[petsc-dev] snes_monitor_residual

[Matthew Knepley]

On Thu, Dec 22, 2016 at 7:30 AM, Mark Adams <mfadams at lbl.gov> wrote:

>
>> That will stash vectors in the HDF5 file, but you still need to put in
>> the DM as well
>>
>>   -dm_view hdf5:ex1.h5
>>  -snes_monitor_residual hdf5:ex1.h5::append
>>  -snes_monitor_solution hdf5:ex1.h5::append
>>
>
> I tried:
>
> #PETSc Option Table entries:
> -dm_view hdf5:res.h5
> -snes_monitor_residual hdf5:res.h5::append
>
> And see this:
>  ...
> #End of PETSc Option Table entries
> There is one unused database option. It is:
> Option left: name:-dm_view value: hdf5:res.h5
>
> And, of course, I get the same bad h5 file as before. In other codes I
> have had to add code. I tried simply adding
>
> ierr = DMViewFromOptions(ctx->dm,NULL,"-dm_view");CHKERRQ(ierr);
>

1) You need this in the code. Its in all my examples.

2) Did you put it before the vec views? Otherwise, it need 'append'.

   Matt


> before the solve, but that did not change anything (same bad h5 file)
> other than remove the 'options left' warning.
>

I tried to clone the code that I use for printing vectors manually by
> adding this before the solve:
>
>       ierr = DMViewFromOptions(ctx->dm,NULL,"-dm_view");CHKERRQ(ierr);
>       ierr = PetscOptionsGetViewer(PETSC_COMM_SELF,NULL,"-snes_monitor_
> residual",&viewer,&fmt,&flg);CHKERRQ(ierr);
>       if (flg) {
> ierr = PetscViewerPushFormat(viewer,fmt);CHKERRQ(ierr);
>       }
>
> But got this error in the solve:
>
>     0 SNES Function norm 4.438513482798e+01
> HDF5-DIAG: Error detected in HDF5 (1.8.12) MPI-process 0:
>   #000: H5L.c line 824 in H5Lexists(): unable to get link info
>     major: Symbol table
>     minor: Object not found
>   #001: H5L.c line 2765 in H5L_exists(): path doesn't exist
>     major: Symbol table
>     minor: Object already exists
>   #002: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal
> failed
>     major: Symbol table
>     minor: Object not found
>   #003: H5Gtraverse.c line 596 in H5G_traverse_real(): can't look up
> component
>     major: Symbol table
>     minor: Object not found
>   #004: H5Gobj.c line 1156 in H5G__obj_lookup(): can't locate object
>     major: Symbol table
>     minor: Object not found
>   #005: H5Gstab.c line 907 in H5G__stab_lookup(): not found
>     major: Symbol table
>     minor: Object not found
>   #006: H5B.c line 366 in H5B_find(): can't lookup key in leaf node
>     major: B-Tree node
>     minor: Object not found
>   #007: H5Gnode.c line 545 in H5G_node_found(): unable to protect symbol
> table node
>     major: Symbol table
>     minor: Unable to load metadata into cache
>   #008: H5AC.c line 1329 in H5AC_protect(): H5C_protect() failed.
>     major: Object cache
>     minor: Unable to protect metadata
>   #009: H5C.c line 3574 in H5C_protect(): can't load entry
>     major: Object cache
>     minor: Unable to load metadata into cache
>   #010: H5C.c line 7954 in H5C_load_entry(): unable to load entry
>     major: Object cache
>     minor: Unable to load metadata into cache
>   #011: H5Gcache.c line 169 in H5G_node_load(): bad symbol table node
> signature
>     major: Symbol table
>     minor: Unable to load metadata into cache
> HDF5-DIAG: Error detected in HDF5 (1.8.12) MPI-process 0:
>   #000: H5D.c line 334 in H5Dopen2(): not found
>     major: Dataset
>     minor: Object not found
>   #001: H5Gloc.c line 430 in H5G_loc_find(): can't find object
>     major: Symbol table
>     minor: Object not found
>   #002: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal
> failed
>     major: Symbol table
>     minor: Object not found
>   #003: H5Gtraverse.c line 596 in H5G_traverse_real(): can't look up
> component
>     major: Symbol table
>     minor: Object not found
>   #004: H5Gobj.c line 1156 in H5G__obj_lookup(): can't locate object
>     major: Symbol table
>     minor: Object not found
>   #005: H5Gstab.c line 907 in H5G__stab_lookup(): not found
>     major: Symbol table
>     minor: Object not found
>   #006: H5B.c line 366 in H5B_find(): can't lookup key in leaf node
>     major: B-Tree node
>     minor: Object not found
>   #007: H5Gnode.c line 545 in H5G_node_found(): unable to protect symbol
> table node
>     major: Symbol table
>     minor: Unable to load metadata into cache
>   #008: H5AC.c line 1329 in H5AC_protect(): H5C_protect() failed.
>     major: Object cache
>     minor: Unable to protect metadata
>   #009: H5C.c line 3574 in H5C_protect(): can't load entry
>     major: Object cache
>     minor: Unable to load metadata into cache
>   #010: H5C.c line 7954 in H5C_load_entry(): unable to load entry
>     major: Object cache
>     minor: Unable to load metadata into cache
>   #011: H5Gcache.c line 169 in H5G_node_load(): bad symbol table node
> signature
>     major: Symbol table
>     minor: Unable to load metadata into cache
>   ...
>



-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20161222/6ed7ba04/attachment.html>