It doesn't compile out of the box with master. singularity def file attached.
On Sat, 15 Feb 2020 at 08:03, Richard Beare <[email protected]> wrote: > I will see if I can build with master. The docs for simulatrophy say > 3.6.3.1. > > On Sat, 15 Feb 2020 at 02:47, Junchao Zhang <[email protected]> wrote: > >> Which petsc version do you use? In aij.c of the master branch, I saw >> Barry recently added a useful check to catch number of nonzero overflow, >> ierr = PetscIntCast(nz64,&nz);CHKERRQ(ierr); But you mentioned using >> 64-bit indices did not solve the problem, it might not be the reason. You >> should try the master branch if feasible. Also, vary number of MPI ranks to >> see if error stack changes. >> >> --Junchao Zhang >> >> >> On Fri, Feb 14, 2020 at 5:12 AM Richard Beare via petsc-users < >> [email protected]> wrote: >> >>> No luck - exactly the same error after including the >>> --with-64-bit-indicies=yes --download-mpich=yes options >>> >>> ==8674== Argument 'size' of function memalign has a fishy (possibly >>> negative) value: -17152036540 >>> ==8674== at 0x4C320A6: memalign (in >>> /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) >>> ==8674== by 0x4F0CFF2: PetscMallocAlign(unsigned long, int, char >>> const*, char const*, void**) (mal.c:28) >>> ==8674== by 0x4F0F716: PetscTrMallocDefault(unsigned long, int, char >>> const*, char const*, void**) (mtr.c:188) >>> ==8674== by 0x569AF3E: MatSeqAIJSetPreallocation_SeqAIJ (aij.c:3595) >>> ==8674== by 0x569A531: MatSeqAIJSetPreallocation (aij.c:3539) >>> ==8674== by 0x599080A: DMCreateMatrix_DA_3d_MPIAIJ(_p_DM*, _p_Mat*) >>> (fdda.c:1085) >>> ==8674== by 0x598B937: DMCreateMatrix_DA(_p_DM*, _p_Mat**) >>> (fdda.c:759) >>> ==8674== by 0x58A2BF2: DMCreateMatrix (dm.c:956) >>> ==8674== by 0x5E377B3: KSPSetUp (itfunc.c:262) >>> ==8674== by 0x409FFC: PetscAdLemTaras3D::solveModel(bool) >>> (PetscAdLemTaras3D.hxx:255) >>> ==8674== by 0x4239FB: AdLem3D<3u>::solveModel(bool, bool, bool) >>> (AdLem3D.hxx:551) >>> ==8674== by 0x41BD17: main (PetscAdLemMain.cxx:344) >>> ==8674== >>> On Fri, 14 Feb 2020 at 17:07, Smith, Barry F. <[email protected]> >>> wrote: >>> >>>> >>>> Richard, >>>> >>>> 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. >>>> >>>> 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. >>>> >>>> Good luck and let us know how it works out >>>> >>>> Barry >>>> >>>> Probably the code is built with an older version of PETSc; the >>>> later versions should produce a more useful error message. >>>> >>>> > On Feb 13, 2020, at 11:43 PM, Richard Beare via petsc-users < >>>> [email protected]> wrote: >>>> > >>>> > Hi Everyone, >>>> > I am experimenting with the Simlul@trophy tool ( >>>> https://github.com/Inria-Asclepios/simul-atrophy) 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? >>>> > Thankyou. >>>> > >>>> > valgrind tells me: >>>> > >>>> > ==18175== Argument 'size' of function memalign has a fishy (possibly >>>> negative) value: -17152038144 >>>> > ==18175== at 0x4C320A6: memalign (in >>>> /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) >>>> > ==18175== by 0x4F0F1F2: PetscMallocAlign(unsigned long, int, char >>>> const*, char const*, void**) (mal.c:28) >>>> > ==18175== by 0x56B43CA: MatSeqAIJSetPreallocation_SeqAIJ >>>> (aij.c:3595) >>>> > ==18175== by 0x56B39BD: MatSeqAIJSetPreallocation (aij.c:3539) >>>> > ==18175== by 0x59A9B44: DMCreateMatrix_DA_3d_MPIAIJ(_p_DM*, >>>> _p_Mat*) (fdda.c:1085) >>>> > ==18175== by 0x59A4C71: DMCreateMatrix_DA(_p_DM*, _p_Mat**) >>>> (fdda.c:759) >>>> > ==18175== by 0x58BBD29: DMCreateMatrix (dm.c:956) >>>> > ==18175== by 0x5E509D5: KSPSetUp (itfunc.c:262) >>>> > ==18175== by 0x40A3DE: PetscAdLemTaras3D::solveModel(bool) >>>> (PetscAdLemTaras3D.hxx:269) >>>> > ==18175== by 0x42413F: AdLem3D<3u>::solveModel(bool, bool, bool) >>>> (AdLem3D.hxx:552) >>>> > ==18175== by 0x41C25C: main (PetscAdLemMain.cxx:349) >>>> > ==18175== >>>> > >>>> > -- >>>> > -- >>>> > A/Prof Richard Beare >>>> > Imaging and Bioinformatics, Peninsula Clinical School >>>> > orcid.org/0000-0002-7530-5664 >>>> > [email protected] >>>> > +61 3 9788 1724 >>>> > >>>> > >>>> > >>>> > Geospatial Research: >>>> https://www.monash.edu/medicine/scs/medicine/research/geospatial-analysis >>>> >>>> >>> >>> -- >>> -- >>> A/Prof Richard Beare >>> Imaging and Bioinformatics, Peninsula Clinical School >>> orcid.org/0000-0002-7530-5664 >>> [email protected] >>> +61 3 9788 1724 >>> >>> >>> >>> Geospatial Research: >>> https://www.monash.edu/medicine/scs/medicine/research/geospatial-analysis >>> >> > > -- > -- > A/Prof Richard Beare > Imaging and Bioinformatics, Peninsula Clinical School > orcid.org/0000-0002-7530-5664 > [email protected] > +61 3 9788 1724 > > > > Geospatial Research: > https://www.monash.edu/medicine/scs/medicine/research/geospatial-analysis > -- -- A/Prof Richard Beare Imaging and Bioinformatics, Peninsula Clinical School orcid.org/0000-0002-7530-5664 [email protected] +61 3 9788 1724 Geospatial Research: https://www.monash.edu/medicine/scs/medicine/research/geospatial-analysis
sa.def
Description: Binary data
