---
title: "Creating a Singularity Container to Run HuggingFace Transformers Models in R"
output: github_document #rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Singularity_Container}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

[Singularity](https://apptainer.org/) is a container engine alternative to Docker. Singularity containers are well suited for the requirements of High Performance Computing (HPC) workloads.

A container contains all code as well as *all* its dependencies so that the an application runs reliably on different computers (or different computing environments). It can be used to run on servers or as a way to ensure computational reproducibility (that the code run on other systems, and in the future). For an introduction to the concept of containers see [Computational Reproducibility via Containers in Psychology](https://open.lnu.se/index.php/metapsychology/article/view/892/). Below is code to build a Singularity container for setting up transformers language models from HuggingFace and running the ```text```-package.

## Code to build a singularity container with HuggingFace models in R

``` 
Bootstrap: docker
From: ubuntu:20.04

%environment
  export LANG=C.UTF-8 LC_ALL=C.UTF-8
  export XDG_RUNTIME_DIR=/tmp/.run_$(uuidgen)

%post
    # Install
    apt-get -y update

    export R_VERSION=4.2.2
    echo "export R_VERSION=${R_VERSION}" >> $SINGULARITY_ENVIRONMENT

     # Install R
     apt-get update
     apt-get install -y --no-install-recommends software-properties-common dirmngr  wget uuid-runtime
     wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | \
       tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
     add-apt-repository \
       "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
     apt-get install -y --no-install-recommends \
     r-base=${R_VERSION}* \
     r-base-core=${R_VERSION}* \
     r-base-dev=${R_VERSION}* \
     r-recommended=${R_VERSION}* \
     r-base-html=${R_VERSION}* \
     r-doc-html=${R_VERSION}* \
     libcurl4-openssl-dev \
     libharfbuzz-dev \
     libfribidi-dev \
     libgit2-dev \
     libxml2-dev \
     libfontconfig1-dev \
     libssl-dev \
     libxml2-dev \
     libfreetype6-dev \
     libpng-dev \
     libtiff5-dev \
     libjpeg-dev
     
     # Add a default CRAN mirror
     echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/lib/R/etc/Rprofile.site

     # Fix R package libpaths (helps RStudio Server find the right directories)
     mkdir -p /usr/lib64/R/etc
     echo "R_LIBS_USER='/usr/lib64/R/library'" >> /usr/lib64/R/etc/Renviron
     echo "R_LIBS_SITE='${R_PACKAGE_DIR}'" >> /usr/lib64/R/etc/Renviron
     # Clean up
     rm -rf /var/lib/apt/lists/*

     # Install python3
     apt-get -y install python3 wget
     apt-get -y clean

     # Install Miniconda
     cd /
     wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
     bash Miniconda3-latest-Linux-x86_64.sh -b -p /miniconda

/bin/bash <<EOF
     rm Miniconda3-latest-Linux-x86_64.sh
     source /miniconda/etc/profile.d/conda.sh
     conda update -y conda
     # Install reticulate and text
         Rscript -e 'install.packages("pkgdown")'
     Rscript -e 'install.packages("ragg")'
     Rscript -e 'install.packages("textshaping")'
     Rscript -e 'install.packages("reticulate")'
     Rscript -e 'install.packages("devtools")'
     Rscript -e 'install.packages("glmnet")'
     Rscript -e 'install.packages("tidyverse")'
#     Rscript -e 'install.packages("text")'
     Rscript -e 'devtools::install_github("oscarkjell/text")'
     # Create the Conda environment at a system folder
     Rscript -e 'text::textrpp_install(prompt = FALSE, rpp_version = c("torch==1.11.0", "transformers==4.19.2", "numpy", "nltk"))'
     Rscript -e 'text::textrpp_initialize(save_profile = TRUE, prompt = FALSE, textEmbed_test = TRUE)'
     Rscript -e 'text::textEmbed("hello", model = "distilbert-base-uncased", layers = 5)'
     Rscript -e 'text::textEmbed("hello", model = "roberta-base", layers = 11)'

```

 
