Merge branch 'merge' into 'master'

Merge in upstream changes and update CI See merge request !16

Merge branch 'merge' into 'master'
5aaaf253 · Sylvester Joosten · 867c7bac · ab31a770 · 5aaaf253 · 5aaaf253
Commit 5aaaf253 authored 4 years ago by Sylvester Joosten
--- a/.containers/Dockerfile.in
+++ b/.containers/Dockerfile.in
+FROM eicweb.phy.anl.gov:4567/containers/image_recipes/root_spack:@CONTAINER_TAG@
+LABEL maintainer "Sylvester Joosten <sjoosten@anl.gov>"
+RUN  cd /tmp \
+  && git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/hallac_evio.git \
+  && mkdir hallac_evio/build && cd hallac_evio/build  \
+  && cmake ../.  && make -j20 && make install \
+  && cd /tmp && rm -rf hallac_evio \
+  && git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/analyzer.git \
+  && mkdir analyzer/build && cd analyzer/build   && git pull && git checkout v1.8.3 \
+  && cmake ../.  && make -j20 VERBOSE=1 && make install \
+  && cd /tmp  && rm -rf analyzer
+## 2 layers so we can isolate hcana from the rest of the stack
+RUN cd /tmp \
+  && git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/hcana.git \
+  && mkdir hcana/build && cd hcana/build  \
+  && git pull \
+  && cmake ../.  && make -j20 VERBOSE=1 && make install \
+  && cd /tmp && rm -rf hcana 
--- a/.containers/Makefile
+++ b/.containers/Makefile
+# import config.
+# You can change the default config with `make cnf="config_special.env" build`
+cnf ?= config.env
+include $(cnf)
+# exports variables in config.env as environment variables
+export $(shell sed 's/=.*//' $(cnf))
+SHELL = bash
+# grep the version from the mix file
+VERSION=$(shell bash version.sh)
+TAG_VERSION=$(VERSION)
+LONG_TAG=$(VERSION)-$(PUBLISH_TAG)
+# help will output the help for each task
+# thanks to https://marmelab.com/blog/2016/02/29/auto-documented-makefile.html
+.PHONY: help
+help: ## This help.
+	@awk 'BEGIN {FS = ":.*?## "} /^[a-zA-Z_-]+:.*?## / {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}' $(MAKEFILE_LIST)
+.DEFAULT_GOAL := help
+# ==========================================================================
+#
+build: ## build the image
+	docker build -t $(APP_NAME):$(LONG_TAG) .
+build-nc: ## Build the container without caching (from scratch)
+	docker build --no-cache -t $(APP_NAME):$(LONG_TAG) .
+# ==========================================================================
+#
+login: ## Auto login to AWS-ECR unsing aws-cli
+	@docker login -u ${CI_REGISTRY_USER} -p ${CI_REGISTRY_PASSWORD} ${CI_REGISTRY}
+	echo "Login COMPLETE"
+# ==========================================================================
+#
+publish: login ## Publish a tagged container to ECR
+	@echo 'publish $(PUBLISH_TAG) to $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME)'
+	docker tag $(APP_NAME):$(LONG_TAG) $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):$(PUBLISH_TAG)
+	docker push $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):$(PUBLISH_TAG)
+	docker rmi  $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):$(PUBLISH_TAG)
+publish-version: login ## Publish the `{version}` taged container to ECR
+	@echo 'publish $(VERSION) to $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):$(VERSION)'
+	docker tag $(APP_NAME):$(LONG_TAG) $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):$(VERSION)
+	docker push $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):$(VERSION)
+	docker rmi  $(REG_NAME)/$(GL_REG_GROUP)/$(APP_NAME):$(VERSION)
+# ==========================================================================
+# remove container from registry
+unpublish: login
+	@echo 'removing $(PUBLISH_TAG)'
+	curl --request DELETE --header "PRIVATE-TOKEN: $(CI_JOB_TOKEN)" "$(REG_API_URL)/$(PUBLISH_TAG)"
+# ==========================================================================
+# cleanup docker registry on system used by runner
+cleanup:
+	@echo 'removing $(REG_NAME):$(LONG_TAG)'
+	docker rmi $(REG_NAME):$(LONG_TAG)
--- a/containers/docker/config.env
+++ b/containers/docker/config.env
 # Port to run the container 
-PORT=4000
-REG_TOKEN ?= ${CI_IMAGE_BUILD_PAT}
-REG_USER  ?= whit
-REG_NAME  ?= eicweb.phy.anl.gov:4567
-REG_HOST  ?= eicweb.phy.anl.gov:4567
-# name of alternate build: 
-# Dockerfile.$(ALT_NAME) --> $(APP_NAME)_${ALT_NAME}
-ALT_NAME ?= broadwell
 APP_NAME     = hcana
 REPO_NAME    = hcana
-DH_ORG       = hallac
-GL_GROUP     = jlab/hallc/analyzer_software
-GL_REG_GROUP = jlab/hallc/analyzer_software
-GL_REG_NAME  = hcana
-REPO         = hcana
-TAG_VERSION  = latest
+REG_HOST  ?= eicweb.phy.anl.gov
+REG_NAME  ?= eicweb.phy.anl.gov:4567
+REG_PORT  ?= 4567
+REG_URL   ?= https://$(REG_HOST)
+GL_GROUP     = jlab/hallc/analyzer_software
+GL_REG_GROUP = jlab/hallc/analyzer_software/hcana
+GL_REG_NAME  = $(REG_NAME)
+PUBLISH_TAG = $(HCANA_TAG)
+REG_API_URL = $(REG_URL)/api/v4/projects/$(CI_PROJECT_ID)/registry/repositories/49/tags
--- a/containers/docker/Makefile
+++ b/containers/docker/Makefile
--- a/.containers/hcana.def.in
+++ b/.containers/hcana.def.in
+Bootstrap: docker
+From: eicweb.phy.anl.gov:4567/jlab/hallc/analyzer_software/hcana:@HCANA_TAG@
+%help
+  singularity container for hcana development
+%labels
+  Maintainer "Whitney Armstrong, Sylvester Joosten"
+  Version v1-dev
+%post -c /bin/bash
+  echo "  -------------------------------------------------"
+  echo "  ===> Image setup complete"
+  echo "  -------------------------------------------------"
--- a/containers/singularity/Singularity.broadwell
+++ b/containers/singularity/Singularity.broadwell
--- a/containers/docker/version.sh
+++ b/containers/docker/version.sh
 #!/bin/bash
-echo "0.1"
+cat ../VERSION
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
-image: eicweb.phy.anl.gov:4567/containers/image_recipes/root_base:latest
+variables:
+  CONTAINER_TAG: "1.4.0"
+default: 
+  image: eicweb.phy.anl.gov:4567/containers/image_recipes/ubuntu_dind:latest
+  tags:
+    - silicon
 stages:
+  - config
  - build
-  - build_docker
+  - push
-  - build_sing_img
+  - deploy
-  - data_replays
+  - cleanup
-  - data_tests
-hcana_build:
+workflow:
-  stage: build
+  rules:
-  tags: 
+     - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
-    - sodium
+     - if: '$CI_COMMIT_BRANCH == "master"'
-  script:
+     - if: '$CI_COMMIT_TAG'
-    -  ls -lrth /usr/local/bin
-    - bash bin/compile
-hcana_docker:
-  stage: build_docker  
-  only:
-     - tags
-  tags: 
-     - eic0 docker
-  script:
-     - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
-     - cd containers/docker && make release
-hcana_singularity:
+env:
-  tags: 
+  stage: config 
-     - singularity
-  stage: build_sing_img
-  when: manual
-  dependencies:
-     - hcana_docker
  script:
-     - /bin/bash .gitlabci/setup.sh
+    - export HCANA_TAG="latest"
-     - mkdir -p build
+    - |
-     - pwd
+      if [ "x${CI_PIPELINE_SOURCE}" == "xmerge_request_event" ]; then
-     - cp containers/singularity/Singularity Singularity.hcana
+        export HCANA_TAG="testing-mr-${CI_MERGE_REQUEST_IID}"
-     - cp Singularity.hcana build/.
+      fi
-     - /bin/bash .gitlabci/build.sh Singularity.hcana
+    - echo "CI HCANA_TAG for this pipeline set to ${HCANA_TAG}"
-     - cp Singularity.hcana.simg build/.
+    - echo "HCANA_TAG=$HCANA_TAG" >> hcana.env
  artifacts:
-      paths:
+    reports:
-        - build/Singularity.hcana
+      dotenv: hcana.env
-        - build/Singularity.hcana.simg
-elastic_replay:
+docker:
-  when: manual
+  stage: build
-  tags: 
+  needs:
-     - eic0 docker
+    - env
-  stage: data_replays
-  dependencies: 
-     - hcana_singularity
  script:
-     - bash tests/replay_elastic_data.sh
+    - echo $HCANA_TAG
-  artifacts:
+    - ./.gitlabci/configure.sh .containers/Dockerfile.in
-     paths: 
+    - cd .containers
-       - ROOTfiles/*
+    - make build-nc
-       - build/Singularity.hcana
-       - build/Singularity.hcana.simg
-elastic_test1:
+## for now only publish the stable versions to the registry.
-  when: manual
+## if we change this down the line for some CI-time testing
-  tags: 
+## make sure to also enable the cleanup job
-     - eic0 docker
+publish:
-  stage: data_tests
+  stage: push
-  dependencies: 
+  rules:
-     - elastic_replay
+    - if: '$CI_COMMIT_BRANCH == "master"'
+      when: manual
+    - if: '$CI_COMMIT_TAG'
+      when: manual
+  needs:
+    - env
+    - docker
  script:
-     - bash tests/elastic_test.sh
+    - cd .containers
+    - |
+      if [ "x$CI_COMMIT_TAG" != "x" ]; then
+        make publish publish-version
+      else
+        make publish
+      fi
+  retry:
+    max: 2
+    when:
+      - runner_system_failure
+      - stuck_or_timeout_failure
-elastic_test2:
+.singularity:
-  when: manual
+  stage: deploy
-  tags: 
+  needs: 
-     - eic0 docker
+    - env
-  stage: data_tests
+    - publish
-  dependencies: 
-     - elastic_replay
  script:
-     - bash tests/elastic_test2.sh
+    - ./.gitlabci/configure.sh .containers/hcana.def.in
+    - mkdir -p build
+    - mv .containers/hcana.def build
+    - singularity build build/hcana.sif build/hcana.def
+  retry:
+    max: 2
+    when:
+      - runner_system_failure
+      - stuck_or_timeout_failure
+singularity:latest:
+  extends: .singularity
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "master"'
+      when: manual
+    - if: '$CI_COMMIT_TAG'
+      when: manual
+  artifacts:
+    expire_in: 90 days
+    paths:
+      - build/hcana.sif
+      - build/hcana.def
+purge_image:
+  stage: cleanup
+  needs:
+    - env
+    - publish
+  rules:
+    - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
+      when: never
+  script:
+    - cd .containers
+    - make cleanup || true
+    - make unpublish || true
--- a/.gitlabci/build.sh
+++ b/.gitlabci/build.sh
--- a/.gitlabci/configure.sh
+++ b/.gitlabci/configure.sh
+#!/bin/bash
+## Configure a CI file based on a template file (first and only
+## argument to this script).
+## Known variables that will be substituted:
+## @CONTAINER_TAG@          - docker tag for the ROOT container
+## @HCANA_TAG@         - output tag for the hcana version
+## @HCANA_BRANCH@      - hcana git branch for build
+TEMPLATE_FILE=$1
+OUTPUT_FILE=${TEMPLATE_FILE%.*}
+HCANA_BRANCH="master"
+if [ -n "${CI_MERGE_REQUEST_SOURCE_BRANCH_NAME}" ] ; then
+    HCANA_BRANCH=$CI_MERGE_REQUEST_SOURCE_BRANCH_NAME
+fi
+echo "Configuring CI file: ${TEMPLATE_FILE}"
+echo "Output will be written to: ${OUTPUT_FILE}"
+sed "s/@CONTAINER_TAG@/$CONTAINER_TAG/g" $TEMPLATE_FILE | \
+    sed "s/@HCANA_TAG@/$HCANA_TAG/g" | \
+    sed "s/@HCANA_BRANCH@/$HCANA_BRANCH/g" > ${OUTPUT_FILE}
+echo "Done"
--- a/.gitlabci/setup.sh
+++ b/.gitlabci/setup.sh
-#!/bin/bash
-apt-get update && apt-get install -y wget git \
-                                          build-essential \
-                                          squashfs-tools \
-                                          libtool \
-                                          autotools-dev \
-                                          libarchive-dev \
-                                          automake \
-                                          autoconf \
-                                          uuid-dev \
-                                          python3   \
-                                          libssl-dev
-sed -i -e 's/^Defaults\tsecure_path.*$//' /etc/sudoers
-# Check Python
-echo "Python Version:"
-which python
-python --version
-pip install sregistry[all]
-sregistry version
-echo "sregistry Version:"
-# Install Singularity
-cd /tmp && \
-    git clone -b vault/release-2.5 https://www.github.com/sylabs/singularity.git
-    cd singularity && \
-    ./autogen.sh && \
-    ./configure --prefix=/usr/local && \
-    make -j8 && make install
--- a/.gitlabci/sregistry-gitlab.png
+++ b/.gitlabci/sregistry-gitlab.png
--- a/.gitlabci/sregistry-gitlab.xcf
+++ b/.gitlabci/sregistry-gitlab.xcf
--- a/VERSION
+++ b/VERSION
+1.4.0
--- a/bin/compile
+++ b/bin/compile
-#!/bin/bash
-#set -o nounset
-set -o errexit
-startdir=$(pwd)
-export PYTHONPATH=/usr/local/lib:$PYTHONPATH  
-export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH  
-export PATH=/usr/local/bin:$PATH  
-source /usr/local/bin/thisroot.sh 
-cd /tmp 
-git clone https://github.com/fmtlib/fmt.git && cd fmt 
-git checkout 6.2.1 && mkdir /tmp/build && cd /tmp/build 
-cmake -DBUILD_SHARED_LIBS=TRUE ../fmt 
-make -j20 install 
-cd /tmp && rm -r /tmp/build && rm -r /tmp/fmt 
-cd /tmp  
-git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/hallac_evio.git 
-mkdir hallac_evio/build && cd hallac_evio/build  
-cmake ../.  && make -j20 && make install 
-cd /tmp && rm -rf hallac_evio 
-cd /tmp  
-export PYTHONPATH=/usr/local/lib:$PYTHONPATH  
-export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH  
-export PATH=/usr/local/bin:$PATH  
-git clone --depth 1 https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/analyzer.git 
-mkdir analyzer/build && cd analyzer/build   
-cmake ../.  && make -j20 VERBOSE=1 && make install 
-cd /tmp  && rm -rf analyzer 
-export PYTHONPATH=/usr/local/lib:$PYTHONPATH  
-export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH  
-export PATH=/usr/local/bin:$PATH  
-source /usr/local/bin/thisroot.sh 
-cd $startdir
-mkdir build && cd build  
-cmake ../.  && make -j20 VERBOSE=1 && make install  
--- a/containers/docker/Dockerfile
+++ b/containers/docker/Dockerfile
-FROM eicweb.phy.anl.gov:4567/containers/image_recipes/root_base:latest                                                                                                                                       
-LABEL maintainer "Whitney Armstrong <warmstrong@anl.gov>"
-#
-RUN   ls -lrth /usr/local/lib/lib*.so \
-  && export PYTHONPATH=/usr/local/lib:$PYTHONPATH  \
-  && export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH  \
-  && export PATH=/usr/local/bin:$PATH  \
-  && source /usr/local/bin/thisroot.sh \
-  && cd /tmp \
-  && git clone https://github.com/fmtlib/fmt.git && cd fmt \
-  && git checkout 6.2.1 && mkdir /tmp/build && cd /tmp/build \
-  && cmake -DBUILD_SHARED_LIBS=TRUE ../fmt \
-  &&  make -j20 install \
-  && cd /tmp && rm -r /tmp/build && rm -r /tmp/fmt \
-  && cd /tmp  \
-  && git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/hallac_evio.git \
-  && mkdir hallac_evio/build && cd hallac_evio/build  \
-  && cmake ../.  && make -j20 && make install \
-  && cd /tmp && rm -rf hallac_evio \
-  && cd /tmp  \
-  && export PYTHONPATH=/usr/local/lib:$PYTHONPATH  \
-  && export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH  \
-  && export PATH=/usr/local/bin:$PATH  \
-  && git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/analyzer.git \
-  && mkdir analyzer/build && cd analyzer/build   && git pull && git checkout v1.8.2 \
-  && cmake ../.  && make -j20 VERBOSE=1 && make install \
-  && cd /tmp  && rm -rf analyzer \
-  && export PYTHONPATH=/usr/local/lib:$PYTHONPATH  \
-  && export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH  \
-  && export PATH=/usr/local/bin:$PATH  \
-  && source /usr/local/bin/thisroot.sh \
-  && git clone https://eicweb.phy.anl.gov/jlab/hallc/analyzer_software/hcana.git \
-  && mkdir hcana/build && cd hcana/build  \
-  && git pull \
-  && cmake ../.  && make -j20 VERBOSE=1 && make install \ 
-  && cd /tmp && rm -rf hcana 
-#-DCMAKE_CXX_FLAGS=" -march=haswell -O3 -mfma -malign-data=cacheline -finline-functions "
-#&& wget -O- https://root.cern.ch/download/root_v6.14.06.source.tar.gz | tar -zxvf - \
-#&& mv root-6.14.06 root_master \
-#RUN which c++ && ls -lrth /usr/bin/c++ && cd /tmp/builds/root_build && make -j38 VERBOSE=1 && make install \
-#      && cd /tmp && rm -rf /tmp/root_master && rm -rf /tmp/builds/root_build 
-#RUN useradd -ms /bin/bash -d /opt/user user
-#USER user
-#WORKDIR /opt/bubble_user
-##CMD ["-c" ]
-#ENTRYPOINT ["/bin/bash"]
--- a/containers/docker/Dockerfile.broadwell
+++ b/containers/docker/Dockerfile.broadwell
-# ROOT base
-#
-# A container for the latest root
-#
-FROM  whit/image_recipes/ubuntu_base:latest
-LABEL maintainer "Whitney Armstrong <warmstrong@anl.gov>"
-#
-RUN cd /tmp \
-      && wget http://bitbucket.org/eigen/eigen/get/3.3.4.tar.bz2 \
-      && tar -xvf 3.3.4.tar.bz2 \
-      && cd eigen-* \
-      && mkdir build && cd build \
-      && cmake ../. -DCMAKE_CXX_FLAGS=" -march=haswell -O3 -mfma -malign-data=cacheline -finline-functions " \
-      && make -j10 > /tmp/eigen_build.log && make install
-RUN cd /tmp \
-      && git clone --depth=1 https://gitlab.cern.ch/CLHEP/CLHEP.git \
-      && mkdir -p builds/clhep_build \
-      && cd  builds/clhep_build \
-      && cmake /tmp/CLHEP/.  -DCMAKE_CXX_FLAGS=" -march=haswell -O3 -mfma -malign-data=cacheline -finline-functions "\
-      && make -j38 install > /tmp/clhep_build.log \
-      && cd /tmp && rm -rf /tmp/CLHEP && rm -rf /tmp/builds/clhep_build
-RUN cd /tmp \
-&& git clone https://github.com/VcDevel/Vc.git \
-&& cd  Vc \
-&& git submodule update --init \
-&& mkdir build && cd build \
-&& cmake -DCMAKE_INSTALL_PREFIX=/usr/local -DBUILD_TESTING=OFF -DTARGET_ARCHITECTURE=broadwell ../.  \
-&& make -j30 > /tmp/vc_build.log  \
-&& make install
-# Build root from the repo master
-RUN cd /tmp \
-      && pwd \
-      && git clone --depth=1 https://github.com/root-project/root.git root_master \
-      && cd /tmp && mkdir -p builds/root_build \
-      && cd builds/root_build \
-      && cmake ../../root_master/. -Droot7:BOOL=ON -Dcxx17:BOOL=ON -Dfortran:BOOL=ON \
-             -Dgdml:BOOL=ON -Dmathmore:BOOL=ON -Dminuit2:BOOL=ON  -Dbuiltin_vdt:BOOL=ON -Dbuiltin_veccore:BOOL=ON \
-             -Dvc:BOOL=ON -Dbuiltin_vecgeom:BOOL=ON  -Dunuran:BOOL=ON  \
-      && cd /tmp/builds/root_build && make -j38 > /tmp/root_build.log && make install \
-      && cd /tmp && rm -rf /tmp/root_master && rm -rf /tmp/builds/root_build 
-#-DCMAKE_CXX_FLAGS=" -march=haswell -O3 -mfma -malign-data=cacheline -finline-functions "
-#&& wget -O- https://root.cern.ch/download/root_v6.14.06.source.tar.gz | tar -zxvf - \
-#&& mv root-6.14.06 root_master \
-#RUN which c++ && ls -lrth /usr/bin/c++ && cd /tmp/builds/root_build && make -j38 VERBOSE=1 && make install \
-#      && cd /tmp && rm -rf /tmp/root_master && rm -rf /tmp/builds/root_build 
-#RUN useradd -ms /bin/bash -d /opt/user user
-#USER user
-#WORKDIR /opt/bubble_user
-##CMD ["-c" ]
-#ENTRYPOINT ["/bin/bash"]
--- a/containers/docker/README.md
+++ b/containers/docker/README.md
-Hall A/C Software
-=================
-Images for running containers for all aspects of the SANE experimental 
-analysis.
-The starting point is a pre-built image for the ROOT libraries. (ubuntu + ROOT)
-Main software libraries:
- - `evio`: Built from https://github.com/whit2333/hallac_evio
- - `analyzer`: Hall A analyzer (podd)from https://github.com/whit2333/analyzer
- - `hcana`: Hall C analyzer from  https://github.com/whit2333/hcana
-These are all built using the super build project `cool_halls` (https://github.com/whit2333/cool_halls)
--- a/containers/docker/deploy.env
+++ b/containers/docker/deploy.env
-# You have to define the values in {}
-#DOCKER_REPO={account-nr}.dkr.ecr.{region}.amazonaws.com
-## optional aws-cli options
-#AWS_CLI_PROFILE={aws-cli-profile}
-#AWS_CLI_REGION={aws-cli-region}
--- a/containers/docker/usage.sh
+++ b/containers/docker/usage.sh
-# INSTALL
-# - copy the files deploy.env, config.env, version.sh and Makefile to your repo
-# - replace the vars in deploy.env
-# - define the version script
-# Build the container
-make build
-# Build and publish the container
-make release
-# Publish a container to AWS-ECR.
-# This includes the login to the repo
-make publish
-# Run the container
-make run
-# Build an run the container
-make up
-# Stop the running container
-make stop
-# Build the container with differnt config and deploy file
-make cnf=another_config.env dpl=another_deploy.env build
\ No newline at end of file