Running R Markdown Server in Background Forever: A Comprehensive Guide

Introduction

The servr package is a popular choice for hosting R Markdown files on servers, and its ability to run scripts in the background makes it an ideal tool for automating tasks. However, managing these background jobs can be challenging, especially when it comes to restarting them upon server restarts. In this article, we will explore the best practices for running servr::rmdv2() in the background forever and provide detailed explanations of the technical concepts involved.

Understanding servr and its usage

Before diving into the details of running servr in the background, let’s take a brief look at how it works. The servr package provides two functions: rmdv2() and rmdv2(). The former is used to serve R Markdown files, while the latter is used to render them.

To run servr in the background, you need to use the rscript command with the path to the servr script. The basic syntax is as follows:

Rscript /path/to/servr.R -d /path/to/your/markdown/files -p 8080

In this example, /path/to/servr.R is the path to the servr script, "/path/to/your/markdown/files" is the directory containing your Markdown files, and -p 8080 specifies the port number on which the server will listen.

Running in background using Rscript

One common approach to running servr in the background is to use the Rscript command. This method involves executing the Rscript command with the path to the servr script, followed by any additional arguments required by the script. However, this method has a significant drawback: it will not restart automatically upon server restarts.

To illustrate this, let’s consider an example:

$ Rscript /path/to/servr.R -d /path/to/your/markdown/files -p 8080 &

In this command, we execute Rscript with the path to the servr script and any additional arguments. The & symbol at the end of the command runs the process in the background.

Running in screen session

Another approach is to run servr in a screen session. This method provides more control over the process than running it directly, as you can easily pause or resume the process using screen commands like Ctrl-A + S.

To illustrate this, let’s consider an example:

$ screen -S myservr Rscript /path/to/servr.R -d /path/to/your/markdown/files -p 8080

In this command, we create a new screen session called myservr, followed by the execution of Rscript with the path to the servr script and any additional arguments.

Using nohup

However, running in a screen session has its own limitations. One common issue is that when the server restarts, the screen session will be terminated, causing the process to exit as well. To address this, we can use the nohup command to run the servr script in the background.

The nohup command is used to run a command even after the process has been terminated. It works by setting up an alias for the command that bypasses the standard signal handling mechanisms.

To illustrate this, let’s consider an example:

$ nohup Rscript /path/to/servr.R -d /path/to/your/markdown/files -p 8080 &

In this command, we execute Rscript with the path to the servr script and any additional arguments. The nohup command runs the process in the background, even if the server restarts.

Using crontab

However, using nohup has its own limitations. One common issue is that it will not automatically restart upon server restarts. To address this, we can use the crontab command to schedule regular executions of the servr script.

The crontab command is used to manage cron jobs, which are scheduled tasks that execute at specific times or intervals. By using crontab, we can create a cron job that runs the servr script periodically and restarts it if necessary.

To illustrate this, let’s consider an example:

$ crontab -e

In this command, we edit the current cron table to add a new entry. The -e option allows us to manually edit the file using our favorite editor.

Next, we can add a new line that runs the servr script every hour, followed by the nohup command and an alias for the script:

@hourly /usr/bin/nohup Rscript /path/to/servr.R -d /path/to/your/markdown/files -p 8080 &

In this entry, we specify that the cron job should execute every hour. The nohup command runs the process in the background, even if the server restarts.

Using flock

However, using crontab has its own limitations. One common issue is that it will not ensure that the servr script does not exit prematurely. To address this, we can use the flock command to synchronize access to shared resources.

The flock command is used to create a lock file that prevents other processes from accessing a resource until the current process releases it. By using flock, we can ensure that the servr script does not exit prematurely.

To illustrate this, let’s consider an example:

$ flock -x /path/to/servr.lock Rscript /path/to/servr.R -d /path/to/your/markdown/files -p 8080 &

In this command, we execute Rscript with the path to the servr script and any additional arguments. The flock command creates a lock file that prevents other processes from accessing the resource until we release it.

Conclusion

Running servr::rmdv2() in the background forever requires careful consideration of various technical concepts, including process management, signal handling, and synchronization. In this article, we have explored several approaches to achieving this goal, including using Rscript, running in a screen session, using nohup, scheduling with crontab, and synchronizing access with flock. By understanding these concepts and techniques, you can develop robust solutions for automating your servr tasks.

Troubleshooting common issues

While the approaches outlined in this article should work in most cases, there are several common issues that you may encounter. Here are some troubleshooting tips to help you resolve these problems:

Issue 1: Process exits prematurely

If your process is exiting prematurely, it’s likely due to a signal handling issue. To address this, try using nohup or flock to synchronize access to shared resources.

$ nohup Rscript /path/to/servr.R -d /path/to/your/markdown/files -p 8080 &

$ flock -x /path/to/servr.lock Rscript /path/to/servr.R -d /path/to/your/markdown/files -p 8080 &

Issue 2: Screen session does not persist

If your screen session does not persist, it’s likely due to a configuration issue. To address this, try checking the following:

Ensure that the screen command is installed and configured correctly.
Verify that the session name is correct and matches the one specified in the command.
Check the default directory for screen sessions and ensure that it aligns with your requirements.

$ screen -S myservr Rscript /path/to/servr.R -d /path/to/your/markdown/files -p 8080

Issue 3: Crontab job does not run periodically

If your crontab job does not run periodically, it’s likely due to a configuration issue. To address this, try checking the following:

Verify that the crontab command is installed and configured correctly.
Check the cron table for syntax errors or incorrect timing settings.
Ensure that the script path is correct and matches the one specified in the entry.

$ crontab -e

Note: The above troubleshooting tips are provided as a general guideline and may need to be adjusted based on your specific environment and requirements.

Last modified on 2023-06-02