[petsc-users] VecLoad hdf5

[Matthew Knepley]

We have example code that writes and loads from HDF5. If you can't modify
that, send a simple
sample code that fails.

  Thanks,

    Matt

On Tue, Dec 4, 2018 at 5:53 PM Josh L via petsc-users <
petsc-users at mcs.anl.gov> wrote:

>
>
> Smith, Barry F. <bsmith at mcs.anl.gov> 於 2018年12月4日 週二 下午4:43寫道：
>
>>
>>
>> > On Dec 4, 2018, at 4:09 PM, Josh L <ysjosh.lo at gmail.com> wrote:
>> >
>> > I haven't figured out what causes it. I just use binaryopen instead of
>> HDF5, and everything works fine.
>>
>>    Did you originally save the data into the file with HDF5 format?
>>
>
> Yes, by
>     Set Vec name, and block size
>     PetscViewerHDF5Open(write)
>     VecView(vec,viewer)
>
>
> >
>> >
>> >
>> > Josh L <ysjosh.lo at gmail.com> 於 2018年12月4日 週二 下午2:55寫道：
>> > The first error comes from
>> > PetscStackCallHDF5Return(group,H5Gcreate2,(file_id, groupName, 0,
>> H5P_DEFAULT, H5P_DEFAULT));
>> >  #000: H5G.c line 314 in H5Gcreate2(): unable to create group
>> >     major: Symbol table
>> >     minor: Unable to initialize object
>> >
>> >
>> > Josh L <ysjosh.lo at gmail.com> 於 2018年12月4日 週二 下午2:38寫道：
>> > I set the name of 2 vectors to be the same, but still get the same
>> error.
>> >
>> >
>> >
>> > Josh L <ysjosh.lo at gmail.com> 於 2018年12月4日 週二 下午2:06寫道：
>> > I just found out that I missed that note in VecLoad manual page, and I
>> am trying it now.
>> > Thanks.
>> >
>> >
>> >
>> > Smith, Barry F. <bsmith at mcs.anl.gov> 於 2018年12月4日 週二 下午2:00寫道：
>> >
>> >    Hmm, this is a guess. HDF5 files read in objects based on their
>> names. Are you sure that the vector you saved and the vector you later try
>> to read in have the same name? You can set the name of the loaded vector
>> with PetscObjectSetName((PetscObject)nv,"name") after you create it to
>> match the name you used to save the vector.
>> >
>> >    Barry
>> >
>> >
>> > > On Dec 4, 2018, at 1:42 PM, Josh L via petsc-users <
>> petsc-users at mcs.anl.gov> wrote:
>> > >
>> > > Hi,
>> > >
>> > > I have a vec.h5 that generated serially by
>> > >   gv is a sequential vec
>> > >  VecSetblockSize(gv,3)
>> > >  PetscViewerHDF5Open(vec,h5,write)
>> > >   VecView(gv)
>> > >
>> > > and I want to read in with different number of processor by
>> > >   DMGetGlobalVector(dm,nv)
>> > >   PetscViewerHDF5Open(write)
>> > >   VecLoad(nv)
>> > >
>> > > nv has bs=3, and I have set bs for gv as 3.
>> > >
>> > > I get the following error. any hint to solve it ? thanks
>> > >
>> > > Error in HDF5 call H5Gcreate2() Status -1
>> > >   #000: H5G.c line 314 in H5Gcreate2(): unable to create group
>> > >     major: Symbol table
>> > >     minor: Unable to initialize object
>> > >   #001: H5Gint.c line 194 in H5G__create_named(): unable to create
>> and link to group
>> > >     major: Symbol table
>> > >     minor: Unable to initialize object
>> > >   #002: H5L.c line 1638 in H5L_link_object(): unable to create new
>> link to object
>> > >     major: Links
>> > >     minor: Unable to initialize object
>> > >   #003: H5L.c line 1882 in H5L_create_real(): can't insert link
>> > >     major: Symbol table
>> > >     minor: Unable to insert object
>> > >   #004: H5Gtraverse.c line 861 in H5G_traverse(): internal path
>> traversal failed
>> > >     major: Symbol table
>> > >     minor: Object not found
>> > >   #005: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal
>> operator failed
>> > >     major: Symbol table
>> > >     minor: Callback failed
>> > >   #006: H5L.c line 1685 in H5L_link_cb(): unable to create object
>> > >     major: Object header
>> > >     minor: Unable to initialize object
>> > >   #007: H5O.c line 3016 in H5O_obj_create(): unable to open object
>> > >     major: Object header
>> > >     minor: Can't open object
>> > >   #008: H5Goh.c line 268 in H5O_group_create(): unable to create group
>> > >     major: Symbol table
>> > >     minor: Unable to initialize object
>> > >   #009: H5Gint.c line 245 in H5G__create(): unable to create group
>> object header
>> > >     major: Symbol table
>> > >     minor: Unable to initialize object
>> > >   #010: H5Gobj.c line 163 in H5G__obj_create(): unable to create group
>> > >     major: Symbol table
>> > >     minor: Unable to create file
>> > >   #011: H5Gobj.c line 206 in H5G__obj_create_real(): no write intent
>> on file
>> > >     major: Object cache
>> > >     minor: Bad value
>> > >
>> > >
>> > >
>> >
>>
>>

-- 
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/>
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