On Mon, Apr 15, 2013 at 12:14 PM, Robin Anil <[email protected]> wrote:
> Another crazy idea for the future is to kill the usage of > OpenIntDoubleHashMap entirely and copy parts of it inside RASV which will > only deal with nonzero keys and non zero values. RASV can then keep track > of non-zero elements in a variable to speed up those lookups. > > > Robin Anil | Software Engineer | +1 312 869 2602 | Google Inc. > > > On Mon, Apr 15, 2013 at 2:11 PM, Robin Anil <[email protected]> wrote: > > > The point 3 is coming from the philosophy that all Vectors behave the > same > > way and numNonDefaultElements of a DenseVector is same as that of a > > SparseVector. Eg, if PersonSimilarity relies upon it for document length, > > it should be behave the same way. > > > > The point 4 can be solved by killing the iterator interface entirely and > > creating forEachNonZero(function()) method which will only call if the > > element is nonzero. > Killing iteration would be really really bad, from a useability standpoint. In fact, I've been moving in the other direction: https://reviews.apache.org/r/9867/ adds iterators to the basic collection interface! > > > > > > > > On Mon, Apr 15, 2013 at 2:08 PM, Jake Mannix <[email protected] > >wrote: > > > >> On Mon, Apr 15, 2013 at 11:58 AM, Robin Anil <[email protected]> > >> wrote: > >> > >> > This is what I propose: > >> > > >> > 1) Allow setting value to zero while iterating (e.set(0.0)). > >> > > >> > >> This is in addition to the fact that we already allow setting nonzero > >> values > >> while iterating, right? > >> > >> > >> > 2) Do not allow callers to use vector.set(index, 0.0) during > iterating). > >> > This can cause re-hashing. (Can set a dirty bit in the hashmap during > >> > rehash to throw a concurrent modified exception) > >> > > >> > >> Agreed - this is a commonly accepted requirement: I think in fact we > >> should pro-actively throw ConcurrentModificationException if someone > >> tries to call vector.set / vector.assign while iterating. > >> > >> > >> > 3) Update the numNonDefaultElements to iterate over the array to > >> discount > >> > 0.0 instead of returning the hashMap values. > >> > 4) IterateNonZero may iterate over a few zeros if you did set the > >> dimension > >> > to 0. Most of the statistics code should handle 0 values correctly. > >> > > >> > >> Yeah, are we really strict about getNumNonDefaultElements really always > >> returning exactly the number of nonzeroes? I was under the impression > >> that > >> for e.g. DenseVector, it would give the overal size, even if some were > 0, > >> and that it was basically tracking the amount of space the vector was > >> taking > >> up. But I can see the argument that it really should return what it > says > >> it > >> returns, if that is relied upon. > >> > >> > >> > > >> > > >> > > >> > Robin Anil | Software Engineer | +1 312 869 2602 | Google Inc. > >> > > >> > > >> > On Mon, Apr 15, 2013 at 1:50 PM, Jake Mannix <[email protected]> > >> > wrote: > >> > > >> > > Ah, this was the one corner case I was worried about - we do > >> special-case > >> > > setting to 0, > >> > > as meaning remove from the hashmap, yes. > >> > > > >> > > What's the TL;DR of what you did to work around this? Should we > allow > >> > > this? Even > >> > > if it's through the Vector.Element instance, should it be ok? If > so, > >> how > >> > > to handle? > >> > > > >> > > > >> > > On Mon, Apr 15, 2013 at 11:04 AM, Robin Anil <[email protected]> > >> > wrote: > >> > > > >> > > > I am adding the tests and updating the patch. > >> > > > > >> > > > Robin Anil | Software Engineer | +1 312 869 2602 | Google Inc. > >> > > > > >> > > > > >> > > > On Mon, Apr 15, 2013 at 1:03 PM, Robin Anil <[email protected] > > > >> > > wrote: > >> > > > > >> > > > > You can re-iterate if the state is in iteration. But you cannot > >> > write. > >> > > > > > >> > > > > This is what is happening: > >> > > > > > >> > > > > One of the values are becoming 0. So Vector tries to remove it > >> from > >> > the > >> > > > > underlying hashmap. This changes the layout, if a vector has to > be > >> > > > mutated > >> > > > > while iterating, we have to set 0 value in the hashmap and not > >> remove > >> > > it > >> > > > > like what the Vector layer is doing. This adds another > complexity, > >> > the > >> > > > > vector iterator has to deal with skipping over elements with 0 > >> value. > >> > > > > > >> > > > > > >> > > > > Try this > >> > > > > > >> > > > > Create a vector of length 13 and set the following values. > >> > > > > > >> > > > > > >> > > > > 1. double[] val = new double[] { 0, 2, 0, 0, 8, 3, 0, 6, > >> 0, 1, > >> > > 1, > >> > > > > 2, 1 }; > >> > > > > 2. for (int i = 0; i < val.length; ++i) { > >> > > > > 3. vector.set(i, val[i]); > >> > > > > 4. } > >> > > > > > >> > > > > Iterate again and while iterating set one of the values as zero. > >> > > > > > >> > > > > On Mon, Apr 15, 2013 at 12:56 PM, Dan Filimon < > >> > > > [email protected] > >> > > > > > wrote: > >> > > > > > >> > > > >> What kind of Vector is failing to set() in that code? > >> > > > >> > >> > > > >> About the state enum, what if (for whatever reason, not > >> > > > >> multi-threaded-ness) there are multiple iterators to that > vector? > >> > > > >> Something like a reference count (how many iterators point to > it) > >> > > would > >> > > > >> probably be needed, and keeping it sane would only be possible > in > >> > one > >> > > > >> thread. Although this seems kind of brittle. > >> > > > >> > >> > > > >> +1 for numNonDefault. > >> > > > >> > >> > > > >> > >> > > > >> On Mon, Apr 15, 2013 at 8:36 PM, Robin Anil < > >> [email protected]> > >> > > > wrote: > >> > > > >> > >> > > > >>> Another behavior difference. > >> > > > >>> > >> > > > >>> The numNonDefaultElement for a DenseVector returns the total > >> > length. > >> > > > >>> This causes Pearson Correlation Similarity to differ from if > it > >> was > >> > > > >>> implemented using on of the SparseVector. > >> > > > >>> I am proposing to fix the numNonDefaultElement to correctly > >> iterate > >> > > > over > >> > > > >>> the dense vector to figure out non zero values ? Sounds ok > >> > > > >>> > >> > > > >>> Robin Anil | Software Engineer | +1 312 869 2602 | Google > Inc. > >> > > > >>> > >> > > > >>> > >> > > > >>> On Mon, Apr 15, 2013 at 12:32 PM, Robin Anil < > >> [email protected] > >> > > > >wrote: > >> > > > >>> > >> > > > >>>> Found the bug PearsonCorrelationSimilarity was trying to > mutate > >> > the > >> > > > >>>> object while iterating. > >> > > > >>>> > >> > > > >>>> > >> > > > >>>> 1. while (it.hasNext()) { > >> > > > >>>> 2. Vector.Element e = it.next(); > >> > > > >>>> 3. *vector.set(e.index(),* e.get() - average); > >> > > > >>>> 4. } > >> > > > >>>> > >> > > > >>>> This has a side effect of causing the underlying hash-map or > >> > object > >> > > to > >> > > > >>>> change. > >> > > > >>>> > >> > > > >>>> The right behavior is to set the value of the index while > >> > iterating. > >> > > > >>>> > >> > > > >>>> 1. while (it.hasNext()) { > >> > > > >>>> 2. Vector.Element e = it.next(); > >> > > > >>>> 3. *e.set(e.get()* - average); > >> > > > >>>> 4. } > >> > > > >>>> > >> > > > >>>> I am sure we are incorrectly doing the first style across the > >> code > >> > > at > >> > > > >>>> many places. > >> > > > >>>> > >> > > > >>>> I am proposing this > >> > > > >>>> > >> > > > >>>> When iterating, we lock the set interface on the vector > using a > >> > > State > >> > > > >>>> enum. If anyone tries to mutate, we throw an exception. > >> > > > >>>> We flip the state when we complete iterating (hasNext = > false) > >> or > >> > > when > >> > > > >>>> we explicitly close the iterator (adding a close method on > the > >> > > > iterator). > >> > > > >>>> > >> > > > >>>> Again this is all a single thread fix. if a vector is being > >> > mutated > >> > > > and > >> > > > >>>> iterated across multiple threads, all hell can break loose. > >> > > > >>>> > >> > > > >>>> Robin > >> > > > >>>> > >> > > > >>>> > >> > > > >>>> > >> > > > >>>> On Mon, Apr 15, 2013 at 12:56 AM, Robin Anil < > >> > [email protected] > >> > > > >wrote: > >> > > > >>>> > >> > > > >>>>> Spoke too soon still failure. I am uploading the latest > >> patch. > >> > > These > >> > > > >>>>> are the current failing tests. > >> > > > >>>>> > >> > > > >>>>> > >> > > > > >> > > > >> > > >> > > ClusterClassificationDriverTest.testVectorClassificationWithOutlierRemovalMR:103->assertVectorsWithOutlierRemoval:189->checkClustersWithOutlierRemoval:239->Assert.assertTrue:41->Assert.fail:88 > >> > > > >>>>> not expecting cluster:{0:1.0,1:1.0} > >> > > > >>>>> > >> > > > >>>>> > >> > > > > >> > > > >> > > >> > ClusterClassificationDriverTest.testVectorClassificationWithOutlierRemoval:139->assertVectorsWithOutlierRemoval:189->checkClustersWithOutlierRemoval:239->Assert.assertTrue:41->Assert.fail:88 > >> > > > >>>>> not expecting cluster:{0:1.0,1:1.0} > >> > > > >>>>> > >> > > > >>>>> > >> > > > > >> > > > >> > > >> > ClusterClassificationDriverTest.testVectorClassificationWithoutOutlierRemoval:121->assertVectorsWithoutOutlierRemoval:193->assertFirstClusterWithoutOutlierRemoval:218->Assert.assertTrue:52->Assert.assertTrue:41->Assert.fail:86 > >> > > > >>>>> null > >> > > > >>>>> > >> > > > >>>>> > >> > > > > >> > > > >> > > >> > ClusterOutputPostProcessorTest.testTopDownClustering:102->assertPostProcessedOutput:188->assertTopLevelCluster:115->assertPointsInSecondTopLevelCluster:134->Assert.assertTrue:52->Assert.assertTrue:41->Assert.fail:86 > >> > > > >>>>> null > >> > > > >>>>> > >> > > > >>>>> > >> > > > > >> > > > >> > > >> > VectorSimilarityMeasuresTest.testPearsonCorrelationSimilarity:109->Assert.assertEquals:592->Assert.assertEquals:494->Assert.failNotEquals:743->Assert.fail:88 > >> > > > >>>>> expected:<0.5303300858899108> but was:<0.38729833462074176> > >> > > > >>>>> > >> > > > >>>>> > >> > > > >>>>> Robin Anil | Software Engineer | +1 312 869 2602 | Google > >> Inc. > >> > > > >>>>> > >> > > > >>>>> > >> > > > >>>>> On Mon, Apr 15, 2013 at 12:24 AM, Robin Anil < > >> > [email protected] > >> > > > >wrote: > >> > > > >>>>> > >> > > > >>>>>> Found it, fixed it. I am submitting soon. > >> > > > >>>>>> > >> > > > >>>>>> Robin Anil | Software Engineer | +1 312 869 2602 | Google > >> Inc. > >> > > > >>>>>> > >> > > > >>>>>> > >> > > > >>>>>> On Sun, Apr 14, 2013 at 11:56 PM, Ted Dunning < > >> > > > [email protected]>wrote: > >> > > > >>>>>> > >> > > > >>>>>>> Robin, > >> > > > >>>>>>> > >> > > > >>>>>>> Can you make sure that the patches are somewhere that Dan > >> can > >> > > pick > >> > > > >>>>>>> up this > >> > > > >>>>>>> work? He is in GMT+2 and is probably about to appear on > the > >> > > scene. > >> > > > >>>>>>> > >> > > > >>>>>>> > >> > > > >>>>>>> > >> > > > >>>>>>> On Sun, Apr 14, 2013 at 9:34 PM, Robin Anil < > >> > > [email protected]> > >> > > > >>>>>>> wrote: > >> > > > >>>>>>> > >> > > > >>>>>>> > Strike that there are still failures. Investigating. if > I > >> > cant > >> > > > fix > >> > > > >>>>>>> it in > >> > > > >>>>>>> > the next hour, I will submit them sometime in the > evening > >> > > > tomorrow. > >> > > > >>>>>>> > > >> > > > >>>>>>> > Robin Anil | Software Engineer | +1 312 869 2602 | > Google > >> > Inc. > >> > > > >>>>>>> > > >> > > > >>>>>>> > > >> > > > >>>>>>> > On Sun, Apr 14, 2013 at 11:33 PM, Robin Anil < > >> > > > [email protected]> > >> > > > >>>>>>> wrote: > >> > > > >>>>>>> > > >> > > > >>>>>>> > > Tests pass. Submitting the patches. > >> > > > >>>>>>> > > > >> > > > >>>>>>> > > Robin Anil | Software Engineer | +1 312 869 2602 | > >> Google > >> > > Inc. > >> > > > >>>>>>> > > > >> > > > >>>>>>> > > > >> > > > >>>>>>> > > On Sun, Apr 14, 2013 at 11:17 PM, Robin Anil < > >> > > > >>>>>>> [email protected]> > >> > > > >>>>>>> > wrote: > >> > > > >>>>>>> > > > >> > > > >>>>>>> > >> Added a few more tests. Throw NoSuchElementException > >> like > >> > > Java > >> > > > >>>>>>> > >> Collections when iterating past the end. Things look > >> > solid, > >> > > > >>>>>>> performance > >> > > > >>>>>>> > is > >> > > > >>>>>>> > >> 2x. All Math tests pass. I am now waiting for the > >> entire > >> > > test > >> > > > >>>>>>> suites to > >> > > > >>>>>>> > run > >> > > > >>>>>>> > >> before submitting. > >> > > > >>>>>>> > >> > >> > > > >>>>>>> > >> Robin Anil | Software Engineer | +1 312 869 2602 | > >> Google > >> > > > Inc. > >> > > > >>>>>>> > >> > >> > > > >>>>>>> > >> > >> > > > >>>>>>> > >> On Sun, Apr 14, 2013 at 9:49 PM, Robin Anil < > >> > > > >>>>>>> [email protected]> > >> > > > >>>>>>> > wrote: > >> > > > >>>>>>> > >> > >> > > > >>>>>>> > >>> I am not sure what I did. But removing Guava > Abstract > >> > > > iterator > >> > > > >>>>>>> actually > >> > > > >>>>>>> > >>> sped up the dot, cosine, euclidean by another 60%. > >> Things > >> > > are > >> > > > >>>>>>> now 2x > >> > > > >>>>>>> > faster > >> > > > >>>>>>> > >>> than trunk. While also correcting the behavior (I > >> hope) > >> > > > >>>>>>> > >>> > >> > > > >>>>>>> > >>> > >> > > > >>>>>>> > >>> > >> > > > >>>>>>> > > >> > > > >>>>>>> > >> > > > > >> > > > >> > > >> > https://docs.google.com/spreadsheet/ccc?key=0AhewTD_ZgznddGFQbWJCQTZXSnFULUYzdURfWDRJQlE#gid=1 > >> > > > >>>>>>> > >>> > >> > > > >>>>>>> > >>> Robin Anil | Software Engineer | +1 312 869 2602 | > >> > Google > >> > > > Inc. > >> > > > >>>>>>> > >>> > >> > > > >>>>>>> > >>> > >> > > > >>>>>>> > >>> On Sun, Apr 14, 2013 at 8:56 PM, Robin Anil < > >> > > > >>>>>>> [email protected] > >> > > > >>>>>>> > >wrote: > >> > > > >>>>>>> > >>> > >> > > > >>>>>>> > >>>> Also note that this is code gen, I have to create > >> > > > >>>>>>> > Element$keyType$Value > >> > > > >>>>>>> > >>>> for each and every combination not just int double. > >> and > >> > > also > >> > > > >>>>>>> update > >> > > > >>>>>>> > all > >> > > > >>>>>>> > >>>> callers to user ElementIntDouble instead of > Element. > >> Is > >> > it > >> > > > >>>>>>> worth it ? > >> > > > >>>>>>> > >>>> > >> > > > >>>>>>> > >>>> Robin Anil | Software Engineer | +1 312 869 2602 | > >> > Google > >> > > > >>>>>>> Inc. > >> > > > >>>>>>> > >>>> > >> > > > >>>>>>> > >>>> > >> > > > >>>>>>> > >>>> On Sun, Apr 14, 2013 at 8:46 PM, Ted Dunning < > >> > > > >>>>>>> [email protected] > >> > > > >>>>>>> > >wrote: > >> > > > >>>>>>> > >>>> > >> > > > >>>>>>> > >>>>> Collections (no longer colt collections) are now > >> part > >> > of > >> > > > >>>>>>> mahout math. > >> > > > >>>>>>> > >>>>> No > >> > > > >>>>>>> > >>>>> need to keep them separate. The lower iterator > can > >> > > > reference > >> > > > >>>>>>> > >>>>> Vector.Element > >> > > > >>>>>>> > >>>>> > >> > > > >>>>>>> > >>>>> > >> > > > >>>>>>> > >>>>> On Sun, Apr 14, 2013 at 6:24 PM, Robin Anil < > >> > > > >>>>>>> [email protected]> > >> > > > >>>>>>> > >>>>> wrote: > >> > > > >>>>>>> > >>>>> > >> > > > >>>>>>> > >>>>> > I would have loved to but Element is a sub > >> interface > >> > in > >> > > > >>>>>>> Vector. If > >> > > > >>>>>>> > >>>>> we want > >> > > > >>>>>>> > >>>>> > to keep colt collections separate we have to > keep > >> > this > >> > > > >>>>>>> separation. > >> > > > >>>>>>> > >>>>> > > >> > > > >>>>>>> > >>>>> > >> > > > >>>>>>> > >>>> > >> > > > >>>>>>> > >>>> > >> > > > >>>>>>> > >>> > >> > > > >>>>>>> > >> > >> > > > >>>>>>> > > > >> > > > >>>>>>> > > >> > > > >>>>>>> > >> > > > >>>>>> > >> > > > >>>>>> > >> > > > >>>>> > >> > > > >>>> > >> > > > >>> > >> > > > >> > >> > > > > > >> > > > > >> > > > >> > > > >> > > > >> > > -- > >> > > > >> > > -jake > >> > > > >> > > >> > >> > >> > >> -- > >> > >> -jake > >> > > > > > -- -jake
