Merge branch 'sly2j-master-patch-56912' into 'master'

Fix environment in singularity See merge request !80

Merge branch 'sly2j-master-patch-56912' into 'master'
484b36c6 · Sylvester Joosten · 2751d50f · 7b2deb7f · 484b36c6 · 484b36c6
Commit 484b36c6 authored 3 years ago by Sylvester Joosten
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -30,6 +30,7 @@ stages:
  - build:dev       ## naked dev container image
  - build:release   ## dressed release container image
  - deploy          ## build/deploy singularity images
+  - test            
  - finalize

 default:
@@ -96,7 +97,7 @@ version:
      NIGHTLY_TAG=${NIGHTLY}
      if [ "x${CI_PIPELINE_SOURCE}" == "xmerge_request_event" ]; then
        INTERNAL_TAG="unstable-mr-${CI_MERGE_REQUEST_ID}"
-        NIGHTLY_TAG=
+        NIGHTLY_TAG="${INTERNAL_TAG}-nightly"
        EXPORT_TAG=$UNSTABLE
        EXPORT_TAG2=
      elif [ "$CI_COMMIT_TAG" = "v${VERSION}" ]; then
@@ -208,6 +209,8 @@ jug_xl:nightly:
  rules:
    - if: '$CI_COMMIT_BRANCH == "master"'
      when: on_success
+    - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
+      when: on_success
    - when: never
  needs:
    - version
@@ -220,9 +223,14 @@ jug_xl:nightly:
                   --build-arg INTERNAL_TAG=${INTERNAL_TAG}
                   --build-arg JUG_VERSION=nightly-$(date +%Y-%m-%d_%H-%M-%S)-$(git rev-parse HEAD)
                   containers/jug
+    - |
+      PUSH_FLAG=""
+      if [ "$CI_PIPELINE_SOURCE" == "merge_request_event" ]; then
+        PUSH_FLAG="--eicweb"
+      fi
    - ./gitlab-ci/docker_push.sh -i ${BUILD_IMAGE} -l ${NIGHTLY_TAG} 
                                 -n $DOCKER_NTRIES -t $DOCKER_WAIT_TIME
-                                 ${NIGHTLY_TAG}
+                                 ${NIGHTLY_TAG} ${PUSH_FLAG}

 .singularity:
  stage: deploy
@@ -262,6 +270,8 @@ jug_xl:singularity:nightly:
  rules:
    - if: '$CI_COMMIT_BRANCH == "master"'
      when: on_success
+    - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
+      when: on_success
    - when: never
  artifacts:
      expire_in: 1 days
@@ -289,6 +299,9 @@ juggler:master:
    project: EIC/juggler
  allow_failure: true

+include:
+  - local: 'tests/tutorial/config.yml'
+
 cleanup:
  stage: finalize
  dependencies:
@@ -299,3 +312,7 @@ cleanup:
    - ./gitlab-ci/cleanup_registry.sh -i debian_base -r 66 ${INTERNAL_TAG}
    - ./gitlab-ci/cleanup_registry.sh -i jug_dev -r 68 ${INTERNAL_TAG}
    - ./gitlab-ci/cleanup_registry.sh -i jug_xl -r 69 ${INTERNAL_TAG}
+    - |
+      if [ "$CI_PIPELINE_SOURCE" == "merge_request_event" ]; then
+        ./gitlab-ci/cleanup_registry.sh -i jug_xl -r 69 ${NIGHTLY_TAG}
+      fi
--- a/containers/jug/Dockerfile.dev
+++ b/containers/jug/Dockerfile.dev
@@ -130,9 +130,8 @@ RUN cd /opt/spack-environment                                           \
 && echo -n ""                                                          \
 && echo "Grabbing environment info"                                    \
 && spack env activate --sh -d .                                        \
-        > /etc/profile.d/z10_spack_environment.sh                       \
- && sed -i "s?LD_LIBRARY_PATH=?&/lib/x86_64-linux-gnu:?"                \
-        /etc/profile.d/z10_spack_environment.sh                         \
+        | sed "s?LD_LIBRARY_PATH=?&/lib/x86_64-linux-gnu:?"             \
+    > /etc/profile.d/z10_spack_environment.sh                           \
 && cd /opt/spack-environment                                           \
 && echo -n ""                                                          \
 && echo "Add extra environment variables for Jug, Podio and Gaudi"     \
@@ -220,12 +219,12 @@ RUN --mount=from=staging,target=/staging                                \
    rm -rf /usr/local                                                   \
 && cp -r /staging/opt/software /opt/software                           \
 && cp -r /staging/usr/local /usr/local                                 \
- && cp /staging/etc/profile.d/z10_spack_environment.sh /etc/eic-env.sh  \
- && sed -i '/MANPATH/ s/;$/:;/' /etc/eic-env.sh                         \
 && cp /staging/etc/profile.d/z11_jug_env.sh                            \
       /etc/profile.d/z11_jug_env.sh                                    \
- && cat /etc/profile.d/z11_jug_env.sh >> /etc/eic-env.sh                \
- && cp /etc/eic-env.sh /etc/profile.d/z10_eic-env.sh                    \
+ && cat /staging/etc/profile.d/z10_spack_environment.sh                 \
+       | sed '/MANPATH/ s/;$/:;/'                                       \
+       > /etc/profile.d/z10_spack_env.sh                                \
+ && cat /etc/profile.d/z1*.sh > /etc/eic-env.sh                         \
 && cp /staging/etc/jug_info /etc/jug_info

 ARG JUG_VERSION=1

--- a/containers/jug/eic-shell
+++ b/containers/jug/eic-shell
 #!/usr/bin/env bash

-source /etc/profile
 ## Force environment to be clean
+export LD_LIBRARY_PATH="/lib/x86_64-linux-gnu:/usr/local/lib64:/usr/local/lib"
+export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+[ ! -z "$CC" ] && unset CC
+[ ! -z "$CXX" ] && unset CXX
+[ ! -z "$JUPYTER_CONFIG_DIR" ] && unset JUPYTER_CONFIG_DIR
+[ ! -z "$JUPYTER_PATH" ] && unset JUPYTER_PATH
+[ ! -z "$CLING_STANDARD_PCH" ] && unset CLING_STANDARD_PCH
+[ ! -z "$USER_PATH" ] && unset USER_PATH
+[ ! -z "$SHLIB_PATH ] && unset SHLIB_PATH
+[ ! -z "$LIBPATH ] && unset $LIBPATH
+[ ! -z "$CMAKE_PREFIX_PATH" ] && unset CMAKE_PREFIX_PATH
+[ ! -z "$SOFTWARE_HOME" ] && unset SOFTWARE_HOME
+[ ! -z "$ROOTSYS" ] && unset ROOTSYS
+
+## Properly setup environment
 source /etc/eic-env.sh

 piped_args=()
@@ -15,9 +29,9 @@ fi
 ### Fire off bash
 if [ "${#piped_args[@]}" != "0" ]; then
  echo "${#piped_args[@]}"
-  printf "%s\n" "${piped_args[@]}" | bash
+  printf "%s\n" "${piped_args[@]}" | bash -s -- --norc
 elif [ $# -gt 0 ]; then
-  exec bash -c "$@"
+  exec bash --norc -c "$@"
 else
-  exec bash
+  exec bash --norc
 fi
--- a/install.sh
+++ b/install.sh
@@ -124,6 +124,9 @@ else
    ln -sf /cvmfs/eic.opensciencegrid.org/singularity/athena/${CONTAINER}_v${VERSION}.sif ${SIF}
  elif [ -f /gpfs02/cvmfst0/eic.opensciencegrid.org/singularity/athena/${CONTAINER}_v${VERSION}.sif ]; then
    ln -sf /gpfs02/cvmfst0/eic.opensciencegrid.org/singularity/athena/${CONTAINER}_v${VERSION}.sif ${SIF}
+  ## check if we have an internal CI image we will use for testing purposes
+  elif [ -f $PWD/.gitlab-ci/${CONTAINER}-${VERSION}.sif ]; then
+    ln -sf $PWD/.gitlab-ci/${CONTAINER}-${VERSION}.sif ${SIF}
  ## if not, download the container to the system
  else
    ## get the python installer and run the old-style install

--- a/tests/tutorial/config.yml
+++ b/tests/tutorial/config.yml
+## Ensure the container still works for the new container
+## even with a strange environment setup
+
+
+test:tutorial:
+  stage: test
+  needs:
+    - version
+    - jug_xl:singularity:nightly
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "master"'
+      when: on_success
+    - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
+      when: on_success
+    - when: never
+  script:
+    - mkdir eic && cd eic
+    - mkdir -p .gitlab-ci && mv ../build/jug_xl.sif .gitlab-ci/jug_xl-ci-test.sif
+    # setup our environment to be weird
+    - |
+      echo ROOTSYS=/invalid-path >> ~/.bashrc
+      echo CC=`which gfortran` >> ~/.bashrc
+      echo CXX=`which gfortran` >> ~/.bashrc
+    # setup tutorial starting position
+    - bash ../install.sh -v ci-test
+    # now attempt the tutorial
+    - ./eic-shell tests/tutorial/quick-start.sh
+    - ./eic-shell tests/tutorial/part1.sh
--- a/tests/tutorial/part1.sh
+++ b/tests/tutorial/part1.sh
+#!/bin/bash
+
+source /opt/detector/setup.sh
+
+git clone https://eicweb.phy.anl.gov/EIC/tutorials/ip6_tutorial_1.git part1
+pushd part1
+cmake -B build -S . -DCMAKE_INSTALL_PREFIX=$ATHENA_PREFIX -DCMAKE_CXX_STANDARD=17
+cmake --build build -j4 -- install
+dd_web_display --export gem_tracker.xml
+checkOverlaps -t 0.0001 -c gem_tracker.xml
+npdet_info dump gem_tracker.xml
+npsim  --runType run  --enableG4GPS \
+   --macroFile gps.mac \
+   --compactFile ./gem_tracker.xml \
+   --outputFile gem_tracker_sim.root
+
+root -b -q scripts/tutorial1_hit_position.cxx+
+root -b -q scripts/tutorial2_cell_size.cxx+
+popd
--- a/tests/tutorial/quick-start.sh
+++ b/tests/tutorial/quick-start.sh
+#!/bin/bash
+
+git clone https://eicweb.phy.anl.gov/EIC/detectors/athena.git
+git clone https://eicweb.phy.anl.gov/EIC/detectors/ip6.git
+ln -s ../ip6/ip6 athena/ip6
+
+echo "PART 1: QUICK START"
+pushd athena
+source /opt/detector/setup.sh
+dd_web_display --export athena.xml
+popd