April 2012 - petsc-dev - mailman3.cels.anl.gov

Meeting Tuesday
by Barry Smith 21 Apr '12

21 Apr '12

Scott and Travis, Let's say we will have a meeting regarding commercial packaging of PETSc at 9 AM on Tuesday You can come to my office before then, building 240 (the penitentiary) Everyone is welcome to join the meeting, if anyone (Matt) wants to call in we can do that. Barry

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Re: [petsc-dev] Fwd: Sou-Cheng Choi awarded SIAM linear prize
by Barry Smith 20 Apr '12

20 Apr '12

On Apr 20, 2012, at 4:13 PM, Jed Brown wrote: > Sou-Cheng set up PETSc on her computer last week. She posted about it on Facebook, which I interpret as a good sign. +1 > > On Apr 20, 2012 3:55 PM, "Barry Smith" <bsmith(a)mcs.anl.gov> wrote: > > Is this fantastic algorithm available in KSP? If not, why not, since it is of world shattering performance. > > Barry > > > Begin forwarded message: > > > From: Stefan Wild <wild(a)mcs.anl.gov> > > Date: April 20, 2012 11:35:29 AM CDT > > To: mcs(a)lists.mcs.anl.gov > > Cc: lans-all(a)lists.mcs.anl.gov > > Subject: Sou-Cheng Choi awarded SIAM linear prize > > > > Congratulations are due to Argonne/UChicago/Computation Institute computational mathematician Sou-Cheng Choi for being awarded the 2012 SIAM SIAG/Linear Algebra Prize! > > > > This award is given once every three years and is one of the most prestigious awards given in the area of numerical linear algebra, I'm sure you'll recognize many of the previous winners > > http://www.siam.org/prizes/sponsored/siagla.php . > > > > The citation (from http://connect.siam.org/) is below. > > > > Congrats Sou-Cheng! > > > > Stefan > > > > > > > > Sou-Cheng Choi, Christopher Paige, and Michael Saunders will be awarded the 2012 SIAG/LA Prize for their paper, “MINRES-QLP: A Krylov Subspace Method for Indefinite or Singular Symmetric Systems,” SIAM Journal on Scientific Computing, 33:1810-1836, 2011. According to the prize committee: “The authors improve on MINRES, an elegant, efficient and widely used iterative method for linear systems, achieving optimal accuracy and extending the algorithm to the solution of least squares problems.” > > >

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Re: [petsc-dev] Fwd: Sou-Cheng Choi awarded SIAM linear prize
by Jed Brown 20 Apr '12

20 Apr '12

Sou-Cheng set up PETSc on her computer last week. She posted about it on Facebook, which I interpret as a good sign. On Apr 20, 2012 3:55 PM, "Barry Smith" <bsmith(a)mcs.anl.gov> wrote: > > Is this fantastic algorithm available in KSP? If not, why not, since it > is of world shattering performance. > > Barry > > > Begin forwarded message: > > > From: Stefan Wild <wild(a)mcs.anl.gov> > > Date: April 20, 2012 11:35:29 AM CDT > > To: mcs(a)lists.mcs.anl.gov > > Cc: lans-all(a)lists.mcs.anl.gov > > Subject: Sou-Cheng Choi awarded SIAM linear prize > > > > Congratulations are due to Argonne/UChicago/Computation Institute > computational mathematician Sou-Cheng Choi for being awarded the 2012 SIAM > SIAG/Linear Algebra Prize! > > > > This award is given once every three years and is one of the most > prestigious awards given in the area of numerical linear algebra, I'm sure > you'll recognize many of the previous winners > > http://www.siam.org/prizes/sponsored/siagla.php . > > > > The citation (from http://connect.siam.org/) is below. > > > > Congrats Sou-Cheng! > > > > Stefan > > > > > > > > Sou-Cheng Choi, Christopher Paige, and Michael Saunders will be awarded > the 2012 SIAG/LA Prize for their paper, “MINRES-QLP: A Krylov Subspace > Method for Indefinite or Singular Symmetric Systems,” SIAM Journal on > Scientific Computing, 33:1810-1836, 2011. According to the prize > committee: “The authors improve on MINRES, an elegant, efficient and widely > used iterative method for linear systems, achieving optimal accuracy and > extending the algorithm to the solution of least squares problems.” > > > >

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Fwd: Sou-Cheng Choi awarded SIAM linear prize
by Barry Smith 20 Apr '12

20 Apr '12

Is this fantastic algorithm available in KSP? If not, why not, since it is of world shattering performance. Barry Begin forwarded message: > From: Stefan Wild <wild(a)mcs.anl.gov> > Date: April 20, 2012 11:35:29 AM CDT > To: mcs(a)lists.mcs.anl.gov > Cc: lans-all(a)lists.mcs.anl.gov > Subject: Sou-Cheng Choi awarded SIAM linear prize > > Congratulations are due to Argonne/UChicago/Computation Institute computational mathematician Sou-Cheng Choi for being awarded the 2012 SIAM SIAG/Linear Algebra Prize! > > This award is given once every three years and is one of the most prestigious awards given in the area of numerical linear algebra, I'm sure you'll recognize many of the previous winners > http://www.siam.org/prizes/sponsored/siagla.php . > > The citation (from http://connect.siam.org/) is below. > > Congrats Sou-Cheng! > > Stefan > > > > Sou-Cheng Choi, Christopher Paige, and Michael Saunders will be awarded the 2012 SIAG/LA Prize for their paper, “MINRES-QLP: A Krylov Subspace Method for Indefinite or Singular Symmetric Systems,” SIAM Journal on Scientific Computing, 33:1810-1836, 2011. According to the prize committee: “The authors improve on MINRES, an elegant, efficient and widely used iterative method for linear systems, achieving optimal accuracy and extending the algorithm to the solution of least squares problems.” >

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Re: [petsc-dev] MatAXPY with DIFFERENT_NONZERO_PATTERN
by Jed Brown 20 Apr '12

20 Apr '12

On Fri, Apr 20, 2012 at 05:18, Matthew Knepley <knepley(a)gmail.com> wrote: > Did someone intend to fix this, and then > stop? MatAXPY_BasicWithPreallocation() is the same as MatAXPY_Basic(). > Look how it's called. I don't know what's going on here. ierr = MatAXPYGetPreallocation_SeqAIJ(yy->A,xx->A,nnz_d);CHKERRQ(ierr); ierr = MatAXPYGetPreallocation_SeqAIJ(yy->B,xx->B,nnz_o);CHKERRQ(ierr); ierr = MatMPIAIJSetPreallocation(B,0,nnz_d,0,nnz_o);CHKERRQ(ierr); ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr);

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Re: [petsc-dev] MatAXPY with DIFFERENT_NONZERO_PATTERN
by Matthew Knepley 20 Apr '12

20 Apr '12

On Fri, Apr 20, 2012 at 8:05 AM, Alexander Grayver <agrayver(a)gfz-potsdam.de>wrote: > On 20.04.2012 14:02, Matthew Knepley wrote: > >> Yes, we started to require that everything be correctly allocated, rather >> than have hidden performance problems. >> > > Matt, can you point me to the patch of this issue? > Did someone intend to fix this, and then stop? MatAXPY_BasicWithPreallocation() is the same as MatAXPY_Basic(). Matt > >> Matt >> > > > -- > Regards, > Alexander > > -- 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

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Re: [petsc-dev] MatAXPY with DIFFERENT_NONZERO_PATTERN
by Alexander Grayver 20 Apr '12

20 Apr '12

On 20.04.2012 14:02, Matthew Knepley wrote: > Yes, we started to require that everything be correctly allocated, > rather than have hidden performance problems. Matt, can you point me to the patch of this issue? > > Matt -- Regards, Alexander

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Re: [petsc-dev] MatAXPY with DIFFERENT_NONZERO_PATTERN
by Matthew Knepley 20 Apr '12

20 Apr '12

On Fri, Apr 20, 2012 at 6:07 AM, Alexander Grayver <agrayver(a)gfz-potsdam.de>wrote: > Hello, > > Calling MatAYPX with MatStructure == DIFFERENT_NONZERO_PATTERN produces > following errors: > > [30]PETSC ERROR: --------------------- Error Message > ------------------------------**------ > [30]PETSC ERROR: Argument out of range! > [30]PETSC ERROR: New nonzero at (0,8486) caused a malloc! > [30]PETSC ERROR: ------------------------------** > ------------------------------**------------ > [30]PETSC ERROR: Petsc Development HG revision: > 7c3c3f8c0d65b793aea33c138419de**755b591ca7 HG Date: Thu Feb 09 14:42:30 > 2012 -0600 > [30]PETSC ERROR: See docs/changes/index.html for recent updates. > [30]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > [30]PETSC ERROR: See docs/index.html for manual pages. > [30]PETSC ERROR: ------------------------------** > ------------------------------**------------ > [30]PETSC ERROR: /home/prog on a openmpi-i named node229 by agrayver Fri > Apr 20 11:33:55 2012 > [30]PETSC ERROR: Libraries linked from /home/lib/petsc-dev/openmpi-** > intel-complex-debug-f/lib > [30]PETSC ERROR: Configure run at Fri Feb 10 09:28:34 2012 > [30]PETSC ERROR: Configure options --with-petsc-arch=openmpi-**intel-complex-debug-f > --with-fortran-interfaces=1 --with-scalapack-lib=/opt/** > intel/Compiler/11.1/072/mkl/**lib/em64t/libmkl_scalapack_**lp64.a > --with-scalapack-include=/opt/**intel/Compiler/11.1/072/mkl/**include > --with-blacs-lib=/opt/intel/**Compiler/11.1/072/mkl/lib/** > em64t/libmkl_blacs_openmpi_**lp64.a --with-blacs-include=/opt/** > intel/Compiler/11.1/072/mkl/**include --with-mpi-dir=/opt/mpi/intel/**openmpi-1.4.2 > --with-scalar-type=complex --with-blas-lapack-lib="[/opt/** > intel/Compiler/11.1/072/mkl/**lib/em64t/libmkl_intel_lp64.a,** > /opt/intel/Compiler/11.1/072/**mkl/lib/em64t/libmkl_intel_** > thread.a,/opt/intel/Compiler/**11.1/072/mkl/lib/em64t/libmkl_** > core.a,/opt/intel/Compiler/11.**1/072/lib/intel64/libiomp5.a]" > --with-precision=double --with-x=0 > [30]PETSC ERROR: ------------------------------** > ------------------------------**------------ > [30]PETSC ERROR: MatSetValues_MPIAIJ() line 538 in > /home/lib/petsc-dev/src/mat/**impls/aij/mpi/mpiaij.c > [30]PETSC ERROR: MatSetValues() line 1129 in /home/lib/petsc-dev/src/mat/* > *interface/matrix.c > [30]PETSC ERROR: MatAXPY_**BasicWithPreallocation() line 108 in > /home/lib/petsc-dev/src/mat/**utils/axpy.c > [30]PETSC ERROR: MatAXPY_MPIAIJ() line 2235 in /home/lib/petsc-dev/src/mat/ > **impls/aij/mpi/mpiaij.c > [30]PETSC ERROR: MatAXPY() line 39 in /home/lib/petsc-dev/src/mat/** > utils/axpy.c > [30]PETSC ERROR: MatAYPX() line 272 in /home/lib/petsc-dev/src/mat/** > utils/axpy.c > > > I guess it has something to do with recent changes in mataij > implementation, doesn't it? Yes, we started to require that everything be correctly allocated, rather than have hidden performance problems. Matt > -- > Regards, > Alexander > -- 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

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MatAXPY with DIFFERENT_NONZERO_PATTERN
by Alexander Grayver 20 Apr '12

20 Apr '12

Hello, Calling MatAYPX with MatStructure == DIFFERENT_NONZERO_PATTERN produces following errors: [30]PETSC ERROR: --------------------- Error Message ------------------------------------ [30]PETSC ERROR: Argument out of range! [30]PETSC ERROR: New nonzero at (0,8486) caused a malloc! [30]PETSC ERROR: ------------------------------------------------------------------------ [30]PETSC ERROR: Petsc Development HG revision: 7c3c3f8c0d65b793aea33c138419de755b591ca7 HG Date: Thu Feb 09 14:42:30 2012 -0600 [30]PETSC ERROR: See docs/changes/index.html for recent updates. [30]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [30]PETSC ERROR: See docs/index.html for manual pages. [30]PETSC ERROR: ------------------------------------------------------------------------ [30]PETSC ERROR: /home/prog on a openmpi-i named node229 by agrayver Fri Apr 20 11:33:55 2012 [30]PETSC ERROR: Libraries linked from /home/lib/petsc-dev/openmpi-intel-complex-debug-f/lib [30]PETSC ERROR: Configure run at Fri Feb 10 09:28:34 2012 [30]PETSC ERROR: Configure options --with-petsc-arch=openmpi-intel-complex-debug-f --with-fortran-interfaces=1 --with-scalapack-lib=/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_scalapack_lp64.a --with-scalapack-include=/opt/intel/Compiler/11.1/072/mkl/include --with-blacs-lib=/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_blacs_openmpi_lp64.a --with-blacs-include=/opt/intel/Compiler/11.1/072/mkl/include --with-mpi-dir=/opt/mpi/intel/openmpi-1.4.2 --with-scalar-type=complex --with-blas-lapack-lib="[/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.a,/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_thread.a,/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.a,/opt/intel/Compiler/11.1/072/lib/intel64/libiomp5.a]" --with-precision=double --with-x=0 [30]PETSC ERROR: ------------------------------------------------------------------------ [30]PETSC ERROR: MatSetValues_MPIAIJ() line 538 in /home/lib/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c [30]PETSC ERROR: MatSetValues() line 1129 in /home/lib/petsc-dev/src/mat/interface/matrix.c [30]PETSC ERROR: MatAXPY_BasicWithPreallocation() line 108 in /home/lib/petsc-dev/src/mat/utils/axpy.c [30]PETSC ERROR: MatAXPY_MPIAIJ() line 2235 in /home/lib/petsc-dev/src/mat/impls/aij/mpi/mpiaij.c [30]PETSC ERROR: MatAXPY() line 39 in /home/lib/petsc-dev/src/mat/utils/axpy.c [30]PETSC ERROR: MatAYPX() line 272 in /home/lib/petsc-dev/src/mat/utils/axpy.c I guess it has something to do with recent changes in mataij implementation, doesn't it? -- Regards, Alexander

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Re: [petsc-dev] configure error
by Satish Balay 19 Apr '12

19 Apr '12

On Thu, 19 Apr 2012, Lisandro Dalcin wrote: > On 19 April 2012 18:04, Jed Brown <jedbrown(a)mcs.anl.gov> wrote: > > On Thu, Apr 19, 2012 at 08:01, Mark F. Adams <mark.adams(a)columbia.edu> > > wrote: > >> > >> [I sent this error message but it "Your message to petsc-dev awaits > >> moderator approval" because the configure.log was > 512 Kb???] > > > > > > Configure issues (and especially configure.log attachments) belong on > > petsc-maint, not petsc-dev. > > Have ever considered an email filter for petsc-dev looking for a > configure.log attachement that automatically forwards the email to > petsc-maint and reply the OP informing that? Is this possible with mailman? [I could't locate appropriate options]. For now - I'm just forwarding such messages manually to petsc-maint [and ocassionally approve them on petsc-dev/petsc-users mailing list- when it makes sense] Satish

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