On 05.06.2013 10:31, Andreas Hilboll wrote: > On 05.06.2013 03:29, Tim Burgess wrote: >> I was playing around with in-memory HDF5 prior to the 3.0 release. >> Here's an example based on what I was doing. >> I looked over the docs and it does mention that there is an option to >> throw away the 'file' rather than write it to disk. >> Not sure how to do that and can't actually think of a use case where I >> would want to :-) >> >> And be wary, it is H5FD_CORE. >> >> >> On Jun 05, 2013, at 08:38 AM, Anthony Scopatz <scop...@gmail.com> wrote: >>> >>> I think that you want to set parameters.DRIVER to H5DF_CORE [1]. I >>> haven't ever used this personally, but it would be great to have an >>> example script, if someone wants to write one ;) >>> >> >> >> import numpy as np >> import tables >> >> CHUNKY = 30 >> CHUNKX = 8640 >> >> if __name__ == '__main__': >> >> # create dataset and add global attrs >> >> file_path = 'demofile_chunk%sx%d.h5' % (CHUNKY, CHUNKX) >> >> with tables.open_file(file_path, 'w', title='PyTables HDF5 In-memory >> example', driver='H5FD_CORE') as h5f: >> >> # dummy some data >> lats = np.empty([4320]) >> lons = np.empty([8640]) >> >> # create some simple arrays >> lat_node = h5f.create_array('/', 'lat', lats, title='latitude') >> lon_node = h5f.create_array('/', 'lon', lons, title='longitude') >> >> # create a 365 x 4320 x 8640 CArray of 32bit float >> shape = (365, 4320, 8640) >> atom = tables.Float32Atom(dflt=np.nan) >> >> # chunk into daily slices and then further chunk days >> sst_node = h5f.create_carray(h5f.root, 'sst', atom, shape, >> chunkshape=(1, CHUNKY, CHUNKX)) >> >> # dummy up an ndarray >> sst = np.empty([4320, 8640], dtype=np.float32) >> sst.fill(30.0) >> >> # write ndarray to a 2D plane in the HDF5 >> sst_node[0] = sst > > Thanks Tim, > > I adapted your example for my use case (I'm using the EArray class, > because I need to continuously update my database), and it works well. > > However, when I use this with my own data (but also creating the arrays > like you did), I'm running into errors like "Could not wait on barrier". > It seems like the HDF library is spawing several threads. > > Any idea what's going wrong? Can I somehow avoid HDF5 multithreading at > runtime?
Update: When setting max_blosc_threads=2 and max_numexpr_threads=2, everything seems to work as expected (but a bit on the slow side ...). With max_blosc_threads=4, the error pops up. Cheers, Andreas. ------------------------------------------------------------------------------ How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j _______________________________________________ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users