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Running a Simple R Script on Bacalhau

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You can use official Docker containers for each language like R or Python. In this example, we will use the official R container and run it on Bacalhau.

In this tutorial example, we will run a "hello world" R script on Bacalhau.

Prerequisites​

To get started, you need to install the Bacalhau client, see more information here

1. Running an R Script Locally​

To install R follow these instructions A Installing R and RStudio | Hands-On Programming with R. After R and RStudio are installed, create and run a script called hello.R:

%%writefile hello.R
print("hello world")

Run the script:

%%bash
Rscript hello.R

Next, upload the script to your public storage (in our case, IPFS). We've already uploaded the script to IPFS and the CID is: QmVHSWhAL7fNkRiHfoEJGeMYjaYZUsKHvix7L54SptR8ie. You can look at this by browsing to one of the HTTP IPFS proxies like ipfs.io or w3s.link.

2. Running a Job on Bacalhau​

Now it's time to run the script on Bacalhau:

%%bash --out job_id
bacalhau docker run \
    --wait \
    --id-only \
    -i ipfs://QmQRVx3gXVLaRXywgwo8GCTQ63fHqWV88FiwEqCidmUGhk:/hello.R \
    r-base \
    -- Rscript hello.R

Structure of the command​

bacalhau docker run: call to Bacalhau

i ipfs://QmQRVx3gXVLaRXywgwo8GCTQ63fHqWV88FiwEqCidmUGhk:/hello.R: Mounting the uploaded dataset at /inputs in the execution. It takes two arguments, the first is the IPFS CID (QmQRVx3gXVLaRXywgwo8GCTQ63fHqWV88FiwEqCidmUGhk) and the second is file path within IPFS (/hello.R)

r-base: docker official image we are using

Rscript hello.R: execute the R script

When a job is submitted, Bacalhau prints out the related job_id. We store that in an environment variable so that we can reuse it later on:

%env JOB_ID={job_id}

3. Checking the State of your Jobs​

Job status: You can check the status of the job using bacalhau list.

%%bash
bacalhau list --id-filter ${JOB_ID}

When it says Published or Completed, that means the job is done, and we can get the results.

Job information: You can find out more information about your job by using bacalhau describe.

%%bash
bacalhau describe  ${JOB_ID}

Job download: You can download your job results directly by using bacalhau get. Alternatively, you can choose to create a directory to store your results. In the command below, we created a directory (results) and downloaded our job output to be stored in that directory.

%%bash
rm -rf results && mkdir results
bacalhau get ${JOB_ID} --output-dir results

4. Viewing your Job Output​

To view the file, run the following command:

%%bash
cat results/stdout

Futureproofing your R Scripts​

You can generate the job request using bacalhau describe with the --spec flag. This will allow you to re-run that job in the future:

%%bash
bacalhau describe ${JOB_ID} --spec > job.yaml
%%bash
cat job.yaml

Support​

If you have questions or need support or guidance, please reach out to the Bacalhau team via Slack (#general channel).