[petsc-users] Correct approach for updating deprecated code

Richard Beare richard.beare at monash.edu
Mon Mar 2 22:45:12 CST 2020 

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 <knepley at gmail.com> wrote:

> On Sun, Feb 23, 2020 at 6:45 PM Richard Beare <richard.beare at monash.edu>
> 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 <knepley at gmail.com> wrote:
>>
>>> On Sun, Feb 23, 2020 at 6:25 PM Richard Beare via petsc-users <
>>> petsc-users at mcs.anl.gov> 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
>>>> Richard.Beare at monash.edu
>>>> +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
>> Richard.Beare at monash.edu
>> +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
Richard.Beare at monash.edu
+61 3 9788 1724



Geospatial Research:
https://www.monash.edu/medicine/scs/medicine/research/geospatial-analysis
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