Hi Ed, After fixing the issue, does performance has been enhanced? I'm the one who put the warning, so I'm curious on whether this actually helps people or not.
Thanks, Francesc On 6/10/13 3:28 PM, Edward Vogel wrote: > Yes, exactly. > I'm pulling data out of C that has a 1 to many relationship, and > dumping it into pytables for easier analysis. I'm creating extension > classes in cython to get access to the C structures. > It looks like this (basically, each cv1 has several cv2s): > > h5.create_table('/', 'cv1', schema_cv1) > h5.create_table('/', 'cv2', schema_cv2) > cv1_row = h5.root.cv1.row > cv2_row = h5.root.cv2.row > for cv in sf.itercv(): > cv1_row['addr'] = cv['addr'] > ... > cv1_row.append() > for cv2 in cv.itercv2(): > cv2_row['cv1_addr'] = cv['addr'] > cv2_row['foo'] = cv2_row['foo'] > ... > cv2_row.append() > h5.root.cv2.flush() # This fixes issue > > Adding the flush after the inner loop does fix the issue. (Thanks!) > So, my followup question, why do I need a flush after the inner loop, > but not when moving from the outer loop to the inner loop? > > Thanks! > > > > On Mon, Jun 10, 2013 at 2:48 PM, Anthony Scopatz <scop...@gmail.com > <mailto:scop...@gmail.com>> wrote: > > Hi Ed, > > Are you inside of a nested loop? You probably just need to flush > after the innermost loop. > > Do you have some sample code you can share? > > Be Well > Anthony > > > On Mon, Jun 10, 2013 at 1:44 PM, Edward Vogel > <edwardvog...@gmail.com <mailto:edwardvog...@gmail.com>> wrote: > > I have a dataset that I want to split between two tables. But, > when I iterate over the data and append to both tables, I get > a warning: > > /usr/local/lib/python2.7/site-packages/tables/table.py:2967: > PerformanceWarning: table ``/cv2`` is being preempted from > alive nodes without its buffers being flushed or with some > index being dirty. This may lead to very ineficient use of > resources and even to fatal errors in certain situations. > Please do a call to the .flush() or .reindex_dirty() methods > on this table before start using other nodes. > > However, if I flush after every append, I get awful performance. > Is there a correct way to append to two tables without doing a > flush? > Note, I don't have any indices defined, so it seems > reindex_dirty() doesn't apply. > > Thanks, > Ed > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > Pytables-users mailing list > Pytables-users@lists.sourceforge.net > <mailto:Pytables-users@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/pytables-users > > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > _______________________________________________ > Pytables-users mailing list > Pytables-users@lists.sourceforge.net > <mailto:Pytables-users@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/pytables-users > > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Windows: > > Build for Windows Store. > > http://p.sf.net/sfu/windows-dev2dev > > > _______________________________________________ > Pytables-users mailing list > Pytables-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pytables-users -- Francesc Alted ------------------------------------------------------------------------------ This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users