Re: [petsc-users] Algorithms to remove null spaces in a singular system

2016-10-11 Thread Kong, Fande
Barry, Thanks so much for your explanation. It helps me a lot. On Mon, Oct 10, 2016 at 4:00 PM, Barry Smith wrote: > > > On Oct 10, 2016, at 4:01 PM, Kong, Fande wrote: > > > > Hi All, > > > > I know how to remove the null spaces from a singular system

Re: [petsc-users] SuperLU_dist issue in 3.7.4

2016-10-11 Thread Anton Popov
Valgrind immediately detects interesting stuff: ==25673== Use of uninitialised value of size 8 ==25673==at 0x178272C: static_schedule (static_schedule.c:960) ==25674== Use of uninitialised value of size 8 ==25674==at 0x178272C: static_schedule (static_schedule.c:960) ==25674==by

Re: [petsc-users] SuperLU_dist issue in 3.7.4

2016-10-11 Thread Anton Popov
On 10/10/2016 07:11 PM, Satish Balay wrote: Thats from petsc-3.5 Anton - please post the stack trace you get with --download-superlu_dist-commit=origin/maint I guess this is it: [0]PETSC ERROR: [0] SuperLU_DIST:pdgssvx line 421

[petsc-users] Autoconf tests

2016-10-11 Thread CLAUS HELLMUTH WARNER HETZER
Hi everybody- Figured I’d ask this here before I go reinventing the wheel. I’m writing an autoconf installer (the standard Linux configure/make package) for an acoustic wave propagation modeling package that builds PETSc and SLEPc as part of the installation process. I’d like to be able to

Re: [petsc-users] large PetscCommDuplicate overhead

2016-10-11 Thread Matthew Overholt
Barry, Subsequent tests with the same code and a problem (input) having a much smaller vertex (equation) count (i.e. a much smaller matrix to invert for the solution) have NOT had PetscCommDuplicate() account for any significant time, so I'm not surprised that your test didn't find any problem.

Re: [petsc-users] SuperLU_dist issue in 3.7.4

2016-10-11 Thread Anton
On 10/11/16 7:44 PM, Barry Smith wrote: You can run your code with -ksp_view_mat binary -ksp_view_rhs binary this will cause it to save the matrices and right hand sides to the linear systems in a file called binaryoutput, then email the file to petsc-ma...@mcs.anl.gov (don't worry this

Re: [petsc-users] SuperLU_dist issue in 3.7.4

2016-10-11 Thread Satish Balay
On Tue, 11 Oct 2016, Anton wrote: > > > On 10/11/16 7:44 PM, Barry Smith wrote: > > You can run your code with -ksp_view_mat binary -ksp_view_rhs binary > > this will cause it to save the matrices and right hand sides to the > > linear systems in a file called binaryoutput, then

Re: [petsc-users] SuperLU_dist issue in 3.7.4

2016-10-11 Thread Anton
On 10/11/16 7:19 PM, Satish Balay wrote: This log looks truncated. Are there any valgrind mesages before this? [like from your application code - or from MPI] Yes it is indeed truncated. I only included relevant messages. Perhaps you can send the complete log - with: valgrind -q

Re: [petsc-users] large PetscCommDuplicate overhead

2016-10-11 Thread Jed Brown
Matthew Overholt writes: > Barry, > > Subsequent tests with the same code and a problem (input) having a much > smaller vertex (equation) count (i.e. a much smaller matrix to invert for > the solution) have NOT had PetscCommDuplicate() account for any significant > time, so

Re: [petsc-users] Algorithms to remove null spaces in a singular system

2016-10-11 Thread Kong, Fande
On Tue, Oct 11, 2016 at 10:39 AM, Barry Smith wrote: > > > On Oct 11, 2016, at 9:33 AM, Kong, Fande wrote: > > > > Barry, Thanks so much for your explanation. It helps me a lot. > > > > On Mon, Oct 10, 2016 at 4:00 PM, Barry Smith

Re: [petsc-users] Algorithms to remove null spaces in a singular system

2016-10-11 Thread Barry Smith
> On Oct 11, 2016, at 9:33 AM, Kong, Fande wrote: > > Barry, Thanks so much for your explanation. It helps me a lot. > > On Mon, Oct 10, 2016 at 4:00 PM, Barry Smith wrote: > > > On Oct 10, 2016, at 4:01 PM, Kong, Fande wrote: > >

Re: [petsc-users] SuperLU_dist issue in 3.7.4

2016-10-11 Thread Barry Smith
You can run your code with -ksp_view_mat binary -ksp_view_rhs binary this will cause it to save the matrices and right hand sides to the linear systems in a file called binaryoutput, then email the file to petsc-ma...@mcs.anl.gov (don't worry this email address accepts large attachments).

Re: [petsc-users] SuperLU_dist issue in 3.7.4

2016-10-11 Thread Satish Balay
This log looks truncated. Are there any valgrind mesages before this? [like from your application code - or from MPI] Perhaps you can send the complete log - with: valgrind -q --tool=memcheck --leak-check=yes --num-callers=20 --track-origins=yes [and if there were more valgrind messages from

Re: [petsc-users] Algorithms to remove null spaces in a singular system

2016-10-11 Thread Kong, Fande
Barry, I am trying to reproduce this issue using a pure PETSc code. VecLoad does not work for me. I do not know why. Anyway, I can reproduce this using a very small system. Here are some info: Mat, A Mat Object:() 2 MPI processes type: mpiaij row 0: (0, 1.) row 1: (0, -0.820827) (1, 1.51669)

Re: [petsc-users] Algorithms to remove null spaces in a singular system

2016-10-11 Thread Barry Smith
Fande, Could you send me (petsc-ma...@mcs.anl.gov) a non symmetric matrix you have that has a different null space for A and A'. This would be one that is failing with right preconditioning. Smaller the better but whatever size you have. Run the code with -ksp_view_mat binary and send

Re: [petsc-users] Algorithms to remove null spaces in a singular system

2016-10-11 Thread Kong, Fande
On Tue, Oct 11, 2016 at 12:18 PM, Barry Smith wrote: > > > On Oct 11, 2016, at 12:01 PM, Kong, Fande wrote: > > > > > > > > On Tue, Oct 11, 2016 at 10:39 AM, Barry Smith > wrote: > > > > > On Oct 11, 2016, at 9:33 AM, Kong, Fande

Re: [petsc-users] Autoconf tests

2016-10-11 Thread Barry Smith
You don't want to get the debug mode from PETSC_ARCH since there may not be a PETSC_ARCH (for PETSc --prefix installs) or because the user did not put the string in it. You can check for the PETSC_USE_DEBUG symbol in the petscconf.h file by linking a C program against and #if