## What changes were proposed in this pull request?
This PR proposes to add **Single threading model design (pinned thread model)** mode which is an experimental mode to sync threads on PVM and JVM. See https://www.py4j.org/advanced_topics.html#using-single-threading-model-pinned-thread
### Multi threading model
Currently, PySpark uses this model. Threads on PVM and JVM are independent. For instance, in a different Python thread, callbacks are received and relevant Python codes are executed. JVM threads are reused when possible.
Py4J will create a new thread every time a command is received and there is no thread available. See the current model we're using - https://www.py4j.org/advanced_topics.html#the-multi-threading-model
One problem in this model is that we can't sync threads on PVM and JVM out of the box. This leads to some problems in particular at some codes related to threading in JVM side. See:
7056e004ee/core/src/main/scala/org/apache/spark/SparkContext.scala (L334)
Due to reusing JVM threads, seems the job groups in Python threads cannot be set in each thread as described in the JIRA.
### Single threading model design (pinned thread model)
This mode pins and syncs the threads on PVM and JVM to work around the problem above. For instance, in the same Python thread, callbacks are received and relevant Python codes are executed. See https://www.py4j.org/advanced_topics.html#the-single-threading-model
Even though this mode can sync threads on PVM and JVM for other thread related code paths,
this might cause another problem: seems unable to inherit properties as below (assuming multi-thread mode still creates new threads when existing threads are busy, I suspect this issue already exists when multiple jobs are submitted in multi-thread mode; however, it can be always seen in single threading mode):
```bash
$ PYSPARK_PIN_THREAD=true ./bin/pyspark
```
```python
import threading
spark.sparkContext.setLocalProperty("a", "hi")
def print_prop():
print(spark.sparkContext.getLocalProperty("a"))
threading.Thread(target=print_prop).start()
```
```
None
```
Unlike Scala side:
```scala
spark.sparkContext.setLocalProperty("a", "hi")
new Thread(new Runnable {
def run() = println(spark.sparkContext.getLocalProperty("a"))
}).start()
```
```
hi
```
This behaviour potentially could cause weird issues but this PR currently does not target this fix this for now since this mode is experimental.
### How does this PR fix?
Basically there are two types of Py4J servers `GatewayServer` and `ClientServer`. The former is for multi threading and the latter is for single threading. This PR adds a switch to use the latter.
In Scala side:
The logic to select a server is encapsulated in `Py4JServer` and use `Py4JServer` at `PythonRunner` for Spark summit and `PythonGatewayServer` for Spark shell. Each uses `ClientServer` when `PYSPARK_PIN_THREAD` is `true` and `GatewayServer` otherwise.
In Python side:
Simply do an if-else to switch the server to talk. It uses `ClientServer` when `PYSPARK_PIN_THREAD` is `true` and `GatewayServer` otherwise.
This is disabled by default for now.
## How was this patch tested?
Manually tested. This can be tested via:
```python
PYSPARK_PIN_THREAD=true ./bin/pyspark
```
and/or
```bash
cd python
./run-tests --python-executables=python --testnames "pyspark.tests.test_pin_thread"
```
Also, ran the Jenkins tests with `PYSPARK_PIN_THREAD` enabled.
Closes#24898 from HyukjinKwon/pinned-thread.
Authored-by: HyukjinKwon <gurwls223@apache.org>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
### What changes were proposed in this pull request?
Remove automatically generated param setters in _shared_params_code_gen.py
### Why are the changes needed?
To keep parity between scala and python
### Does this PR introduce any user-facing change?
Yes
Add some setters in Python ML XXXModels
### How was this patch tested?
unit tests
Closes#26232 from huaxingao/spark-29093.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: zhengruifeng <ruifengz@foxmail.com>
### What changes were proposed in this pull request?
change PySpark ml ```Params._clear``` to ```Params.clear```
### Why are the changes needed?
PySpark ML currently has a private _clear() method that will unset a param. This should be made public to match the Scala API and give users a way to unset a user supplied param.
### Does this PR introduce any user-facing change?
Yes. PySpark ml ```Params._clear``` ---> ```Params.clear```
### How was this patch tested?
Add test.
Closes#26130 from huaxingao/spark-29464.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Bryan Cutler <cutlerb@gmail.com>
### What changes were proposed in this pull request?
Binarizer support multi-column by extending `HasInputCols`/`HasOutputCols`/`HasThreshold`/`HasThresholds`
### Why are the changes needed?
similar algs in `ml.feature` already support multi-column, like `Bucketizer`/`StringIndexer`/`QuantileDiscretizer`
### Does this PR introduce any user-facing change?
yes, add setter/getter of `thresholds`/`inputCols`/`outputCols`
### How was this patch tested?
added suites
Closes#26064 from zhengruifeng/binarizer_multicols.
Authored-by: zhengruifeng <ruifengz@foxmail.com>
Signed-off-by: zhengruifeng <ruifengz@foxmail.com>
### What changes were proposed in this pull request?
add column setters/getters support in Pyspark feature models
### Why are the changes needed?
keep parity between Pyspark and Scala
### Does this PR introduce any user-facing change?
Yes.
After the change, Pyspark feature models have column setters/getters support.
### How was this patch tested?
Add some doctests
Closes#25908 from huaxingao/spark-29143.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
### What changes were proposed in this pull request?
Add some common classes in Python to make it have the same structure as Scala
1. Scala has ClassifierParams/Classifier/ClassificationModel:
```
trait ClassifierParams
extends PredictorParams with HasRawPredictionCol
abstract class Classifier
extends Predictor with ClassifierParams {
def setRawPredictionCol
}
abstract class ClassificationModel
extends PredictionModel with ClassifierParams {
def setRawPredictionCol
}
```
This PR makes Python has the following:
```
class JavaClassifierParams(HasRawPredictionCol, JavaPredictorParams):
pass
class JavaClassifier(JavaPredictor, JavaClassifierParams):
def setRawPredictionCol
class JavaClassificationModel(JavaPredictionModel, JavaClassifierParams):
def setRawPredictionCol
```
2. Scala has ProbabilisticClassifierParams/ProbabilisticClassifier/ProbabilisticClassificationModel:
```
trait ProbabilisticClassifierParams
extends ClassifierParams with HasProbabilityCol with HasThresholds
abstract class ProbabilisticClassifier
extends Classifier with ProbabilisticClassifierParams {
def setProbabilityCol
def setThresholds
}
abstract class ProbabilisticClassificationModel
extends ClassificationModel with ProbabilisticClassifierParams {
def setProbabilityCol
def setThresholds
}
```
This PR makes Python have the following:
```
class JavaProbabilisticClassifierParams(HasProbabilityCol, HasThresholds, JavaClassifierParams):
pass
class JavaProbabilisticClassifier(JavaClassifier, JavaProbabilisticClassifierParams):
def setProbabilityCol
def setThresholds
class JavaProbabilisticClassificationModel(JavaClassificationModel, JavaProbabilisticClassifierParams):
def setProbabilityCol
def setThresholds
```
3. Scala has PredictorParams/Predictor/PredictionModel:
```
trait PredictorParams extends Params
with HasLabelCol with HasFeaturesCol with HasPredictionCol
abstract class Predictor
extends Estimator with PredictorParams {
def setLabelCol
def setFeaturesCol
def setPredictionCol
}
abstract class PredictionModel
extends Model with PredictorParams {
def setFeaturesCol
def setPredictionCol
def numFeatures
def predict
}
```
This PR makes Python have the following:
```
class JavaPredictorParams(HasLabelCol, HasFeaturesCol, HasPredictionCol):
pass
class JavaPredictor(JavaEstimator, JavaPredictorParams):
def setLabelCol
def setFeaturesCol
def setPredictionCol
class JavaPredictionModel(JavaModel, JavaPredictorParams):
def setFeaturesCol
def setPredictionCol
def numFeatures
def predict
```
### Why are the changes needed?
Have parity between Python and Scala ML
### Does this PR introduce any user-facing change?
Yes. Add the following changes:
```
LinearSVCModel
- get/setFeatureCol
- get/setPredictionCol
- get/setLabelCol
- get/setRawPredictionCol
- predict
```
```
LogisticRegressionModel
DecisionTreeClassificationModel
RandomForestClassificationModel
GBTClassificationModel
NaiveBayesModel
MultilayerPerceptronClassificationModel
- get/setFeatureCol
- get/setPredictionCol
- get/setLabelCol
- get/setRawPredictionCol
- get/setProbabilityCol
- predict
```
```
LinearRegressionModel
IsotonicRegressionModel
DecisionTreeRegressionModel
RandomForestRegressionModel
GBTRegressionModel
AFTSurvivalRegressionModel
GeneralizedLinearRegressionModel
- get/setFeatureCol
- get/setPredictionCol
- get/setLabelCol
- predict
```
### How was this patch tested?
Add a few doc tests.
Closes#25776 from huaxingao/spark-28985.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
### What changes were proposed in this pull request?
Bucketizer support multi-column in the python side
### Why are the changes needed?
Bucketizer should support multi-column like the scala side.
### Does this PR introduce any user-facing change?
yes, this PR add new Python API
### How was this patch tested?
added testsuites
Closes#25801 from zhengruifeng/20542_py.
Authored-by: zhengruifeng <ruifengz@foxmail.com>
Signed-off-by: zhengruifeng <ruifengz@foxmail.com>
### What changes were proposed in this pull request?
- Remove SQLContext.createExternalTable and Catalog.createExternalTable, deprecated in favor of createTable since 2.2.0, plus tests of deprecated methods
- Remove HiveContext, deprecated in 2.0.0, in favor of `SparkSession.builder.enableHiveSupport`
- Remove deprecated KinesisUtils.createStream methods, plus tests of deprecated methods, deprecate in 2.2.0
- Remove deprecated MLlib (not Spark ML) linear method support, mostly utility constructors and 'train' methods, and associated docs. This includes methods in LinearRegression, LogisticRegression, Lasso, RidgeRegression. These have been deprecated since 2.0.0
- Remove deprecated Pyspark MLlib linear method support, including LogisticRegressionWithSGD, LinearRegressionWithSGD, LassoWithSGD
- Remove 'runs' argument in KMeans.train() method, which has been a no-op since 2.0.0
- Remove deprecated ChiSqSelector isSorted protected method
- Remove deprecated 'yarn-cluster' and 'yarn-client' master argument in favor of 'yarn' and deploy mode 'cluster', etc
Notes:
- I was not able to remove deprecated DataFrameReader.json(RDD) in favor of DataFrameReader.json(Dataset); the former was deprecated in 2.2.0, but, it is still needed to support Pyspark's .json() method, which can't use a Dataset.
- Looks like SQLContext.createExternalTable was not actually deprecated in Pyspark, but, almost certainly was meant to be? Catalog.createExternalTable was.
- I afterwards noted that the toDegrees, toRadians functions were almost removed fully in SPARK-25908, but Felix suggested keeping just the R version as they hadn't been technically deprecated. I'd like to revisit that. Do we really want the inconsistency? I'm not against reverting it again, but then that implies leaving SQLContext.createExternalTable just in Pyspark too, which seems weird.
- I *kept* LogisticRegressionWithSGD, LinearRegressionWithSGD, LassoWithSGD, RidgeRegressionWithSGD in Pyspark, though deprecated, as it is hard to remove them (still used by StreamingLogisticRegressionWithSGD?) and they are not fully removed in Scala. Maybe should not have been deprecated.
### Why are the changes needed?
Deprecated items are easiest to remove in a major release, so we should do so as much as possible for Spark 3. This does not target items deprecated 'recently' as of Spark 2.3, which is still 18 months old.
### Does this PR introduce any user-facing change?
Yes, in that deprecated items are removed from some public APIs.
### How was this patch tested?
Existing tests.
Closes#25684 from srowen/SPARK-28980.
Lead-authored-by: Sean Owen <sean.owen@databricks.com>
Co-authored-by: HyukjinKwon <gurwls223@apache.org>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
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### What changes were proposed in this pull request?
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This PR proposes to fix both tests below:
```
======================================================================
FAIL: test_raw_and_probability_prediction (pyspark.ml.tests.test_algorithms.MultilayerPerceptronClassifierTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/dongjoon/APACHE/spark-master/python/pyspark/ml/tests/test_algorithms.py", line 89, in test_raw_and_probability_prediction
self.assertTrue(np.allclose(result.rawPrediction, expected_rawPrediction, atol=1E-4))
AssertionError: False is not true
```
```
File "/Users/dongjoon/APACHE/spark-master/python/pyspark/mllib/clustering.py", line 386, in __main__.GaussianMixtureModel
Failed example:
abs(softPredicted[0] - 1.0) < 0.001
Expected:
True
Got:
False
**********************************************************************
File "/Users/dongjoon/APACHE/spark-master/python/pyspark/mllib/clustering.py", line 388, in __main__.GaussianMixtureModel
Failed example:
abs(softPredicted[1] - 0.0) < 0.001
Expected:
True
Got:
False
```
to pass in JDK 11.
The root cause seems to be different float values being understood via Py4J. This issue also was found in https://github.com/apache/spark/pull/25132 before.
When floats are transferred from Python to JVM, the values are sent as are. Python floats are not "precise" due to its own limitation - https://docs.python.org/3/tutorial/floatingpoint.html.
For some reasons, the floats from Python on JDK 8 and JDK 11 are different, which is already explicitly not guaranteed.
This seems why only some tests in PySpark with floats are being failed.
So, this PR fixes it by increasing tolerance in identified test cases in PySpark.
### Why are the changes needed?
<!--
Please clarify why the changes are needed. For instance,
1. If you propose a new API, clarify the use case for a new API.
2. If you fix a bug, you can clarify why it is a bug.
-->
To fully support JDK 11. See, for instance, https://github.com/apache/spark/pull/25443 and https://github.com/apache/spark/pull/25423 for ongoing efforts.
### Does this PR introduce any user-facing change?
<!--
If yes, please clarify the previous behavior and the change this PR proposes - provide the console output, description and/or an example to show the behavior difference if possible.
If no, write 'No'.
-->
No.
### How was this patch tested?
<!--
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If it was tested in a way different from regular unit tests, please clarify how you tested step by step, ideally copy and paste-able, so that other reviewers can test and check, and descendants can verify in the future.
If tests were not added, please describe why they were not added and/or why it was difficult to add.
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Manually tested as described in JIRAs:
```
$ build/sbt -Phadoop-3.2 test:package
$ python/run-tests --testnames 'pyspark.ml.tests.test_algorithms' --python-executables python
```
```
$ build/sbt -Phadoop-3.2 test:package
$ python/run-tests --testnames 'pyspark.mllib.clustering' --python-executables python
```
Closes#25475 from HyukjinKwon/SPARK-28735.
Authored-by: HyukjinKwon <gurwls223@apache.org>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
## What changes were proposed in this pull request?
Update HashingTF to use new implementation of MurmurHash3
Make HashingTF use the old MurmurHash3 when a model from pre 3.0 is loaded
## How was this patch tested?
Change existing unit tests. Also add one unit test to make sure HashingTF use the old MurmurHash3 when a model from pre 3.0 is loaded
Closes#25303 from huaxingao/spark-23469.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
## What changes were proposed in this pull request?
I remove the deprecate `ImageSchema.readImages`.
Move some useful methods from class `ImageSchema` into class `ImageFileFormat`.
In pyspark, I rename `ImageSchema` class to be `ImageUtils`, and keep some useful python methods in it.
## How was this patch tested?
UT.
Please review https://spark.apache.org/contributing.html before opening a pull request.
Closes#25245 from WeichenXu123/remove_image_schema.
Authored-by: WeichenXu <weichen.xu@databricks.com>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
## What changes were proposed in this pull request?
Currently, pretty skipped message added by f7435bec6a mechanism seems not working when xmlrunner is installed apparently.
This PR fixes two things:
1. When `xmlrunner` is installed, seems `xmlrunner` does not respect `vervosity` level in unittests (default is level 1).
So the output looks as below
```
Running tests...
----------------------------------------------------------------------
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
----------------------------------------------------------------------
```
So it is not caught by our message detection mechanism.
2. If we manually set the `vervocity` level to `xmlrunner`, it prints messages as below:
```
test_mixed_udf (pyspark.sql.tests.test_pandas_udf_scalar.ScalarPandasUDFTests) ... SKIP (0.000s)
test_mixed_udf_and_sql (pyspark.sql.tests.test_pandas_udf_scalar.ScalarPandasUDFTests) ... SKIP (0.000s)
...
```
This is different in our Jenkins machine:
```
test_createDataFrame_column_name_encoding (pyspark.sql.tests.test_arrow.ArrowTests) ... skipped 'Pandas >= 0.23.2 must be installed; however, it was not found.'
test_createDataFrame_does_not_modify_input (pyspark.sql.tests.test_arrow.ArrowTests) ... skipped 'Pandas >= 0.23.2 must be installed; however, it was not found.'
...
```
Note that last `SKIP` is different. This PR fixes the regular expression to catch `SKIP` case as well.
## How was this patch tested?
Manually tested.
**Before:**
```
Starting test(python2.7): pyspark....
Finished test(python2.7): pyspark.... (0s)
...
Tests passed in 562 seconds
========================================================================
...
```
**After:**
```
Starting test(python2.7): pyspark....
Finished test(python2.7): pyspark.... (48s) ... 93 tests were skipped
...
Tests passed in 560 seconds
Skipped tests pyspark.... with python2.7:
pyspark...(...) ... SKIP (0.000s)
...
========================================================================
...
```
Closes#24927 from HyukjinKwon/SPARK-28130.
Authored-by: HyukjinKwon <gurwls223@apache.org>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
Before, you could have this code
```
A = SparseMatrix(2, 2, [0, 2, 3], [0], [2])
B = DenseMatrix(2, 2, [2, 0, 0, 0])
B == A # False
A == B # True
```
The second would be `True` as `SparseMatrix` already checks for semantic
equality. This commit changes `DenseMatrix` so that equality is
semantical as well.
## What changes were proposed in this pull request?
Better semantic equality for DenseMatrix
## How was this patch tested?
Unit tests were added, plus manual testing. Note that the code falls back to the old behavior when `other` is not a SparseMatrix.
Closes#17968 from gglanzani/SPARK-9792.
Authored-by: Giovanni Lanzani <giovanni@lanzani.nl>
Signed-off-by: Holden Karau <holden@pigscanfly.ca>
## What changes were proposed in this pull request?
The hashSeed method allocates 64 bytes instead of 8. Other bytes are always zeros (thanks to default behavior of ByteBuffer). And they could be excluded from hash calculation because they don't differentiate inputs.
## How was this patch tested?
By running the existing tests - XORShiftRandomSuite
Closes#20793 from MaxGekk/hash-buff-size.
Lead-authored-by: Maxim Gekk <maxim.gekk@databricks.com>
Co-authored-by: Maxim Gekk <max.gekk@gmail.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
## What changes were proposed in this pull request?
Add RawPrediction to OneVsRest in PySpark to make it consistent with scala implementation
## How was this patch tested?
Add doctest
Closes#23910 from huaxingao/spark-27007.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
## What changes were proposed in this pull request?
Add multiple column support to PySpark StringIndexer
## How was this patch tested?
Add doctest
Closes#23741 from huaxingao/spark-22798.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
## What changes were proposed in this pull request?
Add PMML export support for ML KMeans to PySpark.
## How was this patch tested?
Add tests in ml.tests.PersistenceTest.
Closes#23592 from huaxingao/spark-16838.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
## What changes were proposed in this pull request?
This change exposes the `df` (document frequency) as a public val along with the number of documents (`m`) as part of the IDF model.
* The document frequency is returned as an `Array[Long]`
* If the minimum document frequency is set, this is considered in the df calculation. If the count is less than minDocFreq, the df is 0 for such terms
* numDocs is not very required. But it can be useful, if we plan to provide a provision in future for user to give their own idf function, instead of using a default (log((1+m)/(1+df))). In such cases, the user can provide a function taking input of `m` and `df` and returning the idf value
* Pyspark changes
## How was this patch tested?
The existing test case was edited to also check for the document frequency values.
I am not very good with python or pyspark. I have committed and run tests based on my understanding. Kindly let me know if I have missed anything
Reviewer request: mengxr zjffdu yinxusen
Closes#23549 from purijatin/master.
Authored-by: Jatin Puri <purijatin@gmail.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
## What changes were proposed in this pull request?
This PR is a small follow up that puts some logic and functions into smaller scope and make it localized, and deduplicate.
## How was this patch tested?
Manually tested. Jenkins tests as well.
Closes#23200 from HyukjinKwon/followup-SPARK-26034-SPARK-26033.
Authored-by: Hyukjin Kwon <gurwls223@apache.org>
Signed-off-by: Bryan Cutler <cutlerb@gmail.com>
## What changes were proposed in this pull request?
Currently, some of PySpark tests sill assume the tests could be ran in Python 2.6 by importing `unittest2`. For instance:
```python
if sys.version_info[:2] <= (2, 6):
try:
import unittest2 as unittest
except ImportError:
sys.stderr.write('Please install unittest2 to test with Python 2.6 or earlier')
sys.exit(1)
else:
import unittest
```
While I am here, I removed some of unused imports and reordered imports per PEP 8.
We officially dropped Python 2.6 support a while ago and started to discuss about Python 2 drop. It's better to remove them out.
## How was this patch tested?
Manually tests, and existing tests via Jenkins.
Closes#23077 from HyukjinKwon/SPARK-26105.
Lead-authored-by: hyukjinkwon <gurwls223@apache.org>
Co-authored-by: Bryan Cutler <cutlerb@gmail.com>
Signed-off-by: hyukjinkwon <gurwls223@apache.org>
## What changes were proposed in this pull request?
This PR breaks down the large ml/tests.py file that contains all Python ML unit tests into several smaller test files to be easier to read and maintain.
The tests are broken down as follows:
```
pyspark
├── __init__.py
...
├── ml
│ ├── __init__.py
...
│ ├── tests
│ │ ├── __init__.py
│ │ ├── test_algorithms.py
│ │ ├── test_base.py
│ │ ├── test_evaluation.py
│ │ ├── test_feature.py
│ │ ├── test_image.py
│ │ ├── test_linalg.py
│ │ ├── test_param.py
│ │ ├── test_persistence.py
│ │ ├── test_pipeline.py
│ │ ├── test_stat.py
│ │ ├── test_training_summary.py
│ │ ├── test_tuning.py
│ │ └── test_wrapper.py
...
├── testing
...
│ ├── mlutils.py
...
```
## How was this patch tested?
Ran tests manually by module to ensure test count was the same, and ran `python/run-tests --modules=pyspark-ml` to verify all passing with Python 2.7 and Python 3.6.
Closes#23063 from BryanCutler/python-test-breakup-ml-SPARK-26033.
Authored-by: Bryan Cutler <cutlerb@gmail.com>
Signed-off-by: hyukjinkwon <gurwls223@apache.org>
