October 2022 - petsc-users - mailman3.cels.anl.gov

How to combine different element types into a single DMPlex?
by Eric Chamberland 01 Aug '24

01 Aug '24

Hi, while playing with DMPlexBuildFromCellListParallel, I noticed we have to specify "numCorners" which is a fixed value, then gives a fixed number of nodes for a series of elements. How can I then add, for example, triangles and quadrangles into a DMPlex? Thanks, Eric -- Eric Chamberland, ing., M. Ing Professionnel de recherche GIREF/Université Laval (418) 656-2131 poste 41 22 42

4 13

HDF5 corruption
by Adrian Croucher 13 May '24

13 May '24

hi, One of the users of my PETSc-based code has reported that HDF5 output files can be corrupted and unusable if e.g. the run is killed. I've just done a bit of reading about this and it appears to be a known issue with HDF5. Some people suggest flushing the HDF5 file periodically to help prevent data loss. I had a look at PetscViewerFlush() but it doesn't seem to be implemented for the HDF5 viewer- is that correct? I am currently calling PetscViewerHDF5Open() once at the start of the run and closing it at the end. Some other people suggest doing this before and after each write instead. Is there likely to be a significant performance penalty in doing that? I gather HDF5 journaling has been promised for a while to get around this problem but as far as I can see it hasn't materialised yet... Regards, Adrian -- Dr Adrian Croucher Senior Research Fellow Department of Engineering Science University of Auckland, New Zealand email: a.croucher(a)auckland.ac.nz tel: +64 (0)9 923 4611

4 17

How to find the map between the high order coordinates of DMPlex and vertex numbering?
by Zongze Yang 15 May '23

15 May '23

Hi, if I load a `gmsh` file with second-order elements, the coordinates will be stored in a DG-P2 space. After obtaining the coordinates of a cell, how can I map the coordinates to vertex and edge? Below is some code load the gmsh file, I want to know the relation between `cl` and `cell_coords`. ``` import firedrake as fd import numpy as np # Load gmsh file (2rd) plex = fd.mesh._from_gmsh('test-fd-load-p2-rect.msh') cs, ce = plex.getHeightStratum(0) cdm = plex.getCoordinateDM() csec = dm.getCoordinateSection() coords_gvec = dm.getCoordinates() for i in range(cs, ce): cell_coords = cdm.getVecClosure(csec, coords_gvec, i) print(f'coordinates for cell {i} :\n{cell_coords.reshape([-1, 3])}') cl = dm.getTransitiveClosure(i) print('closure:', cl) break ``` Best wishes, Zongze

3 20

DMPlex PETSCViewer for Surface Component
by Mike Michell 30 Mar '23

30 Mar '23

Hi, I am a user of DMPlex object in 3D grid topology. Currently the solution field is printed out using viewer PETSCVIEWERVTK in .vtu format. By doing that the entire volume components are written in the file. I was wondering if there is an option that I can tell PETSc viewer to print out only surface component, instead of the entire volume. Best, Mike

3 4

DMPlex Reordering
by Nicholas Arnold-Medabalimi 08 Feb '23

08 Feb '23

Hi Petsc users, I have been working on how to read in meshes into a DMPlex object. The process of building the cones has been relatively straightforward. The mesh files in question have sets of faces that I use to derive the cell vertex cones. The method is basically identical to that used in DMPlexCreateFluent. After I setup the DMPlex cones and call Symmetrize and Stratify, I then load in all the coordinates corresponding to the vertices and then use DMInterpolate to generate the intermediate edges The issue that I am running into is that because I am deriving the cell-vertex relationship from independent sets of face-vertex relationships, I can end up with cells that have improper mesh ordering. For example a cell with the coordinates: point 0: 0.000000 0.000000 point 1: 0.000000 2.500000 point 2: 0.100000 0.000000 point 3: 0.100000 2.500000 As you can see instead of going around the perimeter of the cell the path from 1 to 2 instead bisects the cell. I can manually reorder these after I read in the coordinates by manually checking right-handedness but I was wondering if there is an easier way to reorder the cones? If there isn't once I do reorder the cones manually is there anything I need to do as far as station keeping on the DM? I apologize if I missed any resources on this. Thanks Nicholas -- Nicholas Arnold-Medabalimi Ph.D. Candidate Computational Aeroscience Lab University of Michigan

2 3

locate DMSwarm particles with respect to a background DMDA mesh
by Semplice Matteo 12 Jan '23

12 Jan '23

Dear Petsc developers, I am trying to use a DMSwarm to locate a cloud of points with respect to a background mesh. In the real application the points will be loaded from disk, but I have created a small demo in which * each processor creates Npart particles, all within the domain covered by the mesh, but not all in the local portion of the mesh * migrate the particles After migration most particles are not any more in the DMSwarm (how many and which ones seems to depend on the number of cpus, but it never happens that all particle survive the migration process). I am clearly missing some step, since I'd expect that a DMDA would be able to locate particles without the need to go through a DMShell as it is done in src/dm/tutorials/swarm_ex3.c.html<https://petsc.org/main/src/dm/tutorials/swarm_ex3.c.html> I attach my demo code. Could someone give me a hint? Best Matteo

5 18

Loading labels from a hdf5 mesh file in parallel
by Yi Jiang 30 Nov '22

30 Nov '22

Dear Petsc developers, We are trying to use the HDF5_XDMF parallel I/O feature to read/write unstructured meshes. By trying some tests, we found that the topology and geometry data (i.e., cells and vertices) can be efficiently loaded in a scalable way, which is very impressive! However, we also found that all labels (such as `cell sets', `face sets') in the .h5 file are ignored (the .h5 file was converted from an EXODUSII mesh, by using a PetscViewer with PETSC_VIEWER_HDF5_XDMF format). Hence, we are wondering, does the latest Petsc also support to import these labels in parallel? In particular, we would like to redistribute the mesh after it is parallelly loaded by the naive partition. If so, could you please show me where to find an example to learn the techniques? Thank you very much for devoting the continuous efforts to the community and keep developing these wonderful features. Best regards, YJ

2 1

About Q3 tensor product Hermite element
by Duan Junming 30 Nov '22

30 Nov '22

Dear all, I need to use Q3 tensor product Hermite element in 2D (point value, gradient, and mixed derivative at 4 vertices in a cell as unknowns). Is it available in PETSc FEM module now? I found that only Lagrange element is available. If not, what is the correct path to implement Q3 tensor product Hermite element? I think I should create my own petscspace and petscdualspace? Or is there any package that has already provided this? Thanks for any suggestions!

2 1

Report Bug TaoALMM class
by Stephan Köhler 11 Nov '22

11 Nov '22

Dear PETSc/Tao team, it seems to be that there is a bug in the TaoALMM class: In the methods TaoALMMSubsolverObjective_Private and TaoALMMSubsolverObjectiveAndGradient_Private the vector where the function value for the augmented Lagrangian is evaluate is copied into the current solution, see, e.g., https://petsc.org/release/src/tao/constrained/impls/almm/almm.c.html line 672 or 682. This causes subsolver routine to not converge if the line search for the subsolver rejects the step length 1. for some update. In detail: Suppose the current iterate is xk and the current update is dxk. The line search evaluates the augmented Lagrangian now at (xk + dxk). This causes that the value (xk + dxk) is copied in the current solution. If the point (xk + dxk) is rejected, the line search should try the point (xk + alpha * dxk), where alpha < 1. But due to the copying, what happens is that the point ((xk + dxk) + alpha * dxk) is evaluated, see, e.g., https://petsc.org/release/src/tao/linesearch/impls/armijo/armijo.c.html line 191. Best regards Stephan Köhler -- Stephan Köhler TU Bergakademie Freiberg Institut für numerische Mathematik und Optimierung Akademiestraße 6 09599 Freiberg Gebäudeteil Mittelbau, Zimmer 2.07 Telefon: +49 (0)3731 39-3173 (Büro)

2 8

Periodic boundary condition
by Sepideh Kavousi 03 Nov '22

03 Nov '22

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 and 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== Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

3 12