Re: [petsc-users] Question about TSComputeRHSJacobianConstant
Sorry this code has not been changed. Barry > On Sep 30, 2019, at 4:24 PM, Sajid Ali > wrote: > > Hi PETSc-developers, > > Has this bug been fixed in the new 3.12 release ? > > Thank You, > Sajid Ali > Applied Physics > Northwestern University > s-sajid-ali.github.io
Re: [petsc-users] Question about TSComputeRHSJacobianConstant
Hi PETSc-developers, Has this bug been fixed in the new 3.12 release ? Thank You, Sajid Ali Applied Physics Northwestern University s-sajid-ali.github.io
[petsc-users] PETSc 3.12 release
We are pleased to announce the release of PETSc version 3.12 at http://www.mcs.anl.gov/petsc The major changes and updates can be found at http://www.mcs.anl.gov/petsc/documentation/changes/312.html We recommend upgrading to PETSc 3.12 soon. As always, please report problems to petsc-ma...@mcs.anl.gov and ask questions at petsc-users@mcs.anl.gov This release includes contributions from Alex Lindsay Alp Dener Barry Smith Boris Boutkov Chris Eldred Dave May David Wells Debojyoti Ghosh deepblu2718 Emil Constantinescu Fande Kong Florian Wechsung Glenn Hammond Hannah Morgan Hansol Suh Hendrik Ranocha Hong Zhang Hong Zhang Jacob Faibussowitsch Jakub Kružík Jed Brown Jeffrey Larson Joe Wallwork Jose E. Roman Julian Giordani Junchao Zhang Karl Rupp Lawrence Mitchell Lisandro Dalcin Lu luzhanghpp Mark Adams Martin Diehl Matthew G. Knepley Patrick Farrell Patrick Sanan Pierre Jolivet Richard Tran Mills Sajid Ali Satish Balay Scott Kruger Siegfried Cools Stefano Zampini Thibaut Appel Tristan Konolige Václav Hapla valeriabarr Volker Jacht William Gropp and bug reports/patches/proposed improvements received from 장승언 Adina Püsök Andrea Gallegati "Appel, Thibaut" Åsmund Ervik "Aulisa, Eugenio" Barry Smith "Betrie, Getnet" Brad Aagaard Carl Steefel Clausen Pascal Danyang Su Dave A. May David Dang Veselin Dobrev Dylan P. Brennan Ed Bueler Elias Karabelas Fabian Jakub Fande Kong Glenn E. Hammond "Guenther, Stefanie" Hannah Mairs Morgan Hapla Vaclav Heeho Park Hong Zhang Hubert Weissmann Ian Lin Jacob Faibussowitsch Jakub Kruzik Jaysaval, Piyoosh Jed Brown Joe Wallwork Jose E. Roman Junchao Zhang Karl Lin Karl Rupp Daniel Kokron Lardelli Nicolo Jeffery Larson Leon Avery Lisandro Dalcin Magne Rudshaug Manuel Colera Rico Mark Adams Matthew Knepley Matthias Beaupere Mohammad Asghar Mouralidaran Arrutselvi "Nair, Nirmal Jayaprasad" Nick Papior Oana Marin Paolo Orsini Patrick Sanan Paul Seibert Pierre Jolivet Piyoosh Jaysaval Prince Joseph Richard Katz Richard Tran Mills Robert Nr Nourgaliev Sajid Ali Satish Balay "Schanen, Michel" Sergi Molins Rafa Sophie Blondel Stefano Zampini Steve Thibaut Appel Tim Steinhoff Todd Munson Tom Goffrey Vaclav Hapla "Wells, David" Xiangdong Xiang Huang Yuyun Yang "Zhang, Hong" "Zhang, Junchao"
Re: [petsc-users] Computing part of the inverse of a large matrix
The Python wrapper for PETSc may be missing some functionality; there is a manual process involved in creating new ones. You could poke around the petsc4py source and see how easy it would be to add more functionality that you need. > On Sep 30, 2019, at 10:13 AM, Jan Grießer wrote: > > I configured PETSc with MUMPS and tested it already for the spectrum slicing > method in Slepc4py but i have problems in setting up the LU factorization in > the PETSc4py. Since i do not find the corresponding methods and commands in > the source code. Thats why is was wondering if this is even possible in the > python version. > > Am Mo., 30. Sept. 2019 um 16:57 Uhr schrieb Smith, Barry F. > : > > If you want a parallal LU (and hence the ability to build the inverse in > parallel) you need to configure PETSc with --download-mumps > --download-scalapack > > Barry > > > > On Sep 30, 2019, at 9:44 AM, Jan Grießer > > wrote: > > > > Is the MatMumpsGetInverse also wrapped to the python version in PETSc4py ? > > If yes is there any example for using it ? > > My other question is related to the LU factoriation > > (https://www.mcs.anl.gov/petsc/documentation/faq.html#invertmatrix). > > Is the LU factorization only possible for sequential Aij matrices ? I read > > in the docs that this is the case for ordering. > > After setting up my matrix A, B and x i tried: > > r, c = dynamical_matrix_nn.getOrdering("nd") > > fac_dyn_matrix = dynamical_matrix_nn.factorLU(r,c) > > > > resulting in an error: > > [0] No support for this operation for this object type > > [0] Mat type mpiaij > > > > Am Fr., 27. Sept. 2019 um 16:26 Uhr schrieb Zhang, Hong > > : > > See ~petsc/src/mat/examples/tests/ex214.c on how to compute selected > > entries of inv(A) using mumps. > > Hong > > > > On Fri, Sep 27, 2019 at 8:04 AM Smith, Barry F. via petsc-users > > wrote: > > > > MatMumpsGetInverse() maybe useful. Also simply using MatMatSolve() with the > > first 1000 columns of the identity and "throwing away" the part you don't > > need may be most effective. > > > >Barry > > > > > > > > > On Sep 27, 2019, at 3:34 AM, Jan Grießer via petsc-users > > > wrote: > > > > > > Hi all, > > > i am using petsc4py. I am dealing with rather large sparse matrices up to > > > 600kx600k and i am interested in calculating a part of the inverse of the > > > matrix(I know it will be a dense matrix). Due to the nature of my > > > problem, I am only interested in approximately the first 1000 rows and > > > 1000 columns (i.e. a large block in the upper left ofthe matrix). Before > > > I start to play around now, I wanted to ask if there is a clever way to > > > tackle this kind of problem in PETSc in principle. For any input I would > > > be very grateful! > > > Greetings Jan > > >
Re: [petsc-users] Computing part of the inverse of a large matrix
I configured PETSc with MUMPS and tested it already for the spectrum slicing method in Slepc4py but i have problems in setting up the LU factorization in the PETSc4py. Since i do not find the corresponding methods and commands in the source code. Thats why is was wondering if this is even possible in the python version. Am Mo., 30. Sept. 2019 um 16:57 Uhr schrieb Smith, Barry F. < bsm...@mcs.anl.gov>: > > If you want a parallal LU (and hence the ability to build the inverse in > parallel) you need to configure PETSc with --download-mumps > --download-scalapack > > Barry > > > > On Sep 30, 2019, at 9:44 AM, Jan Grießer > wrote: > > > > Is the MatMumpsGetInverse also wrapped to the python version in PETSc4py > ? If yes is there any example for using it ? > > My other question is related to the LU factoriation ( > https://www.mcs.anl.gov/petsc/documentation/faq.html#invertmatrix). > > Is the LU factorization only possible for sequential Aij matrices ? I > read in the docs that this is the case for ordering. > > After setting up my matrix A, B and x i tried: > > r, c = dynamical_matrix_nn.getOrdering("nd") > > fac_dyn_matrix = dynamical_matrix_nn.factorLU(r,c) > > > > resulting in an error: > > [0] No support for this operation for this object type > > [0] Mat type mpiaij > > > > Am Fr., 27. Sept. 2019 um 16:26 Uhr schrieb Zhang, Hong < > hzh...@mcs.anl.gov>: > > See ~petsc/src/mat/examples/tests/ex214.c on how to compute selected > entries of inv(A) using mumps. > > Hong > > > > On Fri, Sep 27, 2019 at 8:04 AM Smith, Barry F. via petsc-users < > petsc-users@mcs.anl.gov> wrote: > > > > MatMumpsGetInverse() maybe useful. Also simply using MatMatSolve() with > the first 1000 columns of the identity and "throwing away" the part you > don't need may be most effective. > > > >Barry > > > > > > > > > On Sep 27, 2019, at 3:34 AM, Jan Grießer via petsc-users < > petsc-users@mcs.anl.gov> wrote: > > > > > > Hi all, > > > i am using petsc4py. I am dealing with rather large sparse matrices up > to 600kx600k and i am interested in calculating a part of the inverse of > the matrix(I know it will be a dense matrix). Due to the nature of my > problem, I am only interested in approximately the first 1000 rows and 1000 > columns (i.e. a large block in the upper left ofthe matrix). Before I > start to play around now, I wanted to ask if there is a clever way to > tackle this kind of problem in PETSc in principle. For any input I would be > very grateful! > > > Greetings Jan > > > >
Re: [petsc-users] Computing part of the inverse of a large matrix
If you want a parallal LU (and hence the ability to build the inverse in parallel) you need to configure PETSc with --download-mumps --download-scalapack Barry > On Sep 30, 2019, at 9:44 AM, Jan Grießer wrote: > > Is the MatMumpsGetInverse also wrapped to the python version in PETSc4py ? If > yes is there any example for using it ? > My other question is related to the LU factoriation > (https://www.mcs.anl.gov/petsc/documentation/faq.html#invertmatrix). > Is the LU factorization only possible for sequential Aij matrices ? I read in > the docs that this is the case for ordering. > After setting up my matrix A, B and x i tried: > r, c = dynamical_matrix_nn.getOrdering("nd") > fac_dyn_matrix = dynamical_matrix_nn.factorLU(r,c) > > resulting in an error: > [0] No support for this operation for this object type > [0] Mat type mpiaij > > Am Fr., 27. Sept. 2019 um 16:26 Uhr schrieb Zhang, Hong : > See ~petsc/src/mat/examples/tests/ex214.c on how to compute selected entries > of inv(A) using mumps. > Hong > > On Fri, Sep 27, 2019 at 8:04 AM Smith, Barry F. via petsc-users > wrote: > > MatMumpsGetInverse() maybe useful. Also simply using MatMatSolve() with the > first 1000 columns of the identity and "throwing away" the part you don't > need may be most effective. > >Barry > > > > > On Sep 27, 2019, at 3:34 AM, Jan Grießer via petsc-users > > wrote: > > > > Hi all, > > i am using petsc4py. I am dealing with rather large sparse matrices up to > > 600kx600k and i am interested in calculating a part of the inverse of the > > matrix(I know it will be a dense matrix). Due to the nature of my problem, > > I am only interested in approximately the first 1000 rows and 1000 columns > > (i.e. a large block in the upper left ofthe matrix). Before I start to > > play around now, I wanted to ask if there is a clever way to tackle this > > kind of problem in PETSc in principle. For any input I would be very > > grateful! > > Greetings Jan >
Re: [petsc-users] Computing part of the inverse of a large matrix
Is the MatMumpsGetInverse also wrapped to the python version in PETSc4py ? If yes is there any example for using it ? My other question is related to the LU factoriation ( https://www.mcs.anl.gov/petsc/documentation/faq.html#invertmatrix). Is the LU factorization only possible for sequential Aij matrices ? I read in the docs that this is the case for ordering. After setting up my matrix A, B and x i tried: r, c = dynamical_matrix_nn.getOrdering("nd") fac_dyn_matrix = dynamical_matrix_nn.factorLU(r,c) resulting in an error: [0] No support for this operation for this object type [0] Mat type mpiaij Am Fr., 27. Sept. 2019 um 16:26 Uhr schrieb Zhang, Hong : > See ~petsc/src/mat/examples/tests/ex214.c on how to compute selected > entries of inv(A) using mumps. > Hong > > On Fri, Sep 27, 2019 at 8:04 AM Smith, Barry F. via petsc-users < > petsc-users@mcs.anl.gov> wrote: > >> >> MatMumpsGetInverse() maybe useful. Also simply using MatMatSolve() with >> the first 1000 columns of the identity and "throwing away" the part you >> don't need may be most effective. >> >>Barry >> >> >> >> > On Sep 27, 2019, at 3:34 AM, Jan Grießer via petsc-users < >> petsc-users@mcs.anl.gov> wrote: >> > >> > Hi all, >> > i am using petsc4py. I am dealing with rather large sparse matrices up >> to 600kx600k and i am interested in calculating a part of the inverse of >> the matrix(I know it will be a dense matrix). Due to the nature of my >> problem, I am only interested in approximately the first 1000 rows and 1000 >> columns (i.e. a large block in the upper left ofthe matrix). Before I >> start to play around now, I wanted to ask if there is a clever way to >> tackle this kind of problem in PETSc in principle. For any input I would be >> very grateful! >> > Greetings Jan >> >>