- Use custom R libraries on OSG
- Getting Help
This tutorial describes how to create custom R libraries for use in jobs on OSG Connect.
The material in this tutorial builds up on the [Run R Scripts on OSG] (https://support.opensciencegrid.org/support/solutions/articles/12000056217-run-r-scripts-on-osg) tutorial. If you are not already familiar with how to run R jobs on OSG Connect, please see that tutorial first.
Use custom R libraries on OSG
Often we may need to add R external libraries that are not part of the base R installation. As a user, we could add the libraries in our home (or stash) directory and then compress the library to make them available on remote machines for job executions.
Setup Workflow Files
First we'll need to create a working directory, you can either run
$ tutorial R-addlib or type the following:
$ mkdir tutorial-R-addlib $ cd tutorial-R-addlib
In the previous tutorial, recall that we created the script
that contained the following:
We also created a wrapper script called
R-wrapper.sh to execute our R
script. The contents of that file is shown below:
#!/bin/bash module load r Rscript --no-save hello_world.R
Finally, we had the
R.submit submit script which we used to submit the
job to OSG Connect:
universe = vanilla log = R.log.$(Cluster).$(Process) error = R.err.$(Cluster).$(Process) output = R.out.$(Cluster).$(Process) executable = R-wrapper.sh transfer_input_files = hello_world.R request_cpus = 1 request_memory = 1GB request_disk = 1GB requirements = OSGVO_OS_STRING == "RHEL 7" && Arch == "X86_64" && HAS_MODULES == True queue 1
Build external packages for R under userspace
It is helpful to create a dedicated directory to install the package
into. This will facilitate zipping the library so it can be transported
with the job. Say, you decided to built the library in the path
/home/username/R_libs/lubridate_R.3.5. If it does not already exist,
make the necessary directory by typing the following in your shell prompt:
$ mkdir -p ~/R_libs/lubridate_R.3.5
After defining the path, we set the
R_LIBS environment variable so R
knows where to find our custom library directory:
$ export R_LIBS=~/R_libs/lubridate_R.3.5
Now we can run R and check that our library location is being used (here
> is the R-prompt):
$ module load r $ R ... > .libPaths()  "/home/user/R_libs/lubridate_R.3.5"  "/cvmfs/connect.opensciencegrid.org/modules/packages/linux-rhel7-x86_64/gcc-6.4.0spack/r-3.5.1-eoot7bzcbxp3pwf4dxlqrssdk7clylwd/rlib/R/library"
Excellent. We can see the location listed as library path
. We can
also check for available libraries within R.
q to close that display.
To install packages within R, we use the command (where “XYZ” is the name of the target package):
> install.packages("XYZ", repos = "http://cloud.r-project.org/", dependencies = TRUE)
For this tutorial, we are going to use the
lubridate package. To install
lubridate, enter this command:
> install.packages("lubridate", repos="http://cloud.r-project.org/", dependencies=TRUE)
Install multiple packages at once
If you have multiple packages to be added, it may be better to list each of
install.packages() commands within a separate R script and source the
file to R. For example, if we needed to install
tidyr, we can list them to be installed in a script called
which would contain the following:
install.packages("ggplot2", repos="http://cloud.r-project.org/", dependencies = TRUE) install.packages("dplyr", repos="http://cloud.r-project.org/", dependencies = TRUE) install.packages("tidyr", repos="http://cloud.r-project.org/", dependencies = TRUE)
Then, install all of the packages by running the setup file within R:
Prepare a tarball of the add-on packages
Proceeding with the
lubridate package, the next step is create a tarball of
the package so we can send the tarball along with the job.
Exit from the R prompt by typing:
In either case, be sure to say
n when prompted to
Save workspace image? [y/n/c]:.
To tar the package directory, type the following at the shell prompt:
$ cd /home/user/R_libs $ tar -cvzf lubridate_R.3.5.tar.gz lubridate_R.3.5
Now copy the tarball to the job directory where the R program, job wrapper script and condor job description file are.
Use the packages in your OSG job
Now, let's change the
hello_world job to use the new package. First, modify the
hello_world.R R script by adding the following lines:
This will add a print out of the local date to the output of the job.
Define the libPaths() in the wrapper script
R library locations are set upon launch and can be modified using the
environmental variable. To set this correctly, we need to modify the wrapper script.
Change the file
R-wrapper.sh so it matches the following:
#!/bin/bash module load r # Uncompress the tarball tar -xzf lubridate_R.3.5.tar.gz # Set the library location export R_LIBS="$PWD/lubridate_R.3.5" # run the R program Rscript --no-save hello_world.R
Once you have edited the file, make the wrapper script executable and test it by using the commands below:
$ chmod +x R-wrapper.sh $ ./R-wrapper.sh  "Hello World!"
Next, we need to modify the submit script so that the package tarball is
transferred correctly with the job. Change the submit script
R.submit so that
arguments are set correctly. The completed file,
which can bee seen in
R.submit should look like below:
universe = vanilla log = R.log.$(Cluster).$(Process) error = R.err.$(Cluster).$(Process) output = R.out.$(Cluster).$(Process) executable = R-wrapper.sh transfer_input_files = lubridate_R.3.5.tar.gz, hello_world.R request_cpus = 1 request_memory = 1GB request_disk = 1GB requirements = OSGVO_OS_STRING == "RHEL 7" && Arch == "X86_64" && HAS_MODULES == True queue 1
Job submission and output
Now we are ready to submit the job:
$ condor_submit R.submit
and check the job status:
$ condor_q username
Once the job finished running, check the output files as before. They should now look like this:
$ cat R.out.3796676.0  "2019-05-13"  "Hello World!"
This page was updated on Dec 22, 2020 at 22:54 from tutorials/tutorial-R-addlibSNA/README.md.