This chapter contains the following information:
Parent topic: Greenplum Database Reference Guide
PL/R is a procedural language. With the Greenplum Database PL/R extension you can write database functions in the R programming language and use R packages that contain R functions and data sets.
For information about supported PL/R versions, see the Greenplum Database Release Notes.
The PL/R extension is available as a package. Download the package from Broadcom Support Portal under the desired Greemplum release and install it with the Greenplum Package Manager (gppkg
).
NoteFor more information about download prerequisites, troubleshooting, and instructions, see Download Broadcom products and software.
The gppkg
utility installs Greenplum Database extensions, along with any dependencies, on all hosts across a cluster. It also automatically installs extensions on new hosts in the case of system expansion and segment recovery.
For information about gppkg
, see the Greenplum Database Utility Guide.
Before you install the PL/R extension, make sure that your Greenplum Database is running, you have sourced greenplum_path.sh
, and that the $MASTER_DATA_DIRECTORY
and $GPHOME
variables are set.
Download the PL/R extension package from Broadcom Support Portal under the desired Greemplum release.
Follow the instructions in Verifying the Greenplum Database Software Download to verify the integrity of the Greenplum Procedural Languages PL/R software.
Copy the PL/R package to the Greenplum Database master host.
Install the software extension package by running the gppkg
command. This example installs the PL/R extension on a Linux system:
$ gppkg -i plr-2.3.1-gp5-rhel6-x86_64.gppkg
Source the file $GPHOME/greenplum_path.sh
.
Restart the database.
$ gpstop -r
The extension and the R environment is installed in this directory:
$GPHOME/ext/R-3.3.3/
Note: The version of some shared libraries installed with the operating system might not be compatible with the Greenplum Database PL/R extension.
If a shared library is not compatible, edit the file $GPHOME/greenplum_path.sh
in all Greenplum Database master and segment hosts and set environment variable LD_LIBRARY_PATH
to specify the location that is installed with the PL/R extension.
export *LD\_LIBRARY\_PATH=
$GPHOME/ext/R-3.3.3/lib:$LD\_LIBRARY\_PATH*
For each database that requires its use, register the PL/R language with the SQL command CREATE EXTENSION
. Because PL/R is an untrusted language, only superusers can register PL/R with a database. For example, run this command as the gpadmin
user to register the language with the database named testdb
:
$ psql -d testdb -c 'CREATE EXTENSION plr;'
PL/R is registered as an untrusted language.
When you remove PL/R language support from a database, the PL/R routines that you created in the database will no longer work.
For a database that no longer requires the PL/R language, remove support for PL/R with the SQL command DROP EXTENSION
. Because PL/R is an untrusted language, only superusers can remove support for the PL/R language from a database. For example, run this command as the gpadmin
user to remove support for PL/R from the database named testdb
:
$ psql -d testdb -c 'DROP EXTENSION plr;'
The default command fails if any existing objects (such as functions) depend on the language. Specify the CASCADE
option to also drop all dependent objects, including functions that you created with PL/R.
If no databases have PL/R as a registered language, uninstall the Greenplum PL/R extension with the gppkg
utility. This example uninstalls PL/R package version 2.3.1
$ gppkg -r plr-2.3.1
You can run the gppkg
utility with the options -q --all
to list the installed extensions and their versions.
Restart the database.
$ gpstop -r
The following are simple PL/R examples.
This function generates an array of numbers with a normal distribution using the R function rnorm()
.
CREATE OR REPLACE FUNCTION r_norm(n integer, mean float8,
std_dev float8) RETURNS float8[ ] AS
$$
x<-rnorm(n,mean,std_dev)
return(x)
$$
LANGUAGE 'plr';
The following CREATE TABLE command uses the r_norm function to populate the table. The r_norm function creates an array of 10 numbers.
CREATE TABLE test_norm_var
AS SELECT id, r_norm(10,0,1) as x
FROM (SELECT generate_series(1,30:: bigint) AS ID) foo
DISTRIBUTED BY (id);
Assuming your PL/R function returns an R data.frame
as its output, unless you want to use arrays of arrays, some work is required to see your data.frame
from PL/R as a simple SQL table:
Create a TYPE
in a Greenplum database with the same dimensions as your R data.frame:
CREATE TYPE t1 AS ...
Use this TYPE
when defining your PL/R function
... RETURNS SET OF t1 AS ...
Sample SQL for this is given in the next example.
The SQL below defines a TYPE
and runs hierarchical regression using PL/R:
--Create TYPE to store model results
DROP TYPE IF EXISTS wj_model_results CASCADE;
CREATE TYPE wj_model_results AS (
cs text, coefext float, ci_95_lower float, ci_95_upper float,
ci_90_lower, float, ci_90_upper float, ci_80_lower,
float, ci_80_upper float);
--Create PL/R function to run model in R
DROP FUNCTION wj.plr.RE(response float [ ], cs text [ ])
RETURNS SETOF wj_model_results AS
$$
library(arm)
y<- log(response)
cs<- cs
d_temp<- data.frame(y,cs)
m0 <- lmer (y ~ 1 + (1 | cs), data=d_temp)
cs_unique<- sort(unique(cs))
n_cs_unique<- length(cs_unique)
temp_m0<- data.frame(matrix0,n_cs_unique, 7))
for (i in 1:n_cs_unique){temp_m0[i,]<-
c(exp(coef(m0)$cs[i,1] + c(0,-1.96,1.96,-1.65,1.65
-1.28,1.28)*se.ranef(m0)$cs[i]))}
names(temp_m0)<- c("Coefest", "CI_95_Lower",
"CI_95_Upper", "CI_90_Lower", "CI_90_Upper",
"CI_80_Lower", "CI_80_Upper")
temp_m0_v2<- data.frames(cs_unique, temp_m0)
return(temp_m0_v2)
$$
LANGUAGE 'plr';
--Run modeling plr function and store model results in a
--table
DROP TABLE IF EXISTS wj_model_results_roi;
CREATE TABLE wj_model_results_roi AS SELECT *
FROM wj.plr_RE((SELECT wj.droi2_array),
(SELECT cs FROM wj.droi2_array));
R packages are modules that contain R functions and data sets. You can install R packages to extend R and PL/R functionality in Greenplum Database.
Greenplum Database provides a collection of data science-related R libraries that can be used with the Greenplum Database PL/R language. You can download these libraries in .gppkg
format from Broadcom Support Portal under the desired Greemplum release. For information about the libraries, see R Data Science Library Package.
NoteFor more information about download prerequisites, troubleshooting, and instructions, see Download Broadcom products and software.
Note: If you expand Greenplum Database and add segment hosts, you must install the R packages in the R installation of the new hosts.
For an R package, identify all dependent R packages and each package web URL. The information can be found by selecting the given package from the following navigation page:
http://cran.r-project.org/web/packages/available_packages_by_name.html
As an example, the page for the R package arm indicates that the package requires the following R libraries: Matrix, lattice, lme4, R2WinBUGS, coda, abind, foreign, and MASS.
You can also try installing the package with R CMD INSTALL
command to determine the dependent packages.
For the R installation included with the Greenplum Database PL/R extension, the required R packages are installed with the PL/R extension. However, the Matrix package requires a newer version.
From the command line, use the wget
utility to download the tar.gz
files for the arm package to the Greenplum Database master host:
wget http://cran.r-project.org/src/contrib/Archive/arm/arm_1.5-03.tar.gz
wget http://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_0.9996875-1.tar.gz
Use the gpscp
utility and the hosts_all
file to copy the tar.gz
files to the same directory on all nodes of the Greenplum Database cluster. The hosts_all
file contains a list of all the Greenplum Database segment hosts. You might require root access to do this.
gpscp -f hosts_all Matrix_0.9996875-1.tar.gz =:/home/gpadmin
gpscp -f /hosts_all arm_1.5-03.tar.gz =:/home/gpadmin
Use the gpssh
utility in interactive mode to log into each Greenplum Database segment host (gpssh -f all_hosts
). Install the packages from the command prompt using the R CMD INSTALL
command. Note that this may require root access. For example, this R install command installs the packages for the arm package.
$R_HOME/bin/R CMD INSTALL Matrix_0.9996875-1.tar.gz arm_1.5-03.tar.gz
Ensure that the package is installed in the $R_HOME/library
directory on all the segments (the gpssh
can be use to install the package). For example, this gpssh
command list the contents of the R library directory.
gpssh -s -f all_hosts "ls $R_HOME/library"
The gpssh
option -s
sources the greenplum_path.sh
file before running commands on the remote hosts.
Test if the R package can be loaded.
This function performs a simple test to if an R package can be loaded:
CREATE OR REPLACE FUNCTION R_test_require(fname text)
RETURNS boolean AS
$BODY$
return(require(fname,character.only=T))
$BODY$
LANGUAGE 'plr';
This SQL command checks if the R package arm can be loaded:
SELECT R_test_require('arm');
You can use the R command line to display information about the installed libraries and functions on the Greenplum Database host. You can also add and remove libraries from the R installation. To start the R command line on the host, log into the host as the gadmin
user and run the script R from the directory $GPHOME/ext/R-3.3.3/bin
.
This R function lists the available R packages from the R command line:
> library()
Display the documentation for a particular R package
> library(help="<package_name>")
> help(package="<package_name>")
Display the help file for an R function:
> help("<function_name>")
> ?<function_name>
To see what packages are installed, use the R command installed.packages()
. This will return a matrix with a row for each package that has been installed. Below, we look at the first 5 rows of this matrix.
> installed.packages()
Any package that does not appear in the installed packages matrix must be installed and loaded before its functions can be used.
An R package can be installed with install.packages()
:
> install.packages("<package_name>")
> install.packages("mypkg", dependencies = TRUE, type="source")
Load a package from the R command line.
> library(" <package_name> ")
An R package can be removed with remove.packages
> remove.packages("<package_name>")
You can use the R command -e
option to run functions from the command line. For example, this command displays help on the R package MASS.
$ R -e 'help("MASS")'
http://www.r-project.org/ - The R Project home page
https://cran.r-project.org/web/packages/PivotalR/ - The home page for PivotalR, a package that provides an R interface to operate on Greenplum Database tables and views that is similar to the R data.frame. PivotalR also supports using the machine learning package MADlib directly from R.
R documentation is installed with the Greenplum R package:
$GPHOME/ext/R-3.3.3/doc