Re: [petsc-users] Periodic boundary condition

20 Oct 2022

      Some of the valgrind information does not appear to make sense

PetscMemcpy() is not calling SNESSolve() so I suspect there must be some serious corruption of something to this impossible stack trace

==236074==    by 0x6FD160F: SNESSolve (snes.c:4569)
==236074==    by 0x711917E: PetscMemcpy (bdf.c:223)

From

==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x5F10977: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:146)
==236074==    by 0x5F10977: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284)
==236074==    by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242)
==236074==    by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79)
==236074==    by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717)
==236074==    by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324)
==236074==    by 0x6FD160F: SNESSolve (snes.c:4569)
==236074==    by 0x711917E: PetscMemcpy (bdf.c:223)
==236074==    by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074==    by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074==    by 0x70C363A: TSStep (ts.c:3757)
==236074==    by 0x70C1999: TSSolve (ts.c:4154)
==236074==    by 0x402594: main (one.c:391)

I suggest you run with -malloc_debug instead of valgrind and see if any errors are reported. If so you can add the macro CHKMEMQ; inside your function evaluation where you write to memory to see if anything is writing to the wrong location. For example wherever you assign aF such as

	aF[j][i].vx=(x3+x4+x5+x6+x7+x8+x9-x1-x2)*user->hx;

this can help you determine the exact line number where you are writing to the wrong location and determine what might be the cause.
...
On Oct 20, 2022, at 6:45 PM, Sepideh Kavousi <[email protected]> wrote:
Hello,
I want to solve my 5 PDEs based on finite  difference method using periodic BC in x-direction and non-periodic in y-direction but I run into error (Segmentation Violation, probably memory access out of range).
For this, I discretize my equation in FormFunction function. My PDE discretization in (i,j) node needs data on (i+1,j), (i+2,j), (i-1,j), (i-2,j), (i,j+1), (i,j+2), (i,j-1), (i,j-2) points.
In my previous codes that the x-direction was non-periodic (no flux) boundary condition, I:
i)                    implemented the no flux BC for i=0 and i=Nx-1,
ii)                   set i+2= Nx-1 in discretizing (Nx-2,j) and i+2= 0 in discretizing (1,j)
iii)                 discretized my equation for i=1..Nx-2.
I am not sure how I should do the periodic BC. From the following discussions (https://lists.mcs.anl.gov/pipermail/petsc-users/2012-May/013476.html <https://lists.mcs.anl.gov/pipermail/petsc-users/2012-May/013476.html>  andhttps://lists.mcs.anl.gov/pipermail/petsc-users/2016-May/029273.html <https://lists.mcs.anl.gov/pipermail/petsc-users/2016-May/029273.html>), I guess I should not do step (i) (stated above) for the x-boundaries and just do step (iii) for i=0..Nx-1. If I just focus on solving 2 of the PDEs which does need data on (i+2,j), (i-2,j), (i,j+2), (i,j-2) points for discretizing equation in (i,j) node, I still run into error:
Running with Valgrind (just 1 processor) gave the following file. I did not find any information which gives me hint on the error source.
Can you please help me to find the error? 
Best,
Sepideh
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x4C29E39: malloc (vg_replace_malloc.c:309)
==236074==    by 0x1B79E59B: MPID_Init (mpid_init.c:1649)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x2183B805: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218323C1: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218341C7: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x400F9C2: _dl_init (in /usr/lib64/ld-2.17.so)
==236074==    by 0x401459D: dl_open_worker (in /usr/lib64/ld-2.17.so)
==236074==    by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074==    by 0x4013B8A: _dl_open (in /usr/lib64/ld-2.17.so)
==236074==    by 0x1AEA4FAA: dlopen_doit (in /usr/lib64/libdl-2.17.so)
==236074==    by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074==    by 0x1AEA55AC: _dlerror_run (in /usr/lib64/libdl-2.17.so)
==236074==    by 0x1AEA5040: dlopen@@GLIBC_2.2.5 (in /usr/lib64/libdl-2.17.so)
==236074==    by 0x1B8198DC: MPID_nem_ofi_init (ofi_init.c:158)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x2183B810: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218323C1: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218341C7: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x400F9C2: _dl_init (in /usr/lib64/ld-2.17.so)
==236074==    by 0x401459D: dl_open_worker (in /usr/lib64/ld-2.17.so)
==236074==    by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074==    by 0x4013B8A: _dl_open (in /usr/lib64/ld-2.17.so)
==236074==    by 0x1AEA4FAA: dlopen_doit (in /usr/lib64/libdl-2.17.so)
==236074==    by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074==    by 0x1AEA55AC: _dlerror_run (in /usr/lib64/libdl-2.17.so)
==236074==    by 0x1AEA5040: dlopen@@GLIBC_2.2.5 (in /usr/lib64/libdl-2.17.so)
==236074==    by 0x1B8198DC: MPID_nem_ofi_init (ofi_init.c:158)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x218323C8: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218341C7: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x400F9C2: _dl_init (in /usr/lib64/ld-2.17.so)
==236074==    by 0x401459D: dl_open_worker (in /usr/lib64/ld-2.17.so)
==236074==    by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074==    by 0x4013B8A: _dl_open (in /usr/lib64/ld-2.17.so)
==236074==    by 0x1AEA4FAA: dlopen_doit (in /usr/lib64/libdl-2.17.so)
==236074==    by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074==    by 0x1AEA55AC: _dlerror_run (in /usr/lib64/libdl-2.17.so)
==236074==    by 0x1AEA5040: dlopen@@GLIBC_2.2.5 (in /usr/lib64/libdl-2.17.so)
==236074==    by 0x1B8198DC: MPID_nem_ofi_init (ofi_init.c:158)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Use of uninitialised value of size 8
==236074==    at 0x218323CF: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218341C7: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x400F9C2: _dl_init (in /usr/lib64/ld-2.17.so)
==236074==    by 0x401459D: dl_open_worker (in /usr/lib64/ld-2.17.so)
==236074==    by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074==    by 0x4013B8A: _dl_open (in /usr/lib64/ld-2.17.so)
==236074==    by 0x1AEA4FAA: dlopen_doit (in /usr/lib64/libdl-2.17.so)
==236074==    by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074==    by 0x1AEA55AC: _dlerror_run (in /usr/lib64/libdl-2.17.so)
==236074==    by 0x1AEA5040: dlopen@@GLIBC_2.2.5 (in /usr/lib64/libdl-2.17.so)
==236074==    by 0x1B8198DC: MPID_nem_ofi_init (ofi_init.c:158)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Use of uninitialised value of size 8
==236074==    at 0x218323E5: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218341C7: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x400F9C2: _dl_init (in /usr/lib64/ld-2.17.so)
==236074==    by 0x401459D: dl_open_worker (in /usr/lib64/ld-2.17.so)
==236074==    by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074==    by 0x4013B8A: _dl_open (in /usr/lib64/ld-2.17.so)
==236074==    by 0x1AEA4FAA: dlopen_doit (in /usr/lib64/libdl-2.17.so)
==236074==    by 0x400F7D3: _dl_catch_error (in /usr/lib64/ld-2.17.so)
==236074==    by 0x1AEA55AC: _dlerror_run (in /usr/lib64/libdl-2.17.so)
==236074==    by 0x1AEA5040: dlopen@@GLIBC_2.2.5 (in /usr/lib64/libdl-2.17.so)
==236074==    by 0x1B8198DC: MPID_nem_ofi_init (ofi_init.c:158)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x2183B805: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218323C1: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218343EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2180E4F3: psm2_init (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2112D7E6: psmx2_getinfo (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x210AC753: fi_getinfo@@FABRIC_1.2 (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x1B819AB7: MPID_nem_ofi_init (ofi_init.c:245)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x2183B810: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218323C1: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218343EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2180E4F3: psm2_init (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2112D7E6: psmx2_getinfo (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x210AC753: fi_getinfo@@FABRIC_1.2 (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x1B819AB7: MPID_nem_ofi_init (ofi_init.c:245)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x218323C8: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218343EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2180E4F3: psm2_init (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2112D7E6: psmx2_getinfo (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x210AC753: fi_getinfo@@FABRIC_1.2 (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x1B819AB7: MPID_nem_ofi_init (ofi_init.c:245)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Use of uninitialised value of size 8
==236074==    at 0x218323CF: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218343EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2180E4F3: psm2_init (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2112D7E6: psmx2_getinfo (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x210AC753: fi_getinfo@@FABRIC_1.2 (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x1B819AB7: MPID_nem_ofi_init (ofi_init.c:245)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Use of uninitialised value of size 8
==236074==    at 0x218323E5: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218343EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2180E4F3: psm2_init (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2112D7E6: psmx2_getinfo (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x210AC753: fi_getinfo@@FABRIC_1.2 (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x1B819AB7: MPID_nem_ofi_init (ofi_init.c:245)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x2183B69A: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x21836F9A: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x21834872: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217F7F5D: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155)
==236074==    by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x2183B7B8: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x21836F9A: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x21834872: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217F7F5D: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155)
==236074==    by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x2183B69A: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217F88C8: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155)
==236074==    by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x2183B7B8: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217F88C8: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155)
==236074==    by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x2183B69A: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217F916B: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155)
==236074==    by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x2183B7B8: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x218371EC: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x21837077: hfi_get_port_lid (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217F916B: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217FDC29: ??? (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x217FCA91: psm2_ep_open (in /usr/lib64/libpsm2.so.2.2)
==236074==    by 0x2112FB19: psmx2_trx_ctxt_alloc (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x21138089: psmx2_ep_open (in /opt/apps/libfabric/1.7.0/lib/libfabric.so.1.10.0)
==236074==    by 0x1B81A6A1: fi_endpoint (fi_endpoint.h:155)
==236074==    by 0x1B81A6A1: MPID_nem_ofi_init (ofi_init.c:377)
==236074==    by 0x1B7B5C55: ??? (mpid_nem_init.c:231)
==236074==    by 0x1B7B3F92: MPID_nem_init_ckpt (mpid_nem_init.c:954)
==236074==    by 0x1B580640: MPIDI_CH3_Init (ch3_init.c:125)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x1B1DA260: __I_MPI___intel_sse2_strncmp (in /opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib/libmpifort.so.12.0)
==236074==    by 0x1B8CFBA1: ??? (simple_pmi.c:2376)
==236074==    by 0x1B8CBDAD: PMIi_InitIfSingleton (simple_pmi.c:2883)
==236074==    by 0x1B8CBDAD: iPMI_KVS_Get (simple_pmi.c:751)
==236074==    by 0x1B7CCC1E: ??? (mpidi_pg.c:949)
==236074==    by 0x1B817EAA: MPID_nem_ofi_post_init (ofi_init.c:1736)
==236074==    by 0x1B7B3575: MPID_nem_init_post (mpid_nem_init.c:1421)
==236074==    by 0x1B5806E3: MPIDI_CH3_Init (ch3_init.c:146)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x1B1DA383: __I_MPI___intel_sse2_strncmp (in /opt/intel/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib/libmpifort.so.12.0)
==236074==    by 0x1B8CFBA1: ??? (simple_pmi.c:2376)
==236074==    by 0x1B8CBDAD: PMIi_InitIfSingleton (simple_pmi.c:2883)
==236074==    by 0x1B8CBDAD: iPMI_KVS_Get (simple_pmi.c:751)
==236074==    by 0x1B7CCC1E: ??? (mpidi_pg.c:949)
==236074==    by 0x1B817EAA: MPID_nem_ofi_post_init (ofi_init.c:1736)
==236074==    by 0x1B7B3575: MPID_nem_init_post (mpid_nem_init.c:1421)
==236074==    by 0x1B5806E3: MPIDI_CH3_Init (ch3_init.c:146)
==236074==    by 0x1B79F02D: MPID_Init (mpid_init.c:1857)
==236074==    by 0x1B73FAEA: MPIR_Init_thread (initthread.c:717)
==236074==    by 0x1B73D795: PMPI_Init_thread (initthread.c:1061)
==236074==    by 0x5264A94: PetscInitialize (pinit.c:907)
==236074==    by 0x40219D: main (one.c:335)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x1E48032E: __intel_sse4_strcpy (in /opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64_lin/libirc.so)
==236074==    by 0x51FD8BE: PetscStrcpy (str.c:354)
==236074==    by 0x51FD7A3: PetscStrallocpy (str.c:188)
==236074==    by 0x52A39CE: PetscEventRegLogRegister (eventlog.c:313)
==236074==    by 0x527D89A: PetscLogEventRegister (plog.c:693)
==236074==    by 0x6A56A20: PCBDDCInitializePackage (bddc.c:3115)
==236074==    by 0x6E1A515: PCInitializePackage (dlregisksp.c:59)
==236074==    by 0x6DB1A86: PCCreate (precon.c:382)
==236074==    by 0x6E05167: KSPGetPC (itfunc.c:1837)
==236074==    by 0x6E0FC5C: KSPSetDM (iterativ.c:1150)
==236074==    by 0x6FDD27B: SNESSetDM (snes.c:5402)
==236074==    by 0x70B85F7: TSGetSNES (ts.c:2914)
==236074==    by 0x70BE430: TSSetDM (ts.c:4949)
==236074==    by 0x402496: main (one.c:378)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x1E4782BA: __intel_ssse3_strncpy (in /opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64_lin/libirc.so)
==236074==    by 0x51FFD24: PetscStrncpy (str.c:392)
==236074==    by 0x51FEB03: PetscStrreplace (str.c:1142)
==236074==    by 0x52C9958: PetscViewerFileSetName (filev.c:659)
==236074==    by 0x52B743B: PetscViewerVTKOpen (vtkv.c:279)
==236074==    by 0x70C76E6: TSMonitorSolutionVTK (ts.c:5580)
==236074==    by 0x40313C: FormFunction (one.c:120)
==236074==    by 0x7066531: TSComputeIFunction_DMDA (dmdats.c:82)
==236074==    by 0x70BA5EF: TSComputeIFunction (ts.c:857)
==236074==    by 0x711E2DC: SNESTSFormFunction_BDF (bdf.c:368)
==236074==    by 0x70C6E46: SNESTSFormFunction (ts.c:5014)
==236074==    by 0x6FDC8A6: SNESComputeFunction (snes.c:2383)
==236074==    by 0x7023556: SNESSolve_NEWTONTR (tr.c:297)
==236074==    by 0x6FD160F: SNESSolve (snes.c:4569)
==236074==    by 0x711917E: PetscMemcpy (bdf.c:223)
==236074==    by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074==    by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074==    by 0x70C363A: TSStep (ts.c:3757)
==236074==    by 0x70C1999: TSSolve (ts.c:4154)
==236074==    by 0x402594: main (one.c:391)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x1E4782BA: __intel_ssse3_strncpy (in /opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64_lin/libirc.so)
==236074==    by 0x51FFD24: PetscStrncpy (str.c:392)
==236074==    by 0x51FEB03: PetscStrreplace (str.c:1142)
==236074==    by 0x5224E4B: PetscFOpen (mpiuopen.c:52)
==236074==    by 0x63A074B: DMDAVTKWriteAll_VTS.A (grvtk.c:72)
==236074==    by 0x639A589: DMDAVTKWriteAll (grvtk.c:545)
==236074==    by 0x52B66F3: PetscViewerFlush_VTK (vtkv.c:100)
==236074==    by 0x52CFAAE: PetscViewerFlush (flush.c:26)
==236074==    by 0x52CEA95: PetscViewerDestroy (view.c:113)
==236074==    by 0x70C7717: TSMonitorSolutionVTK (ts.c:5582)
==236074==    by 0x40313C: FormFunction (one.c:120)
==236074==    by 0x7066531: TSComputeIFunction_DMDA (dmdats.c:82)
==236074==    by 0x70BA5EF: TSComputeIFunction (ts.c:857)
==236074==    by 0x711E2DC: SNESTSFormFunction_BDF (bdf.c:368)
==236074==    by 0x70C6E46: SNESTSFormFunction (ts.c:5014)
==236074==    by 0x6FDC8A6: SNESComputeFunction (snes.c:2383)
==236074==    by 0x7023556: SNESSolve_NEWTONTR (tr.c:297)
==236074==    by 0x6FD160F: SNESSolve (snes.c:4569)
==236074==    by 0x711917E: PetscMemcpy (bdf.c:223)
==236074==    by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074==    by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074==    by 0x70C363A: TSStep (ts.c:3757)
==236074== 
==236074== Conditional jump or move depends on uninitialised value(s)
==236074==    at 0x5F10977: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:146)
==236074==    by 0x5F10977: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284)
==236074==    by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242)
==236074==    by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79)
==236074==    by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717)
==236074==    by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324)
==236074==    by 0x6FD160F: SNESSolve (snes.c:4569)
==236074==    by 0x711917E: PetscMemcpy (bdf.c:223)
==236074==    by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074==    by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074==    by 0x70C363A: TSStep (ts.c:3757)
==236074==    by 0x70C1999: TSSolve (ts.c:4154)
==236074==    by 0x402594: main (one.c:391)
==236074== 
==236074== Invalid write of size 4
==236074==    at 0x5F10983: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:150)
==236074==    by 0x5F10983: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284)
==236074==    by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242)
==236074==    by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79)
==236074==    by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717)
==236074==    by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324)
==236074==    by 0x6FD160F: SNESSolve (snes.c:4569)
==236074==    by 0x711917E: PetscMemcpy (bdf.c:223)
==236074==    by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074==    by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074==    by 0x70C363A: TSStep (ts.c:3757)
==236074==    by 0x70C1999: TSSolve (ts.c:4154)
==236074==    by 0x402594: main (one.c:391)
==236074==  Address 0x3a94fa80 is 0 bytes after a block of size 73,960,000 alloc'd
==236074==    at 0x4C2C480: memalign (vg_replace_malloc.c:909)
==236074==    by 0x522FFE2: PetscMallocAlign (mal.c:52)
==236074==    by 0x52305F9: PetscMallocA (mal.c:418)
==236074==    by 0x5F10778: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:125)
==236074==    by 0x5F10778: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284)
==236074==    by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242)
==236074==    by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79)
==236074==    by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717)
==236074==    by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324)
==236074==    by 0x6FD160F: SNESSolve (snes.c:4569)
==236074==    by 0x711917E: PetscMemcpy (bdf.c:223)
==236074==    by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074==    by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074==    by 0x70C363A: TSStep (ts.c:3757)
==236074==    by 0x70C1999: TSSolve (ts.c:4154)
==236074==    by 0x402594: main (one.c:391)
==236074== 
==236074== Invalid write of size 8
==236074==    at 0x5F10991: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:151)
==236074==    by 0x5F10991: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284)
==236074==    by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242)
==236074==    by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79)
==236074==    by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717)
==236074==    by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324)
==236074==    by 0x6FD160F: SNESSolve (snes.c:4569)
==236074==    by 0x711917E: PetscMemcpy (bdf.c:223)
==236074==    by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074==    by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074==    by 0x70C363A: TSStep (ts.c:3757)
==236074==    by 0x70C1999: TSSolve (ts.c:4154)
==236074==    by 0x402594: main (one.c:391)
==236074==  Address 0x3a94fa88 is 8 bytes after a block of size 73,960,000 alloc'd
==236074==    at 0x4C2C480: memalign (vg_replace_malloc.c:909)
==236074==    by 0x522FFE2: PetscMallocAlign (mal.c:52)
==236074==    by 0x52305F9: PetscMallocA (mal.c:418)
==236074==    by 0x5F10778: MatFDColoringSetUpBlocked_AIJ_Private (fdaij.c:125)
==236074==    by 0x5F10778: MatFDColoringSetUp_SeqXAIJ.A (fdaij.c:284)
==236074==    by 0x585892A: MatFDColoringSetUp (fdmatrix.c:242)
==236074==    by 0x6FE5037: SNESComputeJacobianDefaultColor (snesj2.c:79)
==236074==    by 0x6FC8E4E: SNESComputeJacobian (snes.c:2717)
==236074==    by 0x70236E7: SNESSolve_NEWTONTR (tr.c:324)
==236074==    by 0x6FD160F: SNESSolve (snes.c:4569)
==236074==    by 0x711917E: PetscMemcpy (bdf.c:223)
==236074==    by 0x711917E: PetscCitationsRegister (petscsys.h:2689)
==236074==    by 0x711917E: TSStep_BDF.A (bdf.c:265)
==236074==    by 0x70C363A: TSStep (ts.c:3757)
==236074==    by 0x70C1999: TSSolve (ts.c:4154)
==236074==    by 0x402594: main (one.c:391)
==236074==
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Re: [petsc-users] Periodic boundary condition

Barry Smith