0.7.0 Release Prep #408

pbauman · 2016-05-26T20:43:31Z

Updated CHANGES, added @nicholasmalaya to AUTHORS (thanks!), fixed one test that didn't run with mpiexec -np 8 (or any -np except 1), distcheck fixes, updated so we don't distribute the license tool (that way it's only used in a repo clone, not a tarball), and updated LICENSE date to 2016.

pbauman · 2016-05-26T20:58:07Z

Barring any comments, will merge this COB tomorrow and do the release.

pbauman · 2016-05-29T23:22:50Z

@roystgnr says he's getting a compilation failure, but I can't reproduce with GCC 4.8.5, GCC 4.9.3, or GCC 5.3. Going to hold off on tagging this until we can sort that out.

roystgnr · 2016-05-30T22:13:46Z

Working on a fix in https://github.com/roystgnr/grins/tree/fix_metaprogramming - I'll try to have it done late tonight.

This test is effectively identical to its parsed_qoi.sh cousin, it just has a few extra qois. So, use the same solver options so we can successfully run the test in parallel.

Only run if it's a cloned repo. This way, we get rid of those annoying warnings that come out in a build from a tarball.

This takes care of grinsfem#410.

pbauman · 2016-05-31T14:27:05Z

Rebased on #411.

Going to clean up some new warnings that showed up with GCC 6.1 and then I think this should be good.

roystgnr · 2016-05-31T15:13:34Z

After the fix, Everything passes for me with -np 1. With -np 4, GRINS master, I get

FAIL: exact_soln/poisson_periodic_2d_x.sh
FAIL: exact_soln/poisson_periodic_2d_y.sh
FAIL: exact_soln/poisson_periodic_3d_xz.sh
FAIL: exact_soln/poisson_periodic_3d_yz.sh
FAIL: exact_soln/poisson_periodic_3d_xy.sh
FAIL: regression/penalty_poiseuille_stab.sh

In that last regression, linear solvers are failing to converge after 2500 steps and leading to nonlinear solver convergence failure too.

In the former cases it looks like I'm getting segfaults. I'll see if I can hunt down where.

pbauman · 2016-05-31T15:14:27Z

Crap, thanks for pointing these out. I'll take care of the "after the fix" cases.

Although the current use cases will never be the SCALAR type, there may be needs in the future. This fixes warnings emitted by GCC 6.1.0.

Now we run the tests again if Antioch is enabled.

pbauman · 2016-05-31T16:44:33Z

OK, the test/run_tests_parallel_loop.sh script is almost through -np 12 and here's what I've got:

[12:36:25][pbauman@fry:/fry1/data/users/pbauman/research/grins/build/0.7.0-prep/devel/test]$ grep -e LIBMESH_RUN -e FAIL parallel_loop_check_tests.log | grep -v XFAIL
LIBMESH_RUN is mpiexec -np 1
# FAIL:  0
LIBMESH_RUN is mpiexec -np 2
# FAIL:  0
LIBMESH_RUN is mpiexec -np 3
LIBMESH_RUN is mpiexec -np 1
# FAIL:  0
LIBMESH_RUN is mpiexec -np 2
# FAIL:  0
LIBMESH_RUN is mpiexec -np 3
# FAIL:  0
LIBMESH_RUN is mpiexec -np 4
FAIL: regression/penalty_poiseuille_stab.sh
# FAIL:  1
LIBMESH_RUN is mpiexec -np 5
FAIL: regression/reacting_low_mach_antioch_kinetics_theory.sh
# FAIL:  1
LIBMESH_RUN is mpiexec -np 6
# FAIL:  0
LIBMESH_RUN is mpiexec -np 7
# FAIL:  0
LIBMESH_RUN is mpiexec -np 8
# FAIL:  0
LIBMESH_RUN is mpiexec -np 9
# FAIL:  0
LIBMESH_RUN is mpiexec -np 10
# FAIL:  0
LIBMESH_RUN is mpiexec -np 11
# FAIL:  0
LIBMESH_RUN is mpiexec -np 12

I don't know how regressions got in for those two cases. I'll fix them. I'm not seeing the Poisson-periodic failures. I'm running with SerialMesh - were your failures with ParallelMesh @roystgnr?

roystgnr · 2016-05-31T16:51:36Z

They are indeed with ParallelMesh. So if you'll worry about the solvers I'll worry about the segfaults.

pbauman · 2016-05-31T17:08:40Z

They are indeed with ParallelMesh. So if you'll worry about the solvers I'll worry about the segfaults.

👍

pbauman · 2016-05-31T17:11:09Z

Just for completeness, here's the final result of ./run_tests_parallel_loop.sh 16

LIBMESH_RUN is mpiexec -np 1
# FAIL:  0
LIBMESH_RUN is mpiexec -np 2
# FAIL:  0
LIBMESH_RUN is mpiexec -np 3
LIBMESH_RUN is mpiexec -np 1
# FAIL:  0
LIBMESH_RUN is mpiexec -np 2
# FAIL:  0
LIBMESH_RUN is mpiexec -np 3
# FAIL:  0
LIBMESH_RUN is mpiexec -np 4
FAIL: regression/penalty_poiseuille_stab.sh
# FAIL:  1
LIBMESH_RUN is mpiexec -np 5
FAIL: regression/reacting_low_mach_antioch_kinetics_theory.sh
# FAIL:  1
LIBMESH_RUN is mpiexec -np 6
# FAIL:  0
LIBMESH_RUN is mpiexec -np 7
# FAIL:  0
LIBMESH_RUN is mpiexec -np 8
# FAIL:  0
LIBMESH_RUN is mpiexec -np 9
# FAIL:  0
LIBMESH_RUN is mpiexec -np 10
# FAIL:  0
LIBMESH_RUN is mpiexec -np 11
# FAIL:  0
LIBMESH_RUN is mpiexec -np 12
FAIL: regression/reacting_low_mach_antioch_kinetics_theory.sh
# FAIL:  1
LIBMESH_RUN is mpiexec -np 13
# FAIL:  0
LIBMESH_RUN is mpiexec -np 14
# FAIL:  0
LIBMESH_RUN is mpiexec -np 15
# FAIL:  0
LIBMESH_RUN is mpiexec -np 16
FAIL: regression/reacting_low_mach_antioch_statmech_constant_prandtl.sh
# FAIL:  1

Going to focus first on PETSc versions to see if that's the issue.

pbauman · 2016-05-31T17:49:34Z

Good lord. I'm focusing on regression/penalty_poiseuille_stab.sh and going back to the revision that we both ran successfully now fails with mpiexec -np 4. I trolled through the issues and couldn't find what PETSc version we were using so I'll run through various PETSc versions to see if I can get success out of that commit again.

roystgnr · 2016-05-31T18:03:56Z

So the other regressions are clearly a libMesh failure, and not an easy one to fix. Don't let them hold up 0.7.0. If you want to hard-code mesh type == serial into the periodic BC tests that might be a good stopgap.

pbauman · 2016-05-31T18:25:31Z

So the other regressions are clearly a libMesh failure, and not an easy one to fix. Don't let them hold up 0.7.0. If you want to hard-code mesh type == serial into the periodic BC tests that might be a good stopgap.

Glad I added the tests those tests then! I'll hardcode the test as you suggest and I'll add a check in the periodic boundary condition factory that throws an error that references the libMesh issue (that we can remove once it's sorted).

Then, once I sort out these other solver-related regressions, I'll update this ticket.

pbauman · 2016-05-31T20:15:45Z

Update: So I thought our original test updating was with switch from PETSC 3.5.x to PETSC 3.6.y, but apparently not for regression/penalty_poiseuille_stab.sh. Going back d4a432e (which is after the "robustness tweaks" and before shuffling I did down stream (that shouldn't have affected the convergence behavior of the test)) I get pass with mpiexec -np 4 with PETSc 3.5.4 and fail with PETSc 3.6.0, all other things unchanged.

I'll work on updating options for this test and see if the other failures behave similarly.

pbauman · 2016-05-31T20:24:35Z

Update: Going back to the tip of this branch (pbauman/0.7.0-prep) and using PETSc 3.5.4, all the previous failing processor/test combinations pass.

This get me consistency across PETSc 3.5.4, 3.6.0, and 3.6.4, both debug and opt versions, for LIBMESH_RUN="mpiexec -np 1" through LIBMESH_RUN="mpiexec -np 16". Previously, everything was fine for 3.5.4, but then moving to PETSc 3.6, something changed (beyond the default pc_factor_shift_type and I haven't been able to ascertain what). Hopefully, these will be more consistent options.

This way we can restrict the TESTS that it runs when going through all the processor variations.

pbauman · 2016-06-02T16:56:21Z

OK, in theory, we should be good again. I've run this through PETSc 3.5.4, 3.6.4, and 3.7.1 using GCC 4.8.5 and GCC 6.1.0 using the parallel loop test up to 16 cores. I had to adjust a few a long the way. I'm resisting the urge to go back and change all the tests that use (implicitly or explicitly) -sub_pc_type ilu to -sub_pc_type lu. If this becomes a problem again, I'll probably do that to try and get more stability out of the tests again compiler/petsc changes. I did go ahead and update the parallel loop test script to take the TESTS="..." argument in 59c1876.

Two things left to do: tidy up some warnings when antioch and cantera are off and "serialize" the periodic tests/throw error for ParallelMesh in PeriodBoundary conditions.

See libMesh/libmesh#977

pbauman · 2016-06-02T19:37:20Z

OK, I think we're ready to go. I snuck in adding accessors for the Neumann bcs that I'd forgotten to put in the boundary conditions PR.

We're almost to the point where we could add -Werror for Antioch enabled and Cantera disabled. Just a couple of warnings to clear up in ParsedFunction and ParsedFEMFunction on the libMesh side.

roystgnr · 2016-06-02T19:45:13Z

🏆

pbauman · 2016-06-02T19:47:48Z

Have to run now, but will merge, tag, and release tonight.

pbauman · 2016-06-02T19:48:16Z

(not merging now in case anyone wants to look a little closer before tonight)

roystgnr closed this May 30, 2016

roystgnr reopened this May 30, 2016

pbauman mentioned this pull request May 31, 2016

Antioch tests aren't getting disabled when Antioch is #410

Closed

pbauman added 9 commits May 31, 2016 10:26

Updated CHANGES for 0.7.0 release

1016f86

Add @nicholasmalaya to AUTHORS

d00c280

Fix unused variable warning

5e476c2

Add PETSC_OPTIONS to regression/parsed_qoi_scalar.sh test

b17f017

This test is effectively identical to its parsed_qoi.sh cousin, it just has a few extra qois. So, use the same solver options so we can successfully run the test in parallel.

distcheck fixes

ae0e1b5

Remove svn cruft from build system

334ec37

Don't distribute license tool

9329336

Only run if it's a cloned repo. This way, we get rid of those annoying warnings that come out in a build from a tarball.

For real, it's 2016

b60652f

Skip Antioch regression test when Antioch not present

64ac014

This takes care of grinsfem#410.

pbauman force-pushed the 0.7.0-prep branch from 0dd005a to 64ac014 Compare May 31, 2016 14:26

pbauman added 2 commits May 31, 2016 11:27

Pass Elem* to build_new_fe helper function

8859cb2

Although the current use cases will never be the SCALAR type, there may be needs in the future. This fixes warnings emitted by GCC 6.1.0.

Fix wrong variable for GRINS_ANTIOCH_ENABLED in tests

9a97d60

Now we run the tests again if Antioch is enabled.

roystgnr mentioned this pull request May 31, 2016

delete_remote_elements(DistributedMesh) deletes periodic neighbor elements libMesh/libmesh#977

Closed

pbauman added 3 commits June 1, 2016 13:28

Needed to soften up this test for GCC 6.1/PETSc 3.6.4

58bb855

Add optional second argument for parallel loop test script

59c1876

This way we can restrict the TESTS that it runs when going through all the processor variations.

pbauman added 4 commits June 2, 2016 14:52

Clean-up warnings with both Antioch and Cantera are disabled

e299fb4

Use SerialMesh only in periodic tests

cb13f10

See libMesh/libmesh#977

Throw error for ParallelMesh+periodic boundary conditions

03b1146

Add accessors for neumann bcs in MultiphysicsSystem

59ad051

pbauman merged commit 7de3104 into grinsfem:master Jun 3, 2016

pbauman deleted the 0.7.0-prep branch June 3, 2016 00:56

dmcdougall mentioned this pull request Oct 4, 2016

Fix licence tool libqueso/queso#470

Merged

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0.7.0 Release Prep #408

0.7.0 Release Prep #408

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0.7.0 Release Prep #408

0.7.0 Release Prep #408

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