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 <[email protected]
> <mailto:[email protected]>> 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
> <[email protected] <mailto:[email protected]>> 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
>
>
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Francesc Alted
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