[petsc-users] Issue with DMPlexRestoreCone from Fortran
Fabian.Jakub
Fabian.Jakub at physik.uni-muenchen.de
Wed Jul 3 13:03:42 CDT 2019
Found the change...
it was in Commit 6d563f2afc7bcefff9dc7869193a6debf1d639a5
Date: Wed Jun 26 12:32:01 2019 +0000
remove remnants of non-existing
DMPlexRestore{Cone,ConeOrientation,Support}
The patch removed the fortran stubs but not the C functions.
In this case I guess that the fortran compiler reverts to the default
calling convention and thus does not nullify the cone pointers but
rather nulls the values in the cone.
I suggest you remove the C functions to get a compiler error or revert
the path.
Many thanks,
Fabian
On 7/3/19 3:18 PM, Matthew Knepley wrote:
> 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.
>>
>>
>
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