 203.052572(60)
Grid_Origin -12.173547013257 -12.173547643166 -6.503806944026
Cell_Volume = 7983.277982894211 (Bohr^3)
GridVol = 0.010607033885 (Bohr^3)
Grid_Origin -12.173547013257 -12.173547643166 -6.503806944026
Cell_Volume = 7983.277982894211 (Bohr^3)
GridVol = 0.010607033885 (Bohr^3)
<UCell_Box> Info. of cutoff energy and num. of grids
lattice vectors (bohr)
A = 24.566437851526, 0.000000000000, 0.000000000000
B = 0.000000000000, 24.566437851526, 0.000000000000
C = 0.000000000000, 0.000000000000, 13.228081920052
reciprocal lattice vectors (bohr^-1)
RA = 0.255762978139, 0.000000000000, 0.000000000000
RB = 0.000000000000, 0.255762978139, 0.000000000000
RB = 0.000000000000, 0.000000000000, 0.474988387973
Trial cutoff energies (a,b,c) = 0.801 (7), 0.801 (7), 0.902 (4)
Trial cutoff energies (a,b,c) = 3.205 (14), 3.205 (14), 3.610 (8)
Trial cutoff energies (a,b,c) = 7.212 (21), 7.212 (21), 8.122 (12)
Trial cutoff energies (a,b,c) = 12.821 (28), 12.821 (28), 14.439 (16)
Trial cutoff energies (a,b,c) = 20.033 (35), 20.033 (35), 22.561 (20)
Trial cutoff energies (a,b,c) = 28.848 (42), 28.848 (42), 32.488 (24)
Trial cutoff energies (a,b,c) = 39.265 (49), 39.265 (49), 44.220 (28)
Trial cutoff energies (a,b,c) = 51.285 (56), 51.285 (56), 57.757 (32)
Trial cutoff energies (a,b,c) = 64.908 (63), 64.908 (63), 73.099 (36)
Trial cutoff energies (a,b,c) = 80.133 (70), 80.133 (70), 90.246 (40)
Trial cutoff energies (a,b,c) = 96.961 (77), 96.961 (77), 109.197 (44)
Trial cutoff energies (a,b,c) = 115.392 (84), 115.392 (84), 129.954 (48)
Trial cutoff energies (a,b,c) = 135.425 (91), 135.425 (91), 152.515 (52)
Trial cutoff energies (a,b,c) = 157.061 (98), 157.061 (98), 176.881 (56)
Trial cutoff energies (a,b,c) = 180.299 (105), 180.299 (105), 203.053 (60)
Trial cutoff energies (a,b,c) = 205.141 (112), 205.141 (112), 231.029 (64)
UCell_Box: Cutoff=205.140502(112) 205.140502(112) 231.028704(64)
UCell_Box: (tuned) Cutoff=205.140502(112) 205.140502(112) 203.052572(60)
Required cutoff energy (Ryd) for 3D-grids = 200.0000
Used cutoff energy (Ryd) for 3D-grids = 205.1405, 205.1405, 203.0526
Num. of grids of a-, b-, and c-axes = 112, 112, 60
Grid_Origin -12.173547013257 -12.173547643166 -6.503806944026
Cell_Volume = 7983.277982894211 (Bohr^3)
GridVol = 0.010607033885 (Bohr^3)
Cell vectors (bohr) of the grid cell (gtv)
gtv_a = 0.219343195103, 0.000000000000, 0.000000000000
gtv_b = 0.000000000000, 0.219343195103, 0.000000000000
gtv_c = 0.000000000000, 0.000000000000, 0.220468032001
|gtv_a| = 0.219343195103
|gtv_b| = 0.219343195103
|gtv_c| = 0.220468032001
Num. of grids overlapping with atom 1 = 49344
Num. of grids overlapping with atom 2 = 49354
Num. of grids overlapping with atom 3 = 49362
Num. of grids overlapping with atom 4 = 49344
Num. of grids overlapping with atom 5 = 49354
Num. of grids overlapping with atom 6 = 49362
Num. of grids overlapping with atom 7 = 49346
Num. of grids overlapping with atom 8 = 49352
Num. of grids overlapping with atom 9 = 49360
Num. of grids overlapping with atom 10 = 49346
Num. of grids overlapping with atom 11 = 49352
Num. of grids overlapping with atom 12 = 49360
*******************************************************
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_=0x6934450 src_=0x6934450 len_=240
internal ABORT - process 0
===================================================================================
then I tried to run it in parallel
but this time I got more errors
mpirun -np 4 ../source/openmx -runtest
===================================================================================
The number of threads in each node for OpenMP parallelization is 1.
*******************************************************
*******************************************************
Welcome to OpenMX Ver. 3.6
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.
*******************************************************
*******************************************************
OpenMX is now in the mode to check whether OpenMX runs normally
on your machine or not by comparing the stored *.out and
generated *.out
14 dat files are found in the directory 'input_example'.
*******************************************************
*******************************************************
Welcome to OpenMX Ver. 3.6
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.
*******************************************************
*******************************************************
<Input_std> Your input file was normally read.
<Input_std> The system includes 2 species and 12 atoms.
*******************************************************
PAO and VPS
*******************************************************
MESSAGES SIMILAR TO SERIAL RUN
*******************************************************
<Cluster> Solving the eigenvalue problem...
Assertion failed in file ch3u_buffer.c at line 77: FALSE
memcpy argument memory ranges overlap, dst_=0x35cb920 src_=0x35cb920 len_=64
Assertion failed in file ch3u_buffer.c at line 77: FALSE
memcpy argument memory ranges overlap, dst_=0x32f7240 src_=0x32f7240 len_=64
internal ABORT - process 1
Assertion failed in file ch3u_buffer.c at line 77: FALSE
memcpy argument memory ranges overlap, dst_=0x35bb3b0 src_=0x35bb3b0 len_=64
internal ABORT - process 2
Assertion failed in file ch3u_buffer.c at line 77: FALSE
memcpy argument memory ranges overlap, dst_=0x26e4090 src_=0x26e4090 len_=72
internal ABORT - process 3
internal ABORT - process 0
======================================================================================
I don't know why I am getting such type of errors (even after successfully compiling the code). My machine configuration is
OS : Fedora 15 (x86_64)
RAM : 8 GB
HDD : 1 TB
# of Processors : 8 (Intel Core i7)
Please help, thanks in advance.
-Surender
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Re: problem with 'Automatic Running Test"