April 2011 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] change to MatIsTranspose() and failing test
by Hong Zhang 28 Apr '11

28 Apr '11

Lisandro : > BTW, do you fully agree with my previous fix? Should MatIsTranspose() > generate an error if the test is not implemented? Or should it just > return PETSC_FALSE? I agree with you: generate an error if the test is not implemented - consistent with entire petsc style 'PETSC_FALSE' is simply one of output of this routine. Hong >> On Wed, Apr 27, 2011 at 2:04 PM, Lisandro Dalcin <dalcinl(a)gmail.com> wrote: >>> After wasting as considerable amount of time debugging issues related >>> to uninitialized variables passed to MatIsTranspose, I've pushed this: >>> >>> changeset: 18869:3bdc748ba073 >>> tag: tip >>> user: Lisandro Dalcin <dalcinl(a)gmail.com> >>> date: Wed Apr 27 15:59:56 2011 -0300 >>> summary: MatIsTranspose(): error if any matrix does not support the test >>> >>> And now, the best below fails, becase SeqBAIJ does not support transpose test. >>> >>> [dalcinl@trantor tests]$ cd $PETSC_DIR/src/ksp/ksp/examples/tests >>> [dalcinl@trantor tests]$ make runex32_aij_sbaij_icc >>> make: [runex32_aij_sbaij_icc] Error 56 (ignored) >>> 1,19c1,7 >>> < [0]PETSC ERROR: --------------------- Error Message >>> ------------------------------------ >>> < [0]PETSC ERROR: No support for this operation for this object type! >>> < [0]PETSC ERROR: Matrix of type <seqbaij> does not support checking >>> for transpose! >>> < [0]PETSC ERROR: >>> ------------------------------------------------------------------------ >>> < [0]PETSC ERROR: Petsc Development HG revision: >>> a02bb9bcaf33cf16868e2771c3c8306d52235c69 HG Date: Fri Apr 22 13:15:40 >>> 2011 -0500 >>> < [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: ./ex32 on a arch-linu named trantor by dalcinl Wed >>> Apr 27 16:00:08 2011 >>> < [0]PETSC ERROR: Libraries linked from >>> /home/devel/petsc/dev/arch-linux2-c-debug/lib >>> < [0]PETSC ERROR: Configure run at Sat Apr 23 17:40:22 2011 >>> < [0]PETSC ERROR: Configure options --with-shared-libraries=1 >>> PETSC_ARCH=arch-linux2-c-debug >>> < [0]PETSC ERROR: >>> ------------------------------------------------------------------------ >>> < [0]PETSC ERROR: MatIsTranspose() line 4383 in >>> /home/devel/petsc/dev/src/mat/interface/matrix.c >>> < [0]PETSC ERROR: main() line 69 in src/ksp/ksp/examples/tests/ex32.c >>> < application called MPI_Abort(MPI_COMM_WORLD, 56) - process 0 >>> < rank 0 in job 3534 trantor_56062 caused collective abort of all ranks >>> < exit status of rank 0: return code 56 >>> --- >>>> 0 KSP Residual norm 0.210648 >>>> 1 KSP Residual norm 0.07826 >>>> 2 KSP Residual norm 0.0115565 >>>> 3 KSP Residual norm 0.00113989 >>>> 4 KSP Residual norm 0.00013248 >>>> 5 KSP Residual norm 9.04476e-06 >>>> 6 KSP Residual norm 4.52149e-07 >>> Possible problem with ex32_aij_sbaij_icc, diffs above >>> >>> -- >>> Lisandro Dalcin >>> --------------- >>> CIMEC (INTEC/CONICET-UNL) >>> Predio CONICET-Santa Fe >>> Colectora RN 168 Km 472, Paraje El Pozo >>> 3000 Santa Fe, Argentina >>> Tel: +54-342-4511594 (ext 1011) >>> Tel/Fax: +54-342-4511169 >>> >> > > > > -- > Lisandro Dalcin > --------------- > CIMEC (INTEC/CONICET-UNL) > Predio CONICET-Santa Fe > Colectora RN 168 Km 472, Paraje El Pozo > 3000 Santa Fe, Argentina > Tel: +54-342-4511594 (ext 1011) > Tel/Fax: +54-342-4511169 >

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Re: [petsc-dev] change to MatIsTranspose() and failing test
by Lisandro Dalcin 28 Apr '11

28 Apr '11

On 28 April 2011 13:48, Hong Zhang <hzhang(a)mcs.anl.gov> wrote: > Pushed MatIsTranspose_SeqBAIJ(). > Many thanks! BTW, do you fully agree with my previous fix? Should MatIsTranspose() generate an error if the test is not implemented? Or should it just return PETSC_FALSE? > Hong > > On Wed, Apr 27, 2011 at 2:04 PM, Lisandro Dalcin <dalcinl(a)gmail.com> wrote: >> After wasting as considerable amount of time debugging issues related >> to uninitialized variables passed to MatIsTranspose, I've pushed this: >> >> changeset: 18869:3bdc748ba073 >> tag: tip >> user: Lisandro Dalcin <dalcinl(a)gmail.com> >> date: Wed Apr 27 15:59:56 2011 -0300 >> summary: MatIsTranspose(): error if any matrix does not support the test >> >> And now, the best below fails, becase SeqBAIJ does not support transpose test. >> >> [dalcinl@trantor tests]$ cd $PETSC_DIR/src/ksp/ksp/examples/tests >> [dalcinl@trantor tests]$ make runex32_aij_sbaij_icc >> make: [runex32_aij_sbaij_icc] Error 56 (ignored) >> 1,19c1,7 >> < [0]PETSC ERROR: --------------------- Error Message >> ------------------------------------ >> < [0]PETSC ERROR: No support for this operation for this object type! >> < [0]PETSC ERROR: Matrix of type <seqbaij> does not support checking >> for transpose! >> < [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> < [0]PETSC ERROR: Petsc Development HG revision: >> a02bb9bcaf33cf16868e2771c3c8306d52235c69 HG Date: Fri Apr 22 13:15:40 >> 2011 -0500 >> < [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: ./ex32 on a arch-linu named trantor by dalcinl Wed >> Apr 27 16:00:08 2011 >> < [0]PETSC ERROR: Libraries linked from >> /home/devel/petsc/dev/arch-linux2-c-debug/lib >> < [0]PETSC ERROR: Configure run at Sat Apr 23 17:40:22 2011 >> < [0]PETSC ERROR: Configure options --with-shared-libraries=1 >> PETSC_ARCH=arch-linux2-c-debug >> < [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> < [0]PETSC ERROR: MatIsTranspose() line 4383 in >> /home/devel/petsc/dev/src/mat/interface/matrix.c >> < [0]PETSC ERROR: main() line 69 in src/ksp/ksp/examples/tests/ex32.c >> < application called MPI_Abort(MPI_COMM_WORLD, 56) - process 0 >> < rank 0 in job 3534 trantor_56062 caused collective abort of all ranks >> < exit status of rank 0: return code 56 >> --- >>> 0 KSP Residual norm 0.210648 >>> 1 KSP Residual norm 0.07826 >>> 2 KSP Residual norm 0.0115565 >>> 3 KSP Residual norm 0.00113989 >>> 4 KSP Residual norm 0.00013248 >>> 5 KSP Residual norm 9.04476e-06 >>> 6 KSP Residual norm 4.52149e-07 >> Possible problem with ex32_aij_sbaij_icc, diffs above >> >> -- >> Lisandro Dalcin >> --------------- >> CIMEC (INTEC/CONICET-UNL) >> Predio CONICET-Santa Fe >> Colectora RN 168 Km 472, Paraje El Pozo >> 3000 Santa Fe, Argentina >> Tel: +54-342-4511594 (ext 1011) >> Tel/Fax: +54-342-4511169 >> > -- Lisandro Dalcin --------------- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169

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Re: [petsc-dev] change to MatIsTranspose() and failing test
by Hong Zhang 28 Apr '11

28 Apr '11

Pushed MatIsTranspose_SeqBAIJ(). Hong On Wed, Apr 27, 2011 at 2:04 PM, Lisandro Dalcin <dalcinl(a)gmail.com> wrote: > After wasting as considerable amount of time debugging issues related > to uninitialized variables passed to MatIsTranspose, I've pushed this: > > changeset: 18869:3bdc748ba073 > tag: tip > user: Lisandro Dalcin <dalcinl(a)gmail.com> > date: Wed Apr 27 15:59:56 2011 -0300 > summary: MatIsTranspose(): error if any matrix does not support the test > > And now, the best below fails, becase SeqBAIJ does not support transpose test. > > [dalcinl@trantor tests]$ cd $PETSC_DIR/src/ksp/ksp/examples/tests > [dalcinl@trantor tests]$ make runex32_aij_sbaij_icc > make: [runex32_aij_sbaij_icc] Error 56 (ignored) > 1,19c1,7 > < [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > < [0]PETSC ERROR: No support for this operation for this object type! > < [0]PETSC ERROR: Matrix of type <seqbaij> does not support checking > for transpose! > < [0]PETSC ERROR: > ------------------------------------------------------------------------ > < [0]PETSC ERROR: Petsc Development HG revision: > a02bb9bcaf33cf16868e2771c3c8306d52235c69 HG Date: Fri Apr 22 13:15:40 > 2011 -0500 > < [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: ./ex32 on a arch-linu named trantor by dalcinl Wed > Apr 27 16:00:08 2011 > < [0]PETSC ERROR: Libraries linked from > /home/devel/petsc/dev/arch-linux2-c-debug/lib > < [0]PETSC ERROR: Configure run at Sat Apr 23 17:40:22 2011 > < [0]PETSC ERROR: Configure options --with-shared-libraries=1 > PETSC_ARCH=arch-linux2-c-debug > < [0]PETSC ERROR: > ------------------------------------------------------------------------ > < [0]PETSC ERROR: MatIsTranspose() line 4383 in > /home/devel/petsc/dev/src/mat/interface/matrix.c > < [0]PETSC ERROR: main() line 69 in src/ksp/ksp/examples/tests/ex32.c > < application called MPI_Abort(MPI_COMM_WORLD, 56) - process 0 > < rank 0 in job 3534 trantor_56062 caused collective abort of all ranks > < exit status of rank 0: return code 56 > --- >> 0 KSP Residual norm 0.210648 >> 1 KSP Residual norm 0.07826 >> 2 KSP Residual norm 0.0115565 >> 3 KSP Residual norm 0.00113989 >> 4 KSP Residual norm 0.00013248 >> 5 KSP Residual norm 9.04476e-06 >> 6 KSP Residual norm 4.52149e-07 > Possible problem with ex32_aij_sbaij_icc, diffs above > > -- > Lisandro Dalcin > --------------- > CIMEC (INTEC/CONICET-UNL) > Predio CONICET-Santa Fe > Colectora RN 168 Km 472, Paraje El Pozo > 3000 Santa Fe, Argentina > Tel: +54-342-4511594 (ext 1011) > Tel/Fax: +54-342-4511169 >

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Re: [petsc-dev] change to MatIsTranspose() and failing test
by Hong Zhang 27 Apr '11

27 Apr '11

I'll check it. Hong On Wed, Apr 27, 2011 at 2:04 PM, Lisandro Dalcin <dalcinl(a)gmail.com> wrote: > After wasting as considerable amount of time debugging issues related > to uninitialized variables passed to MatIsTranspose, I've pushed this: > > changeset: 18869:3bdc748ba073 > tag: tip > user: Lisandro Dalcin <dalcinl(a)gmail.com> > date: Wed Apr 27 15:59:56 2011 -0300 > summary: MatIsTranspose(): error if any matrix does not support the test > > And now, the best below fails, becase SeqBAIJ does not support transpose test. > > [dalcinl@trantor tests]$ cd $PETSC_DIR/src/ksp/ksp/examples/tests > [dalcinl@trantor tests]$ make runex32_aij_sbaij_icc > make: [runex32_aij_sbaij_icc] Error 56 (ignored) > 1,19c1,7 > < [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > < [0]PETSC ERROR: No support for this operation for this object type! > < [0]PETSC ERROR: Matrix of type <seqbaij> does not support checking > for transpose! > < [0]PETSC ERROR: > ------------------------------------------------------------------------ > < [0]PETSC ERROR: Petsc Development HG revision: > a02bb9bcaf33cf16868e2771c3c8306d52235c69 HG Date: Fri Apr 22 13:15:40 > 2011 -0500 > < [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: ./ex32 on a arch-linu named trantor by dalcinl Wed > Apr 27 16:00:08 2011 > < [0]PETSC ERROR: Libraries linked from > /home/devel/petsc/dev/arch-linux2-c-debug/lib > < [0]PETSC ERROR: Configure run at Sat Apr 23 17:40:22 2011 > < [0]PETSC ERROR: Configure options --with-shared-libraries=1 > PETSC_ARCH=arch-linux2-c-debug > < [0]PETSC ERROR: > ------------------------------------------------------------------------ > < [0]PETSC ERROR: MatIsTranspose() line 4383 in > /home/devel/petsc/dev/src/mat/interface/matrix.c > < [0]PETSC ERROR: main() line 69 in src/ksp/ksp/examples/tests/ex32.c > < application called MPI_Abort(MPI_COMM_WORLD, 56) - process 0 > < rank 0 in job 3534 trantor_56062 caused collective abort of all ranks > < exit status of rank 0: return code 56 > --- >> 0 KSP Residual norm 0.210648 >> 1 KSP Residual norm 0.07826 >> 2 KSP Residual norm 0.0115565 >> 3 KSP Residual norm 0.00113989 >> 4 KSP Residual norm 0.00013248 >> 5 KSP Residual norm 9.04476e-06 >> 6 KSP Residual norm 4.52149e-07 > Possible problem with ex32_aij_sbaij_icc, diffs above > > -- > Lisandro Dalcin > --------------- > CIMEC (INTEC/CONICET-UNL) > Predio CONICET-Santa Fe > Colectora RN 168 Km 472, Paraje El Pozo > 3000 Santa Fe, Argentina > Tel: +54-342-4511594 (ext 1011) > Tel/Fax: +54-342-4511169 >

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change to MatIsTranspose() and failing test
by Lisandro Dalcin 27 Apr '11

27 Apr '11

After wasting as considerable amount of time debugging issues related to uninitialized variables passed to MatIsTranspose, I've pushed this: changeset: 18869:3bdc748ba073 tag: tip user: Lisandro Dalcin <dalcinl(a)gmail.com> date: Wed Apr 27 15:59:56 2011 -0300 summary: MatIsTranspose(): error if any matrix does not support the test And now, the best below fails, becase SeqBAIJ does not support transpose test. [dalcinl@trantor tests]$ cd $PETSC_DIR/src/ksp/ksp/examples/tests [dalcinl@trantor tests]$ make runex32_aij_sbaij_icc make: [runex32_aij_sbaij_icc] Error 56 (ignored) 1,19c1,7 < [0]PETSC ERROR: --------------------- Error Message ------------------------------------ < [0]PETSC ERROR: No support for this operation for this object type! < [0]PETSC ERROR: Matrix of type <seqbaij> does not support checking for transpose! < [0]PETSC ERROR: ------------------------------------------------------------------------ < [0]PETSC ERROR: Petsc Development HG revision: a02bb9bcaf33cf16868e2771c3c8306d52235c69 HG Date: Fri Apr 22 13:15:40 2011 -0500 < [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: ./ex32 on a arch-linu named trantor by dalcinl Wed Apr 27 16:00:08 2011 < [0]PETSC ERROR: Libraries linked from /home/devel/petsc/dev/arch-linux2-c-debug/lib < [0]PETSC ERROR: Configure run at Sat Apr 23 17:40:22 2011 < [0]PETSC ERROR: Configure options --with-shared-libraries=1 PETSC_ARCH=arch-linux2-c-debug < [0]PETSC ERROR: ------------------------------------------------------------------------ < [0]PETSC ERROR: MatIsTranspose() line 4383 in /home/devel/petsc/dev/src/mat/interface/matrix.c < [0]PETSC ERROR: main() line 69 in src/ksp/ksp/examples/tests/ex32.c < application called MPI_Abort(MPI_COMM_WORLD, 56) - process 0 < rank 0 in job 3534 trantor_56062 caused collective abort of all ranks < exit status of rank 0: return code 56 --- > 0 KSP Residual norm 0.210648 > 1 KSP Residual norm 0.07826 > 2 KSP Residual norm 0.0115565 > 3 KSP Residual norm 0.00113989 > 4 KSP Residual norm 0.00013248 > 5 KSP Residual norm 9.04476e-06 > 6 KSP Residual norm 4.52149e-07 Possible problem with ex32_aij_sbaij_icc, diffs above -- Lisandro Dalcin --------------- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo 3000 Santa Fe, Argentina Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169

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Re: [petsc-dev] KSP monitor
by Barry Smith 26 Apr '11

26 Apr '11

On Apr 26, 2011, at 6:50 AM, Nathan Collier wrote: > Good day, > > I am solving a linear problem using finite elements with PETSC and I > want to look at the H1 norm of my true error as a function of KSP > iterations. I registered my own monitor function with KSP which looks > something like the last function in this example: > > http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-dev/src/ksp/ksp/examp… > > where I get the current state of the solution vector using > > KSPBuildSolution(kps,PETSC_NULL,&U) Try using KSPBuildSolution(ksp,work,0); where you create the work vector in your monitor routine. There could be a bug in the usuage you are using. Let us know if this works. Barry > > Then I use U to compute the H1 norm. As per the documentation I do not > Destroy U after. When I have this monitor function registered, my H1 > norm diverges while the KSP residual converges. Also, I compute the > final H1 norm (outside of the monitor) and it is divergent, which > matches the last iteration. If I remove my monitor function, things > work well. > > What am I screwing up? How can I access the current solution vector in > a KSP monitor? Do I need to use a vector that I create from a DA since > my FEM matrix assembly is based in DAs? > > Thanks, > NAte > > -- > Nathan Collier > Postdoctoral Researcher > King Abdullah University of Science and Technology (KAUST) > nathaniel.collier(a)gmail.com > nathaniel.collier(a)kaust.edu.sa

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Re: [petsc-dev] KSP monitor
by Jed Brown 26 Apr '11

26 Apr '11

On Tue, Apr 26, 2011 at 13:50, Nathan Collier <nathaniel.collier(a)gmail.com>wrote: > When I have this monitor function registered, my H1 > norm diverges while the KSP residual converges. Also, I compute the > final H1 norm (outside of the monitor) and it is divergent, which > matches the last iteration. If I remove my monitor function, things > work well. > Is your monitor forgetting to zero some internal variable? What happens if you just call your monitor twice with the same arguments? Also, does -ksp_monitor_true_residual change anything?

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KSP monitor
by Nathan Collier 26 Apr '11

26 Apr '11

Good day, I am solving a linear problem using finite elements with PETSC and I want to look at the H1 norm of my true error as a function of KSP iterations. I registered my own monitor function with KSP which looks something like the last function in this example: http://www.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-dev/src/ksp/ksp/examp… where I get the current state of the solution vector using KSPBuildSolution(kps,PETSC_NULL,&U) Then I use U to compute the H1 norm. As per the documentation I do not Destroy U after. When I have this monitor function registered, my H1 norm diverges while the KSP residual converges. Also, I compute the final H1 norm (outside of the monitor) and it is divergent, which matches the last iteration. If I remove my monitor function, things work well. What am I screwing up? How can I access the current solution vector in a KSP monitor? Do I need to use a vector that I create from a DA since my FEM matrix assembly is based in DAs? Thanks, NAte -- Nathan Collier Postdoctoral Researcher King Abdullah University of Science and Technology (KAUST) nathaniel.collier(a)gmail.com nathaniel.collier(a)kaust.edu.sa

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Re: [petsc-dev] RSS feed for API breaks?
by Jed Brown 26 Apr '11

26 Apr '11

On Tue, Apr 26, 2011 at 10:47, Aron Ahmadia <aron.ahmadia(a)kaust.edu.sa>wrote: > I don't follow PETSc-dev as closely as I should, but it looks like I will > be supporting some development repositories in the near future. Is there > any chance we can get an RSS feed for the content here: > http://www.mcs.anl.gov/petsc/petsc-as/documentation/changes/dev.html > I think this is a good idea. Even more slick (but maybe not worth the effort) would be to harvest the API changes from markup in commit messages, I often paste between changes/dev.html and the commit message. API Change: [Mat] Added matrix type MATNEST to eliminate copies when using PCFIELDSPLIT and reduce storage requirements for multiphysics problems.

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RSS feed for API breaks?
by Aron Ahmadia 26 Apr '11

26 Apr '11

I don't follow PETSc-dev as closely as I should, but it looks like I will be supporting some development repositories in the near future. Is there any chance we can get an RSS feed for the content here: http://www.mcs.anl.gov/petsc/petsc-as/documentation/changes/dev.html It might make it a little easier for developers aside from myself to keep their repos from breaking if they know how and when changes to the API are being introduced. A

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