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From Robin Anil <robina...@apache.org>
Subject Re: Review Request: MAHOUT-1192 [2]: Speed up Vector Operations
Date Thu, 25 Apr 2013 17:04:53 GMT
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 <dangeorge.filimon@gmail.com>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 <robinanil@apache.org> 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" <dangeorge.filimon@gmail.com>
>> 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 <robinanil@apache.org>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 <
>>>> dangeorge.filimon@gmail.com> 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 <robinanil@apache.org>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 <robinanil@apache.org>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 <robinanil@apache.org>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 <robinanil@apache.org>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/>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>

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