[petsc-users] Problems imposing boundary conditions

Fri Mar 3 11:37:28 CST 2017

Hello,

I am working on a transient structural FEM code with PETSc. I managed to create a slow but functioning program with the use of petscFE and a TS solver. The code runs fine until I try to restrict movement in all three spatial directions for one face. I then get the error which is attached below.
So apparently DMPlexMatSetClosure tries to write/read beyond what was priorly allocated. I do however not call MatSeqAIJSetPreallocation myself in the code. So I’m unsure where to start looking for the bug. In my understanding, PETSc should know from the DM how much space to allocate.
Could you kindly give me a hint?

Thanks,

Max

0 SNES Function norm 2.508668036663e-06 
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Argument out of range
[0]PETSC ERROR: New nonzero at (41754,5) caused a malloc
Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to turn off this check
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.7.5-3223-g99077fc  GIT Date: 2017-02-28 13:41:43 -0600
[0]PETSC ERROR: ./S3 on a arch-linux-gnu-intel named XXXXXXX by hartig Fri Mar  3 17:55:57 2017
[0]PETSC ERROR: Configure options PETSC_ARCH=arch-linux-gnu-intel --with-cc=/opt/intel/compilers_and_libraries/linux/mpi/intel64/bin/mpiicc --with-cxx=/opt/intel/compilers_and_libraries/linux/mpi/intel64/bin/mpiicpc --with-fc=/opt/intel/compilers_and_libraries/linux/mpi/intel64/bin/mpiifort --download-ml
[0]PETSC ERROR: #1 MatSetValues_SeqAIJ() line 455 in /home/hartig/petsc/src/mat/impls/aij/seq/aij.c
[0]PETSC ERROR: #2 MatSetValues() line 1270 in /home/hartig/petsc/src/mat/interface/matrix.c
[0]PETSC ERROR: [0]ERROR in DMPlexMatSetClosure
[0]mat for sieve point 60
[0]mat row indices[0] = 41754
[0]mat row indices[1] = 41755
[0]mat row indices[2] = 41756
[0]mat row indices[3] = 41760
[0]mat row indices[4] = 41761
[0]mat row indices[5] = 41762
[0]mat row indices[6] = 41766
[0]mat row indices[7] = -41768
[0]mat row indices[8] = 41767
[0]mat row indices[9] = 41771
[0]mat row indices[10] = -41773
[0]mat row indices[11] = 41772
[0]mat row indices[12] = 41776
[0]mat row indices[13] = 41777
[0]mat row indices[14] = 41778
[0]mat row indices[15] = 41782
[0]mat row indices[16] = -41784
[0]mat row indices[17] = 41783
[0]mat row indices[18] = 261
[0]mat row indices[19] = -263
[0]mat row indices[20] = 262
[0]mat row indices[21] = 24318
[0]mat row indices[22] = 24319
[0]mat row indices[23] = 24320
[0]mat row indices[24] = -7
[0]mat row indices[25] = -8
[0]mat row indices[26] = 6
[0]mat row indices[27] = 1630
[0]mat row indices[28] = -1632
[0]mat row indices[29] = 1631
[0]mat row indices[30] = 41757
[0]mat row indices[31] = 41758
[0]mat row indices[32] = 41759
[0]mat row indices[33] = 41763
[0]mat row indices[34] = 41764
[0]mat row indices[35] = 41765
[0]mat row indices[36] = 41768
[0]mat row indices[37] = 41769
[0]mat row indices[38] = 41770
[0]mat row indices[39] = 41773
[0]mat row indices[40] = 41774
[0]mat row indices[41] = 41775
[0]mat row indices[42] = 41779
[0]mat row indices[43] = 41780
[0]mat row indices[44] = 41781
[0]mat row indices[45] = 41784
[0]mat row indices[46] = 41785
[0]mat row indices[47] = 41786
[0]mat row indices[48] = 263
[0]mat row indices[49] = 264
[0]mat row indices[50] = 265
[0]mat row indices[51] = 24321
[0]mat row indices[52] = 24322
[0]mat row indices[53] = 24323
[0]mat row indices[54] = 5
[0]mat row indices[55] = 6
[0]mat row indices[56] = 7
[0]mat row indices[57] = 1632
[0]mat row indices[58] = 1633
[0]mat row indices[59] = 1634
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[0] -2.39586 -0.206902 0.33027 -2.37741 0.011448 -0.33027 -2.44501 -0.417727 6.38053e-17 1.1468 -0.165724 0.165135 4.88671 0.435454 0. 1.18146 -0.0565489 -0.165135 0.307839 0.0658628 -0.0412838 -0.00807774 0.18 0. 0.303413 0.038569 0.0412838 -0.599871 0.115568 0. 4.17288e-11 0. 0. 4.17288e-11 0. 0. 2.08644e-11 0. 0. 4.17288e-11 0. 0. 8.34577e-11 0. 0. 4.17288e-11 0. 0. -1.56483e-11 0. 0. -1.04322e-11 0. 0. -1.56483e-11 0. 0. -1.04322e-11 0. 0.
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[0] 0.0500786 -0.197561 -0.0160508 0.24647 -0.171351 -0.00845384 -0.148706 -0.657189 0.0284819 0.00886356 0.360043 0.0163395 -0.0565489 0.270936 -0.0524184 0.0265907 1.08549 0.0349425 0.00748035 0.0412255 -0.00239755 -0.02 0.00816465 0.00641026 -0.0540894 -0.309066 -0.00600133 -0.0601388 -0.430693 -0.000852265 0. 2.08644e-11 0. 0. 4.17288e-11 0. 0. 4.17288e-11 0. 0. 4.17288e-11 0. 0. 4.17288e-11 0. 0. 8.34577e-11 0. 0. -1.56483e-11 0. 0. -1.56483e-11 0. 0. -1.04322e-11 0. 0. -1.04322e-11 0.
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[0] -0.0974804 -0.138996 0.0312437 -0.00838243 -0.0212853 -0.0117288 0.0476669 0.0715157 0.0279687 -0.175069 -0.326529 0.0128652 0.0658628 0.111396 -0.00669434 0.0174804 0.0412255 -0.00560268 0.112441 0.197005 -0.0360388 0.02 0.0244427 -0.00641026 -0.0283824 -0.045728 -0.00531859 0.0458628 0.0869535 -0.000284088 0. -1.04322e-11 0. 0. -1.56483e-11 0. 0. -1.04322e-11 0. 0. -1.04322e-11 0. 0. -1.56483e-11 0. 0. -1.56483e-11 0. 0. 1.56483e-11 0. 0. 2.60805e-12 0. 0. 2.60805e-12 0. 0. 2.60805e-12 0.
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[0] 0. 1.99342e-06 0. 0. 1.32894e-06 0. 0. 1.32894e-06 0. 0. 1.99342e-06 0. 0. 1.99342e-06 0. 0. 1.32894e-06 0. 0. -3.32236e-07 0. 0. -3.32236e-07 0. 0. -1.99342e-06 0. 0. -3.32236e-07 0. 0. -9.96708e-10 0. 0. -6.64472e-10 0. 0. -6.64472e-10 0. 0. -9.96708e-10 0. 0. -9.96708e-10 0. 0. -6.64472e-10 0. 0. 1.66118e-10 0. 0. 1.66118e-10 0. 0. 9.96708e-10 0. 0. 1.66118e-10 0.
[0] 0. 0. 1.99342e-06 0. 0. 1.32894e-06 0. 0. 1.32894e-06 0. 0. 1.99342e-06 0. 0. 1.99342e-06 0. 0. 1.32894e-06 0. 0. -3.32236e-07 0. 0. -3.32236e-07 0. 0. -1.99342e-06 0. 0. -3.32236e-07 0. 0. -9.96708e-10 0. 0. -6.64472e-10 0. 0. -6.64472e-10 0. 0. -9.96708e-10 0. 0. -9.96708e-10 0. 0. -6.64472e-10 0. 0. 1.66118e-10 0. 0. 1.66118e-10 0. 0. 9.96708e-10 0. 0. 1.66118e-10
[0] 1.99342e-06 0. 0. 1.99342e-06 0. 0. 1.99342e-06 0. 0. 1.32894e-06 0. 0. 1.32894e-06 0. 0. 1.32894e-06 0. 0. -3.32236e-07 0. 0. -3.32236e-07 0. 0. -3.32236e-07 0. 0. -1.99342e-06 0. 0. -9.96708e-10 0. 0. -9.96708e-10 0. 0. -9.96708e-10 0. 0. -6.64472e-10 0. 0. -6.64472e-10 0. 0. -6.64472e-10 0. 0. 1.66118e-10 0. 0. 1.66118e-10 0. 0. 1.66118e-10 0. 0. 9.96708e-10 0. 0.
[0] 0. 1.99342e-06 0. 0. 1.99342e-06 0. 0. 1.99342e-06 0. 0. 1.32894e-06 0. 0. 1.32894e-06 0. 0. 1.32894e-06 0. 0. -3.32236e-07 0. 0. -3.32236e-07 0. 0. -3.32236e-07 0. 0. -1.99342e-06 0. 0. -9.96708e-10 0. 0. -9.96708e-10 0. 0. -9.96708e-10 0. 0. -6.64472e-10 0. 0. -6.64472e-10 0. 0. -6.64472e-10 0. 0. 1.66118e-10 0. 0. 1.66118e-10 0. 0. 1.66118e-10 0. 0. 9.96708e-10 0.
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[0]PETSC ERROR: #3 DMPlexMatSetClosure() line 5480 in /home/hartig/petsc/src/dm/impls/plex/plex.c
[0]PETSC ERROR: #4 DMPlexComputeJacobian_Internal() line 2301 in /home/hartig/petsc/src/snes/utils/dmplexsnes.c
[0]PETSC ERROR: #5 DMPlexTSComputeIJacobianFEM() line 233 in /home/hartig/petsc/src/ts/utils/dmplexts.c
[0]PETSC ERROR: #6 TSComputeIJacobian_DMLocal() line 131 in /home/hartig/petsc/src/ts/utils/dmlocalts.c
[0]PETSC ERROR: #7 TSComputeIJacobian() line 882 in /home/hartig/petsc/src/ts/interface/ts.c
[0]PETSC ERROR: #8 SNESTSFormJacobian_Theta() line 515 in /home/hartig/petsc/src/ts/impls/implicit/theta/theta.c
[0]PETSC ERROR: #9 SNESTSFormJacobian() line 5044 in /home/hartig/petsc/src/ts/interface/ts.c
[0]PETSC ERROR: #10 SNESComputeJacobian() line 2276 in /home/hartig/petsc/src/snes/interface/snes.c
[0]PETSC ERROR: #11 SNESSolve_NEWTONLS() line 222 in /home/hartig/petsc/src/snes/impls/ls/ls.c
[0]PETSC ERROR: #12 SNESSolve() line 3967 in /home/hartig/petsc/src/snes/interface/snes.c
[0]PETSC ERROR: #13 TS_SNESSolve() line 171 in /home/hartig/petsc/src/ts/impls/implicit/theta/theta.c
[0]PETSC ERROR: #14 TSStep_Theta() line 211 in /home/hartig/petsc/src/ts/impls/implicit/theta/theta.c
[0]PETSC ERROR: #15 TSStep() line 3809 in /home/hartig/petsc/src/ts/interface/ts.c