Here's [1] the most recent benchmarks, after refactoring the Assign into separate classes. It's now using a 10 second runtime and a 1 second lead time and these are only the benchmarks involving assign().
Oddly enough there are regressions with RandomAccessSparseVectors' plus() and minus() despite these working like trunk from what I can tell from the tests (VectorBinaryAssignTest). Also, there's quite a bit of variance for some reason... Clone, Create are just two of the odd ones. [1] https://docs.google.com/spreadsheet/ccc?key=0AochdzPoBmWodG9RTms1UG40YlNQd3ByUFpQY0FLWmc#gid=4 On Fri, Apr 26, 2013 at 1:30 AM, Robin Anil <[email protected]> wrote: > Do in place for rand an dense. Assign a bug to me to speed up rasv > GetElement. > On Apr 25, 2013 2:56 PM, "Dan Filimon" <[email protected]> > wrote: > > > Nearly done splitting the code up, but I'm not sure what the costs should > > ideally be. > > > > Robin, you proposed: cost of iteration + cost of lookup + cost of update > > (if its not in-place) > > > > This sounds like it's per element, rather than for the entire vector. > Also, > > are we just going to assume that there will be as many updates as > non-zeros > > or as large as the array is? How does the cost of an update factor in? > > > > And, is "in-place" just for DenseVectors? > > > > > > On Thu, Apr 25, 2013 at 8:04 PM, Robin Anil <[email protected]> > wrote: > > > > > Depends on the speed of copying a 1M double array v/s doing a calloc + > > > copying 1000 non zeros (Assuming java is doing that underneath). > > > > > > ------ > > > Robin Anil > > > > > > > > > > > > On Thu, Apr 25, 2013 at 2:18 AM, Dan Filimon < > > [email protected] > > > >wrote: > > > > > > > Right, but is clone() generally slower than assigning? That strikes > me > > as > > > > odd; doesn't Java optimize copying the internal structures (there are > > > > arrays underneath after all)? > > > > > > > > > > > > On Thu, Apr 25, 2013 at 10:14 AM, Robin Anil <[email protected]> > > > wrote: > > > > > > > >> Seems like for dense clone is slower than like().assign I need to > test > > > it > > > >> with different sizes to be sure. I kept it from the old behavior. > > > >> On Apr 25, 2013 2:12 AM, "Dan Filimon" <[email protected] > > > > > >> wrote: > > > >> > > > >>> Okay, so I should split it further into smaller sub-cases that > handle > > > >>> each Vector type. I tried making so that these match the cases in > the > > > >>> document to the extent possible. > > > >>> You're right. It is ugly and I need to split it up. > > > >>> > > > >>> I removed the OrderedIntDoubleMapping (but with another if...) but > > one > > > >>> more thing that helped is making the assign() only go through the > > > non-zeros > > > >>> when setting up a new copy. > > > >>> > > > >>> About the copying, I saw that the optimized copy doesn't always > call > > > >>> clone clone on the Vector. Why is this? > > > >>> > > > >>> Thanks for the test and the feedback! :) > > > >>> > > > >>> > > > >>> On Thu, Apr 25, 2013 at 8:30 AM, Robin Anil <[email protected] > > > >wrote: > > > >>> > > > >>>> Yes its reaching dev. I checked out your code to take a look. I > > > >>>> understand you are trying to still mix isSequentialAccess etc in > the > > > >>>> validity calculation. The whole point of this architecture is to > > > completely > > > >>>> unroll things to be more modular instead of creating a giant > > spaghetti > > > >>>> > > > >>>> Here is an example of what I am trying to say. > > > >>>> > > > >>>> This is your current implementation of > AssignIterateOneLookupOther. > > > >>>> There are so many conditionals > > > >>>> > > > >>>> > > > >>>> 1. @Override > > > >>>> 2. public Vector assign(Vector x, Vector y, > > > >>>> DoubleDoubleFunction f) { > > > >>>> 3. return !swap ? assignInner(x, y, f) : assignInner(y, > x, > > > f); > > > >>>> 4. } > > > >>>> 5. > > > >>>> 6. public Vector assignInner(Vector x, Vector y, > > > >>>> DoubleDoubleFunction f) { > > > >>>> 7. Iterator<Vector.Element> xi = x.iterateNonZero(); > > > >>>> 8. Vector.Element xe; > > > >>>> 9. Vector.Element ye; > > > >>>> 10. OrderedIntDoubleMapping updates = > > > newOrderedIntDoubleMapping(); > > > >>>> 11. while (xi.hasNext()) { > > > >>>> 12. xe = xi.next(); > > > >>>> 13. ye = y.getElement(xe.index()); > > > >>>> 14. if (!swap) { > > > >>>> 15. xe.set(f.apply(xe.get(), ye.get())); > > > >>>> 16. } else { > > > >>>> 17. if (ye.get() != 0.0 || y.isAddConstantTime()) { > > > >>>> 18. ye.set(f.apply(ye.get(), xe.get())); > > > >>>> 19. } else { > > > >>>> 20. updates.set(xe.index(), f.apply(ye.get(), > > > >>>> xe.get())); > > > >>>> 21. } > > > >>>> 22. } > > > >>>> 23. } > > > >>>> 24. if (swap && !y.isAddConstantTime()) { > > > >>>> 25. y.mergeUpdates(updates); > > > >>>> 26. } > > > >>>> 27. return swap ? y : x; > > > >>>> 28. } > > > >>>> 29. } > > > >>>> > > > >>>> Split this into. > > > >>>> > > > >>>> IterateThisLookupThatInplaceUpdate > > > >>>> IterateThatLookupThisInplaceUpdate > > > >>>> IterateThisLookupThatMergeUpdate > > > >>>> IterateThatLookupThisMergeUpdate > > > >>>> > > > >>>> Removing the conditionals itself will speedup the operations you > see > > > >>>> regression on. > > > >>>> > > > >>>> Also note that getElement() is not constant Add time for RASV. In > > > >>>> earlier version we tried at best to set in place. That reduced the > > > extra > > > >>>> hashkey computation. getElement in AbstractVector is really > > optimized > > > for > > > >>>> DenseVector and it does indicate as the cause of regression you > are > > > seeing > > > >>>> in RASV. Another one is the unused new OrderedIntDoubleMapping(). > > > Removing > > > >>>> all these will bring back the loss. > > > >>>> > > > >>>> Now the cost for each can be computed as: cost of iteration + cost > > of > > > >>>> lookup + cost of update (if its not in-place) > > > >>>> > > > >>>> See the attached file for a mock test. You will have to rework the > > > >>>> expectations but the framework should be understandable. > > > >>>> > > > >>>> > > > >>>> ------ > > > >>>> Robin Anil > > > >>>> > > > >>>> > > > >>>> > > > >>>> On Tue, Apr 23, 2013 at 4:09 AM, Dan Filimon < > > > >>>> [email protected]> wrote: > > > >>>> > > > >>>>> Here's [1] a link to the "design document" of the new vector > > > >>>>> operations so I can lay out the ideas behind what I'm doing more > > > clearly. > > > >>>>> > > > >>>>> I'd like anyone who can to have a look and comment. > > > >>>>> > > > >>>>> Ted, > > > >>>>> I know you'd like me to get back to working on clustering, but > > > >>>>> currently, BallKMeans is roughly 2x as slow as Mahout's KMeans. > > > >>>>> This is because of centroid.update() for one (it doesn't have > > > >>>>> "interesting" properties that are exploited in the current) and > > also > > > >>>>> because we're using we're just doing lots of Vector operations: > dot > > > >>>>> products for projections, hash codes for unique sets of > candidates, > > > >>>>> equality checks etc. > > > >>>>> > > > >>>>> Here's a snapshot of the hotspots for one run of BallKMeans (20 > > > >>>>> newsgroups, unprojected, i.e 20K sparse vectors with 200K > > dimensions > > > and > > > >>>>> ~100 nonzero values): > > > >>>>> Name Time (ms) > org.apache.mahout.math.AbstractVector.dot(Vector) > > > >>>>> 104069 org.apache.mahout.math.DelegatingVector.hashCode() 30159 > > > org.apache.mahout.math.AbstractVector.assignIterateBoth(Iterator, > > > >>>>> Iterator, DoubleDoubleFunction) 13720 > > > >>>>> > > > > > > org.apache.mahout.math.OrderedIntDoubleMapping.merge(OrderedIntDoubleMapping) > > > >>>>> 2911 java.lang.ClassLoader.loadClass(String, boolean) 2620 > > > sun.misc.Launcher$AppClassLoader.loadClass(String, > > > >>>>> boolean) 2620 > > > >>>>> > > > >>>>> > > > >>>>> You can see that the most time is spent doing Vector operations. > > > >>>>> Combined, the first three rows account for 91% of the runtime. > > > >>>>> > > > >>>>> Thanks for your help! > > > >>>>> > > > >>>>> PS: Is this reaching dev@? > > > >>>>> > > > >>>>> [1] > > > >>>>> > > > > > > https://docs.google.com/document/d/1g1PjUuvjyh2LBdq2_rKLIcUiDbeOORA1sCJiSsz-JVU/edit# > > > >>>>> > > > >>>>> > > > >>>>> On Tue, Apr 23, 2013 at 7:53 AM, Robin Anil < > [email protected] > > > >wrote: > > > >>>>> > > > >>>>>> Few more brain dump ideas > > > >>>>>> > > > >>>>>> For any operation (assign, aggregate) you are trying to do. > > > >>>>>> Compute set of "feasible" solutions: Based on all the properties > > of > > > >>>>>> functions > > > >>>>>> Choose the solution that minimises the cost. > > > >>>>>> > > > >>>>>> For this you may need to refactor all the special kinds of > > > iterations > > > >>>>>> and aggregations subclassing from AssignOperation and > > > AggregateOperation. > > > >>>>>> Each operation would return the cost given two input vectors > > (based > > > on > > > >>>>>> their cost properties) > > > >>>>>> > > > >>>>>> > > > >>>>>> > > > >>>>>> ------ > > > >>>>>> Robin Anil > > > >>>>>> > > > >>>>>> > > > >>>>>> > > > >>>>>> On Mon, Apr 22, 2013 at 8:46 PM, Robin Anil < > [email protected] > > > >wrote: > > > >>>>>> > > > >>>>>>> Strike that. I think the code is very confusing. You will have > > > >>>>>>> better luck if you create method for the three implementations. > > It > > > will > > > >>>>>>> make things explicit and easy to debug. > > > >>>>>>> > > > >>>>>>> public final double getIterationCost() { > > > >>>>>>> return one of {cardinality, 1.2*numNonDefault, numNonDefault} > > > >>>>>>> } > > > >>>>>>> > > > >>>>>>> public final double getLookupCost() { > > > >>>>>>> return one of {1, 1.5(lets say), log_2(numNonDefault)} > > > >>>>>>> } > > > >>>>>>> > > > >>>>>>> All your logic then becomes a minimization of the total cost. > > > >>>>>>> > > > >>>>>>> This is more extendable than current isDense(), isSequential(), > > > >>>>>>> isSparse(), isRandom() and doesn't assume what the underlying > > > >>>>>>> implementation is. > > > >>>>>>> > > > >>>>>>> > > > >>>>>>> ------ > > > >>>>>>> Robin Anil > > > >>>>>>> > > > >>>>>>> > > > >>>>>>> > > > >>>>>>> On Mon, Apr 22, 2013 at 8:09 PM, Robin Anil < > > [email protected] > > > >wrote: > > > >>>>>>> > > > >>>>>>>> Also the calculation for cost is wrong. RASV is HashMap based > > its > > > >>>>>>>> cost O(n) not O(log n) > > > >>>>>>>> > > > >>>>>>>> ------ > > > >>>>>>>> Robin Anil > > > >>>>>>>> > > > >>>>>>>> > > > >>>>>>>> > > > >>>>>>>> On Mon, Apr 22, 2013 at 4:43 PM, Robin Anil < > > [email protected] > > > >wrote: > > > >>>>>>>> > > > >>>>>>>>> This is an automatically generated e-mail. To reply, > visit: > > > >>>>>>>>> https://reviews.apache.org/r/10669/ > > > >>>>>>>>> > > math/src/main/java/org/apache/mahout/math/AbstractVector.java< > > > > https://reviews.apache.org/r/10669/diff/2/?file=283185#file283185line56> > > > (Diff > > > >>>>>>>>> revision 2) > > > >>>>>>>>> > > > >>>>>>>>> None > > > >>>>>>>>> > > > >>>>>>>>> 55 > > > >>>>>>>>> > > > >>>>>>>>> boolean commutativeAndAssociative = > > > aggregator.isCommutative() && aggregator.isAssociative(); > > > >>>>>>>>> > > > >>>>>>>>> This should be a method in AbstractFunction interface > > > >>>>>>>>> > > > >>>>>>>>> > > > >>>>>>>>> > > math/src/main/java/org/apache/mahout/math/AbstractVector.java< > > > > > > https://reviews.apache.org/r/10669/diff/2/?file=283185#file283185line1037> > > > (Diff > > > >>>>>>>>> revision 2) > > > >>>>>>>>> > > > >>>>>>>>> {'text': 'public int getNumNonZeroElements() {', 'line': 726, > > > 'expand_offset': 2} > > > >>>>>>>>> > > > >>>>>>>>> {'text': 'public int getNumNonZeroElements() {', 'line': 927, > > > 'expand_offset': 2} > > > >>>>>>>>> > > > >>>>>>>>> 942 > > > >>>>>>>>> > > > >>>>>>>>> // Make all the non-zero values 0. > > > >>>>>>>>> > > > >>>>>>>>> vector.clear() > > > >>>>>>>>> > > > >>>>>>>>> > > > >>>>>>>>> > > math/src/main/java/org/apache/mahout/math/AbstractVector.java< > > > > > > https://reviews.apache.org/r/10669/diff/2/?file=283185#file283185line1047> > > > (Diff > > > >>>>>>>>> revision 2) > > > >>>>>>>>> > > > >>>>>>>>> {'text': 'public int getNumNonZeroElements() {', 'line': 726, > > > 'expand_offset': 2} > > > >>>>>>>>> > > > >>>>>>>>> {'text': 'public int getNumNonZeroElements() {', 'line': 927, > > > 'expand_offset': 2} > > > >>>>>>>>> > > > >>>>>>>>> 952 > > > >>>>>>>>> > > > >>>>>>>>> while (it.hasNext()) { > > > >>>>>>>>> > > > >>>>>>>>> There is no guarantee of ordered iteration. The updates is > > > unsorted. merge typically implies that input is sorted > > > >>>>>>>>> > > > >>>>>>>>> > > > >>>>>>>>> > > math/src/main/java/org/apache/mahout/math/AbstractVector.java< > > > > > > https://reviews.apache.org/r/10669/diff/2/?file=283185#file283185line1074> > > > (Diff > > > >>>>>>>>> revision 2) > > > >>>>>>>>> > > > >>>>>>>>> {'text': 'public int getNumNonZeroElements() {', 'line': 726, > > > 'expand_offset': 2} > > > >>>>>>>>> > > > >>>>>>>>> {'text': 'public int getNumNonZeroElements() {', 'line': 927, > > > 'expand_offset': 2} > > > >>>>>>>>> > > > >>>>>>>>> 979 > > > >>>>>>>>> > > > >>>>>>>>> element.set(values[index]); > > > >>>>>>>>> > > > >>>>>>>>> What if there are values that are not in the existing > data. I > > > dont this is correct > > > >>>>>>>>> > > > >>>>>>>>> > > > >>>>>>>>> > > math/src/main/java/org/apache/mahout/math/AbstractVector.java< > > > > > > https://reviews.apache.org/r/10669/diff/2/?file=283185#file283185line1100> > > > (Diff > > > >>>>>>>>> revision 2) > > > >>>>>>>>> > > > >>>>>>>>> {'text': 'public int getNumNonZeroElements() {', 'line': 726, > > > 'expand_offset': 2} > > > >>>>>>>>> > > > >>>>>>>>> {'text': 'public int getNumNonZeroElements() {', 'line': 927, > > > 'expand_offset': 2} > > > >>>>>>>>> > > > >>>>>>>>> 999 > > > >>>>>>>>> > > > >>>>>>>>> invalidateCachedLength(); > > > >>>>>>>>> > > > >>>>>>>>> move invalidateCachedLength to the set method. Instead of > > > dispersing it everywhere. > > > >>>>>>>>> > > > >>>>>>>>> > > > >>>>>>>>> > > math/src/main/java/org/apache/mahout/math/AbstractVector.java< > > > > > > https://reviews.apache.org/r/10669/diff/2/?file=283185#file283185line1115> > > > (Diff > > > >>>>>>>>> revision 2) > > > >>>>>>>>> > > > >>>>>>>>> None > > > >>>>>>>>> > > > >>>>>>>>> {'text': ' private Vector > assignIterateBoth(Iterator<Element> > > > thisIterator, Iterator<Element> thatIterator,', 'line': 1070} > > > >>>>>>>>> > > > >>>>>>>>> 1014 > > > >>>>>>>>> > > > >>>>>>>>> protected Vector > assignSkipZerosIterateOne(Iterator<Element> > > > thisIterator, Vector other, > > > >>>>>>>>> > > > >>>>>>>>> be consistent, this that or thisIterator that Iterator. > > > >>>>>>>>> > > > >>>>>>>>> > > > >>>>>>>>> > > math/src/main/java/org/apache/mahout/math/AbstractVector.java< > > > > > > https://reviews.apache.org/r/10669/diff/2/?file=283185#file283185line1171> > > > (Diff > > > >>>>>>>>> revision 2) > > > >>>>>>>>> > > > >>>>>>>>> None > > > >>>>>>>>> > > > >>>>>>>>> {'text': ' private Vector > assignIterateBoth(Iterator<Element> > > > thisIterator, Iterator<Element> thatIterator,', 'line': 1070} > > > >>>>>>>>> > > > >>>>>>>>> 1070 > > > >>>>>>>>> > > > >>>>>>>>> private Vector assignIterateBoth(Iterator<Element> > > > thisIterator, Iterator<Element> thatIterator, > > > >>>>>>>>> > > > >>>>>>>>> This expects the data to to be sorted. indicate that in a > > > comment. Similarly comment other places > > > >>>>>>>>> > > > >>>>>>>>> > > > >>>>>>>>> > > > >>>>>>>>> > > > math/src/main/java/org/apache/mahout/math/function/Functions.java< > > > > https://reviews.apache.org/r/10669/diff/2/?file=283202#file283202line900 > > > > > > (Diff > > > >>>>>>>>> revision 2) > > > >>>>>>>>> > > > >>>>>>>>> None > > > >>>>>>>>> > > > >>>>>>>>> {'text': ' public boolean isLikeLeftMult() {', 'line': > > 892} > > > >>>>>>>>> > > > >>>>>>>>> 896 > > > >>>>>>>>> > > > >>>>>>>>> /** > > > >>>>>>>>> > > > >>>>>>>>> Move this comments to the base class > > > >>>>>>>>> > > > >>>>>>>>> > > > >>>>>>>>> - Robin > > > >>>>>>>>> > > > >>>>>>>>> On April 22nd, 2013, 8:45 p.m., Dan Filimon wrote: > > > >>>>>>>>> Review request for mahout, Ted Dunning, Sebastian Schelter, > > and > > > >>>>>>>>> Robin Anil. > > > >>>>>>>>> By Dan Filimon. > > > >>>>>>>>> > > > >>>>>>>>> *Updated April 22, 2013, 8:45 p.m.* > > > >>>>>>>>> Description > > > >>>>>>>>> > > > >>>>>>>>> This patch contains code cleaning up AbstractVector and > making > > > the operations as fast as possible while still having a high level > > > interface. > > > >>>>>>>>> > > > >>>>>>>>> The main changes are in AbstractVector as well as new methods > > in > > > DoubleDoubleFunction. > > > >>>>>>>>> > > > >>>>>>>>> Testing > > > >>>>>>>>> > > > >>>>>>>>> The vectors test pass but it's likely that the patch in it's > > > current state is broken as other, unrelated tests (BallKMeans...) are > > > failing. > > > >>>>>>>>> Also, my Hadoop conf is broken so I didn't run all the core > > > tests. Anyone? > > > >>>>>>>>> > > > >>>>>>>>> I can't seem to find the bug, so _please_ have a closer look. > > > It's still a work in progress. > > > >>>>>>>>> > > > >>>>>>>>> The benchmarks seem comparable (although there are some > jarring > > > diferences – Minkowski distance seems a lot slower in new-dan-1 than > > > old-trunk-2). It may be however that this is just variance due to the > > load > > > of the machine at the time. I'm having trouble interpreting the > > benchmarks > > > in general, so anyone who could give me a hand is more than welcome. > > > >>>>>>>>> > > > >>>>>>>>> Diffs > > > >>>>>>>>> > > > >>>>>>>>> - > > > math/src/main/java/org/apache/mahout/math/AbstractMatrix.java > > > >>>>>>>>> (e12aa38) > > > >>>>>>>>> - > > > math/src/main/java/org/apache/mahout/math/AbstractVector.java > > > >>>>>>>>> (090aa7a) > > > >>>>>>>>> - math/src/main/java/org/apache/mahout/math/Centroid.java > > > >>>>>>>>> (0c42196) > > > >>>>>>>>> - > > > math/src/main/java/org/apache/mahout/math/ConstantVector.java > > > >>>>>>>>> (51d67d4) > > > >>>>>>>>> - > > > math/src/main/java/org/apache/mahout/math/DelegatingVector.java > > > >>>>>>>>> (12220d4) > > > >>>>>>>>> - > math/src/main/java/org/apache/mahout/math/DenseVector.java > > > >>>>>>>>> (41c356b) > > > >>>>>>>>> - > > > > > > math/src/main/java/org/apache/mahout/math/FileBasedSparseBinaryMatrix.java > > > >>>>>>>>> (094003b) > > > >>>>>>>>> - > math/src/main/java/org/apache/mahout/math/MatrixSlice.java > > > >>>>>>>>> (7f79c96) > > > >>>>>>>>> - > > > math/src/main/java/org/apache/mahout/math/MatrixVectorView.java > > > >>>>>>>>> (af70727) > > > >>>>>>>>> - > math/src/main/java/org/apache/mahout/math/NamedVector.java > > > >>>>>>>>> (4b7a41d) > > > >>>>>>>>> - > > > math/src/main/java/org/apache/mahout/math/OrderedIntDoubleMapping.java > > > >>>>>>>>> (650d82d) > > > >>>>>>>>> - > > > math/src/main/java/org/apache/mahout/math/PermutedVectorView.java > > > >>>>>>>>> (d1ea93a) > > > >>>>>>>>> - > > > math/src/main/java/org/apache/mahout/math/RandomAccessSparseVector.java > > > >>>>>>>>> (6f85692) > > > >>>>>>>>> - > > > > > > math/src/main/java/org/apache/mahout/math/SequentialAccessSparseVector.java > > > >>>>>>>>> (21982f9) > > > >>>>>>>>> - math/src/main/java/org/apache/mahout/math/Vector.java > > > >>>>>>>>> (2f8b417) > > > >>>>>>>>> - > math/src/main/java/org/apache/mahout/math/VectorView.java > > > >>>>>>>>> (add2a60) > > > >>>>>>>>> - > > > math/src/main/java/org/apache/mahout/math/WeightedVector.java > > > >>>>>>>>> (06fbd05) > > > >>>>>>>>> - > > > > > > math/src/main/java/org/apache/mahout/math/function/DoubleDoubleFunction.java > > > >>>>>>>>> (82b350a) > > > >>>>>>>>> - > > > math/src/main/java/org/apache/mahout/math/function/Functions.java > > > >>>>>>>>> (eb2e42f) > > > >>>>>>>>> - > > > math/src/main/java/org/apache/mahout/math/function/PlusMult.java > > > >>>>>>>>> (60587b1) > > > >>>>>>>>> - > > > math/src/main/java/org/apache/mahout/math/function/TimesFunction.java > > > >>>>>>>>> (8ab0bb1) > > > >>>>>>>>> - > > > math/src/main/java/org/apache/mahout/math/jet/math/Constants.java > > > >>>>>>>>> (53535d6) > > > >>>>>>>>> - > > > math/src/test/java/org/apache/mahout/math/AbstractVectorTest.java > > > >>>>>>>>> (2b11199) > > > >>>>>>>>> - > math/src/test/java/org/apache/mahout/math/VectorTest.java > > > >>>>>>>>> (d6d554b) > > > >>>>>>>>> > > > >>>>>>>>> View Diff <https://reviews.apache.org/r/10669/diff/> > > > >>>>>>>>> > > > >>>>>>>> > > > >>>>>>>> > > > >>>>>>> > > > >>>>>> > > > >>>>> > > > >>>> > > > >>> > > > > > > > > > >
