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
