After increasing the lead time to 15 seconds, I believe I am giving enough time for JIT to take place. This way we are measuring only the JITed code not the interpreted code. There is a flag in JVM with which you can change the threshold -XX:+CompileThreshold (default: 10000). I didnt want to mess with it to make it as close as possible to the real world.
I have also disabled the cluster benchmarks as they are not executed enough times for JIT to compile them. I have to look more at them. for now ignore them for your patch. But you can see that variance is greatly reduced (See Sheet Version8) https://docs.google.com/spreadsheet/ccc?key=0AochdzPoBmWodG9RTms1UG40YlNQd3ByUFpQY0FLWmc#gid=8 There are only a handful of regressions Norm1 (for Seq and Rand), Minus and Plus (for Rand) and a few others. Robin Anil | Software Engineer | +1 312 869 2602 | Google Inc. On Mon, Apr 29, 2013 at 11:37 AM, Robin Anil <[email protected]> wrote: > I have a few ideas to tweak around with the JIT to make the benchmarks > more stable. I will ping back once I get some time to do something. > > Robin Anil | Software Engineer | +1 312 869 2602 | Google Inc. > > > On Mon, Apr 29, 2013 at 10:32 AM, Dan Filimon <[email protected] > > wrote: > >> That's the weirdness, it's _exactly_ the same code. >> >> >> On Mon, Apr 29, 2013 at 6:31 PM, Robin Anil <[email protected]> wrote: >> >> > I will pull your Patch in and take a look a close look at it tonight. >> Whats >> > different in Run3 in Version7 v/s Run2 and Run1. Because Run3 looks >> really >> > good and the regressions of 30% in some are actually not as bad and >> nothing >> > no longer looks ridiculously blocking the patch. >> > >> > >> > On Mon, Apr 29, 2013 at 10:13 AM, Dan Filimon >> > <[email protected]>wrote: >> > >> > > I uploaded the latest patch to my vector branch on github [0]. >> > > >> > > The latest revision is, as always, here [1], "Version 7 >> > (Assign/Aggregate; >> > > 1 sec runtime)". Tests pass for this one except for some aggregate >> tests >> > > (it's not clear if aggregate should throw an exception when the >> vectors >> > are >> > > empty or return 0; I chose return 0). >> > > >> > > There's quite a bit of variance, a lot of it even in code that I >> haven't >> > > changed between runs. So, norm2 shows regressions in version 7 and >> > > improvements in version 6 and the code not having been changed. >> > > >> > > The dot product is also oscillating in version 7, showing different >> > results >> > > in the different runs (of the same algorithm). >> > > >> > > Except for some cleanup, I don't think I can do much better than >> this, so >> > > could someone please also run the benchmarks and I'll update the >> patch on >> > > ReviewBoard? >> > > >> > > [0] https://github.com/dfilimon/mahout/tree/vector >> > > [1] >> > > >> > > >> > >> https://docs.google.com/spreadsheet/ccc?key=0AochdzPoBmWodG9RTms1UG40YlNQd3ByUFpQY0FLWmc#gid=7 >> > > >> > > >> > > On Sun, Apr 28, 2013 at 11:18 PM, Ted Dunning <[email protected]> >> > > wrote: >> > > >> > > > It would *really* help to put a legend on these spreadsheets even if >> > you >> > > > have described it in the past. >> > > > >> > > > I take it that these are number of ops and bigger is better, right? >> > > > >> > > > And where is a description of what patch runs 1 and 2 actually are? >> > > > >> > > > >> > > > >> > > > On Sun, Apr 28, 2013 at 2:23 AM, Dan Filimon < >> > > [email protected]>wrote: >> > > > >> > > >> 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/ >> > >> > > >>> > > >>>>>>>>> >> > > >>> > > >>>>>>>> >> > > >>> > > >>>>>>>> >> > > >>> > > >>>>>>> >> > > >>> > > >>>>>> >> > > >>> > > >>>>> >> > > >>> > > >>>> >> > > >>> > > >>> >> > > >>> > > > >> > > >>> > > >> > > >>> > >> > > >>> >> > > >> >> > > >> >> > > > >> > > >> > >> > >
