diff options
| -rw-r--r-- | .nea/.gitlab-ci.yml | 214 | ||||
| -rw-r--r-- | .nea/docker/Dockerfile.slim | 51 | ||||
| -rw-r--r-- | .nea/docker/entrypoint.sh | 22 | ||||
| -rw-r--r-- | README.md | 131 |
4 files changed, 418 insertions, 0 deletions
diff --git a/.nea/.gitlab-ci.yml b/.nea/.gitlab-ci.yml new file mode 100644 index 0000000..45b1787 --- /dev/null +++ b/.nea/.gitlab-ci.yml @@ -0,0 +1,214 @@ +variables: + GIT_STRATEGY: clone + GIT_SUBMODULE_STRATEGY: recursive + GET_SOURCES_ATTEMPTS: 3 + DOCKER_BASE_REPO: docker.oecd-nea.org + + +stages: + - build + - test + - deploy +# - release + +default: + tags: + - podman + +.release_rules: &RELEASE_RULES + rules: + # Run this job only when a tag is created + - if: '$CI_COMMIT_TAG =~ /v+\d+\.\d+\.\d+/' + +.apt_setup: &APT_SETUP | + sed -i 's|http://archive.ubuntu.com|http://debmirror.nea.fr:9999/archive.ubuntu.com|g' /etc/apt/sources.list + sed -i 's|http://security.ubuntu.com|http://debmirror.nea.fr:9999/security.ubuntu.com|g' /etc/apt/sources.list + apt-get update -o Acquire::ForceIPv4=true + +.apt2_setup: &APT2_SETUP | + sed -i 's|http://archive.ubuntu.com|http://debmirror.nea.fr:9999/archive.ubuntu.com|g' /etc/apt/sources.list.d/ubuntu.sources + sed -i 's|http://security.ubuntu.com|http://debmirror.nea.fr:9999/security.ubuntu.com|g' /etc/apt/sources.list.d/ubuntu.sources + apt-get update -o Acquire::ForceIPv4=true + +.apt_deb_setup: &APT_DEB_SETUP | + sed -i 's|http://deb.debian.org|http://debmirror.nea.fr:9999/deb.debian.org|g' /etc/apt/sources.list + apt-get update -o Acquire::ForceIPv4=true + +.apt_deb2_setup: &APT_DEB2_SETUP | + sed -i 's|http://deb.debian.org|http://debmirror.nea.fr:9999/deb.debian.org|g' /etc/apt/sources.list.d/debian.sources + apt-get update -o Acquire::ForceIPv4=true + +.build_with_hdf5: &BUILD_WITH_HDF5 | + cd Donjon + make hdf5=1 openmp=1 + cd ../PyGan + make hdf5=1 openmp=1 + + +.build_linux_template: + stage: build + before_script: + - *APT_SETUP + - | + env DEBIAN_FRONTEND=noninteractive apt-get install -yq --no-install-recommends \ + make gfortran python3 python3-dev python3-numpy python3-distutils libhdf5-serial-dev libomp-dev + after_script: + - mkdir 5.1 + - mv Donjon 5.1/ + - mv Dragon 5.1/ + - mv Ganlib 5.1/ + - mv PyGan 5.1/ + - mv Trivac 5.1/ + - mv script 5.1/ + artifacts: + paths: + - 5.1/**/rdonjon + - 5.1/**/rdragon + - 5.1/**/rganlib + - 5.1/**/rpython + - 5.1/**/rtrivac + - 5.1/**/bin + - 5.1/**/lib + - 5.1/**/data + - 5.1/PyGan/Makefile + - 5.1/script + expire_in: 1 day + when: always + +build_ubuntu20: + extends: .build_linux_template + image: docker.oecd-nea.org/dragon/5.1/ubuntu:20.04 + script: + - export HDF5_INC=/usr/include/hdf5/serial + - export HDF5_API=/usr/lib/x86_64-linux-gnu/hdf5/serial + - export FORTRANPATH=/usr/lib/gcc/x86_64-linux-gnu/9 + - *BUILD_WITH_HDF5 + +build_ubuntu22: + extends: .build_linux_template + image: docker.oecd-nea.org/dragon/5.1/ubuntu:22.04 + script: + - export HDF5_INC=/usr/include/hdf5/serial + - export HDF5_API=/usr/lib/x86_64-linux-gnu/hdf5/serial + - export FORTRANPATH=/usr/lib/gcc/x86_64-linux-gnu/11 + - *BUILD_WITH_HDF5 + +# uses python 3.12 +build_ubuntu24: + extends: .build_linux_template + image: docker.oecd-nea.org/dragon/5.1/ubuntu:24.04 + before_script: + - *APT2_SETUP + - | + env DEBIAN_FRONTEND=noninteractive apt-get install -yq --no-install-recommends \ + make gfortran python3 python3-dev python3-numpy python3-setuptools libhdf5-serial-dev libomp-dev + script: + - export HDF5_INC=/usr/include/hdf5/serial + - export HDF5_API=/usr/lib/x86_64-linux-gnu/hdf5/serial + - export FORTRANPATH=/usr/lib/gcc/x86_64-linux-gnu/13 + - *BUILD_WITH_HDF5 + +.test_template: + stage: test + image: docker.oecd-nea.org/dragon/5.1/ubuntu:22.04 + variables: + GIT_STRATEGY: none + needs: + - job: build_ubuntu22 + artifacts: true + before_script: + - *APT_SETUP + # Note that the binaries require gfortran (a matching version) at runtime + - | + env DEBIAN_FRONTEND=noninteractive apt-get install -yq --no-install-recommends \ + python3 python3-numpy python3-distutils python3-matplotlib libomp-dev \ + make gfortran wget libhdf5-serial-dev libomp-dev + - export HDF5_INC=/usr/include/hdf5/serial + - export HDF5_API=/usr/lib/x86_64-linux-gnu/hdf5/serial + - export DRAGON_HOME=$CI_PROJECT_DIR/dragon + - export DRAGON_LIB_DIR=$DRAGON_HOME/libraries/l_endian + - export DRAGON_CODE_DIR=$DRAGON_HOME/5.1 + - mkdir -p ${DRAGON_LIB_DIR} + - mv 5.1 ${DRAGON_HOME}/ + +test_ganlib_ubuntu22: + extends: .test_template + script: + - cd ${DRAGON_CODE_DIR}/Ganlib + - ./rganlib -q testgan1.x2m + - ./rganlib -q testgan2.x2m + - ./rganlib -q testgan3.x2m + - ./rganlib -q testgan4.x2m + + +test_dragon_ubuntu22: + extends: .test_template + script: + - cd ${DRAGON_LIB_DIR} + # get JEF 2.2 for testing + - wget --no-check-certificate https://git.oecd-nea.org/dragon/libraries/-/raw/main/l_endian/draglibJef2p2.gz + # get JEF 3.1.1 for OpenMP testing + - wget --no-check-certificate https://git.oecd-nea.org/dragon/libraries/-/raw/main/l_endian/draglibJeff3p1p1SHEM295_v5p1.gz + - cd ${DRAGON_CODE_DIR}/Dragon + - ./rdragon -q salmacro.x2m + - ./rdragon -q tdraglib.x2m + - ./rdragon -q pincell_mpo.x2m + - ./rdragon -q -p 8 uo2_295_kec1_openMP.x2m + + +test_donjon_ubuntu22: + extends: .test_template + script: + - cd ${DRAGON_LIB_DIR} + # get JEF 2.2 for testing + - wget --no-check-certificate https://git.oecd-nea.org/dragon/libraries/-/raw/main/l_endian/draglibJef2p2Apolib99_v5p1.gz + - cd ${DRAGON_CODE_DIR}/Donjon + - ./rdonjon -q rep900_msap.x2m + - ./rdonjon -q Reflector_beavrs_DF-RT_Jef2p2Apolib99.x2m + - ./rdonjon -q Fessenheim.x2m + + +test_pygan_ubuntu22: + extends: .test_template + script: + - cd ${DRAGON_LIB_DIR} + # get JEF 2.2 for testing + - wget --no-check-certificate https://git.oecd-nea.org/dragon/libraries/-/raw/main/l_endian/draglibJeff3p1p1SHEM295_v5p1.gz + - cd ${DRAGON_CODE_DIR}/PyGan + - make tests hdf5=1 openmp=1 + +docker_ubuntu24_slim: + stage: deploy + image: + # recommended image for building with kaniko + # https://docs.gitlab.com/ee/ci/docker/using_kaniko.html#building-a-docker-image-with-kaniko + name: ${DOCKER_BASE_REPO}/dragon/5.1/kaniko:v1.23.0-debug + entrypoint: [""] + needs: + - job: test_ganlib_ubuntu22 + artifacts: false + - job: test_dragon_ubuntu22 + artifacts: false + - job: test_donjon_ubuntu22 + artifacts: false + - job: test_pygan_ubuntu22 + artifacts: false + script: + - | + cat <<EOF > /kaniko/.docker/config.json + { + "auths": { + "docker.oecd-nea.org": { + "username": "$CI_DEPLOY_USER", + "password": "$CI_DEPLOY_PASSWORD" + } + } + } + EOF + # TODO: change the hardcoded docker tag to use a git tag + - > + /kaniko/executor + --context "${CI_PROJECT_DIR}" + --dockerfile "${CI_PROJECT_DIR}/.nea/docker/Dockerfile.slim" + --destination "${DOCKER_BASE_REPO}/${CI_PROJECT_NAMESPACE}/${CI_PROJECT_NAME}:v5.1.0-slim" + --single-snapshot --cache=false diff --git a/.nea/docker/Dockerfile.slim b/.nea/docker/Dockerfile.slim new file mode 100644 index 0000000..ebfae15 --- /dev/null +++ b/.nea/docker/Dockerfile.slim @@ -0,0 +1,51 @@ +FROM docker.oecd-nea.org/dragon/5.1/ubuntu:24.04 + +COPY ./.nea/docker/entrypoint.sh /entrypoint.sh + +ENV DRAGON_HOME=/dragon +ENV DRAGON_CODE_DIR=$DRAGON_HOME/5.1 + +ENV HDF5_INC=/usr/include/hdf5/serial +ENV HDF5_API=/usr/lib/x86_64-linux-gnu/hdf5/serial +ENV FORTRANPATH=/usr/lib/gcc/x86_64-linux-gnu/13 + +RUN AG="env DEBIAN_FRONTEND=noninteractive apt-get -yq" && \ + ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \ + # NEA special for our internal apt mirrors + cp /etc/apt/sources.list.d/ubuntu.sources /ubuntu.sources.original && \ + sed -i 's|http://archive.ubuntu.com|http://debmirror.nea.fr:9999/archive.ubuntu.com|g' /etc/apt/sources.list.d/ubuntu.sources && \ + sed -i 's|http://security.ubuntu.com|http://debmirror.nea.fr:9999/security.ubuntu.com|g' /etc/apt/sources.list.d/ubuntu.sources && \ + $AG update && \ + $AG upgrade --no-install-recommends && \ + $AG install --no-install-recommends openssl git git-lfs wget curl make gfortran python3 python3-dev python3-numpy python3-setuptools libhdf5-serial-dev libomp-dev && \ + $AG autoremove && \ + $AG autoclean && \ + $AG clean && \ + # Put the normal apt sources back after installing deps + mv /ubuntu.sources.original /etc/apt/sources.list.d/ubuntu.sources && \ + openssl s_client -showcerts -connect git.oecd-nea.org:443 < /dev/null | sed -ne '/-BEGIN CERTIFICATE-/,/-END CERTIFICATE-/p' > /ca.crt && \ + git config --global http.sslCAInfo /ca.crt && \ + mkdir ${DRAGON_HOME} && cd ${DRAGON_HOME} && \ + git clone https://git.oecd-nea.org/dragon/5.1 && \ + cd ${DRAGON_CODE_DIR} && \ + # to keep it slim we can remove the .git folder, and the data folders + rm -rf .git Donjon/data Dragon/data Trivac/data doc && \ + cd ${DRAGON_CODE_DIR}/Donjon && \ + make hdf5=1 openmp=1 && \ + # this doesn't remove the binaries, just the *.o and the *.a and *.mod files + make clean && \ + cd ../PyGan && \ + make hdf5=1 openmp=1 && \ + # this doesn't remove the binaries, just the *.o and the *.a and *.mod files + make clean && \ + cd ../Ganlib && \ + ./rganlib -q testgan1.x2m && \ + ./rganlib -q testgan2.x2m && \ + ./rganlib -q testgan3.x2m && \ + chmod +x /entrypoint.sh + +# ENV DRAGON_LIB_DIR=$DRAGON_HOME/libraries/l_endian + +WORKDIR /dragon/5.1/ + +ENTRYPOINT [ "/entrypoint.sh" ] diff --git a/.nea/docker/entrypoint.sh b/.nea/docker/entrypoint.sh new file mode 100644 index 0000000..416fac5 --- /dev/null +++ b/.nea/docker/entrypoint.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +RED='\033[1;91m' +GREEN='\033[1;92m' +BLUE='\033[1;94m' +NC='\033[0m' + + +tryit(){ + "$@" + local status=$? + if [ $status -ne 0 ]; then + echo -e "${RED}Error occurred with $1 ${NC}" >&2 + exit $status + fi + return $status +} + + +# run donjon as the default entrypoint, as donjon can run dragon +cd Donjon +tryit ./rdonjon $@ diff --git a/README.md b/README.md new file mode 100644 index 0000000..fdc2bc6 --- /dev/null +++ b/README.md @@ -0,0 +1,131 @@ +# Dragon v5.1 + +This is the repository for the Dragon code. +Version5 is a 64-bit clean distribution of the reactor physics codes developed at Polytechnique Montréal. + + +## License + +The license is [GNU General Public License](http://www.gnu.org/licenses/lgpl.html). + + +## Documentation + +For comprehensive documentation please refer to the [Merlin site](http://merlin.polymtl.ca/version5.htm). +Additionally, you can build the documentation yourself using Latex, see the subdirectory [doc](./doc) for more. + + +## Dependencies + +In order to compile and run Dragon you must have a Fortran compiler (2003 or later standard) and Python3. + +Optional dependencies are [OpenMP](https://www.openmp.org/resources/openmp-compilers-tools/) and [HDF5](https://www.hdfgroup.org/download-hdf5/). + + +## Installation + +Dragon is supported on Linux and Unix machines. For Windows users we recommend using the Windows Subsystem for Linux (WSL). + +The installation is based on `make`, particularly `gmake` for Unix systems. + +Please go to the [Merlin site](http://merlin.polymtl.ca/version5.htm) for comprehensive installation instructions. + + +## Run the code + +A minimum set of cross section files can be found on the [Merlin site](http://merlin.polymtl.ca/version5.htm), for more extensive work download the required files from the NEA data repository [here](../libraries/). + +**Please note that you must preserve the directory structure**. This can be achieved by doing the following: + +If you want all data (note the disk space ~10GB) follow these steps: + +```bash +mkdir dragon +cd dragon +git clone https://git.oecd-nea.org/dragon/5.1 +git clone https://git.oecd-nea.org/dragon/libraries +``` + +For those with limited disk space, you will need to specify which data files you want. + +For example: + +```bash +mkdir dragon +cd dragon +git clone https://git.oecd-nea.org/dragon/5.1 +GIT_LFS_SKIP_SMUDGE=1 git clone https://git.oecd-nea.org/dragon/libraries +cd libraries +# For JEFF 3.1.1 SHEM 361 use the following +git lfs pull -I l_endian/draglibJeff3p1p1SHEM361_v5p1.gz +``` + +## Docker + +If you don't want to compile the code on your machine, we offer pre-built Docker images for you to use to bypass this, and you just require docker installed on your machine. + +For Windows users you can use [Docker Desktop](https://docs.docker.com/desktop/setup/install/windows-install/) (if you don't have WSL). + + +### Get image + +To get a docker images (Ubuntu 22.04) with PHITS already setup and paths set, you may pull this image via: + +```bash +docker pull docker.oecd-nea.org/dragon/5.1:v5.1.0-slim +``` + +### Running image + +A template command is provided below and you only need to change the text in the `<>` sections, specific to your installation. Note that the paths on the right hand side of the colon (:) should be to your **host** machine, the paths on the right hand side do not need to be changed and match to paths inside the docker container. + + +```bash +docker run -v <my_path_to_libs>:/dragon/libraries:ro + -v <my_path_to_inputs>:/dragon/5.1/Donjon/data/:ro + -v <my_path_to_outputs>:/dragon/5.1/Donjon/Linux_x86_64 + docker.oecd-nea.org/dragon/5.1:v5.1.0-slim + "-q <my_input_file.x2m>" +``` + +You therefore need 4 parameters to set: + +1. `<my_path_to_libs>` should point to the directory containing your Dragon nuclear data library file (`*.gz`). + +2. `<my_path_to_inputs>` should point to a directory on your host machine containing the input data files (`*.x2m` and other related files). This should be a different directory to number 1. + +3. `<my_path_to_outputs>` should point to a directory on your host machine which will be used to keep the output files from each code run i.e (including the `*.result` file). This should be different to 1. and 2. + +4. `<my_input_file.x2m>` should be the name of the input data file which should exist in directory number 2. + + +An example of this is given below: + + +```bash +docker run -v /home/user/dragon/libraries:/dragon/libraries:ro + -v /home/user/dragon/inputs:/dragon/5.1/Donjon/data/:ro + -v /home/user/dragon/outputs:/dragon/5.1/Donjon/Linux_x86_64 + docker.oecd-nea.org/dragon/5.1:v5.1.0-slim + "-q VanDerGucht.x2m" +``` + + +given the following directory contents: + +```bash +$ls /home/user/dragon/libraries +README.md ascii hdf5 l_endian pynjoy +``` + +```bash +$ls /home/user/dragon/inputs +VanDerGucht.access VanDerGucht.x2m VanDerGucht_proc +``` + +will give me the following outputs + +```bash +$ls /home/user/dragon/outputs +VanDerGucht.result +```
\ No newline at end of file |