Re: [petsc-users] unsorted local columns in 3.8?

I've merged this branch to maint. Satish On Sat, 11 Nov 2017, Satish Balay wrote: > Will have a build tonight of this branch in next-tmp - and then look > at merging it tomorrow.

Re: [petsc-users] unsorted local columns in 3.8?

On Fri, Nov 10, 2017 at 6:09 PM, Hong wrote: > Satish : > >> I don't see any changes hzhang/fix-submat_samerowdist in past few >> days. So how did this error get fixed? >> > > I've never seen valgrind error for ex56 from nightly tests. > Mark told me about Valgrind error on

Re: [petsc-users] unsorted local columns in 3.8?

Ok - I just ran this example with valgrind (and parmetis) on my laptop - and got no valgrind errors. Will have a build tonight of this branch in next-tmp - and then look at merging it tomorrow. BTW: if the destination for this branch is maint - then its best to use the name

Re: [petsc-users] unsorted local columns in 3.8?

Satish : > I don't see any changes hzhang/fix-submat_samerowdist in past few > days. So how did this error get fixed? > I've never seen valgrind error for ex56 from nightly tests. Mark told me about Valgrind error on his mac, and I reproduced it on our linux machine with my own configure, which

Re: [petsc-users] unsorted local columns in 3.8?

I don't see any changes hzhang/fix-submat_samerowdist in past few days. So how did this error get fixed? please do not merge yet. Satish On Fri, 10 Nov 2017, Mark Adams wrote: > I don't see a problem with this. As far as what branch to merge it into, > that is a Barry/Satish/etc decision. >

Re: [petsc-users] unsorted local columns in 3.8?

I don't see a problem with this. As far as what branch to merge it into, that is a Barry/Satish/etc decision. On Fri, Nov 10, 2017 at 5:17 PM, Hong wrote: > Mark: > >> I would add: >> >> '--download-fblaslapack=1', >> >> This is what I have on my Linux machine (cg at

Re: [petsc-users] unsorted local columns in 3.8?

Mark: > I would add: > > '--download-fblaslapack=1', > > This is what I have on my Linux machine (cg at ANL) and it runs clean. > I do not see any error report from nightly tests for ex56. Should I merge this branch to maint? Hong > > On Fri, Nov 10, 2017 at 11:03 AM, Hong

Re: [petsc-users] unsorted local columns in 3.8?

I would add: '--download-fblaslapack=1', This is what I have on my Linux machine (cg at ANL) and it runs clean. On Fri, Nov 10, 2017 at 11:03 AM, Hong wrote: > I use > Using configure Options: --download-metis --download-mpich > --download-mumps --download-parmetis

Re: [petsc-users] unsorted local columns in 3.8?

I use Using configure Options: --download-metis --download-mpich --download-mumps --download-parmetis --download-scalapack --download-superlu --download-superlu_dist --download-suitesparse --download-hypre --download-ptscotch --download-chaco --with-ctable=1 --download-cmake --with-cc=gcc

Re: [petsc-users] unsorted local columns in 3.8?

This must be a configure issue. I don't see these warning: #!/usr/bin/python if __name__ == '__main__': import sys import os sys.path.insert(0, os.path.abspath('config')) import configure configure_options = [ '--with-cc=clang', '--with-cc++=clang++', '--download-mpich=1',

Re: [petsc-users] unsorted local columns in 3.8?

This is comming from blas. How did you configure blas? On Fri, Nov 10, 2017 at 10:38 AM, Hong wrote: > Using petsc machine, I get > hzhang@petsc /sandbox/hzhang/petsc/src/snes/examples/tutorials > (hzhang/fix-submat_samerowdist) > $ mpiexec -n 2 valgrind ./ex56 -cells 2,2,1

Re: [petsc-users] unsorted local columns in 3.8?

Using petsc machine, I get hzhang@petsc /sandbox/hzhang/petsc/src/snes/examples/tutorials (hzhang/fix-submat_samerowdist) $ mpiexec -n 2 valgrind ./ex56 -cells 2,2,1 -max_conv_its 3 -petscspace_order 2 -snes_max_it 2 -ksp_max_it 100 -ksp_type cg -ksp_rtol 1.e-11 -ksp_norm_type unpreconditioned

Re: [petsc-users] unsorted local columns in 3.8?

This printed a little funny in gmail, snes/ex56 is running clean in the first few loops (appended), but the last one is the one with a reduced processor set. Still waiting. This is with 32 bit integers. I'm running another with 64 bit integers. ... [0] 27 global equations, 9 vertices [0] 27

Re: [petsc-users] unsorted local columns in 3.8?

On Thu, Nov 9, 2017 at 1:56 PM, Hong wrote: > Mark: > >> OK, well, just go with the Linux machine for the regression test. I will >> keep trying to reproduce this on my Mac with an O build. >> > > Valgrind error occurs on linux machines with g-build. I cannot merge this >

Re: [petsc-users] unsorted local columns in 3.8?

Mark: > OK, well, just go with the Linux machine for the regression test. I will > keep trying to reproduce this on my Mac with an O build. > Valgrind error occurs on linux machines with g-build. I cannot merge this branch to maint until the bug is fixed. Hong > > On Wed, Nov 8, 2017 at 12:24

Re: [petsc-users] unsorted local columns in 3.8?

OK, well, just go with the Linux machine for the regression test. I will keep trying to reproduce this on my Mac with an O build. On Wed, Nov 8, 2017 at 12:24 PM, Hong wrote: > mpiexec -n 2 valgrind ./ex56 -cells 2,2,1 -max_conv_its 3 > -petscspace_order 2 -snes_max_it 2

Re: [petsc-users] unsorted local columns in 3.8?

mpiexec -n 2 valgrind ./ex56 -cells 2,2,1 -max_conv_its 3 -petscspace_order 2 -snes_max_it 2 -ksp_max_it 100 -ksp_type cg -ksp_rtol 1.e-11 -ksp_norm_type unpreconditioned -snes_rtol 1.e-10 -pc_type gamg -pc_gamg_type agg -pc_gamg_agg_nsmooths 1 -pc_gamg_coarse_eq_limit 10

Re: [petsc-users] unsorted local columns in 3.8?

On Wed, Nov 8, 2017 at 11:09 AM, Hong wrote: > Mark: > >> Hong, is >> > 0-cells: 12 12 0 0 >> > 1-cells: 20 20 0 0 >> > 2-cells: 11 11 0 0 >> > 3-cells: 2 2 0 0 >> >> from the old version? >> > In O-build on my macPro, I get the above. In g-build, I get > >> >>

Re: [petsc-users] unsorted local columns in 3.8?

Mark: > Hong, is > > 0-cells: 12 12 0 0 > > 1-cells: 20 20 0 0 > > 2-cells: 11 11 0 0 > > 3-cells: 2 2 0 0 > > from the old version? > In O-build on my macPro, I get the above. In g-build, I get > > 0-cells: 8 8 8 8 > 1-cells: 12 12 12 12 > 2-cells: 6 6 6 6 > 3-cells: 1 1 1 1 > I

Re: [petsc-users] unsorted local columns in 3.8?

Hong, is > 0-cells: 12 12 0 0 > 1-cells: 20 20 0 0 > 2-cells: 11 11 0 0 > 3-cells: 2 2 0 0 from the old version? I am seeing 0-cells: 8 8 8 8 1-cells: 12 12 12 12 2-cells: 6 6 6 6 3-cells: 1 1 1 1 Thanks, On Tue, Nov 7, 2017 at 10:13 PM, Hong wrote: >

Re: [petsc-users] unsorted local columns in 3.8?

Mark: I removed option '-ex56_dm_view'. Hong Humm, this looks a little odd, but it may be OK. Is this this diffing with > the old non-repartition data? (more below) > > On Tue, Nov 7, 2017 at 11:45 AM, Hong wrote: > >> Mark, >> The fix is merged to next branch for tests

Re: [petsc-users] unsorted local columns in 3.8?

Humm, this looks a little odd, but it may be OK. Is this this diffing with the old non-repartition data? (more below) On Tue, Nov 7, 2017 at 11:45 AM, Hong wrote: > Mark, > The fix is merged to next branch for tests which show diff as > > *** Testing:

Re: [petsc-users] unsorted local columns in 3.8?

Mark, The fix is merged to next branch for tests which show diff as *** Testing: testexamples_PARMETIS *** 5c5 < 1 SNES Function norm 1.983e-10 --- > 1 SNES Function norm 1.990e-10 10,13c10,13 < 0-cells: 8 8 8 8 < 1-cells: 12 12 12 12 < 2-cells: 6 6 6 6 < 3-cells: 1 1 1 1 ---

Re: [petsc-users] unsorted local columns in 3.8?

Mark: Bug is fixed in branch hzhang/fix-submat_samerowdist https://bitbucket.org/petsc/petsc/branch/hzhang/fix-submat_samerowdist I also add the test runex56. Please test it and let me know if there is a problem. Hong Also, I have been using -petscpartition_type but now I see >

Re: [petsc-users] unsorted local columns in 3.8?

Also, I have been using -petscpartition_type but now I see -pc_gamg_mat_partitioning_type. Is -petscpartition_type depreciated for GAMG? Is this some sort of auto generated portmanteau? I can not find pc_gamg_mat_partitioning_type in the source. On Thu, Nov 2, 2017 at 6:44 PM, Mark Adams

Re: [petsc-users] unsorted local columns in 3.8?

Great, thanks, And could you please add these parameters to a regression test? As I recall we have with-parmetis regression test. On Thu, Nov 2, 2017 at 6:35 PM, Hong wrote: > Mark: > I used petsc/src/ksp/ksp/examples/tutorials/ex56.c :-( > Now testing

Re: [petsc-users] unsorted local columns in 3.8?

Mark: I used petsc/src/ksp/ksp/examples/tutorials/ex56.c :-( Now testing src/snes/examples/tutorials/ex56.c with your options, I can reproduce the error. I'll fix it. Hong Hong, > > I've tested with master and I get the same error. Maybe the partitioning > parameters are wrong.

Re: [petsc-users] unsorted local columns in 3.8?

Hong, I've tested with master and I get the same error. Maybe the partitioning parameters are wrong. -pc_gamg_mat_partitioning_type is new to me. Can you run this (snes ex56) w/o the error? 17:33 *master* *= ~*/Codes/petsc/src/snes/examples/tutorials*$ make runex

Re: [petsc-users] unsorted local columns in 3.8?

Mark : I realize that using maint or master branch, I cannot reproduce the same error. For this example, you must use a parallel partitioner, e.g.,'current' gives me following error: [0]PETSC ERROR: This is the DEFAULT NO-OP partitioner, it currently only supports one domain per processor use

Re: [petsc-users] unsorted local columns in 3.8?

On Thu, Nov 2, 2017 at 11:07 AM, Hong wrote: > Mark, > I can reproduce this in an old branch, but not in current maint and master. > Which branch are you using to produce this error? > I am using a branch from Matt. Let me try to merge it with master. > Hong > > > On Thu,

Re: [petsc-users] unsorted local columns in 3.8?

Randy: I can reproduce it in maint branch (=v3.8) with option '-pc_gamg_mat_partitioning_type current'. My petsc is built with parmetis, thus it uses '-pc_gamg_mat_partitioning_type parmetis' by default and works well. Replacing it with 'current', I am able to see the error -- will fix it.

Re: [petsc-users] unsorted local columns in 3.8?

I used: git checkout v3.8 On Thu, Nov 2, 2017 at 10:07 AM, Hong wrote: > Mark, > I can reproduce this in an old branch, but not in current maint and master. > Which branch are you using to produce this error? > Hong > > > On Thu, Nov 2, 2017 at 9:28 AM, Mark Adams

Re: [petsc-users] unsorted local columns in 3.8?

Mark, I can reproduce this in an old branch, but not in current maint and master. Which branch are you using to produce this error? Hong On Thu, Nov 2, 2017 at 9:28 AM, Mark Adams wrote: > I am able to reproduce this with snes ex56 with 2 processors and adding >

Re: [petsc-users] unsorted local columns in 3.8?

I am able to reproduce this with snes ex56 with 2 processors and adding -pc_gamg_repartition true I'm not sure how to fix it. 10:26 1 knepley/feature-plex-boxmesh-create *= ~/Codes/petsc/src/snes/examples/tutorials$ make PETSC_DIR=/Users/markadams/Codes/petsc PETSC_ARCH=arch-macosx-gnu-g runex

Re: [petsc-users] unsorted local columns in 3.8?

Thanks Mark, both your suggestions of using pc hypre or turning off repartitioning does indeed make the error go away. On Thu, Nov 2, 2017 at 8:51 AM, Mark Adams wrote: > > > On Wed, Nov 1, 2017 at 9:36 PM, Randy Michael Churchill > wrote: > >> Doing some

Re: [petsc-users] unsorted local columns in 3.8?

On Wed, Nov 1, 2017 at 9:36 PM, Randy Michael Churchill wrote: > Doing some additional testing, the issue goes away when removing the gamg > preconditioner line from the petsc.rc: > -pc_type gamg > Yea, this is GAMG setup. This is the code. findices is create with

Re: [petsc-users] unsorted local columns in 3.8?

Doing some additional testing, the issue goes away when removing the gamg preconditioner line from the petsc.rc: -pc_type gamg On Wed, Nov 1, 2017 at 8:23 PM, Hong wrote: > Randy: > Thanks, I'll check it tomorrow. > Hong > > OK, this might not be completely satisfactory,

Re: [petsc-users] unsorted local columns in 3.8?

Randy: Thanks, I'll check it tomorrow. Hong > OK, this might not be completely satisfactory, because it doesn't show the > partitioning or how the matrix is created, but this reproduces the problem. > I wrote out my matrix, Amat, from the larger simulation, and load it in > this script. This must

Re: [petsc-users] unsorted local columns in 3.8?

Randy: It could be a bug or a missing feature in our new MatCreateSubMatrix_MPIAIJ_ SameRowDist(). It would be helpful if you can provide us a simple example that produces this example. Hong I'm running a Fortran code that was just changed over to using petsc 3.8 > (previously petsc 3.7.6). An

[petsc-users] unsorted local columns in 3.8?

I'm running a Fortran code that was just changed over to using petsc 3.8 (previously petsc 3.7.6). An error was thrown during a KSPSetUp() call. The error is "unsorted iscol_local is not implemented yet" (see full error below). I tried to trace down the difference in the source files, but where