Sorry for the delay in dealing with this. If you do Pkg.update(), it should be
fixed now.
--Tim
On Monday, March 10, 2014 03:21:01 PM Zachary Roth wrote:
> I'm having some trouble loading saved data, and I haven't had any luck in
> looking for solutions online. I've reduced the code to as short of an
> example as I could:
>
> using HDF5, JLD
>
> type Test
> values::Vector{Integer}
> end
>
> x = Test([])
> @save "test.jld" x
> @load "test.jld" x
>
> When I run the above code, I get the following error:
>
> Error dereferencing object
> while loading In[1], in expression starting on line 9
> in h5r_dereference at /home/zroth/.julia/HDF5/src/plain.jl:1673
> in getindex at /home/zroth/.julia/HDF5/src/jld.jl:178
> in getrefs at /home/zroth/.julia/HDF5/src/jld.jl:413
> in read at /home/zroth/.julia/HDF5/src/jld.jl:344
> in read at /home/zroth/.julia/HDF5/src/jld.jl:220
> in getrefs at /home/zroth/.julia/HDF5/src/jld.jl:415
> in read at /home/zroth/.julia/HDF5/src/jld.jl:384
> in read at /home/zroth/.julia/HDF5/src/jld.jl:220
> in read at /home/zroth/.julia/HDF5/src/jld.jl:209
> in anonymous at no file
>
>
> HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 139795549558592:
> #000: ../../../src/H5R.c line 533 in H5Rdereference(): unable dereference
> object major: References
> minor: Unable to initialize object
> #001: ../../../src/H5R.c line 419 in H5R_dereference(): dereferencing
> deleted object major: References
> minor: Bad object header link count
> #002: ../../../src/H5O.c line 1542 in H5O_link(): unable to load object
> header major: Object header
> minor: Unable to load metadata into cache
> #003: ../../../src/H5AC.c line 1831 in H5AC_protect(): H5C_protect()
> failed. major: Object cache
> minor: Unable to protect metadata
> #004: ../../../src/H5C.c line 6160 in H5C_protect(): can't load entry
> major: Object cache
> minor: Unable to load metadata into cache
> #005: ../../../src/H5C.c line 10990 in H5C_load_entry(): unable to load
> entry major: Object cache
> minor: Unable to load metadata into cache
> #006: ../../../src/H5Ocache.c line 154 in H5O_load(): unable to read
> object header major: Object header
> minor: Read failed
> #007: ../../../src/H5Fio.c line 113 in H5F_block_read(): read from
> metadata accumulator failed major: Low-level I/O
> minor: Read failed
> #008: ../../../src/H5Faccum.c line 196 in H5F_accum_read(): driver read
> request failed major: Low-level I/O
> minor: Read failed
> #009: ../../../src/H5FDint.c line 142 in H5FD_read(): driver read request
> failed major: Virtual File Layer
> minor: Read failed
> #010: ../../../src/H5FDsec2.c line 739 in H5FD_sec2_read(): addr overflow
> major: Invalid arguments to routine
> minor: Address overflowed
>
>
> The problem only seems to occur when [] is passed to Test; for example,
> saving the output of Test([1:4]) works just fine for me. (For the record,
> I am working with real data that will sometimes be empty; it took me a
> while to track down that empty vectors were causing the problem.) And from
> what I can tell, the resultant file doesn't seem to be corrupted. If
> somebody can help me out, I'd greatly appreciate it.
