On Wednesday 03 March 2010 18:17:31 Mark Miller wrote:
> I think the '5' in the HP5set_fapl_core means to allocate only 5 more
> bytes each time it needs to allocate. I think that is too small and
> maybe a problem since its an odd number and not a power of 2.
>
> Although I would not necessarily expect that to have failed in the way
> you are seeing either.
>
> Try '5<<20' instead of '5'
I found this in h5test.c, function h5_fileaccess()
/* In-core temporary file with 1MB increment */
if (H5Pset_fapl_core(fapl, (size_t)1, TRUE)<0) return -1;
Anyway, using a number like 5<<20 did not make a difference, it still
aborts...
Cheers,
Thorben
>
> Other than that, I don't see anything wrong with what your are doing.
> Except that maybe allocating the 30 gigabyte buffer in HDF5 to read your
> file into core is failing due to too large a request. I guess that is
> possible. To see if that is happening, if your HDF5 installation was
> compiled with tracing/debugging features turned on, then try setting
> HDF5_DEBUG=all in your enviornment where you are running your
> application.
>
> Mark
>
> On Wed, 2010-03-03 at 09:07, Thorben Kröger wrote:
> > > > On Wednesday 03 March 2010 16:47:20 Mark Miller wrote:
> > > > > Hello Thorben,
> > > > >
> > > > > However, did you in fact try using HDF5-1.8.4
> > > > > and reading the file with the CORE vfd (H5Pset_fapl_core)
> >
> > instead of opening my file like this:
> >
> > hdf5geometryFile_ = H5Fopen(filename.c_str(), H5F_ACC_RDONLY,
> > H5P_DEFAULT);
> >
> > I am now doing this:
> >
> > hid_t fapl = H5Pcreate(H5P_FILE_ACCESS);
> > if(fapl < 0) {throw std::runtime_error("fapl < 0");}
> > hid_t ret = H5Pset_fapl_core(fapl, 5/*MB?*/, 0 /*no backing store*/);
> > if(ret < 0) {throw std::runtime_error("could not create fapl core");}
> > hdf5geometryFile_ = H5Fopen(filename.c_str(), H5F_ACC_RDONLY, fapl);
> >
> > But using the second way, it cannot open any of my datasets:
> >
> > HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
> > #000: H5D.c line 321 in H5Dopen2(): not found
> >
> > major: Dataset
> > minor: Object not found
> >
> > #001: H5Gloc.c line 468 in H5G_loc_find(): can't find object
> >
> > major: Symbol table
> > minor: Object not found
> >
> > #002: H5Gtraverse.c line 877 in H5G_traverse(): internal path traversal
> >
> > failed
> >
> > major: Symbol table
> > minor: Object not found
> >
> > #003: H5Gtraverse.c line 665 in H5G_traverse_real(): can't look up
> > component
> >
> > major: Symbol table
> > minor: Object not found
> >
> > #004: H5Gobj.c line 1047 in H5G_obj_lookup(): can't locate object
> >
> > major: Symbol table
> > minor: Object not found
> >
> > #005: H5Gstab.c line 860 in H5G_stab_lookup(): not found
> >
> > major: Symbol table
> > minor: Object not found
> >
> > #006: H5B.c line 360 in H5B_find(): can't lookup key in leaf node
> >
> > major: B-Tree node
> > minor: Object not found
> >
> > #007: H5Gnode.c line 522 in H5G_node_found(): unable to protect symbol
> > table
> >
> > node
> >
> > major: Symbol table
> > minor: Unable to load metadata into cache
> >
> > #008: H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
> >
> > major: Object cache
> > minor: Unable to protect metadata
> >
> > #009: H5C.c line 6160 in H5C_protect(): can't load entry
> >
> > major: Object cache
> > minor: Unable to load metadata into cache
> >
> > #010: H5C.c line 10990 in H5C_load_entry(): unable to load entry
> >
> > major: Object cache
> > minor: Unable to load metadata into cache
> >
> > #011: H5Gcache.c line 176 in H5G_node_load(): bad symbol table node
> >
> > signature
> >
> > major: Symbol table
> > minor: Unable to load metadata into cache
> >
> > I'm at a loss now, what am I doing wrong here?
> >
> > Cheers,
> > Thorben
> >
> > _______________________________________________
> > Hdf-forum is for HDF software users discussion.
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