[petsc-users] Issue with DMPlexRestoreCone from Fortran
Matthew Knepley
knepley at gmail.com
Wed Jul 3 08:18:05 CDT 2019
On Wed, Jul 3, 2019 at 7:38 AM Fabian.Jakub via petsc-users <
petsc-users at mcs.anl.gov> wrote:
> Dear Matt, Dear Petsc
>
> After my recent pull of petsc master I encounter test fails that use
> dmplex meshes.
>
> I attached a simple script to show an issue where DMPlexRestoreCone
> mangles the cone relationships in the DM.
>
> The behaviour happens with gcc 7.4.0 aswell as icc 19.0.3.199
> @ current petsc/master d3dc048301fdb3e4c282b528e7b28910551cfe13
>
> We recently had a system update and I am not 100% sure if this is some
> weird stuff going on at my end or if this is indeed Plex related or if I
> should not call Restore in the inner loop.
>
> Anyway, I would be most grateful if you could try to reproduce the error
> and hint me towards a solution.
>
Hi Fabian,
I think it might be your system update. Seems to run fine for me:
master *:~/Downloads/tmp$ ./plex_prism
Cone 0 : 1 2 3 4
5
Cone 1 : 6 7 8
Cone 2 : 12 13 14
Cone 3 : 7 9 11 13
Cone 4 : 6 9 10 12
Cone 5 : 8 10 11 14
Cone 6 : 15 16
Cone 7 : 15 17
Cone 8 : 16 17
Cone 9 : 15 18
Cone 10 : 16 19
Cone 11 : 17 20
Cone 12 : 18 19
Cone 13 : 18 20
Cone 14 : 19 20
Cone 15 :
Cone 16 :
Cone 17 :
Cone 18 :
Cone 19 :
Cone 20 :
master *:~/Downloads/tmp$ ./plex_prism -show_plex ::ascii_info_detail
DM Object: testplex 1 MPI processes
type: plex
testplex in 3 dimensions:
Supports:
[0] Max support size: 3
[0]: 1 ----> 0
[0]: 2 ----> 0
[0]: 3 ----> 0
[0]: 4 ----> 0
[0]: 5 ----> 0
[0]: 6 ----> 1
[0]: 6 ----> 4
[0]: 7 ----> 1
[0]: 7 ----> 3
[0]: 8 ----> 1
[0]: 8 ----> 5
[0]: 9 ----> 3
[0]: 9 ----> 4
[0]: 10 ----> 4
[0]: 10 ----> 5
[0]: 11 ----> 3
[0]: 11 ----> 5
[0]: 12 ----> 2
[0]: 12 ----> 4
[0]: 13 ----> 2
[0]: 13 ----> 3
[0]: 14 ----> 2
[0]: 14 ----> 5
[0]: 15 ----> 6
[0]: 15 ----> 7
[0]: 15 ----> 9
[0]: 16 ----> 6
[0]: 16 ----> 8
[0]: 16 ----> 10
[0]: 17 ----> 7
[0]: 17 ----> 8
[0]: 17 ----> 11
[0]: 18 ----> 9
[0]: 18 ----> 12
[0]: 18 ----> 13
[0]: 19 ----> 10
[0]: 19 ----> 12
[0]: 19 ----> 14
[0]: 20 ----> 11
[0]: 20 ----> 13
[0]: 20 ----> 14
Cones:
[0] Max cone size: 5
[0]: 0 <---- 1 (0)
[0]: 0 <---- 2 (0)
[0]: 0 <---- 3 (0)
[0]: 0 <---- 4 (0)
[0]: 0 <---- 5 (0)
[0]: 1 <---- 6 (0)
[0]: 1 <---- 7 (0)
[0]: 1 <---- 8 (0)
[0]: 2 <---- 12 (0)
[0]: 2 <---- 13 (0)
[0]: 2 <---- 14 (0)
[0]: 3 <---- 7 (0)
[0]: 3 <---- 9 (0)
[0]: 3 <---- 11 (0)
[0]: 3 <---- 13 (0)
[0]: 4 <---- 6 (0)
[0]: 4 <---- 9 (0)
[0]: 4 <---- 10 (0)
[0]: 4 <---- 12 (0)
[0]: 5 <---- 8 (0)
[0]: 5 <---- 10 (0)
[0]: 5 <---- 11 (0)
[0]: 5 <---- 14 (0)
[0]: 6 <---- 15 (0)
[0]: 6 <---- 16 (0)
[0]: 7 <---- 15 (0)
[0]: 7 <---- 17 (0)
[0]: 8 <---- 16 (0)
[0]: 8 <---- 17 (0)
[0]: 9 <---- 15 (0)
[0]: 9 <---- 18 (0)
[0]: 10 <---- 16 (0)
[0]: 10 <---- 19 (0)
[0]: 11 <---- 17 (0)
[0]: 11 <---- 20 (0)
[0]: 12 <---- 18 (0)
[0]: 12 <---- 19 (0)
[0]: 13 <---- 18 (0)
[0]: 13 <---- 20 (0)
[0]: 14 <---- 19 (0)
[0]: 14 <---- 20 (0)
coordinates with 1 fields
field 0 with 3 components
Process 0:
( 0) dim 0 offset 0
( 1) dim 0 offset 0
( 2) dim 0 offset 0
( 3) dim 0 offset 0
( 4) dim 0 offset 0
( 5) dim 0 offset 0
( 6) dim 0 offset 0
( 7) dim 0 offset 0
( 8) dim 0 offset 0
( 9) dim 0 offset 0
( 10) dim 0 offset 0
( 11) dim 0 offset 0
( 12) dim 0 offset 0
( 13) dim 0 offset 0
( 14) dim 0 offset 0
( 15) dim 3 offset 0 0. 0. 0.
( 16) dim 3 offset 3 0. 2. 0.
( 17) dim 3 offset 6 2. 1. 0.
( 18) dim 3 offset 9 0. 0. 1.
( 19) dim 3 offset 12 0. 2. 1.
( 20) dim 3 offset 15 2. 1. 1.
Cone 0 : 1 2 3 4
5
Cone 1 : 6 7 8
Cone 2 : 12 13 14
Cone 3 : 7 9 11 13
Cone 4 : 6 9 10 12
Cone 5 : 8 10 11 14
Cone 6 : 15 16
Cone 7 : 15 17
Cone 8 : 16 17
Cone 9 : 15 18
Cone 10 : 16 19
Cone 11 : 17 20
Cone 12 : 18 19
Cone 13 : 18 20
Cone 14 : 19 20
Cone 15 :
Cone 16 :
Cone 17 :
Cone 18 :
Cone 19 :
Cone 20 :
DM Object: testplex 1 MPI processes
type: plex
testplex in 3 dimensions:
Supports:
[0] Max support size: 3
[0]: 1 ----> 0
[0]: 2 ----> 0
[0]: 3 ----> 0
[0]: 4 ----> 0
[0]: 5 ----> 0
[0]: 6 ----> 1
[0]: 6 ----> 4
[0]: 7 ----> 1
[0]: 7 ----> 3
[0]: 8 ----> 1
[0]: 8 ----> 5
[0]: 9 ----> 3
[0]: 9 ----> 4
[0]: 10 ----> 4
[0]: 10 ----> 5
[0]: 11 ----> 3
[0]: 11 ----> 5
[0]: 12 ----> 2
[0]: 12 ----> 4
[0]: 13 ----> 2
[0]: 13 ----> 3
[0]: 14 ----> 2
[0]: 14 ----> 5
[0]: 15 ----> 6
[0]: 15 ----> 7
[0]: 15 ----> 9
[0]: 16 ----> 6
[0]: 16 ----> 8
[0]: 16 ----> 10
[0]: 17 ----> 7
[0]: 17 ----> 8
[0]: 17 ----> 11
[0]: 18 ----> 9
[0]: 18 ----> 12
[0]: 18 ----> 13
[0]: 19 ----> 10
[0]: 19 ----> 12
[0]: 19 ----> 14
[0]: 20 ----> 11
[0]: 20 ----> 13
[0]: 20 ----> 14
Cones:
[0] Max cone size: 5
[0]: 0 <---- 1 (0)
[0]: 0 <---- 2 (0)
[0]: 0 <---- 3 (0)
[0]: 0 <---- 4 (0)
[0]: 0 <---- 5 (0)
[0]: 1 <---- 6 (0)
[0]: 1 <---- 7 (0)
[0]: 1 <---- 8 (0)
[0]: 2 <---- 12 (0)
[0]: 2 <---- 13 (0)
[0]: 2 <---- 14 (0)
[0]: 3 <---- 7 (0)
[0]: 3 <---- 9 (0)
[0]: 3 <---- 11 (0)
[0]: 3 <---- 13 (0)
[0]: 4 <---- 6 (0)
[0]: 4 <---- 9 (0)
[0]: 4 <---- 10 (0)
[0]: 4 <---- 12 (0)
[0]: 5 <---- 8 (0)
[0]: 5 <---- 10 (0)
[0]: 5 <---- 11 (0)
[0]: 5 <---- 14 (0)
[0]: 6 <---- 15 (0)
[0]: 6 <---- 16 (0)
[0]: 7 <---- 15 (0)
[0]: 7 <---- 17 (0)
[0]: 8 <---- 16 (0)
[0]: 8 <---- 17 (0)
[0]: 9 <---- 15 (0)
[0]: 9 <---- 18 (0)
[0]: 10 <---- 16 (0)
[0]: 10 <---- 19 (0)
[0]: 11 <---- 17 (0)
[0]: 11 <---- 20 (0)
[0]: 12 <---- 18 (0)
[0]: 12 <---- 19 (0)
[0]: 13 <---- 18 (0)
[0]: 13 <---- 20 (0)
[0]: 14 <---- 19 (0)
[0]: 14 <---- 20 (0)
coordinates with 1 fields
field 0 with 3 components
Process 0:
( 0) dim 0 offset 0
( 1) dim 0 offset 0
( 2) dim 0 offset 0
( 3) dim 0 offset 0
( 4) dim 0 offset 0
( 5) dim 0 offset 0
( 6) dim 0 offset 0
( 7) dim 0 offset 0
( 8) dim 0 offset 0
( 9) dim 0 offset 0
( 10) dim 0 offset 0
( 11) dim 0 offset 0
( 12) dim 0 offset 0
( 13) dim 0 offset 0
( 14) dim 0 offset 0
( 15) dim 3 offset 0 0. 0. 0.
( 16) dim 3 offset 3 0. 2. 0.
( 17) dim 3 offset 6 2. 1. 0.
( 18) dim 3 offset 9 0. 0. 1.
( 19) dim 3 offset 12 0. 2. 1.
( 20) dim 3 offset 15 2. 1. 1.
Thanks,
Matt
> As always, many many thanks!
>
> Fabian
>
> P.S. here the output of
> make run
>
> and note the cones, the second time they are outputted...
>
> ./plex_prism -show_plex ::ascii_info_detail
> DM Object: testplex 1 MPI processes
> type: plex
> testplex in 3 dimensions:
> Supports:
> [0] Max support size: 3
> [0]: 1 ----> 0
> [0]: 2 ----> 0
> [0]: 3 ----> 0
> [0]: 4 ----> 0
> [0]: 5 ----> 0
> [0]: 6 ----> 1
> [0]: 6 ----> 4
> [0]: 7 ----> 1
> [0]: 7 ----> 3
> [0]: 8 ----> 1
> [0]: 8 ----> 5
> [0]: 9 ----> 3
> [0]: 9 ----> 4
> [0]: 10 ----> 4
> [0]: 10 ----> 5
> [0]: 11 ----> 3
> [0]: 11 ----> 5
> [0]: 12 ----> 2
> [0]: 12 ----> 4
> [0]: 13 ----> 2
> [0]: 13 ----> 3
> [0]: 14 ----> 2
> [0]: 14 ----> 5
> [0]: 15 ----> 6
> [0]: 15 ----> 7
> [0]: 15 ----> 9
> [0]: 16 ----> 6
> [0]: 16 ----> 8
> [0]: 16 ----> 10
> [0]: 17 ----> 7
> [0]: 17 ----> 8
> [0]: 17 ----> 11
> [0]: 18 ----> 9
> [0]: 18 ----> 12
> [0]: 18 ----> 13
> [0]: 19 ----> 10
> [0]: 19 ----> 12
> [0]: 19 ----> 14
> [0]: 20 ----> 11
> [0]: 20 ----> 13
> [0]: 20 ----> 14
> Cones:
> [0] Max cone size: 5
> [0]: 0 <---- 1 (0)
> [0]: 0 <---- 2 (0)
> [0]: 0 <---- 3 (0)
> [0]: 0 <---- 4 (0)
> [0]: 0 <---- 5 (0)
> [0]: 1 <---- 6 (0)
> [0]: 1 <---- 7 (0)
> [0]: 1 <---- 8 (0)
> [0]: 2 <---- 12 (0)
> [0]: 2 <---- 13 (0)
> [0]: 2 <---- 14 (0)
> [0]: 3 <---- 7 (0)
> [0]: 3 <---- 9 (0)
> [0]: 3 <---- 11 (0)
> [0]: 3 <---- 13 (0)
> [0]: 4 <---- 6 (0)
> [0]: 4 <---- 9 (0)
> [0]: 4 <---- 10 (0)
> [0]: 4 <---- 12 (0)
> [0]: 5 <---- 8 (0)
> [0]: 5 <---- 10 (0)
> [0]: 5 <---- 11 (0)
> [0]: 5 <---- 14 (0)
> [0]: 6 <---- 15 (0)
> [0]: 6 <---- 16 (0)
> [0]: 7 <---- 15 (0)
> [0]: 7 <---- 17 (0)
> [0]: 8 <---- 16 (0)
> [0]: 8 <---- 17 (0)
> [0]: 9 <---- 15 (0)
> [0]: 9 <---- 18 (0)
> [0]: 10 <---- 16 (0)
> [0]: 10 <---- 19 (0)
> [0]: 11 <---- 17 (0)
> [0]: 11 <---- 20 (0)
> [0]: 12 <---- 18 (0)
> [0]: 12 <---- 19 (0)
> [0]: 13 <---- 18 (0)
> [0]: 13 <---- 20 (0)
> [0]: 14 <---- 19 (0)
> [0]: 14 <---- 20 (0)
> coordinates with 1 fields
> field 0 with 3 components
> Process 0:
> ( 0) dim 0 offset 0
> ( 1) dim 0 offset 0
> ( 2) dim 0 offset 0
> ( 3) dim 0 offset 0
> ( 4) dim 0 offset 0
> ( 5) dim 0 offset 0
> ( 6) dim 0 offset 0
> ( 7) dim 0 offset 0
> ( 8) dim 0 offset 0
> ( 9) dim 0 offset 0
> ( 10) dim 0 offset 0
> ( 11) dim 0 offset 0
> ( 12) dim 0 offset 0
> ( 13) dim 0 offset 0
> ( 14) dim 0 offset 0
> ( 15) dim 3 offset 0 0. 0. 0.
> ( 16) dim 3 offset 3 0. 2. 0.
> ( 17) dim 3 offset 6 2. 1. 0.
> ( 18) dim 3 offset 9 0. 0. 1.
> ( 19) dim 3 offset 12 0. 2. 1.
> ( 20) dim 3 offset 15 2. 1. 1.
>
>
>
>
>
>
>
>
>
> DM Object: testplex 1 MPI processes
> type: plex
> testplex in 3 dimensions:
> Supports:
> [0] Max support size: 3
> [0]: 1 ----> 0
> [0]: 2 ----> 0
> [0]: 3 ----> 0
> [0]: 4 ----> 0
> [0]: 5 ----> 0
> [0]: 6 ----> 1
> [0]: 6 ----> 4
> [0]: 7 ----> 1
> [0]: 7 ----> 3
> [0]: 8 ----> 1
> [0]: 8 ----> 5
> [0]: 9 ----> 3
> [0]: 9 ----> 4
> [0]: 10 ----> 4
> [0]: 10 ----> 5
> [0]: 11 ----> 3
> [0]: 11 ----> 5
> [0]: 12 ----> 2
> [0]: 12 ----> 4
> [0]: 13 ----> 2
> [0]: 13 ----> 3
> [0]: 14 ----> 2
> [0]: 14 ----> 5
> [0]: 15 ----> 6
> [0]: 15 ----> 7
> [0]: 15 ----> 9
> [0]: 16 ----> 6
> [0]: 16 ----> 8
> [0]: 16 ----> 10
> [0]: 17 ----> 7
> [0]: 17 ----> 8
> [0]: 17 ----> 11
> [0]: 18 ----> 9
> [0]: 18 ----> 12
> [0]: 18 ----> 13
> [0]: 19 ----> 10
> [0]: 19 ----> 12
> [0]: 19 ----> 14
> [0]: 20 ----> 11
> [0]: 20 ----> 13
> [0]: 20 ----> 14
> Cones:
> [0] Max cone size: 5
> [0]: 0 <---- 0 (0)
> [0]: 0 <---- 0 (0)
> [0]: 0 <---- 3 (0)
> [0]: 0 <---- 4 (0)
> [0]: 0 <---- 5 (0)
> [0]: 1 <---- 0 (0)
> [0]: 1 <---- 0 (0)
> [0]: 1 <---- 8 (0)
> [0]: 2 <---- 0 (0)
> [0]: 2 <---- 0 (0)
> [0]: 2 <---- 14 (0)
> [0]: 3 <---- 0 (0)
> [0]: 3 <---- 0 (0)
> [0]: 3 <---- 11 (0)
> [0]: 3 <---- 13 (0)
> [0]: 4 <---- 0 (0)
> [0]: 4 <---- 0 (0)
> [0]: 4 <---- 10 (0)
> [0]: 4 <---- 12 (0)
> [0]: 5 <---- 0 (0)
> [0]: 5 <---- 0 (0)
> [0]: 5 <---- 11 (0)
> [0]: 5 <---- 14 (0)
> [0]: 6 <---- 0 (0)
> [0]: 6 <---- 0 (0)
> [0]: 7 <---- 0 (0)
> [0]: 7 <---- 0 (0)
> [0]: 8 <---- 0 (0)
> [0]: 8 <---- 0 (0)
> [0]: 9 <---- 0 (0)
> [0]: 9 <---- 0 (0)
> [0]: 10 <---- 0 (0)
> [0]: 10 <---- 0 (0)
> [0]: 11 <---- 0 (0)
> [0]: 11 <---- 0 (0)
> [0]: 12 <---- 0 (0)
> [0]: 12 <---- 0 (0)
> [0]: 13 <---- 0 (0)
> [0]: 13 <---- 0 (0)
> [0]: 14 <---- 0 (0)
> [0]: 14 <---- 0 (0)
> coordinates with 1 fields
> field 0 with 3 components
> Process 0:
> ( 0) dim 0 offset 0
> ( 1) dim 0 offset 0
> ( 2) dim 0 offset 0
> ( 3) dim 0 offset 0
> ( 4) dim 0 offset 0
> ( 5) dim 0 offset 0
> ( 6) dim 0 offset 0
> ( 7) dim 0 offset 0
> ( 8) dim 0 offset 0
> ( 9) dim 0 offset 0
> ( 10) dim 0 offset 0
> ( 11) dim 0 offset 0
> ( 12) dim 0 offset 0
> ( 13) dim 0 offset 0
> ( 14) dim 0 offset 0
> ( 15) dim 3 offset 0 0. 0. 0.
> ( 16) dim 3 offset 3 0. 2. 0.
> ( 17) dim 3 offset 6 2. 1. 0.
> ( 18) dim 3 offset 9 0. 0. 1.
> ( 19) dim 3 offset 12 0. 2. 1.
> ( 20) dim 3 offset 15 2. 1. 1.
>
>
--
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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