December 2018 - petsc-dev - mailman3.cels.anl.gov

testing code which use partitioners
by Smith, Barry F. 30 Dec '18

30 Dec '18

It really irks me that we can't use the various partitioners in our nightly tests because they use rand() and produce different results on different machines. Here is what I propose 1) add ./configure flag --with-petsc-rand 2) if the flag is set then provide our own rand() and srand() (by crudely wrapping PetscRandom()) in pinit.c which is compiled if the flag is set 3) add the --with-petsc-rand to all the nightlybuilds Problems with this plan? Barry

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Re: [petsc-dev] Faulty logic in MatHYPRESetPreallocation?
by Stefano Zampini 29 Dec '18

29 Dec '18

Barry, Probably this is an oversight from me. When I coded the MATHYPRE class, I did not make much attention to the preallocation. Also, hypre did not seem very robust to matrix reusage at the time. Take a look at the comments at line 85 in ex115 from mat tests. Probably Pierre's fix will curate that problem too. Stefano Il giorno Sab 22 Dic 2018, 06:30 Smith, Barry F. <bsmith(a)mcs.anl.gov> ha scritto: > > Stefeno, > > Doe this look right to you? > > Thanks > > Barry > > > > On Dec 17, 2018, at 3:18 AM, Pierre Jolivet via petsc-dev < > petsc-dev(a)mcs.anl.gov> wrote: > > > > Hello, > > I am not sure the hypre routines are called in the right order in > MatHYPRESetPreallocation. > > Indeed, attached, you’ll find two Massif logs, one with the current > order (massif.out.bad), and the other (massif.out.better) with the attached > patch applied. > > In the former, you can see at the snapshot #31 that there is a call to > hypre_CTAlloc in hypre_AuxParCSRMatrixInitialize (aux_parcsr_matrix.c:163). > > This means that hypre is allocating memory as if it was not aware of the > number of nonzero per row, even though I supply in my application the two > arrays dnnz and onnz. > > > > Am I missing something? > > > > Thanks, > > Pierre > > > > <massif.out.bad><massif.out.better><patch-hypre.txt> > >

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Re: [petsc-dev] Faulty logic in MatHYPRESetPreallocation?
by Smith, Barry F. 28 Dec '18

28 Dec '18

Pierre, Could you make a pull request on this? Thanks Barry > On Dec 17, 2018, at 3:18 AM, Pierre Jolivet via petsc-dev <petsc-dev(a)mcs.anl.gov> wrote: > > Hello, > I am not sure the hypre routines are called in the right order in MatHYPRESetPreallocation. > Indeed, attached, you’ll find two Massif logs, one with the current order (massif.out.bad), and the other (massif.out.better) with the attached patch applied. > In the former, you can see at the snapshot #31 that there is a call to hypre_CTAlloc in hypre_AuxParCSRMatrixInitialize (aux_parcsr_matrix.c:163). > This means that hypre is allocating memory as if it was not aware of the number of nonzero per row, even though I supply in my application the two arrays dnnz and onnz. > > Am I missing something? > > Thanks, > Pierre > > <massif.out.bad><massif.out.better><patch-hypre.txt>

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Re: [petsc-dev] Fwd: PETSc blame digest (next-tmp) 2018-12-24
by Matthew Knepley 26 Dec '18

26 Dec '18

On Wed, Dec 26, 2018 at 10:18 AM Balay, Satish <balay(a)mcs.anl.gov> wrote: > Ah - I see the fix in https://bitbucket.org/arcowie/alpetsc > arcowie-rem/feature-error-logging > > I've: > > - updated pr1206/arcowie-rem/feature-error-logging/master with this change > - deleted duplcate branch origin/arcowie-rem/feature-error-logging > - updated next-tmp with pr1206/arcowie-rem/feature-error-logging/master > Thanks man. I messed up with the last push to origin/arcowie-rem/feature-error-logging Matt > Satish > > On Wed, 26 Dec 2018, Balay, Satish via petsc-dev wrote: > > > Which branch did you push fixes to? I don't see them in 'arcowie' > branches. > > > > Satish > > > > > > On Wed, 26 Dec 2018, Matthew Knepley via petsc-dev wrote: > > > > > Okay, Satish I have pushed fixes for this. > > > > > > Thanks, > > > > > > Matt > > > > > > On Tue, Dec 25, 2018 at 4:12 PM Smith, Barry F. <bsmith(a)mcs.anl.gov> > wrote: > > > > > > > > > > > --with-log=0 > > > > > > > > and you don't have code to manage this case. Take a look at the > petsclog.h > > > > for #else after the defined(PETSC_USE_LOG) you need macros that > return 0 > > > > for those two things. > > > > > > > > > > > > > On Dec 25, 2018, at 11:49 AM, Matthew Knepley via petsc-dev < > > > > petsc-dev(a)mcs.anl.gov> wrote: > > > > > > > > > > This makes no sense, > > > > > > > > > > petscvonest.h includes > > > > > petscsnes.h includes > > > > > petsksp.h includes > > > > > petscpc.h includes > > > > > petscmat.h includes > > > > > petscvec.h includes > > > > > petscis.h includes > > > > > petscsys.h includes > > > > > petsclog.h includes the declaration. > > > > > > > > > > Thanks, > > > > > > > > > > Matt > > > > > > > > > > ---------- Forwarded message --------- > > > > > From: PETSc checkBuilds <petsc-checkbuilds(a)mcs.anl.gov> > > > > > Date: Mon, Dec 24, 2018 at 4:28 PM > > > > > Subject: PETSc blame digest (next-tmp) 2018-12-24 > > > > > To: Matthew Knepley <knepley(a)gmail.com>, PETSc checkBuilds < > > > > petsc-checkbuilds(a)mcs.anl.gov> > > > > > > > > > > > > > > > > > > > > > > > > > Dear PETSc developer, > > > > > > > > > > This email contains listings of contributions attributed to you by > > > > > `git blame` that caused compiler errors or warnings in PETSc > automated > > > > > testing. Follow the links to see the full log files. Please > attempt to > > > > fix > > > > > the issues promptly or let us know at petsc-dev(a)mcs.anl.gov if > you are > > > > unable > > > > > to resolve the issues. > > > > > > > > > > Thanks, > > > > > The PETSc development team > > > > > > > > > > ---- > > > > > > > > > > warnings attributed to commit > > > > https://bitbucket.org/petsc/petsc/commits/a56d3bf > > > > > ConvEst: Separately fit convergence rate for each field > > > > > > > > > > src/snes/utils/convest.c:362 > > > > > [ > > > > > http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2018/12/24/build_next-… > > > > ] > > > > > > "/export/home/petsc/petsc.next-tmp-2/src/snes/utils/convest.c", > > > > line 362: warning: implicit function declaration: PetscLogEventSetDof > > > > > > > > > > src/snes/utils/convest.c:363 > > > > > [ > > > > > http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2018/12/24/build_next-… > > > > ] > > > > > > "/export/home/petsc/petsc.next-tmp-2/src/snes/utils/convest.c", > > > > line 363: warning: implicit function declaration: > PetscLogEventSetError > > > > > > > > > > ---- > > > > > To opt-out from receiving these messages - send a request to > > > > petsc-dev(a)mcs.anl.gov. > > > > > > > > > > > > > > > -- > > > > > What most experimenters take for granted before they begin their > > > > experiments is infinitely more interesting than any results to which > their > > > > experiments lead. > > > > > -- Norbert Wiener > > > > > > > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > > > > > > > > > > > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [petsc-dev] Fwd: PETSc blame digest (next-tmp) 2018-12-24
by Balay, Satish 26 Dec '18

26 Dec '18

Ah - I see the fix in https://bitbucket.org/arcowie/alpetsc arcowie-rem/feature-error-logging I've: - updated pr1206/arcowie-rem/feature-error-logging/master with this change - deleted duplcate branch origin/arcowie-rem/feature-error-logging - updated next-tmp with pr1206/arcowie-rem/feature-error-logging/master Satish On Wed, 26 Dec 2018, Balay, Satish via petsc-dev wrote: > Which branch did you push fixes to? I don't see them in 'arcowie' branches. > > Satish > > > On Wed, 26 Dec 2018, Matthew Knepley via petsc-dev wrote: > > > Okay, Satish I have pushed fixes for this. > > > > Thanks, > > > > Matt > > > > On Tue, Dec 25, 2018 at 4:12 PM Smith, Barry F. <bsmith(a)mcs.anl.gov> wrote: > > > > > > > > --with-log=0 > > > > > > and you don't have code to manage this case. Take a look at the petsclog.h > > > for #else after the defined(PETSC_USE_LOG) you need macros that return 0 > > > for those two things. > > > > > > > > > > On Dec 25, 2018, at 11:49 AM, Matthew Knepley via petsc-dev < > > > petsc-dev(a)mcs.anl.gov> wrote: > > > > > > > > This makes no sense, > > > > > > > > petscvonest.h includes > > > > petscsnes.h includes > > > > petsksp.h includes > > > > petscpc.h includes > > > > petscmat.h includes > > > > petscvec.h includes > > > > petscis.h includes > > > > petscsys.h includes > > > > petsclog.h includes the declaration. > > > > > > > > Thanks, > > > > > > > > Matt > > > > > > > > ---------- Forwarded message --------- > > > > From: PETSc checkBuilds <petsc-checkbuilds(a)mcs.anl.gov> > > > > Date: Mon, Dec 24, 2018 at 4:28 PM > > > > Subject: PETSc blame digest (next-tmp) 2018-12-24 > > > > To: Matthew Knepley <knepley(a)gmail.com>, PETSc checkBuilds < > > > petsc-checkbuilds(a)mcs.anl.gov> > > > > > > > > > > > > > > > > > > > > Dear PETSc developer, > > > > > > > > This email contains listings of contributions attributed to you by > > > > `git blame` that caused compiler errors or warnings in PETSc automated > > > > testing. Follow the links to see the full log files. Please attempt to > > > fix > > > > the issues promptly or let us know at petsc-dev(a)mcs.anl.gov if you are > > > unable > > > > to resolve the issues. > > > > > > > > Thanks, > > > > The PETSc development team > > > > > > > > ---- > > > > > > > > warnings attributed to commit > > > https://bitbucket.org/petsc/petsc/commits/a56d3bf > > > > ConvEst: Separately fit convergence rate for each field > > > > > > > > src/snes/utils/convest.c:362 > > > > [ > > > http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2018/12/24/build_next-… > > > ] > > > > "/export/home/petsc/petsc.next-tmp-2/src/snes/utils/convest.c", > > > line 362: warning: implicit function declaration: PetscLogEventSetDof > > > > > > > > src/snes/utils/convest.c:363 > > > > [ > > > http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2018/12/24/build_next-… > > > ] > > > > "/export/home/petsc/petsc.next-tmp-2/src/snes/utils/convest.c", > > > line 363: warning: implicit function declaration: PetscLogEventSetError > > > > > > > > ---- > > > > To opt-out from receiving these messages - send a request to > > > petsc-dev(a)mcs.anl.gov. > > > > > > > > > > > > -- > > > > What most experimenters take for granted before they begin their > > > experiments is infinitely more interesting than any results to which their > > > experiments lead. > > > > -- Norbert Wiener > > > > > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > > > > > >

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Re: [petsc-dev] Fwd: PETSc blame digest (next-tmp) 2018-12-24
by Balay, Satish 26 Dec '18

26 Dec '18

Which branch did you push fixes to? I don't see them in 'arcowie' branches. Satish On Wed, 26 Dec 2018, Matthew Knepley via petsc-dev wrote: > Okay, Satish I have pushed fixes for this. > > Thanks, > > Matt > > On Tue, Dec 25, 2018 at 4:12 PM Smith, Barry F. <bsmith(a)mcs.anl.gov> wrote: > > > > > --with-log=0 > > > > and you don't have code to manage this case. Take a look at the petsclog.h > > for #else after the defined(PETSC_USE_LOG) you need macros that return 0 > > for those two things. > > > > > > > On Dec 25, 2018, at 11:49 AM, Matthew Knepley via petsc-dev < > > petsc-dev(a)mcs.anl.gov> wrote: > > > > > > This makes no sense, > > > > > > petscvonest.h includes > > > petscsnes.h includes > > > petsksp.h includes > > > petscpc.h includes > > > petscmat.h includes > > > petscvec.h includes > > > petscis.h includes > > > petscsys.h includes > > > petsclog.h includes the declaration. > > > > > > Thanks, > > > > > > Matt > > > > > > ---------- Forwarded message --------- > > > From: PETSc checkBuilds <petsc-checkbuilds(a)mcs.anl.gov> > > > Date: Mon, Dec 24, 2018 at 4:28 PM > > > Subject: PETSc blame digest (next-tmp) 2018-12-24 > > > To: Matthew Knepley <knepley(a)gmail.com>, PETSc checkBuilds < > > petsc-checkbuilds(a)mcs.anl.gov> > > > > > > > > > > > > > > > Dear PETSc developer, > > > > > > This email contains listings of contributions attributed to you by > > > `git blame` that caused compiler errors or warnings in PETSc automated > > > testing. Follow the links to see the full log files. Please attempt to > > fix > > > the issues promptly or let us know at petsc-dev(a)mcs.anl.gov if you are > > unable > > > to resolve the issues. > > > > > > Thanks, > > > The PETSc development team > > > > > > ---- > > > > > > warnings attributed to commit > > https://bitbucket.org/petsc/petsc/commits/a56d3bf > > > ConvEst: Separately fit convergence rate for each field > > > > > > src/snes/utils/convest.c:362 > > > [ > > http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2018/12/24/build_next-… > > ] > > > "/export/home/petsc/petsc.next-tmp-2/src/snes/utils/convest.c", > > line 362: warning: implicit function declaration: PetscLogEventSetDof > > > > > > src/snes/utils/convest.c:363 > > > [ > > http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2018/12/24/build_next-… > > ] > > > "/export/home/petsc/petsc.next-tmp-2/src/snes/utils/convest.c", > > line 363: warning: implicit function declaration: PetscLogEventSetError > > > > > > ---- > > > To opt-out from receiving these messages - send a request to > > petsc-dev(a)mcs.anl.gov. > > > > > > > > > -- > > > What most experimenters take for granted before they begin their > > experiments is infinitely more interesting than any results to which their > > experiments lead. > > > -- Norbert Wiener > > > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > >

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Re: [petsc-dev] Fwd: PETSc blame digest (next-tmp) 2018-12-24
by Matthew Knepley 26 Dec '18

26 Dec '18

Okay, Satish I have pushed fixes for this. Thanks, Matt On Tue, Dec 25, 2018 at 4:12 PM Smith, Barry F. <bsmith(a)mcs.anl.gov> wrote: > > --with-log=0 > > and you don't have code to manage this case. Take a look at the petsclog.h > for #else after the defined(PETSC_USE_LOG) you need macros that return 0 > for those two things. > > > > On Dec 25, 2018, at 11:49 AM, Matthew Knepley via petsc-dev < > petsc-dev(a)mcs.anl.gov> wrote: > > > > This makes no sense, > > > > petscvonest.h includes > > petscsnes.h includes > > petsksp.h includes > > petscpc.h includes > > petscmat.h includes > > petscvec.h includes > > petscis.h includes > > petscsys.h includes > > petsclog.h includes the declaration. > > > > Thanks, > > > > Matt > > > > ---------- Forwarded message --------- > > From: PETSc checkBuilds <petsc-checkbuilds(a)mcs.anl.gov> > > Date: Mon, Dec 24, 2018 at 4:28 PM > > Subject: PETSc blame digest (next-tmp) 2018-12-24 > > To: Matthew Knepley <knepley(a)gmail.com>, PETSc checkBuilds < > petsc-checkbuilds(a)mcs.anl.gov> > > > > > > > > > > Dear PETSc developer, > > > > This email contains listings of contributions attributed to you by > > `git blame` that caused compiler errors or warnings in PETSc automated > > testing. Follow the links to see the full log files. Please attempt to > fix > > the issues promptly or let us know at petsc-dev(a)mcs.anl.gov if you are > unable > > to resolve the issues. > > > > Thanks, > > The PETSc development team > > > > ---- > > > > warnings attributed to commit > https://bitbucket.org/petsc/petsc/commits/a56d3bf > > ConvEst: Separately fit convergence rate for each field > > > > src/snes/utils/convest.c:362 > > [ > http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2018/12/24/build_next-… > ] > > "/export/home/petsc/petsc.next-tmp-2/src/snes/utils/convest.c", > line 362: warning: implicit function declaration: PetscLogEventSetDof > > > > src/snes/utils/convest.c:363 > > [ > http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2018/12/24/build_next-… > ] > > "/export/home/petsc/petsc.next-tmp-2/src/snes/utils/convest.c", > line 363: warning: implicit function declaration: PetscLogEventSetError > > > > ---- > > To opt-out from receiving these messages - send a request to > petsc-dev(a)mcs.anl.gov. > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [petsc-dev] Fwd: PETSc blame digest (next-tmp) 2018-12-24
by Smith, Barry F. 25 Dec '18

25 Dec '18

--with-log=0 and you don't have code to manage this case. Take a look at the petsclog.h for #else after the defined(PETSC_USE_LOG) you need macros that return 0 for those two things. > On Dec 25, 2018, at 11:49 AM, Matthew Knepley via petsc-dev <petsc-dev(a)mcs.anl.gov> wrote: > > This makes no sense, > > petscvonest.h includes > petscsnes.h includes > petsksp.h includes > petscpc.h includes > petscmat.h includes > petscvec.h includes > petscis.h includes > petscsys.h includes > petsclog.h includes the declaration. > > Thanks, > > Matt > > ---------- Forwarded message --------- > From: PETSc checkBuilds <petsc-checkbuilds(a)mcs.anl.gov> > Date: Mon, Dec 24, 2018 at 4:28 PM > Subject: PETSc blame digest (next-tmp) 2018-12-24 > To: Matthew Knepley <knepley(a)gmail.com>, PETSc checkBuilds <petsc-checkbuilds(a)mcs.anl.gov> > > > > > Dear PETSc developer, > > This email contains listings of contributions attributed to you by > `git blame` that caused compiler errors or warnings in PETSc automated > testing. Follow the links to see the full log files. Please attempt to fix > the issues promptly or let us know at petsc-dev(a)mcs.anl.gov if you are unable > to resolve the issues. > > Thanks, > The PETSc development team > > ---- > > warnings attributed to commit https://bitbucket.org/petsc/petsc/commits/a56d3bf > ConvEst: Separately fit convergence rate for each field > > src/snes/utils/convest.c:362 > [http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2018/12/24/build_next-…] > "/export/home/petsc/petsc.next-tmp-2/src/snes/utils/convest.c", line 362: warning: implicit function declaration: PetscLogEventSetDof > > src/snes/utils/convest.c:363 > [http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2018/12/24/build_next-…] > "/export/home/petsc/petsc.next-tmp-2/src/snes/utils/convest.c", line 363: warning: implicit function declaration: PetscLogEventSetError > > ---- > To opt-out from receiving these messages - send a request to petsc-dev(a)mcs.anl.gov. > > > -- > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/

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Fwd: PETSc blame digest (next-tmp) 2018-12-24
by Matthew Knepley 25 Dec '18

25 Dec '18

This makes no sense, petscvonest.h includes petscsnes.h includes petsksp.h includes petscpc.h includes petscmat.h includes petscvec.h includes petscis.h includes petscsys.h includes petsclog.h includes the declaration. Thanks, Matt ---------- Forwarded message --------- From: PETSc checkBuilds <petsc-checkbuilds(a)mcs.anl.gov> Date: Mon, Dec 24, 2018 at 4:28 PM Subject: PETSc blame digest (next-tmp) 2018-12-24 To: Matthew Knepley <knepley(a)gmail.com>, PETSc checkBuilds < petsc-checkbuilds(a)mcs.anl.gov> Dear PETSc developer, This email contains listings of contributions attributed to you by `git blame` that caused compiler errors or warnings in PETSc automated testing. Follow the links to see the full log files. Please attempt to fix the issues promptly or let us know at petsc-dev(a)mcs.anl.gov if you are unable to resolve the issues. Thanks, The PETSc development team ---- warnings attributed to commit https://bitbucket.org/petsc/petsc/commits/a56d3bf ConvEst: Separately fit convergence rate for each field src/snes/utils/convest.c:362 [ http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2018/12/24/build_next-… ] "/export/home/petsc/petsc.next-tmp-2/src/snes/utils/convest.c", line 362: warning: implicit function declaration: PetscLogEventSetDof src/snes/utils/convest.c:363 [ http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2018/12/24/build_next-… ] "/export/home/petsc/petsc.next-tmp-2/src/snes/utils/convest.c", line 363: warning: implicit function declaration: PetscLogEventSetError ---- To opt-out from receiving these messages - send a request to petsc-dev(a)mcs.anl.gov. -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [petsc-dev] Faulty logic in MatHYPRESetPreallocation?
by Smith, Barry F. 22 Dec '18

22 Dec '18

Stefeno, Doe this look right to you? Thanks Barry > On Dec 17, 2018, at 3:18 AM, Pierre Jolivet via petsc-dev <petsc-dev(a)mcs.anl.gov> wrote: > > Hello, > I am not sure the hypre routines are called in the right order in MatHYPRESetPreallocation. > Indeed, attached, you’ll find two Massif logs, one with the current order (massif.out.bad), and the other (massif.out.better) with the attached patch applied. > In the former, you can see at the snapshot #31 that there is a call to hypre_CTAlloc in hypre_AuxParCSRMatrixInitialize (aux_parcsr_matrix.c:163). > This means that hypre is allocating memory as if it was not aware of the number of nonzero per row, even though I supply in my application the two arrays dnnz and onnz. > > Am I missing something? > > Thanks, > Pierre > > <massif.out.bad><massif.out.better><patch-hypre.txt>

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