From: Kyunghoon Lee <aeronova.mailing@gm...>  20111027 23:23:58

Hi all, I compiled petsc with complex variable support using the following options: ./configure prefix=/Users/aeronova/ Development/local/lib64/petsc/petsc3.2p4 downloadmpich=1 downloadblacs=1 downloadparmetis=1 downloadscalapack=1 downloadmumps=1 withscalartype=complex withclanguage=cxx Then, rebuild slepc & libmesh (svn version). As I test libmesh with examples, I got an error for ex17 (plz see the below). I'd appreciate if someone could help me with this problem. (ex7, complex variable example, seemed ok, though there were a couple of warnings such as WARNING! There are options you set that were not used!, WARNING! could be spelling mistake, etc!, Option left: name:f value: .5) [0]PETSC ERROR:  Error Message  [0]PETSC ERROR: IPNorm: The inner product is not well defined! [0]PETSC ERROR:  [0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 13:37:48 CDT 2011 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:  [0]PETSC ERROR: ./ex17dbg on a darwin10. named spike.local by aeronova Fri Oct 28 05:13:59 2011 [0]PETSC ERROR: Libraries linked from /Users/aeronova/Development/local/lib64/petsc/petsc3.1p8/lib [0]PETSC ERROR: Configure run at Fri Oct 28 04:12:19 2011 [0]PETSC ERROR: Configure options prefix=/Users/aeronova/Development/local/lib64/petsc/petsc3.1p8 downloadmpich=1 downloadblacs=1 downloadparmetis=1 downloadscalapack=1 downloadmumps=1 withscalartype=complex withclanguage=cxx [0]PETSC ERROR:  [0]PETSC ERROR: IPNorm() line 70 in src/ip/ipdot.c [0]PETSC ERROR: IPOrthogonalize() line 338 in src/ip/iporthog.c [0]PETSC ERROR: EPSGetStartVector() line 1487 in src/eps/interface/solve.c [0]PETSC ERROR: EPSSolve_ARNOLDI() line 387 in src/eps/impls/krylov/arnoldi/arnoldi.c [0]PETSC ERROR: EPSSolve() line 146 in src/eps/interface/solve.c [0]PETSC ERROR: User provided function() line 488 in "unknowndirectory/"src/solvers/slepc_eigen_solver.C application called MPI_Abort(comm=0x84000000, 1)  process 0[unset]: aborting job: application called MPI_Abort(comm=0x84000000, 1)  process 0 make[2]: *** [run] Error 1 make[1]: *** [run] Error 1 make: *** [run_examples] Error 2 
From: Roy Stogner <roystgnr@ic...>  20111027 23:30:18

What options did you use to configure libMesh? I'll see if I can reproduce this. We currently have enablecomplex BuildBot tests and enableslepc tests but I don't think we're testing the combination of the two...  Roy On Fri, 28 Oct 2011, Kyunghoon Lee wrote: > Hi all, > > I compiled petsc with complex variable support using the following options: > > ./configure prefix=/Users/aeronova/ > Development/local/lib64/petsc/petsc3.2p4 downloadmpich=1 > downloadblacs=1 downloadparmetis=1 downloadscalapack=1 > downloadmumps=1 withscalartype=complex withclanguage=cxx > > Then, rebuild slepc & libmesh (svn version). As I test libmesh with > examples, I got an error for ex17 (plz see the below). I'd appreciate if > someone could help me with this problem. (ex7, complex variable example, > seemed ok, though there were a couple of warnings such as WARNING! There are > options you set that were not used!, WARNING! could be spelling mistake, > etc!, Option left: name:f value: .5) > > > [0]PETSC ERROR:  Error Message >  > [0]PETSC ERROR: IPNorm: The inner product is not well defined! > [0]PETSC ERROR: >  > [0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 13:37:48 > CDT 2011 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR: >  > [0]PETSC ERROR: ./ex17dbg on a darwin10. named spike.local by aeronova Fri > Oct 28 05:13:59 2011 > [0]PETSC ERROR: Libraries linked from > /Users/aeronova/Development/local/lib64/petsc/petsc3.1p8/lib > [0]PETSC ERROR: Configure run at Fri Oct 28 04:12:19 2011 > [0]PETSC ERROR: Configure options > prefix=/Users/aeronova/Development/local/lib64/petsc/petsc3.1p8 > downloadmpich=1 downloadblacs=1 downloadparmetis=1 > downloadscalapack=1 downloadmumps=1 withscalartype=complex > withclanguage=cxx > [0]PETSC ERROR: >  > [0]PETSC ERROR: IPNorm() line 70 in src/ip/ipdot.c > [0]PETSC ERROR: IPOrthogonalize() line 338 in src/ip/iporthog.c > [0]PETSC ERROR: EPSGetStartVector() line 1487 in src/eps/interface/solve.c > [0]PETSC ERROR: EPSSolve_ARNOLDI() line 387 in > src/eps/impls/krylov/arnoldi/arnoldi.c > [0]PETSC ERROR: EPSSolve() line 146 in src/eps/interface/solve.c > [0]PETSC ERROR: User provided function() line 488 in > "unknowndirectory/"src/solvers/slepc_eigen_solver.C > application called MPI_Abort(comm=0x84000000, 1)  process 0[unset]: > aborting job: > application called MPI_Abort(comm=0x84000000, 1)  process 0 > make[2]: *** [run] Error 1 > make[1]: *** [run] Error 1 > make: *** [run_examples] Error 2 >  > The demand for IT networking professionals continues to grow, and the > demand for specialized networking skills is growing even more rapidly. > Take a complimentary Learning@... SelfAssessment and learn > about Cisco certifications, training, and career opportunities. > http://p.sf.net/sfu/ciscodev2dev > _______________________________________________ > Libmeshusers mailing list > Libmeshusers@... > https://lists.sourceforge.net/lists/listinfo/libmeshusers > > 
From: Roy Stogner <roystgnr@ic...>  20111101 19:28:28

We're testing SLEPc + complex now, and seeing the same IPNorm error. The problem seems to be some issue with the default iterative solvers we tell SLEPc to use; it looks like for some reason they're getting a "norm" of their initial random starting vector that isn't a nonnegative real number. I'm not sure how this would happen, though a Google search suggests that we're not the first people to run into this IPNorm error when doing a generalized eigenproblem. Running with LIBMESH_OPTIONS="eps_type lapack" comes up with results; I presume that's switching to a direct solver. This probably isn't SLEPc's fault, but if you're doing eigen problems with complexvalued PDEs then you might want to ask them about this issue anyway; I don't know enough about our SLEPc interface or about the various methods they have available to advise you on which to use. For now I'm going to put "eps_type lapack" in our ex17 Makefile just to get it passing tests; however if you learn more about what we might be doing wrong that's confusing their Arnoldi solver then I'd appreciate hearing about it. Thanks,  Roy On Thu, 27 Oct 2011, Roy Stogner wrote: > What options did you use to configure libMesh? > > I'll see if I can reproduce this. We currently have enablecomplex > BuildBot tests and enableslepc tests but I don't think we're > testing the combination of the two... >  > Roy > > On Fri, 28 Oct 2011, Kyunghoon Lee wrote: > >> Hi all, >> >> I compiled petsc with complex variable support using the following options: >> >> ./configure prefix=/Users/aeronova/ >> Development/local/lib64/petsc/petsc3.2p4 downloadmpich=1 >> downloadblacs=1 downloadparmetis=1 downloadscalapack=1 >> downloadmumps=1 withscalartype=complex withclanguage=cxx >> >> Then, rebuild slepc & libmesh (svn version). As I test libmesh with >> examples, I got an error for ex17 (plz see the below). I'd appreciate if >> someone could help me with this problem. (ex7, complex variable example, >> seemed ok, though there were a couple of warnings such as WARNING! There >> are >> options you set that were not used!, WARNING! could be spelling mistake, >> etc!, Option left: name:f value: .5) >> >> >> [0]PETSC ERROR:  Error Message >>  >> [0]PETSC ERROR: IPNorm: The inner product is not well defined! >> [0]PETSC ERROR: >>  >> [0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 13:37:48 >> CDT 2011 >> [0]PETSC ERROR: See docs/changes/index.html for recent updates. >> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >> [0]PETSC ERROR: See docs/index.html for manual pages. >> [0]PETSC ERROR: >>  >> [0]PETSC ERROR: ./ex17dbg on a darwin10. named spike.local by aeronova Fri >> Oct 28 05:13:59 2011 >> [0]PETSC ERROR: Libraries linked from >> /Users/aeronova/Development/local/lib64/petsc/petsc3.1p8/lib >> [0]PETSC ERROR: Configure run at Fri Oct 28 04:12:19 2011 >> [0]PETSC ERROR: Configure options >> prefix=/Users/aeronova/Development/local/lib64/petsc/petsc3.1p8 >> downloadmpich=1 downloadblacs=1 downloadparmetis=1 >> downloadscalapack=1 downloadmumps=1 withscalartype=complex >> withclanguage=cxx >> [0]PETSC ERROR: >>  >> [0]PETSC ERROR: IPNorm() line 70 in src/ip/ipdot.c >> [0]PETSC ERROR: IPOrthogonalize() line 338 in src/ip/iporthog.c >> [0]PETSC ERROR: EPSGetStartVector() line 1487 in src/eps/interface/solve.c >> [0]PETSC ERROR: EPSSolve_ARNOLDI() line 387 in >> src/eps/impls/krylov/arnoldi/arnoldi.c >> [0]PETSC ERROR: EPSSolve() line 146 in src/eps/interface/solve.c >> [0]PETSC ERROR: User provided function() line 488 in >> "unknowndirectory/"src/solvers/slepc_eigen_solver.C >> application called MPI_Abort(comm=0x84000000, 1)  process 0[unset]: >> aborting job: >> application called MPI_Abort(comm=0x84000000, 1)  process 0 >> make[2]: *** [run] Error 1 >> make[1]: *** [run] Error 1 >> make: *** [run_examples] Error 2 >> >>  >> The demand for IT networking professionals continues to grow, and the >> demand for specialized networking skills is growing even more rapidly. >> Take a complimentary Learning@... SelfAssessment and learn >> about Cisco certifications, training, and career opportunities. >> http://p.sf.net/sfu/ciscodev2dev >> _______________________________________________ >> Libmeshusers mailing list >> Libmeshusers@... >> https://lists.sourceforge.net/lists/listinfo/libmeshusers >> >> > 
From: David Knezevic <dknezevic@se...>  20111101 19:38:02

On 11/01/2011 03:28 PM, Roy Stogner wrote: > We're testing SLEPc + complex now, and seeing the same IPNorm error. > > The problem seems to be some issue with the default iterative solvers > we tell SLEPc to use; it looks like for some reason they're getting a > "norm" of their initial random starting vector that isn't a > nonnegative real number. I'm not sure how this would happen, though > a Google search suggests that we're not the first people to run into > this IPNorm error when doing a generalized eigenproblem. Interesting. So it's not a bug per se, good to know. > Running with LIBMESH_OPTIONS="eps_type lapack" comes up with results; > I presume that's switching to a direct solver. The lapack solver uses the QR algorithm (or something similar) to find all the eigenvalues I believe. Its very robust, but only works for small problems since it treats the matrix as dense. Dave >> What options did you use to configure libMesh? >> >> I'll see if I can reproduce this. We currently have enablecomplex >> BuildBot tests and enableslepc tests but I don't think we're >> testing the combination of the two... >>  >> Roy >> >> On Fri, 28 Oct 2011, Kyunghoon Lee wrote: >> >>> Hi all, >>> >>> I compiled petsc with complex variable support using the following options: >>> >>> ./configure prefix=/Users/aeronova/ >>> Development/local/lib64/petsc/petsc3.2p4 downloadmpich=1 >>> downloadblacs=1 downloadparmetis=1 downloadscalapack=1 >>> downloadmumps=1 withscalartype=complex withclanguage=cxx >>> >>> Then, rebuild slepc& libmesh (svn version). As I test libmesh with >>> examples, I got an error for ex17 (plz see the below). I'd appreciate if >>> someone could help me with this problem. (ex7, complex variable example, >>> seemed ok, though there were a couple of warnings such as WARNING! There >>> are >>> options you set that were not used!, WARNING! could be spelling mistake, >>> etc!, Option left: name:f value: .5) >>> >>> >>> [0]PETSC ERROR:  Error Message >>>  >>> [0]PETSC ERROR: IPNorm: The inner product is not well defined! >>> [0]PETSC ERROR: >>>  >>> [0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 13:37:48 >>> CDT 2011 >>> [0]PETSC ERROR: See docs/changes/index.html for recent updates. >>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >>> [0]PETSC ERROR: See docs/index.html for manual pages. >>> [0]PETSC ERROR: >>>  >>> [0]PETSC ERROR: ./ex17dbg on a darwin10. named spike.local by aeronova Fri >>> Oct 28 05:13:59 2011 >>> [0]PETSC ERROR: Libraries linked from >>> /Users/aeronova/Development/local/lib64/petsc/petsc3.1p8/lib >>> [0]PETSC ERROR: Configure run at Fri Oct 28 04:12:19 2011 >>> [0]PETSC ERROR: Configure options >>> prefix=/Users/aeronova/Development/local/lib64/petsc/petsc3.1p8 >>> downloadmpich=1 downloadblacs=1 downloadparmetis=1 >>> downloadscalapack=1 downloadmumps=1 withscalartype=complex >>> withclanguage=cxx >>> [0]PETSC ERROR: >>>  >>> [0]PETSC ERROR: IPNorm() line 70 in src/ip/ipdot.c >>> [0]PETSC ERROR: IPOrthogonalize() line 338 in src/ip/iporthog.c >>> [0]PETSC ERROR: EPSGetStartVector() line 1487 in src/eps/interface/solve.c >>> [0]PETSC ERROR: EPSSolve_ARNOLDI() line 387 in >>> src/eps/impls/krylov/arnoldi/arnoldi.c >>> [0]PETSC ERROR: EPSSolve() line 146 in src/eps/interface/solve.c >>> [0]PETSC ERROR: User provided function() line 488 in >>> "unknowndirectory/"src/solvers/slepc_eigen_solver.C >>> application called MPI_Abort(comm=0x84000000, 1)  process 0[unset]: >>> aborting job: >>> application called MPI_Abort(comm=0x84000000, 1)  process 0 >>> make[2]: *** [run] Error 1 >>> make[1]: *** [run] Error 1 >>> make: *** [run_examples] Error 2 >>> >>>  >>> The demand for IT networking professionals continues to grow, and the >>> demand for specialized networking skills is growing even more rapidly. >>> Take a complimentary Learning@... SelfAssessment and learn >>> about Cisco certifications, training, and career opportunities. >>> http://p.sf.net/sfu/ciscodev2dev >>> _______________________________________________ >>> Libmeshusers mailing list >>> Libmeshusers@... >>> https://lists.sourceforge.net/lists/listinfo/libmeshusers >>> >>> >  > RSA® Conference 2012 > Save $700 by Nov 18 > Register now! > http://p.sf.net/sfu/rsasfdev2dev1 > _______________________________________________ > Libmeshusers mailing list > Libmeshusers@... > https://lists.sourceforge.net/lists/listinfo/libmeshusers 
From: Roy Stogner <roystgnr@ic...>  20111101 19:41:58

On Tue, 1 Nov 2011, David Knezevic wrote: > On 11/01/2011 03:28 PM, Roy Stogner wrote: >> The problem seems to be some issue with the default iterative solvers >> we tell SLEPc to use; it looks like for some reason they're getting a >> "norm" of their initial random starting vector that isn't a >> nonnegative real number. I'm not sure how this would happen, though >> a Google search suggests that we're not the first people to run into >> this IPNorm error when doing a generalized eigenproblem. > > Interesting. So it's not a bug per se, good to know. It might still point to a bug. Our matrices in ex17 should both be realvalued symmetric, right? The stiffness matrix is not invertible, but I don't see how that would cause a problem in C but not in R.  Roy 
From: Jed Brown <jed@59...>  20111101 19:48:47

Kyunghoon, the error messages say petsc3.1p8, but the configure line makes it look like you are trying to use petsc3.2. Which is it? I assume that Roy reproduced with a clean petsc3.2/slepc3.2 configuration. Jose, do you know what is causing this error? On Tue, Nov 1, 2011 at 13:28, Roy Stogner <roystgnr@...> wrote: > > We're testing SLEPc + complex now, and seeing the same IPNorm error. > > The problem seems to be some issue with the default iterative solvers > we tell SLEPc to use; it looks like for some reason they're getting a > "norm" of their initial random starting vector that isn't a > nonnegative real number. I'm not sure how this would happen, though > a Google search suggests that we're not the first people to run into > this IPNorm error when doing a generalized eigenproblem. > > Running with LIBMESH_OPTIONS="eps_type lapack" comes up with results; > I presume that's switching to a direct solver. > > This probably isn't SLEPc's fault, but if you're doing eigen problems > with complexvalued PDEs then you might want to ask them about this > issue anyway; I don't know enough about our SLEPc interface or about > the various methods they have available to advise you on which to use. > > For now I'm going to put "eps_type lapack" in our ex17 Makefile just > to get it passing tests; however if you learn more about what we might > be doing wrong that's confusing their Arnoldi solver then I'd > appreciate hearing about it. > > Thanks, >  > Roy > > On Thu, 27 Oct 2011, Roy Stogner wrote: > > > What options did you use to configure libMesh? > > > > I'll see if I can reproduce this. We currently have enablecomplex > > BuildBot tests and enableslepc tests but I don't think we're > > testing the combination of the two... > >  > > Roy > > > > On Fri, 28 Oct 2011, Kyunghoon Lee wrote: > > > >> Hi all, > >> > >> I compiled petsc with complex variable support using the following > options: > >> > >> ./configure prefix=/Users/aeronova/ > >> Development/local/lib64/petsc/petsc3.2p4 downloadmpich=1 > >> downloadblacs=1 downloadparmetis=1 downloadscalapack=1 > >> downloadmumps=1 withscalartype=complex withclanguage=cxx > >> > >> Then, rebuild slepc & libmesh (svn version). As I test libmesh with > >> examples, I got an error for ex17 (plz see the below). I'd appreciate > if > >> someone could help me with this problem. (ex7, complex variable > example, > >> seemed ok, though there were a couple of warnings such as WARNING! There > >> are > >> options you set that were not used!, WARNING! could be spelling mistake, > >> etc!, Option left: name:f value: .5) > >> > >> > >> [0]PETSC ERROR:  Error Message > >>  > >> [0]PETSC ERROR: IPNorm: The inner product is not well defined! > >> [0]PETSC ERROR: > >>  > >> [0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 > 13:37:48 > >> CDT 2011 > >> [0]PETSC ERROR: See docs/changes/index.html for recent updates. > >> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > >> [0]PETSC ERROR: See docs/index.html for manual pages. > >> [0]PETSC ERROR: > >>  > >> [0]PETSC ERROR: ./ex17dbg on a darwin10. named spike.local by aeronova > Fri > >> Oct 28 05:13:59 2011 > >> [0]PETSC ERROR: Libraries linked from > >> /Users/aeronova/Development/local/lib64/petsc/petsc3.1p8/lib > >> [0]PETSC ERROR: Configure run at Fri Oct 28 04:12:19 2011 > >> [0]PETSC ERROR: Configure options > >> prefix=/Users/aeronova/Development/local/lib64/petsc/petsc3.1p8 > >> downloadmpich=1 downloadblacs=1 downloadparmetis=1 > >> downloadscalapack=1 downloadmumps=1 withscalartype=complex > >> withclanguage=cxx > >> [0]PETSC ERROR: > >>  > >> [0]PETSC ERROR: IPNorm() line 70 in src/ip/ipdot.c > >> [0]PETSC ERROR: IPOrthogonalize() line 338 in src/ip/iporthog.c > >> [0]PETSC ERROR: EPSGetStartVector() line 1487 in > src/eps/interface/solve.c > >> [0]PETSC ERROR: EPSSolve_ARNOLDI() line 387 in > >> src/eps/impls/krylov/arnoldi/arnoldi.c > >> [0]PETSC ERROR: EPSSolve() line 146 in src/eps/interface/solve.c > >> [0]PETSC ERROR: User provided function() line 488 in > >> "unknowndirectory/"src/solvers/slepc_eigen_solver.C > >> application called MPI_Abort(comm=0x84000000, 1)  process 0[unset]: > >> aborting job: > >> application called MPI_Abort(comm=0x84000000, 1)  process 0 > >> make[2]: *** [run] Error 1 > >> make[1]: *** [run] Error 1 > >> make: *** [run_examples] Error 2 > >> > >> >  > >> The demand for IT networking professionals continues to grow, and the > >> demand for specialized networking skills is growing even more rapidly. > >> Take a complimentary Learning@... SelfAssessment and learn > >> about Cisco certifications, training, and career opportunities. > >> http://p.sf.net/sfu/ciscodev2dev > >> _______________________________________________ > >> Libmeshusers mailing list > >> Libmeshusers@... > >> https://lists.sourceforge.net/lists/listinfo/libmeshusers > >> > >> > > > > >  > RSA® Conference 2012 > Save $700 by Nov 18 > Register now! > http://p.sf.net/sfu/rsasfdev2dev1 > _______________________________________________ > Libmeshusers mailing list > Libmeshusers@... > https://lists.sourceforge.net/lists/listinfo/libmeshusers > 
From: Roy Stogner <roystgnr@ic...>  20111101 19:55:37

On Tue, 1 Nov 2011, Jed Brown wrote: > Kyunghoon, the error messages say petsc3.1p8, but the configure line makes it look like you are trying to use petsc3.2. Which > is it? I assume that Roy reproduced with a clean petsc3.2/slepc3.2 configuration. Actually, no  I just built against the newest versions we had lying around: petsc3.1p5 and slepc3.1p4. I'd be happy to upgrade and test the latest if it'd be helpful with any bug hunting, though.  Roy 
From: Kyunghoon Lee <aeronova.mailing@gm...>  20111102 00:28:55

Jed, I have tested two different sets: petsc3.1/slpec3.1 and petsc3.2/slepc3.2  both cases ex17 failed generating the same error log. On Wed, Nov 2, 2011 at 3:48 AM, Jed Brown <jed@...> wrote: > Kyunghoon, the error messages say petsc3.1p8, but the configure line > makes it look like you are trying to use petsc3.2. Which is it? I assume > that Roy reproduced with a clean petsc3.2/slepc3.2 configuration. > > Jose, do you know what is causing this error? > > On Tue, Nov 1, 2011 at 13:28, Roy Stogner <roystgnr@...>wrote: > >> >> We're testing SLEPc + complex now, and seeing the same IPNorm error. >> >> The problem seems to be some issue with the default iterative solvers >> we tell SLEPc to use; it looks like for some reason they're getting a >> "norm" of their initial random starting vector that isn't a >> nonnegative real number. I'm not sure how this would happen, though >> a Google search suggests that we're not the first people to run into >> this IPNorm error when doing a generalized eigenproblem. >> >> Running with LIBMESH_OPTIONS="eps_type lapack" comes up with results; >> I presume that's switching to a direct solver. >> >> This probably isn't SLEPc's fault, but if you're doing eigen problems >> with complexvalued PDEs then you might want to ask them about this >> issue anyway; I don't know enough about our SLEPc interface or about >> the various methods they have available to advise you on which to use. >> >> For now I'm going to put "eps_type lapack" in our ex17 Makefile just >> to get it passing tests; however if you learn more about what we might >> be doing wrong that's confusing their Arnoldi solver then I'd >> appreciate hearing about it. >> >> Thanks, >>  >> Roy >> >> On Thu, 27 Oct 2011, Roy Stogner wrote: >> >> > What options did you use to configure libMesh? >> > >> > I'll see if I can reproduce this. We currently have enablecomplex >> > BuildBot tests and enableslepc tests but I don't think we're >> > testing the combination of the two... >> >  >> > Roy >> > >> > On Fri, 28 Oct 2011, Kyunghoon Lee wrote: >> > >> >> Hi all, >> >> >> >> I compiled petsc with complex variable support using the following >> options: >> >> >> >> ./configure prefix=/Users/aeronova/ >> >> Development/local/lib64/petsc/petsc3.2p4 downloadmpich=1 >> >> downloadblacs=1 downloadparmetis=1 downloadscalapack=1 >> >> downloadmumps=1 withscalartype=complex withclanguage=cxx >> >> >> >> Then, rebuild slepc & libmesh (svn version). As I test libmesh with >> >> examples, I got an error for ex17 (plz see the below). I'd appreciate >> if >> >> someone could help me with this problem. (ex7, complex variable >> example, >> >> seemed ok, though there were a couple of warnings such as WARNING! >> There >> >> are >> >> options you set that were not used!, WARNING! could be spelling >> mistake, >> >> etc!, Option left: name:f value: .5) >> >> >> >> >> >> [0]PETSC ERROR:  Error Message >> >>  >> >> [0]PETSC ERROR: IPNorm: The inner product is not well defined! >> >> [0]PETSC ERROR: >> >> >>  >> >> [0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17 >> 13:37:48 >> >> CDT 2011 >> >> [0]PETSC ERROR: See docs/changes/index.html for recent updates. >> >> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. >> >> [0]PETSC ERROR: See docs/index.html for manual pages. >> >> [0]PETSC ERROR: >> >> >>  >> >> [0]PETSC ERROR: ./ex17dbg on a darwin10. named spike.local by >> aeronova Fri >> >> Oct 28 05:13:59 2011 >> >> [0]PETSC ERROR: Libraries linked from >> >> /Users/aeronova/Development/local/lib64/petsc/petsc3.1p8/lib >> >> [0]PETSC ERROR: Configure run at Fri Oct 28 04:12:19 2011 >> >> [0]PETSC ERROR: Configure options >> >> prefix=/Users/aeronova/Development/local/lib64/petsc/petsc3.1p8 >> >> downloadmpich=1 downloadblacs=1 downloadparmetis=1 >> >> downloadscalapack=1 downloadmumps=1 withscalartype=complex >> >> withclanguage=cxx >> >> [0]PETSC ERROR: >> >> >>  >> >> [0]PETSC ERROR: IPNorm() line 70 in src/ip/ipdot.c >> >> [0]PETSC ERROR: IPOrthogonalize() line 338 in src/ip/iporthog.c >> >> [0]PETSC ERROR: EPSGetStartVector() line 1487 in >> src/eps/interface/solve.c >> >> [0]PETSC ERROR: EPSSolve_ARNOLDI() line 387 in >> >> src/eps/impls/krylov/arnoldi/arnoldi.c >> >> [0]PETSC ERROR: EPSSolve() line 146 in src/eps/interface/solve.c >> >> [0]PETSC ERROR: User provided function() line 488 in >> >> "unknowndirectory/"src/solvers/slepc_eigen_solver.C >> >> application called MPI_Abort(comm=0x84000000, 1)  process 0[unset]: >> >> aborting job: >> >> application called MPI_Abort(comm=0x84000000, 1)  process 0 >> >> make[2]: *** [run] Error 1 >> >> make[1]: *** [run] Error 1 >> >> make: *** [run_examples] Error 2 >> >> >> >> >>  >> >> The demand for IT networking professionals continues to grow, and the >> >> demand for specialized networking skills is growing even more rapidly. >> >> Take a complimentary Learning@... SelfAssessment and learn >> >> about Cisco certifications, training, and career opportunities. >> >> http://p.sf.net/sfu/ciscodev2dev >> >> _______________________________________________ >> >> Libmeshusers mailing list >> >> Libmeshusers@... >> >> https://lists.sourceforge.net/lists/listinfo/libmeshusers >> >> >> >> >> > >> >> >>  >> RSA® Conference 2012 >> Save $700 by Nov 18 >> Register now! >> http://p.sf.net/sfu/rsasfdev2dev1 >> _______________________________________________ >> Libmeshusers mailing list >> Libmeshusers@... >> https://lists.sourceforge.net/lists/listinfo/libmeshusers >> > > 
From: David Knezevic <dknezevic@se...>  20111101 19:51:35

On 11/01/2011 03:41 PM, Roy Stogner wrote: > > On Tue, 1 Nov 2011, David Knezevic wrote: > >> On 11/01/2011 03:28 PM, Roy Stogner wrote: > >>> The problem seems to be some issue with the default iterative solvers >>> we tell SLEPc to use; it looks like for some reason they're getting a >>> "norm" of their initial random starting vector that isn't a >>> nonnegative real number. I'm not sure how this would happen, though >>> a Google search suggests that we're not the first people to run into >>> this IPNorm error when doing a generalized eigenproblem. >> >> Interesting. So it's not a bug per se, good to know. > > It might still point to a bug. Our matrices in ex17 should both be > realvalued symmetric, right? The stiffness matrix is not invertible, > but I don't see how that would cause a problem in C but not in R. True. One thought is that I've always thought that ex17 was a bit strange since we're looking for sup_v a(v,v) / m(v,v) which is unbounded as h > 0. Perhaps things are more fragile because of this highfrequency mode? Does ex17 work with complex numbers if you uncomment the line: eigen_system.eigen_solver>set_position_of_spectrum(SMALLEST_MAGNITUDE); 
From: Roy Stogner <roystgnr@ic...>  20111101 20:10:23

On Tue, 1 Nov 2011, David Knezevic wrote: > One thought is that I've always thought that ex17 was a bit strange since > we're looking for > > sup_v a(v,v) / m(v,v) > > which is unbounded as h > 0. Perhaps things are more fragile because of > this highfrequency mode? Does ex17 work with complex numbers if you > uncomment the line: > > eigen_system.eigen_solver>set_position_of_spectrum(SMALLEST_MAGNITUDE); Still fails for me. As I'd expect it to, I think. Even with an illdefined infinitedimensional problem, we ought to be getting something vaguely resembling the highest frequency mode capturable by the mesh for the discretized problem.  Roy 
From: David Knezevic <dknezevic@se...>  20111101 20:16:19

On 11/01/2011 04:10 PM, Roy Stogner wrote: > > On Tue, 1 Nov 2011, David Knezevic wrote: > >> One thought is that I've always thought that ex17 was a bit strange >> since we're looking for >> >> sup_v a(v,v) / m(v,v) >> >> which is unbounded as h > 0. Perhaps things are more fragile >> because of this highfrequency mode? Does ex17 work with complex >> numbers if you uncomment the line: >> >> eigen_system.eigen_solver>set_position_of_spectrum(SMALLEST_MAGNITUDE); > > Still fails for me. > > As I'd expect it to, I think. Even with an illdefined > infinitedimensional problem, we ought to be getting something vaguely > resembling the highest frequency mode capturable by the mesh for the > discretized problem. OK, no big deal. Yeah, we do get an approximation to the highest frequency mode on the mesh in the real case. I just thought that changing to the lowest mode would make the problem "easier" and let us see if slepc is more fragile in the complex case... 
From: Jed Brown <jed@59...>  20111101 20:13:15

On Tue, Nov 1, 2011 at 14:06, Jose E. Roman <jroman@...> wrote: > > El 01/11/2011, a las 20:55, Roy Stogner escribió: > > > > > On Tue, 1 Nov 2011, Jed Brown wrote: > > > >> Kyunghoon, the error messages say petsc3.1p8, but the configure line > makes it look like you are trying to use petsc3.2. Which > >> is it? I assume that Roy reproduced with a clean petsc3.2/slepc3.2 > configuration. > > > > Actually, no  I just built against the newest versions we had lying > > around: petsc3.1p5 and slepc3.1p4. I'd be happy to upgrade and > > test the latest if it'd be helpful with any bug hunting, though. > >  > > Roy > > > The error "IPNorm: The inner product is not well defined!" is usually due > to the fact that the B matrix of the eigenproblem is not positive (semi) > definite. Are you sure your eigenproblem is definite? In that case, I would > be interested in trying these matrices to track down the problem. > It is supposed to be a finite element generalized eigenproblem where A is the Laplacian and B is a mass matrix (using Q_1 quadrilateral elements on [1,1]^2). 
From: John Peterson <jwpeterson@gm...>  20111101 20:20:25

On Tue, Nov 1, 2011 at 2:13 PM, Jed Brown <jed@...> wrote: > On Tue, Nov 1, 2011 at 14:06, Jose E. Roman <jroman@...> wrote: > >> >> El 01/11/2011, a las 20:55, Roy Stogner escribió: >> >> > >> > On Tue, 1 Nov 2011, Jed Brown wrote: >> > >> >> Kyunghoon, the error messages say petsc3.1p8, but the configure line >> makes it look like you are trying to use petsc3.2. Which >> >> is it? I assume that Roy reproduced with a clean petsc3.2/slepc3.2 >> configuration. >> > >> > Actually, no  I just built against the newest versions we had lying >> > around: petsc3.1p5 and slepc3.1p4. I'd be happy to upgrade and >> > test the latest if it'd be helpful with any bug hunting, though. >> >  >> > Roy >> >> >> The error "IPNorm: The inner product is not well defined!" is usually due >> to the fact that the B matrix of the eigenproblem is not positive (semi) >> definite. Are you sure your eigenproblem is definite? In that case, I would >> be interested in trying these matrices to track down the problem. >> > > It is supposed to be a finite element generalized eigenproblem where A is > the Laplacian and B is a mass matrix (using Q_1 quadrilateral elements on > [1,1]^2). I actually don't see where we define boundary conditions on either of the matrices in ex17. So does that mean the problem is indefinite?  John 
From: Roy Stogner <roystgnr@ic...>  20111101 20:31:29

On Tue, 1 Nov 2011, Jed Brown wrote: > The error "IPNorm: The inner product is not well defined!" is > usually due to the fact that the B matrix of the eigenproblem is not > positive (semi) definite. Are you sure your eigenproblem is > definite? It's definitely *supposed* to be; this is just the ex17 code that builds a laplacian stiffness and L2 mass matrix, as you said. I can even switch from Q_1 quads to P_1 line segments, and as long as I use at least 3 of them (4 nodes) I still get that IPNorm error. Although, tweaking the mesh does seem to change the stack trace; the IPNorm starts coming from different calls to IPOrthogonalize, then from EPSComputeVectors_Hermitian, as I shrink things. > In that case, I would be interested in trying these > matrices to track down the problem. matrix_A = [Real part: 1.5 1.5 0 0 1.5 3 1.5 0 0 1.5 3 1.5 0 0 1.5 1.5 Imaginary part: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ]; matrix_B = [Real part: 0.222222 0.111111 0 0 0.111111 0.444444 0.111111 0 0 0.111111 0.444444 0.111111 0 0 0.111111 0.222222 Imaginary part: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ]; I forgot to set_precision() on that, but you get the idea. matrix_B is SPD. matrix_A isn't, but that just ought to mean that one of our eigenvalues is 0, right?  Roy 
From: David Knezevic <dknezevic@se...>  20111101 20:41:37

On 11/01/2011 04:31 PM, Roy Stogner wrote: > On Tue, 1 Nov 2011, Jed Brown wrote: > >> The error "IPNorm: The inner product is not well defined!" is >> usually due to the fact that the B matrix of the eigenproblem is not >> positive (semi) definite. Are you sure your eigenproblem is >> definite? > It's definitely *supposed* to be; this is just the ex17 code that > builds a laplacian stiffness and L2 mass matrix, as you said. I can > even switch from Q_1 quads to P_1 line segments, and as long as I use > at least 3 of them (4 nodes) I still get that IPNorm error. Although, > tweaking the mesh does seem to change the stack trace; the IPNorm > starts coming from different calls to IPOrthogonalize, then from > EPSComputeVectors_Hermitian, as I shrink things. > >> In that case, I would be interested in trying these >> matrices to track down the problem. > matrix_A = [Real part: > 1.5 1.5 0 0 > 1.5 3 1.5 0 > 0 1.5 3 1.5 > 0 0 1.5 1.5 > > Imaginary part: > 0 0 0 0 > 0 0 0 0 > 0 0 0 0 > 0 0 0 0 > ]; > > matrix_B = [Real part: > 0.222222 0.111111 0 0 > 0.111111 0.444444 0.111111 0 > 0 0.111111 0.444444 0.111111 > 0 0 0.111111 0.222222 > > Imaginary part: > 0 0 0 0 > 0 0 0 0 > 0 0 0 0 > 0 0 0 0 > ]; > > I forgot to set_precision() on that, but you get the idea. > > matrix_B is SPD. matrix_A isn't, but that just ought to mean that one > of our eigenvalues is 0, right? Yeah, I agree. Plus, it works with eps_type lapack, so the problem can't be illposed... 
From: David Knezevic <dknezevic@se...>  20111101 21:27:47

On 11/01/2011 04:31 PM, Roy Stogner wrote: > On Tue, 1 Nov 2011, Jed Brown wrote: > >> The error "IPNorm: The inner product is not well defined!" is >> usually due to the fact that the B matrix of the eigenproblem is not >> positive (semi) definite. Are you sure your eigenproblem is >> definite? > It's definitely *supposed* to be; this is just the ex17 code that > builds a laplacian stiffness and L2 mass matrix, as you said. I can > even switch from Q_1 quads to P_1 line segments, and as long as I use > at least 3 of them (4 nodes) I still get that IPNorm error. Although, > tweaking the mesh does seem to change the stack trace; the IPNorm > starts coming from different calls to IPOrthogonalize, then from > EPSComputeVectors_Hermitian, as I shrink things. > >> In that case, I would be interested in trying these >> matrices to track down the problem. > matrix_A = [Real part: > 1.5 1.5 0 0 > 1.5 3 1.5 0 > 0 1.5 3 1.5 > 0 0 1.5 1.5 > > Imaginary part: > 0 0 0 0 > 0 0 0 0 > 0 0 0 0 > 0 0 0 0 > ]; > > matrix_B = [Real part: > 0.222222 0.111111 0 0 > 0.111111 0.444444 0.111111 0 > 0 0.111111 0.444444 0.111111 > 0 0 0.111111 0.222222 > > Imaginary part: > 0 0 0 0 > 0 0 0 0 > 0 0 0 0 > 0 0 0 0 > ]; > > I forgot to set_precision() on that, but you get the idea. > > matrix_B is SPD. matrix_A isn't, but that just ought to mean that one > of our eigenvalues is 0, right? Roy, I've attached a version of ex17 with dirichlet boundary conditions, if you're interested in testing that out in complex mode. (Note: it uses CondensedEigenSystem, which I use in rbOOmit in order to compute eigenvalues without introducing spurious behavior due to the presence of Dirichlet dofs) David 
From: Roy Stogner <roystgnr@ic...>  20111101 21:37:16

On Tue, 1 Nov 2011, David Knezevic wrote: > Roy, I've attached a version of ex17 with dirichlet boundary conditions, if > you're interested in testing that out in complex mode. (Note: it uses > CondensedEigenSystem, which I use in rbOOmit in order to compute eigenvalues > without introducing spurious behavior due to the presence of Dirichlet dofs) It was worth a try, anyway. I get the same error, but now it takes 5 EDGE2 elements rather than 3 to trigger it.  Roy 