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andyatmiamiandyatmiami
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feat(upgrade): bi-annual RStudio package update
This commit is related to the ongoing work to release the `2025a` software upgrade. Upgrades: - `R` - `4.4.1` -> `4.4.3` - `RStudio` - rstudio-server-rhel-2024.04.2-764-x86_64.rpm -> rstudio-server-rhel-2024.12.1-563-x86_64.rpm - `tidymodels` - `1.2.0` -> `1.3.0` - `plumber` - `1.2.2` -> `1.3.0` A couple other "quality of life" improvements were included: - Refactored `Dockerfile` to combine `RUN` statements where obvious/low-risk - Better use of `ARG` references to reduce copy-pasta in `Dockerfile` instructions - `install_packages.R` script externalizes the userland software installs in an external script to better "share" across `cpu` + `cuda` `Dockerfile` variants - Fixed issue(s) with `kustomize` `cuda` `overlay` so now `kubectl apply -k overlays/accelerator/cuda` works Related-to: https://issues.redhat.com/browse/RHOAIENG-19484
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‎rstudio/c9s-python-3.11/Dockerfile.cpu

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@@ -46,7 +46,7 @@ LABEL name="odh-notebook-rstudio-server-c9s-python-3.11" \
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USER 0
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ENV R_VERSION=4.4.1
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ENV R_VERSION=4.4.3
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# Install R
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RUN yum install -y yum-utils && \
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yum -y clean all --enablerepo='*'
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# set R library to default (used in install.r from littler)
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RUN chmod -R a+w /usr/lib64/R/library
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ENV LIBLOC=/usr/lib64/R/library
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# set User R Library path
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RUN mkdir -p /opt/app-root/bin/Rpackages/4.4 && chmod -R a+w /opt/app-root/bin/Rpackages/4.4
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ENV R_LIBS_USER=/opt/app-root/bin/Rpackages/4.4
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RUN chmod -R a+w ${LIBLOC} && \
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# create User R Library path
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mkdir -p ${R_LIBS_USER} && \
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chmod -R a+w ${R_LIBS_USER}
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WORKDIR /tmp/
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# Install RStudio
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RUN wget --progress=dot:giga https://download2.rstudio.org/server/rhel9/x86_64/rstudio-server-rhel-2024.04.2-764-x86_64.rpm && \
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yum install -y rstudio-server-rhel-2024.04.2-764-x86_64.rpm && \
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rm rstudio-server-rhel-2024.04.2-764-x86_64.rpm && \
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yum -y clean all --enablerepo='*'
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# Specific RStudio config and fixes
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RUN chmod 1777 /var/run/rstudio-server && \
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mkdir -p /usr/share/doc/R
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ARG RSTUDIO_RPM=rstudio-server-rhel-2024.12.1-563-x86_64.rpm
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RUN wget --progress=dot:giga https://download2.rstudio.org/server/rhel8/x86_64/${RSTUDIO_RPM} && \
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yum install -y ${RSTUDIO_RPM} && \
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rm ${RSTUDIO_RPM} && \
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yum -y clean all --enablerepo='*' && \
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# Specific RStudio config and fixes
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chmod 1777 /var/run/rstudio-server && \
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mkdir -p /usr/share/doc/R && \
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# package installation
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# install necessary texlive-framed package to make Knit R markup to PDF rendering possible
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dnf install -y libsodium-devel.x86_64 libgit2-devel.x86_64 libcurl-devel harfbuzz-devel.x86_64 fribidi-devel.x86_64 cmake "flexiblas-*" texlive-framed && \
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dnf clean all && \
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rm -rf /var/cache/yum
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COPY ${RSTUDIO_SOURCE_CODE}/rsession.conf /etc/rstudio/rsession.conf
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# package installation
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# install necessary texlive-framed package to make Knit R markup to PDF rendering possible
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RUN dnf install -y libsodium-devel.x86_64 libgit2-devel.x86_64 libcurl-devel harfbuzz-devel.x86_64 fribidi-devel.x86_64 cmake "flexiblas-*" texlive-framed \
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&& dnf clean all && rm -rf /var/cache/yum
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# Install R packages
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RUN R -e "install.packages('remotes')"
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RUN R -e "require('remotes'); \
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remotes::install_version('Rcpp','1.0.14'); \
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remotes::install_version('tidyverse','2.0.0'); \
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remotes::install_version('tidymodels','1.2.0'); \
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remotes::install_version('plumber','1.2.2'); \
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remotes::install_version('vetiver','0.2.5'); \
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remotes::install_version('devtools','2.4.5');"
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# https://cran.r-project.org/web/packages
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COPY ${RSTUDIO_SOURCE_CODE}/install_packages.R ./
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RUN R -f ./install_packages.R && \
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rm ./install_packages.R
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# Install NGINX to proxy RStudio and pass probes check
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ENV NGINX_VERSION=1.24 \

‎rstudio/c9s-python-3.11/Dockerfile.cuda

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@@ -137,7 +137,7 @@ RUN yum install -y \
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${NV_CUDNN_PACKAGE_DEV} \
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&& yum clean all \
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&& rm -rf /var/cache/yum/*
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# Set this flag so that libraries can find the location of CUDA
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ENV XLA_FLAGS=--xla_gpu_cuda_data_dir=/usr/local/cuda
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@@ -170,7 +170,7 @@ LABEL name="odh-notebook-rstudio-server-cuda-c9s-python-3.11" \
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USER 0
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ENV R_VERSION=4.4.1
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ENV R_VERSION=4.4.3
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# Install R
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RUN yum install -y yum-utils && \
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yum -y clean all --enablerepo='*'
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# set R library to default (used in install.r from littler)
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RUN chmod -R a+w /usr/lib64/R/library
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ENV LIBLOC=/usr/lib64/R/library
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# set User R Library path
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RUN mkdir -p /opt/app-root/bin/Rpackages/4.4 && chmod -R a+w /opt/app-root/bin/Rpackages/4.4
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ENV R_LIBS_USER=/opt/app-root/bin/Rpackages/4.4
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RUN chmod -R a+w ${LIBLOC} && \
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# create User R Library path
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mkdir -p ${R_LIBS_USER} && \
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chmod -R a+w ${R_LIBS_USER}
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WORKDIR /tmp/
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# Install RStudio
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RUN wget --progress=dot:giga https://download2.rstudio.org/server/rhel9/x86_64/rstudio-server-rhel-2024.04.2-764-x86_64.rpm && \
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yum install -y rstudio-server-rhel-2024.04.2-764-x86_64.rpm && \
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rm rstudio-server-rhel-2024.04.2-764-x86_64.rpm && \
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yum -y clean all --enablerepo='*'
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# Specific RStudio config and fixes
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RUN chmod 1777 /var/run/rstudio-server && \
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mkdir -p /usr/share/doc/R
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ARG RSTUDIO_RPM=rstudio-server-rhel-2024.12.1-563-x86_64.rpm
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RUN wget --progress=dot:giga https://download2.rstudio.org/server/rhel8/x86_64/${RSTUDIO_RPM} && \
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yum install -y ${RSTUDIO_RPM} && \
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rm ${RSTUDIO_RPM} && \
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yum -y clean all --enablerepo='*' && \
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# Specific RStudio config and fixes
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chmod 1777 /var/run/rstudio-server && \
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mkdir -p /usr/share/doc/R && \
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# package installation
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# install necessary texlive-framed package to make Knit R markup to PDF rendering possible
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dnf install -y libsodium-devel.x86_64 libgit2-devel.x86_64 libcurl-devel harfbuzz-devel.x86_64 fribidi-devel.x86_64 cmake "flexiblas-*" texlive-framed && \
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dnf clean all && \
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rm -rf /var/cache/yum
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COPY ${RSTUDIO_SOURCE_CODE}/rsession.conf /etc/rstudio/rsession.conf
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# package installation
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# install necessary texlive-framed package to make Knit R markup to PDF rendering possible
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RUN dnf install -y libsodium-devel.x86_64 libgit2-devel.x86_64 libcurl-devel harfbuzz-devel.x86_64 fribidi-devel.x86_64 cmake "flexiblas-*" texlive-framed \
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&& dnf clean all && rm -rf /var/cache/yum
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# Install R packages
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RUN R -e "install.packages('remotes')"
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RUN R -e "require('remotes'); \
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remotes::install_version('Rcpp','1.0.14'); \
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remotes::install_version('tidyverse','2.0.0'); \
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remotes::install_version('tidymodels','1.2.0'); \
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remotes::install_version('plumber','1.2.2'); \
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remotes::install_version('vetiver','0.2.5'); \
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remotes::install_version('devtools','2.4.5');"
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# https://cran.r-project.org/web/packages
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COPY ${RSTUDIO_SOURCE_CODE}/install_packages.R ./
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RUN R -f ./install_packages.R && \
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rm ./install_packages.R
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# Install NGINX to proxy RStudio and pass probes check
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ENV NGINX_VERSION=1.24 \

‎rstudio/c9s-python-3.11/install_packages.R

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# install_packages.R
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# Load or install 'remotes' package
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if (!requireNamespace("remotes", quietly = TRUE)) {
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install.packages("remotes")
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}
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# Install specific versions of packages
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remotes::install_version('Rcpp', '1.0.14')
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remotes::install_version('tidyverse', '2.0.0')
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remotes::install_version('tidymodels', '1.3.0')
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remotes::install_version('plumber', '1.3.0')
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remotes::install_version('vetiver', '0.2.5')
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remotes::install_version('devtools', '2.4.5')

‎rstudio/c9s-python-3.11/kustomize/components/accelerator/pod-patch.yaml

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name: pod
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spec:
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containers:
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- name: runtime
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- name: rstudio
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resources:
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limits:
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memory: 6Gi

‎rstudio/c9s-python-3.11/kustomize/overlays/accelerator/cuda/pod-patch.yaml

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@@ -7,7 +7,7 @@ spec:
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nodeSelector:
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accelerator: cuda
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containers:
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- name: runtime
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- name: rstudio
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resources:
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limits:
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nvidia.com/gpu: '1'

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