From 2fe2e0571bbfeb5e9f993205808a1b034e9794ac Mon Sep 17 00:00:00 2001
From: Tony Kew <tony.d.r.kew@gmail.com>
Date: Thu, 23 Oct 2025 17:18:26 -0400
Subject: [PATCH 1/8] Initial commit of R Rocker Project container files

Tony
---
 .../R-Rocker_Project/R_rocker_4.5.1.def       | 232 ++++++++++++++++++
 .../R-Rocker_Project/estimate_pi.R            |  30 +++
 .../R-Rocker_Project/slurm_ARM64_example.bash |  34 +++
 .../R-Rocker_Project/slurm_example.bash       |  35 +++
 4 files changed, 331 insertions(+)
 create mode 100644 containers/2_ApplicationSpecific/R-Rocker_Project/R_rocker_4.5.1.def
 create mode 100644 containers/2_ApplicationSpecific/R-Rocker_Project/estimate_pi.R
 create mode 100755 containers/2_ApplicationSpecific/R-Rocker_Project/slurm_ARM64_example.bash
 create mode 100755 containers/2_ApplicationSpecific/R-Rocker_Project/slurm_example.bash

diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/R_rocker_4.5.1.def b/containers/2_ApplicationSpecific/R-Rocker_Project/R_rocker_4.5.1.def
new file mode 100644
index 00000000..8df8784e
--- /dev/null
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/R_rocker_4.5.1.def
@@ -0,0 +1,232 @@
+Bootstrap: docker
+From: ghcr.io/rocker-org/r-ver:4.5.1
+
+%post -c /bin/bash
+  # Set the timezone, if unset
+  test -h /etc/localtime || ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime
+
+  cp /etc/apt/sources.list /etc/apt/sources.list~
+  sed -E -i 's/^# deb-src /deb-src /' /etc/apt/sources.list
+  apt-get -y update
+
+  # Install man & man pages - this section can be removed if not needed
+  # NOTE: Do this before installing anything else so their man pages are installed
+  sed -e '\|/usr/share/man|s|^#*|#|g' -i /etc/dpkg/dpkg.cfg.d/excludes
+  DEBIAN_FRONTEND=noninteractive apt-get -y install apt-utils groff dialog man-db manpages manpages-posix manpages-dev
+  rm -f /usr/bin/man
+  dpkg-divert --quiet --remove --rename /usr/bin/man
+
+  # O/S package updates:
+  DEBIAN_FRONTEND=noninteractive apt-get -y upgrade
+
+  DEBIAN_FRONTEND=noninteractive apt-get -y install \
+   bash-completion \
+   ca-certificates \
+   tzdata \
+   locales \
+   zip \
+   unzip \
+   wget \
+   git \
+   libgit2-dev \
+   subversion \
+   gawk \
+   file \
+   gnupg2 \
+   gpg \
+   gpg-agent \
+   libssh2-1-dev \
+   libsasl2-dev \
+   build-essential \
+   autoconf \
+   automake \
+   pkg-config \
+   cmake \
+   cmake-data \
+   cmake-extras \
+   cmake-format \
+   libclang-dev \
+   python3 \
+   python3-pip \
+   python3-setuptools \
+   python3-sphinx \
+   python3-sphinx-rtd-theme \
+   python3-dev \
+   python-is-python3 \
+   libpython3-dev \
+   devscripts \
+   perl \
+   zstd \
+   gnulib \
+   libicu-dev \
+   libssl-dev \
+   zlib1g-dev \
+   libzstd-dev \
+   libbz2-dev \
+   lbzip2 \
+   xz-utils \
+   libncurses5-dev \
+   libncursesw5-dev \
+   libreadline-dev \
+   liblzma-dev \
+   liblz4-tool \
+   libcurl4-gnutls-dev \
+   libdeflate-dev \
+   libx11-dev \
+   x11proto-core-dev \
+   xfonts-base \
+   xvfb \
+   xauth \
+   xtail \
+   xzdec \
+   libxt-dev \
+   libxt6 \
+   libxtst6 \
+   xorg-dev \
+   fonts-roboto \
+   fonts-texgyre \
+   gsfonts \
+   ghostscript \
+   libpng-dev \
+   libtiff5-dev \
+   libfreetype6-dev \
+   libjpeg-dev \
+   libjpeg-turbo8-dev \
+   libjq-dev \
+   liblzma-dev \
+   texinfo \
+   texlive \
+   texlive-base \
+   texlive-fonts-recommended \
+   texlive-fonts-extra \
+   texlive-font-utils \
+   texlive-lang-all \
+   texlive-extra-utils \
+   texlive-latex-recommended \
+   texlive-latex-extra \
+   libpcre2-posix3 \
+   libpcre2-dev \
+   openjdk-21-jdk-headless \
+   nvidia-cuda-dev \
+   nvidia-cuda-toolkit \
+   libxml2-dev \
+   libudunits2-dev \
+   libgdal-dev \
+   libharfbuzz-dev \
+   libfribidi-dev \
+   libmagick++-dev \
+   libgsl-dev \
+   libfftw3-dev \
+   libcairo2-dev \
+   libpango1.0-dev \
+   libgmp-dev \
+   tk-dev \
+   tcl-dev \
+   libmpfr-dev \
+   libnetcdf-dev \
+   libhdf4-alt-dev \
+   libhdf5-dev \
+   libhts3 \
+   libhts-dev \
+   libhtscodecs2 \
+   libhtscodecs-dev \
+   libopenblas64-0 \
+   libopenblas64-dev \
+   liblapack3 \
+   liblapack-dev \
+   liblapacke-dev \
+   libscalapack-openmpi-dev \
+   openmpi-bin \
+   openmpi-common \
+   libopenmpi-dev \
+   libpmix2t64 \
+   libpmix-dev \
+   libgl1-mesa-dev \
+   libglpk-dev \
+   libglu1-mesa-dev \
+   libgmp3-dev \
+   libgsl0-dev \
+   gdebi-core \
+   libgeos-dev \
+   libhunspell-dev \
+   libpq-dev \
+   libproj-dev \
+   libprotobuf-dev \
+   protobuf-compiler \
+   libsqlite3-dev \
+   unixodbc-dev \
+   sqlite3 \
+   libv8-dev \
+   libzmq3-dev \
+   postgis \
+   psmisc \
+   hugo \
+   swig \
+   curl \
+   jq \
+   nano \
+   vim \
+   less \
+   apt-file
+
+  # NOTE: apt-file is generally not needed to run, but can be useful during development
+  apt-file update
+
+  # These steps are necessary to configure Perl and can cause issues with Python if omitted
+  sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
+  dpkg-reconfigure --frontend=noninteractive locales
+  update-locale LANG=en_US.UTF-8
+
+  # Libraries in /usr/local/lib
+  # Include files in /usr/local/include
+  export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib"
+  export CFLAGS="${CFLAGS} -I/usr/local/include"
+  export CPPFLAGS="${CPPFLAGS} -I/usr/local/include"
+  export CXXFLAGS="${CXXFLAGS} -I/usr/local/include"
+  export FFLAGS="${FFLAGS} -I/usr/local/include"
+  export LDFLAGS="${LDFLAGS} -L/usr/local/lib -Xlinker -rpath -Xlinker \"/usr/local/lib\""
+  export CMAKE_BUILD_PARALLEL_LEVEL="$(nproc)"
+  pip_install_dir="$(python3 -c 'import sys; print("/usr/local/lib/python" + str(sys.version_info.major) + "." + str(sys.version_info.minor) + "/dist-packages")')"
+  export PYTHONPATH="${pip_install_dir}:${PYTHONPATH}"
+  export PATH="${PATH}:${pip_install_dir}/bin"
+
+  # distro from the Ubuntu package clashes with the one from pip
+  DEBIAN_FRONTEND=noninteractive apt-get -y remove python3-distro
+  pip install --prefix="/usr" distro setuptools
+
+  # make sure TMPDIR is on a local filesystem
+  export TMPDIR="${SLURMTMPDIR:-/var/tmp}"
+  # container setting required from some builds:
+  export container="oci"
+  # CUDA installed with Ubuntu packages, so set CUDA_HOME to /usr
+  export CUDA_HOME="/usr"
+
+  R --version
+
+###  # Sample code to add R packages from CRAN inside this container
+###  for package in \
+###    Rcpp \
+###    RcppEigen
+###  do
+###    R -e "install.packages(pkgs = \"${package}\", repos = \"https://cran.r-project.org\",
+###     lib = \"/usr/local/lib/R/library\", type = \"source\", dependencies = TRUE)"
+###  done
+
+%environment
+  # make sure TMPDIR is on a local filesystem
+  export TMPDIR="${SLURMTMPDIR:-/var/tmp}"
+  # container setting required from some builds:
+  export container="oci"
+  # CUDA installed with Ubuntu packages, so set CUDA_HOME to /usr
+  export CUDA_HOME="/usr"
+  export LANG=en_US.UTF-8 
+  export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/lib"
+  export PYTHONPATH="$(python3 -c 'import sys; print("/usr/local/lib/python" + str(sys.version_info.major) + "." + str(sys.version_info.minor) + "/dist-packages")'):${PYTHONPATH}"
+  export PATH="$(python3 -c 'import sys; print("/usr/local/lib/python" + str(sys.version_info.major) + "." + str(sys.version_info.minor) + "/dist-packages/bin")'):${PATH}"
+
+%runscript
+  #!/bin/bash
+  export PS1="rocker-R> "
+  # Exec passed command (required for Modal ENTRYPOINT compatibility)
+  exec "$@"
+
diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/estimate_pi.R b/containers/2_ApplicationSpecific/R-Rocker_Project/estimate_pi.R
new file mode 100644
index 00000000..78636356
--- /dev/null
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/estimate_pi.R
@@ -0,0 +1,30 @@
+#
+# Estimating Pi Using Monte Carlo Simulation in R
+# by Andrea Gustafsen
+#
+# https://rpubs.com/andrea_gustafsen/839901
+#
+estimate_pi <- function(seed = 28, iterations = 1000){
+    # set seed for reproducibility
+    set.seed(seed)
+    
+    # generate the (x, y) points
+    x <- runif(n = iterations, min = 0, max = 1)
+    y <- runif(n = iterations, min = 0, max = 1)
+    
+    # calculate 
+    sum_sq_xy <- sqrt(x^2 + y^2) 
+    
+    # see how many points are within circle
+    index_within_circle <- which(sum_sq_xy <= 1)
+    points_within_circle = length(index_within_circle)
+    
+    # estimate pi
+    pi_est <- 4 * points_within_circle / iterations
+    return(pi_est)
+}
+no_of_iterations <- c(10, 100, 1000, 10000, 100000, 1000000, 10000000, 100000000, 1000000000)
+res <- sapply(no_of_iterations, function(n)estimate_pi(iterations = n))
+names(res) <- no_of_iterations
+res
+
diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_ARM64_example.bash b/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_ARM64_example.bash
new file mode 100755
index 00000000..597a51e5
--- /dev/null
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_ARM64_example.bash
@@ -0,0 +1,34 @@
+#!/bin/bash -l
+
+## This file is intended to serve as a template to be downloaded and modified for your use case.
+## For more information, refer to the following resources whenever referenced in the script-
+## README- https://github.com/ubccr/ccr-examples/tree/main/slurm/README.md
+## DOCUMENTATION- https://docs.ccr.buffalo.edu/en/latest/hpc/jobs
+
+#SBATCH --cluster="ub-hpc"
+#SBATCH --partition="arm64"
+#SBATCH --qos="arm64"
+
+## Select an account that has access to the arm64 partition (see `slimits | grep arm64`)
+#SBATCH --account="[SlurmAccountName]"
+
+## Job runtime limit, the job will be canceled once this limit is reached. Format- dd-hh:mm:ss
+#SBATCH --time=00:20:00
+
+## NOTE: R uses only one core, unless you specifically use functions that take
+##       advantage of multiple cores, such as the 'parallel' package.
+##       This example allocates 6 cores, so apptainer has a thread for itself,
+##       plus a thread for each bind mount, leaving one core for the R process
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=6
+#SBATCH --mem=36GB
+
+R_version="4.5.1"
+
+# Run containerized R
+apptainer run \
+ -B /projects:/projects,/scratch:/scratch,/util:/util,/vscratch:/vscratch \
+ R_rocker_${R_version}-$(arch).sif \
+ Rscript estimate_pi.R
+
diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_example.bash b/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_example.bash
new file mode 100755
index 00000000..3ee0a945
--- /dev/null
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_example.bash
@@ -0,0 +1,35 @@
+#!/bin/bash -l
+
+## This file is intended to serve as a template to be downloaded and modified for your use case.
+## For more information, refer to the following resources whenever referenced in the script-
+## README- https://github.com/ubccr/ccr-examples/tree/main/slurm/README.md
+## DOCUMENTATION- https://docs.ccr.buffalo.edu/en/latest/hpc/jobs
+
+## Select a cluster, partition, qos and account that is appropriate for your use case
+## Available options and more details are provided in CCR's documentation:
+##   https://docs.ccr.buffalo.edu/en/latest/hpc/jobs/#slurm-directives-partitions-qos
+#SBATCH --cluster="[cluster]"
+#SBATCH --partition="[partition]"
+#SBATCH --qos="[qos]"
+#SBATCH --account="[SlurmAccountName]"
+
+## Job runtime limit, the job will be canceled once this limit is reached. Format- dd-hh:mm:ss
+#SBATCH --time=00:20:00
+
+## NOTE: R uses only one core, unless you specifically use functions that take
+##       advantage of multiple cores, such as the 'parallel' package.
+##       This example allocates 6 cores, so apptainer has a thread for itself,
+##       plus a thread for each bind mount, leaving one core for the R process
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=6
+#SBATCH --mem=36GB
+
+R_version="4.5.1"
+
+# Run containerized R
+apptainer run \
+ -B /projects:/projects,/scratch:/scratch,/util:/util,/vscratch:/vscratch \
+ R_rocker_${R_version}-$(arch).sif \
+ Rscript estimate_pi.R
+

From bc4b384d6e41f6bf1cca58395ba8fb5606626772 Mon Sep 17 00:00:00 2001
From: Tony Kew <tony.d.r.kew@gmail.com>
Date: Thu, 23 Oct 2025 17:34:36 -0400
Subject: [PATCH 2/8] Added new documentation files

Tony
---
 .../R-Rocker_Project/BUILD-ARM64.md           | 243 ++++++++++++++++
 .../R-Rocker_Project/EXAMPLE.md               | 102 +++++++
 .../R-Rocker_Project/README.md                | 266 ++++++++++++++++++
 .../R-Rocker_Project/SLURM_ARM64_EXAMPLE.md   |  84 ++++++
 .../R-Rocker_Project/SLURM_EXAMPLE.md         |  75 +++++
 5 files changed, 770 insertions(+)
 create mode 100644 containers/2_ApplicationSpecific/R-Rocker_Project/BUILD-ARM64.md
 create mode 100644 containers/2_ApplicationSpecific/R-Rocker_Project/EXAMPLE.md
 create mode 100644 containers/2_ApplicationSpecific/R-Rocker_Project/README.md
 create mode 100644 containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md
 create mode 100644 containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md

diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/BUILD-ARM64.md b/containers/2_ApplicationSpecific/R-Rocker_Project/BUILD-ARM64.md
new file mode 100644
index 00000000..acf1f279
--- /dev/null
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/BUILD-ARM64.md
@@ -0,0 +1,243 @@
+# Build the R_rocker container on ARM64
+
+
+## Building the container
+
+1. Start an interactive job on an ARM64 node
+
+```
+tmp_file="$(mktemp)"
+salloc --partition=arm64 --qos=arm64 --constraint=ARM64 --no-shell \
+ --exclusive --time=1:00:00 2>&1 | tee "${tmp_file}"
+SLURM_JOB_ID="$(head -1 "${tmp_file}" | awk '{print $NF}')"
+rm "${tmp_file}"
+srun --jobid="${SLURM_JOB_ID}" --export=HOME,TERM,SHELL --pty /bin/bash --login
+```
+
+sample outout:
+
+> ```
+> salloc: Pending job allocation 22171515
+> salloc: job 22171515 queued and waiting for resources
+> salloc: job 22171515 has been allocated resources
+> salloc: Granted job allocation 22171515
+> salloc: Nodes cpn-f06-38 are ready for job
+> CCRusername@cpn-f06-38:~$ 
+> ```
+
+2. Navigate to your build directory and use the Slurm job local temporary directory for cache
+
+
+Change to your R directory
+
+```
+cd /projects/academic/[YourGroupName]/R
+```
+
+Then set the apptainer cache dir:
+
+```
+export APPTAINER_CACHEDIR=${SLURMTMPDIR}
+```
+
+The `R_rocker_4.5.1.def` file will already be in the directory if you have already built
+on the x86_64 platform, if not, download the .def file:
+
+```
+test -f R_rocker_4.5.1.def || curl -o R_rocker_4.5.1.def https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/R_rocker_4.5.1.def
+```
+
+sample output:
+
+> ```
+>   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
+>                                  Dload  Upload   Total   Spent    Left  Speed
+> 100  6126  100  6126    0     0   103k      0 --:--:-- --:--:-- --:--:--  104k
+> ```
+
+
+3. Build your container
+
+Building the R container takes about ten minutes
+
+```
+apptainer build --fakeroot R_rocker_4.5.1-$(arch).sif R_rocker_4.5.1.def
+```
+
+sample truncated output:
+
+> ```
+> [....]
+> INFO:    Adding environment to container
+> INFO:    Creating SIF file...
+> INFO:    Build complete: R_rocker_4.5.1-aarch64.sif
+> ```
+
+Quick test of the new container .sif image
+
+```
+apptainer run \
+ -B /projects:/projects,/scratch:/scratch,/util:/util,/vscratch:/vscratch \
+ R_rocker_4.5.1-$(arch).sif \
+ R --version
+````
+
+Sample output:
+
+> ```
+> R version 4.5.1 (2025-06-13) -- "Great Square Root"
+> Copyright (C) 2025 The R Foundation for Statistical Computing
+> Platform: x86_64-pc-linux-gnu
+> 
+> R is free software and comes with ABSOLUTELY NO WARRANTY.
+> You are welcome to redistribute it under the terms of the
+> GNU General Public License versions 2 or 3.
+> For more information about these matters see
+> https://www.gnu.org/licenses/.
+> 
+> ```
+
+Exit the Slurm interactive session
+
+```
+exit
+```
+
+sample output:
+
+> ```
+> CCRusername@login1$ 
+> ```
+
+End the Slurm job
+
+```
+scancel "${SLURM_JOB_ID}"
+unset SLURM_JOB_ID
+``` 
+
+4. Running the container
+
+Start an interactive job on an ARM64 node
+Notes: 
+  R uses only one core, unless you specifically use functions that take
+  advantage of multiple cores, such as the 'parallel' package.  This example
+  allocates 6 cores, so apptainer has a thread for itself, plus a thread for
+  each bind mount, leaving one core for the R process.  Request more cores if
+  you are running parallel code.
+
+  If you use R packages that uses CUDA, add the Slurm directive to request
+  GPU(s) e.g. "--gpus-per-node=1" and add tht "--nv" opion to apptainer so the
+  requested GPU(s) are available inside the container.
+
+```
+tmp_file="$(mktemp)"
+salloc --partition=arm64 --qos=arm64 --constraint=ARM64 --no-shell \
+ --nodes=1 --ntasks-per-node=1 --cpus-per-task=6 --mem=32GB \
+ --time=1:00:00 2>&1 | tee "${tmp_file}"
+SLURM_JOB_ID="$(head -1 "${tmp_file}" | awk '{print $NF}')"
+rm "${tmp_file}"
+srun --jobid="${SLURM_JOB_ID}" --export=HOME,TERM,SHELL --pty /bin/bash --login
+```
+
+sample outout:
+
+> ```
+> salloc: Pending job allocation 22171524
+> salloc: job 22171524 queued and waiting for resources
+> salloc: job 22171524 has been allocated resources
+> salloc: Granted job allocation 22171524
+> salloc: Nodes cpn-f06-38 are ready for job
+> CCRusername@cpn-f06-38:~$
+> ```
+
+Change to your R directory
+
+```
+cd /projects/academic/[YourGroupName]/R
+```
+
+Start the R container instance
+
+```
+apptainer shell \
+ -B /projects:/projects,/scratch:/scratch,/util:/util,/vscratch:/vscratch \
+ ./R_rocker_4.5.1-$(arch).sif
+```
+
+All the following commands are run from the "Apptainer> " prompt
+run R
+
+```
+R
+```
+
+Sampleoutput:
+
+> ```
+> 
+> R version 4.5.1 (2025-06-13) -- "Great Square Root"
+> Copyright (C) 2025 The R Foundation for Statistical Computing
+> Platform: x86_64-pc-linux-gnu
+> 
+> R is free software and comes with ABSOLUTELY NO WARRANTY.
+> You are welcome to redistribute it under certain conditions.
+> Type 'license()' or 'licence()' for distribution details.
+> 
+>   Natural language support but running in an English locale
+> 
+> R is a collaborative project with many contributors.
+> Type 'contributors()' for more information and
+> 'citation()' on how to cite R or R packages in publications.
+> 
+> Type 'demo()' for some demos, 'help()' for on-line help, or
+> 'help.start()' for an HTML browser interface to help.
+> Type 'q()' to quit R.
+> 
+> > 
+> ```
+
+exit R from the ">" prompt with:
+
+```
+q()
+```
+
+Expected output
+
+> ```
+> Apptainer> 
+> ```
+
+Exit the Apptainer container instance
+From the "Apptainer>" prompt:
+
+```
+exit
+```
+
+sample output:
+> ```
+> CCRusername@cpn-d01-39~$ 
+> ```
+
+Exit the Slurm interactive session
+
+```
+exit
+```
+
+sample output:
+
+> ```
+> logout
+> CCRusername@login1$ 
+> ```
+
+End the Slurm job
+
+```
+scancel "${SLURM_JOB_ID}"
+unset SLURM_JOB_ID
+```
+
diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/EXAMPLE.md b/containers/2_ApplicationSpecific/R-Rocker_Project/EXAMPLE.md
new file mode 100644
index 00000000..aa2db49a
--- /dev/null
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/EXAMPLE.md
@@ -0,0 +1,102 @@
+# R_rocker Example
+
+Start an interactive job in the "debug" partition
+
+```
+tmp_file="$(mktemp)"
+salloc --cluster=ub-hpc --partition=debug --qos=debug --no-shell \
+ --nodes=1 --cpus-per-task=1 --tasks-per-node=6 --mem=36GB \
+ --account="[SlurmAccountName]" --time=1:00:00 2>&1 | tee "${tmp_file}"
+SLURM_JOB_ID="$(head -1 "${tmp_file}" | awk '{print $NF}')"
+rm "${tmp_file}"
+srun --jobid="${SLURM_JOB_ID}" --export=HOME,TERM,SHELL --pty /bin/bash --login
+```
+
+sample outout:
+
+> ```
+> salloc: Pending job allocation 22172066
+> salloc: job 22172066 queued and waiting for resources
+> salloc: job 22172066 has been allocated resources
+> salloc: Granted job allocation 22172066
+> salloc: Nodes cpn-d01-39 are ready for job
+> CCRusername@cpn-d01-39~$ 
+> ```
+
+Change to your R directory
+
+```
+cd /projects/academic/[YourGroupName]/R
+```
+
+Start the R container instance
+
+```
+apptainer shell \
+ -B /projects:/projects,/scratch:/scratch,/util:/util,/vscratch:/vscratch \
+ ./R_rocker_4.5.1-$(arch).sif
+```
+
+Download the exmaple R script [estimate_pi.R](https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/estimate_pi.R)
+This code is writen by Andrea Gustafsen - see:
+https://rpubs.com/andrea_gustafsen/839901
+
+```
+test -f estimate_pi.R || curl -o estimate_pi.R https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/estimate_pi.R
+```
+
+sample output:
+
+> ```
+>   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
+>                                  Dload  Upload   Total   Spent    Left  Speed
+> 100   874  100   874    0     0   7536      0 --:--:-- --:--:-- --:--:--  7600
+> ```
+
+Run the R script
+Note: This script takes about 2 minutes to run, during which there is no output
+
+```
+Rscript estimate_pi.R
+```
+
+Sample output:
+
+> ```
+>       10      100     1000    10000    1e+05    1e+06    1e+07    1e+08 
+> 2.400000 3.160000 3.184000 3.158400 3.138760 3.143816 3.141868 3.141650 
+>    1e+09 
+> 3.141679 
+> ```
+
+Exit the Apptainer container instance
+From the "Apptainer>" prompt:
+
+```
+exit
+```
+
+sample output:
+> ```
+> CCRusername@cpn-d01-39~$ 
+> ```
+
+Exit the Slurm interactive session
+
+```
+exit
+```
+
+sample output:
+
+> ```
+> CCRusername@login1$ 
+> ```
+
+End the Slurm job
+
+```
+scancel "${SLURM_JOB_ID}"
+unset SLURM_JOB_ID
+``` 
+
diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/README.md b/containers/2_ApplicationSpecific/R-Rocker_Project/README.md
new file mode 100644
index 00000000..ea8131de
--- /dev/null
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/README.md
@@ -0,0 +1,266 @@
+# Example R container, based on the Rocker Project "r-ver" image
+
+The [Rocker Project](https://rocker-project.org) provides a number of [GPL 2 or later](https://opensource.org/license/gpl-2-0) licenced ["R" containers](https://rocker-project.org/images/) 
+This example is based on the [r-ver](https://rocker-project.org/images/versioned/r-ver.html) image which is, in turn, based on the [r-base](https://hub.docker.com/_/r-base) 
+offical R image 
+The [r-ver](https://rocker-project.org/images/versioned/r-ver.html) image uses Ubuntu LTS rather than Debian, with an emphasis on 
+reproducibility.
+
+
+## Building the container
+
+A brief guide to building the R_rocker container follows:<br/>
+Please refer to CCR's [container documentation](https://docs.ccr.buffalo.edu/en/latest/howto/containerization/) for more detailed information on building and using Apptainer.
+
+NOTE: for building on the ARM64 platform see [BUILD-ARM64.md](./BUILD-ARM64.md)
+
+1. Start an interactive job
+
+Apptainer is not available on the CCR login nodes and the compile nodes may not provide enough resources for you to build a container.  We recommend requesting an interactive job on a compute node to conduct this build process.<br/>
+See CCR docs for more info on [running jobs](https://docs.ccr.buffalo.edu/en/latest/hpc/jobs/#interactive-job-submission)
+
+```
+tmp_file="$(mktemp)"
+salloc --cluster=ub-hpc --partition=debug --qos=debug --no-shell --exclusive \
+ --account="[SlurmAccountName]" --mem=0 --time=1:00:00 2>&1 | tee "${tmp_file}"
+SLURM_JOB_ID="$(head -1 "${tmp_file}" | awk '{print $NF}')"
+rm "${tmp_file}"
+srun --jobid="${SLURM_JOB_ID}" --export=HOME,TERM,SHELL --pty /bin/bash --login
+```
+
+sample outout:
+
+> ```
+> salloc: Pending job allocation 22171515
+> salloc: job 22171515 queued and waiting for resources
+> salloc: job 22171515 has been allocated resources
+> salloc: Granted job allocation 22171515
+> salloc: Nodes cpn-d01-39 are ready for job
+> CCRusername@pn-d01-39:~$ 
+> ```
+
+2. Navigate to your build directory and use the Slurm job local temporary directory for cache
+
+You should now be on the compute node allocated to you. 
+In this example we're using our project directory for our build directory.
+
+Change to your R directory
+
+```
+cd /projects/academic/[YourGroupName]/R
+```
+
+Then set the apptainer cache dir:
+
+```
+export APPTAINER_CACHEDIR=${SLURMTMPDIR}
+```
+
+Download the .def file
+
+```
+test -f R_rocker_4.5.1.def || curl -o R_rocker_4.5.1.def https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/R_rocker_4.5.1.def
+```
+
+sample output:
+
+> ```
+>   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
+>                                  Dload  Upload   Total   Spent    Left  Speed
+> 100  6126  100  6126    0     0  97501      0 --:--:-- --:--:-- --:--:-- 98806
+> ```
+
+3. Build your container
+
+Building the R container takes about ten minutes
+
+```
+apptainer build --fakeroot R_rocker_4.5.1-$(arch).sif R_rocker_4.5.1.def
+```
+
+sample truncated output:
+
+> ```
+> [....]
+> INFO:    Adding environment to container
+> INFO:    Creating SIF file...
+> INFO:    Build complete: R_rocker_4.5.1-x86_64.sif
+> ```
+
+Quick test of the new container .sif image
+
+```
+apptainer run \
+ -B /projects:/projects,/scratch:/scratch,/util:/util,/vscratch:/vscratch \
+ R_rocker_4.5.1-$(arch).sif \
+ R --version
+````
+
+Sample output:
+
+> ```
+> R version 4.5.1 (2025-06-13) -- "Great Square Root"
+> Copyright (C) 2025 The R Foundation for Statistical Computing
+> Platform: x86_64-pc-linux-gnu
+> 
+> R is free software and comes with ABSOLUTELY NO WARRANTY.
+> You are welcome to redistribute it under the terms of the
+> GNU General Public License versions 2 or 3.
+> For more information about these matters see
+> https://www.gnu.org/licenses/.
+> 
+> ```
+
+Exit the Slurm interactive session
+
+```
+exit
+```
+
+sample output:
+
+> ```
+> CCRusername@login1$ 
+> ```
+
+End the Slurm job
+
+```
+scancel "${SLURM_JOB_ID}"
+unset SLURM_JOB_ID
+``` 
+
+4. Running the container
+
+Start an interactive job e.g.
+
+```
+tmp_file="$(mktemp)"
+salloc --cluster=ub-hpc --partition=general-compute --qos=general-compute \
+ --no-shell --mem=128GB --nodes=1 --cpus-per-task=1 --tasks-per-node=12 \
+ --account="[SlurmAccountName]" --time=5:00:00 2>&1 | tee "${tmp_file}"
+SLURM_JOB_ID="$(head -1 "${tmp_file}" | awk '{print $NF}')"
+rm "${tmp_file}"
+srun --jobid="${SLURM_JOB_ID}" --export=HOME,TERM,SHELL --pty /bin/bash --login
+```
+
+sample outout:
+
+> ```
+> salloc: Pending job allocation 22171524
+> salloc: job 22171524 queued and waiting for resources
+> salloc: job 22171524 has been allocated resources
+> salloc: Granted job allocation 22171524
+> salloc: Nodes cpn-d01-19 are ready for job
+> ```
+
+Change to your R directory
+
+```
+cd /projects/academic/[YourGroupName]/R
+```
+
+Start the R container instance
+
+```
+apptainer shell \
+ -B /projects:/projects,/scratch:/scratch,/util:/util,/vscratch:/vscratch \
+ ./R_rocker_4.5.1-$(arch).sif
+```
+
+All the following commands are run from the "Apptainer> " prompt
+run R
+
+```
+R
+```
+
+Sampleoutput:
+
+> ```
+> 
+> R version 4.5.1 (2025-06-13) -- "Great Square Root"
+> Copyright (C) 2025 The R Foundation for Statistical Computing
+> Platform: x86_64-pc-linux-gnu
+> 
+> R is free software and comes with ABSOLUTELY NO WARRANTY.
+> You are welcome to redistribute it under certain conditions.
+> Type 'license()' or 'licence()' for distribution details.
+> 
+>   Natural language support but running in an English locale
+> 
+> R is a collaborative project with many contributors.
+> Type 'contributors()' for more information and
+> 'citation()' on how to cite R or R packages in publications.
+> 
+> Type 'demo()' for some demos, 'help()' for on-line help, or
+> 'help.start()' for an HTML browser interface to help.
+> Type 'q()' to quit R.
+> 
+> > 
+> ```
+
+exit R from the ">" prompt with:
+
+```
+q()
+```
+
+Expected output
+
+> ```
+> Apptainer> 
+> ```
+
+Exit the Apptainer container instance
+From the "Apptainer>" prompt:
+
+```
+exit
+```
+
+sample output:
+> ```
+> CCRusername@cpn-d01-39~$ 
+> ```
+
+Exit the Slurm interactive session
+
+```
+exit
+```
+
+sample output:
+
+> ```
+> logout
+> CCRusername@login1$ 
+> ```
+
+End the Slurm job
+
+```
+scancel "${SLURM_JOB_ID}"
+unset SLURM_JOB_ID
+```
+
+
+See the [EXAMPLES file](./EXAMPLES.md) for more info.
+
+## Sample Slurm scripts
+
+Slurm script examples:
+
+### x86_64 example
+[R example](https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_example.bash)  
+
+### ARM64 example
+[R ARM64 example](https://raw.githubusercontent.com/ubccr/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_ARM64_example.bash)  
+
+
+## Documentation Resources
+
+For more information on R see the [R project website](https://www.r-project.org), the [R Documentation](https://www.r-project.org/other-docs.html),
+the [Rocker Project website](https://rocker-project.org), the [Rocker Project Images](https://rocker-project.org/images), 
+and the [Rocker Project Versioned 2 github repo](https://github.com/rocker-org/rocker-versioned2)
+
diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md
new file mode 100644
index 00000000..e4079a20
--- /dev/null
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md
@@ -0,0 +1,84 @@
+# R_rocker ARM64 Slurm example
+
+Change to your R directory
+
+```
+cd /projects/academic/[YourGroupName]/R
+```
+
+Download the slurm sample scrip and the exmaple R script [estimate_pi.R](https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/estimate_pi.R)
+The example code is writen by Andrea Gustafsen - see:
+https://rpubs.com/andrea_gustafsen/839901
+
+```
+test -f estimate_pi.R || curl -o estimate_pi.R https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/estimate_pi.R
+test -f slurm_ARM64_example.bash || curl -o slurm_ARM64_example.bash https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_ARM64_example.bash
+```
+
+sample output:
+
+> ```
+>   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
+>                                  Dload  Upload   Total   Spent    Left  Speed
+> 100   874  100   874    0     0  14616      0 --:--:-- --:--:-- --:--:-- 14813
+>   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
+>                                  Dload  Upload   Total   Spent    Left  Speed
+> 100  1268  100  1268    0     0   9810      0 --:--:-- --:--:-- --:--:--  9829
+> ```
+
+Modify the Slurm script - change the account to one that has access to the
+"arm64" partition (see `slimits | grep arm64`)
+
+For example:
+
+```
+slimits | grep arm64
+```
+
+sample output:
+
+> ```
+>     ub-hpc         ccradmintest   tkewtest                      	arm64,class,debug,eai-test,general-compute,industry,scavenger,viz
+> ```
+
+So my test account has access to the "arm64" partition using the account
+"ccradmintest"
+
+```
+cat slurm_ARM64_example.bash
+```
+
+abridged sample output:
+
+> ```
+> [...]
+#SBATCH --account="ccradmintest"
+> [...]
+> ```
+
+Submit the Slurm script
+
+```
+sbatch ./slurm_ARM64_example.bash
+```
+
+sample output:
+
+> ```
+> Submitted batch job 22173297 on cluster ub-hpc
+> ```
+
+The Slurm output file in this case is slurm-22173297.out
+Once this Slurm job completed:
+
+```
+cat slurm-22173297.out
+```
+
+> ```
+>       10      100     1000    10000    1e+05    1e+06    1e+07    1e+08 
+> 2.400000 3.160000 3.184000 3.158400 3.138760 3.143816 3.141868 3.141650 
+>    1e+09 
+> 3.141679 
+> ```
+
diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md
new file mode 100644
index 00000000..be1dabb7
--- /dev/null
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md
@@ -0,0 +1,75 @@
+# R_rocker Slurm example
+
+Change to your R directory
+
+```
+cd /projects/academic/[YourGroupName]/R
+```
+
+Download the slurm sample scrip and the exmaple R script [estimate_pi.R](https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/estimate_pi.R)
+The example code is writen by Andrea Gustafsen - see:
+https://rpubs.com/andrea_gustafsen/839901
+
+```
+test -f estimate_pi.R || curl -o estimate_pi.R https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/estimate_pi.R
+test -f slurm_example.bash || curl -o slurm_example.bash https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_example.bash
+```
+
+sample output:
+
+> ```
+>   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
+>                                  Dload  Upload   Total   Spent    Left  Speed
+> 100   874  100   874    0     0  14577      0 --:--:-- --:--:-- --:--:-- 14813
+>   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
+>                                  Dload  Upload   Total   Spent    Left  Speed
+> 100  1434  100  1434    0     0  12964      0 --:--:-- --:--:-- --:--:-- 13036
+> ```
+
+Modify the Slurm script - change the cluster, partition, qos and account
+You can use the `slimits` command to see what accounts and QOS settings yoa
+have access to.
+
+For example:
+
+```
+cat slurm_example.bash
+```
+
+abridged sample output:
+
+> ```
+> [...]
+#SBATCH --cluster="ub-hpc"
+#SBATCH --partition="debug"
+#SBATCH --qos="debug"
+#SBATCH --account="ccradmintest"
+> [...]
+> ```
+
+Submit the Slurm script
+
+```
+sbatch ./slurm_example.bash
+```
+
+sample output:
+
+> ```
+> Submitted batch job 22173265 on cluster ub-hpc
+> ```
+
+The Slurm output file in this case is slurm-22173265.out
+Once this Slurm job completed:
+
+```
+cat slurm-22173265.out
+```
+
+> ```
+>       10      100     1000    10000    1e+05    1e+06    1e+07    1e+08 
+> 2.400000 3.160000 3.184000 3.158400 3.138760 3.143816 3.141868 3.141650 
+>    1e+09 
+> 3.141679 
+> ```
+

From 522f4fd456abf0a08a8a66db21e6e7c289d1ffc3 Mon Sep 17 00:00:00 2001
From: Tony Kew <tony.d.r.kew@gmail.com>
Date: Thu, 23 Oct 2025 17:44:41 -0400
Subject: [PATCH 3/8] Added links to Slurm example docs & updated the menu
 README.md

Tony
---
 containers/2_ApplicationSpecific/R-Rocker_Project/README.md | 6 ++++--
 containers/2_ApplicationSpecific/README.md                  | 1 +
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/README.md b/containers/2_ApplicationSpecific/R-Rocker_Project/README.md
index ea8131de..c8532833 100644
--- a/containers/2_ApplicationSpecific/R-Rocker_Project/README.md
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/README.md
@@ -252,10 +252,12 @@ See the [EXAMPLES file](./EXAMPLES.md) for more info.
 Slurm script examples:
 
 ### x86_64 example
-[R example](https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_example.bash)  
+[R x86_64 Slurm example script](https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_example.bash)  
+[Docs for running the R x86_64 Slurm example script](./SLURM_EXAMPLE.md)  
 
 ### ARM64 example
-[R ARM64 example](https://raw.githubusercontent.com/ubccr/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_ARM64_example.bash)  
+[R ARM64 Slurm example script](https://raw.githubusercontent.com/ubccr/ccr-examples/refs/heads/R-Rocker_Project/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_ARM64_example.bash)  
+[Docs for running the R ARM64 Slurm example script](./SLURM_ARM64_EXAMPLE.md)  
 
 
 ## Documentation Resources
diff --git a/containers/2_ApplicationSpecific/README.md b/containers/2_ApplicationSpecific/README.md
index 25c4ef32..8bcd2327 100644
--- a/containers/2_ApplicationSpecific/README.md
+++ b/containers/2_ApplicationSpecific/README.md
@@ -17,6 +17,7 @@ Please refer to CCR's [container documentation](https://docs.ccr.buffalo.edu/en/
 | [OpenFF-Toolkit](./Open_Force_Field_toolkit)  | Open Force Field toolkit container with steps for building and running via Apptainer |
 | [OpenFOAM](./OpenFOAM)               | OpenFOAM container with steps for building and running via Apptainer and Slurm |
 | [OpenSees](./OpenSees)               | OpenSees container with steps for building and running via Apptainer |
+| [R - Rocker Project](./R-Rocker_Project) | R container based on the Rocker Project "r-ver" image - Apptainer build, run and Slurm scripts |
 | [SAS](./sas)                         | Guide for running SAS using Apptainer via Slurm batch script, command line, and GUI access |
 | [Seurat](./seurat)                   | Seurat container with example scRNA analysis |
 | [VASP](./vasp)                       | Example VASP container with steps for building and running via Apptainer |

From e5aebfd28fe80ce37b120c309d79c5981657ee6e Mon Sep 17 00:00:00 2001
From: Tony Kew <tony.d.r.kew@gmail.com>
Date: Thu, 23 Oct 2025 17:51:59 -0400
Subject: [PATCH 4/8] Fix formatting

Tony
---
 .../R-Rocker_Project/SLURM_ARM64_EXAMPLE.md               | 2 +-
 .../R-Rocker_Project/SLURM_EXAMPLE.md                     | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md
index e4079a20..119f7144 100644
--- a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md
@@ -52,7 +52,7 @@ abridged sample output:
 
 > ```
 > [...]
-#SBATCH --account="ccradmintest"
+> #SBATCH --account="ccradmintest"
 > [...]
 > ```
 
diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md
index be1dabb7..92b2c0d4 100644
--- a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md
@@ -40,10 +40,10 @@ abridged sample output:
 
 > ```
 > [...]
-#SBATCH --cluster="ub-hpc"
-#SBATCH --partition="debug"
-#SBATCH --qos="debug"
-#SBATCH --account="ccradmintest"
+> #SBATCH --cluster="ub-hpc"
+> #SBATCH --partition="debug"
+> #SBATCH --qos="debug"
+> #SBATCH --account="ccradmintest"
 > [...]
 > ```
 

From 4285c493ed99193d8ce50a27bb3cd1666215a201 Mon Sep 17 00:00:00 2001
From: Tony Kew <tony.d.r.kew@gmail.com>
Date: Fri, 24 Oct 2025 10:06:49 -0400
Subject: [PATCH 5/8] Fixed ARM64 slurm script

Tony
---
 .../R-Rocker_Project/SLURM_ARM64_EXAMPLE.md                 | 6 +++---
 .../R-Rocker_Project/slurm_ARM64_example.bash               | 4 +++-
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md
index 119f7144..a5c70554 100644
--- a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md
@@ -65,14 +65,14 @@ sbatch ./slurm_ARM64_example.bash
 sample output:
 
 > ```
-> Submitted batch job 22173297 on cluster ub-hpc
+> Submitted batch job 22179954 on cluster ub-hpc
 > ```
 
-The Slurm output file in this case is slurm-22173297.out
+The Slurm output file in this case is slurm-22179954.out
 Once this Slurm job completed:
 
 ```
-cat slurm-22173297.out
+cat slurm-22179954.out
 ```
 
 > ```
diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_ARM64_example.bash b/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_ARM64_example.bash
index 597a51e5..5850b589 100755
--- a/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_ARM64_example.bash
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/slurm_ARM64_example.bash
@@ -8,8 +8,10 @@
 #SBATCH --cluster="ub-hpc"
 #SBATCH --partition="arm64"
 #SBATCH --qos="arm64"
+## Make sure the x86_64 (head node) environment is not used on the ARM64 node
+#SBATCH --export=HOME,TERM,SHELL
 
-## Select an account that has access to the arm64 partition (see `slimits | grep arm64`)
+## Select an account that has access to the arm64 partition (see "slimits | grep arm64")
 #SBATCH --account="[SlurmAccountName]"
 
 ## Job runtime limit, the job will be canceled once this limit is reached. Format- dd-hh:mm:ss

From 02ee512cf884fe4d947bb00b86fa61c56163122f Mon Sep 17 00:00:00 2001
From: Tony Kew <tony.d.r.kew@gmail.com>
Date: Fri, 24 Oct 2025 10:31:56 -0400
Subject: [PATCH 6/8] Clarify "slimits" output & fix a typo

Tony
---
 .../R-Rocker_Project/SLURM_ARM64_EXAMPLE.md                   | 4 ++--
 .../2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md   | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md
index a5c70554..bf67b923 100644
--- a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md
@@ -41,8 +41,8 @@ sample output:
 >     ub-hpc         ccradmintest   tkewtest                      	arm64,class,debug,eai-test,general-compute,industry,scavenger,viz
 > ```
 
-So my test account has access to the "arm64" partition using the account
-"ccradmintest"
+The second field in the Slurm account name, so my test account has access to
+the "arm64" partition using the account "ccradmintest"
 
 ```
 cat slurm_ARM64_example.bash
diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md
index 92b2c0d4..73cc0c57 100644
--- a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md
@@ -27,7 +27,7 @@ sample output:
 > ```
 
 Modify the Slurm script - change the cluster, partition, qos and account
-You can use the `slimits` command to see what accounts and QOS settings yoa
+You can use the `slimits` command to see what accounts and QOS settings you
 have access to.
 
 For example:

From 03cf084ae7824c4c9102d4952dba13035cc92672 Mon Sep 17 00:00:00 2001
From: Tony Kew <tony.d.r.kew@gmail.com>
Date: Fri, 24 Oct 2025 18:24:20 -0400
Subject: [PATCH 7/8] Added "slimits" examples for Slurm account information

Use SALLOC_ACCOUNT for the Slurm account name so the following
"salloc" code block can be copied & pasted without change.

Tried using SALLOC_[...] variables for all the "salloc" settings,
infortunately there are not SALLOC veraibles for several
"salloc" options such as "--nodes=" "--ntasks-per-node=" and
"--cpus-per-task="

The end result may be worse than before...

Tony
---
 .../R-Rocker_Project/BUILD-ARM64.md           | 44 ++++++++-
 .../R-Rocker_Project/EXAMPLE.md               | 34 ++++++-
 .../R-Rocker_Project/README.md                | 95 ++++++++++++++++---
 .../R-Rocker_Project/SLURM_ARM64_EXAMPLE.md   |  8 +-
 .../R-Rocker_Project/SLURM_EXAMPLE.md         |  2 +-
 5 files changed, 163 insertions(+), 20 deletions(-)

diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/BUILD-ARM64.md b/containers/2_ApplicationSpecific/R-Rocker_Project/BUILD-ARM64.md
index acf1f279..a4c9f52d 100644
--- a/containers/2_ApplicationSpecific/R-Rocker_Project/BUILD-ARM64.md
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/BUILD-ARM64.md
@@ -5,6 +5,36 @@
 
 1. Start an interactive job on an ARM64 node
 
+You can use the `slimits` command to see what accounts and QOS settings you
+have access to.
+
+To find which Slurm account you can use to run an interactive job in the "arm64"
+partition:
+
+```
+slimits | grep "arm64"
+```
+
+sample output:
+
+> ```
+>     ub-hpc         SlurmAccountName   CCRusername                      	arm64,debug,general-compute,scavenger,viz
+> ```
+
+The second field in the Slurm account name, so my test account has access to
+the "arm64" partition using the account "SlurmAccountName"
+
+Set the environment variable "SBATCH_ACCOUNT" to the Slurm account you want
+to use.
+e.g.
+
+```
+export SBATCH_ACCOUNT="SlurmAccountName"
+```
+
+You can now start an interactive job in the "arm64" partition with the 
+following:
+
 ```
 tmp_file="$(mktemp)"
 salloc --partition=arm64 --qos=arm64 --constraint=ARM64 --no-shell \
@@ -113,7 +143,7 @@ End the Slurm job
 
 ```
 scancel "${SLURM_JOB_ID}"
-unset SLURM_JOB_ID
+unset SLURM_JOB_ID SBATCH_ACCOUNT
 ``` 
 
 4. Running the container
@@ -130,6 +160,16 @@ Notes:
   GPU(s) e.g. "--gpus-per-node=1" and add tht "--nv" opion to apptainer so the
   requested GPU(s) are available inside the container.
 
+Set the Slurm account you want to use for this interactive job (see `slimits`
+for the account(s) you can use
+
+```
+export SBATCH_ACCOUNT="SlurmAccountName"
+```
+
+You can now start an interactive job in the "arm64" partition with the
+following:
+
 ```
 tmp_file="$(mktemp)"
 salloc --partition=arm64 --qos=arm64 --constraint=ARM64 --no-shell \
@@ -238,6 +278,6 @@ End the Slurm job
 
 ```
 scancel "${SLURM_JOB_ID}"
-unset SLURM_JOB_ID
+unset SLURM_JOB_ID SBATCH_ACCOUNT
 ```
 
diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/EXAMPLE.md b/containers/2_ApplicationSpecific/R-Rocker_Project/EXAMPLE.md
index aa2db49a..1d7889a3 100644
--- a/containers/2_ApplicationSpecific/R-Rocker_Project/EXAMPLE.md
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/EXAMPLE.md
@@ -2,11 +2,41 @@
 
 Start an interactive job in the "debug" partition
 
+You can use the `slimits` command to see what accounts and QOS settings you
+have access to.
+
+To find which Slurm account you can use to run an interactive job in the debug
+partition:
+
+```
+slimits | grep "debug"
+```
+
+sample output:
+
+> ```
+>     ub-hpc         SlurmAccountName   CCRusername                      	arm64,debug,general-compute,scavenger,viz
+> ```
+
+The second field in the Slurm account name, so this example has access to the
+"debug" partition using the Slurm account "SlurmAccountName"
+
+Set the environment variable "SBATCH_ACCOUNT" to the Slurm account you want
+to use.
+e.g.
+
+```
+export SBATCH_ACCOUNT="SlurmAccountName"
+```
+
+You can now start an interactive job in the "debug" partition with the 
+following:
+
 ```
 tmp_file="$(mktemp)"
 salloc --cluster=ub-hpc --partition=debug --qos=debug --no-shell \
  --nodes=1 --cpus-per-task=1 --tasks-per-node=6 --mem=36GB \
- --account="[SlurmAccountName]" --time=1:00:00 2>&1 | tee "${tmp_file}"
+ --time=1:00:00 2>&1 | tee "${tmp_file}"
 SLURM_JOB_ID="$(head -1 "${tmp_file}" | awk '{print $NF}')"
 rm "${tmp_file}"
 srun --jobid="${SLURM_JOB_ID}" --export=HOME,TERM,SHELL --pty /bin/bash --login
@@ -97,6 +127,6 @@ End the Slurm job
 
 ```
 scancel "${SLURM_JOB_ID}"
-unset SLURM_JOB_ID
+unset SLURM_JOB_ID SBATCH_ACCOUNT
 ``` 
 
diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/README.md b/containers/2_ApplicationSpecific/R-Rocker_Project/README.md
index c8532833..8b76d305 100644
--- a/containers/2_ApplicationSpecific/R-Rocker_Project/README.md
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/README.md
@@ -10,19 +10,62 @@ reproducibility.
 ## Building the container
 
 A brief guide to building the R_rocker container follows:<br/>
-Please refer to CCR's [container documentation](https://docs.ccr.buffalo.edu/en/latest/howto/containerization/) for more detailed information on building and using Apptainer.
+Please refer to CCR's [container documentation](https://docs.ccr.buffalo.edu/en/latest/howto/containerization/) for more detailed information on
+building and using Apptainer.
 
 NOTE: for building on the ARM64 platform see [BUILD-ARM64.md](./BUILD-ARM64.md)
 
-1. Start an interactive job
+1. Start an interactive job in the "debug" partition
 
-Apptainer is not available on the CCR login nodes and the compile nodes may not provide enough resources for you to build a container.  We recommend requesting an interactive job on a compute node to conduct this build process.<br/>
+Apptainer is not available on the CCR login nodes and the compile nodes may not
+provide enough resources for you to build a container.  We recommend requesting
+an interactive job on a compute node to conduct this build process.<br/>
 See CCR docs for more info on [running jobs](https://docs.ccr.buffalo.edu/en/latest/hpc/jobs/#interactive-job-submission)
 
+You can use the `slimits` command to see what accounts and QOS settings you
+have access to.
+For example, to find the Slurm accoun(s) you can use to run an interactive job
+in the "debug" partition:
+
+```
+slimits | grep "debug"
+```
+
+sample output:
+
+> ```
+>     ub-hpc         SlurmAccountName   CCRusername                      	arm64,debug,general-compute,scavenger,viz
+> ```
+
+The second field in the Slurm account name, so this example has access to the
+"debug" partition using the Slurm account "SlurmAccountName"
+
+Set the environment variable "SALLOC_ACCOUNT" to the Slurm account you want
+to use.
+e.g.
+
+```
+export SALLOC_ACCOUNT="SlurmAccountName"
+```
+
+The following variables will request exclusive use of a "debug" partition node
+for an hour with the salloc comand that follows
+
+```
+export SALLOC_CLUSTERS="ub-hpc"
+export SALLOC_PARTITION="debug"
+export SALLOC_QOS="debug"
+export SALLOC_EXCLUSIVE=""
+export SALLOC_MEM_PER_NODE="0"
+export SALLOC_TIMELIMIT="01:00:00"
+```
+
+You can now start an interactive job in the "debug" partition with the 
+following:
+
 ```
 tmp_file="$(mktemp)"
-salloc --cluster=ub-hpc --partition=debug --qos=debug --no-shell --exclusive \
- --account="[SlurmAccountName]" --mem=0 --time=1:00:00 2>&1 | tee "${tmp_file}"
+salloc --nodes=1 --no-shell 2>&1 | tee "${tmp_file}"
 SLURM_JOB_ID="$(head -1 "${tmp_file}" | awk '{print $NF}')"
 rm "${tmp_file}"
 srun --jobid="${SLURM_JOB_ID}" --export=HOME,TERM,SHELL --pty /bin/bash --login
@@ -123,22 +166,52 @@ sample output:
 > CCRusername@login1$ 
 > ```
 
-End the Slurm job
+End the Slurm job and remove the environment variables set for the job
 
 ```
 scancel "${SLURM_JOB_ID}"
 unset SLURM_JOB_ID
+eval $(set | grep ^SALLOC_ | awk -F= '{print "unset " $1}')
 ``` 
 
 4. Running the container
 
-Start an interactive job e.g.
+Start an interactive job - the following example uses the "general-compute"
+partition
+
+To find which Slurm account you can use to run an interactive job in the
+"general-compute" partition:
+
+```
+slimits | grep "general-compute"
+```
+
+sample output:
+
+> ```
+>     ub-hpc         SlurmAccountName   CCRusername                      	arm64,debug,general-compute,scavenger,viz
+> ```
+
+
+The second field in the Slurm account name, so this example has access to the
+"general-compute" partition using the Slurm account "SlurmAccountName"
+
+Set the environment variable "SALLOC_ACCOUNT" to the Slurm account you want
+to use.
+e.g.
+
+```
+export SALLOC_ACCOUNT="SlurmAccountName"
+```
+
+This example runs an interactive job in the "general-compute" partition, with
+64GB RAM and 6 cores on a single node for 5 hours:
 
 ```
 tmp_file="$(mktemp)"
 salloc --cluster=ub-hpc --partition=general-compute --qos=general-compute \
- --no-shell --mem=128GB --nodes=1 --cpus-per-task=1 --tasks-per-node=12 \
- --account="[SlurmAccountName]" --time=5:00:00 2>&1 | tee "${tmp_file}"
+ --no-shell --mem=64GB --nodes=1 --cpus-per-task=1 --tasks-per-node=6 \
+ --time=5:00:00 2>&1 | tee "${tmp_file}"
 SLURM_JOB_ID="$(head -1 "${tmp_file}" | awk '{print $NF}')"
 rm "${tmp_file}"
 srun --jobid="${SLURM_JOB_ID}" --export=HOME,TERM,SHELL --pty /bin/bash --login
@@ -237,11 +310,11 @@ sample output:
 > CCRusername@login1$ 
 > ```
 
-End the Slurm job
+End the Slurm job and remove the environment variables set for the job
 
 ```
 scancel "${SLURM_JOB_ID}"
-unset SLURM_JOB_ID
+unset SLURM_JOB_ID SALLOC_ACCOUNT
 ```
 
 
diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md
index bf67b923..cca1d276 100644
--- a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_ARM64_EXAMPLE.md
@@ -38,11 +38,11 @@ slimits | grep arm64
 sample output:
 
 > ```
->     ub-hpc         ccradmintest   tkewtest                      	arm64,class,debug,eai-test,general-compute,industry,scavenger,viz
+>     ub-hpc         SlurmAccountName   CCRusername                      	arm64,debug,general-compute,scavenger,viz
 > ```
 
-The second field in the Slurm account name, so my test account has access to
-the "arm64" partition using the account "ccradmintest"
+The second field in the Slurm account name, so this example has access to the
+"arm64" partition using the Slurm account "SlurmAccountName"
 
 ```
 cat slurm_ARM64_example.bash
@@ -52,7 +52,7 @@ abridged sample output:
 
 > ```
 > [...]
-> #SBATCH --account="ccradmintest"
+> #SBATCH --account="SlurmAccountName"
 > [...]
 > ```
 
diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md
index 73cc0c57..323b09c7 100644
--- a/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/SLURM_EXAMPLE.md
@@ -43,7 +43,7 @@ abridged sample output:
 > #SBATCH --cluster="ub-hpc"
 > #SBATCH --partition="debug"
 > #SBATCH --qos="debug"
-> #SBATCH --account="ccradmintest"
+> #SBATCH --account="SlurmAccountName"
 > [...]
 > ```
 

From 416f82cc100a2feac285362662a0e7b1eec286d5 Mon Sep 17 00:00:00 2001
From: Tony Kew <tony.d.r.kew@gmail.com>
Date: Mon, 3 Nov 2025 10:12:28 -0500
Subject: [PATCH 8/8] Add the 32bit openblas (as well as the 64 bit openblas)

Tony
---
 .../2_ApplicationSpecific/R-Rocker_Project/R_rocker_4.5.1.def   | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/containers/2_ApplicationSpecific/R-Rocker_Project/R_rocker_4.5.1.def b/containers/2_ApplicationSpecific/R-Rocker_Project/R_rocker_4.5.1.def
index 8df8784e..a1f89abb 100644
--- a/containers/2_ApplicationSpecific/R-Rocker_Project/R_rocker_4.5.1.def
+++ b/containers/2_ApplicationSpecific/R-Rocker_Project/R_rocker_4.5.1.def
@@ -132,6 +132,8 @@ From: ghcr.io/rocker-org/r-ver:4.5.1
    libhtscodecs-dev \
    libopenblas64-0 \
    libopenblas64-dev \
+   libopenblas-dev \
+   libopenblas64-dev \
    liblapack3 \
    liblapack-dev \
    liblapacke-dev \