There was a relevant change in PETSc 3.8, you now need to call DMSetUp() after DMDACreate1d(), DMDACreate2d(), or DMDACreate3d().
https://www.mcs.anl.gov/petsc/documentation/changes/38.html "Replace calls to DMDACreateXd() with DMDACreateXd(), [DMSetFromOptions()] DMSetUp()" Am Di., 3. März 2020 um 05:46 Uhr schrieb Richard Beare via petsc-users < [email protected]>: > This is the error. Maybe nothing to do with the viewer part and something > to do with changes in initialization? Something that has happened since > version 3.6.3, perhaps. > > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Operation done in wrong order > [0]PETSC ERROR: You should call DMSetUp() first > [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > [0]PETSC ERROR: Petsc Development GIT revision: v3.12.4-753-gbac983c101 > GIT Date: 2020-02-18 15:05:54 +0000 > [0]PETSC ERROR: simul_atrophy on a named m3j007 by rbeare Tue Mar 3 > 14:12:22 2020 > [0]PETSC ERROR: Configure options --with-cc=gcc-6 --with-cxx=g++-6 > --with-fc=gfortran --download-mpich --download-fblaslapack --with-clangu > age=cxx --prefix=/opt/petsc/ --with-64-bit-indices=yes > [0]PETSC ERROR: #1 DMDASetFieldName() line 68 in > /petsc/src/dm/impls/da/dacorn.c > [0]PETSC ERROR: #2 PetscAdLemTaras3D() line 68 in > /simul-atrophy/src/includes/PetscAdLemTaras3D.hxx > terminate called after throwing an instance of 'std::runtime_error' > what(): Error detected in C PETSc > SIGABRT: abort > PC=0x47282b m=0 sigcode=0 > > goroutine 1 [running, locked to thread]: > syscall.RawSyscall(0x3e, 0x5cbd, 0x6, 0x0, 0xc0001e3ef0, 0x48f422, 0x5cbd) > /usr/local/go/1.11.1/src/syscall/asm_linux_amd64.s:78 +0x2b > fp=0xc0001e3eb8 sp=0xc0001e3eb0 pc=0x47282b > syscall.Kill(0x5cbd, 0x6, 0x4377de, 0xc0001e3f20) > /usr/local/go/1.11.1/src/syscall/zsyscall_linux_amd64.go:597 +0x4b > fp=0xc0001e3f00 sp=0xc0001e3eb8 pc=0x46f1db > github.com/sylabs/singularity/internal/app/starter.Master.func4() > internal/app/starter/master_linux.go:158 +0x3e fp=0xc0001e3f38 > sp=0xc0001e3f00 pc=0x8d51be > github.com/sylabs/singularity/internal/pkg/util/mainthread.Execute.func1() > internal/pkg/util/mainthread/mainthread.go:20 +0x2f > fp=0xc0001e3f60 sp=0xc0001e3f38 pc=0x87472f > main.main() > cmd/starter/main_linux.go:102 +0x68 fp=0xc0001e3f98 > sp=0xc0001e3f60 pc=0x8d59f8 > runtime.main() > /usr/local/go/1.11.1/src/runtime/proc.go:201 +0x207 > fp=0xc0001e3fe0 sp=0xc0001e3f98 pc=0x42faa7 > runtime.goexit() > /usr/local/go/1.11.1/src/runtime/asm_amd64.s:1333 +0x1 > fp=0xc0001e3fe8 sp=0xc0001e3fe0 pc=0x45b4f1 > > goroutine 5 [syscall]: > os/signal.signal_recv(0xaa2620) > /usr/local/go/1.11.1/src/runtime/sigqueue.go:139 +0x9c > os/signal.loop() > /usr/local/go/1.11.1/src/os/signal/signal_unix.go:23 +0x22 > created by os/signal.init.0 > /usr/local/go/1.11.1/src/os/signal/signal_unix.go:29 +0x41 > > goroutine 7 [chan receive]: > > github.com/sylabs/singularity/internal/pkg/util/mainthread.Execute(0xc0003e83a0) > internal/pkg/util/mainthread/mainthread.go:23 +0xb4 > github.com/sylabs/singularity/internal/app/starter.Master(0x4, 0xa, > 0x2300, 0x5cca, 0xc000213e00) > internal/app/starter/master_linux.go:157 +0x44e > main.startup() > cmd/starter/main_linux.go:73 +0x563 > created by main.main > cmd/starter/main_linux.go:98 +0x3e > > On Tue, 25 Feb 2020 at 03:04, Matthew Knepley <[email protected]> wrote: > >> On Sun, Feb 23, 2020 at 6:45 PM Richard Beare <[email protected]> >> wrote: >> >>> That's what I did (see below), but I got ordering errors (unfortunately >>> deleted those logs too soon). I'll rerun if no one recognises what I've >>> done wrong. >>> >>> PetscViewer viewer1; >>> ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,fileName.c_str >>> (),FILE_MODE_WRITE,&viewer1);CHKERRQ(ierr); >>> //ierr = >>> PetscViewerSetFormat(viewer1,PETSC_VIEWER_BINARY_MATLAB);CHKERRQ(ierr); >>> ierr = PetscViewerPushFormat(viewer1,PETSC_VIEWER_BINARY_MATLAB);CHKERRQ >>> (ierr); >>> >> >> This should not cause problems. However, is it possible that somewhere >> you are pushing a format >> again and again without popping? This could exceed the stack size. >> >> Thanks, >> >> Matt >> >> >>> ierr = PetscObjectSetName((PetscObject)mX,"x");CHKERRQ(ierr); >>> ierr = PetscObjectSetName((PetscObject)mB,"b");CHKERRQ(ierr); >>> >>> On Mon, 24 Feb 2020 at 10:43, Matthew Knepley <[email protected]> wrote: >>> >>>> On Sun, Feb 23, 2020 at 6:25 PM Richard Beare via petsc-users < >>>> [email protected]> wrote: >>>> >>>>> >>>>> Hi, >>>>> The following code gives a deprecation warning. What is the correct >>>>> way of updating the use of ViewerSetFormat to ViewerPushFormat (which I >>>>> presume is the preferred replacement). My first attempt gave errors >>>>> concerning ordering. >>>>> >>>> >>>> You can't just change SetFormat to PushFormat here? >>>> >>>> Matt >>>> >>>> >>>>> Thanks >>>>> >>>>> PetscViewer viewer1; >>>>> ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,fileName.c_str >>>>> (),FILE_MODE_WRITE,&viewer1);CHKERRQ(ierr); >>>>> ierr = PetscViewerSetFormat(viewer1,PETSC_VIEWER_BINARY_MATLAB); >>>>> CHKERRQ(ierr); >>>>> >>>>> ierr = PetscObjectSetName((PetscObject)mX,"x");CHKERRQ(ierr); >>>>> ierr = PetscObjectSetName((PetscObject)mB,"b");CHKERRQ(ierr); >>>>> >>>>> ierr = VecView(mX,viewer1);CHKERRQ(ierr); >>>>> ierr = VecView(mB,viewer1);CHKERRQ(ierr); >>>>> >>>>> >>>>> -- >>>>> -- >>>>> 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 >>>>> >>>> >>>> >>>> -- >>>> What most experimenters take for granted before they begin their >>>> experiments is infinitely more interesting than any results to which their >>>> experiments lead. >>>> -- Norbert Wiener >>>> >>>> https://www.cse.buffalo.edu/~knepley/ >>>> <http://www.cse.buffalo.edu/~knepley/> >>>> >>> >>> >>> -- >>> -- >>> 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 >>> >> >> >> -- >> What most experimenters take for granted before they begin their >> experiments is infinitely more interesting than any results to which their >> experiments lead. >> -- Norbert Wiener >> >> https://www.cse.buffalo.edu/~knepley/ >> <http://www.cse.buffalo.edu/~knepley/> >> > > > -- > -- > 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 >
