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<div class="moz-cite-prefix">Thanks, I have corrected the shift
amount option and I get the same error as when using the
-st_pc_factor_shift_amount 1 <br>
<br>
I have been using the PETSc IO module to convert my matrix from
sparse coordinate format into PETSc binary. I am guessing there is
some problem with this step. I use the function:<br>
PetscBinaryIO.PetscBinaryIO().writeMatSciPy( fh, matrix) <br>
to convert into Petsc binary format. Is there something wrong with
this? Do I need to manually put zeros into the diagonal elements
of zero rows of B?<br>
<br>
When I solve the problem using scipy I use dense matrices. There
are definitely entries in the matrix A at row 2395. I used python
to confirm this before I convert it to petsc format:<br>
<br>
column | value <br>
LHS: 1795 10.9955742876j<br>
1198 (76+0j)<br>
1196 (72+0j)<br>
595 0.02j<br>
<br>
However, the matrix is all zeros at row 2395 in B. As far as I
understand, this doesn't make my problem singular. I am sure that
the problem is not rank deficient when I solve it in scipy.<br>
<br>
Thanks again,<br>
Toby<br>
<br>
<br>
On 25/07/2013 12:51, Matthew Knepley wrote:<br>
</div>
<blockquote
cite="mid:CAMYG4GmkbYmfUyAo9JFJpdg+2mVeRgb=QzBtUbnR0UjQ8tnPQw@mail.gmail.com"
type="cite">
<div dir="ltr">On Thu, Jul 25, 2013 at 6:46 AM, Toby <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:T.W.Searle@sms.ed.ac.uk" target="_blank">T.W.Searle@sms.ed.ac.uk</a>></span>
wrote:<br>
<div class="gmail_extra">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><br>
Ok, it looks like the -st_pc_factor_shift_type option is
now being used, thanks. Unfortunately it hasn't fixed the
problem.<br>
<br>
if I use the NONZERO type and a shift amount, the shift
amount option is not recognised and I still get the zero
pivot error. If I use the POSITIVE_DEFINITE type I also
get the pivot error. Output is below<br>
<br>
Thanks,<br>
Toby<br>
<br>
tobymac:SLEPC toby$ mpiexec ./ex7 -f1
LHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc -f2
RHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc -st_pc_type lu
-st_pc_factor_shift_type NONZERO -st_pc_shift_type_amount
1<br>
<br>
Generalized eigenproblem stored in file.<br>
<br>
Reading COMPLEX matrices from binary files...<br>
[0]PETSC ERROR: --------------------- Error Message
------------------------------------<br>
[0]PETSC ERROR: Detected zero pivot in LU factorization:<br>
see <a moz-do-not-send="true"
href="http://www.mcs.anl.gov/petsc/documentation/faq.html#ZeroPivot"
target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#ZeroPivot</a>!<br>
[0]PETSC ERROR: Empty row in matrix: row in original
ordering 2395 in permuted ordering 3600!<br>
</blockquote>
<div><br>
</div>
<div>1) You misspelled the option:
-st_pc_factor_shift_amount 1</div>
<div><br>
</div>
<div>2) It was used, and fixed you problem on row 0, now you
have a problem on row 2395, namely that it is missing. No</div>
<div> LU factorization routine will succeed here. You
must at least put a diagonal 0.0 on all rows.</div>
<div><br>
</div>
<div>3) Same goes for the run below.</div>
<div><br>
</div>
<div>4) A completely empty row means your matrix is indeed
rank deficient. I have no idea what results are coming out
of</div>
<div> scipy, but they are not using factorization.</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">[0]PETSC
ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 5, Sat
Dec 1 15:10:41 CST 2012<br>
[0]PETSC ERROR: See docs/changes/index.html for recent
updates.<br>
[0]PETSC ERROR: See docs/faq.html for hints about trouble
shooting.<br>
[0]PETSC ERROR: See docs/index.html for manual pages.<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: ./ex7 on a arch-darw named tobymac by toby
Thu Jul 25 12:41:57 2013<br>
[0]PETSC ERROR: Libraries linked from /opt/local/lib<br>
[0]PETSC ERROR: Configure run at Tue Jul 23 15:11:27 2013<br>
[0]PETSC ERROR: Configure options --prefix=/opt/local
--with-valgrind-dir=/opt/local --with-shared-libraries
--with-scalar-type=complex --with-clanguage=C++
--with-superlu-dir=/opt/local --with-blacs-dir=/opt/local
--with-scalapack-dir=/opt/local
--with-mumps-dir=/opt/local --with-metis-dir=/opt/local
--with-parmetis-dir=/opt/local --COPTFLAGS=-O2
--CXXOPTFLAGS=-O2 --FOPTFLAGS=-O2
--LDFLAGS=-L/opt/local/lib --CFLAGS="-O2 -mtune=native"
--CXXFLAGS="-O2 -mtune=native"<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: MatLUFactorSymbolic_SeqAIJ() line 334 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/mat/impls/aij/seq/aijfact.c<br>
[0]PETSC ERROR: MatLUFactorSymbolic() line 2750 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/mat/interface/matrix.c<br>
[0]PETSC ERROR: PCSetUp_LU() line 135 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/ksp/pc/impls/factor/lu/lu.c<br>
[0]PETSC ERROR: PCSetUp() line 832 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/ksp/pc/interface/precon.c<br>
[0]PETSC ERROR: KSPSetUp() line 278 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/ksp/ksp/interface/itfunc.c<br>
[0]PETSC ERROR: STSetUp_Shift() line 94 in
src/st/impls/shift/shift.c<br>
[0]PETSC ERROR: STSetUp() line 280 in
src/st/interface/stsolve.c<br>
[0]PETSC ERROR: EPSSetUp() line 204 in
src/eps/interface/setup.c<br>
[0]PETSC ERROR: EPSSolve() line 109 in
src/eps/interface/solve.c<br>
Number of iterations of the method: 0<br>
Number of linear iterations of the method: 0<br>
Number of requested eigenvalues: 1<br>
Stopping condition: tol=1e-08, maxit=750<br>
Number of converged approximate eigenpairs: 0<br>
<br>
WARNING! There are options you set that were not used!<br>
WARNING! could be spelling mistake, etc!<br>
Option left: name:-st_pc_shift_type_amount value: 1<br>
<br>
mpiexec ./ex7 -f1 LHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc
-f2 RHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc -st_pc_type
lu -st_pc_factor_shift_type POSITIVE_DEFINITE<br>
<br>
Generalized eigenproblem stored in file.<br>
<br>
Reading COMPLEX matrices from binary files...<br>
[0]PETSC ERROR: --------------------- Error Message
------------------------------------<br>
[0]PETSC ERROR: Detected zero pivot in LU factorization:<br>
see <a moz-do-not-send="true"
href="http://www.mcs.anl.gov/petsc/documentation/faq.html#ZeroPivot"
target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#ZeroPivot</a>!<br>
[0]PETSC ERROR: Empty row in matrix: row in original
ordering 2395 in permuted ordering 3600!<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 5, Sat
Dec 1 15:10:41 CST 2012<br>
[0]PETSC ERROR: See docs/changes/index.html for recent
updates.<br>
[0]PETSC ERROR: See docs/faq.html for hints about trouble
shooting.<br>
[0]PETSC ERROR: See docs/index.html for manual pages.<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: ./ex7 on a arch-darw named tobymac by toby
Thu Jul 25 12:40:20 2013<br>
[0]PETSC ERROR: Libraries linked from /opt/local/lib<br>
[0]PETSC ERROR: Configure run at Tue Jul 23 15:11:27 2013<br>
[0]PETSC ERROR: Configure options --prefix=/opt/local
--with-valgrind-dir=/opt/local --with-shared-libraries
--with-scalar-type=complex --with-clanguage=C++
--with-superlu-dir=/opt/local --with-blacs-dir=/opt/local
--with-scalapack-dir=/opt/local
--with-mumps-dir=/opt/local --with-metis-dir=/opt/local
--with-parmetis-dir=/opt/local --COPTFLAGS=-O2
--CXXOPTFLAGS=-O2 --FOPTFLAGS=-O2
--LDFLAGS=-L/opt/local/lib --CFLAGS="-O2 -mtune=native"
--CXXFLAGS="-O2 -mtune=native"<br>
[0]PETSC ERROR: ------------------------------------------------------------------------<br>
[0]PETSC ERROR: MatLUFactorSymbolic_SeqAIJ() line 334 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/mat/impls/aij/seq/aijfact.c<br>
[0]PETSC ERROR: MatLUFactorSymbolic() line 2750 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/mat/interface/matrix.c<br>
[0]PETSC ERROR: PCSetUp_LU() line 135 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/ksp/pc/impls/factor/lu/lu.c<br>
[0]PETSC ERROR: PCSetUp() line 832 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/ksp/pc/interface/precon.c<br>
[0]PETSC ERROR: KSPSetUp() line 278 in
/opt/local/var/macports/build/_Users_toby_MyPorts_scienceports_math_petsc/petsc/work/petsc-3.3-p5/src/ksp/ksp/interface/itfunc.c<br>
[0]PETSC ERROR: STSetUp_Shift() line 94 in
src/st/impls/shift/shift.c<br>
[0]PETSC ERROR: STSetUp() line 280 in
src/st/interface/stsolve.c<br>
[0]PETSC ERROR: EPSSetUp() line 204 in
src/eps/interface/setup.c<br>
[0]PETSC ERROR: EPSSolve() line 109 in
src/eps/interface/solve.c<br>
Number of iterations of the method: 0<br>
Number of linear iterations of the method: 0<br>
Number of requested eigenvalues: 1<br>
Stopping condition: tol=1e-08, maxit=750<br>
Number of converged approximate eigenpairs: 0<br>
<br>
<br>
<br>
<br>
On 25/07/2013 12:34, Jose E. Roman wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
El 25/07/2013, a las 13:30, Toby escribió:<br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px
0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Hi
Matt,<br>
<br>
Thanks for the speedy reply. I tried using the options
you suggested:<br>
<br>
mpiexec ./ex7 -f1 LHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc
-f2 RHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc
-st_pc_factor_shift_type NONZERO
-st_pc_shift_type_amount 1<br>
<br>
But I still get the warnings:<br>
Option left: name:-st_pc_factor_shift_type value:
NONZERO<br>
Option left: name:-st_pc_shift_type_amount value: 1<br>
</blockquote>
By default, ST is using PCREDUNDANT. In order to use the
above options you must change it to e.g. PCLU.<br>
That is, add -st_pc_type lu<br>
<br>
Jose<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px
0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">I
have tried it with just the -st_pc_type jacobi and
-st_ksp_view. This gives me some eigenvalues, but I
don't believe them (they do not appear on the spectrum
which I solve using LAPACK where all eigenvalues have
a real part less than 0). The output was very large,
but consists of repetitions of this:<br>
<br>
mpiexec ./ex7 -f1 LHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc
-f2 RHS-N7-M40-Re0.0-b0.1-Wi5.0-amp0.02.petsc
-st_pc_type jacobi -st_ksp_view<br>
<br>
Generalized eigenproblem stored in file.<br>
<br>
Reading COMPLEX matrices from binary files...<br>
KSP Object:(st_) 1 MPI processes<br>
type: preonly<br>
maximum iterations=10000, initial guess is zero<br>
tolerances: relative=1e-08, absolute=1e-50,
divergence=10000<br>
left preconditioning<br>
using NONE norm type for convergence test<br>
PC Object:(st_) 1 MPI processes<br>
type: jacobi<br>
linear system matrix = precond matrix:<br>
Matrix Object: 1 MPI processes<br>
type: seqaij<br>
rows=6000, cols=6000<br>
total: nonzeros=3600, allocated nonzeros=3600<br>
total number of mallocs used during MatSetValues
calls =0<br>
using I-node routines: found 4080 nodes, limit
used is 5<br>
<br>
...<br>
<br>
Number of iterations of the method: 189<br>
Number of linear iterations of the method: 1520<br>
Number of requested eigenvalues: 1<br>
Stopping condition: tol=1e-08, maxit=750<br>
Number of converged approximate eigenpairs: 2<br>
<br>
k ||Ax-kBx||/||kx||<br>
----------------- ------------------<br>
1388.774454+0.001823 i 0.751726<br>
1388.774441+0.001820 i 0.912665<br>
<br>
<br>
Thanks again,<br>
Toby<br>
</blockquote>
<br>
<span class=""><font color="#888888">
</font></span></blockquote>
<span class=""><font color="#888888">
<br>
<br>
-- <br>
The University of Edinburgh is a charitable body,
registered in<br>
Scotland, with registration number SC005336.<br>
<br>
</font></span></blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
What most experimenters take for granted before they begin
their experiments is infinitely more interesting than any
results to which their experiments lead.<br>
-- Norbert Wiener
</div>
</div>
</blockquote>
<br>
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