[petsc-users] VecView to hdf5 broken for large (complex) vectors

[Smith, Barry F.]

   You can run with -start_in_debugger  -debugger_nodes 0 and in that one debugger window put a break point in the needed vector routine to print the chunk sizes at the appropriate line. 

  Barry


> On Apr 16, 2019, at 9:32 AM, Sajid Ali via petsc-users <petsc-users at mcs.anl.gov> wrote:
> 
> Hi PETSc developers,
> 
> I’m trying to write a large vector created with VecCreateMPI (size 32768x32768) concurrently from 4 nodes (+32 tasks per node, total 128 mpi-ranks) and I see the following (indicative) error : [Full error log is here : https://file.io/CdjUfe] 
> 
> HDF5-DIAG: Error detected in HDF5 (1.10.5) MPI-process 52:
>   #000: H5D.c line 145 in H5Dcreate2(): unable to create dataset
>     major: Dataset
>     minor: Unable to initialize object
>   #001: H5Dint.c line 329 in H5D__create_named(): unable to create and link to dataset
>     major: Dataset
>     minor: Unable to initialize object
>   #002: H5L.c line 1557 in H5L_link_object(): unable to create new link to object
>     major: Links
>     minor: Unable to initialize object
>   #003: H5L.c line 1798 in H5L__create_real(): can't insert link
>     major: Links
>     minor: Unable to insert object
>   #004: H5Gtraverse.c line 851 in H5G_traverse(): internal path traversal failed
>     major: Symbol table
> HDF5-DIAG: Error detected in HDF5 (1.10.5) MPI-process 59:                              
>   #000: H5D.c line 145 in H5Dcreate2(): unable to create dataset                        
>     major: Dataset                                                                      
>     minor: Unable to initialize object                                                  
>   #001: H5Dint.c line 329 in H5D__create_named(): unable to create and link to dataset  
>     major: Dataset                                                                      
>     minor: Unable to initialize object                                                  
>   #002: H5L.c line 1557 in H5L_link_object(): unable to create new link to object       
>     major: Links                                                                        
>     minor: Unable to initialize object                                                  
>   #003: H5L.c line 1798 in H5L__create_real(): can't insert link                        
>     major: Links                                                                        
>     minor: Unable to insert object                                                      
>   #004: H5Gtraverse.c line 851 in H5G_traverse(): internal path traversal failed        
>     major: Symbol table                                                                 
>     minor: Object not found                                                             
>   #005: H5Gtraverse.c line 627 in H5G__traverse_real(): traversal operator failed       
>     major: Symbol table                                                                 
>     minor: Callback failed                                                              
>   #006: H5L.c line 1604 in H5L__link_cb(): unable to create object                      
>     major: Links                                                                        
>     minor: Unable to initialize object                                                  
>   #007: H5Oint.c line 2453 in H5O_obj_create(): unable to open object                   
>     major: Object header                                                                
>     minor: Can't open object                                                            
>   #008: H5Doh.c line 300 in H5O__dset_create(): unable to create dataset                
>     minor: Object not found                                                             
>   #005: H5Gtraverse.c line 627 in H5G__traverse_real(): traversal operator failed       
>     major: Symbol table                                                                 
>     minor: Callback failed                                                              
>   #006: H5L.c line 1604 in H5L__link_cb(): unable to create object                      
>     major: Links                                                                        
>     minor: Unable to initialize object                                                  
>   #007: H5Oint.c line 2453 in H5O_obj_create(): unable to open object                   
>     major: Object header                                                                
>     minor: Can't open object                                                            
>   #008: H5Doh.c line 300 in H5O__dset_create(): unable to create dataset                
>     major: Dataset                                                                      
>     minor: Unable to initialize object                                                  
>   #009: H5Dint.c line 1274 in H5D__create(): unable to construct layout information
>     major: Dataset
>     minor: Unable to initialize object
>   #010: H5Dchunk.c line 872 in H5D__chunk_construct(): unable to set chunk sizes
>     major: Dataset
>     minor: Bad value
>   #011: H5Dchunk.c line 831 in H5D__chunk_set_sizes(): chunk size must be < 4GB
>     major: Dataset
>     minor: Unable to initialize object
>     major: Dataset
>     minor: Unable to initialize object
>   #009: H5Dint.c line 1274 in H5D__create(): unable to construct layout information
>     major: Dataset
>     minor: Unable to initialize object
>   #010: H5Dchunk.c line 872 in H5D__chunk_construct(): unable to set chunk sizes
>     major: Dataset
>     minor: Bad value
>   #011: H5Dchunk.c line 831 in H5D__chunk_set_sizes(): chunk size must be < 4GB
>     major: Dataset
>     minor: Unable to initialize object
> .......
> 
> I spoke to Barry last evening who said that this is a known error that was fixed for DMDA vecs but is broken for non-dmda vecs.
> 
> Could this be fixed ?
> 
> 
> Thank You, 
> Sajid Ali
> Applied Physics
> Northwestern University