SystemML Standalone Guide


This tutorial provides a quick introduction to using SystemML by running existing SystemML algorithms in standalone mode.

What is SystemML

SystemML enables large-scale machine learning (ML) via a high-level declarative language with R-like syntax called DML and Python-like syntax called PyDML. DML and PyDML allow data scientists to express their ML algorithms with full flexibility but without the need to fine-tune distributed runtime execution plans and system configurations. These ML programs are dynamically compiled and optimized based on data and cluster characteristics using rule-based and cost-based optimization techniques. The compiler automatically generates hybrid runtime execution plans ranging from in-memory, single node execution to distributed computation for Hadoop or Spark Batch execution. SystemML features a suite of algorithms for Descriptive Statistics, Classification, Clustering, Regression, Matrix Factorization, and Survival Analysis. Detailed descriptions of these algorithms can be found in the Algorithms Reference.

Download SystemML

Apache incubator releases of SystemML are available from the Downloads page.

SystemML can also be downloaded from GitHub and built with Maven. The SystemML project is available on GitHub at https://github.com/apache/incubator-systemml. Instructions to build SystemML can be found in the Engine Developer Guide.

Standalone vs Distributed Execution Mode

SystemML’s standalone mode is designed to allow data scientists to rapidly prototype algorithms on a single machine. In standalone mode, all operations occur on a single node in a non-Hadoop environment. Standalone mode is not appropriate for large datasets.

For large-scale production environments, SystemML algorithm execution can be distributed across multi-node clusters using Apache Hadoop or Apache Spark. We will make use of standalone mode throughout this tutorial.

Choosing Test Data

In this tutorial we will use the Haberman’s Survival Data Set which can be downloaded in CSV format from the Center for Machine Learning and Intelligent Systems

$ wget -P data/ http://archive.ics.uci.edu/ml/machine-learning-databases/haberman/haberman.data

The Haberman Data Set has 306 instances and 4 attributes (including the class attribute):

  1. Age of patient at time of operation (numerical)
  2. Patient’s year of operation (year - 1900, numerical)
  3. Number of positive axillary nodes detected (numerical)
  4. Survival status (class attribute)
    • 1 = the patient survived 5 years or longer
    • 2 = the patient died within 5 year

We will need to create a metadata file (MTD) which stores metadata information about the content of the data file. The name of the MTD file associated with the data file <filename> must be <filename>.mtd.

$ echo '{"rows": 306, "cols": 4, "format": "csv"}' > data/haberman.data.mtd

Example 1 - Univariate Statistics

Let’s start with a simple example, computing certain univariate statistics for each feature column using the algorithm Univar-Stats.dml which requires 3 arguments:

We need to create a file types.csv that describes the type of each column in the data along with its metadata file types.csv.mtd.

$ echo '1,1,1,2' > data/types.csv
$ echo '{"rows": 1, "cols": 4, "format": "csv"}' > data/types.csv.mtd

To run the Univar-Stats.dml algorithm, issue the following command (we set the optional argument CONSOLE_OUTPUT to TRUE to print the statistics to the console):

$ ./runStandaloneSystemML.sh scripts/algorithms/Univar-Stats.dml -nvargs X=data/haberman.data TYPES=data/types.csv STATS=data/univarOut.mtx CONSOLE_OUTPUT=TRUE

[...]
-------------------------------------------------
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

In addition to writing statistics to the console, the Univar-Stats.dml script writes the computed statistics to the data/univarOut.mtx file specified by the STATS input parameter.

univarOut.mtx file

1 1 30.0
1 2 58.0
2 1 83.0
2 2 69.0
2 3 52.0
3 1 53.0
3 2 11.0
3 3 52.0
4 1 52.45751633986928
4 2 62.85294117647059
4 3 4.026143790849673
5 1 116.71458266366658
5 2 10.558630665380907
5 3 51.691117539912135
6 1 10.803452349303281
6 2 3.2494046632238507
6 3 7.189653506248555
7 1 0.6175922641866753
7 2 0.18575610076612029
7 3 0.41100513466216837
8 1 0.20594669940735139
8 2 0.051698529971741194
8 3 1.7857418611299172
9 1 0.1450718616532357
9 2 0.07798443581479181
9 3 2.954633471088322
10 1 -0.6150152487211726
10 2 -1.1324380182967442
10 3 11.425776549251449
11 1 0.13934809593495995
11 2 0.13934809593495995
11 3 0.13934809593495995
12 1 0.277810485320835
12 2 0.277810485320835
12 3 0.277810485320835
13 1 52.0
13 2 63.0
13 3 1.0
14 1 52.16013071895425
14 2 62.80392156862745
14 3 1.2483660130718954
15 4 2.0
16 4 1.0
17 4 1.0

The following table lists the number and name of each univariate statistic. The row numbers below correspond to the elements of the first column in the output matrix above. The signs “+” show applicability to scale or/and to categorical features.

Row Name of Statistic Scale Categ.
1 Minimum +  
2 Maximum +  
3 Range +  
4 Mean +  
5 Variance +  
6 Standard deviation +  
7 Standard error of mean +  
8 Coefficient of variation +  
9 Skewness +  
10 Kurtosis +  
11 Standard error of skewness +  
12 Standard error of kurtosis +  
13 Median +  
14 Inter quartile mean +  
15 Number of categories   +
16 Mode   +
17 Number of modes   +

Example 2 - Binary-class Support Vector Machines

Let’s take the same haberman.data to explore the binary-class support vector machines algorithm l2-svm.dml. This example also illustrates how to use of the sampling algorithm sample.dml and the data split algorithm spliXY.dml.

Sampling the Test Data

First we need to use the sample.dml algorithm to separate the input into one training data set and one data set for model prediction.

Parameters:

We will create the file perc.csv and perc.csv.mtd to define the sampling vector with a sampling rate of 50% to generate 2 data sets:

$ printf "0.5\n0.5" > data/perc.csv
$ echo '{"rows": 2, "cols": 1, "format": "csv"}' > data/perc.csv.mtd

Let’s run the sampling algorithm to create the two data samples:

$ ./runStandaloneSystemML.sh scripts/utils/sample.dml -nvargs X=data/haberman.data sv=data/perc.csv O=data/haberman.part ofmt="csv"

Splitting Labels from Features

Next we use the splitXY.dml algorithm to separate the feature columns from the label column(s).

Parameters:

We specify y=4 as the 4th column contains the labels to be predicted and run the splitXY.dml algorithm on our training and test data sets.

$ ./runStandaloneSystemML.sh scripts/utils/splitXY.dml -nvargs X=data/haberman.part/1 y=4 OX=data/haberman.train.data.csv OY=data/haberman.train.labels.csv ofmt="csv"

$ ./runStandaloneSystemML.sh scripts/utils/splitXY.dml -nvargs X=data/haberman.part/2 y=4 OX=data/haberman.test.data.csv  OY=data/haberman.test.labels.csv  ofmt="csv"

Training and Testing the Model

Now we need to train our model using the l2-svm.dml algorithm.

Parameters:

The l2-svm.dml algorithm is used on our training data sample to train the model.

$ ./runStandaloneSystemML.sh scripts/algorithms/l2-svm.dml -nvargs X=data/haberman.train.data.csv Y=data/haberman.train.labels.csv model=data/l2-svm-model.csv fmt="csv" Log=data/l2-svm-log.csv

The l2-svm-predict.dml algorithm is used on our test data sample to predict the labels based on the trained model.

$ ./runStandaloneSystemML.sh scripts/algorithms/l2-svm-predict.dml -nvargs X=data/haberman.test.data.csv Y=data/haberman.test.labels.csv model=data/l2-svm-model.csv fmt="csv" confusion=data/l2-svm-confusion.csv

The console output should show the accuracy of the trained model in percent, i.e.:

15/09/01 01:32:51 INFO api.DMLScript: BEGIN DML run 09/01/2015 01:32:51
15/09/01 01:32:51 INFO conf.DMLConfig: Updating localtmpdir with value /tmp/systemml
15/09/01 01:32:51 INFO conf.DMLConfig: Updating scratch with value scratch_space
15/09/01 01:32:51 INFO conf.DMLConfig: Updating optlevel with value 2
15/09/01 01:32:51 INFO conf.DMLConfig: Updating numreducers with value 10
15/09/01 01:32:51 INFO conf.DMLConfig: Updating jvmreuse with value false
15/09/01 01:32:51 INFO conf.DMLConfig: Updating defaultblocksize with value 1000
15/09/01 01:32:51 INFO conf.DMLConfig: Updating dml.yarn.appmaster with value false
15/09/01 01:32:51 INFO conf.DMLConfig: Updating dml.yarn.appmaster.mem with value 2048
15/09/01 01:32:51 INFO conf.DMLConfig: Updating dml.yarn.mapreduce.mem with value 2048
15/09/01 01:32:51 INFO conf.DMLConfig: Updating dml.yarn.app.queue with value default
15/09/01 01:32:51 INFO conf.DMLConfig: Updating cp.parallel.matrixmult with value true
15/09/01 01:32:51 INFO conf.DMLConfig: Updating cp.parallel.textio with value true
Accuracy (%): 74.14965986394557
15/09/01 01:32:52 INFO api.DMLScript: SystemML Statistics:
Total execution time:		0.130 sec.
Number of executed MR Jobs:	0.

The generated file l2-svm-confusion.csv should contain the following confusion matrix of this form:

|0   1.0 2.0|
|1.0 t1  t2 |
|2.0 t3  t4 |

If the confusion matrix looks like this …

0,1.0,2.0
1.0,107.0,38.0
2.0,0.0,2.0

… then the accuracy of the model is (t1+t4)/(t1+t2+t3+t4) = (107+2)/107+38+0+2) = 0.741496599


Refer to the Algorithms Reference for more details.

Example 3 - Linear Regression

For this example, we’ll use a standalone wrapper executable, bin/systemml, that is available to be run directly within the project’s source directory when built locally.

After you build SystemML from source (mvn clean package), the standalone mode can be executed either on Linux or OS X using the ./bin/systemml script, or on Windows using the .\bin\systemml.bat batch file.

If you run from the script from the project root folder ./ or from the ./bin folder, then the output files from running SystemML will be created inside the ./temp folder to keep them separate from the SystemML source files managed by Git. The output files for this example will be created under the ./temp folder.

The runtime behavior and logging behavior of SystemML can be customized by editing the files ./conf/SystemML-config.xml and ./conf/log4j.properties. Both files will be created from their corresponding *.template files during the first execution of the SystemML executable script.

When invoking the ./bin/systemml or .\bin\systemml.bat with any of the prepackaged DML scripts you can omit the relative path to the DML script file. The following two commands are equivalent:

./bin/systemml ./scripts/datagen/genLinearRegressionData.dml -nvargs numSamples=1000 numFeatures=50 maxFeatureValue=5 maxWeight=5 addNoise=FALSE b=0 sparsity=0.7 output=linRegData.csv format=csv perc=0.5

./bin/systemml genLinearRegressionData.dml -nvargs numSamples=1000 numFeatures=50 maxFeatureValue=5 maxWeight=5 addNoise=FALSE b=0 sparsity=0.7 output=linRegData.csv format=csv perc=0.5

In this guide we invoke the command with the relative folder to make it easier to look up the source of the DML scripts.

Linear Regression Example

As an example of the capabilities and power of SystemML and DML, let’s consider the Linear Regression algorithm. We require sets of data to train and test our model. To obtain this data, we can either use real data or generate data for our algorithm. The UCI Machine Learning Repository Datasets is one location for real data. Use of real data typically involves some degree of data wrangling. In the following example, we will use SystemML to generate random data to train and test our model.

This example consists of the following parts:

SystemML is distributed in several packages, including a standalone package. We’ll operate in Standalone mode in this example.

Run DML Script to Generate Random Data

We can execute the genLinearRegressionData.dml script in Standalone mode using either the systemml or systemml.bat file. In this example, we’ll generate a matrix of 1000 rows of 50 columns of test data, with sparsity 0.7. In addition to this, a 51st column consisting of labels will be appended to the matrix.

./bin/systemml ./scripts/datagen/genLinearRegressionData.dml -nvargs numSamples=1000 numFeatures=50 maxFeatureValue=5 maxWeight=5 addNoise=FALSE b=0 sparsity=0.7 output=linRegData.csv format=csv perc=0.5

This generates the following files inside the ./temp folder:

linRegData.csv      # 1000 rows of 51 columns of doubles (50 data columns and 1 label column), csv format
linRegData.csv.mtd  # Metadata file
perc.csv            # Used to generate two subsets of the data (for training and testing)
perc.csv.mtd        # Metadata file
scratch_space       # SystemML scratch_space directory

Divide Generated Data into Two Sample Groups

Next, we’ll create two subsets of the generated data, each of size ~50%. We can accomplish this using the sample.dml script with the perc.csv file created in the previous step:

0.5
0.5

The sample.dml script will randomly sample rows from the linRegData.csv file and place them into 2 files based on the percentages specified in perc.csv. This will create two sample groups of roughly 50 percent each.

./bin/systemml ./scripts/utils/sample.dml -nvargs X=linRegData.csv sv=perc.csv O=linRegDataParts ofmt=csv

This script creates two partitions of the original data and places them in a linRegDataParts folder. The files created are as follows:

linRegDataParts/1       # first partition of data, ~50% of rows of linRegData.csv, csv format
linRegDataParts/1.mtd   # metadata
linRegDataParts/2       # second partition of data, ~50% of rows of linRegData.csv, csv format
linRegDataParts/2.mtd   # metadata

The 1 file contains the first partition of data, and the 2 file contains the second partition of data. An associated metadata file describes the nature of each partition of data. If we open 1 and 2 and look at the number of rows, we can see that typically the partitions are not exactly 50% but instead are close to 50%. However, we find that the total number of rows in the original data file equals the sum of the number of rows in 1 and 2.

Split Label Column from First Sample

The next task is to split the label column from the first sample. We can do this using the splitXY.dml script.

./bin/systemml ./scripts/utils/splitXY.dml -nvargs X=linRegDataParts/1 y=51 OX=linRegData.train.data.csv OY=linRegData.train.labels.csv ofmt=csv

This splits column 51, the label column, off from the data. When done, the following files have been created.

linRegData.train.data.csv        # training data of 50 columns, csv format
linRegData.train.data.csv.mtd    # metadata
linRegData.train.labels.csv      # training labels of 1 column, csv format
linRegData.train.labels.csv.mtd  # metadata

Split Label Column from Second Sample

We also need to split the label column from the second sample.

./bin/systemml ./scripts/utils/splitXY.dml -nvargs X=linRegDataParts/2 y=51 OX=linRegData.test.data.csv OY=linRegData.test.labels.csv ofmt=csv

This splits column 51 off the data, resulting in the following files:

linRegData.test.data.csv        # test data of 50 columns, csv format
linRegData.test.data.csv.mtd    # metadata
linRegData.test.labels.csv      # test labels of 1 column, csv format
linRegData.test.labels.csv.mtd  # metadata

Train Model on First Sample

Now, we can train our model based on the first sample. To do this, we utilize the LinearRegDS.dml (Linear Regression Direct Solve) script. Note that SystemML also includes a LinearRegCG.dml (Linear Regression Conjugate Gradient) algorithm for situations where the number of features is large.

./bin/systemml ./scripts/algorithms/LinearRegDS.dml -nvargs X=linRegData.train.data.csv Y=linRegData.train.labels.csv B=betas.csv fmt=csv

This will generate the following files:

betas.csv      # betas, 50 rows of 1 column, csv format
betas.csv.mtd  # metadata

The LinearRegDS.dml script generates statistics to standard output similar to the following.

BEGIN LINEAR REGRESSION SCRIPT
Reading X and Y...
Calling the Direct Solver...
Computing the statistics...
AVG_TOT_Y,-2.160284487670675
STDEV_TOT_Y,66.86434576808432
AVG_RES_Y,-3.3127468704080085E-10
STDEV_RES_Y,1.7231785003947183E-8
DISPERSION,2.963950542926297E-16
PLAIN_R2,1.0
ADJUSTED_R2,1.0
PLAIN_R2_NOBIAS,1.0
ADJUSTED_R2_NOBIAS,1.0
PLAIN_R2_VS_0,1.0
ADJUSTED_R2_VS_0,1.0
Writing the output matrix...
END LINEAR REGRESSION SCRIPT

Now that we have our betas.csv, we can test our model with our second set of data.

Test Model on Second Sample

To test our model on the second sample, we can use the GLM-predict.dml script. This script can be used for both prediction and scoring. Here, we’re using it for scoring since we include the Y named argument. Our betas.csv file is specified as the B named argument.

./bin/systemml ./scripts/algorithms/GLM-predict.dml -nvargs X=linRegData.test.data.csv Y=linRegData.test.labels.csv B=betas.csv fmt=csv

This generates statistics similar to the following to standard output.

LOGLHOOD_Z,,FALSE,NaN
LOGLHOOD_Z_PVAL,,FALSE,NaN
PEARSON_X2,,FALSE,1.895530994504798E-13
PEARSON_X2_BY_DF,,FALSE,4.202951207327712E-16
PEARSON_X2_PVAL,,FALSE,1.0
DEVIANCE_G2,,FALSE,0.0
DEVIANCE_G2_BY_DF,,FALSE,0.0
DEVIANCE_G2_PVAL,,FALSE,1.0
LOGLHOOD_Z,,TRUE,NaN
LOGLHOOD_Z_PVAL,,TRUE,NaN
PEARSON_X2,,TRUE,1.895530994504798E-13
PEARSON_X2_BY_DF,,TRUE,4.202951207327712E-16
PEARSON_X2_PVAL,,TRUE,1.0
DEVIANCE_G2,,TRUE,0.0
DEVIANCE_G2_BY_DF,,TRUE,0.0
DEVIANCE_G2_PVAL,,TRUE,1.0
AVG_TOT_Y,1,,1.0069397725436522
STDEV_TOT_Y,1,,68.29092137526905
AVG_RES_Y,1,,-4.1450397073455047E-10
STDEV_RES_Y,1,,2.0519206226041048E-8
PRED_STDEV_RES,1,TRUE,1.0
PLAIN_R2,1,,1.0
ADJUSTED_R2,1,,1.0
PLAIN_R2_NOBIAS,1,,1.0
ADJUSTED_R2_NOBIAS,1,,1.0

We see that the STDEV_RES_Y value of the testing phase is of similar magnitude to the value obtained from the model training phase.

For convenience, we can encapsulate our DML invocations in a single script:

#!/bin/bash

./bin/systemml ./scripts/datagen/genLinearRegressionData.dml -nvargs numSamples=1000 numFeatures=50 maxFeatureValue=5 maxWeight=5 addNoise=FALSE b=0 sparsity=0.7 output=linRegData.csv format=csv perc=0.5

./bin/systemml ./scripts/utils/sample.dml -nvargs X=linRegData.csv sv=perc.csv O=linRegDataParts ofmt=csv

./bin/systemml ./scripts/utils/splitXY.dml -nvargs X=linRegDataParts/1 y=51 OX=linRegData.train.data.csv OY=linRegData.train.labels.csv ofmt=csv

./bin/systemml ./scripts/utils/splitXY.dml -nvargs X=linRegDataParts/2 y=51 OX=linRegData.test.data.csv OY=linRegData.test.labels.csv ofmt=csv

./bin/systemml ./scripts/algorithms/LinearRegDS.dml -nvargs X=linRegData.train.data.csv Y=linRegData.train.labels.csv B=betas.csv fmt=csv

./bin/systemml ./scripts/algorithms/GLM-predict.dml -nvargs X=linRegData.test.data.csv Y=linRegData.test.labels.csv B=betas.csv fmt=csv

Troubleshooting

If you encounter a "java.lang.OutOfMemoryError" you can edit the invocation script (runStandaloneSystemML.sh or runStandaloneSystemML.bat) to increase the memory available to the JVM, i.e:

java -Xmx16g -Xms4g -Xmn1g -cp ${CLASSPATH} org.apache.sysml.api.DMLScript \
     -f ${SCRIPT_FILE} -exec singlenode -config=SystemML-config.xml \
     $@