Commit graph

10756 commits

Author SHA1 Message Date
Joseph K. Bradley b1ef6a60ff [SPARK-7259] [ML] VectorIndexer: do not copy non-ML metadata to output column
Changed VectorIndexer so it does not carry non-ML metadata from the input to the output column.  Removed ml.util.TestingUtils since VectorIndexer was the only use.

CC: mengxr

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #5789 from jkbradley/vector-indexer-metadata and squashes the following commits:

b28e159 [Joseph K. Bradley] Changed VectorIndexer so it does not carry non-ML metadata from the input to the output column.  Removed ml.util.TestingUtils since VectorIndexer was the only use.
2015-04-29 16:35:17 -07:00
Cheng Hao f8cbb0a4b3 [SPARK-7229] [SQL] SpecificMutableRow should take integer type as internal representation for Date
Author: Cheng Hao <hao.cheng@intel.com>

Closes #5772 from chenghao-intel/specific_row and squashes the following commits:

2cd064d [Cheng Hao] scala style issue
60347a2 [Cheng Hao] SpecificMutableRow should take integer type as internal representation for DateType
2015-04-29 16:23:34 -07:00
yongtang 3fc6cfd079 [SPARK-7155] [CORE] Allow newAPIHadoopFile to support comma-separated list of files as input
See JIRA: https://issues.apache.org/jira/browse/SPARK-7155

SparkContext's newAPIHadoopFile() does not support comma-separated list of files. For example, the following:
```scala
sc.newAPIHadoopFile("/root/file1.txt,/root/file2.txt", classOf[TextInputFormat], classOf[LongWritable], classOf[Text])
```
will throw
```
org.apache.hadoop.mapreduce.lib.input.InvalidInputException: Input path does not exist: file:/root/file1.txt,/root/file2.txt
```
However, the other API hadoopFile() is able to process comma-separated list of files correctly. In addition, since sc.textFile() uses hadoopFile(), it is also able to process comma-separated list of files correctly.

That means the behaviors of hadoopFile() and newAPIHadoopFile() are not aligned.

This pull request fix this issue and allows newAPIHadoopFile() to support comma-separated list of files as input.

A unit test has also been added in SparkContextSuite.scala. It creates two temporary text files as the input and tested against sc.textFile(), sc.hadoopFile(), and sc.newAPIHadoopFile().

Note: The contribution is my original work and that I license the work to the project under the project's open source license.

Author: yongtang <yongtang@users.noreply.github.com>

Closes #5708 from yongtang/SPARK-7155 and squashes the following commits:

654c80c [yongtang] [SPARK-7155] [CORE] Remove unneeded temp file deletion in unit test as parent dir is already temporary.
26faa6a [yongtang] [SPARK-7155] [CORE] Support comma-separated list of files as input for newAPIHadoopFile, wholeTextFiles, and binaryFiles. Use setInputPaths for consistency.
73e1f16 [yongtang] [SPARK-7155] [CORE] Allow newAPIHadoopFile to support comma-separated list of files as input.
2015-04-29 23:55:51 +01:00
Qiping Li 7f4b583733 [SPARK-7181] [CORE] fix inifite loop in Externalsorter's mergeWithAggregation
see [SPARK-7181](https://issues.apache.org/jira/browse/SPARK-7181).

Author: Qiping Li <liqiping1991@gmail.com>

Closes #5737 from chouqin/externalsorter and squashes the following commits:

2924b93 [Qiping Li] fix inifite loop in Externalsorter's mergeWithAggregation
2015-04-29 23:52:16 +01:00
Burak Yavuz d7dbce8f7d [SPARK-7156][SQL] support RandomSplit in DataFrames
This is built on top of kaka1992 's PR #5711 using Logical plans.

Author: Burak Yavuz <brkyvz@gmail.com>

Closes #5761 from brkyvz/random-sample and squashes the following commits:

a1fb0aa [Burak Yavuz] remove unrelated file
69669c3 [Burak Yavuz] fix broken test
1ddb3da [Burak Yavuz] copy base
6000328 [Burak Yavuz] added python api and fixed test
3c11d1b [Burak Yavuz] fixed broken test
f400ade [Burak Yavuz] fix build errors
2384266 [Burak Yavuz] addressed comments v0.1
e98ebac [Burak Yavuz] [SPARK-7156][SQL] support RandomSplit in DataFrames
2015-04-29 15:34:05 -07:00
Xusen Yin c9d530e2e5 [SPARK-6529] [ML] Add Word2Vec transformer
See JIRA issue [here](https://issues.apache.org/jira/browse/SPARK-6529).

There are some notes:

1. I add `learningRate` in sharedParams since it is a common parameter for ML algorithms.
2. We will not support transform of finding synonyms from a `Vector`, which will support in further JIRA issues.
3. Word2Vec is different with other ML models that its training set and transformed set are different. Its training set is an `RDD[Iterable[String]]` which represents documents, but the transformed set we want is an `RDD[String]` that represents unique words. So you have to switch your `inputCol` in these two stages.

Author: Xusen Yin <yinxusen@gmail.com>

Closes #5596 from yinxusen/SPARK-6529 and squashes the following commits:

ee2b37a [Xusen Yin] merge with former HEAD
4945462 [Xusen Yin] merge with #5626
3bc2cbd [Xusen Yin] change foldLeft to for loop and use blas
5dd4ee7 [Xusen Yin] fix scala style
743e0d5 [Xusen Yin] fix comments and code style
04c48e9 [Xusen Yin] ensure the functionality
a190f2c [Xusen Yin] fix code style and refine the transform function of word2vec
02848fa [Xusen Yin] refine comments
34a55c0 [Xusen Yin] fix errors
109d124 [Xusen Yin] add test suite and pass it
04dde06 [Xusen Yin] add shared params
c594095 [Xusen Yin] add word2vec transformer
23d77fa [Xusen Yin] merge with #5626
e8cfaf7 [Xusen Yin] fix conflict with master
66e7bd3 [Xusen Yin] change foldLeft to for loop and use blas
566ec20 [Xusen Yin] fix scala style
b54399f [Xusen Yin] fix comments and code style
1211e86 [Xusen Yin] ensure the functionality
6b97ec8 [Xusen Yin] fix code style and refine the transform function of word2vec
7cde18f [Xusen Yin] rm sharedParams
618abd0 [Xusen Yin] refine comments
e29680a [Xusen Yin] fix errors
fe3afe9 [Xusen Yin] add test suite and pass it
02767fb [Xusen Yin] add shared params
6a514f1 [Xusen Yin] add word2vec transformer
2015-04-29 14:55:32 -07:00
DB Tsai 15995c883a [SPARK-7222] [ML] Added mathematical derivation in comment and compressed the model, removed the correction terms in LinearRegression with ElasticNet
Added detailed mathematical derivation of how scaling and LeastSquaresAggregator work. Refactored the code so the model is compressed based on the storage. We may try compression based on the prediction time.

Also, I found that diffSum will be always zero mathematically, so no corrections are required.

Author: DB Tsai <dbt@netflix.com>

Closes #5767 from dbtsai/lir-doc and squashes the following commits:

5e346c9 [DB Tsai] refactoring
fc9f582 [DB Tsai] doc
58456d8 [DB Tsai] address feedback
69757b8 [DB Tsai] actually diffSum is mathematically zero! No correction is needed.
5929e49 [DB Tsai] typo
63f7d1e [DB Tsai] Added compression to the model based on storage
203a295 [DB Tsai] Add more documentation to LinearRegression in new ML framework.
2015-04-29 14:53:37 -07:00
Josh Rosen 3a180c19a4 [SPARK-6629] cancelJobGroup() may not work for jobs whose job groups are inherited from parent threads
When a job is submitted with a job group and that job group is inherited from a parent thread, there are multiple bugs that may prevent this job from being cancelable via `SparkContext.cancelJobGroup()`:

- When filtering jobs based on their job group properties, DAGScheduler calls `get()` instead of `getProperty()`, which does not respect inheritance, so it will skip over jobs whose job group properties were inherited.
- `Properties` objects are mutable, but we do not make defensive copies / snapshots, so modifications of the parent thread's job group will cause running jobs' groups to change; this also breaks cancelation.

Both of these issues are easy to fix: use `getProperty()` and perform defensive copying.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #5288 from JoshRosen/localProperties-mutability-race and squashes the following commits:

9e29654 [Josh Rosen] Fix style issue
5d90750 [Josh Rosen] Merge remote-tracking branch 'origin/master' into localProperties-mutability-race
3f7b9e8 [Josh Rosen] Add JIRA reference; move clone into DAGScheduler
707e417 [Josh Rosen] Clone local properties to prevent mutations from breaking job cancellation.
b376114 [Josh Rosen] Fix bug that prevented jobs with inherited job group properties from being cancelled.
2015-04-29 13:31:52 -07:00
Tathagata Das a9c4e29950 [SPARK-6752] [STREAMING] [REOPENED] Allow StreamingContext to be recreated from checkpoint and existing SparkContext
Original PR #5428 got reverted due to issues between MutableBoolean and Hadoop 1.0.4 (see JIRA). This replaces MutableBoolean with AtomicBoolean.

srowen pwendell

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #5773 from tdas/SPARK-6752 and squashes the following commits:

a0c0ead [Tathagata Das] Fix for hadoop 1.0.4
70ae85b [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into SPARK-6752
94db63c [Tathagata Das] Fix long line.
524f519 [Tathagata Das] Many changes based on PR comments.
eabd092 [Tathagata Das] Added Function0, Java API and unit tests for StreamingContext.getOrCreate
36a7823 [Tathagata Das] Minor changes.
204814e [Tathagata Das] Added StreamingContext.getOrCreate with existing SparkContext
2015-04-29 13:10:31 -07:00
Tathagata Das 1868bd40dc [SPARK-7056] [STREAMING] Make the Write Ahead Log pluggable
Users may want the WAL data to be written to non-HDFS data storage systems. To allow that, we have to make the WAL pluggable. The following design doc outlines the plan.

https://docs.google.com/a/databricks.com/document/d/1A2XaOLRFzvIZSi18i_luNw5Rmm9j2j4AigktXxIYxmY/edit?usp=sharing

Things to add.
* Unit tests for WriteAheadLogUtils

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #5645 from tdas/wal-pluggable and squashes the following commits:

2c431fd [Tathagata Das] Minor fixes.
c2bc7384 [Tathagata Das] More changes based on PR comments.
569a416 [Tathagata Das] fixed long line
bde26b1 [Tathagata Das] Renamed segment to record handle everywhere
b65e155 [Tathagata Das] More changes based on PR comments.
d7cd15b [Tathagata Das] Fixed test
1a32a4b [Tathagata Das] Fixed test
e0d19fb [Tathagata Das] Fixed defaults
9310cbf [Tathagata Das] style fix.
86abcb1 [Tathagata Das] Refactored WriteAheadLogUtils, and consolidated all WAL related configuration into it.
84ce469 [Tathagata Das] Added unit test and fixed compilation error.
bce5e75 [Tathagata Das] Fixed long lines.
837c4f5 [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into wal-pluggable
754fbf8 [Tathagata Das] Added license and docs.
09bc6fe [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into wal-pluggable
7dd2d4b [Tathagata Das] Added pluggable WriteAheadLog interface, and refactored all code along with it
2015-04-29 13:06:11 -07:00
Xusen Yin c0c0ba6d2a Fix a typo of "threshold"
mengxr

Author: Xusen Yin <yinxusen@gmail.com>

Closes #5769 from yinxusen/patch-1 and squashes the following commits:

43235f4 [Xusen Yin] Update PearsonCorrelation.scala
f7287ee [Xusen Yin] Fix a typo of "threshold"
2015-04-29 10:13:48 -07:00
Wenchen Fan 81ea42bf39 [SQL][Minor] fix java doc for DataFrame.agg
Author: Wenchen Fan <cloud0fan@outlook.com>

Closes #5712 from cloud-fan/minor and squashes the following commits:

be23064 [Wenchen Fan] fix java doc for DataFrame.agg
2015-04-29 09:49:24 -07:00
ksonj 3df9c5dd0c Better error message on access to non-existing attribute
I believe column access via `__getattr__` is bad and shouldn't be implicitly encouraged by the error message when accessing a non-existing attribute on DataFrame. This patch changes the error message from 'no such column'  to the more generic 'no such attribute', which is also what Pandas DFs will throw.

Author: ksonj <kson@siberie.de>

Closes #5771 from ksonj/master and squashes the following commits:

bcc2220 [ksonj] Better error message on access to non-existing attribute
2015-04-29 09:48:47 -07:00
Reynold Xin 687273d915 [SPARK-7223] Rename RPC askWithReply -> askWithReply, sendWithReply -> ask.
The old naming scheme was very confusing between askWithReply and sendWithReply. I also divided RpcEnv.scala into multiple files.

Author: Reynold Xin <rxin@databricks.com>

Closes #5768 from rxin/rpc-rename and squashes the following commits:

a84058e [Reynold Xin] [SPARK-7223] Rename RPC askWithReply -> askWithReply, sendWithReply -> ask.
2015-04-29 09:46:37 -07:00
Dean Chen baed3f2c73 [SPARK-6918] [YARN] Secure HBase support.
Obtain HBase security token with Kerberos credentials locally to be sent to executors. Tested on eBay's secure HBase cluster.

Similar to obtainTokenForNamenodes and fails gracefully if HBase classes are not included in path.

Requires hbase-site.xml to be in the classpath(typically via conf dir) for the zookeeper configuration. Should that go in the docs somewhere? Did not see an HBase section.

Author: Dean Chen <deanchen5@gmail.com>

Closes #5586 from deanchen/master and squashes the following commits:

0c190ef [Dean Chen] [SPARK-6918][YARN] Secure HBase support.
2015-04-29 08:58:33 -05:00
Josh Rosen f49284b5bf [SPARK-7076][SPARK-7077][SPARK-7080][SQL] Use managed memory for aggregations
This patch adds managed-memory-based aggregation to Spark SQL / DataFrames. Instead of working with Java objects, this new aggregation path uses `sun.misc.Unsafe` to manipulate raw memory.  This reduces the memory footprint for aggregations, resulting in fewer spills, OutOfMemoryErrors, and garbage collection pauses.  As a result, this allows for higher memory utilization.  It can also result in better cache locality since objects will be stored closer together in memory.

This feature can be eanbled by setting `spark.sql.unsafe.enabled=true`.  For now, this feature is only supported when codegen is enabled and only supports aggregations for which the grouping columns are primitive numeric types or strings and aggregated values are numeric.

### Managing memory with sun.misc.Unsafe

This patch supports both on- and off-heap managed memory.

- In on-heap mode, memory addresses are identified by the combination of a base Object and an offset within that object.
- In off-heap mode, memory is addressed directly with 64-bit long addresses.

To support both modes, functions that manipulate memory accept both `baseObject` and `baseOffset` fields.  In off-heap mode, we simply pass `null` as `baseObject`.

We allocate memory in large chunks, so memory fragmentation and allocation speed are not significant bottlenecks.

By default, we use on-heap mode.  To enable off-heap mode, set `spark.unsafe.offHeap=true`.

To track allocated memory, this patch extends `SparkEnv` with an `ExecutorMemoryManager` and supplies each `TaskContext` with a `TaskMemoryManager`.  These classes work together to track allocations and detect memory leaks.

### Compact tuple format

This patch introduces `UnsafeRow`, a compact row layout.  In this format, each tuple has three parts: a null bit set, fixed length values, and variable-length values:

![image](https://cloud.githubusercontent.com/assets/50748/7328538/2fdb65ce-ea8b-11e4-9743-6c0f02bb7d1f.png)

- Rows are always 8-byte word aligned (so their sizes will always be a multiple of 8 bytes)
- The bit set is used for null tracking:
	- Position _i_ is set if and only if field _i_ is null
	- The bit set is aligned to an 8-byte word boundary.
- Every field appears as an 8-byte word in the fixed-length values part:
	- If a field is null, we zero out the values.
	- If a field is variable-length, the word stores a relative offset (w.r.t. the base of the tuple) that points to the beginning of the field's data in the variable-length part.
- Each variable-length data type can have its own encoding:
	- For strings, the first word stores the length of the string and is followed by UTF-8 encoded bytes.  If necessary, the end of the string is padded with empty bytes in order to ensure word-alignment.

For example, a tuple that consists 3 fields of type (int, string, string), with value (null, “data”, “bricks”) would look like this:

![image](https://cloud.githubusercontent.com/assets/50748/7328526/1e21959c-ea8b-11e4-9a28-a4350fe4a7b5.png)

This format allows us to compare tuples for equality by directly comparing their raw bytes.  This also enables fast hashing of tuples.

### Hash map for performing aggregations

This patch introduces `UnsafeFixedWidthAggregationMap`, a hash map for performing aggregations where the aggregation result columns are fixed-with.  This map's keys and values are `Row` objects. `UnsafeFixedWidthAggregationMap` is implemented on top of `BytesToBytesMap`, an append-only map which supports byte-array keys and values.

`BytesToBytesMap` stores pointers to key and value tuples.  For each record with a new key, we copy the key and create the aggregation value buffer for that key and put them in a buffer. The hash table then simply stores pointers to the key and value. For each record with an existing key, we simply run the aggregation function to update the values in place.

This map is implemented using open hashing with triangular sequence probing.  Each entry stores two words in a long array: the first word stores the address of the key and the second word stores the relative offset from the key tuple to the value tuple, as well as the key's 32-bit hashcode.  By storing the full hashcode, we reduce the number of equality checks that need to be performed to handle position collisions ()since the chance of hashcode collision is much lower than position collision).

`UnsafeFixedWidthAggregationMap` allows regular Spark SQL `Row` objects to be used when probing the map.  Internally, it encodes these rows into `UnsafeRow` format using `UnsafeRowConverter`.  This conversion has a small overhead that can be eliminated in the future once we use UnsafeRows in other operators.

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Author: Josh Rosen <joshrosen@databricks.com>

Closes #5725 from JoshRosen/unsafe and squashes the following commits:

eeee512 [Josh Rosen] Add converters for Null, Boolean, Byte, and Short columns.
81f34f8 [Josh Rosen] Follow 'place children last' convention for GeneratedAggregate
1bc36cc [Josh Rosen] Refactor UnsafeRowConverter to avoid unnecessary boxing.
017b2dc [Josh Rosen] Remove BytesToBytesMap.finalize()
50e9671 [Josh Rosen] Throw memory leak warning even in case of error; add warning about code duplication
70a39e4 [Josh Rosen] Split MemoryManager into ExecutorMemoryManager and TaskMemoryManager:
6e4b192 [Josh Rosen] Remove an unused method from ByteArrayMethods.
de5e001 [Josh Rosen] Fix debug vs. trace in logging message.
a19e066 [Josh Rosen] Rename unsafe Java test suites to match Scala test naming convention.
78a5b84 [Josh Rosen] Add logging to MemoryManager
ce3c565 [Josh Rosen] More comments, formatting, and code cleanup.
529e571 [Josh Rosen] Measure timeSpentResizing in nanoseconds instead of milliseconds.
3ca84b2 [Josh Rosen] Only zero the used portion of groupingKeyConversionScratchSpace
162caf7 [Josh Rosen] Fix test compilation
b45f070 [Josh Rosen] Don't redundantly store the offset from key to value, since we can compute this from the key size.
a8e4a3f [Josh Rosen] Introduce MemoryManager interface; add to SparkEnv.
0925847 [Josh Rosen] Disable MiMa checks for new unsafe module
cde4132 [Josh Rosen] Add missing pom.xml
9c19fc0 [Josh Rosen] Add configuration options for heap vs. offheap
6ffdaa1 [Josh Rosen] Null handling improvements in UnsafeRow.
31eaabc [Josh Rosen] Lots of TODO and doc cleanup.
a95291e [Josh Rosen] Cleanups to string handling code
afe8dca [Josh Rosen] Some Javadoc cleanup
f3dcbfe [Josh Rosen] More mod replacement
854201a [Josh Rosen] Import and comment cleanup
06e929d [Josh Rosen] More warning cleanup
ef6b3d3 [Josh Rosen] Fix a bunch of FindBugs and IntelliJ inspections
29a7575 [Josh Rosen] Remove debug logging
49aed30 [Josh Rosen] More long -> int conversion.
b26f1d3 [Josh Rosen] Fix bug in murmur hash implementation.
765243d [Josh Rosen] Enable optional performance metrics for hash map.
23a440a [Josh Rosen] Bump up default hash map size
628f936 [Josh Rosen] Use ints intead of longs for indexing.
92d5a06 [Josh Rosen] Address a number of minor code review comments.
1f4b716 [Josh Rosen] Merge Unsafe code into the regular GeneratedAggregate, guarded by a configuration flag; integrate planner support and re-enable all tests.
d85eeff [Josh Rosen] Add basic sanity test for UnsafeFixedWidthAggregationMap
bade966 [Josh Rosen] Comment update (bumping to refresh GitHub cache...)
b3eaccd [Josh Rosen] Extract aggregation map into its own class.
d2bb986 [Josh Rosen] Update to implement new Row methods added upstream
58ac393 [Josh Rosen] Use UNSAFE allocator in GeneratedAggregate (TODO: make this configurable)
7df6008 [Josh Rosen] Optimizations related to zeroing out memory:
c1b3813 [Josh Rosen] Fix bug in UnsafeMemoryAllocator.free():
738fa33 [Josh Rosen] Add feature flag to guard UnsafeGeneratedAggregate
c55bf66 [Josh Rosen] Free buffer once iterator has been fully consumed.
62ab054 [Josh Rosen] Optimize for fact that get() is only called on String columns.
c7f0b56 [Josh Rosen] Reuse UnsafeRow pointer in UnsafeRowConverter
ae39694 [Josh Rosen] Add finalizer as "cleanup method of last resort"
c754ae1 [Josh Rosen] Now that the store*() contract has been stregthened, we can remove an extra lookup
f764d13 [Josh Rosen] Simplify address + length calculation in Location.
079f1bf [Josh Rosen] Some clarification of the BytesToBytesMap.lookup() / set() contract.
1a483c5 [Josh Rosen] First version that passes some aggregation tests:
fc4c3a8 [Josh Rosen] Sketch how the converters will be used in UnsafeGeneratedAggregate
53ba9b7 [Josh Rosen] Start prototyping Java Row -> UnsafeRow converters
1ff814d [Josh Rosen] Add reminder to free memory on iterator completion
8a8f9df [Josh Rosen] Add skeleton for GeneratedAggregate integration.
5d55cef [Josh Rosen] Add skeleton for Row implementation.
f03e9c1 [Josh Rosen] Play around with Unsafe implementations of more string methods.
ab68e08 [Josh Rosen] Begin merging the UTF8String implementations.
480a74a [Josh Rosen] Initial import of code from Databricks unsafe utils repo.
2015-04-29 01:07:26 -07:00
Patrick Wendell 1fd6ed9a56 [SPARK-7204] [SQL] Fix callSite for Dataframe and SQL operations
This patch adds SQL to the set of excluded libraries when
generating a callSite. This makes the callSite mechanism work
properly for the data frame API. I also added a small improvement for
JDBC queries where we just use the string "Spark JDBC Server Query"
instead of trying to give a callsite that doesn't make any sense
to the user.

Before (DF):
![screen shot 2015-04-28 at 1 29 26 pm](https://cloud.githubusercontent.com/assets/320616/7380170/ef63bfb0-edae-11e4-989c-f88a5ba6bbee.png)

After (DF):
![screen shot 2015-04-28 at 1 34 58 pm](https://cloud.githubusercontent.com/assets/320616/7380181/fa7f6d90-edae-11e4-9559-26f163ed63b8.png)

After (JDBC):
![screen shot 2015-04-28 at 2 00 10 pm](https://cloud.githubusercontent.com/assets/320616/7380185/02f5b2a4-edaf-11e4-8e5b-99bdc3df66dd.png)

Author: Patrick Wendell <patrick@databricks.com>

Closes #5757 from pwendell/dataframes and squashes the following commits:

0d931a4 [Patrick Wendell] Attempting to fix PySpark tests
85bf740 [Patrick Wendell] [SPARK-7204] Fix callsite for dataframe operations.
2015-04-29 00:35:08 -07:00
Burak Yavuz fe917f5ec9 [SPARK-7188] added python support for math DataFrame functions
Adds support for the math functions for DataFrames in PySpark.

rxin I love Davies.

Author: Burak Yavuz <brkyvz@gmail.com>

Closes #5750 from brkyvz/python-math-udfs and squashes the following commits:

7c4f563 [Burak Yavuz] removed is_math
3c4adde [Burak Yavuz] cleanup imports
d5dca3f [Burak Yavuz] moved math functions to mathfunctions
25e6534 [Burak Yavuz] addressed comments v2.0
d3f7e0f [Burak Yavuz] addressed comments and added tests
7b7d7c4 [Burak Yavuz] remove tests for removed methods
33c2c15 [Burak Yavuz] fixed python style
3ee0c05 [Burak Yavuz] added python functions
2015-04-29 00:09:24 -07:00
Patrick Wendell 8dee2746b5 MAINTENANCE: Automated closing of pull requests.
This commit exists to close the following pull requests on Github:

Closes #3205 (close requested by 'srowen')
Closes #5478 (close requested by 'andrewor14')
Closes #4910 (close requested by 'srowen')
Closes #5080 (close requested by 'marmbrus')
Closes #537 (close requested by 'srowen')
Closes #5691 (close requested by 'srowen')
Closes #5469 (close requested by 'marmbrus')
2015-04-28 23:38:59 -07:00
Burak Yavuz f98773a90d [SPARK-7205] Support .ivy2/local and .m2/repositories/ in --packages
In addition, I made a small change that will allow users to import 2 different artifacts with the same name. That change is made in `[organization]_[artifact]-[revision].[ext]`. This used to be only `[artifact].[ext]` which might have caused collisions between artifacts with the same artifactId, but different groupId's.

cc pwendell

Author: Burak Yavuz <brkyvz@gmail.com>

Closes #5755 from brkyvz/local-caches and squashes the following commits:

c47c9c5 [Burak Yavuz] Small fixes to --packages
2015-04-28 23:05:02 -07:00
Burak Yavuz 271c4c621d [SPARK-7215] made coalesce and repartition a part of the query plan
Coalesce and repartition now show up as part of the query plan, rather than resulting in a new `DataFrame`.

cc rxin

Author: Burak Yavuz <brkyvz@gmail.com>

Closes #5762 from brkyvz/df-repartition and squashes the following commits:

b1e76dd [Burak Yavuz] added documentation on repartitions
5807e35 [Burak Yavuz] renamed coalescepartitions
fa4509f [Burak Yavuz] rename coalesce
2c349b5 [Burak Yavuz] address comments
f2e6af1 [Burak Yavuz] add ticks
686c90b [Burak Yavuz] made coalesce and repartition a part of the query plan
2015-04-28 22:48:04 -07:00
Xiangrui Meng 5ef006fc4d [SPARK-6756] [MLLIB] add toSparse, toDense, numActives, numNonzeros, and compressed to Vector
Add `compressed` to `Vector` with some other methods: `numActives`, `numNonzeros`, `toSparse`, and `toDense`. jkbradley

Author: Xiangrui Meng <meng@databricks.com>

Closes #5756 from mengxr/SPARK-6756 and squashes the following commits:

8d4ecbd [Xiangrui Meng] address comment and add mima excludes
da54179 [Xiangrui Meng] add toSparse, toDense, numActives, numNonzeros, and compressed to Vector
2015-04-28 21:49:53 -07:00
Joseph K. Bradley a8aeadb7d4 [SPARK-7208] [ML] [PYTHON] Added Matrix, SparseMatrix to __all__ list in linalg.py
Added Matrix, SparseMatrix to __all__ list in linalg.py

CC: mengxr

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #5759 from jkbradley/SPARK-7208 and squashes the following commits:

deb51a2 [Joseph K. Bradley] Added Matrix, SparseMatrix to __all__ list in linalg.py
2015-04-28 21:15:47 -07:00
Tathagata Das 5c8f4bd5fa [SPARK-7138] [STREAMING] Add method to BlockGenerator to add multiple records to BlockGenerator with single callback
This is to ensure that receivers that receive data in small batches (like Kinesis) and want to add them but want the callback function to be called only once. This is for internal use only for improvement to Kinesis Receiver that we are planning to do.

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #5695 from tdas/SPARK-7138 and squashes the following commits:

a35cf7d [Tathagata Das] Fixed style.
a7a4cb9 [Tathagata Das] Added extra method to BlockGenerator.
2015-04-28 19:31:57 -07:00
Xiangrui Meng d36e67350c [SPARK-6965] [MLLIB] StringIndexer handles numeric input.
Cast numeric types to String for indexing. Boolean type is not handled in this PR. jkbradley

Author: Xiangrui Meng <meng@databricks.com>

Closes #5753 from mengxr/SPARK-6965 and squashes the following commits:

2e34f3c [Xiangrui Meng] add actual type in the error message
ad938bf [Xiangrui Meng] StringIndexer handles numeric input.
2015-04-28 17:41:09 -07:00
Xiangrui Meng 555213ebbf Closes #4807
Closes #5055
Closes #3583
2015-04-28 14:21:25 -07:00
Xiangrui Meng f0a1f90f53 [SPARK-7201] [MLLIB] move Identifiable to ml.util
It shouldn't live directly under `spark.ml`.

Author: Xiangrui Meng <meng@databricks.com>

Closes #5749 from mengxr/SPARK-7201 and squashes the following commits:

53847f9 [Xiangrui Meng] move Identifiable to ml.util
2015-04-28 14:07:26 -07:00
Marcelo Vanzin 28b1af7420 [MINOR] [CORE] Warn users who try to cache RDDs with dynamic allocation on.
Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #5751 from vanzin/cached-rdd-warning and squashes the following commits:

554cc07 [Marcelo Vanzin] Change message.
9efb9da [Marcelo Vanzin] [minor] [core] Warn users who try to cache RDDs with dynamic allocation on.
2015-04-28 13:49:29 -07:00
Timothy Chen 53befacced [SPARK-5338] [MESOS] Add cluster mode support for Mesos
This patch adds the support for cluster mode to run on Mesos.
It introduces a new Mesos framework dedicated to launch new apps/drivers, and can be called with the spark-submit script and specifying --master flag to the cluster mode REST interface instead of Mesos master.

Example:
./bin/spark-submit --deploy-mode cluster --class org.apache.spark.examples.SparkPi --master mesos://10.0.0.206:8077 --executor-memory 1G --total-executor-cores 100 examples/target/spark-examples_2.10-1.3.0-SNAPSHOT.jar 30

Part of this patch is also to abstract the StandaloneRestServer so it can have different implementations of the REST endpoints.

Features of the cluster mode in this PR:
- Supports supervise mode where scheduler will keep trying to reschedule exited job.
- Adds a new UI for the cluster mode scheduler to see all the running jobs, finished jobs, and supervise jobs waiting to be retried
- Supports state persistence to ZK, so when the cluster scheduler fails over it can pick up all the queued and running jobs

Author: Timothy Chen <tnachen@gmail.com>
Author: Luc Bourlier <luc.bourlier@typesafe.com>

Closes #5144 from tnachen/mesos_cluster_mode and squashes the following commits:

069e946 [Timothy Chen] Fix rebase.
e24b512 [Timothy Chen] Persist submitted driver.
390c491 [Timothy Chen] Fix zk conf key for mesos zk engine.
e324ac1 [Timothy Chen] Fix merge.
fd5259d [Timothy Chen] Address review comments.
1553230 [Timothy Chen] Address review comments.
c6c6b73 [Timothy Chen] Pass spark properties to mesos cluster tasks.
f7d8046 [Timothy Chen] Change app name to spark cluster.
17f93a2 [Timothy Chen] Fix head of line blocking in scheduling drivers.
6ff8e5c [Timothy Chen] Address comments and add logging.
df355cd [Timothy Chen] Add metrics to mesos cluster scheduler.
20f7284 [Timothy Chen] Address review comments
7252612 [Timothy Chen] Fix tests.
a46ad66 [Timothy Chen] Allow zk cli param override.
920fc4b [Timothy Chen] Fix scala style issues.
862b5b5 [Timothy Chen] Support asking driver status when it's retrying.
7f214c2 [Timothy Chen] Fix RetryState visibility
e0f33f7 [Timothy Chen] Add supervise support and persist retries.
371ce65 [Timothy Chen] Handle cluster mode recovery and state persistence.
3d4dfa1 [Luc Bourlier] Adds support to kill submissions
febfaba [Timothy Chen] Bound the finished drivers in memory
543a98d [Timothy Chen] Schedule multiple jobs
6887e5e [Timothy Chen] Support looking at SPARK_EXECUTOR_URI env variable in schedulers
8ec76bc [Timothy Chen] Fix Mesos dispatcher UI.
d57d77d [Timothy Chen] Add documentation
825afa0 [Luc Bourlier] Supports more spark-submit parameters
b8e7181 [Luc Bourlier] Adds a shutdown latch to keep the deamon running
0fa7780 [Luc Bourlier] Launch task through the mesos scheduler
5b7a12b [Timothy Chen] WIP: Making a cluster mode a mesos framework.
4b2f5ef [Timothy Chen] Specify user jar in command to be replaced with local.
e775001 [Timothy Chen] Support fetching remote uris in driver runner.
7179495 [Timothy Chen] Change Driver page output and add logging
880bc27 [Timothy Chen] Add Mesos Cluster UI to display driver results
9986731 [Timothy Chen] Kill drivers when shutdown
67cbc18 [Timothy Chen] Rename StandaloneRestClient to RestClient and add sbin scripts
e3facdd [Timothy Chen] Add Mesos Cluster dispatcher
2015-04-28 13:33:57 -07:00
Zhang, Liye 80098109d9 [SPARK-6314] [CORE] handle JsonParseException for history server
This is handled in the same way with [SPARK-6197](https://issues.apache.org/jira/browse/SPARK-6197). The result of this PR is that exception showed in history server log will be replaced by a warning, and the application that with un-complete history log file will be listed on history server webUI

Author: Zhang, Liye <liye.zhang@intel.com>

Closes #5736 from liyezhang556520/SPARK-6314 and squashes the following commits:

b8d2d88 [Zhang, Liye] handle JsonParseException for history server
2015-04-28 12:36:10 -07:00
Ilya Ganelin 2d222fb39d [SPARK-5932] [CORE] Use consistent naming for size properties
I've added an interface to JavaUtils to do byte conversion and added hooks within Utils.scala to handle conversion within Spark code (like for time strings). I've added matching tests for size conversion, and then updated all deprecated configs and documentation as per SPARK-5933.

Author: Ilya Ganelin <ilya.ganelin@capitalone.com>

Closes #5574 from ilganeli/SPARK-5932 and squashes the following commits:

11f6999 [Ilya Ganelin] Nit fixes
49a8720 [Ilya Ganelin] Whitespace fix
2ab886b [Ilya Ganelin] Scala style
fc85733 [Ilya Ganelin] Got rid of floating point math
852a407 [Ilya Ganelin] [SPARK-5932] Added much improved overflow handling. Can now handle sizes up to Long.MAX_VALUE Petabytes instead of being capped at Long.MAX_VALUE Bytes
9ee779c [Ilya Ganelin] Simplified fraction matches
22413b1 [Ilya Ganelin] Made MAX private
3dfae96 [Ilya Ganelin] Fixed some nits. Added automatic conversion of old paramter for kryoserializer.mb to new values.
e428049 [Ilya Ganelin] resolving merge conflict
8b43748 [Ilya Ganelin] Fixed error in pattern matching for doubles
84a2581 [Ilya Ganelin] Added smoother handling of fractional values for size parameters. This now throws an exception and added a warning for old spark.kryoserializer.buffer
d3d09b6 [Ilya Ganelin] [SPARK-5932] Fixing error in KryoSerializer
fe286b4 [Ilya Ganelin] Resolved merge conflict
c7803cd [Ilya Ganelin] Empty lines
54b78b4 [Ilya Ganelin] Simplified byteUnit class
69e2f20 [Ilya Ganelin] Updates to code
f32bc01 [Ilya Ganelin] [SPARK-5932] Fixed error in API in SparkConf.scala where Kb conversion wasn't being done properly (was Mb). Added test cases for both timeUnit and ByteUnit conversion
f15f209 [Ilya Ganelin] Fixed conversion of kryo buffer size
0f4443e [Ilya Ganelin]     Merge remote-tracking branch 'upstream/master' into SPARK-5932
35a7fa7 [Ilya Ganelin] Minor formatting
928469e [Ilya Ganelin] [SPARK-5932] Converted some longs to ints
5d29f90 [Ilya Ganelin] [SPARK-5932] Finished documentation updates
7a6c847 [Ilya Ganelin] [SPARK-5932] Updated spark.shuffle.file.buffer
afc9a38 [Ilya Ganelin] [SPARK-5932] Updated spark.broadcast.blockSize and spark.storage.memoryMapThreshold
ae7e9f6 [Ilya Ganelin] [SPARK-5932] Updated spark.io.compression.snappy.block.size
2d15681 [Ilya Ganelin] [SPARK-5932] Updated spark.executor.logs.rolling.size.maxBytes
1fbd435 [Ilya Ganelin] [SPARK-5932] Updated spark.broadcast.blockSize
eba4de6 [Ilya Ganelin] [SPARK-5932] Updated spark.shuffle.file.buffer.kb
b809a78 [Ilya Ganelin] [SPARK-5932] Updated spark.kryoserializer.buffer.max
0cdff35 [Ilya Ganelin] [SPARK-5932] Updated to use bibibytes in method names. Updated spark.kryoserializer.buffer.mb and spark.reducer.maxMbInFlight
475370a [Ilya Ganelin] [SPARK-5932] Simplified ByteUnit code, switched to using longs. Updated docs to clarify that we use kibi, mebi etc instead of kilo, mega
851d691 [Ilya Ganelin] [SPARK-5932] Updated memoryStringToMb to use new interfaces
a9f4fcf [Ilya Ganelin] [SPARK-5932] Added unit tests for unit conversion
747393a [Ilya Ganelin] [SPARK-5932] Added unit tests for ByteString conversion
09ea450 [Ilya Ganelin] [SPARK-5932] Added byte string conversion to Jav utils
5390fd9 [Ilya Ganelin] Merge remote-tracking branch 'upstream/master' into SPARK-5932
db9a963 [Ilya Ganelin] Closing second spark context
1dc0444 [Ilya Ganelin] Added ref equality check
8c884fa [Ilya Ganelin] Made getOrCreate synchronized
cb0c6b7 [Ilya Ganelin] Doc updates and code cleanup
270cfe3 [Ilya Ganelin] [SPARK-6703] Documentation fixes
15e8dea [Ilya Ganelin] Updated comments and added MiMa Exclude
0e1567c [Ilya Ganelin] Got rid of unecessary option for AtomicReference
dfec4da [Ilya Ganelin] Changed activeContext to AtomicReference
733ec9f [Ilya Ganelin] Fixed some bugs in test code
8be2f83 [Ilya Ganelin] Replaced match with if
e92caf7 [Ilya Ganelin] [SPARK-6703] Added test to ensure that getOrCreate both allows creation, retrieval, and a second context if desired
a99032f [Ilya Ganelin] Spacing fix
d7a06b8 [Ilya Ganelin] Updated SparkConf class to add getOrCreate method. Started test suite implementation
2015-04-28 12:18:55 -07:00
Iulian Dragos 8aab94d898 [SPARK-4286] Add an external shuffle service that can be run as a daemon.
This allows Mesos deployments to use the shuffle service (and implicitly dynamic allocation). It does so by adding a new "main" class and two corresponding scripts in `sbin`:

- `sbin/start-shuffle-service.sh`
- `sbin/stop-shuffle-service.sh`

Specific options can be passed in `SPARK_SHUFFLE_OPTS`.

This is picking up work from #3861 /cc tnachen

Author: Iulian Dragos <jaguarul@gmail.com>

Closes #4990 from dragos/feature/external-shuffle-service and squashes the following commits:

6c2b148 [Iulian Dragos] Import order and wrong name fixup.
07804ad [Iulian Dragos] Moved ExternalShuffleService to the `deploy` package + other minor tweaks.
4dc1f91 [Iulian Dragos] Reviewer’s comments:
8145429 [Iulian Dragos] Add an external shuffle service that can be run as a daemon.
2015-04-28 12:08:18 -07:00
Zhang, Liye 52ccf1d373 [Core][test][minor] replace try finally block with tryWithSafeFinally
Author: Zhang, Liye <liye.zhang@intel.com>

Closes #5739 from liyezhang556520/trySafeFinally and squashes the following commits:

55683e5 [Zhang, Liye] replace try finally block with tryWithSafeFinally
2015-04-28 10:24:00 -07:00
Xiangrui Meng b14cd23649 [SPARK-7140] [MLLIB] only scan the first 16 entries in Vector.hashCode
The Python SerDe calls `Object.hashCode`, which is very expensive for Vectors. It is not necessary to scan the whole vector, especially for large ones. In this PR, we only scan the first 16 nonzeros. srowen

Author: Xiangrui Meng <meng@databricks.com>

Closes #5697 from mengxr/SPARK-7140 and squashes the following commits:

2abc86d [Xiangrui Meng] typo
8fb7d74 [Xiangrui Meng] update impl
1ebad60 [Xiangrui Meng] only scan the first 16 nonzeros in Vector.hashCode
2015-04-28 09:59:36 -07:00
DB Tsai 6a827d5d1e [SPARK-5253] [ML] LinearRegression with L1/L2 (ElasticNet) using OWLQN
Author: DB Tsai <dbt@netflix.com>
Author: DB Tsai <dbtsai@alpinenow.com>

Closes #4259 from dbtsai/lir and squashes the following commits:

a81c201 [DB Tsai] add import org.apache.spark.util.Utils back
9fc48ed [DB Tsai] rebase
2178b63 [DB Tsai] add comments
9988ca8 [DB Tsai] addressed feedback and fixed a bug. TODO: documentation and build another synthetic dataset which can catch the bug fixed in this commit.
fcbaefe [DB Tsai] Refactoring
4eb078d [DB Tsai] first commit
2015-04-28 09:46:08 -07:00
Masayoshi TSUZUKI 268c419f15 [SPARK-6435] spark-shell --jars option does not add all jars to classpath
Modified to accept double-quotated args properly in spark-shell.cmd.

Author: Masayoshi TSUZUKI <tsudukim@oss.nttdata.co.jp>

Closes #5227 from tsudukim/feature/SPARK-6435-2 and squashes the following commits:

ac55787 [Masayoshi TSUZUKI] removed unnecessary argument.
60789a7 [Masayoshi TSUZUKI] Merge branch 'master' of https://github.com/apache/spark into feature/SPARK-6435-2
1fee420 [Masayoshi TSUZUKI] fixed test code for escaping '='.
0d4dc41 [Masayoshi TSUZUKI] - escaped comman and semicolon in CommandBuilderUtils.java - added random string to the temporary filename - double-quotation followed by `cmd /c` did not worked properly - no need to escape `=` by `^` - if double-quoted string ended with `\` like classpath, the last `\` is parsed as the escape charactor and the closing `"` didn't work properly
2a332e5 [Masayoshi TSUZUKI] Merge branch 'master' into feature/SPARK-6435-2
04f4291 [Masayoshi TSUZUKI] [SPARK-6435] spark-shell --jars option does not add all jars to classpath
2015-04-28 07:56:36 -04:00
Jim Carroll 75905c57cd [SPARK-7100] [MLLIB] Fix persisted RDD leak in GradientBoostTrees
This fixes a leak of a persisted RDD where GradientBoostTrees can call persist but never unpersists.

Jira: https://issues.apache.org/jira/browse/SPARK-7100

Discussion: http://apache-spark-developers-list.1001551.n3.nabble.com/GradientBoostTrees-leaks-a-persisted-RDD-td11750.html

Author: Jim Carroll <jim@dontcallme.com>

Closes #5669 from jimfcarroll/gb-unpersist-fix and squashes the following commits:

45f4b03 [Jim Carroll] [SPARK-7100][MLLib] Fix persisted RDD leak in GradientBoostTrees
2015-04-28 07:51:02 -04:00
Sean Owen 7f3b3b7eb7 [SPARK-7168] [BUILD] Update plugin versions in Maven build and centralize versions
Update Maven build plugin versions and centralize plugin version management

Author: Sean Owen <sowen@cloudera.com>

Closes #5720 from srowen/SPARK-7168 and squashes the following commits:

98a8947 [Sean Owen] Make install, deploy plugin versions explicit
4ecf3b2 [Sean Owen] Update Maven build plugin versions and centralize plugin version management
2015-04-28 07:48:34 -04:00
Pei-Lun Lee e13cd86567 [SPARK-6352] [SQL] Custom parquet output committer
Add new config "spark.sql.parquet.output.committer.class" to allow custom parquet output committer and an output committer class specific to use on s3.
Fix compilation error introduced by https://github.com/apache/spark/pull/5042.
Respect ParquetOutputFormat.ENABLE_JOB_SUMMARY flag.

Author: Pei-Lun Lee <pllee@appier.com>

Closes #5525 from ypcat/spark-6352 and squashes the following commits:

54c6b15 [Pei-Lun Lee] error handling
472870e [Pei-Lun Lee] add back custom parquet output committer
ddd0f69 [Pei-Lun Lee] Merge branch 'master' of https://github.com/apache/spark into spark-6352
9ece5c5 [Pei-Lun Lee] compatibility with hadoop 1.x
8413fcd [Pei-Lun Lee] Merge branch 'master' of https://github.com/apache/spark into spark-6352
fe65915 [Pei-Lun Lee] add support for parquet config parquet.enable.summary-metadata
e17bf47 [Pei-Lun Lee] Merge branch 'master' of https://github.com/apache/spark into spark-6352
9ae7545 [Pei-Lun Lee] [SPARL-6352] [SQL] Change to allow custom parquet output committer.
0d540b9 [Pei-Lun Lee] [SPARK-6352] [SQL] add license
c42468c [Pei-Lun Lee] [SPARK-6352] [SQL] add test case
0fc03ca [Pei-Lun Lee] [SPARK-6532] [SQL] hide class DirectParquetOutputCommitter
769bd67 [Pei-Lun Lee] DirectParquetOutputCommitter
f75e261 [Pei-Lun Lee] DirectParquetOutputCommitter
2015-04-28 16:50:18 +08:00
Reynold Xin d94cd1a733 [SPARK-7135][SQL] DataFrame expression for monotonically increasing IDs.
Author: Reynold Xin <rxin@databricks.com>

Closes #5709 from rxin/inc-id and squashes the following commits:

7853611 [Reynold Xin] private sql.
a9fda0d [Reynold Xin] Missed a few numbers.
343d896 [Reynold Xin] Self review feedback.
a7136cb [Reynold Xin] [SPARK-7135][SQL] DataFrame expression for monotonically increasing IDs.
2015-04-28 00:39:08 -07:00
Andrew Or bf35edd9d4 [SPARK-7187] SerializationDebugger should not crash user code
rxin

Author: Andrew Or <andrew@databricks.com>

Closes #5734 from andrewor14/ser-deb and squashes the following commits:

e8aad6c [Andrew Or] NonFatal
57d0ef4 [Andrew Or] try catch improveException
2015-04-28 00:38:14 -07:00
jerryshao 9e4e82b7bc [SPARK-5946] [STREAMING] Add Python API for direct Kafka stream
Currently only added `createDirectStream` API, I'm not sure if `createRDD` is also needed, since some Java object needs to be wrapped in Python. Please help to review, thanks a lot.

Author: jerryshao <saisai.shao@intel.com>
Author: Saisai Shao <saisai.shao@intel.com>

Closes #4723 from jerryshao/direct-kafka-python-api and squashes the following commits:

a1fe97c [jerryshao] Fix rebase issue
eebf333 [jerryshao] Address the comments
da40f4e [jerryshao] Fix Python 2.6 Syntax error issue
5c0ee85 [jerryshao] Style fix
4aeac18 [jerryshao] Fix bug in example code
7146d86 [jerryshao] Add unit test
bf3bdd6 [jerryshao] Add more APIs and address the comments
f5b3801 [jerryshao] Small style fix
8641835 [Saisai Shao] Rebase and update the code
589c05b [Saisai Shao] Fix the style
d6fcb6a [Saisai Shao] Address the comments
dfda902 [Saisai Shao] Style fix
0f7d168 [Saisai Shao] Add the doc and fix some style issues
67e6880 [Saisai Shao] Fix test bug
917b0db [Saisai Shao] Add Python createRDD API for Kakfa direct stream
c3fc11d [jerryshao] Modify the docs
2c00936 [Saisai Shao] address the comments
3360f44 [jerryshao] Fix code style
e0e0f0d [jerryshao] Code clean and bug fix
338c41f [Saisai Shao] Add python API and example for direct kafka stream
2015-04-27 23:48:02 -07:00
Burak Yavuz 29576e7860 [SPARK-6829] Added math functions for DataFrames
Implemented almost all math functions found in scala.math (max, min and abs were already present).

cc mengxr marmbrus

Author: Burak Yavuz <brkyvz@gmail.com>

Closes #5616 from brkyvz/math-udfs and squashes the following commits:

fb27153 [Burak Yavuz] reverted exception message
836a098 [Burak Yavuz] fixed test and addressed small comment
e5f0d13 [Burak Yavuz] addressed code review v2.2
b26c5fb [Burak Yavuz] addressed review v2.1
2761f08 [Burak Yavuz] addressed review v2
6588a5b [Burak Yavuz] fixed merge conflicts
b084e10 [Burak Yavuz] Addressed code review
029e739 [Burak Yavuz] fixed atan2 test
534cc11 [Burak Yavuz] added more tests, addressed comments
fa68dbe [Burak Yavuz] added double specific test data
937d5a5 [Burak Yavuz] use doubles instead of ints
8e28fff [Burak Yavuz] Added apache header
7ec8f7f [Burak Yavuz] Added math functions for DataFrames
2015-04-27 23:10:14 -07:00
zsxwing 874a2ca93d [SPARK-7174][Core] Move calling TaskScheduler.executorHeartbeatReceived to another thread
`HeartbeatReceiver` will call `TaskScheduler.executorHeartbeatReceived`, which is a blocking operation because `TaskScheduler.executorHeartbeatReceived` will call

```Scala
    blockManagerMaster.driverEndpoint.askWithReply[Boolean](
      BlockManagerHeartbeat(blockManagerId), 600 seconds)
```

finally. Even if it asks from a local Actor, it may block the current Akka thread. E.g., the reply may be dispatched to the same thread of the ask operation. So the reply cannot be processed. An extreme case is setting the thread number of Akka dispatch thread pool to 1.

jstack log:

```
"sparkDriver-akka.actor.default-dispatcher-14" daemon prio=10 tid=0x00007f2a8c02d000 nid=0x725 waiting on condition [0x00007f2b1d6d0000]
   java.lang.Thread.State: TIMED_WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00000006197a0868> (a scala.concurrent.impl.Promise$CompletionLatch)
	at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:226)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer.doAcquireSharedNanos(AbstractQueuedSynchronizer.java:1033)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer.tryAcquireSharedNanos(AbstractQueuedSynchronizer.java:1326)
	at scala.concurrent.impl.Promise$DefaultPromise.tryAwait(Promise.scala:208)
	at scala.concurrent.impl.Promise$DefaultPromise.ready(Promise.scala:218)
	at scala.concurrent.impl.Promise$DefaultPromise.result(Promise.scala:223)
	at scala.concurrent.Await$$anonfun$result$1.apply(package.scala:107)
	at akka.dispatch.MonitorableThreadFactory$AkkaForkJoinWorkerThread$$anon$3.block(ThreadPoolBuilder.scala:169)
	at scala.concurrent.forkjoin.ForkJoinPool.managedBlock(ForkJoinPool.java:3640)
	at akka.dispatch.MonitorableThreadFactory$AkkaForkJoinWorkerThread.blockOn(ThreadPoolBuilder.scala:167)
	at scala.concurrent.Await$.result(package.scala:107)
	at org.apache.spark.rpc.RpcEndpointRef.askWithReply(RpcEnv.scala:355)
	at org.apache.spark.scheduler.DAGScheduler.executorHeartbeatReceived(DAGScheduler.scala:169)
	at org.apache.spark.scheduler.TaskSchedulerImpl.executorHeartbeatReceived(TaskSchedulerImpl.scala:367)
	at org.apache.spark.HeartbeatReceiver$$anonfun$receiveAndReply$1.applyOrElse(HeartbeatReceiver.scala:103)
	at org.apache.spark.rpc.akka.AkkaRpcEnv.org$apache$spark$rpc$akka$AkkaRpcEnv$$processMessage(AkkaRpcEnv.scala:182)
	at org.apache.spark.rpc.akka.AkkaRpcEnv$$anonfun$actorRef$lzycompute$1$1$$anon$1$$anonfun$receiveWithLogging$1$$anonfun$applyOrElse$4.apply$mcV$sp(AkkaRpcEnv.scala:128)
	at org.apache.spark.rpc.akka.AkkaRpcEnv.org$apache$spark$rpc$akka$AkkaRpcEnv$$safelyCall(AkkaRpcEnv.scala:203)
	at org.apache.spark.rpc.akka.AkkaRpcEnv$$anonfun$actorRef$lzycompute$1$1$$anon$1$$anonfun$receiveWithLogging$1.applyOrElse(AkkaRpcEnv.scala:127)
	at scala.runtime.AbstractPartialFunction$mcVL$sp.apply$mcVL$sp(AbstractPartialFunction.scala:33)
	at scala.runtime.AbstractPartialFunction$mcVL$sp.apply(AbstractPartialFunction.scala:33)
	at scala.runtime.AbstractPartialFunction$mcVL$sp.apply(AbstractPartialFunction.scala:25)
	at org.apache.spark.util.ActorLogReceive$$anon$1.apply(ActorLogReceive.scala:59)
	at org.apache.spark.util.ActorLogReceive$$anon$1.apply(ActorLogReceive.scala:42)
	at scala.PartialFunction$class.applyOrElse(PartialFunction.scala:118)
	at org.apache.spark.util.ActorLogReceive$$anon$1.applyOrElse(ActorLogReceive.scala:42)
	at akka.actor.Actor$class.aroundReceive(Actor.scala:465)
	at org.apache.spark.rpc.akka.AkkaRpcEnv$$anonfun$actorRef$lzycompute$1$1$$anon$1.aroundReceive(AkkaRpcEnv.scala:94)
	at akka.actor.ActorCell.receiveMessage(ActorCell.scala:516)
	at akka.actor.ActorCell.invoke(ActorCell.scala:487)
	at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:238)
	at akka.dispatch.Mailbox.run(Mailbox.scala:220)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:393)
	at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
	at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
	at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
	at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
```

This PR moved this blocking operation to a separated thread.

Author: zsxwing <zsxwing@gmail.com>

Closes #5723 from zsxwing/SPARK-7174 and squashes the following commits:

98bfe48 [zsxwing] Use a single thread for checking timeout and reporting executorHeartbeatReceived
5b3b545 [zsxwing] Move calling `TaskScheduler.executorHeartbeatReceived` to another thread to avoid blocking the Akka thread pool
2015-04-27 21:45:40 -07:00
Yuhao Yang 4d9e560b54 [SPARK-7090] [MLLIB] Introduce LDAOptimizer to LDA to further improve extensibility
jira: https://issues.apache.org/jira/browse/SPARK-7090

LDA was implemented with extensibility in mind. And with the development of OnlineLDA and Gibbs Sampling, we are collecting more detailed requirements from different algorithms.
As Joseph Bradley jkbradley proposed in https://github.com/apache/spark/pull/4807 and with some further discussion, we'd like to adjust the code structure a little to present the common interface and extension point clearly.
Basically class LDA would be a common entrance for LDA computing. And each LDA object will refer to a LDAOptimizer for the concrete algorithm implementation. Users can customize LDAOptimizer with specific parameters and assign it to LDA.

Concrete changes:

1. Add a trait `LDAOptimizer`, which defines the common iterface for concrete implementations. Each subClass is a wrapper for a specific LDA algorithm.

2. Move EMOptimizer to file LDAOptimizer and inherits from LDAOptimizer, rename to EMLDAOptimizer. (in case a more generic EMOptimizer comes in the future)
        -adjust the constructor of EMOptimizer, since all the parameters should be passed in through initialState method. This can avoid unwanted confusion or overwrite.
        -move the code from LDA.initalState to initalState of EMLDAOptimizer

3. Add property ldaOptimizer to LDA and its getter/setter, and EMLDAOptimizer is the default Optimizer.

4. Change the return type of LDA.run from DistributedLDAModel to LDAModel.

Further work:
add OnlineLDAOptimizer and other possible Optimizers once ready.

Author: Yuhao Yang <hhbyyh@gmail.com>

Closes #5661 from hhbyyh/ldaRefactor and squashes the following commits:

0e2e006 [Yuhao Yang] respond to review comments
08a45da [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaRefactor
e756ce4 [Yuhao Yang] solve mima exception
d74fd8f [Yuhao Yang] Merge remote-tracking branch 'upstream/master' into ldaRefactor
0bb8400 [Yuhao Yang] refactor LDA with Optimizer
ec2f857 [Yuhao Yang] protoptype for discussion
2015-04-27 19:02:51 -07:00
GuoQiang Li 62888a4ded [SPARK-7162] [YARN] Launcher error in yarn-client
jira: https://issues.apache.org/jira/browse/SPARK-7162

Author: GuoQiang Li <witgo@qq.com>

Closes #5716 from witgo/SPARK-7162 and squashes the following commits:

b64564c [GuoQiang Li] Launcher error in yarn-client
2015-04-27 19:52:41 -04:00
Sean Owen ab5adb7a97 [SPARK-7145] [CORE] commons-lang (2.x) classes used instead of commons-lang3 (3.x); commons-io used without dependency
Remove use of commons-lang in favor of commons-lang3 classes; remove commons-io use in favor of Guava

Author: Sean Owen <sowen@cloudera.com>

Closes #5703 from srowen/SPARK-7145 and squashes the following commits:

21fbe03 [Sean Owen] Remove use of commons-lang in favor of commons-lang3 classes; remove commons-io use in favor of Guava
2015-04-27 19:50:55 -04:00
Marcelo Vanzin 5d45e1f600 [SPARK-3090] [CORE] Stop SparkContext if user forgets to.
Set up a shutdown hook to try to stop the Spark context in
case the user forgets to do it. The main effect is that any
open logs files are flushed and closed, which is particularly
interesting for event logs.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #5696 from vanzin/SPARK-3090 and squashes the following commits:

3b554b5 [Marcelo Vanzin] [SPARK-3090] [core] Stop SparkContext if user forgets to.
2015-04-27 19:46:17 -04:00
Hong Shen 8e1c00dbf4 [SPARK-6738] [CORE] Improve estimate the size of a large array
Currently, SizeEstimator.visitArray is not correct in the follow case,
```
array size > 200,
elem has the share object
```

when I add a debug log in SizeTracker.scala:
```
 System.err.println(s"numUpdates:$numUpdates, size:$ts, bytesPerUpdate:$bytesPerUpdate, cost time:$b")
```
I get the following log:
```
 numUpdates:1, size:262448, bytesPerUpdate:0.0, cost time:35
 numUpdates:2, size:420698, bytesPerUpdate:158250.0, cost time:35
 numUpdates:4, size:420754, bytesPerUpdate:28.0, cost time:32
 numUpdates:7, size:420754, bytesPerUpdate:0.0, cost time:27
 numUpdates:12, size:420754, bytesPerUpdate:0.0, cost time:28
 numUpdates:20, size:420754, bytesPerUpdate:0.0, cost time:25
 numUpdates:32, size:420754, bytesPerUpdate:0.0, cost time:21
 numUpdates:52, size:420754, bytesPerUpdate:0.0, cost time:20
 numUpdates:84, size:420754, bytesPerUpdate:0.0, cost time:20
 numUpdates:135, size:420754, bytesPerUpdate:0.0, cost time:20
 numUpdates:216, size:420754, bytesPerUpdate:0.0, cost time:11
 numUpdates:346, size:420754, bytesPerUpdate:0.0, cost time:6
 numUpdates:554, size:488911, bytesPerUpdate:327.67788461538464, cost time:8
 numUpdates:887, size:2312259426, bytesPerUpdate:6942253.798798799, cost time:198
15/04/21 14:27:26 INFO collection.ExternalAppendOnlyMap: Thread 51 spilling in-memory map of 3.0 GB to disk (1 time so far)
15/04/21 14:27:26 INFO collection.ExternalAppendOnlyMap: /data11/yarnenv/local/usercache/spark/appcache/application_1426746631567_11745/spark-local-20150421142719-c001/30/temp_local_066af981-c2fc-4b70-a00e-110e23006fbc
```
But in fact the file size is only 162K:
```
$ ll -h /data11/yarnenv/local/usercache/spark/appcache/application_1426746631567_11745/spark-local-20150421142719-c001/30/temp_local_066af981-c2fc-4b70-a00e-110e23006fbc
-rw-r----- 1 spark users 162K Apr 21 14:27 /data11/yarnenv/local/usercache/spark/appcache/application_1426746631567_11745/spark-local-20150421142719-c001/30/temp_local_066af981-c2fc-4b70-a00e-110e23006fbc
```

In order to test case, I change visitArray to:
```
       var size = 0l
         for (i <- 0 until length) {
          val obj = JArray.get(array, i)
          size += SizeEstimator.estimate(obj, state.visited).toLong
        }
       state.size += size
```
I get the following log:
```
...
14895 277016088 566.9046118590662 time:8470
23832 281840544 552.3308270676691 time:8031
38132 289891824 539.8294729775092 time:7897
61012 302803640 563.0265734265735 time:13044
97620 322904416 564.3276223776223 time:13554
15/04/14 11:46:43 INFO collection.ExternalAppendOnlyMap: Thread 51 spilling in-memory map of 314.5 MB to disk (1 time so far)
15/04/14 11:46:43 INFO collection.ExternalAppendOnlyMap: /data1/yarnenv/local/usercache/spark/appcache/application_1426746631567_8477/spark-local-20150414114020-2fcb/14/temp_local_5b6b98d5-5bfa-47e2-8216-059482ccbda0
```
 the file size is 85M.
```
$ ll -h /data1/yarnenv/local/usercache/spark/appcache/application_1426746631567_8477/spark- local-20150414114020-2fcb/14/
total 85M
-rw-r----- 1 spark users 85M Apr 14 11:46 temp_local_5b6b98d5-5bfa-47e2-8216-059482ccbda0
```

The following log is when I use this patch,
```
....
numUpdates:32, size:365484, bytesPerUpdate:0.0, cost time:7
numUpdates:52, size:365484, bytesPerUpdate:0.0, cost time:5
numUpdates:84, size:365484, bytesPerUpdate:0.0, cost time:5
numUpdates:135, size:372208, bytesPerUpdate:131.84313725490196, cost time:86
numUpdates:216, size:379020, bytesPerUpdate:84.09876543209876, cost time:21
numUpdates:346, size:1865208, bytesPerUpdate:11432.215384615385, cost time:23
numUpdates:554, size:2052380, bytesPerUpdate:899.8653846153846, cost time:16
numUpdates:887, size:2142820, bytesPerUpdate:271.59159159159157, cost time:15
..
numUpdates:14895, size:251675500, bytesPerUpdate:438.5263157894737, cost time:13
numUpdates:23832, size:257010268, bytesPerUpdate:596.9305135951662, cost time:14
numUpdates:38132, size:263922396, bytesPerUpdate:483.3655944055944, cost time:15
numUpdates:61012, size:268962596, bytesPerUpdate:220.28846153846155, cost time:24
numUpdates:97620, size:286980644, bytesPerUpdate:492.1888111888112, cost time:22
15/04/21 14:45:12 INFO collection.ExternalAppendOnlyMap: Thread 53 spilling in-memory map of 328.7 MB to disk (1 time so far)
15/04/21 14:45:12 INFO collection.ExternalAppendOnlyMap: /data4/yarnenv/local/usercache/spark/appcache/application_1426746631567_11758/spark-local-20150421144456-a2a5/2a/temp_local_9c109510-af16-4468-8f23-48cad04da88f
```
 the file size is 88M.
```
$ ll -h /data4/yarnenv/local/usercache/spark/appcache/application_1426746631567_11758/spark-local-20150421144456-a2a5/2a/
total 88M
-rw-r----- 1 spark users 88M Apr 21 14:45 temp_local_9c109510-af16-4468-8f23-48cad04da88f
```

Author: Hong Shen <hongshen@tencent.com>

Closes #5608 from shenh062326/my_change5 and squashes the following commits:

5506bae [Hong Shen] Fix compile error
c275dd3 [Hong Shen] Alter code style
fe202a2 [Hong Shen] Change the code style and add documentation.
a9fca84 [Hong Shen] Add test case for SizeEstimator
4877eee [Hong Shen] Improve estimate the size of a large array
a2ea7ac [Hong Shen] Alter code style
4c28e36 [Hong Shen] Improve estimate the size of a large array
2015-04-27 18:59:45 -04:00
Steven She b9de9e040a [SPARK-7103] Fix crash with SparkContext.union when RDD has no partitioner
Added a check to the SparkContext.union method to check that a partitioner is defined on all RDDs when instantiating a PartitionerAwareUnionRDD.

Author: Steven She <steven@canopylabs.com>

Closes #5679 from stevencanopy/SPARK-7103 and squashes the following commits:

5a3d846 [Steven She] SPARK-7103: Fix crash with SparkContext.union when at least one RDD has no partitioner
2015-04-27 18:55:02 -04:00