[petsc-users] Question with setting up KSP solver parameters.
Song Gao
song.gao2 at mail.mcgill.ca
Mon May 5 10:00:34 CDT 2014
Thank you.
Runing with
mpirun -np 1 valgrind --track-origins=yes
~/mycodes/fensapngnew/bin/fensapMPI_LINUX64_DEBUG
-ksp_monitor_true_residual -ksp_view
gives the following information.
==8222== Conditional jump or move depends on uninitialised value(s)
==8222== at 0x216E9A7: SearchPath (in
/home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64_DEBUG)
==8222== by 0x216E1EC: mkl_cfg_file (in
/home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64_DEBUG)
==8222== by 0x216AC14: DDOT (in
/home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64_DEBUG)
==8222== by 0x1291100: VecNorm_Seq (bvec2.c:239)
==8222== by 0x126F431: VecNorm (rvector.c:166)
==8222== by 0x127039D: VecNormalize (rvector.c:261)
==8222== by 0x1405507: KSPGMRESCycle (gmres.c:127)
==8222== by 0x140695F: KSPSolve_GMRES (gmres.c:231)
==8222== by 0x1BEEF66: KSPSolve (itfunc.c:446)
==8222== by 0x13F95E8: kspsolve_ (itfuncf.c:219)
==8222== by 0xC5E51F: petsolv_ (PETSOLV.F:375)
==8222== by 0x612C35: flowsol_ng_ (flowsol_ng.F:275)
==8222== Uninitialised value was created by a stack allocation
==8222== at 0x216E97F: SearchPath (in
/home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64_DEBUG)
==8222==
==8222== Conditional jump or move depends on uninitialised value(s)
==8222== at 0x216E9D1: SearchPath (in
/home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64_DEBUG)
==8222== by 0x216E1EC: mkl_cfg_file (in
/home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64_DEBUG)
==8222== by 0x216AC14: DDOT (in
/home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64_DEBUG)
==8222== by 0x1291100: VecNorm_Seq (bvec2.c:239)
==8222== by 0x126F431: VecNorm (rvector.c:166)
==8222== by 0x127039D: VecNormalize (rvector.c:261)
==8222== by 0x1405507: KSPGMRESCycle (gmres.c:127)
==8222== by 0x140695F: KSPSolve_GMRES (gmres.c:231)
==8222== by 0x1BEEF66: KSPSolve (itfunc.c:446)
==8222== by 0x13F95E8: kspsolve_ (itfuncf.c:219)
==8222== by 0xC5E51F: petsolv_ (PETSOLV.F:375)
==8222== by 0x612C35: flowsol_ng_ (flowsol_ng.F:275)
==8222== Uninitialised value was created by a stack allocation
==8222== at 0x216E97F: SearchPath (in
/home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64_DEBUG)
==8222==
On Mon, May 5, 2014 at 10:03 AM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
> If you run valgrind with the debug version of the libraries it will
> provide more information about the line numbers where the problem occurred,
> etc. recommend doing that.
>
> Either your initial solution or right hand side has garbage in it or
> the wrong blas may be being linked in. But there is definitely a problem
>
> Barry
>
> On May 5, 2014, at 8:28 AM, Song Gao <song.gao2 at mail.mcgill.ca> wrote:
>
> > Thanks for reply. What do you mean by a “happier” state? I check the
> converged solution (the one which call kspgmressetrestart twice), the
> solution should be correct.
> >
> > I run with valgrind both codes (one call kspgmressetrestart once and
> another call kspgmressetrestart twice)
> > Both of them have the errors: what does this
> mean? Thank you in advance.
> > ==7858== Conditional jump or move depends on uninitialised value(s)
> > ==7858== at 0xE71DFB: SearchPath (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0xE71640: mkl_cfg_file (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0xE6E068: DDOT (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x73281A: VecNorm_Seq (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x730BF4: VecNormalize (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x7BC5A8: KSPSolve_GMRES (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0xB8A06E: KSPSolve (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x7B659F: kspsolve_ (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x5EAE84: petsolv_ (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x4ECD46: flowsol_ng_ (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x507E4E: iterprc_ (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x51D1B4: solnalg_ (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858==
> > ==7858== Conditional jump or move depends on uninitialised value(s)
> > ==7858== at 0xE71E25: SearchPath (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0xE71640: mkl_cfg_file (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0xE6E068: DDOT (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x73281A: VecNorm_Seq (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x730BF4: VecNormalize (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x7BC5A8: KSPSolve_GMRES (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0xB8A06E: KSPSolve (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x7B659F: kspsolve_ (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x5EAE84: petsolv_ (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x4ECD46: flowsol_ng_ (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x507E4E: iterprc_ (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858== by 0x51D1B4: solnalg_ (in
> /home/cfd/sgao/mycodes/fensapngnew/bin/fensapMPI_LINUX64)
> > ==7858==
> >
> >
> > On Fri, May 2, 2014 at 7:25 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >
> > On May 2, 2014, at 5:29 PM, Song Gao <song.gao2 at mail.mcgill.ca> wrote:
> >
> > > Thanks for your quick reply. What confused me is that why would the
> code works fine if I reset the gmres restart number by recalling
> kspgmressetrestart just before kspsolve?
> >
> > It isn’t really working. Something is going wrong (run with valgrind)
> and setting that restart number and starting the solver just puts it in a
> “happier” state so it seems to make more progress.
> >
> > Barry
> >
> > >
> > > Sent from my iPhone
> > >
> > >> On May 2, 2014, at 6:03 PM, "Barry Smith" <bsmith at mcs.anl.gov> wrote:
> > >>
> > >>
> > >> Your shell matrix is buggy in some way. Whenever the residual norm
> jumps like crazy at a restart it means that something is wrong with the
> operator.
> > >>
> > >> Barry
> > >>
> > >>> On May 2, 2014, at 4:41 PM, Song Gao <song.gao2 at mail.mcgill.ca>
> wrote:
> > >>>
> > >>> Dear PETSc users,
> > >>>
> > >>> I'm solving a linear system in KSP and trying to setup the solver in
> codes. But I feel strange because my codes don't converge unless I call
> KSPGMRESSetRestart twice.
> > >>>
> > >>> My codes looks like
> > >>>
> > >>> call KSPSetOperators ( pet_solv, pet_mat_mf_shell, pet_matp,
> DIFFERENT_NONZERO_PATTERN, ierpetsc )
> > >>> call KSPSetType ( pet_solv, 'gmres', ierpetsc )
> > >>> call KSPGMRESSetRestart ( pet_solv, 30, ierpetsc )
> > >>> call KSPGetPC ( pet_solv, pet_precon, ierpetsc )
> > >>> call PCSetType ( pet_precon, 'asm', ierpetsc )
> > >>> call PCASMSetOverlap ( pet_precon, 1, ierpetsc )
> > >>> call KSPSetUp ( pet_solv, ierpetsc )
> > >>> call PCASMGetSubKSP ( pet_precon, n_local, first_local,
> pet_solv_sub, ierpetsc ) ! n_local is one
> > >>> call KSPGetPC ( pet_solv_sub(1), pet_precon_sub, ierpetsc )
> > >>> call PCSetType ( pet_precon_sub, 'jacobi', ierpetsc )
> > >>> call PCJacobiSetUseRowMax ( pet_precon_sub, ierpetsc )
> > >>> call KSPSetFromOptions ( pet_solv, ierpetsc )
> > >>> call KSPGMRESSetRestart ( pet_solv, 29, ierpetsc ) !
> adding this line, the codes converge
> > >>> call KSPSolve ( pet_solv, pet_rhsp, pet_solup, ierpetsc )
> > >>>
> > >>> runing with 1 CPU WITHOUT the line with red color and the codes
> don't converge
> > >>>
> > >>> runtime options: -ksp_monitor_true_residual -ksp_view
> > >>> 0 KSP preconditioned resid norm 6.585278940829e+00 true resid norm
> 9.619278462343e-03 ||r(i)||/||b|| 1.000000000000e+00
> > >>> 1 KSP preconditioned resid norm 6.585278219510e+00 true resid norm
> 9.619278462343e-03 ||r(i)||/||b|| 1.000000000000e+00
> > >>> 2 KSP preconditioned resid norm 2.198638170622e+00 true resid norm
> 1.365132713014e-01 ||r(i)||/||b|| 1.419163317039e+01
> > >>> 3 KSP preconditioned resid norm 1.599896387215e+00 true resid norm
> 1.445988845022e-01 ||r(i)||/||b|| 1.503219654865e+01
> > >>> .......
> > >>> 28 KSP preconditioned resid norm 4.478466011191e-01 true resid norm
> 1.529879309381e-01 ||r(i)||/||b|| 1.590430420920e+01
> > >>> 29 KSP preconditioned resid norm 4.398129572260e-01 true resid norm
> 1.530132924055e-01 ||r(i)||/||b|| 1.590694073413e+01
> > >>> 30 KSP preconditioned resid norm 2.783227613716e+12 true resid norm
> 1.530369123550e-01 ||r(i)||/||b|| 1.590939621450e+01
> > >>>
> > >>> KSP Object: 1 MPI processes
> > >>> type: gmres
> > >>> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
> Orthogonalization with no iterative refinement
> > >>> GMRES: happy breakdown tolerance 1e-30
> > >>> maximum iterations=10000, initial guess is zero
> > >>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
> > >>> left preconditioning
> > >>> using PRECONDITIONED norm type for convergence test
> > >>> PC Object: 1 MPI processes
> > >>> type: asm
> > >>> Additive Schwarz: total subdomain blocks = 1, amount of overlap = 1
> > >>> Additive Schwarz: restriction/interpolation type - RESTRICT
> > >>> [0] number of local blocks = 1
> > >>> Local solve info for each block is in the following KSP and PC
> objects:
> > >>> - - - - - - - - - - - - - - - - - -
> > >>> [0] local block number 0, size = 22905
> > >>> KSP Object: (sub_) 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: (sub_) 1 MPI processes
> > >>> type: jacobi
> > >>> linear system matrix = precond matrix:
> > >>> Matrix Object: 1 MPI processes
> > >>> type: seqbaij
> > >>> rows=22905, cols=22905, bs=5
> > >>> total: nonzeros=785525, allocated nonzeros=785525
> > >>> total number of mallocs used during MatSetValues calls =0
> > >>> block size is 5
> > >>> - - - - - - - - - - - - - - - - - -
> > >>> linear system matrix followed by preconditioner matrix:
> > >>> Matrix Object: 1 MPI processes
> > >>> type: shell
> > >>> rows=22905, cols=22905
> > >>> Matrix Object: 1 MPI processes
> > >>> type: seqbaij
> > >>> rows=22905, cols=22905, bs=5
> > >>> total: nonzeros=785525, allocated nonzeros=785525
> > >>> total number of mallocs used during MatSetValues calls =0
> > >>> block size is 5
> > >>> WARNING: zero iteration in iterative solver
> > >>>
> > >>> runing with 1 CPU WITH the line with red color and the codes
> converge
> > >>>
> > >>> runtime options: -ksp_monitor_true_residual -ksp_view
> > >>> 0 KSP preconditioned resid norm 6.585278940829e+00 true resid norm
> 9.619278462343e-03 ||r(i)||/||b|| 1.000000000000e+00
> > >>> 1 KSP preconditioned resid norm 2.566248171026e+00 true resid norm
> 4.841043870812e-03 ||r(i)||/||b|| 5.032647604250e-01
> > >>> 2 KSP preconditioned resid norm 1.410418402651e+00 true resid norm
> 3.347509391208e-03 ||r(i)||/||b|| 3.480000505561e-01
> > >>> 3 KSP preconditioned resid norm 9.665409287757e-01 true resid norm
> 2.289877121679e-03 ||r(i)||/||b|| 2.380508195748e-01
> > >>> 4 KSP preconditioned resid norm 4.469486152454e-01 true resid norm
> 1.283813398084e-03 ||r(i)||/||b|| 1.334625463968e-01
> > >>> 5 KSP preconditioned resid norm 2.474889829653e-01 true resid norm
> 7.956009139680e-04 ||r(i)||/||b|| 8.270900120862e-02
> > >>> ............
> > >>> 24 KSP preconditioned resid norm 9.518780877620e-05 true resid norm
> 6.273993696172e-07 ||r(i)||/||b|| 6.522312167937e-05
> > >>> 25 KSP preconditioned resid norm 6.837876679998e-05 true resid norm
> 4.612861071815e-07 ||r(i)||/||b|| 4.795433555514e-05
> > >>> 26 KSP preconditioned resid norm 4.864361942316e-05 true resid norm
> 3.394754589076e-07 ||r(i)||/||b|| 3.529115621682e-05
> > >>> KSP Object: 1 MPI processes
> > >>> type: gmres
> > >>> GMRES: restart=29, using Classical (unmodified) Gram-Schmidt
> Orthogonalization with no iterative refinement
> > >>> GMRES: happy breakdown tolerance 1e-30
> > >>> maximum iterations=10000, initial guess is zero
> > >>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
> > >>> left preconditioning
> > >>> using PRECONDITIONED norm type for convergence test
> > >>> PC Object: 1 MPI processes
> > >>> type: asm
> > >>> Additive Schwarz: total subdomain blocks = 1, amount of overlap = 1
> > >>> Additive Schwarz: restriction/interpolation type - RESTRICT
> > >>> [0] number of local blocks = 1
> > >>> Local solve info for each block is in the following KSP and PC
> objects:
> > >>> - - - - - - - - - - - - - - - - - -
> > >>> [0] local block number 0, size = 22905
> > >>> KSP Object: (sub_) 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: (sub_) 1 MPI processes
> > >>> type: jacobi
> > >>> linear system matrix = precond matrix:
> > >>> Matrix Object: 1 MPI processes
> > >>> type: seqbaij
> > >>> rows=22905, cols=22905, bs=5
> > >>> total: nonzeros=785525, allocated nonzeros=785525
> > >>> total number of mallocs used during MatSetValues calls =0
> > >>> block size is 5
> > >>> - - - - - - - - - - - - - - - - - -
> > >>> linear system matrix followed by preconditioner matrix:
> > >>> Matrix Object: 1 MPI processes
> > >>> type: shell
> > >>> rows=22905, cols=22905
> > >>> Matrix Object: 1 MPI processes
> > >>> type: seqbaij
> > >>> rows=22905, cols=22905, bs=5
> > >>> total: nonzeros=785525, allocated nonzeros=785525
> > >>> total number of mallocs used during MatSetValues calls =0
> > >>> block size is 5
> > >>> WARNING: zero iteration in iterative solver
> > >>>
> > >>>
> > >>> What would be my error here? Thank you.
> > >>
> >
> >
>
>
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