Hi Hong,
Thanks for checking this. A mechanical model was added at the time when
the solver failed, causing some problem. We need to improve this part in
the code.
Thanks again and best wishes,
Danyang
On 15-12-08 08:10 PM, Hong wrote:
Danyang :
Your matrices are ill-conditioned, numerically singular with
Recip. condition number = 6.000846e-16
Recip. condition number = 2.256434e-27
Recip. condition number = 1.256452e-18
i.e., condition numbers = O(1.e16 - 1.e27), there is no accuracy in
computed solution.
I checked your matrix 168 - 172, got Recip. condition number
= 1.548816e-12.
You need check your model to understand why the matrices are so
ill-conditioned.
Hong
Hi Hong,
Sorry to bother you again. The modified code works much better
than before using both superlu or mumps. However, it still
encounters failure. The case is similar with the previous one,
ill-conditioned matrices.
The code crashed after a long time simulation if I use
superlu_dist, but will not fail if use superlu. I restart the
simulation before the time it crashes and can reproduce the
following error
timestep: 22 time: 1.750E+04 years delt: 2.500E+00 years
iter: 1 max.sia: 5.053E-03 tol.sia: 1.000E-01
Newton Iteration Convergence Summary:
Newton maximum maximum solver
iteration updatePa updateTemp residual iterations
maxvolpa maxvoltemp nexvolpa nexvoltemp
1 0.1531E+08 0.1755E+04 0.6920E-05 1
5585 4402 5814 5814
*** Error in `../program_test': malloc(): memory corruption:
0x0000000003a70d50 ***
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
The solver failed at timestep 22, Newton iteration 2. I exported
the matrices at timestep 1 (matrix 1) and timestep 22 (matrix 140
and 141). Matrix 141 is where it failed. The three matrices here
are not ill-conditioned form the estimated value.
I did the same using the new modified ex52f code and found pretty
different results for matrix 141. The norm by superlu is much
acceptable than superlu_dist. In this test, memory corruption was
not detected. The codes and example data can be download from the
link below.
https://www.dropbox.com/s/i1ls0bg0vt7gu0v/petsc-superlu-test2.tar.gz?dl=0
****************More test on matrix_and_rhs_bin2*******************
mpiexec.hydra -n 1 ./ex52f -f0
./matrix_and_rhs_bin2/a_flow_check_1.bin -rhs
./matrix_and_rhs_bin2/b_flow_check_1.bin -loop_matrices flow_check
-loop_folder ./matrix_and_rhs_bin2 -matrix_index_start 140
-matrix_index_end 141 -pc_type lu -pc_factor_mat_solver_package
superlu -ksp_monitor_true_residual -mat_superlu_conditionnumber
-->loac matrix a
-->load rhs b
size l,m,n,mm 90000 90000 90000 90000
Recip. condition number = 6.000846e-16
0 KSP preconditioned resid norm 1.146871454377e+08 true resid
norm 4.711091037809e+03 ||r(i)||/||b|| 1.000000000000e+00
1 KSP preconditioned resid norm 2.071118508260e-06 true resid
norm 3.363767171515e-08 ||r(i)||/||b|| 7.140102249181e-12
Norm of error 3.3638E-08 iterations 1
-->Test for matrix 140
Recip. condition number = 2.256434e-27
0 KSP preconditioned resid norm 2.084372893355e+14 true resid
norm 4.711091037809e+03 ||r(i)||/||b|| 1.000000000000e+00
1 KSP preconditioned resid norm 4.689629276419e+00 true resid
norm 1.037236635337e-01 ||r(i)||/||b|| 2.201690918330e-05
Norm of error 1.0372E-01 iterations 1
-->Test for matrix 141
Recip. condition number = 1.256452e-18
0 KSP preconditioned resid norm 1.055488964519e+08 true resid
norm 4.711091037809e+03 ||r(i)||/||b|| 1.000000000000e+00
1 KSP preconditioned resid norm 2.998827511681e-04 true resid
norm 4.805214542776e-04 ||r(i)||/||b|| 1.019979130994e-07
Norm of error 4.8052E-04 iterations 1
--> End of test, bye
mpiexec.hydra -n 1 ./ex52f -f0
./matrix_and_rhs_bin2/a_flow_check_1.bin -rhs
./matrix_and_rhs_bin2/b_flow_check_1.bin -loop_matrices flow_check
-loop_folder ./matrix_and_rhs_bin2 -matrix_index_start 140
-matrix_index_end 141 -pc_type lu -pc_factor_mat_solver_package
superlu_dist
-->loac matrix a
-->load rhs b
size l,m,n,mm 90000 90000 90000 90000
Norm of error 3.6752E-08 iterations 1
-->Test for matrix 140
Norm of error 1.6335E-01 iterations 1
-->Test for matrix 141
Norm of error 3.4345E+01 iterations 1
--> End of test, bye
Thanks,
Danyang
On 15-12-07 12:01 PM, Hong wrote:
Danyang:
Add 'call MatSetFromOptions(A,ierr)' to your code.
Attached below is ex52f.F modified from your ex52f.F to be
compatible with petsc-dev.
Hong
Hello Hong,
Thanks for the quick reply and the option
"-mat_superlu_dist_fact SamePattern" works like a charm, if I
use this option from the command line.
How can I add this option as the default. I tried using
PetscOptionsInsertString("-mat_superlu_dist_fact
SamePattern",ierr) in my code but this does not work.
Thanks,
Danyang
On 15-12-07 10:42 AM, Hong wrote:
Danyang :
Adding '-mat_superlu_dist_fact SamePattern' fixed the
problem. Below is how I figured it out.
1. Reading ex52f.F, I see '-superlu_default' =
'-pc_factor_mat_solver_package superlu_dist', the later
enables runtime options for other packages. I use
superlu_dist-4.2 and superlu-4.1 for the tests below.
2. Use the Matrix 168 to setup KSP solver and factorization,
all packages, petsc, superlu_dist and mumps give same
correct results:
./ex52f -f0 matrix_and_rhs_bin/a_flow_check_168.bin -rhs
matrix_and_rhs_bin/b_flow_check_168.bin -loop_matrices
flow_check -loop_folder matrix_and_rhs_bin -pc_type lu
-pc_factor_mat_solver_package petsc
-->loac matrix a
-->load rhs b
size l,m,n,mm 90000 90000 90000 90000
Norm of error 7.7308E-11 iterations 1
-->Test for matrix 168
..
-->Test for matrix 172
Norm of error 3.8461E-11 iterations 1
./ex52f -f0 matrix_and_rhs_bin/a_flow_check_168.bin -rhs
matrix_and_rhs_bin/b_flow_check_168.bin -loop_matrices
flow_check -loop_folder matrix_and_rhs_bin -pc_type lu
-pc_factor_mat_solver_package superlu_dist
Norm of error 9.4073E-11 iterations 1
-->Test for matrix 168
...
-->Test for matrix 172
Norm of error 3.8187E-11 iterations 1
3. Use superlu, I get
./ex52f -f0 matrix_and_rhs_bin/a_flow_check_168.bin -rhs
matrix_and_rhs_bin/b_flow_check_168.bin -loop_matrices
flow_check -loop_folder matrix_and_rhs_bin -pc_type lu
-pc_factor_mat_solver_package superlu
Norm of error 1.0191E-06 iterations 1
-->Test for matrix 168
...
-->Test for matrix 172
Norm of error 9.7858E-07 iterations 1
Replacing default DiagPivotThresh: 1. to 0.0, I get same
solutions as other packages:
./ex52f -f0 matrix_and_rhs_bin/a_flow_check_168.bin -rhs
matrix_and_rhs_bin/b_flow_check_168.bin -loop_matrices
flow_check -loop_folder matrix_and_rhs_bin -pc_type lu
-pc_factor_mat_solver_package superlu
-mat_superlu_diagpivotthresh 0.0
Norm of error 8.3614E-11 iterations 1
-->Test for matrix 168
...
-->Test for matrix 172
Norm of error 3.7098E-11 iterations 1
4.
using '-mat_view ascii::ascii_info', I found that
a_flow_check_1.bin and a_flow_check_168.bin seem have same
structure:
-->loac matrix a
Mat Object: 1 MPI processes
type: seqaij
rows=90000, cols=90000
total: nonzeros=895600, allocated nonzeros=895600
total number of mallocs used during MatSetValues calls =0
using I-node routines: found 45000 nodes, limit used is 5
5.
Using a_flow_check_1.bin, I am able to reproduce the error
you reported: all packages give correct results except
superlu_dist:
./ex52f -f0 matrix_and_rhs_bin/a_flow_check_1.bin -rhs
matrix_and_rhs_bin/b_flow_check_168.bin -loop_matrices
flow_check -loop_folder matrix_and_rhs_bin -pc_type lu
-pc_factor_mat_solver_package superlu_dist
Norm of error 2.5970E-12 iterations 1
-->Test for matrix 168
Norm of error 1.3936E-01 iterations 34
-->Test for matrix 169
I guess the error might come from reuse of matrix factor.
Replacing default
-mat_superlu_dist_fact <SamePattern_SameRowPerm> with
-mat_superlu_dist_fact SamePattern, I get
./ex52f -f0 matrix_and_rhs_bin/a_flow_check_1.bin -rhs
matrix_and_rhs_bin/b_flow_check_168.bin -loop_matrices
flow_check -loop_folder matrix_and_rhs_bin -pc_type lu
-pc_factor_mat_solver_package superlu_dist
-mat_superlu_dist_fact SamePattern
Norm of error 2.5970E-12 iterations 1
-->Test for matrix 168
Norm of error 9.4073E-11 iterations 1
-->Test for matrix 169
Norm of error 6.4303E-11 iterations 1
-->Test for matrix 170
Norm of error 7.4327E-11 iterations 1
-->Test for matrix 171
Norm of error 5.4162E-11 iterations 1
-->Test for matrix 172
Norm of error 3.4440E-11 iterations 1
--> End of test, bye
Sherry may tell you why SamePattern_SameRowPerm cause the
difference here.
Best on the above experiments, I would set following as default
'-mat_superlu_diagpivotthresh 0.0' in petsc/superlu interface.
'-mat_superlu_dist_fact SamePattern' in petsc/superlu_dist
interface.
Hong
Hi Hong,
I did more test today and finally found that the
solution accuracy depends on the initial (first) matrix
quality. I modified the ex52f.F to do the test. There
are 6 matrices and right-hand-side vectors. All these
matrices and rhs are from my reactive transport
simulation. Results will be quite different depending on
which one you use to do factorization. Results will also
be different if you run with different options. My code
is similar to the First or the Second test below. When
the matrix is well conditioned, it works fine. But if
the initial matrix is well conditioned, it likely to
crash when the matrix become ill-conditioned. Since most
of my case are well conditioned so I didn't detect the
problem before. This case is a special one.
How can I avoid this problem? Shall I redo
factorization? Can PETSc automatically detect this
prolbem or is there any option available to do this?
All the data and test code (modified ex52f) can be found
via the dropbox link below.
_
__https://www.dropbox.com/s/4al1a60creogd8m/petsc-superlu-test.tar.gz?dl=0_
Summary of my test is shown below.
First, use the Matrix 1 to setup KSP solver and
factorization, then solve 168 to 172
mpiexec.hydra -n 1 ./ex52f -f0
/home/dsu/work/petsc-superlu-test/matrix_and_rhs_bin/a_flow_check_1.bin
-rhs
/home/dsu/work/petsc-superlu-test/matrix_and_rhs_bin/b_flow_check_1.bin
-loop_matrices flow_check -loop_folder
/home/dsu/work/petsc-superlu-test/matrix_and_rhs_bin
-pc_type lu -pc_factor_mat_solver_package superlu_dist
Norm of error 3.8815E-11 iterations 1
-->Test for matrix 168
Norm of error 4.2307E-01 iterations 32
-->Test for matrix 169
Norm of error 3.0528E-01 iterations 32
-->Test for matrix 170
Norm of error 3.1177E-01 iterations 32
-->Test for matrix 171
Norm of error 3.2793E-01 iterations 32
-->Test for matrix 172
Norm of error 3.1251E-01 iterations 31
Second, use the Matrix 1 to setup KSP solver and
factorization using the implemented SuperLU relative
codes. I thought this will generate the same results as
the First test, but it actually not.
mpiexec.hydra -n 1 ./ex52f -f0
/home/dsu/work/petsc-superlu-test/matrix_and_rhs_bin/a_flow_check_1.bin
-rhs
/home/dsu/work/petsc-superlu-test/matrix_and_rhs_bin/b_flow_check_1.bin
-loop_matrices flow_check -loop_folder
/home/dsu/work/petsc-superlu-test/matrix_and_rhs_bin
-superlu_default
Norm of error 2.2632E-12 iterations 1
-->Test for matrix 168
Norm of error 1.0817E+04 iterations 1
-->Test for matrix 169
Norm of error 1.0786E+04 iterations 1
-->Test for matrix 170
Norm of error 1.0792E+04 iterations 1
-->Test for matrix 171
Norm of error 1.0792E+04 iterations 1
-->Test for matrix 172
Norm of error 1.0792E+04 iterations 1
Third, use the Matrix 168 to setup KSP solver and
factorization, then solve 168 to 172
mpiexec.hydra -n 1 ./ex52f -f0
/home/dsu/work/petsc-superlu-test/matrix_and_rhs_bin/a_flow_check_168.bin
-rhs
/home/dsu/work/petsc-superlu-test/matrix_and_rhs_bin/b_flow_check_168.bin
-loop_matrices flow_check -loop_folder
/home/dsu/work/petsc-superlu-test/matrix_and_rhs_bin
-pc_type lu -pc_factor_mat_solver_package superlu_dist
Norm of error 9.5528E-10 iterations 1
-->Test for matrix 168
Norm of error 9.4945E-10 iterations 1
-->Test for matrix 169
Norm of error 6.4279E-10 iterations 1
-->Test for matrix 170
Norm of error 7.4633E-10 iterations 1
-->Test for matrix 171
Norm of error 7.4863E-10 iterations 1
-->Test for matrix 172
Norm of error 8.9701E-10 iterations 1
Fourth, use the Matrix 168 to setup KSP solver and
factorization using the implemented SuperLU relative
codes. I thought this will generate the same results as
the Third test, but it actually not.
mpiexec.hydra -n 1 ./ex52f -f0
/home/dsu/work/petsc-superlu-test/matrix_and_rhs_bin/a_flow_check_168.bin
-rhs
/home/dsu/work/petsc-superlu-test/matrix_and_rhs_bin/b_flow_check_168.bin
-loop_matrices flow_check -loop_folder
/home/dsu/work/petsc-superlu-test/matrix_and_rhs_bin
-superlu_default
Norm of error 3.7017E-11 iterations 1
-->Test for matrix 168
Norm of error 3.6420E-11 iterations 1
-->Test for matrix 169
Norm of error 3.7184E-11 iterations 1
-->Test for matrix 170
Norm of error 3.6847E-11 iterations 1
-->Test for matrix 171
Norm of error 3.7883E-11 iterations 1
-->Test for matrix 172
Norm of error 3.8805E-11 iterations 1
Thanks very much,
Danyang
On 15-12-03 01:59 PM, Hong wrote:
Danyang :
Further testing a_flow_check_168.bin,
./ex10 -f0
/Users/Hong/Downloads/matrix_and_rhs_bin/a_flow_check_168.bin
-rhs
/Users/Hong/Downloads/matrix_and_rhs_bin/x_flow_check_168.bin
-pc_type lu -pc_factor_mat_solver_package superlu
-ksp_monitor_true_residual -mat_superlu_conditionnumber
Recip. condition number = 1.610480e-12
0 KSP preconditioned resid norm 6.873340313547e+09 true
resid norm 7.295020990196e+03 ||r(i)||/||b||
1.000000000000e+00
1 KSP preconditioned resid norm 2.051833296449e-02 true
resid norm 2.976859070118e-02 ||r(i)||/||b||
4.080672384793e-06
Number of iterations = 1
Residual norm 0.0297686
condition number of this matrix = 1/1.610480e-12 = 1.e+12,
i.e., this matrix is ill-conditioned.
Hong
Hi Hong,
The binary format of matrix, rhs and solution can
be downloaded via the link below.
https://www.dropbox.com/s/cl3gfi0s0kjlktf/matrix_and_rhs_bin.tar.gz?dl=0
Thanks,
Danyang
On 15-12-03 10:50 AM, Hong wrote:
Danyang:
To my surprising, solutions from SuperLU at
timestep 29 seems not correct for the first 4
Newton iterations, but the solutions from
iteration solver and MUMPS are correct.
Please find all the matrices, rhs and
solutions at timestep 29 via the link below.
The data is a bit large so that I just share
it through Dropbox. A piece of matlab code to
read these data and then computer the norm has
also been attached.
_https://www.dropbox.com/s/rr8ueysgflmxs7h/results-check.tar.gz?dl=0_
Can you send us matrix in petsc binary format?
e.g., call MatView(M,
PETSC_VIEWER_BINARY_(PETSC_COMM_WORLD))
or '-ksp_view_mat binary'
Hong
Below is a summary of the norm from the three
solvers at timestep 29, newton iteration 1 to 5.
Timestep 29
Norm of residual seq 1.661321e-09, superlu
1.657103e+04, mumps 3.731225e-11
Norm of residual seq 1.753079e-09, superlu
6.675467e+02, mumps 1.509919e-13
Norm of residual seq 4.914971e-10, superlu
1.236362e-01, mumps 2.139303e-17
Norm of residual seq 3.532769e-10, superlu
1.304670e-04, mumps 5.387000e-20
Norm of residual seq 3.885629e-10, superlu
2.754876e-07, mumps 4.108675e-21
Would anybody please check if SuperLU can
solve these matrices? Another possibility is
that something is wrong in my own code. But so
far, I cannot find any problem in my code
since the same code works fine if I using
iterative solver or direct solver MUMPS. But
for other cases I have tested, all these
solvers work fine.
Please let me know if I did not write down the
problem clearly.
Thanks,
Danyang
