Spark MLContext Programming Guide
- Overview
- Spark Shell Example
- Start Spark Shell with SystemML
- Create MLContext
- Hello World
- LeNet on MNIST Example
- DataFrame Example
- RDD Example
- Matrix Output
- Univariate Statistics on Haberman Data
- Script Information
- Clearing Scripts and MLContext
- Statistics
- GPU
- Explain
- Script Creation and ScriptFactory
- ScriptExecutor
- MatrixMetadata
- Matrix Data Conversions and Performance
- Project Information
- Jupyter (PySpark) Notebook Example - Poisson Nonnegative Matrix Factorization
- Recommended Spark Configuration Settings
Overview
The Spark MLContext API offers a programmatic interface for interacting with SystemML from Spark using languages
such as Scala, Java, and Python. As a result, it offers a convenient way to interact with SystemML from the Spark
Shell and from Notebooks such as Jupyter and Zeppelin.
Spark Shell Example
Start Spark Shell with SystemML
To use SystemML with Spark Shell, the SystemML jar can be referenced using Spark Shell’s --jars option.
spark-shell --executor-memory 4G --driver-memory 4G --jars SystemML.jarpyspark --executor-memory 4G --driver-memory 4G --jars SystemML.jar --driver-class-path SystemML.jarCreate MLContext
All primary classes that a user interacts with are located in the org.apache.sysml.api.mlcontext package.
For convenience, we can additionally add a static import of ScriptFactory to shorten the syntax for creating Script objects.
An MLContext object can be created by passing its constructor a reference to the SparkSession (spark) or SparkContext (sc).
If successful, you should see a “Welcome to Apache SystemML!” message.
import org.apache.sysml.api.mlcontext._
import org.apache.sysml.api.mlcontext.ScriptFactory._
val ml = new MLContext(spark)scala> import org.apache.sysml.api.mlcontext._
import org.apache.sysml.api.mlcontext._
scala> import org.apache.sysml.api.mlcontext.ScriptFactory._
import org.apache.sysml.api.mlcontext.ScriptFactory._
scala> val ml = new MLContext(spark)
Welcome to Apache SystemML!
ml: org.apache.sysml.api.mlcontext.MLContext = org.apache.sysml.api.mlcontext.MLContext@12139db0from systemml import MLContext, dml, dmlFromResource, dmlFromFile, dmlFromUrl
ml = MLContext(spark)>>> from systemml import MLContext, dml, dmlFromResource, dmlFromFile, dmlFromUrl
>>> ml = MLContext(spark)
Welcome to Apache SystemML!
Version 1.0.0-SNAPSHOTHello World
The ScriptFactory class allows DML and PYDML scripts to be created from Strings, Files, URLs, and InputStreams.
Here, we’ll use the dml method to create a DML “hello world” script based on a String. Notice that the script
reports that it has no inputs or outputs.
We execute the script using MLContext’s execute method, which displays “hello world” to the console.
The execute method returns an MLResults object, which contains no results since the script has
no outputs.
val helloScript = dml("print('hello world')")
ml.execute(helloScript)scala> val helloScript = dml("print('hello world')")
helloScript: org.apache.sysml.api.mlcontext.Script =
Inputs:
None
Outputs:
None
scala> ml.execute(helloScript)
hello world
res0: org.apache.sysml.api.mlcontext.MLResults =
NonehelloScript = dml("print('hello world')")
ml.execute(helloScript)>>> helloScript = dml("print('hello world')")
>>> ml.execute(helloScript)
hello world
SystemML Statistics:
Total execution time: 0.001 sec.
Number of executed Spark inst: 0.
MLResultsLeNet on MNIST Example
SystemML features the DML-based nn library for deep learning.
At project build time, SystemML automatically generates wrapper classes for DML scripts
to enable convenient access to scripts and execution of functions.
In the example below, we obtain a reference (clf) to the LeNet on MNIST example.
We generate dummy data, train a convolutional net using the LeNet architecture,
compute the class probability predictions, and then evaluate the convolutional net.
Note that these automatic script wrappers are currently not available in Python but will be made available in the near future.
val clf = ml.nn.examples.Mnist_lenet
val dummy = clf.generate_dummy_data
val dummyVal = clf.generate_dummy_data
val params = clf.train(dummy.X, dummy.Y, dummyVal.X, dummyVal.Y, dummy.C, dummy.Hin, dummy.Win, 1)
val probs = clf.predict(dummy.X, dummy.C, dummy.Hin, dummy.Win, params.W1, params.b1, params.W2, params.b2, params.W3, params.b3, params.W4, params.b4)
val perf = clf.eval(probs, dummy.Y)scala> val clf = ml.nn.examples.Mnist_lenet
clf: org.apache.sysml.scripts.nn.examples.Mnist_lenet =
Inputs:
None
Outputs:
None
scala> val dummy = clf.generate_dummy_data
SystemML Statistics:
Total execution time: 0.144 sec.
Number of executed Spark inst: 0.
dummy: org.apache.sysml.scripts.nn.examples.mnist_lenet.Generate_dummy_data_output =
X (Matrix): MatrixObject: scratch_space//_p64701_192.168.1.103//_t0/temp0_0, [1024 x 784, nnz=802816, blocks (1000 x 1000)], binaryblock, dirty
Y (Matrix): MatrixObject: scratch_space//_p64701_192.168.1.103//_t0/temp4_4, [1024 x 10, nnz=1024, blocks (1000 x 1000)], binaryblock, dirty
C (long): 1
Hin (long): 28
Win (long): 28
scala> val dummyVal = clf.generate_dummy_data
SystemML Statistics:
Total execution time: 0.147 sec.
Number of executed Spark inst: 0.
dummyVal: org.apache.sysml.scripts.nn.examples.mnist_lenet.Generate_dummy_data_output =
X (Matrix): MatrixObject: scratch_space//_p64701_192.168.1.103//_t0/temp5_5, [1024 x 784, nnz=802816, blocks (1000 x 1000)], binaryblock, dirty
Y (Matrix): MatrixObject: scratch_space//_p64701_192.168.1.103//_t0/temp9_9, [1024 x 10, nnz=1024, blocks (1000 x 1000)], binaryblock, dirty
C (long): 1
Hin (long): 28
Win (long): 28
scala> val params = clf.train(dummy.X, dummy.Y, dummyVal.X, dummyVal.Y, dummy.C, dummy.Hin, dummy.Win, 1)
17/06/05 15:52:09 WARN SparkExecutionContext: Configuration parameter spark.driver.maxResultSize set to 1 GB. You can set it through Spark default configuration setting either to 0 (unlimited) or to available memory budget of size 2 GB.
Starting optimization
17/06/05 15:52:10 WARN TaskSetManager: Stage 0 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:11 WARN TaskSetManager: Stage 1 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:11 WARN TaskSetManager: Stage 2 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:11 WARN TaskSetManager: Stage 3 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:13 WARN TaskSetManager: Stage 4 contains a task of very large size (296 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:13 WARN TaskSetManager: Stage 5 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:14 WARN TaskSetManager: Stage 6 contains a task of very large size (118 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:14 WARN TaskSetManager: Stage 7 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:14 WARN TaskSetManager: Stage 8 contains a task of very large size (115 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:14 WARN TaskSetManager: Stage 9 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:15 WARN TaskSetManager: Stage 11 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:15 WARN TaskSetManager: Stage 13 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:16 WARN TaskSetManager: Stage 15 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:16 WARN TaskSetManager: Stage 17 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:17 WARN TaskSetManager: Stage 19 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:17 WARN TaskSetManager: Stage 21 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:18 WARN TaskSetManager: Stage 23 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:18 WARN TaskSetManager: Stage 25 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:19 WARN TaskSetManager: Stage 27 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:19 WARN TaskSetManager: Stage 29 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
17/06/05 15:52:20 WARN TaskSetManager: Stage 31 contains a task of very large size (508 KB). The maximum recommended task size is 100 KB.
SystemML Statistics:
Total execution time: 11.261 sec.
Number of executed Spark inst: 32.
params: org.apache.sysml.scripts.nn.examples.mnist_lenet.Train_output =
W1 (Matrix): MatrixObject: scratch_space//_p64701_192.168.1.103//_t0/temp2203_1606, [32 x 25, nnz=800, blocks (1000 x 1000)], binaryblock, dirty
b1 (Matrix): MatrixObject: scratch_space//_p64701_192.168.1.103//_t0/temp2205_1608, [32 x 1, nnz=32, blocks (1000 x 1000)], binaryblock, dirty
W2 (Matrix): MatrixObject: scratch_space//_p64701_192.168.1.103//_t0/temp2196_1599, [64 x 800, nnz=51200, blocks (1000 x 1000)], binaryblock, dirty
b2 (Matrix): MatrixObject: scratch_space//_p64701_192.168.1.103//_t0/temp2200_1603, [64 x 1, nnz=64, blocks (1000 x 1000)], binaryblock, dirty
W3 (Matrix): MatrixObject: scratch_space//_p64701_192.168.1.103//_t0/temp2186_1589, [3136 x 512, nnz=1605632, blocks (1000 x 1000)], binaryblock, ...
scala> val probs = clf.predict(dummy.X, dummy.C, dummy.Hin, dummy.Win, params.W1, params.b1, params.W2, params.b2, params.W3, params.b3, params.W4, params.b4)
SystemML Statistics:
Total execution time: 2.148 sec.
Number of executed Spark inst: 48.
probs: org.apache.sysml.api.mlcontext.Matrix = MatrixObject: scratch_space//_p64701_192.168.1.103//_t0/temp2505_1865, [1024 x 10, nnz=10240, blocks (1000 x 1000)], binaryblock, dirty
scala> val perf = clf.eval(probs, dummy.Y)
SystemML Statistics:
Total execution time: 0.007 sec.
Number of executed Spark inst: 48.
perf: org.apache.sysml.scripts.nn.examples.mnist_lenet.Eval_output =
loss (double): 2.2681513307168797
accuracy (double): 0.1435546875DataFrame Example
For demonstration purposes, we’ll use Spark to create a DataFrame called df of random doubles from 0 to 1 consisting of 10,000 rows and 100 columns.
import org.apache.spark.sql._
import org.apache.spark.sql.types.{StructType,StructField,DoubleType}
import scala.util.Random
val numRows = 10000
val numCols = 100
val data = sc.parallelize(0 to numRows-1).map { _ => Row.fromSeq(Seq.fill(numCols)(Random.nextDouble)) }
val schema = StructType((0 to numCols-1).map { i => StructField("C" + i, DoubleType, true) } )
val df = spark.createDataFrame(data, schema)scala> import org.apache.spark.sql._
import org.apache.spark.sql._
scala> import org.apache.spark.sql.types.{StructType,StructField,DoubleType}
import org.apache.spark.sql.types.{StructType, StructField, DoubleType}
scala> import scala.util.Random
import scala.util.Random
scala> val numRows = 10000
numRows: Int = 10000
scala> val numCols = 100
numCols: Int = 100
scala> val data = sc.parallelize(0 to numRows-1).map { _ => Row.fromSeq(Seq.fill(numCols)(Random.nextDouble)) }
data: org.apache.spark.rdd.RDD[org.apache.spark.sql.Row] = MapPartitionsRDD[1] at map at <console>:42
scala> val schema = StructType((0 to numCols-1).map { i => StructField("C" + i, DoubleType, true) } )
schema: org.apache.spark.sql.types.StructType = StructType(StructField(C0,DoubleType,true), StructField(C1,DoubleType,true), StructField(C2,DoubleType,true), StructField(C3,DoubleType,true), StructField(C4,DoubleType,true), StructField(C5,DoubleType,true), StructField(C6,DoubleType,true), StructField(C7,DoubleType,true), StructField(C8,DoubleType,true), StructField(C9,DoubleType,true), StructField(C10,DoubleType,true), StructField(C11,DoubleType,true), StructField(C12,DoubleType,true), StructField(C13,DoubleType,true), StructField(C14,DoubleType,true), StructField(C15,DoubleType,true), StructField(C16,DoubleType,true), StructField(C17,DoubleType,true), StructField(C18,DoubleType,true), StructField(C19,DoubleType,true), StructField(C20,DoubleType,true), StructField(C21,DoubleType,true), ...
scala> val df = spark.createDataFrame(data, schema)
df: org.apache.spark.sql.DataFrame = [C0: double, C1: double, C2: double, C3: double, C4: double, C5: double, C6: double, C7: double, C8: double, C9: double, C10: double, C11: double, C12: double, C13: double, C14: double, C15: double, C16: double, C17: double, C18: double, C19: double, C20: double, C21: double, C22: double, C23: double, C24: double, C25: double, C26: double, C27: double, C28: double, C29: double, C30: double, C31: double, C32: double, C33: double, C34: double, C35: double, C36: double, C37: double, C38: double, C39: double, C40: double, C41: double, C42: double, C43: double, C44: double, C45: double, C46: double, C47: double, C48: double, C49: double, C50: double, C51: double, C52: double, C53: double, C54: double, C55: double, C56: double, C57: double, C58: double, C5...numRows = 10000
numCols = 100
from random import random
from pyspark.sql.types import *
data = sc.parallelize(range(numRows)).map(lambda x : [ random() for i in range(numCols) ])
schema = StructType([ StructField("C" + str(i), DoubleType(), True) for i in range(numCols) ])
df = spark.createDataFrame(data, schema)>>> numRows = 10000
>>> numCols = 100
>>> from random import random
>>> from pyspark.sql.types import *
>>> data = sc.parallelize(range(numRows)).map(lambda x : [ random() for i in range(numCols) ])
>>> schema = StructType([ StructField("C" + str(i), DoubleType(), True) for i in range(numCols) ])
>>> df = spark.createDataFrame(data, schema)We’ll create a DML script to find the minimum, maximum, and mean values in a matrix. This
script has one input variable, matrix Xin, and three output variables, minOut, maxOut, and meanOut.
For performance, we’ll specify metadata indicating that the matrix has 10,000 rows and 100 columns.
We’ll create a DML script using the ScriptFactory dml method with the minMaxMean script String. The
input variable is specified to be our DataFrame df with MatrixMetadata mm. The output
variables are specified to be minOut, maxOut, and meanOut. Notice that inputs are supplied by the
in method, and outputs are supplied by the out method.
We execute the script and obtain the results as a Tuple by calling getTuple on the results, specifying
the types and names of the output variables.
val minMaxMean =
"""
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
"""
val mm = new MatrixMetadata(numRows, numCols)
val minMaxMeanScript = dml(minMaxMean).in("Xin", df, mm).out("minOut", "maxOut", "meanOut")
val (min, max, mean) = ml.execute(minMaxMeanScript).getTuple[Double, Double, Double]("minOut", "maxOut", "meanOut")scala> val minMaxMean =
| """
| minOut = min(Xin)
| maxOut = max(Xin)
| meanOut = mean(Xin)
| """
minMaxMean: String =
"
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
"
scala> val mm = new MatrixMetadata(numRows, numCols)
mm: org.apache.sysml.api.mlcontext.MatrixMetadata = rows: 10000, columns: 100, non-zeros: None, rows per block: None, columns per block: None
scala> val minMaxMeanScript = dml(minMaxMean).in("Xin", df, mm).out("minOut", "maxOut", "meanOut")
minMaxMeanScript: org.apache.sysml.api.mlcontext.Script =
Inputs:
[1] (DataFrame) Xin: [C0: double, C1: double, C2: double, C3: double, C4: double, C5: double, C6: double, C7: double, ...
Outputs:
[1] minOut
[2] maxOut
[3] meanOut
scala> val (min, max, mean) = ml.execute(minMaxMeanScript).getTuple[Double, Double, Double]("minOut", "maxOut", "meanOut")
min: Double = 2.6257349849956313E-8
max: Double = 0.9999999686609718
mean: Double = 0.49996223966662934minMaxMean = """
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
"""
minMaxMeanScript = dml(minMaxMean).input("Xin", df).output("minOut", "maxOut", "meanOut")
min, max, mean = ml.execute(minMaxMeanScript).get("minOut", "maxOut", "meanOut")>>> minMaxMean = """
... minOut = min(Xin)
... maxOut = max(Xin)
... meanOut = mean(Xin)
... """
>>> minMaxMeanScript = dml(minMaxMean).input("Xin", df).output("minOut", "maxOut", "meanOut")
>>> min, max, mean = ml.execute(minMaxMeanScript).get("minOut", "maxOut", "meanOut")
SystemML Statistics:
Total execution time: 0.570 sec.
Number of executed Spark inst: 0.Many different types of input and output variables are automatically allowed. These types include
Boolean, Long, Double, String, Array[Array[Double]], RDD<String> and JavaRDD<String>
in CSV (dense) and IJV (sparse) formats, DataFrame, Matrix, and
Frame. RDDs and JavaRDDs are assumed to be CSV format unless MatrixMetadata is supplied indicating
IJV format.
RDD Example
Let’s take a look at an example of input matrices as RDDs in CSV format. We’ll create two 2x2 matrices and input these into a DML script. This script will sum each matrix and create a message based on which sum is greater. We will output the sums and the message.
For fun, we’ll write the script String to a file and then use ScriptFactory’s dmlFromFile method
(in Python, this method is under the systemml package)
to create the script object based on the file. We’ll also specify the inputs using a Map, although
we could have also chained together two in methods to specify the same inputs.
val rdd1 = sc.parallelize(Array("1.0,2.0", "3.0,4.0"))
val rdd2 = sc.parallelize(Array("5.0,6.0", "7.0,8.0"))
val sums = """
s1 = sum(m1);
s2 = sum(m2);
if (s1 > s2) {
message = "s1 is greater"
} else if (s2 > s1) {
message = "s2 is greater"
} else {
message = "s1 and s2 are equal"
}
"""
scala.tools.nsc.io.File("sums.dml").writeAll(sums)
val sumScript = dmlFromFile("sums.dml").in(Map("m1"-> rdd1, "m2"-> rdd2)).out("s1", "s2", "message")
val sumResults = ml.execute(sumScript)
val s1 = sumResults.getDouble("s1")
val s2 = sumResults.getDouble("s2")
val message = sumResults.getString("message")scala> val rdd1 = sc.parallelize(Array("1.0,2.0", "3.0,4.0"))
rdd1: org.apache.spark.rdd.RDD[String] = ParallelCollectionRDD[42] at parallelize at <console>:38
scala> val rdd2 = sc.parallelize(Array("5.0,6.0", "7.0,8.0"))
rdd2: org.apache.spark.rdd.RDD[String] = ParallelCollectionRDD[43] at parallelize at <console>:38
scala> val sums = """
| s1 = sum(m1);
| s2 = sum(m2);
| if (s1 > s2) {
| message = "s1 is greater"
| } else if (s2 > s1) {
| message = "s2 is greater"
| } else {
| message = "s1 and s2 are equal"
| }
| """
sums: String =
"
s1 = sum(m1);
s2 = sum(m2);
if (s1 > s2) {
message = "s1 is greater"
} else if (s2 > s1) {
message = "s2 is greater"
} else {
message = "s1 and s2 are equal"
}
"
scala> scala.tools.nsc.io.File("sums.dml").writeAll(sums)
scala> val sumScript = dmlFromFile("sums.dml").in(Map("m1"-> rdd1, "m2"-> rdd2)).out("s1", "s2", "message")
sumScript: org.apache.sysml.api.mlcontext.Script =
Inputs:
[1] (RDD) m1: ParallelCollectionRDD[42] at parallelize at <console>:38
[2] (RDD) m2: ParallelCollectionRDD[43] at parallelize at <console>:38
Outputs:
[1] s1
[2] s2
[3] message
scala> val sumResults = ml.execute(sumScript)
sumResults: org.apache.sysml.api.mlcontext.MLResults =
[1] (Double) s1: 10.0
[2] (Double) s2: 26.0
[3] (String) message: s2 is greater
scala> val s1 = sumResults.getDouble("s1")
s1: Double = 10.0
scala> val s2 = sumResults.getDouble("s2")
s2: Double = 26.0
scala> val message = sumResults.getString("message")
message: String = s2 is greaterrdd1 = sc.parallelize(["1.0,2.0", "3.0,4.0"])
rdd2 = sc.parallelize(["5.0,6.0", "7.0,8.0"])
sums = """
s1 = sum(m1);
s2 = sum(m2);
if (s1 > s2) {
message = "s1 is greater"
} else if (s2 > s1) {
message = "s2 is greater"
} else {
message = "s1 and s2 are equal"
}
"""
with open("sums.dml", "w") as text_file:
text_file.write(sums)
sumScript = dmlFromFile("sums.dml").input(m1=rdd1, m2= rdd2).output("s1", "s2", "message")
sumResults = ml.execute(sumScript)
s1 = sumResults.get("s1")
s2 = sumResults.get("s2")
message = sumResults.get("message")>>> rdd1 = sc.parallelize(["1.0,2.0", "3.0,4.0"])
>>> rdd2 = sc.parallelize(["5.0,6.0", "7.0,8.0"])
>>> sums = """
... s1 = sum(m1);
... s2 = sum(m2);
... if (s1 > s2) {
... message = "s1 is greater"
... } else if (s2 > s1) {
... message = "s2 is greater"
... } else {
... message = "s1 and s2 are equal"
... }
... """
>>> with open("sums.dml", "w") as text_file:
... text_file.write(sums)
...
>>> sumScript = dmlFromFile("sums.dml").input(m1=rdd1, m2= rdd2).output("s1", "s2", "message")
>>> sumResults = ml.execute(sumScript)
s1 = sumResults.get("s1")
s2 = sumResults.get("s2")
message = sumResults.get("message")
SystemML Statistics:
Total execution time: 0.933 sec.
Number of executed Spark inst: 4.
>>> s1 = sumResults.get("s1")
>>> s2 = sumResults.get("s2")
>>> message = sumResults.get("message")
>>> s1
10.0
>>> s2
26.0
>>> message
u's2 is greater'If you have metadata that you would like to supply along with the input matrices, this can be accomplished using a Scala Seq, List, or Array. This feature is currently not available in Python.
val rdd1Metadata = new MatrixMetadata(2, 2)
val rdd2Metadata = new MatrixMetadata(2, 2)
val sumScript = dmlFromFile("sums.dml").in(Seq(("m1", rdd1, rdd1Metadata), ("m2", rdd2, rdd2Metadata))).out("s1", "s2", "message")
val (firstSum, secondSum, sumMessage) = ml.execute(sumScript).getTuple[Double, Double, String]("s1", "s2", "message")scala> val rdd1Metadata = new MatrixMetadata(2, 2)
rdd1Metadata: org.apache.sysml.api.mlcontext.MatrixMetadata = rows: 2, columns: 2, non-zeros: None, rows per block: None, columns per block: None
scala> val rdd2Metadata = new MatrixMetadata(2, 2)
rdd2Metadata: org.apache.sysml.api.mlcontext.MatrixMetadata = rows: 2, columns: 2, non-zeros: None, rows per block: None, columns per block: None
scala> val sumScript = dmlFromFile("sums.dml").in(Seq(("m1", rdd1, rdd1Metadata), ("m2", rdd2, rdd2Metadata))).out("s1", "s2", "message")
sumScript: org.apache.sysml.api.mlcontext.Script =
Inputs:
[1] (RDD) m1: ParallelCollectionRDD[42] at parallelize at <console>:38
[2] (RDD) m2: ParallelCollectionRDD[43] at parallelize at <console>:38
Outputs:
[1] s1
[2] s2
[3] message
scala> val (firstSum, secondSum, sumMessage) = ml.execute(sumScript).getTuple[Double, Double, String]("s1", "s2", "message")
firstSum: Double = 10.0
secondSum: Double = 26.0
sumMessage: String = s2 is greaterThe same inputs with metadata can be supplied by chaining in methods, as in the example below, which shows that out methods can also be
chained.
val sumScript = dmlFromFile("sums.dml").in("m1", rdd1, rdd1Metadata).in("m2", rdd2, rdd2Metadata).out("s1").out("s2").out("message")
val (firstSum, secondSum, sumMessage) = ml.execute(sumScript).getTuple[Double, Double, String]("s1", "s2", "message")scala> val sumScript = dmlFromFile("sums.dml").in("m1", rdd1, rdd1Metadata).in("m2", rdd2, rdd2Metadata).out("s1").out("s2").out("message")
sumScript: org.apache.sysml.api.mlcontext.Script =
Inputs:
[1] (RDD) m1: ParallelCollectionRDD[42] at parallelize at <console>:38
[2] (RDD) m2: ParallelCollectionRDD[43] at parallelize at <console>:38
Outputs:
[1] s1
[2] s2
[3] message
scala> val (firstSum, secondSum, sumMessage) = ml.execute(sumScript).getTuple[Double, Double, String]("s1", "s2", "message")
firstSum: Double = 10.0
secondSum: Double = 26.0
sumMessage: String = s2 is greatersumScript = dmlFromFile("sums.dml").input(m1=rdd1).input(m2= rdd2).output("s1").output("s2").output("message")
sumResults = ml.execute(sumScript)
s1, s2, message = sumResults.get("s1", "s2", "message")>>> sumScript = dmlFromFile("sums.dml").input(m1=rdd1).input(m2= rdd2).output("s1").output("s2").output("message")
>>> sumResults = ml.execute(sumScript)
SystemML Statistics:
Total execution time: 1.057 sec.
Number of executed Spark inst: 4.
>>> s1, s2, message = sumResults.get("s1", "s2", "message")
>>> s1
10.0
>>> s2
26.0
>>> message
u's2 is greater'Matrix Output
Let’s look at an example of reading a matrix out of SystemML. We’ll create a DML script
in which we create a 2x2 matrix m. We’ll set the variable n to be the sum of the cells in the matrix.
We create a script object using String s, and we set m and n as the outputs. We execute the script, and in
the results we see we have Matrix m and Double n. The n output variable has a value of 110.0.
We get Matrix m and Double n as a Tuple of values x and y.
In Scala, we then convert Matrix m to an RDD of IJV values, an RDD of CSV values, a DataFrame, and a two-dimensional Double Array, and we display
the values in each of these data structures.
In Python, we use the methods toDF() and toNumPy() to get the matrix as PySpark DataFrame or NumPy array respectively.
val s =
"""
m = matrix("11 22 33 44", rows=2, cols=2)
n = sum(m)
"""
val scr = dml(s).out("m", "n");
val res = ml.execute(scr)
val (x, y) = res.getTuple[Matrix, Double]("m", "n")
x.toRDDStringIJV.collect.foreach(println)
x.toRDDStringCSV.collect.foreach(println)
x.toDF.collect.foreach(println)
x.to2DDoubleArrayscala> val s =
| """
| m = matrix("11 22 33 44", rows=2, cols=2)
| n = sum(m)
| """
s: String =
"
m = matrix("11 22 33 44", rows=2, cols=2)
n = sum(m)
"
scala> val scr = dml(s).out("m", "n");
scr: org.apache.sysml.api.mlcontext.Script =
Inputs:
None
Outputs:
[1] m
[2] n
scala> val res = ml.execute(scr)
res: org.apache.sysml.api.mlcontext.MLResults =
[1] (Matrix) m: Matrix: scratch_space//_p12059_9.31.117.12//_t0/temp26_14, [2 x 2, nnz=4, blocks (1000 x 1000)], binaryblock, dirty
[2] (Double) n: 110.0
scala> val (x, y) = res.getTuple[Matrix, Double]("m", "n")
x: org.apache.sysml.api.mlcontext.Matrix = Matrix: scratch_space//_p12059_9.31.117.12//_t0/temp26_14, [2 x 2, nnz=4, blocks (1000 x 1000)], binaryblock, dirty
y: Double = 110.0
scala> x.toRDDStringIJV.collect.foreach(println)
1 1 11.0
1 2 22.0
2 1 33.0
2 2 44.0
scala> x.toRDDStringCSV.collect.foreach(println)
11.0,22.0
33.0,44.0
scala> x.toDF.collect.foreach(println)
[0.0,11.0,22.0]
[1.0,33.0,44.0]
scala> x.to2DDoubleArray
res10: Array[Array[Double]] = Array(Array(11.0, 22.0), Array(33.0, 44.0))s = """
m = matrix("11 22 33 44", rows=2, cols=2)
n = sum(m)
"""
scr = dml(s).output("m", "n");
res = ml.execute(scr)
x, y = res.get("m", "n")
x.toDF().show()
x.toNumPy()>>> s = """
... m = matrix("11 22 33 44", rows=2, cols=2)
... n = sum(m)
... """
>>> scr = dml(s).output("m", "n");
>>> res = ml.execute(scr)
SystemML Statistics:
Total execution time: 0.000 sec.
Number of executed Spark inst: 0.
>>> x, y = res.get("m", "n")
>>> x
Matrix
>>> y
110.0
>>> x.toDF().show()
+-------+----+----+
|__INDEX| C1| C2|
+-------+----+----+
| 1.0|11.0|22.0|
| 2.0|33.0|44.0|
+-------+----+----+
>>> x.toNumPy()
array([[ 11., 22.],
[ 33., 44.]])Univariate Statistics on Haberman Data
Our next example will involve Haberman’s Survival Data Set in CSV format from the Center for Machine Learning and Intelligent Systems. We will run the SystemML Univariate Statistics (“Univar-Stats.dml”) script on this data.
We’ll pull the data from a URL and convert it to an RDD, habermanRDD. Next, we’ll create metadata, habermanMetadata,
stating that the matrix consists of 306 rows and 4 columns.
As we can see from the comments in the script
here, the
script requires a ‘TYPES’ input matrix that lists the types of the features (1 for scale, 2 for nominal, 3 for
ordinal), so we create a typesRDD matrix consisting of 1 row and 4 columns, with corresponding metadata, typesMetadata.
Next, we create the DML script object called uni using ScriptFactory’s dmlFromUrl method, specifying the GitHub URL where the
DML script is located. We bind the habermanRDD matrix to the A variable in Univar-Stats.dml, and we bind
the typesRDD matrix to the K variable. In addition, we supply a $CONSOLE_OUTPUT parameter with a Boolean value
of true, which indicates that we’d like to output labeled results to the console. We’ll explain why we bind to the A and K
variables in the Input Variables vs Input Parameters
section below.
val habermanUrl = "http://archive.ics.uci.edu/ml/machine-learning-databases/haberman/haberman.data"
val habermanList = scala.io.Source.fromURL(habermanUrl).mkString.split("\n")
val habermanRDD = sc.parallelize(habermanList)
val habermanMetadata = new MatrixMetadata(306, 4)
val typesRDD = sc.parallelize(Array("1.0,1.0,1.0,2.0"))
val typesMetadata = new MatrixMetadata(1, 4)
val scriptUrl = "https://raw.githubusercontent.com/apache/systemml/master/scripts/algorithms/Univar-Stats.dml"
val uni = dmlFromUrl(scriptUrl).in("A", habermanRDD, habermanMetadata).in("K", typesRDD, typesMetadata).in("$CONSOLE_OUTPUT", true)
ml.execute(uni)scala> val habermanUrl = "http://archive.ics.uci.edu/ml/machine-learning-databases/haberman/haberman.data"
habermanUrl: String = http://archive.ics.uci.edu/ml/machine-learning-databases/haberman/haberman.data
scala> val habermanList = scala.io.Source.fromURL(habermanUrl).mkString.split("\n")
habermanList: Array[String] = Array(30,64,1,1, 30,62,3,1, 30,65,0,1, 31,59,2,1, 31,65,4,1, 33,58,10,1, 33,60,0,1, 34,59,0,2, 34,66,9,2, 34,58,30,1, 34,60,1,1, 34,61,10,1, 34,67,7,1, 34,60,0,1, 35,64,13,1, 35,63,0,1, 36,60,1,1, 36,69,0,1, 37,60,0,1, 37,63,0,1, 37,58,0,1, 37,59,6,1, 37,60,15,1, 37,63,0,1, 38,69,21,2, 38,59,2,1, 38,60,0,1, 38,60,0,1, 38,62,3,1, 38,64,1,1, 38,66,0,1, 38,66,11,1, 38,60,1,1, 38,67,5,1, 39,66,0,2, 39,63,0,1, 39,67,0,1, 39,58,0,1, 39,59,2,1, 39,63,4,1, 40,58,2,1, 40,58,0,1, 40,65,0,1, 41,60,23,2, 41,64,0,2, 41,67,0,2, 41,58,0,1, 41,59,8,1, 41,59,0,1, 41,64,0,1, 41,69,8,1, 41,65,0,1, 41,65,0,1, 42,69,1,2, 42,59,0,2, 42,58,0,1, 42,60,1,1, 42,59,2,1, 42,61,4,1, 42,62,20,1, 42,65,0,1, 42,63,1,1, 43,58,52,2, 43,59,2,2, 43,64,0,2, 43,64,0,2, 43,63,14,1, 43,64,2,1, 43...
scala> val habermanRDD = sc.parallelize(habermanList)
habermanRDD: org.apache.spark.rdd.RDD[String] = ParallelCollectionRDD[159] at parallelize at <console>:43
scala> val habermanMetadata = new MatrixMetadata(306, 4)
habermanMetadata: org.apache.sysml.api.mlcontext.MatrixMetadata = rows: 306, columns: 4, non-zeros: None, rows per block: None, columns per block: None
scala> val typesRDD = sc.parallelize(Array("1.0,1.0,1.0,2.0"))
typesRDD: org.apache.spark.rdd.RDD[String] = ParallelCollectionRDD[160] at parallelize at <console>:39
scala> val typesMetadata = new MatrixMetadata(1, 4)
typesMetadata: org.apache.sysml.api.mlcontext.MatrixMetadata = rows: 1, columns: 4, non-zeros: None, rows per block: None, columns per block: None
scala> val scriptUrl = "https://raw.githubusercontent.com/apache/systemml/master/scripts/algorithms/Univar-Stats.dml"
scriptUrl: String = https://raw.githubusercontent.com/apache/systemml/master/scripts/algorithms/Univar-Stats.dml
scala> val uni = dmlFromUrl(scriptUrl).in("A", habermanRDD, habermanMetadata).in("K", typesRDD, typesMetadata).in("$CONSOLE_OUTPUT", true)
uni: org.apache.sysml.api.mlcontext.Script =
Inputs:
[1] (RDD) A: ParallelCollectionRDD[159] at parallelize at <console>:43
[2] (RDD) K: ParallelCollectionRDD[160] at parallelize at <console>:39
[3] (Boolean) $CONSOLE_OUTPUT: true
Outputs:
None
scala> ml.execute(uni)
...
-------------------------------------------------
Feature [1]: Scale
(01) Minimum | 30.0
(02) Maximum | 83.0
(03) Range | 53.0
(04) Mean | 52.45751633986928
(05) Variance | 116.71458266366658
(06) Std deviation | 10.803452349303281
(07) Std err of mean | 0.6175922641866753
(08) Coeff of variation | 0.20594669940735139
(09) Skewness | 0.1450718616532357
(10) Kurtosis | -0.6150152487211726
(11) Std err of skewness | 0.13934809593495995
(12) Std err of kurtosis | 0.277810485320835
(13) Median | 52.0
(14) Interquartile mean | 52.16013071895425
-------------------------------------------------
Feature [2]: Scale
(01) Minimum | 58.0
(02) Maximum | 69.0
(03) Range | 11.0
(04) Mean | 62.85294117647059
(05) Variance | 10.558630665380907
(06) Std deviation | 3.2494046632238507
(07) Std err of mean | 0.18575610076612029
(08) Coeff of variation | 0.051698529971741194
(09) Skewness | 0.07798443581479181
(10) Kurtosis | -1.1324380182967442
(11) Std err of skewness | 0.13934809593495995
(12) Std err of kurtosis | 0.277810485320835
(13) Median | 63.0
(14) Interquartile mean | 62.80392156862745
-------------------------------------------------
Feature [3]: Scale
(01) Minimum | 0.0
(02) Maximum | 52.0
(03) Range | 52.0
(04) Mean | 4.026143790849673
(05) Variance | 51.691117539912135
(06) Std deviation | 7.189653506248555
(07) Std err of mean | 0.41100513466216837
(08) Coeff of variation | 1.7857418611299172
(09) Skewness | 2.954633471088322
(10) Kurtosis | 11.425776549251449
(11) Std err of skewness | 0.13934809593495995
(12) Std err of kurtosis | 0.277810485320835
(13) Median | 1.0
(14) Interquartile mean | 1.2483660130718954
-------------------------------------------------
Feature [4]: Categorical (Nominal)
(15) Num of categories | 2
(16) Mode | 1
(17) Num of modes | 1
res23: org.apache.sysml.api.mlcontext.MLResults =
NonehabermanUrl = "http://archive.ics.uci.edu/ml/machine-learning-databases/haberman/haberman.data"
import urllib
urllib.urlretrieve(habermanUrl, "haberman.data")
habermanList = [line.rstrip("\n") for line in open("haberman.data")]
habermanRDD = sc.parallelize(habermanList)
typesRDD = sc.parallelize(["1.0,1.0,1.0,2.0"])
scriptUrl = "https://raw.githubusercontent.com/apache/systemml/master/scripts/algorithms/Univar-Stats.dml"
uni = dmlFromUrl(scriptUrl).input(A=habermanRDD, K=typesRDD).input("$CONSOLE_OUTPUT", True)
ml.execute(uni)>>> habermanUrl = "http://archive.ics.uci.edu/ml/machine-learning-databases/haberman/haberman.data"
>>> import urllib
>>> urllib.urlretrieve(habermanUrl, "haberman.data")
habermanList = [line.rstrip("\n") for line in open("haberman.data")]
habermanRDD = sc.parallelize(habermanList)
typesRDD = sc.parallelize(["1.0,1.0,1.0,2.0"])
scriptUrl = "https://raw.githubusercontent.com/apache/systemml/master/scripts/algorithms/Univar-Stats.dml"
uni = dmlFromUrl(scriptUrl).input(A=habermanRDD, K=typesRDD).input("$CONSOLE_OUTPUT", True)
ml.execute(uni)('haberman.data', <httplib.HTTPMessage instance at 0x7f601ef2e3b0>)
>>> habermanList = [line.rstrip("\n") for line in open("haberman.data")]
>>> habermanRDD = sc.parallelize(habermanList)
>>> typesRDD = sc.parallelize(["1.0,1.0,1.0,2.0"])
>>> scriptUrl = "https://raw.githubusercontent.com/apache/systemml/master/scripts/algorithms/Univar-Stats.dml"
>>> uni = dmlFromUrl(scriptUrl).input(A=habermanRDD, K=typesRDD).input("$CONSOLE_OUTPUT", True)
>>> ml.execute(uni)
17/07/22 13:42:57 WARN RewriteRemovePersistentReadWrite: Non-registered persistent write of variable 'baseStats' (line 186).
-------------------------------------------------
(01) Minimum | 30.0
(02) Maximum | 83.0
(03) Range | 53.0
(04) Mean | 52.45751633986928
(05) Variance | 116.71458266366658
(06) Std deviation | 10.803452349303281
(07) Std err of mean | 0.6175922641866753
(08) Coeff of variation | 0.20594669940735139
(09) Skewness | 0.1450718616532357
(10) Kurtosis | -0.6150152487211726
(11) Std err of skewness | 0.13934809593495995
(12) Std err of kurtosis | 0.277810485320835
(13) Median | 52.0
(14) Interquartile mean | 52.16013071895425
Feature [1]: Scale
-------------------------------------------------
(01) Minimum | 58.0
(02) Maximum | 69.0
(03) Range | 11.0
(04) Mean | 62.85294117647059
(05) Variance | 10.558630665380907
(06) Std deviation | 3.2494046632238507
(07) Std err of mean | 0.18575610076612029
(08) Coeff of variation | 0.051698529971741194
(09) Skewness | 0.07798443581479181
(10) Kurtosis | -1.1324380182967442
(11) Std err of skewness | 0.13934809593495995
(12) Std err of kurtosis | 0.277810485320835
(13) Median | 63.0
(14) Interquartile mean | 62.80392156862745
Feature [2]: Scale
-------------------------------------------------
(01) Minimum | 0.0
(02) Maximum | 52.0
(03) Range | 52.0
(04) Mean | 4.026143790849673
(05) Variance | 51.691117539912135
(06) Std deviation | 7.189653506248555
(07) Std err of mean | 0.41100513466216837
(08) Coeff of variation | 1.7857418611299172
(09) Skewness | 2.954633471088322
(10) Kurtosis | 11.425776549251449
(11) Std err of skewness | 0.13934809593495995
(12) Std err of kurtosis | 0.277810485320835
(13) Median | 1.0
(14) Interquartile mean | 1.2483660130718954
Feature [3]: Scale
-------------------------------------------------
Feature [4]: Categorical (Nominal)
(15) Num of categories | 2
(16) Mode | 1
(17) Num of modes | 1
SystemML Statistics:
Total execution time: 0.733 sec.
Number of executed Spark inst: 4.
MLResults
>>>Alternatively, we could supply a java.net.URL to the Script in method. Note that if the URL matrix data is in IJV
format, metadata needs to be supplied for the matrix. This feature is not available in Python.
val habermanUrl = "http://archive.ics.uci.edu/ml/machine-learning-databases/haberman/haberman.data"
val typesRDD = sc.parallelize(Array("1.0,1.0,1.0,2.0"))
val scriptUrl = "https://raw.githubusercontent.com/apache/systemml/master/scripts/algorithms/Univar-Stats.dml"
val uni = dmlFromUrl(scriptUrl).in("A", new java.net.URL(habermanUrl)).in("K", typesRDD).in("$CONSOLE_OUTPUT", true)
ml.execute(uni)scala> val habermanUrl = "http://archive.ics.uci.edu/ml/machine-learning-databases/haberman/haberman.data"
habermanUrl: String = http://archive.ics.uci.edu/ml/machine-learning-databases/haberman/haberman.data
scala> val typesRDD = sc.parallelize(Array("1.0,1.0,1.0,2.0"))
typesRDD: org.apache.spark.rdd.RDD[String] = ParallelCollectionRDD[50] at parallelize at <console>:33
scala> val scriptUrl = "https://raw.githubusercontent.com/apache/systemml/master/scripts/algorithms/Univar-Stats.dml"
scriptUrl: String = https://raw.githubusercontent.com/apache/systemml/master/scripts/algorithms/Univar-Stats.dml
scala> val uni = dmlFromUrl(scriptUrl).in("A", new java.net.URL(habermanUrl)).in("K", typesRDD).in("$CONSOLE_OUTPUT", true)
uni: org.apache.sysml.api.mlcontext.Script =
Inputs:
[1] (URL) A: http://archive.ics.uci.edu/ml/machine-learning-databases/haberman/haberman.data
[2] (RDD) K: ParallelCollectionRDD[50] at parallelize at <console>:33
[3] (Boolean) $CONSOLE_OUTPUT: true
Outputs:
None
scala> ml.execute(uni)
...
-------------------------------------------------
(01) Minimum | 30.0
(02) Maximum | 83.0
(03) Range | 53.0
(04) Mean | 52.45751633986928
(05) Variance | 116.71458266366658
(06) Std deviation | 10.803452349303281
(07) Std err of mean | 0.6175922641866753
(08) Coeff of variation | 0.20594669940735139
(09) Skewness | 0.1450718616532357
(10) Kurtosis | -0.6150152487211726
(11) Std err of skewness | 0.13934809593495995
(12) Std err of kurtosis | 0.277810485320835
(13) Median | 52.0
(14) Interquartile mean | 52.16013071895425
Feature [1]: Scale
-------------------------------------------------
(01) Minimum | 58.0
(02) Maximum | 69.0
(03) Range | 11.0
(04) Mean | 62.85294117647059
(05) Variance | 10.558630665380907
(06) Std deviation | 3.2494046632238507
(07) Std err of mean | 0.18575610076612029
(08) Coeff of variation | 0.051698529971741194
(09) Skewness | 0.07798443581479181
(10) Kurtosis | -1.1324380182967442
(11) Std err of skewness | 0.13934809593495995
(12) Std err of kurtosis | 0.277810485320835
(13) Median | 63.0
(14) Interquartile mean | 62.80392156862745
Feature [2]: Scale
-------------------------------------------------
(01) Minimum | 0.0
(02) Maximum | 52.0
(03) Range | 52.0
(04) Mean | 4.026143790849673
(05) Variance | 51.691117539912135
(06) Std deviation | 7.189653506248555
(07) Std err of mean | 0.41100513466216837
(08) Coeff of variation | 1.7857418611299172
(09) Skewness | 2.954633471088322
(10) Kurtosis | 11.425776549251449
(11) Std err of skewness | 0.13934809593495995
(12) Std err of kurtosis | 0.277810485320835
(13) Median | 1.0
(14) Interquartile mean | 1.2483660130718954
Feature [3]: Scale
-------------------------------------------------
Feature [4]: Categorical (Nominal)
(15) Num of categories | 2
(16) Mode | 1
(17) Num of modes | 1
res5: org.apache.sysml.api.mlcontext.MLResults =
NoneAs another example, we can also conveniently obtain a Univariate Statistics DML Script object
via ml.scripts.algorithms.Univar_Stats, as shown below. This feature is not available in Python.
val habermanUrl = "http://archive.ics.uci.edu/ml/machine-learning-databases/haberman/haberman.data"
val typesRDD = sc.parallelize(Array("1.0,1.0,1.0,2.0"))
val scriptUrl = "https://raw.githubusercontent.com/apache/systemml/master/scripts/algorithms/Univar-Stats.dml"
ml.scripts.algorithms.Univar_Stats.in("A", new java.net.URL(habermanUrl)).in("K", typesRDD).in("$CONSOLE_OUTPUT", true).executescala> val habermanUrl = "http://archive.ics.uci.edu/ml/machine-learning-databases/haberman/haberman.data"
habermanUrl: String = http://archive.ics.uci.edu/ml/machine-learning-databases/haberman/haberman.data
scala> val typesRDD = sc.parallelize(Array("1.0,1.0,1.0,2.0"))
typesRDD: org.apache.spark.rdd.RDD[String] = ParallelCollectionRDD[21] at parallelize at <console>:30
scala> val scriptUrl = "https://raw.githubusercontent.com/apache/systemml/master/scripts/algorithms/Univar-Stats.dml"
scriptUrl: String = https://raw.githubusercontent.com/apache/systemml/master/scripts/algorithms/Univar-Stats.dml
scala> ml.scripts.algorithms.Univar_Stats.in("A", new java.net.URL(habermanUrl)).in("K", typesRDD).in("$CONSOLE_OUTPUT", true).execute
17/06/05 17:23:37 WARN RewriteRemovePersistentReadWrite: Non-registered persistent write of variable 'baseStats' (line 186).
-------------------------------------------------
(01) Minimum | 30.0
(02) Maximum | 83.0
(03) Range | 53.0
(04) Mean | 52.45751633986928
(05) Variance | 116.71458266366658
(06) Std deviation | 10.803452349303281
(07) Std err of mean | 0.6175922641866753
(08) Coeff of variation | 0.20594669940735139
(09) Skewness | 0.1450718616532357
(10) Kurtosis | -0.6150152487211726
(11) Std err of skewness | 0.13934809593495995
(12) Std err of kurtosis | 0.277810485320835
(13) Median | 52.0
(14) Interquartile mean | 52.16013071895425
Feature [1]: Scale
-------------------------------------------------
(01) Minimum | 58.0
(02) Maximum | 69.0
(03) Range | 11.0
(04) Mean | 62.85294117647059
(05) Variance | 10.558630665380907
(06) Std deviation | 3.2494046632238507
(07) Std err of mean | 0.18575610076612029
(08) Coeff of variation | 0.051698529971741194
(09) Skewness | 0.07798443581479181
(10) Kurtosis | -1.1324380182967442
(11) Std err of skewness | 0.13934809593495995
(12) Std err of kurtosis | 0.277810485320835
(13) Median | 63.0
(14) Interquartile mean | 62.80392156862745
Feature [2]: Scale
-------------------------------------------------
(01) Minimum | 0.0
(02) Maximum | 52.0
(03) Range | 52.0
(04) Mean | 4.026143790849673
(05) Variance | 51.691117539912135
(06) Std deviation | 7.189653506248555
(07) Std err of mean | 0.41100513466216837
(08) Coeff of variation | 1.7857418611299172
(09) Skewness | 2.954633471088322
(10) Kurtosis | 11.425776549251449
(11) Std err of skewness | 0.13934809593495995
(12) Std err of kurtosis | 0.277810485320835
(13) Median | 1.0
(14) Interquartile mean | 1.2483660130718954
Feature [3]: Scale
-------------------------------------------------
Feature [4]: Categorical (Nominal)
(15) Num of categories | 2
(16) Mode | 1
(17) Num of modes | 1
SystemML Statistics:
Total execution time: 0.211 sec.
Number of executed Spark inst: 8.
res1: org.apache.sysml.api.mlcontext.MLResults =
NoneInput Variables vs Input Parameters
If we examine the
Univar-Stats.dml
file, we see in the comments that it can take 4 input
parameters, $X, $TYPES, $CONSOLE_OUTPUT, and $STATS. Input parameters are typically useful when
executing SystemML in Standalone mode, Spark batch mode, or Hadoop batch mode. For example, $X specifies
the location in the file system where the input data matrix is located, $TYPES specifies the location in the file system
where the input types matrix is located, $CONSOLE_OUTPUT specifies whether or not labeled statistics should be
output to the console, and $STATS specifies the location in the file system where the output matrix should be written.
...
# INPUT PARAMETERS:
# -------------------------------------------------------------------------------------------------
# NAME TYPE DEFAULT MEANING
# -------------------------------------------------------------------------------------------------
# X String --- Location of INPUT data matrix
# TYPES String --- Location of INPUT matrix that lists the types of the features:
# 1 for scale, 2 for nominal, 3 for ordinal
# CONSOLE_OUTPUT Boolean FALSE If TRUE, print summary statistics to console
# STATS String --- Location of OUTPUT matrix with summary statistics computed for
# all features (17 statistics - 14 scale, 3 categorical)
# -------------------------------------------------------------------------------------------------
# OUTPUT: Matrix of summary statistics
...
consoleOutput = ifdef($CONSOLE_OUTPUT, FALSE);
A = read($X); # data file
K = read($TYPES); # attribute kind file
...
write(baseStats, $STATS);
...Because MLContext is a programmatic interface, it offers more flexibility. You can still use input parameters and files in the file system, such as this example that specifies file paths to the input matrices and the output matrix:
val script = dmlFromFile("scripts/algorithms/Univar-Stats.dml").in("$X", "data/haberman.data").in("$TYPES", "data/types.csv").in("$STATS", "data/univarOut.mtx").in("$CONSOLE_OUTPUT", true)
ml.execute(script)Using the MLContext API, rather than relying solely on input parameters, we can bind to the variables associated
with the read and write statements. In the fragment of Univar-Stats.dml above, notice that the matrix at
path $X is read to variable A, $TYPES is read to variable
K, and baseStats is written to path $STATS. Therefore, we can bind the Haberman input data matrix to the A variable,
the input types matrix to the K variable, and the output matrix to the baseStats variable.
val uni = dmlFromUrl(scriptUrl).in("A", habermanRDD, habermanMetadata).in("K", typesRDD, typesMetadata).out("baseStats")
val baseStats = ml.execute(uni).getMatrix("baseStats")
baseStats.toRDDStringIJV.collect.slice(0,9).foreach(println)scala> val uni = dmlFromUrl(scriptUrl).in("A", habermanRDD, habermanMetadata).in("K", typesRDD, typesMetadata).out("baseStats")
uni: org.apache.sysml.api.mlcontext.Script =
Inputs:
[1] (RDD) A: ParallelCollectionRDD[159] at parallelize at <console>:43
[2] (RDD) K: ParallelCollectionRDD[160] at parallelize at <console>:39
Outputs:
[1] baseStats
scala> val baseStats = ml.execute(uni).getMatrix("baseStats")
...
baseStats: org.apache.sysml.api.mlcontext.Matrix = Matrix: scratch_space/_p12059_9.31.117.12/parfor/4_resultmerge1, [17 x 4, nnz=44, blocks (1000 x 1000)], binaryblock, dirty
scala> baseStats.toRDDStringIJV.collect.slice(0,9).foreach(println)
1 1 30.0
1 2 58.0
1 3 0.0
1 4 0.0
2 1 83.0
2 2 69.0
2 3 52.0
2 4 0.0
3 1 53.0uni = dmlFromUrl(scriptUrl).input(A=habermanRDD, K=typesRDD).output("baseStats")
baseStats = ml.execute(uni).get("baseStats")
baseStats.toNumPy().flatten()[0:9]>>> uni = dmlFromUrl(scriptUrl).input(A=habermanRDD, K=typesRDD).output("baseStats")
>>> baseStats = ml.execute(uni).get("baseStats")
SystemML Statistics:
Total execution time: 0.690 sec.
Number of executed Spark inst: 4.
>>> baseStats.toNumPy().flatten()[0:9]
array([ 30., 58., 0., 0., 83., 69., 52., 0., 53.])Script Information
The info method on a Script object can provide useful information about a DML or PyDML script, such as
the inputs, output, symbol table, script string, and the script execution string that is passed to the internals of
SystemML.
val minMaxMean =
"""
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
"""
val minMaxMeanScript = dml(minMaxMean).in("Xin", df, mm).out("minOut", "maxOut", "meanOut")
val (min, max, mean) = ml.execute(minMaxMeanScript).getTuple[Double, Double, Double]("minOut", "maxOut", "meanOut")
println(minMaxMeanScript.info)scala> val minMaxMean =
| """
| minOut = min(Xin)
| maxOut = max(Xin)
| meanOut = mean(Xin)
| """
minMaxMean: String =
"
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
"
scala> val minMaxMeanScript = dml(minMaxMean).in("Xin", df, mm).out("minOut", "maxOut", "meanOut")
minMaxMeanScript: org.apache.sysml.api.mlcontext.Script =
Inputs:
[1] (DataFrame) Xin: [C0: double, C1: double, C2: double, C3: double, C4: double, C5: double, C6: double, C7: double, ...
Outputs:
[1] minOut
[2] maxOut
[3] meanOut
scala> val (min, max, mean) = ml.execute(minMaxMeanScript).getTuple[Double, Double, Double]("minOut", "maxOut", "meanOut")
min: Double = 1.4149740823476975E-7
max: Double = 0.9999999956646207
mean: Double = 0.5000954668004209
scala> println(minMaxMeanScript.info)
Script Type: DML
Inputs:
[1] (DataFrame) Xin: [C0: double, C1: double, C2: double, C3: double, C4: double, C5: double, C6: double, C7: double, ...
Outputs:
[1] (Double) minOut: 1.4149740823476975E-7
[2] (Double) maxOut: 0.9999999956646207
[3] (Double) meanOut: 0.5000954668004209
Input Parameters:
None
Input Variables:
[1] Xin
Output Variables:
[1] minOut
[2] maxOut
[3] meanOut
Symbol Table:
[1] (Double) meanOut: 0.5000954668004209
[2] (Double) maxOut: 0.9999999956646207
[3] (Double) minOut: 1.4149740823476975E-7
[4] (Matrix) Xin: Matrix: scratch_space/temp_1166464711339222, [10000 x 100, nnz=1000000, blocks (1000 x 1000)], binaryblock, not-dirty
Script String:
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
Script Execution String:
Xin = read('');
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
write(minOut, '');
write(maxOut, '');
write(meanOut, '');minMaxMean = """
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
"""
minMaxMeanScript = dml(minMaxMean).input(Xin = df).output("minOut", "maxOut", "meanOut")
min, max, mean = ml.execute(minMaxMeanScript).get("minOut", "maxOut", "meanOut")
print(minMaxMeanScript.info())>>> minMaxMean = """
... minOut = min(Xin)
... maxOut = max(Xin)
... meanOut = mean(Xin)
... """
>>> minMaxMeanScript = dml(minMaxMean).input(Xin = df).output("minOut", "maxOut", "meanOut")
min, max, mean = ml.execute(minMaxMeanScript).get("minOut", "maxOut", "meanOut")
print(minMaxMeanScript.info())>>> min, max, mean = ml.execute(minMaxMeanScript).get("minOut", "maxOut", "meanOut")
SystemML Statistics:
Total execution time: 0.521 sec.
Number of executed Spark inst: 0.
>>> print(minMaxMeanScript.info())
Script Type: DML
Inputs:
[1] (Dataset as Matrix) Xin: [C0: double, C1: double ... 98 more fields]
Outputs:
[1] (Double) minOut: 8.754858571102808E-6
[2] (Double) maxOut: 0.9999878908225835
[3] (Double) meanOut: 0.49864912369337505
Input Parameters:
None
Input Variables:
[1] Xin
Output Variables:
[1] minOut
[2] maxOut
[3] meanOut
Symbol Table:
[1] (Double) meanOut: 0.49864912369337505
[2] (Double) maxOut: 0.9999878908225835
[3] (Double) minOut: 8.754858571102808E-6
[4] (Matrix) Xin: MatrixObject: scratch_space/_p20299_10.168.31.110/_t0/temp283, [10000 x 100, nnz=1000000, blocks (1000 x 1000)], binaryblock, not-dirty
Script String:
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
Script Execution String:
Xin = read('');
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
write(minOut, '');
write(maxOut, '');
write(meanOut, '');
>>>Clearing Scripts and MLContext
Dealing with large matrices can require a significant amount of memory. To deal help deal with this, you
can call a Script object’s clearAll method to clear the inputs, outputs, symbol table, and script string.
In terms of memory, the symbol table is most important because it holds references to matrices.
In this example, we display the symbol table of the minMaxMeanScript, call clearAll on the script, and
then display the symbol table, which is empty.
println(minMaxMeanScript.displaySymbolTable)
minMaxMeanScript.clearAll
println(minMaxMeanScript.displaySymbolTable)scala> println(minMaxMeanScript.displaySymbolTable)
Symbol Table:
[1] (Double) meanOut: 0.5000954668004209
[2] (Double) maxOut: 0.9999999956646207
[3] (Double) minOut: 1.4149740823476975E-7
[4] (Matrix) Xin: Matrix: scratch_space/temp_1166464711339222, [10000 x 100, nnz=1000000, blocks (1000 x 1000)], binaryblock, not-dirty
scala> minMaxMeanScript.clearAll
scala> println(minMaxMeanScript.displaySymbolTable)
Symbol Table:
Noneprint(minMaxMeanScript.displaySymbolTable())
minMaxMeanScript.clearAll()
print(minMaxMeanScript.displaySymbolTable())>>> print(minMaxMeanScript.displaySymbolTable())
Symbol Table:
[1] (Double) meanOut: 0.49825964615525964
[2] (Double) maxOut: 0.9999420388455621
[3] (Double) minOut: 2.177681068027404E-5
[4] (Matrix) Xin: MatrixObject: scratch_space/_p30346_10.168.31.110/_t0/temp0, [10000 x 100, nnz=1000000, blocks (1000 x 1000)], binaryblock, not-dirty
>>> minMaxMeanScript.clearAll()
Script
>>> print(minMaxMeanScript.displaySymbolTable())
Symbol Table:
None
>>>The MLContext object holds references to the scripts that have been executed. Calling clear on
the MLContext clears all scripts that it has references to and then removes the references to these
scripts.
ml.clearStatistics
Statistics about script executions can be output to the console by calling MLContext’s setStatistics
method with a value of true.
ml.setStatistics(true)
val minMaxMean =
"""
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
"""
val minMaxMeanScript = dml(minMaxMean).in("Xin", df, mm).out("minOut", "maxOut", "meanOut")
val (min, max, mean) = ml.execute(minMaxMeanScript).getTuple[Double, Double, Double]("minOut", "maxOut", "meanOut")scala> ml.setStatistics(true)
scala> val minMaxMean =
| """
| minOut = min(Xin)
| maxOut = max(Xin)
| meanOut = mean(Xin)
| """
minMaxMean: String =
"
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
"
scala> val minMaxMeanScript = dml(minMaxMean).in("Xin", df, mm).out("minOut", "maxOut", "meanOut")
minMaxMeanScript: org.apache.sysml.api.mlcontext.Script =
Inputs:
[1] (DataFrame) Xin: [C0: double, C1: double, C2: double, C3: double, C4: double, C5: double, C6: double, C7: double, ...
Outputs:
[1] minOut
[2] maxOut
[3] meanOut
scala> val (min, max, mean) = ml.execute(minMaxMeanScript).getTuple[Double, Double, Double]("minOut", "maxOut", "meanOut")
SystemML Statistics:
Total elapsed time: 0.000 sec.
Total compilation time: 0.000 sec.
Total execution time: 0.000 sec.
Number of compiled Spark inst: 0.
Number of executed Spark inst: 0.
Cache hits (Mem, WB, FS, HDFS): 2/0/0/1.
Cache writes (WB, FS, HDFS): 1/0/0.
Cache times (ACQr/m, RLS, EXP): 3.137/0.000/0.001/0.000 sec.
HOP DAGs recompiled (PRED, SB): 0/0.
HOP DAGs recompile time: 0.000 sec.
Spark ctx create time (lazy): 0.000 sec.
Spark trans counts (par,bc,col):0/0/2.
Spark trans times (par,bc,col): 0.000/0.000/6.434 secs.
Total JIT compile time: 112.372 sec.
Total JVM GC count: 54.
Total JVM GC time: 9.664 sec.
Heavy hitter instructions (name, time, count):
-- 1) uamin 3.150 sec 1
-- 2) uamean 0.021 sec 1
-- 3) uamax 0.017 sec 1
-- 4) rmvar 0.000 sec 3
-- 5) assignvar 0.000 sec 3
min: Double = 2.4982850344024143E-8
max: Double = 0.9999997007231808
mean: Double = 0.5002109404821844ml.setStatistics(True)
minMaxMean = """
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
"""
minMaxMeanScript = dml(minMaxMean).input(Xin=df).output("minOut", "maxOut", "meanOut")
min, max, mean = ml.execute(minMaxMeanScript).get("minOut", "maxOut", "meanOut")>>> ml.setStatistics(True)
MLContext
>>> minMaxMean = """
... minOut = min(Xin)
... maxOut = max(Xin)
... meanOut = mean(Xin)
... """
>>> minMaxMeanScript = dml(minMaxMean).input(Xin=df).output("minOut", "maxOut", "meanOut")
>>> min, max, mean = ml.execute(minMaxMeanScript).get("minOut", "maxOut", "meanOut")
SystemML Statistics:
Total elapsed time: 0.608 sec.
Total compilation time: 0.000 sec.
Total execution time: 0.608 sec.
Number of compiled Spark inst: 0.
Number of executed Spark inst: 0.
Cache hits (Mem, WB, FS, HDFS): 2/0/0/1.
Cache writes (WB, FS, HDFS): 1/0/0.
Cache times (ACQr/m, RLS, EXP): 0.586/0.000/0.000/0.000 sec.
HOP DAGs recompiled (PRED, SB): 0/0.
HOP DAGs recompile time: 0.000 sec.
Spark ctx create time (lazy): 0.000 sec.
Spark trans counts (par,bc,col):0/0/1.
Spark trans times (par,bc,col): 0.000/0.000/0.586 secs.
Total JIT compile time: 1.289 sec.
Total JVM GC count: 17.
Total JVM GC time: 0.4 sec.
Heavy hitter instructions:
# Instruction Time(s) Count
1 uamin 0.588 1
2 uamean 0.018 1
3 uamax 0.002 1
4 assignvar 0.000 3
5 rmvar 0.000 1
>>>GPU
If the driver node has a GPU, SystemML may be able to utilize it, subject to memory constraints and what instructions are used in the dml script
ml.setGPU(true)
ml.setStatistics(true)
val matMultScript = dml("""
A = rand(rows=10, cols=1000)
B = rand(rows=1000, cols=10)
C = A %*% B
print(toString(C))
""")
ml.execute(matMultScript)scala> ml.setGPU(true)
scala> ml.setStatistics(true)
scala> val matMultScript = dml("""
| A = rand(rows=10, cols=1000)
| B = rand(rows=1000, cols=10)
| C = A %*% B
| print(toString(C))
| """)
matMultScript: org.apache.sysml.api.mlcontext.Script =
Inputs:
None
Outputs:
None
scala> ml.execute(matMultScript)
249.977 238.545 233.700 234.489 248.556 244.423 249.051 255.043 249.117 251.605
249.226 248.680 245.532 238.258 254.451 249.827 260.957 251.273 250.577 257.571
258.703 246.969 243.463 246.547 250.784 251.758 251.654 258.318 251.817 254.097
248.788 242.960 230.920 244.026 249.159 247.998 251.330 254.718 248.013 255.706
253.251 248.788 235.785 242.941 252.096 248.675 256.865 251.677 252.872 250.490
256.087 245.035 234.124 238.307 248.630 252.522 251.122 251.577 249.171 247.974
245.419 243.114 232.262 239.776 249.583 242.351 250.972 249.244 246.729 251.807
250.081 242.367 230.334 240.955 248.332 240.730 246.940 250.396 244.107 249.729
247.368 239.882 234.353 237.087 252.337 248.801 246.627 249.077 244.305 245.621
252.827 257.352 239.546 246.529 258.916 255.612 260.480 254.805 252.695 257.531
SystemML Statistics:
Total elapsed time: 0.000 sec.
Total compilation time: 0.000 sec.
Total execution time: 0.000 sec.
Number of compiled Spark inst: 0.
Number of executed Spark inst: 0.
CUDA/CuLibraries init time: 0.000/0.003 sec.
Number of executed GPU inst: 8.
GPU mem tx time (alloc/dealloc/toDev/fromDev): 0.003/0.002/0.010/0.002 sec.
GPU mem tx count (alloc/dealloc/toDev/fromDev/evict): 24/24/0/16/8/0.
GPU conversion time (sparseConv/sp2dense/dense2sp): 0.000/0.000/0.000 sec.
GPU conversion count (sparseConv/sp2dense/dense2sp): 0/0/0.
Cache hits (Mem, WB, FS, HDFS): 40/0/0/0.
Cache writes (WB, FS, HDFS): 21/0/0.
Cache times (ACQr/m, RLS, EXP): 0.002/0.002/0.003/0.000 sec.
HOP DAGs recompiled (PRED, SB): 0/0.
HOP DAGs recompile time: 0.000 sec.
Spark ctx create time (lazy): 0.000 sec.
Spark trans counts (par,bc,col):0/0/0.
Spark trans times (par,bc,col): 0.000/0.000/0.000 secs.
Total JIT compile time: 11.426 sec.
Total JVM GC count: 20.
Total JVM GC time: 1.078 sec.
Heavy hitter instructions (name, time, count):
-- 1) toString 0.085 sec 8
-- 2) rand 0.027 sec 16
-- 3) gpu_ba+* 0.018 sec 8
-- 4) print 0.006 sec 8
-- 5) createvar 0.003 sec 24
-- 6) rmvar 0.003 sec 40
res20: org.apache.sysml.api.mlcontext.MLResults =
Noneml.setGPU(True)
ml.setStatistics(True)
matMultScript = dml("""
A = rand(rows=10, cols=1000)
B = rand(rows=1000, cols=10)
C = A %*% B
print(toString(C))
""")
ml.execute(matMultScript)>>> ml.setGPU(True)
MLContext
>>> ml.setStatistics(True)
MLContext
>>> matMultScript = dml("""
... A = rand(rows=10, cols=1000)
... B = rand(rows=1000, cols=10)
... C = A %*% B
... print(toString(C))
... """)
>>> ml.execute(matMultScript)
260.861 262.732 256.630 255.152 254.806 264.448 256.020 250.240 257.520 261.278
257.171 254.891 251.777 246.858 248.947 255.528 247.446 244.370 252.597 253.466
259.844 255.613 257.720 253.652 249.693 261.110 252.608 250.833 251.968 259.176
254.491 247.792 252.551 246.869 244.682 254.734 247.387 244.323 245.981 255.621
259.835 258.062 255.868 252.217 246.304 263.997 255.831 249.846 248.409 260.124
251.598 259.335 255.662 249.818 247.639 257.279 253.946 253.513 251.245 255.922
258.898 258.961 264.036 249.118 250.780 259.547 249.149 258.040 249.100 258.516
250.412 248.424 250.732 243.129 241.684 248.771 237.941 244.719 247.409 247.445
252.990 244.238 248.096 241.145 242.065 253.795 245.352 246.056 251.132 253.063
253.216 249.008 247.910 246.579 242.657 251.078 245.954 244.681 241.878 248.555
SystemML Statistics:
Total elapsed time: 0.042 sec.
Total compilation time: 0.000 sec.
Total execution time: 0.042 sec.
Number of compiled Spark inst: 0.
Number of executed Spark inst: 0.
CUDA/CuLibraries init time: 7.058/0.749 sec.
Number of executed GPU inst: 1.
GPU mem tx time (alloc/dealloc/set0/toDev/fromDev): 0.002/0.000/0.000/0.002/0.000 sec.
GPU mem tx count (alloc/dealloc/set0/toDev/fromDev/evict): 3/3/3/0/2/1/0.
GPU conversion time (sparseConv/sp2dense/dense2sp): 0.000/0.000/0.000 sec.
GPU conversion count (sparseConv/sp2dense/dense2sp): 0/0/0.
Cache hits (Mem, WB, FS, HDFS): 3/0/0/0.
Cache writes (WB, FS, HDFS): 2/0/0.
Cache times (ACQr/m, RLS, EXP): 0.000/0.000/0.000/0.000 sec.
HOP DAGs recompiled (PRED, SB): 0/0.
HOP DAGs recompile time: 0.000 sec.
Spark ctx create time (lazy): 0.000 sec.
Spark trans counts (par,bc,col):0/0/0.
Spark trans times (par,bc,col): 0.000/0.000/0.000 secs.
Total JIT compile time: 1.348 sec.
Total JVM GC count: 9.
Total JVM GC time: 0.264 sec.
Heavy hitter instructions:
# Instruction Time(s) Count
1 rand 0.023 2
2 gpu_ba+* 0.012 1
3 toString 0.004 1
4 createvar 0.000 3
5 rmvar 0.000 3
6 print 0.000 1
18
MLResults
>>>Note that GPU instructions show up prepended with a “gpu” in the statistics.
Explain
A DML or PyDML script is converted into a SystemML program during script execution. Information
about this program can be displayed by calling MLContext’s setExplain method with a value
of true.
ml.setExplain(true)
val minMaxMean =
"""
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
"""
val mm = new MatrixMetadata(numRows, numCols)
val minMaxMeanScript = dml(minMaxMean).in("Xin", df, mm).out("minOut", "maxOut", "meanOut")
val (min, max, mean) = ml.execute(minMaxMeanScript).getTuple[Double, Double, Double]("minOut", "maxOut", "meanOut")scala> ml.setExplain(true)
scala> val minMaxMean =
| """
| minOut = min(Xin)
| maxOut = max(Xin)
| meanOut = mean(Xin)
| """
minMaxMean: String =
"
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
"
scala> val mm = new MatrixMetadata(numRows, numCols)
mm: org.apache.sysml.api.mlcontext.MatrixMetadata = rows: 10000, columns: 100, non-zeros: None, rows per block: None, columns per block: None
scala> val minMaxMeanScript = dml(minMaxMean).in("Xin", df, mm).out("minOut", "maxOut", "meanOut")
minMaxMeanScript: org.apache.sysml.api.mlcontext.Script =
Inputs:
[1] (DataFrame) Xin: [C0: double, C1: double, C2: double, C3: double, C4: double, C5: double, C6: double, C7: double, ...
Outputs:
[1] minOut
[2] maxOut
[3] meanOut
scala> val (min, max, mean) = ml.execute(minMaxMeanScript).getTuple[Double, Double, Double]("minOut", "maxOut", "meanOut")
PROGRAM
--MAIN PROGRAM
----GENERIC (lines 1-8) [recompile=false]
------(12) TRead Xin [10000,100,1000,1000,1000000] {0,0,76 -> 76MB} [chkpt], CP
------(13) ua(minRC) (12) [0,0,-1,-1,-1] {76,0,0 -> 76MB}, CP
------(21) TWrite minOut (13) [0,0,-1,-1,-1] {0,0,0 -> 0MB}, CP
------(14) ua(maxRC) (12) [0,0,-1,-1,-1] {76,0,0 -> 76MB}, CP
------(27) TWrite maxOut (14) [0,0,-1,-1,-1] {0,0,0 -> 0MB}, CP
------(15) ua(meanRC) (12) [0,0,-1,-1,-1] {76,0,0 -> 76MB}, CP
------(33) TWrite meanOut (15) [0,0,-1,-1,-1] {0,0,0 -> 0MB}, CP
min: Double = 5.16651366133658E-9
max: Double = 0.9999999368927975
mean: Double = 0.5001096515241128ml.setExplain(True)
minMaxMean = """
minOut = min(Xin)
maxOut = max(Xin)
meanOut = mean(Xin)
"""
minMaxMeanScript = dml(minMaxMean).input(Xin=df).output("minOut", "maxOut", "meanOut")
min, max, mean = ml.execute(minMaxMeanScript).get("minOut", "maxOut", "meanOut")>>> ml.setExplain(True)
MLContext
>>> minMaxMean = """
... minOut = min(Xin)
... maxOut = max(Xin)
... meanOut = mean(Xin)
... """
>>> minMaxMeanScript = dml(minMaxMean).input(Xin=df).output("minOut", "maxOut", "meanOut")
min, max, mean = ml.execute(minMaxMeanScript).get("minOut", "maxOut", "meanOut")
>>> min, max, mean = ml.execute(minMaxMeanScript).get("minOut", "maxOut", "meanOut")
# EXPLAIN (RUNTIME):
# Memory Budget local/remote = 687MB/?MB/?MB/?MB
# Degree of Parallelism (vcores) local/remote = 24/?
PROGRAM ( size CP/SP = 7/0 )
--MAIN PROGRAM
----GENERIC (lines 1-8) [recompile=false]
------CP uamin Xin.MATRIX.DOUBLE _Var1.SCALAR.DOUBLE 24
------CP uamax Xin.MATRIX.DOUBLE _Var2.SCALAR.DOUBLE 24
------CP uamean Xin.MATRIX.DOUBLE _Var3.SCALAR.DOUBLE 24
------CP assignvar _Var1.SCALAR.DOUBLE.false minOut.SCALAR.DOUBLE
------CP assignvar _Var2.SCALAR.DOUBLE.false maxOut.SCALAR.DOUBLE
------CP assignvar _Var3.SCALAR.DOUBLE.false meanOut.SCALAR.DOUBLE
------CP rmvar _Var1 _Var2 _Var3
SystemML Statistics:
Total execution time: 0.952 sec.
Number of executed Spark inst: 0.
>>>Different explain levels can be set. The explain levels are NONE, HOPS, RUNTIME, RECOMPILE_HOPS, and RECOMPILE_RUNTIME.
ml.setExplainLevel(MLContext.ExplainLevel.RUNTIME)
val (min, max, mean) = ml.execute(minMaxMeanScript).getTuple[Double, Double, Double]("minOut", "maxOut", "meanOut")scala> ml.setExplainLevel(MLContext.ExplainLevel.RUNTIME)
scala> val (min, max, mean) = ml.execute(minMaxMeanScript).getTuple[Double, Double, Double]("minOut", "maxOut", "meanOut")
PROGRAM ( size CP/SP = 9/0 )
--MAIN PROGRAM
----GENERIC (lines 1-8) [recompile=false]
------CP uamin Xin.MATRIX.DOUBLE _Var8.SCALAR.DOUBLE 8
------CP uamax Xin.MATRIX.DOUBLE _Var9.SCALAR.DOUBLE 8
------CP uamean Xin.MATRIX.DOUBLE _Var10.SCALAR.DOUBLE 8
------CP assignvar _Var8.SCALAR.DOUBLE.false minOut.SCALAR.DOUBLE
------CP assignvar _Var9.SCALAR.DOUBLE.false maxOut.SCALAR.DOUBLE
------CP assignvar _Var10.SCALAR.DOUBLE.false meanOut.SCALAR.DOUBLE
------CP rmvar _Var8
------CP rmvar _Var9
------CP rmvar _Var10
min: Double = 5.16651366133658E-9
max: Double = 0.9999999368927975
mean: Double = 0.5001096515241128ml.setExplainLevel("runtime")
min, max, mean = ml.execute(minMaxMeanScript).get("minOut", "maxOut", "meanOut")>>> ml.setExplainLevel("runtime")
MLContext
>>> min, max, mean = ml.execute(minMaxMeanScript).get("minOut", "maxOut", "meanOut")
# EXPLAIN (RUNTIME):
# Memory Budget local/remote = 687MB/?MB/?MB/?MB
# Degree of Parallelism (vcores) local/remote = 24/?
PROGRAM ( size CP/SP = 7/0 )
--MAIN PROGRAM
----GENERIC (lines 1-8) [recompile=false]
------CP uamin Xin.MATRIX.DOUBLE _Var4.SCALAR.DOUBLE 24
------CP uamax Xin.MATRIX.DOUBLE _Var5.SCALAR.DOUBLE 24
------CP uamean Xin.MATRIX.DOUBLE _Var6.SCALAR.DOUBLE 24
------CP assignvar _Var4.SCALAR.DOUBLE.false minOut.SCALAR.DOUBLE
------CP assignvar _Var5.SCALAR.DOUBLE.false maxOut.SCALAR.DOUBLE
------CP assignvar _Var6.SCALAR.DOUBLE.false meanOut.SCALAR.DOUBLE
------CP rmvar _Var4 _Var5 _Var6
SystemML Statistics:
Total execution time: 0.022 sec.
Number of executed Spark inst: 0.
>>>Script Creation and ScriptFactory
Script objects can be created using standard Script constructors. A Script can be of two types: DML (R-based syntax) and PYDML (Python-based syntax). If no ScriptType is specified, the default Script type is DML.
val script = new Script()
println(script.getScriptType)
val script = new Script(ScriptType.PYDML)
println(script.getScriptType)scala> val script = new Script();
...
scala> println(script.getScriptType)
DML
scala> val script = new Script(ScriptType.PYDML);
...
scala> println(script.getScriptType)
PYDMLThe ScriptFactory class offers convenient methods for creating DML and PYDML scripts from a variety of sources. ScriptFactory can create a script object from a String, File, URL, or InputStream.
Script from URL:
Here we create Script object s1 by reading Univar-Stats.dml from a URL.
val uniUrl = "https://raw.githubusercontent.com/apache/systemml/master/scripts/algorithms/Univar-Stats.dml"
val s1 = ScriptFactory.dmlFromUrl(scriptUrl)Script from String:
We create Script objects s2 and s3 from Strings using ScriptFactory’s dml and dmlFromString methods.
Both methods perform the same action. This example reads an algorithm at a URL to String uniString and then
creates two script objects based on this String.
val uniUrl = "https://raw.githubusercontent.com/apache/systemml/master/scripts/algorithms/Univar-Stats.dml"
val uniString = scala.io.Source.fromURL(uniUrl).mkString
val s2 = ScriptFactory.dml(uniString)
val s3 = ScriptFactory.dmlFromString(uniString)Script from File:
We create Script object s4 based on a path to a file using ScriptFactory’s dmlFromFile method. This example
reads a URL to a String, writes this String to a file, and then uses the path to the file to create a Script object.
val uniUrl = "https://raw.githubusercontent.com/apache/systemml/master/scripts/algorithms/Univar-Stats.dml"
val uniString = scala.io.Source.fromURL(uniUrl).mkString
scala.tools.nsc.io.File("uni.dml").writeAll(uniString)
val s4 = ScriptFactory.dmlFromFile("uni.dml")Script from InputStream:
The SystemML jar file contains all the primary algorithm scripts. We can read one of these scripts as an InputStream and use this to create a Script object.
val inputStream = getClass.getResourceAsStream("/scripts/algorithms/Univar-Stats.dml")
val s5 = ScriptFactory.dmlFromInputStream(inputStream)Script from Resource:
As mentioned, the SystemML jar file contains all the primary algorithm script files. For convenience, we can
read these script files or other script files on the classpath using ScriptFactory’s dmlFromResource and pydmlFromResource
methods.
val s6 = ScriptFactory.dmlFromResource("/scripts/algorithms/Univar-Stats.dml");ScriptExecutor
A Script is executed by a ScriptExecutor. If no ScriptExecutor is specified, a default ScriptExecutor will be created to execute a Script. Script execution consists of several steps, as detailed in SystemML’s Optimizer: Plan Generation for Large-Scale Machine Learning Programs. Additional information can be found in the Javadocs for ScriptExecutor.
Advanced users may find it useful to be able to specify their own execution or to override ScriptExecutor methods by subclassing ScriptExecutor.
In this example, we override the parseScript and validateScript methods to display messages to the console
during these execution steps.
class MyScriptExecutor extends org.apache.sysml.api.mlcontext.ScriptExecutor {
override def parseScript{ println("Parsing script"); super.parseScript(); }
override def validateScript{ println("Validating script"); super.validateScript(); }
}
val helloScript = dml("print('hello world')")
ml.execute(helloScript, new MyScriptExecutor)scala> class MyScriptExecutor extends org.apache.sysml.api.mlcontext.ScriptExecutor {
| override def parseScript{ println("Parsing script"); super.parseScript(); }
| override def validateScript{ println("Validating script"); super.validateScript(); }
| }
defined class MyScriptExecutor
scala> val helloScript = dml("print('hello world')")
helloScript: org.apache.sysml.api.mlcontext.Script =
Inputs:
None
Outputs:
None
scala> ml.execute(helloScript, new MyScriptExecutor)
Parsing script
Validating script
hello world
res63: org.apache.sysml.api.mlcontext.MLResults =
NoneMatrixMetadata
When supplying matrix data to Apache SystemML using the MLContext API, matrix metadata can be
supplied using a MatrixMetadata object. Supplying characteristics about a matrix can significantly
improve performance. For some types of input matrices, supplying metadata is mandatory.
Metadata at a minimum typically consists of the number of rows and columns in
a matrix. The number of non-zeros can also be supplied.
Additionally, the number of rows and columns per block can be supplied, although in typical usage it’s probably fine to use the default values used by SystemML (1,000 rows and 1,000 columns per block). SystemML handles a matrix internally by splitting the matrix into chunks, or blocks. The number of rows and columns per block refers to the size of these matrix blocks.
CSV RDD with No Metadata:
Here we see an example of inputting an RDD of Strings in CSV format with no metadata. Note that in general it is recommended that metadata is supplied. We output the sum and mean of the cells in the matrix.
val rddCSV = sc.parallelize(Array("1.0,2.0", "3.0,4.0"))
val sumAndMean = dml("sum = sum(m); mean = mean(m)").in("m", rddCSV).out("sum", "mean")
ml.execute(sumAndMean)scala> val rddCSV = sc.parallelize(Array("1.0,2.0", "3.0,4.0"))
rddCSV: org.apache.spark.rdd.RDD[String] = ParallelCollectionRDD[190] at parallelize at <console>:38
scala> val sumAndMean = dml("sum = sum(m); mean = mean(m)").in("m", rddCSV).out("sum", "mean")
sumAndMean: org.apache.sysml.api.mlcontext.Script =
Inputs:
[1] (RDD) m: ParallelCollectionRDD[190] at parallelize at <console>:38
Outputs:
[1] sum
[2] mean
scala> ml.execute(sumAndMean)
res20: org.apache.sysml.api.mlcontext.MLResults =
[1] (Double) sum: 10.0
[2] (Double) mean: 2.5IJV RDD with Metadata:
Next, we’ll supply an RDD in IJV format. IJV is a sparse format where each line has three space-separated values. The first value indicates the row number, the second value indicates the column number, and the third value indicates the cell value. Since the total numbers of rows and columns can’t be determined from these IJV rows, we need to supply metadata describing the matrix size.
Here, we specify that our matrix has 3 rows and 3 columns.
val rddIJV = sc.parallelize(Array("1 1 1", "2 1 2", "1 2 3", "3 3 4"))
val mm3x3 = new MatrixMetadata(MatrixFormat.IJV, 3, 3)
val sumAndMean = dml("sum = sum(m); mean = mean(m)").in("m", rddIJV, mm3x3).out("sum", "mean")
ml.execute(sumAndMean)scala> val rddIJV = sc.parallelize(Array("1 1 1", "2 1 2", "1 2 3", "3 3 4"))
rddIJV: org.apache.spark.rdd.RDD[String] = ParallelCollectionRDD[202] at parallelize at <console>:38
scala> val mm3x3 = new MatrixMetadata(MatrixFormat.IJV, 3, 3)
mm3x3: org.apache.sysml.api.mlcontext.MatrixMetadata = rows: 3, columns: 3, non-zeros: None, rows per block: None, columns per block: None
scala> val sumAndMean = dml("sum = sum(m); mean = mean(m)").in("m", rddIJV, mm3x3).out("sum", "mean")
sumAndMean: org.apache.sysml.api.mlcontext.Script =
Inputs:
[1] (RDD) m: ParallelCollectionRDD[202] at parallelize at <console>:38
Outputs:
[1] sum
[2] mean
scala> ml.execute(sumAndMean)
res21: org.apache.sysml.api.mlcontext.MLResults =
[1] (Double) sum: 10.0
[2] (Double) mean: 1.1111111111111112Next, we’ll run the same DML, but this time we’ll specify that the input matrix is 4x4 instead of 3x3.
val rddIJV = sc.parallelize(Array("1 1 1", "2 1 2", "1 2 3", "3 3 4"))
val mm4x4 = new MatrixMetadata(MatrixFormat.IJV, 4, 4)
val sumAndMean = dml("sum = sum(m); mean = mean(m)").in("m", rddIJV, mm4x4).out("sum", "mean")
ml.execute(sumAndMean)scala> val rddIJV = sc.parallelize(Array("1 1 1", "2 1 2", "1 2 3", "3 3 4"))
rddIJV: org.apache.spark.rdd.RDD[String] = ParallelCollectionRDD[210] at parallelize at <console>:38
scala> val mm4x4 = new MatrixMetadata(MatrixFormat.IJV, 4, 4)
mm4x4: org.apache.sysml.api.mlcontext.MatrixMetadata = rows: 4, columns: 4, non-zeros: None, rows per block: None, columns per block: None
scala> val sumAndMean = dml("sum = sum(m); mean = mean(m)").in("m", rddIJV, mm4x4).out("sum", "mean")
sumAndMean: org.apache.sysml.api.mlcontext.Script =
Inputs:
[1] (RDD) m: ParallelCollectionRDD[210] at parallelize at <console>:38
Outputs:
[1] sum
[2] mean
scala> ml.execute(sumAndMean)
res22: org.apache.sysml.api.mlcontext.MLResults =
[1] (Double) sum: 10.0
[2] (Double) mean: 0.625Matrix Data Conversions and Performance
Internally, Apache SystemML uses a binary-block matrix representation, where a matrix is represented as a grouping of blocks. Each block is equal in size to the other blocks in the matrix and consists of a number of rows and columns. The default block size is 1,000 rows by 1,000 columns.
Conversion of a large set of data to a SystemML matrix representation can potentially be time-consuming. Therefore, if you use a set of data multiple times, one way to potentially improve performance is to convert it to a SystemML matrix representation and then use this representation rather than performing the data conversion each time.
If you have an input DataFrame, it can be converted to a Matrix, and this Matrix can be passed as an input rather than passing in the DataFrame as an input.
For example, suppose we had a 10000x100 matrix represented as a DataFrame, as we saw in an earlier example. Now suppose we create two Script objects with the DataFrame as an input, as shown below. In the Spark Shell, when executing this code, you can see that each of the two Script object creations requires the time-consuming data conversion step.
import org.apache.spark.sql._
import org.apache.spark.sql.types.{StructType,StructField,DoubleType}
import scala.util.Random
val numRows = 10000
val numCols = 100
val data = sc.parallelize(0 to numRows-1).map { _ => Row.fromSeq(Seq.fill(numCols)(Random.nextDouble)) }
val schema = StructType((0 to numCols-1).map { i => StructField("C" + i, DoubleType, true) } )
val df = spark.createDataFrame(data, schema)
val mm = new MatrixMetadata(numRows, numCols)
val minMaxMeanScript = dml(minMaxMean).in("Xin", df, mm).out("minOut", "maxOut", "meanOut")
val minMaxMeanScript = dml(minMaxMean).in("Xin", df, mm).out("minOut", "maxOut", "meanOut")Rather than passing in a DataFrame each time to the Script object creation, let’s instead create a Matrix object based on the DataFrame and pass this Matrix to the Script object creation. If we run the code below in the Spark Shell, we see that the data conversion step occurs when the Matrix object is created. However, when we create a Script object twice, we see that no conversion penalty occurs, since this conversion occurred when the Matrix was created.
import org.apache.spark.sql._
import org.apache.spark.sql.types.{StructType,StructField,DoubleType}
import scala.util.Random
val numRows = 10000
val numCols = 100
val data = sc.parallelize(0 to numRows-1).map { _ => Row.fromSeq(Seq.fill(numCols)(Random.nextDouble)) }
val schema = StructType((0 to numCols-1).map { i => StructField("C" + i, DoubleType, true) } )
val df = spark.createDataFrame(data, schema)
val mm = new MatrixMetadata(numRows, numCols)
val matrix = new Matrix(df, mm)
val minMaxMeanScript = dml(minMaxMean).in("Xin", matrix).out("minOut", "maxOut", "meanOut")
val minMaxMeanScript = dml(minMaxMean).in("Xin", matrix).out("minOut", "maxOut", "meanOut")When a matrix is returned as an output, it is returned as a Matrix object, which is a wrapper around a SystemML MatrixObject. As a result, an output Matrix is already in a SystemML representation, meaning that it can be passed as an input with no data conversion penalty.
As an example, here we read in matrix x as an RDD in CSV format. We create a Script that adds one to all
values in the matrix. We obtain the resulting matrix y as a Matrix. We execute the
script five times, feeding the output matrix as the input matrix for the next script execution.
val rddCSV = sc.parallelize(Array("1.0,2.0", "3.0,4.0"))
val add = dml("y = x + 1").in("x", rddCSV).out("y")
for (i <- 1 to 5) {
println("#" + i + ":");
val m = ml.execute(add).getMatrix("y")
m.toRDDStringCSV.collect.foreach(println)
add.in("x", m)
}scala> val rddCSV = sc.parallelize(Array("1.0,2.0", "3.0,4.0"))
rddCSV: org.apache.spark.rdd.RDD[String] = ParallelCollectionRDD[341] at parallelize at <console>:53
scala> val add = dml("y = x + 1").in("x", rddCSV).out("y")
add: org.apache.sysml.api.mlcontext.Script =
Inputs:
[1] (RDD) x: ParallelCollectionRDD[341] at parallelize at <console>:53
Outputs:
[1] y
scala> for (i <- 1 to 5) {
| println("#" + i + ":");
| val m = ml.execute(add).getMatrix("y")
| m.toRDDStringCSV.collect.foreach(println)
| add.in("x", m)
| }
#1:
2.0,3.0
4.0,5.0
#2:
3.0,4.0
5.0,6.0
#3:
4.0,5.0
6.0,7.0
#4:
5.0,6.0
7.0,8.0
#5:
6.0,7.0
8.0,9.0Project Information
SystemML project information such as version and build time can be obtained through the
MLContext API. The project version can be obtained by ml.version. The build time can
be obtained by ml.buildTime. The contents of the project manifest can be displayed
using ml.info. Individual properties can be obtained using the ml.info.property
method, as shown below.
print(ml.version)
print(ml.buildTime)
print(ml.info)
print(ml.info.property("Main-Class"))scala> print(ml.version)
1.0.0-SNAPSHOT
scala> print(ml.buildTime)
2017-06-08 17:51:11 UTC
scala> print(ml.info)
Archiver-Version: Plexus Archiver
Artifact-Id: systemml
Build-Jdk: 1.8.0_60
Build-Time: 2017-06-08 17:51:11 UTC
Built-By: sparkuser
Created-By: Apache Maven 3.3.9
Group-Id: org.apache.systemml
Main-Class: org.apache.sysml.api.DMLScript
Manifest-Version: 1.0
Minimum-Recommended-Spark-Version: 2.1.0
Version: 1.0.0-SNAPSHOT
scala> print(ml.info.property("Main-Class"))
org.apache.sysml.api.DMLScriptprint(ml.version())
print(ml.buildTime())
print(ml.info())>>> print(ml.version())
1.0.0-SNAPSHOT
>>> print(ml.buildTime())
2017-07-21 12:39:27 CDT
>>> print(ml.info())
Archiver-Version: Plexus Archiver
Artifact-Id: systemml
Build-Jdk: 1.8.0_111
Build-Time: 2017-07-21 12:39:27 CDT
Built-By: biuser
Created-By: Apache Maven 3.0.5
Group-Id: org.apache.systemml
Main-Class: org.apache.sysml.api.DMLScript
Manifest-Version: 1.0
Minimum-Recommended-Spark-Version: 2.1.0
Version: 1.0.0-SNAPSHOT
>>>Jupyter (PySpark) Notebook Example - Poisson Nonnegative Matrix Factorization
Similar to the Scala API, SystemML also provides a Python MLContext API. Before usage, you’ll need to install it first.
Here, we’ll explore the use of SystemML via PySpark in a Jupyter notebook. This Jupyter notebook example can be nicely viewed in a rendered state on GitHub, and can be downloaded here to a directory of your choice.
From the directory with the downloaded notebook, start Jupyter with PySpark:
PYSPARK_DRIVER_PYTHON=jupyter PYSPARK_DRIVER_PYTHON_OPTS="notebook" pyspark
PYSPARK_PYTHON=python3 PYSPARK_DRIVER_PYTHON=jupyter PYSPARK_DRIVER_PYTHON_OPTS="notebook" pyspark
This will open Jupyter in a browser:
We can then open up the SystemML-PySpark-Recommendation-Demo notebook.
Set up the notebook and download the data
%load_ext autoreload
%autoreload 2
%matplotlib inline
import numpy as np
import matplotlib.pyplot as plt
from systemml import MLContext, dml # pip install systeml
plt.rcParams['figure.figsize'] = (10, 6)%%sh
# Download dataset
curl -O http://snap.stanford.edu/data/amazon0601.txt.gz
gunzip amazon0601.txt.gzUse PySpark to load the data in as a Spark DataFrame
# Load data
import pyspark.sql.functions as F
dataPath = "amazon0601.txt"
X_train = (sc.textFile(dataPath)
.filter(lambda l: not l.startswith("#"))
.map(lambda l: l.split("\t"))
.map(lambda prods: (int(prods[0]), int(prods[1]), 1.0))
.toDF(("prod_i", "prod_j", "x_ij"))
.filter("prod_i < 500 AND prod_j < 500") # Filter for memory constraints
.cache())
max_prod_i = X_train.select(F.max("prod_i")).first()[0]
max_prod_j = X_train.select(F.max("prod_j")).first()[0]
numProducts = max(max_prod_i, max_prod_j) + 1 # 0-based indexing
print("Total number of products: {}".format(numProducts))Create a SystemML MLContext object
# Create SystemML MLContext
ml = MLContext(sc)Define a kernel for Poisson nonnegative matrix factorization (PNMF) in DML
# Define PNMF kernel in SystemML's DSL using the R-like syntax for PNMF
pnmf = """
# data & args
X = X+1 # change product IDs to be 1-based, rather than 0-based
V = table(X[,1], X[,2])
size = ifdef($size, -1)
if(size > -1) {
V = V[1:size,1:size]
}
n = nrow(V)
m = ncol(V)
range = 0.01
W = Rand(rows=n, cols=rank, min=0, max=range, pdf="uniform")
H = Rand(rows=rank, cols=m, min=0, max=range, pdf="uniform")
losses = matrix(0, rows=max_iter, cols=1)
# run PNMF
i=1
while(i <= max_iter) {
# update params
H = (H * (t(W) %*% (V/(W%*%H))))/t(colSums(W))
W = (W * ((V/(W%*%H)) %*% t(H)))/t(rowSums(H))
# compute loss
losses[i,] = -1 * (sum(V*log(W%*%H)) - as.scalar(colSums(W)%*%rowSums(H)))
i = i + 1;
}
"""Execute the algorithm
# Run the PNMF script on SystemML with Spark
script = dml(pnmf).input(X=X_train, max_iter=100, rank=10).output("W", "H", "losses")
W, H, losses = ml.execute(script).get("W", "H", "losses")Retrieve the losses during training and plot them
# Plot training loss over time
xy = losses.toDF().sort("__INDEX").map(lambda r: (r[0], r[1])).collect()
x, y = zip(*xy)
plt.plot(x, y)
plt.xlabel('Iteration')
plt.ylabel('Loss')
plt.title('PNMF Training Loss')
Recommended Spark Configuration Settings
For best performance, we recommend setting the following flags when running SystemML with Spark:
--conf spark.driver.maxResultSize=0 --conf spark.akka.frameSize=128.