docker-spiritroot

This repository provides a Docker image for compiling a specific branch of SpiRITROOT--2024Spring, used in the SpiRIT TPC experiment at RIKEN.

Due to the incompatibility of several outdated dependencies, installing these on modern Linux distributions such as Ubuntu 22.04 or 24.04 is challenging. This Docker image replicates the working setup from Hokusai HPC at RIKEN, starting with a base image of RockyLinux 8.8.

Content

• 1. Pre-requiste
• 2. Usage with Docker
• 3. Usage with Singularity
• 4. How to Contribute

Prerequiste

Before using this repository, ensure you have the following:

• Docker, if you have root privileges.

• [Optional] Singularity, typically pre-installed on HPC systems as an alternative to Docker

• Clone the SpiRITROOT repository:

git clone -b 2024Spring https://github.com/SpiRIT-Collaboration/SpiRITROOT

Usage with Docker

1. pull the docker image, see here

docker pull tck199732/spiritroot:latest

2. run the container

docker run -it -v ${host_dir}:${container_dir} tck199732/spiritroot

• Replace ${host_dir} with the path to the SpiRITROOT directory on your machine.
• Replace ${container_dir} with the desired mount point inside the container (e.g., /root/SpiRITROOT).

3. Compile SpiRITROOT

• [Optional] Compilating SpiRITROOT generates a file VERSION.compiled which indicates the compiled version of SpiRITROOT formatted according to git commits and branch being used. To access these information, one must navigate to the ${container_dir} and run

git config --global --add safe.directory $(pwd)

• Navigate to the mounted directory in the container:

# in the SpiRITROOT directory 
mkdir -p build
cd build
cmake .. -DCMAKE_CXX_COMPILER=g++ \
 -DROOT_CONFIG_EXECUTABLE=${SIMPATH}/bin/root-config \
 -DROOT_CINT_EXECUTABLE=${SIMPATH}/bin/rootcint \
 -DEigen3_DIR=$Eigen3_DIR
make -j4

4. Verify Compilation

• Source the config.sh file

source config.sh

Expected output:

[root@e79fa05ae8ee build]# . config.sh 
System during compilation: Rocky Linux release 8.10 (Green Obsidian)
                           x86_64
System now               : Rocky Linux release 8.10 (Green Obsidian)
                           x86_64
[root@e79fa05ae8ee build]# 

5. Post-Execution

• Exit the container and restore file ownership:

chown -R ${USER}:${USER} SpiRITROOT

Usage with Singularity

It is hard to use Docker without root privileges, especially on HPC. Instead, Singularity is an alternative way to use Docker images⁠. To check if singularity commands are available, do the following:

user@server $ singularity --version
singularity-ce version 3.11.4-1.el8

1. build the singularity image file

user@server $ singularity build image.sif docker://tck199732/spiritroot
INFO:    Starting build...
Getting image source signatures
...
INFO:    Creating SIF file...
INFO:    Build complete: image.sif

This process usually takes a few minutes. You will probably see a lot of warning message warn rootless{opt/root/lib/libASImage.so} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers but it probably does not affect its functionality. An file named image.sif is now generated.

2. Compile SpiRIROOT with singularity image Unlike Docker images, singularity mounts the host system to the container and retains the user privileges. To compile SpiRIROOT, prepare a script for the procedures, i.e.

#!/bin/bash
# compile.sh
mkdir -p build
cd build
cmake .. -DCMAKE_CXX_COMPILER=g++ \
 -DROOT_CONFIG_EXECUTABLE=${SIMPATH}/bin/root-config \
 -DROOT_CINT_EXECUTABLE=${SIMPATH}/bin/rootcint \
 -DEigen3_DIR=$Eigen3_DIR
make -j4
cd ..

and make it an executable and finally run it with singularity

chmod +x ./compile.sh
singularity exec image.sif ./compile.sh

3. Mounting data to singularity container Singularity automatically mounts your user directory but not the shared location of data. To mount it to the container,

user@server $ singularity exec --bind ${host_dir}:${container_dir} ./ana.sh

How to contribute

This section is for developers only. Currently, only the RockyLinux environment is supported. It is, however, helpful in cases to update due to dependency changes or build the container with a different base environment. Here is the procedure to update the repository. First, create a new branch by

git checkout -b ${branch-name}

Then, make neccessary modifications and build the image in the root directory of the project with

docker build -t spirit-root:latest .

After testing, create a pull request to merge to the main branch if needed.