<div dir="ltr"><div>No luck - exactly the same error after including the --with-64-bit-indicies=yes --download-mpich=yes options</div><div><br></div>==8674== Argument 'size' of function memalign has a fishy (possibly negative) value: -17152036540<br>==8674== at 0x4C320A6: memalign (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)<br>==8674== by 0x4F0CFF2: PetscMallocAlign(unsigned long, int, char const*, char const*, void**) (mal.c:28)<br>==8674== by 0x4F0F716: PetscTrMallocDefault(unsigned long, int, char const*, char const*, void**) (mtr.c:188)<br>==8674== by 0x569AF3E: MatSeqAIJSetPreallocation_SeqAIJ (aij.c:3595)<br>==8674== by 0x569A531: MatSeqAIJSetPreallocation (aij.c:3539)<br>==8674== by 0x599080A: DMCreateMatrix_DA_3d_MPIAIJ(_p_DM*, _p_Mat*) (fdda.c:1085)<br>==8674== by 0x598B937: DMCreateMatrix_DA(_p_DM*, _p_Mat**) (fdda.c:759)<br>==8674== by 0x58A2BF2: DMCreateMatrix (dm.c:956)<br>==8674== by 0x5E377B3: KSPSetUp (itfunc.c:262)<br>==8674== by 0x409FFC: PetscAdLemTaras3D::solveModel(bool) (PetscAdLemTaras3D.hxx:255)<br>==8674== by 0x4239FB: AdLem3D<3u>::solveModel(bool, bool, bool) (AdLem3D.hxx:551)<br>==8674== by 0x41BD17: main (PetscAdLemMain.cxx:344)<br>==8674== <br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, 14 Feb 2020 at 17:07, Smith, Barry F. <<a href="mailto:bsmith@mcs.anl.gov" target="_blank">bsmith@mcs.anl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><br>
Richard,<br>
<br>
It is likely that for these problems some of the integers become too large for the int variable to hold them, thus they overflow and become negative.<br>
<br>
You should make a new PETSC_ARCH configuration of PETSc that uses the configure option --with-64-bit-indices, this will change PETSc to use 64 bit integers which will not overflow.<br>
<br>
Good luck and let us know how it works out<br>
<br>
Barry<br>
<br>
Probably the code is built with an older version of PETSc; the later versions should produce a more useful error message.<br>
<br>
> On Feb 13, 2020, at 11:43 PM, Richard Beare via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>> wrote:<br>
> <br>
> Hi Everyone,<br>
> I am experimenting with the Simlul@trophy tool (<a href="https://github.com/Inria-Asclepios/simul-atrophy" rel="noreferrer" target="_blank">https://github.com/Inria-Asclepios/simul-atrophy</a>) that uses petsc to simulate brain atrophy based on segmented MRI data. I am not the author. I have this running on most of a dataset of about 50 scans, but experience crashes with several that I am trying to track down. However I am out of ideas. The problem images are slightly bigger than some of the successful ones, but not substantially so, and I have experimented on machines with sufficient RAM. The error happens very quickly, as part of setup - see the valgrind report below. I haven't managed to get the sgcheck tool to work yet. I can only guess that the ksp object is somehow becoming corrupted during the setup process, but the array sizes that I can track (which derive from image sizes), appear correct at every point I can check. Any suggestions as to how I can check what might go wrong in the setup of the ksp object?<br>
> Thankyou.<br>
> <br>
> valgrind tells me:<br>
> <br>
> ==18175== Argument 'size' of function memalign has a fishy (possibly negative) value: -17152038144<br>
> ==18175== at 0x4C320A6: memalign (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)<br>
> ==18175== by 0x4F0F1F2: PetscMallocAlign(unsigned long, int, char const*, char const*, void**) (mal.c:28)<br>
> ==18175== by 0x56B43CA: MatSeqAIJSetPreallocation_SeqAIJ (aij.c:3595)<br>
> ==18175== by 0x56B39BD: MatSeqAIJSetPreallocation (aij.c:3539)<br>
> ==18175== by 0x59A9B44: DMCreateMatrix_DA_3d_MPIAIJ(_p_DM*, _p_Mat*) (fdda.c:1085)<br>
> ==18175== by 0x59A4C71: DMCreateMatrix_DA(_p_DM*, _p_Mat**) (fdda.c:759)<br>
> ==18175== by 0x58BBD29: DMCreateMatrix (dm.c:956)<br>
> ==18175== by 0x5E509D5: KSPSetUp (itfunc.c:262)<br>
> ==18175== by 0x40A3DE: PetscAdLemTaras3D::solveModel(bool) (PetscAdLemTaras3D.hxx:269)<br>
> ==18175== by 0x42413F: AdLem3D<3u>::solveModel(bool, bool, bool) (AdLem3D.hxx:552)<br>
> ==18175== by 0x41C25C: main (PetscAdLemMain.cxx:349)<br>
> ==18175== <br>
> <br>
> -- <br>
> --<br>
> A/Prof Richard Beare<br>
> Imaging and Bioinformatics, Peninsula Clinical School<br>
> <a href="http://orcid.org/0000-0002-7530-5664" rel="noreferrer" target="_blank">orcid.org/0000-0002-7530-5664</a><br>
> <a href="mailto:Richard.Beare@monash.edu" target="_blank">Richard.Beare@monash.edu</a><br>
> +61 3 9788 1724<br>
> <br>
> <br>
> <br>
> Geospatial Research: <a href="https://www.monash.edu/medicine/scs/medicine/research/geospatial-analysis" rel="noreferrer" target="_blank">https://www.monash.edu/medicine/scs/medicine/research/geospatial-analysis</a><br>
<br>
</blockquote></div></div><br clear="all"><br>-- <br><div dir="ltr"><div dir="ltr"><div>--<br>A/Prof Richard Beare<br>Imaging and Bioinformatics, Peninsula Clinical School</div><div><span><div><span><a href="http://orcid.org/0000-0002-7530-5664" target="_blank">orcid.org/0000-0002-7530-5664</a></span></div></span></div><div><a href="mailto:Richard.Beare@monash.edu" target="_blank">Richard.Beare@monash.edu</a><br>+61 3 9788 1724<br><span><br></span></div><div><br></div><div><span></span><br>Geospatial Research: <a href="https://www.monash.edu/medicine/scs/medicine/research/geospatial-analysis" target="_blank">https://www.monash.edu/medicine/scs/medicine/research/geospatial-analysis</a></div></div></div>