## What changes were proposed in this pull request?
Flush batch timely for pandas UDF.
This could improve performance when multiple pandas UDF plans are pipelined.
When batch being flushed in time, downstream pandas UDFs will get pipelined as soon as possible, and pipeline will help hide the donwstream UDFs computation time. For example:
When the first UDF start computing on batch-3, the second pipelined UDF can start computing on batch-2, and the third pipelined UDF can start computing on batch-1.
If we do not flush each batch in time, the donwstream UDF's pipeline will lag behind too much, which may increase the total processing time.
I add flush at two places:
* JVM process feed data into python worker. In jvm side, when write one batch, flush it
* VM process read data from python worker output, In python worker side, when write one batch, flush it
If no flush, the default buffer size for them are both 65536. Especially in the ML case, in order to make realtime prediction, we will make batch size very small. The buffer size is too large for the case, which cause downstream pandas UDF pipeline lag behind too much.
### Note
* This is only applied to pandas scalar UDF.
* Do not flush for each batch. The minimum interval between two flush is 0.1 second. This avoid too frequent flushing when batch size is small. It works like:
```
last_flush_time = time.time()
for batch in iterator:
writer.write_batch(batch)
flush_time = time.time()
if self.flush_timely and (flush_time - last_flush_time > 0.1):
stream.flush()
last_flush_time = flush_time
```
## How was this patch tested?
### Benchmark to make sure the flush do not cause performance regression
#### Test code:
```
numRows = ...
batchSize = ...
spark.conf.set('spark.sql.execution.arrow.maxRecordsPerBatch', str(batchSize))
df = spark.range(1, numRows + 1, numPartitions=1).select(col('id').alias('a'))
pandas_udf("int", PandasUDFType.SCALAR)
def fp1(x):
return x + 10
beg_time = time.time()
result = df.select(sum(fp1('a'))).head()
print("result: " + str(result[0]))
print("consume time: " + str(time.time() - beg_time))
```
#### Test Result:
params | Consume time (Before) | Consume time (After)
------------ | ----------------------- | ----------------------
numRows=100000000, batchSize=10000 | 23.43s | 24.64s
numRows=100000000, batchSize=1000 | 36.73s | 34.50s
numRows=10000000, batchSize=100 | 35.67s | 32.64s
numRows=1000000, batchSize=10 | 33.60s | 32.11s
numRows=100000, batchSize=1 | 33.36s | 31.82s
### Benchmark pipelined pandas UDF
#### Test code:
```
spark.conf.set('spark.sql.execution.arrow.maxRecordsPerBatch', '1')
df = spark.range(1, 31, numPartitions=1).select(col('id').alias('a'))
pandas_udf("int", PandasUDFType.SCALAR)
def fp1(x):
print("run fp1")
time.sleep(1)
return x + 100
pandas_udf("int", PandasUDFType.SCALAR)
def fp2(x, y):
print("run fp2")
time.sleep(1)
return x + y
beg_time = time.time()
result = df.select(sum(fp2(fp1('a'), col('a')))).head()
print("result: " + str(result[0]))
print("consume time: " + str(time.time() - beg_time))
```
#### Test Result:
**Before**: consume time: 63.57s
**After**: consume time: 32.43s
**So the PR improve performance by make downstream UDF get pipelined early.**
Please review https://spark.apache.org/contributing.html before opening a pull request.
Closes#24734 from WeichenXu123/improve_pandas_udf_pipeline.
Lead-authored-by: WeichenXu <weichen.xu@databricks.com>
Co-authored-by: Xiangrui Meng <meng@databricks.com>
Signed-off-by: gatorsmile <gatorsmile@gmail.com>
## What changes were proposed in this pull request?
Running PySpark tests with Pandas 0.24.x causes a failure in `test_pandas_udf_grouped_map` test_supported_types:
`ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()`
This is because a column is an ArrayType and the method `sqlutils ReusedSQLTestCase.assertPandasEqual ` does not properly check this.
This PR removes `assertPandasEqual` and replaces it with the built-in `pandas.util.testing.assert_frame_equal` which can properly handle columns of ArrayType and also prints out better diff between the DataFrames when an error occurs.
Additionally, imports of pandas and pyarrow were moved to the top of related test files to avoid duplicating the same import many times.
## How was this patch tested?
Existing tests
Closes#24306 from BryanCutler/python-pandas-assert_frame_equal-SPARK-27387.
Authored-by: Bryan Cutler <cutlerb@gmail.com>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
## What changes were proposed in this pull request?
After [SPARK-26856](https://github.com/apache/spark/pull/23797), `Kinesis` Python UT fails with `Found multiple JARs` exception due to a wrong pattern.
- https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/104171/console
```
Exception: Found multiple JARs:
.../spark-streaming-kinesis-asl-assembly-3.0.0-SNAPSHOT.jar,
.../spark-streaming-kinesis-asl-assembly_2.12-3.0.0-SNAPSHOT.jar;
please remove all but one
```
It's because the pattern was changed in a wrong way.
**Original**
```python
kinesis_asl_assembly_dir, "target/scala-*/%s-*.jar" % name_prefix))
kinesis_asl_assembly_dir, "target/%s_*.jar" % name_prefix))
```
**After SPARK-26856**
```python
project_full_path, "target/scala-*/%s*.jar" % jar_name_prefix))
project_full_path, "target/%s*.jar" % jar_name_prefix))
```
The actual kinesis assembly jar files look like the followings.
**SBT Build**
```
-rw-r--r-- 1 dongjoon staff 87459461 Apr 1 19:01 spark-streaming-kinesis-asl-assembly-3.0.0-SNAPSHOT.jar
-rw-r--r-- 1 dongjoon staff 309 Apr 1 18:58 spark-streaming-kinesis-asl-assembly_2.12-3.0.0-SNAPSHOT-tests.jar
-rw-r--r-- 1 dongjoon staff 309 Apr 1 18:58 spark-streaming-kinesis-asl-assembly_2.12-3.0.0-SNAPSHOT.jar
```
**MAVEN Build**
```
-rw-r--r-- 1 dongjoon staff 8.6K Apr 1 18:55 spark-streaming-kinesis-asl-assembly_2.12-3.0.0-SNAPSHOT-sources.jar
-rw-r--r-- 1 dongjoon staff 8.6K Apr 1 18:55 spark-streaming-kinesis-asl-assembly_2.12-3.0.0-SNAPSHOT-test-sources.jar
-rw-r--r-- 1 dongjoon staff 8.7K Apr 1 18:55 spark-streaming-kinesis-asl-assembly_2.12-3.0.0-SNAPSHOT-tests.jar
-rw-r--r-- 1 dongjoon staff 21M Apr 1 18:55 spark-streaming-kinesis-asl-assembly_2.12-3.0.0-SNAPSHOT.jar
```
In addition, after SPARK-26856, the utility function `search_jar` is shared to find `avro` jar files which are identical for both `sbt` and `mvn`. To sum up, The current jar pattern parameter cannot handle both `kinesis` and `avro` jars. This PR splits the single pattern into two patterns.
## How was this patch tested?
Manual. Please note that this will remove only `Found multiple JARs` exception. Kinesis tests need more configurations to run locally.
```
$ build/sbt -Pkinesis-asl test:package streaming-kinesis-asl-assembly/assembly
$ export ENABLE_KINESIS_TESTS=1
$ python/run-tests.py --python-executables python2.7 --module pyspark-streaming
```
Closes#24268 from dongjoon-hyun/SPARK-26856.
Authored-by: Dongjoon Hyun <dhyun@apple.com>
Signed-off-by: Hyukjin Kwon <gurwls223@apache.org>
## What changes were proposed in this pull request?
Avro is built-in but external data source module since Spark 2.4 but `from_avro` and `to_avro` APIs not yet supported in pyspark.
In this PR I've made them available from pyspark.
## How was this patch tested?
Please see the python API examples what I've added.
cd docs/
SKIP_SCALADOC=1 SKIP_RDOC=1 SKIP_SQLDOC=1 jekyll build
Manual webpage check.
Closes#23797 from gaborgsomogyi/SPARK-26856.
Authored-by: Gabor Somogyi <gabor.g.somogyi@gmail.com>
Signed-off-by: Hyukjin Kwon <gurwls223@apache.org>
## 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>
## What changes were proposed in this pull request?
This PR breaks down the large mllib/tests.py file that contains all Python MLlib unit tests into several smaller test files to be easier to read and maintain.
The tests are broken down as follows:
```
pyspark
├── __init__.py
...
├── mllib
│ ├── __init__.py
...
│ ├── tests
│ │ ├── __init__.py
│ │ ├── test_algorithms.py
│ │ ├── test_feature.py
│ │ ├── test_linalg.py
│ │ ├── test_stat.py
│ │ ├── test_streaming_algorithms.py
│ │ └── test_util.py
...
├── testing
...
│ ├── mllibutils.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-mllib` to verify all passing with Python 2.7 and Python 3.6. Also installed scipy to include optional tests in test_linalg.
Closes#23056 from BryanCutler/python-test-breakup-mllib-SPARK-26034.
Authored-by: Bryan Cutler <cutlerb@gmail.com>
Signed-off-by: hyukjinkwon <gurwls223@apache.org>
## What changes were proposed in this pull request?
This PR continues to break down a big large file into smaller files. See https://github.com/apache/spark/pull/23021. It targets to follow https://github.com/numpy/numpy/tree/master/numpy.
Basically this PR proposes to break down `pyspark/streaming/tests.py` into ...:
```
pyspark
├── __init__.py
...
├── streaming
│ ├── __init__.py
...
│ ├── tests
│ │ ├── __init__.py
│ │ ├── test_context.py
│ │ ├── test_dstream.py
│ │ ├── test_kinesis.py
│ │ └── test_listener.py
...
├── testing
...
│ ├── streamingutils.py
...
```
## How was this patch tested?
Existing tests should cover.
`cd python` and .`/run-tests-with-coverage`. Manually checked they are actually being ran.
Each test (not officially) can be ran via:
```bash
SPARK_TESTING=1 ./bin/pyspark pyspark.tests.test_context
```
Note that if you're using Mac and Python 3, you might have to `OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES`.
Closes#23034 from HyukjinKwon/SPARK-26035.
Authored-by: hyukjinkwon <gurwls223@apache.org>
Signed-off-by: hyukjinkwon <gurwls223@apache.org>
## What changes were proposed in this pull request?
This PR continues to break down a big large file into smaller files. See https://github.com/apache/spark/pull/23021. It targets to follow https://github.com/numpy/numpy/tree/master/numpy.
Basically this PR proposes to break down `pyspark/tests.py` into ...:
```
pyspark
...
├── testing
...
│ └── utils.py
├── tests
│ ├── __init__.py
│ ├── test_appsubmit.py
│ ├── test_broadcast.py
│ ├── test_conf.py
│ ├── test_context.py
│ ├── test_daemon.py
│ ├── test_join.py
│ ├── test_profiler.py
│ ├── test_rdd.py
│ ├── test_readwrite.py
│ ├── test_serializers.py
│ ├── test_shuffle.py
│ ├── test_taskcontext.py
│ ├── test_util.py
│ └── test_worker.py
...
```
## How was this patch tested?
Existing tests should cover.
`cd python` and .`/run-tests-with-coverage`. Manually checked they are actually being ran.
Each test (not officially) can be ran via:
```bash
SPARK_TESTING=1 ./bin/pyspark pyspark.tests.test_context
```
Note that if you're using Mac and Python 3, you might have to `OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES`.
Closes#23033 from HyukjinKwon/SPARK-26036.
Authored-by: hyukjinkwon <gurwls223@apache.org>
Signed-off-by: hyukjinkwon <gurwls223@apache.org>
## What changes were proposed in this pull request?
This is the official first attempt to break huge single `tests.py` file - I did it locally before few times and gave up for some reasons. Now, currently it really makes the unittests super hard to read and difficult to check. To me, it even bothers me to to scroll down the big file. It's one single 7000 lines file!
This is not only readability issue. Since one big test takes most of tests time, the tests don't run in parallel fully - although it will costs to start and stop the context.
We could pick up one example and follow. Given my investigation, the current style looks closer to NumPy structure and looks easier to follow. Please see https://github.com/numpy/numpy/tree/master/numpy.
Basically this PR proposes to break down `pyspark/sql/tests.py` into ...:
```bash
pyspark
...
├── sql
...
│ ├── tests # Includes all tests broken down from 'pyspark/sql/tests.py'
│ │ │ # Each matchs to module in 'pyspark/sql'. Additionally, some logical group can
│ │ │ # be added. For instance, 'test_arrow.py', 'test_datasources.py' ...
│ │ ├── __init__.py
│ │ ├── test_appsubmit.py
│ │ ├── test_arrow.py
│ │ ├── test_catalog.py
│ │ ├── test_column.py
│ │ ├── test_conf.py
│ │ ├── test_context.py
│ │ ├── test_dataframe.py
│ │ ├── test_datasources.py
│ │ ├── test_functions.py
│ │ ├── test_group.py
│ │ ├── test_pandas_udf.py
│ │ ├── test_pandas_udf_grouped_agg.py
│ │ ├── test_pandas_udf_grouped_map.py
│ │ ├── test_pandas_udf_scalar.py
│ │ ├── test_pandas_udf_window.py
│ │ ├── test_readwriter.py
│ │ ├── test_serde.py
│ │ ├── test_session.py
│ │ ├── test_streaming.py
│ │ ├── test_types.py
│ │ ├── test_udf.py
│ │ └── test_utils.py
...
├── testing # Includes testing utils that can be used in unittests.
│ ├── __init__.py
│ └── sqlutils.py
...
```
## How was this patch tested?
Existing tests should cover.
`cd python` and `./run-tests-with-coverage`. Manually checked they are actually being ran.
Each test (not officially) can be ran via:
```
SPARK_TESTING=1 ./bin/pyspark pyspark.sql.tests.test_pandas_udf_scalar
```
Note that if you're using Mac and Python 3, you might have to `OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES`.
Closes#23021 from HyukjinKwon/SPARK-25344.
Authored-by: hyukjinkwon <gurwls223@apache.org>
Signed-off-by: hyukjinkwon <gurwls223@apache.org>
