[petsc-users] Help needed with MUMPS solver
Karl Yang
y.juntao at hotmail.com
Mon May 24 21:06:11 CDT 2021
Hi, Barry
I got the following error with -ksp_error_if_not_converged.
I'm making use of the PETSc from dolfin package. So it could also be bugs in dolfin. But still thank you for providing more information.
Regards
Juntao
terminate called after throwing an instance of 'std::runtime_error'
what():
*** -------------------------------------------------------------------------
*** DOLFIN encountered an error. If you are not able to resolve this issue
*** using the information listed below, you can ask for help at
***
*** fenics-support at googlegroups.com
***
*** Remember to include the error message listed below and, if possible,
*** include a *minimal* running example to reproduce the error.
***
*** -------------------------------------------------------------------------
*** Error: Unable to successfully call PETSc function 'KSPSolve'.
*** Reason: PETSc error code is: 76 (Error in external library).
*** Where: This error was encountered inside /tmp/dolfin/dolfin/la/PETScKrylovSolver.cpp.
*** Process: 0
***
*** DOLFIN version: 2019.1.0
*** Git changeset: 74d7efe1e84d65e9433fd96c50f1d278fa3e3f3f
*** -------------------------------------------------------------------------
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 290 RUNNING AT c10236694934
= EXIT CODE: 134
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
Regards
Juntao
On May 24 2021, at 12:17 am, Barry Smith <bsmith at petsc.dev> wrote:
>
> Please run with -ksp_error_if_not_converged and send all the output
>
> Barry
>
>
> > On May 23, 2021, at 10:16 AM, Karl Yang <y.juntao at hotmail.com (https://link.getmailspring.com/link/3C83A41D-E95A-4725-8766-C8F075BB1972@getmailspring.com/0?redirect=mailto%3Ay.juntao%40hotmail.com&recipient=cGV0c2MtdXNlcnNAbWNzLmFubC5nb3Y%3D)> wrote:
> > Hello,
> > I am using MUMPS direct solver for my project. I used the following options for solving my problem and it works in most cases. But for some cases I encounter a divergence error. But I think it is actually error due to MUMPS?
> > I'm not sure how to debug the error. It is appreciated if anyone familiar with MUMPS solver to offer me some guidance.
> > regards
> > Juntao
> >
> > MUMPS options:
> >
> > PetscOptionsSetValue(NULL, "-ksp_type", "preonly");
> > PetscOptionsSetValue(NULL, "-pc_type", "cholesky");
> > PetscOptionsSetValue(NULL, "-pc_factor_mat_solver_type", "mumps");
> > PetscOptionsSetValue(NULL, "-mat_mumps_icntl_1", "1");
> > PetscOptionsSetValue(NULL, "-mat_mumps_icntl_2", "1");
> > PetscOptionsSetValue(NULL, "-mat_mumps_icntl_3", "1");
> > PetscOptionsSetValue(NULL, "-mat_mumps_icntl_4", "3");
> > PetscOptionsSetValue(NULL, "-mat_mumps_icntl_28", "1");
> > PetscOptionsSetValue(NULL, "-mat_mumps_icntl_7", "2");
> > PetscOptionsSetValue(NULL, "-mat_mumps_icntl_24", "1");
> >
> >
> > Log output from MUMPS and error message from PETSC at the bottom
> > Entering DMUMPS 5.2.1 from C interface with JOB, N, NNZ = 1 240 2448
> > executing #MPI = 1, without OMP
> >
> > =================================================
> > MUMPS compiled with option -Dmetis
> > MUMPS compiled with option -Dptscotch
> > MUMPS compiled with option -Dscotch
> > This MUMPS version includes code for SAVE_RESTORE
> > =================================================
> > L D L^T Solver for general symmetric matrices
> > Type of parallelism: Working host
> >
> > ****** ANALYSIS STEP ********
> > Scaling will be computed during analysis
> > Compute maximum matching (Maximum Transversal): 5
> > ... JOB = 5: MAXIMIZE PRODUCT DIAGONAL AND SCALE
> >
> > Entering analysis phase with ...
> > N NNZ LIW INFO(1)
> > 240 2448 5137 0
> > Matrix entries: IRN() ICN()
> > 1 1 1 2 1 3
> > 1 4 1 5 1 6
> > 1 7 1 8 1 9
> > 1 10
> > Average density of rows/columns = 18
> > Average density of rows/columns = 18
> > Ordering based on AMF
> > Constrained Ordering based on AMF
> > Average density of rows/columns = 18
> > Average density of rows/columns = 18
> > NFSIZ(.) = 0 38 14 0 33 33 0 0 0 0
> >
> > FILS (.) = 0 148 4 -96 224 163 20 -43 8 1
> > FRERE(.) = 241 -5 -6 241 0 -2 241 241 241 241
> >
> > Leaving analysis phase with ...
> > INFOG(1) = 0
> > INFOG(2) = 0
> > -- (20) Number of entries in factors (estim.) = 3750
> > -- (3) Real space for factors (estimated) = 4641
> > -- (4) Integer space for factors (estimated) = 2816
> > -- (5) Maximum frontal size (estimated) = 38
> > -- (6) Number of nodes in the tree = 56
> > -- (32) Type of analysis effectively used = 1
> > -- (7) Ordering option effectively used = 2
> > ICNTL(6) Maximum transversal option = 0
> > ICNTL(7) Pivot order option = 2
> > ICNTL(14) Percentage of memory relaxation = 20
> > Number of level 2 nodes = 0
> > Number of split nodes = 0
> > RINFOG(1) Operations during elimination (estim)= 7.137D+04
> > Ordering compressed/constrained (ICNTL(12)) = 3
> >
> > MEMORY ESTIMATIONS ...
> > Estimations with standard Full-Rank (FR) factorization:
> > Total space in MBytes, IC factorization (INFOG(17)): 0
> > Total space in MBytes, OOC factorization (INFOG(27)): 0
> >
> > Elapsed time in analysis driver= 0.0016
> > Entering DMUMPS 5.2.1 from C interface with JOB, N, NNZ = 2 240 2448
> > executing #MPI = 1, without OMP
> >
> >
> >
> > ****** FACTORIZATION STEP ********
> > GLOBAL STATISTICS PRIOR NUMERICAL FACTORIZATION ...
> > Number of working processes = 1
> > ICNTL(22) Out-of-core option = 0
> > ICNTL(35) BLR activation (eff. choice) = 0
> > ICNTL(14) Memory relaxation = 20
> > INFOG(3) Real space for factors (estimated)= 4641
> > INFOG(4) Integer space for factors (estim.)= 2816
> > Maximum frontal size (estimated) = 38
> > Number of nodes in the tree = 56
> > Memory allowed (MB -- 0: N/A ) = 0
> > Memory provided by user, sum of LWK_USER = 0
> > Relative threshold for pivoting, CNTL(1) = 0.1000D-01
> > ZERO PIVOT DETECTION ON, THRESHOLD = 2.8931920285365730E-020
> > INFINITE FIXATION
> > Effective size of S (based on INFO(39))= 7981
> > Elapsed time to reformat/distribute matrix = 0.0001
> > ** Memory allocated, total in Mbytes (INFOG(19)): 0
> > ** Memory effectively used, total in Mbytes (INFOG(22)): 0
> > ** Memory dynamically allocated for CB, total in Mbytes : 0
> >
> > Elapsed time for factorization = 0.0006
> > Leaving factorization with ...
> > RINFOG(2) Operations in node assembly = 5.976D+03
> > ------(3) Operations in node elimination = 1.197D+05
> > INFOG (9) Real space for factors = 6193
> > INFOG(10) Integer space for factors = 3036
> > INFOG(11) Maximum front size = 42
> > INFOG(29) Number of entries in factors = 4896
> > INFOG(12) Number of negative pivots = 79
> > INFOG(13) Number of delayed pivots = 110
> > Number of 2x2 pivots in type 1 nodes = 1
> > Number of 2X2 pivots in type 2 nodes = 0
> > Nb of null pivots detected by ICNTL(24) = 0
> > INFOG(28) Estimated deficiency = 0
> > INFOG(14) Number of memory compress = 0
> >
> > Elapsed time in factorization driver= 0.0009
> > Entering DMUMPS 5.2.1 from C interface with JOB, N, NNZ = 3 240 2448
> > executing #MPI = 1, without OMP
> >
> >
> >
> > ****** SOLVE & CHECK STEP ********
> > GLOBAL STATISTICS PRIOR SOLVE PHASE ...........
> > Number of right-hand-sides = 1
> > Blocking factor for multiple rhs = 1
> > ICNTL (9) = 1
> > --- (10) = 0
> > --- (11) = 0
> > --- (20) = 0
> > --- (21) = 0
> > --- (30) = 0
> > --- (35) = 0
> >
> >
> > Vector solution for column 1
> > RHS
> > -7.828363D-02 -3.255337D+00 1.054729D+00 1.379822D-01 -3.892113D-01
> > 1.433990D-01 1.089250D+00 2.252611D+00 3.215399D+00 -6.788806D-02
> > ** Space in MBYTES used for solve : 0
> >
> > Leaving solve with ...
> > Time to build/scatter RHS = 0.000003
> > Time in solution step (fwd/bwd) = 0.000167
> > .. Time in forward (fwd) step = 0.000053
> > .. Time in backward (bwd) step = 0.000093
> > Time to gather solution(cent.sol)= 0.000000
> > Time to copy/scale dist. solution= 0.000000
> >
> > Elapsed time in solve driver= 0.0004
> > *** Warning: Verbose output for PETScKrylovSolver not implemented, calling PETSc KSPView directly.
> > KSP Object: 1 MPI processes
> > type: preonly
> > maximum iterations=10000, initial guess is zero
> > tolerances: relative=1e-05, absolute=1e-50, divergence=10000.
> > left preconditioning
> > using NONE norm type for convergence test
> > PC Object: 1 MPI processes
> > type: cholesky
> > out-of-place factorization
> > tolerance for zero pivot 2.22045e-14
> > matrix ordering: natural
> > factor fill ratio given 0., needed 0.
> > Factored matrix follows:
> > Mat Object: 1 MPI processes
> > type: mumps
> > rows=240, cols=240
> > package used to perform factorization: mumps
> > total: nonzeros=3750, allocated nonzeros=3750
> > total number of mallocs used during MatSetValues calls=0
> > MUMPS run parameters:
> > SYM (matrix type): 2
> > PAR (host participation): 1
> > ICNTL(1) (output for error): 1
> > ICNTL(2) (output of diagnostic msg): 1
> > ICNTL(3) (output for global info): 6
> > ICNTL(4) (level of printing): 3
> > ICNTL(5) (input mat struct): 0
> > ICNTL(6) (matrix prescaling): 7
> > ICNTL(7) (sequential matrix ordering):2
> > ICNTL(8) (scaling strategy): 77
> > ICNTL(10) (max num of refinements): 0
> > ICNTL(11) (error analysis): 0
> > ICNTL(12) (efficiency control): 0
> > ICNTL(13) (efficiency control): 1
> > ICNTL(14) (percentage of estimated workspace increase): 20
> > ICNTL(18) (input mat struct): 0
> > ICNTL(19) (Schur complement info): 0
> > ICNTL(20) (rhs sparse pattern): 0
> > ICNTL(21) (solution struct): 0
> > ICNTL(22) (in-core/out-of-core facility): 0
> > ICNTL(23) (max size of memory can be allocated locally):0
> > ICNTL(24) (detection of null pivot rows): 1
> > ICNTL(25) (computation of a null space basis): 0
> > ICNTL(26) (Schur options for rhs or solution): 0
> > ICNTL(27) (experimental parameter): -32
> > ICNTL(28) (use parallel or sequential ordering): 1
> > ICNTL(29) (parallel ordering): 0
> > ICNTL(30) (user-specified set of entries in inv(A)): 0
> > ICNTL(31) (factors is discarded in the solve phase): 0
> > ICNTL(33) (compute determinant): 0
> > ICNTL(35) (activate BLR based factorization): 0
> > ICNTL(36) (choice of BLR factorization variant): 0
> > ICNTL(38) (estimated compression rate of LU factors): 333
> > CNTL(1) (relative pivoting threshold): 0.01
> > CNTL(2) (stopping criterion of refinement): 1.49012e-08
> > CNTL(3) (absolute pivoting threshold): 0.
> > CNTL(4) (value of static pivoting): -1.
> > CNTL(5) (fixation for null pivots): 0.
> > CNTL(7) (dropping parameter for BLR): 0.
> > RINFO(1) (local estimated flops for the elimination after analysis):
> > [0] 71368.
> > RINFO(2) (local estimated flops for the assembly after factorization):
> > [0] 5976.
> > RINFO(3) (local estimated flops for the elimination after factorization):
> > [0] 119716.
> > INFO(15) (estimated size of (in MB) MUMPS internal data for running numerical factorization):
> > [0] 0
> > INFO(16) (size of (in MB) MUMPS internal data used during numerical factorization):
> > [0] 0
> > INFO(23) (num of pivots eliminated on this processor after factorization):
> > [0] 240
> > RINFOG(1) (global estimated flops for the elimination after analysis): 71368.
> > RINFOG(2) (global estimated flops for the assembly after factorization): 5976.
> > RINFOG(3) (global estimated flops for the elimination after factorization): 119716.
> > (RINFOG(12) RINFOG(13))*2^INFOG(34) (determinant): (0.,0.)*(2^0)
> > INFOG(3) (estimated real workspace for factors on all processors after analysis): 4641
> > INFOG(4) (estimated integer workspace for factors on all processors after analysis): 2816
> > INFOG(5) (estimated maximum front size in the complete tree): 38
> > INFOG(6) (number of nodes in the complete tree): 56
> > INFOG(7) (ordering option effectively use after analysis): 2
> > INFOG(8) (structural symmetry in percent of the permuted matrix after analysis): 100
> > INFOG(9) (total real/complex workspace to store the matrix factors after factorization): 6193
> > INFOG(10) (total integer space store the matrix factors after factorization): 3036
> > INFOG(11) (order of largest frontal matrix after factorization): 42
> > INFOG(12) (number of off-diagonal pivots): 79
> > INFOG(13) (number of delayed pivots after factorization): 110
> > INFOG(14) (number of memory compress after factorization): 0
> > INFOG(15) (number of steps of iterative refinement after solution): 0
> > INFOG(16) (estimated size (in MB) of all MUMPS internal data for factorization after analysis: value on the most memory consuming processor): 0
> > INFOG(17) (estimated size of all MUMPS internal data for factorization after analysis: sum over all processors): 0
> > INFOG(18) (size of all MUMPS internal data allocated during factorization: value on the most memory consuming processor): 0
> > INFOG(19) (size of all MUMPS internal data allocated during factorization: sum over all processors): 0
> > INFOG(20) (estimated number of entries in the factors): 3750
> > INFOG(21) (size in MB of memory effectively used during factorization - value on the most memory consuming processor): 0
> > INFOG(22) (size in MB of memory effectively used during factorization - sum over all processors): 0
> > INFOG(23) (after analysis: value of ICNTL(6) effectively used): 5
> > INFOG(24) (after analysis: value of ICNTL(12) effectively used): 3
> > INFOG(25) (after factorization: number of pivots modified by static pivoting): 0
> > INFOG(28) (after factorization: number of null pivots encountered): 0
> > INFOG(29) (after factorization: effective number of entries in the factors (sum over all processors)): 4896
> > INFOG(30, 31) (after solution: size in Mbytes of memory used during solution phase): 0, 0
> > INFOG(32) (after analysis: type of analysis done): 1
> > INFOG(33) (value used for ICNTL(8)): -2
> > INFOG(34) (exponent of the determinant if determinant is requested): 0
> > INFOG(35) (after factorization: number of entries taking into account BLR factor compression - sum over all processors): 4896
> > INFOG(36) (after analysis: estimated size of all MUMPS internal data for running BLR in-core - value on the most memory consuming processor): 0
> > INFOG(37) (after analysis: estimated size of all MUMPS internal data for running BLR in-core - sum over all processors): 0
> > INFOG(38) (after analysis: estimated size of all MUMPS internal data for running BLR out-of-core - value on the most memory consuming processor): 0
> > INFOG(39) (after analysis: estimated size of all MUMPS internal data for running BLR out-of-core - sum over all processors): 0
> > linear system matrix = precond matrix:
> > Mat Object: 1 MPI processes
> > type: seqaij
> > rows=240, cols=240
> > total: nonzeros=4656, allocated nonzeros=4656
> > total number of mallocs used during MatSetValues calls=0
> > using I-node routines: found 167 nodes, limit used is 5
> >
> > Entering DMUMPS 5.2.1 from C interface with JOB = -2
> > executing #MPI = 1, without OMP
> > rank: 0 coefficient: 0.132368
> >
> > Entering DMUMPS 5.2.1 from C interface with JOB, N, NNZ = 1 960 9792
> > executing #MPI = 1, without OMP
> >
> > =================================================
> > MUMPS compiled with option -Dmetis
> > MUMPS compiled with option -Dptscotch
> > MUMPS compiled with option -Dscotch
> > This MUMPS version includes code for SAVE_RESTORE
> > =================================================
> > L D L^T Solver for general symmetric matrices
> > Type of parallelism: Working host
> >
> > ****** ANALYSIS STEP ********
> > Scaling will be computed during analysis
> > Compute maximum matching (Maximum Transversal): 5
> > ... JOB = 5: MAXIMIZE PRODUCT DIAGONAL AND SCALE
> >
> > Entering analysis phase with ...
> > N NNZ LIW INFO(1)
> > 960 9792 20545 0
> > Matrix entries: IRN() ICN()
> > 1 1 1 2 1 3
> > 1 4 1 5 1 6
> > 1 7 1 8 1 9
> > 1 10
> > Average density of rows/columns = 18
> > Average density of rows/columns = 18
> > Ordering based on AMF
> > Constrained Ordering based on AMF
> > Average density of rows/columns = 18
> > Average density of rows/columns = 18
> > NFSIZ(.) = 0 0 0 58 0 0 0 73 14 0
> >
> > FILS (.) = 0 -747 -80 922 146 5 6 669 3 1
> > FRERE(.) = 961 961 961 0 961 961 961 -4 -69 961
> >
> > Leaving analysis phase with ...
> > INFOG(1) = 0
> > INFOG(2) = 0
> > -- (20) Number of entries in factors (estim.) = 20336
> > -- (3) Real space for factors (estimated) = 24094
> > -- (4) Integer space for factors (estimated) = 12143
> > -- (5) Maximum frontal size (estimated) = 80
> > -- (6) Number of nodes in the tree = 227
> > -- (32) Type of analysis effectively used = 1
> > -- (7) Ordering option effectively used = 2
> > ICNTL(6) Maximum transversal option = 0
> > ICNTL(7) Pivot order option = 2
> > ICNTL(14) Percentage of memory relaxation = 20
> > Number of level 2 nodes = 0
> > Number of split nodes = 0
> > RINFOG(1) Operations during elimination (estim)= 6.966D+05
> > Ordering compressed/constrained (ICNTL(12)) = 3
> >
> > MEMORY ESTIMATIONS ...
> > Estimations with standard Full-Rank (FR) factorization:
> > Total space in MBytes, IC factorization (INFOG(17)): 1
> > Total space in MBytes, OOC factorization (INFOG(27)): 1
> >
> > Elapsed time in analysis driver= 0.0066
> > Entering DMUMPS 5.2.1 from C interface with JOB, N, NNZ = 2 960 9792
> > executing #MPI = 1, without OMP
> >
> >
> >
> > ****** FACTORIZATION STEP ********
> > GLOBAL STATISTICS PRIOR NUMERICAL FACTORIZATION ...
> > Number of working processes = 1
> > ICNTL(22) Out-of-core option = 0
> > ICNTL(35) BLR activation (eff. choice) = 0
> > ICNTL(14) Memory relaxation = 20
> > INFOG(3) Real space for factors (estimated)= 24094
> > INFOG(4) Integer space for factors (estim.)= 12143
> > Maximum frontal size (estimated) = 80
> > Number of nodes in the tree = 227
> > Memory allowed (MB -- 0: N/A ) = 0
> > Memory provided by user, sum of LWK_USER = 0
> > Relative threshold for pivoting, CNTL(1) = 0.1000D-01
> > ZERO PIVOT DETECTION ON, THRESHOLD = 2.9434468577175697E-020
> > INFINITE FIXATION
> > Effective size of S (based on INFO(39))= 31314
> > Elapsed time to reformat/distribute matrix = 0.0006
> > ** Memory allocated, total in Mbytes (INFOG(19)): 1
> > ** Memory effectively used, total in Mbytes (INFOG(22)): 1
> > ** Memory dynamically allocated for CB, total in Mbytes : 0
> >
> > Elapsed time for (failed) factorization = 0.0032
> > Leaving factorization with ...
> > RINFOG(2) Operations in node assembly = 3.366D+04
> > ------(3) Operations in node elimination = 9.346D+05
> > INFOG (9) Real space for factors = 26980
> > INFOG(10) Integer space for factors = 13047
> > INFOG(11) Maximum front size = 84
> > INFOG(29) Number of entries in factors = 24047
> > INFOG(12) Number of negative pivots = 294
> > INFOG(13) Number of delayed pivots = 452
> > Number of 2x2 pivots in type 1 nodes = 0
> > Number of 2X2 pivots in type 2 nodes = 0
> > Nb of null pivots detected by ICNTL(24) = 0
> > INFOG(28) Estimated deficiency = 0
> > INFOG(14) Number of memory compress = 1
> >
> > Elapsed time in factorization driver= 0.0042
> > On return from DMUMPS, INFOG(1)= -9
> > On return from DMUMPS, INFOG(2)= 22
> > terminate called after throwing an instance of 'std::runtime_error'
> > what():
> >
> > *** -------------------------------------------------------------------------
> > *** DOLFIN encountered an error. If you are not able to resolve this issue
> > *** using the information listed below, you can ask for help at
> > ***
> > *** fenics-support at googlegroups.com (https://link.getmailspring.com/link/3C83A41D-E95A-4725-8766-C8F075BB1972@getmailspring.com/1?redirect=mailto%3Afenics-support%40googlegroups.com&recipient=cGV0c2MtdXNlcnNAbWNzLmFubC5nb3Y%3D)
> > ***
> > *** Remember to include the error message listed below and, if possible,
> > *** include a *minimal* running example to reproduce the error.
> > ***
> > *** -------------------------------------------------------------------------
> > *** Error: Unable to solve linear system using PETSc Krylov solver.
> > *** Reason: Solution failed to converge in 0 iterations (PETSc reason DIVERGED_PC_FAILED, residual norm ||r|| = 0.000000e+00).
> > *** Where: This error was encountered inside PETScKrylovSolver.cpp.
> > *** Process: 0
> > ***
> > *** DOLFIN version: 2019.1.0
> > *** Git changeset: 74d7efe1e84d65e9433fd96c50f1d278fa3e3f3f
> > *** -------------------------------------------------------------------------
> >
> > Aborted (core dumped)
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