diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 9a27aad80a66ca397816f4cee8a1bf487e28c6fd..cdc101d2dc0e18e8ac560229556b37739c9e3aa0 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -3,34 +3,28 @@ stages: - deploy - sync +variables: + SPACK_VERSION: v0.18.1 + BUILD_ENV_DOCKER_IMAGE: docker-registry.ebrains.eu/tc/ebrains-spack-build-env/okd:okd_22.12 + # start an OpenShift Job that will build the Spack environment .deploy-build-environment: stage: deploy script: + # login and select project in openshift - oc login "$OPENSHIFT_SERVER" --token="$OPENSHIFT_TOKEN" - - tar czf ${SPACK_ENV_TAR_FILE} packages/ repo.yaml spack.yaml create_JupyterLab_kernel.sh - - mkdir copy_folder - - mv ${SPACK_ENV_TAR_FILE} copy_folder + - oc project $OC_PROJECT # create job description file - chmod a+x create_job.sh - - ./create_job.sh $INSTALLATION_ROOT $SPACKIFIED_ENV $OP $SPACK_ENV_TAR_FILE $CI_PIPELINE_ID $BUILD_ENV_DOCKER_IMAGE $LAB_KERNEL_PATH $OKD_CLUSTER_UID + - ./create_job.sh $CI_PIPELINE_ID $BUILD_ENV_DOCKER_IMAGE update $INSTALLATION_ROOT $SPACK_VERSION $SPACK_ENV $CI_COMMIT_BRANCH $RELEASE_NAME $LAB_KERNEL_ROOT - cat simplejob.yml - # select the project in openshift - - oc project $OC_PROJECT # start the deploy job - oc create -f simplejob.yml - ## wait for job to finish https://stackoverflow.com/questions/5073453wait-for-kubernetes-job-to-complete-on-either-failure-success-using-command-line - - oc get job/simplejob${CI_PIPELINE_ID} -o=jsonpath='{.status}' -w && oc get job/simplejob${CI_PIPELINE_ID} -o=jsonpath='{.status.conditions[*].type}' | grep -i -E 'failed|complete' || echo 'Failed' - # wait for job's pod to become available so as to copy from the gitlab runner to the OpenShift pod - # the necessary files that define the environment that spack needs to build - - while true; do x=$(oc get pods |grep simplejob${CI_PIPELINE_ID}|awk '{ print $3}');if [ $x == "Running" ]; then break; fi; sleep 10; done - - pod=$(oc get pods |grep simplejob${CI_PIPELINE_ID}|awk '{ print $1}') - - oc rsync copy_folder $pod:/opt/app-root/src - # when build job finishes get the logs - - while true; do sleep 300; x=$(oc get pods |grep $pod|awk '{ print $3}');if [ $x != "Running" ]; then break; fi; done + # wait for job to finish to get the logs + - while true; do sleep 300; x=$(oc get pods | grep simplejob${CI_PIPELINE_ID} | awk '{ print $3}'); if [ $x != "Running" ]; then break; fi; done - oc logs jobs/simplejob${CI_PIPELINE_ID} | tee log.txt # if spack install has failed, fail the pipeline - - if [ $(cat log.txt |grep "No module available for package"|wc -l) -gt 0 ]; then exit 1;fi; + - if [ $(cat log.txt | grep "No module available for package" | wc -l) -gt 0 ]; then exit 1; fi; # delete the job from OpenShift as we have the logs here - oc delete job simplejob${CI_PIPELINE_ID} || true tags: @@ -45,15 +39,11 @@ deploy-int-release-dev-cscs: variables: OPENSHIFT_SERVER: $CSCS_OPENSHIFT_DEV_SERVER OPENSHIFT_TOKEN: $CSCS_OPENSHIFT_DEV_TOKEN - INSTALLATION_ROOT: $CSCS_INSTALLATION_ROOT_DEV - SPACKIFIED_ENV: $CSCS_SPACKIFIED_ENV_DEV - OP: $CSCS_OPERATION_DEV - BUILD_ENV_DOCKER_IMAGE: $CSCS_BUILD_ENV_DOCKER_IMAGE_DEV - LAB_KERNEL_PATH: $CSCS_LAB_KERNEL_PATH_DEV - OKD_CLUSTER_UID: $CSCS_OKD_DEV_UID - #SPACK_ENV_TAR_FILE: ebrains-spack-builds${CI_PIPELINE_ID}.tar.gz - SPACK_ENV_TAR_FILE: ebrains-spack-builds.tar.gz OC_PROJECT: jupyterhub-int + LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/int + INSTALLATION_ROOT: /srv/test-build-2212 + SPACK_ENV: test + RELEASE_NAME: EBRAINS-test resource_group: shared-NFS-mount-dev-cscs only: - master @@ -61,6 +51,7 @@ deploy-int-release-dev-cscs: variables: - $CI_PIPELINE_SOURCE == "schedule" + # Deploy the production release of tools (manual pipeline) # deploy on the production environment of the okd prod cluster at CSCS # runs on protected branches only as the token variable is protected @@ -69,15 +60,11 @@ deploy-prod-release-prod-cscs: variables: OPENSHIFT_SERVER: $CSCS_OPENSHIFT_PROD_SERVER OPENSHIFT_TOKEN: $CSCS_OPENSHIFT_PROD_TOKEN - INSTALLATION_ROOT: $CSCS_INSTALLATION_ROOT_PROD - SPACKIFIED_ENV: $CSCS_SPACKIFIED_ENV_PROD - OP: $CSCS_OPERATION_PROD - BUILD_ENV_DOCKER_IMAGE: $CSCS_BUILD_ENV_DOCKER_IMAGE_PROD - LAB_KERNEL_PATH: $CSCS_LAB_KERNEL_PATH_PROD - OKD_CLUSTER_UID: $CSCS_OKD_PROD_UID - #SPACK_ENV_TAR_FILE: ebrains-spack-builds${CI_PIPELINE_ID}.tar.gz - SPACK_ENV_TAR_FILE: ebrains-spack-builds.tar.gz OC_PROJECT: jupyterhub + LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/prod + INSTALLATION_ROOT: /srv/main-spack-instance-2212 + SPACK_ENV: ebrains-23-01 + RELEASE_NAME: EBRAINS-23.01 resource_group: shared-NFS-mount-prod-cscs rules: - if: '$CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH && $CI_COMMIT_BRANCH =~ /ebrains/' @@ -92,15 +79,11 @@ deploy-prod-release-prod-jsc: variables: OPENSHIFT_SERVER: $JSC_OPENSHIFT_PROD_SERVER OPENSHIFT_TOKEN: $JSC_OPENSHIFT_PROD_TOKEN - INSTALLATION_ROOT: $JSC_INSTALLATION_ROOT_PROD - SPACKIFIED_ENV: $JSC_SPACKIFIED_ENV_PROD - OP: $JSC_OPERATION_PROD - BUILD_ENV_DOCKER_IMAGE: $JSC_BUILD_ENV_DOCKER_IMAGE_PROD - LAB_KERNEL_PATH: $JSC_LAB_KERNEL_PATH_PROD - OKD_CLUSTER_UID: $JSC_OKD_PROD_UID - #SPACK_ENV_TAR_FILE: ebrains-spack-builds${CI_PIPELINE_ID}.tar.gz - SPACK_ENV_TAR_FILE: ebrains-spack-builds.tar.gz OC_PROJECT: jupyterhub + LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/prod + INSTALLATION_ROOT: /srv/main-spack-instance-2212 + SPACK_ENV: ebrains-23-01 + RELEASE_NAME: EBRAINS-23.01 resource_group: shared-NFS-mount-prod-jsc rules: - if: '$CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH && $CI_COMMIT_BRANCH =~ /ebrains/' @@ -117,30 +100,11 @@ deploy-exp-release-dev-cscs: variables: OPENSHIFT_SERVER: $CSCS_OPENSHIFT_DEV_SERVER OPENSHIFT_TOKEN: $CSCS_OPENSHIFT_DEV_TOKEN - INSTALLATION_ROOT: $CSCS_INSTALLATION_ROOT_DEV - SPACKIFIED_ENV: experimental - OP: update - BUILD_ENV_DOCKER_IMAGE: $CSCS_BUILD_ENV_DOCKER_IMAGE_DEV - LAB_KERNEL_PATH: /srv/jupyterlab_kernels/int/experimental - OKD_CLUSTER_UID: $CSCS_OKD_DEV_UID - #SPACK_ENV_TAR_FILE: ebrains-spack-builds${CI_PIPELINE_ID}.tar.gz - SPACK_ENV_TAR_FILE: ebrains-spack-builds.tar.gz OC_PROJECT: jupyterhub-int - before_script: - - | - head -n -9 create_JupyterLab_kernel.sh > tmp.txt && mv tmp.txt create_JupyterLab_kernel.sh - cat << EOS >> create_JupyterLab_kernel.sh - mkdir \$LAB_KERNEL_PATH/spack_experimental_release - cat <<EOF >\$LAB_KERNEL_PATH/spack_experimental_release/kernel.json - { - "argv": ["\$LAB_KERNEL_PATH/bin/env.sh", "{connection_file}", "--profile=default"], - "display_name": "EBRAINS_experimental_release", - "name": "spack_experimental_release", - "language": "python", - "env": { "LAB_KERNEL_NAME": "EBRAINS_experimental_release", "LAB_KERNEL_RELEASE_DATE": "\$(date +"%Y-%m-%d")" } - } - EOF - EOS + LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/int + INSTALLATION_ROOT: /srv/test-build-2212 + SPACK_ENV: experimental + RELEASE_NAME: EBRAINS-experimental resource_group: shared-NFS-mount-dev-cscs only: refs: @@ -159,30 +123,11 @@ deploy-exp-release-prod-cscs: variables: OPENSHIFT_SERVER: $CSCS_OPENSHIFT_PROD_SERVER OPENSHIFT_TOKEN: $CSCS_OPENSHIFT_PROD_TOKEN - INSTALLATION_ROOT: $CSCS_INSTALLATION_ROOT_PROD - SPACKIFIED_ENV: experimental - OP: update - BUILD_ENV_DOCKER_IMAGE: $CSCS_BUILD_ENV_DOCKER_IMAGE_PROD - LAB_KERNEL_PATH: /srv/jupyterlab_kernels/prod/experimental - OKD_CLUSTER_UID: $CSCS_OKD_PROD_UID - #SPACK_ENV_TAR_FILE: ebrains-spack-builds${CI_PIPELINE_ID}.tar.gz - SPACK_ENV_TAR_FILE: ebrains-spack-builds.tar.gz OC_PROJECT: jupyterhub - before_script: - - | - head -n -9 create_JupyterLab_kernel.sh > tmp.txt && mv tmp.txt create_JupyterLab_kernel.sh - cat << EOS >> create_JupyterLab_kernel.sh - mkdir \$LAB_KERNEL_PATH/spack_experimental_release - cat <<EOF >\$LAB_KERNEL_PATH/spack_experimental_release/kernel.json - { - "argv": ["\$LAB_KERNEL_PATH/bin/env.sh", "{connection_file}", "--profile=default"], - "display_name": "EBRAINS_experimental_release", - "name": "spack_experimental_release", - "language": "python", - "env": { "LAB_KERNEL_NAME": "EBRAINS_experimental_release", "LAB_KERNEL_RELEASE_DATE": "\$(date +"%Y-%m-%d")" } - } - EOF - EOS + LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/prod + INSTALLATION_ROOT: /srv/main-spack-instance-2212 + SPACK_ENV: experimental + RELEASE_NAME: EBRAINS-experimental resource_group: shared-NFS-mount-prod-cscs only: refs: @@ -201,30 +146,11 @@ deploy-exp-release-prod-jsc: variables: OPENSHIFT_SERVER: $JSC_OPENSHIFT_PROD_SERVER OPENSHIFT_TOKEN: $JSC_OPENSHIFT_PROD_TOKEN - INSTALLATION_ROOT: $JSC_INSTALLATION_ROOT_PROD - SPACKIFIED_ENV: experimental - OP: update - BUILD_ENV_DOCKER_IMAGE: $JSC_BUILD_ENV_DOCKER_IMAGE_PROD - LAB_KERNEL_PATH: /srv/jupyterlab_kernels/prod/experimental - OKD_CLUSTER_UID: $JSC_OKD_PROD_UID - #SPACK_ENV_TAR_FILE: ebrains-spack-builds${CI_PIPELINE_ID}.tar.gz - SPACK_ENV_TAR_FILE: ebrains-spack-builds.tar.gz OC_PROJECT: jupyterhub - before_script: - - | - head -n -9 create_JupyterLab_kernel.sh > tmp.txt && mv tmp.txt create_JupyterLab_kernel.sh - cat << EOS >> create_JupyterLab_kernel.sh - mkdir \$LAB_KERNEL_PATH/spack_experimental_release - cat <<EOF >\$LAB_KERNEL_PATH/spack_experimental_release/kernel.json - { - "argv": ["\$LAB_KERNEL_PATH/bin/env.sh", "{connection_file}", "--profile=default"], - "display_name": "EBRAINS_experimental_release", - "name": "spack_experimental_release", - "language": "python", - "env": { "LAB_KERNEL_NAME": "EBRAINS_experimental_release", "LAB_KERNEL_RELEASE_DATE": "\$(date +"%Y-%m-%d")" } - } - EOF - EOS + LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/prod + INSTALLATION_ROOT: /srv/main-spack-instance-2212 + SPACK_ENV: experimental + RELEASE_NAME: EBRAINS-experimental resource_group: shared-NFS-mount-prod-jsc only: refs: @@ -241,7 +167,7 @@ build-spack-env-on-runner: tags: - docker-runner - read-only - image: docker-registry.ebrains.eu/tc/ebrains-spack-build-env:gitlab_runners_latest + image: docker-registry.ebrains.eu/tc/ebrains-spack-build-env/gitlab_runners:gitlab_runners_22.09 variables: SPACK_DEV_ENV: ebrains-dev SPACK_DEV_PATH: $CI_PROJECT_DIR/spack @@ -249,28 +175,24 @@ build-spack-env-on-runner: SPACK_USER_CONFIG_PATH: $CI_PROJECT_DIR/.spack TMP: $CI_PROJECT_DIR/.spack-tmp script: - - git clone -c feature.manyFiles=true https://github.com/spack/spack $SPACK_DEV_PATH - - cd $SPACK_DEV_PATH - - git checkout -b ebrains_spack_commit a8d440d3ababcdec20d665ad938ab880cd9b9d17 - - cd ../ + - git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch $SPACK_VERSION https://github.com/spack/spack $SPACK_DEV_PATH - mkdir $TMP - cp packages.yaml $SPACK_DEV_PATH/etc/spack/packages.yaml - | cat <<EOF > $SPACK_DEV_PATH/etc/spack/defaults/upstreams.yaml upstreams: ebrains-gitlab-spack-instance: - install_tree: /mnt/spack/opt/spack + install_tree: /mnt/spack_v0.18.1/opt/spack EOF - . $SPACK_DEV_PATH/share/spack/setup-env.sh - spack find - spack load gcc@10.3.0 - spack compiler find - spack repo add . - - spack repo list - spack env create $SPACK_DEV_ENV spack.yaml - spack env activate $SPACK_DEV_ENV - - spack concretize -f - - spack install --no-check-signature + - spack concretize -f --fresh + - spack install -y --fresh --no-check-signature # cache: # key: spack-cache-$CI_COMMIT_REF_SLUG # paths: @@ -289,21 +211,17 @@ sync-gitlab-spack-instance: tags: - docker-runner - read-write - image: docker-registry.ebrains.eu/tc/ebrains-spack-build-env:gitlab_runners_nfs_latest + image: docker-registry.ebrains.eu/tc/ebrains-spack-build-env/gitlab_runners_nfs:gitlab_runners_nfs_22.09 variables: SPACK_NFS_ENV: ebrains-runner-build - SPACK_PATH: /mnt/spack + SPACK_PATH: /mnt/spack_v0.18.1 SPACK_USER_CACHE_PATH: $SPACK_PATH/.spack SPACK_USER_CONFIG_PATH: $SPACK_PATH/.spack SPACK_REPO_PATH: $SPACK_PATH/ebrains-spack-builds script: - | if [ ! -d $SPACK_PATH ]; then - # git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch $SPACK_VERSION https://github.com/spack/spack $SPACK_PATH - git clone -c feature.manyFiles=true https://github.com/spack/spack $SPACK_PATH - cd $SPACK_PATH - git checkout -b ebrains_spack_commit a8d440d3ababcdec20d665ad938ab880cd9b9d17 - cd ../ + git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch $SPACK_VERSION https://github.com/spack/spack $SPACK_PATH cp $CI_PROJECT_DIR/packages.yaml $SPACK_PATH/etc/spack/packages.yaml fi - . $SPACK_PATH/share/spack/setup-env.sh @@ -322,8 +240,8 @@ sync-gitlab-spack-instance: - spack env list | grep -q $SPACK_NFS_ENV && echo "Environment created already" || spack env create $SPACK_NFS_ENV $CI_PROJECT_DIR/spack.yaml - spack env activate $SPACK_NFS_ENV - cp $CI_PROJECT_DIR/spack.yaml $SPACK_ROOT/var/spack/environments/$SPACK_NFS_ENV/spack.yaml - - spack concretize -f - - spack install --no-check-signature || (cp -r /tmp/spack/spack-stage $CI_PROJECT_DIR/build_logs; exit 1) + - spack concretize -f --fresh + - spack install -y --fresh --no-check-signature || (cp -r /tmp/spack/spack-stage $CI_PROJECT_DIR/build_logs; exit 1) - spack module tcl refresh -y - spack reindex - spack env loads -r diff --git a/.gitlab/issue_templates/build-error.md b/.gitlab/issue_templates/build-error.md index abe8b619ab3e80fb00e82b1fbf03c05a33290a24..e01ec4645acbe56a55d4c6289f0c04fa144b9de6 100644 --- a/.gitlab/issue_templates/build-error.md +++ b/.gitlab/issue_templates/build-error.md @@ -27,9 +27,9 @@ $ spack install <spec> ### Error message <!-- Please post the error message from spack inside the <details> tag below: --> -<details><summary>Error message</summary><pre> +<details><summary>Error message</summary><pre><code> (add error logs here) -</pre></details> +</code></pre></details> ### Information on your system diff --git a/create_JupyterLab_kernel.sh b/create_JupyterLab_kernel.sh index 078c786b51f6c22bdc9a207c7eea2d56f09e778a..8c0d02062b46bc176d5cd42ed3f4996505d42b1b 100644 --- a/create_JupyterLab_kernel.sh +++ b/create_JupyterLab_kernel.sh @@ -1,64 +1,78 @@ #!/bin/bash -#title :create_JupyterLab_kernel.sh -#description :Script to create a spackified JupyterLab kernel conf and place it to NFS where it can be loaded by all users. -#usage :./create_JupyterLab_kernel.sh $INSTALLATION_ROOT $ENV $LAB_KERNEL_PATH -#============================================================================== + +# =========================================================================================================== +# title : create_JupyterLab_kernel.sh +# usage : ./create_JupyterLab_kernel.sh $INSTALLATION_ROOT $EBRAINS_SPACK_ENV $RELEASE_NAME $LAB_KERNEL_ROOT +# description : creates a spackified JupyterLab kernel conf and places it to the NFS where it can be +# loaded by all users. +# =========================================================================================================== INSTALLATION_ROOT=$1 -SPACKIFIED_ENV=$2 -LAB_KERNEL_PATH=$3 +EBRAINS_SPACK_ENV=$2 +RELEASE_NAME=$3 +LAB_KERNEL_ROOT=$4 + +# enable modules +source /usr/share/modules/init/sh # capture the empty env -cd /opt/app-root/src -env >> before.txt +cd ~ +env >> /tmp/before.txt -# load spack, spack repos and spack env -cp -r /srv/$INSTALLATION_ROOT/spack/.spack ~ -source /srv/$INSTALLATION_ROOT/spack/share/spack/setup-env.sh -spack repo add /srv/$INSTALLATION_ROOT/ebrains-spack-builds +# load spack +export SPACK_USER_CACHE_PATH=$INSTALLATION_ROOT/spack/.spack +export SPACK_USER_CONFIG_PATH=$INSTALLATION_ROOT/spack/.spack +source $INSTALLATION_ROOT/spack/share/spack/setup-env.sh # no need to activate as the env is already activated in the context it is used -#spack env activate $SPACKIFIED_ENV +# spack env activate $EBRAINS_SPACK_ENV -module use /srv/$INSTALLATION_ROOT/spack/share/spack/modules/linux-centos7-broadwell/ -module use /srv/$INSTALLATION_ROOT/spack/share/spack/modules/linux-centos7-x86_64/ -source /srv/$INSTALLATION_ROOT/spack/var/spack/environments/$SPACKIFIED_ENV/loads -# add also user's .local python3.8 packages to allow package installation at runtime -# by the user using pip +# load modules +module use $INSTALLATION_ROOT/spack/share/spack/modules/linux-ubuntu20.04-x86_64/ +source $INSTALLATION_ROOT/spack/var/spack/environments/$EBRAINS_SPACK_ENV/loads +# also add user's .local python3.8 packages to allow package installation at runtime by the user using pip export PYTHONPATH=$PYTHONPATH:/opt/app-root/src/.local/lib/python3.8/site-packages export PATH=$PATH:/opt/app-root/src/.local/bin -# export also python modules installed in the base docker Collab image +# and python modules installed in the base docker Collab image export PYTHONPATH=$PYTHONPATH:/usr/local/lib/python3.8/dist-packages # capture the env after spack activation -cd /opt/app-root/src -env >> after.txt +cd ~ +env >> /tmp/after.txt + +# kernel name is lowercase release name +KERNEL_NAME=$(echo "$RELEASE_NAME" | tr '[:upper:]' '[:lower:]') +# kernel dir is a directory inside LAB_KERNEL_ROOT named after the kernel +KERNEL_PATH=$LAB_KERNEL_ROOT/$KERNEL_NAME # prepare the env file required for the JupyterLab kernel -mkdir $LAB_KERNEL_PATH/bin -cat <<EOF > $LAB_KERNEL_PATH/bin/env.sh +mkdir -p $KERNEL_PATH/bin + +# start of env creation +cat <<EOF > $KERNEL_PATH/bin/env.sh #!/usr/bin/env bash set -euxo pipefail EOF -# load here all tools -#spack load --sh -r python@3.8.11 py-ipykernel py-pip py-numpy@1.21.0 py-scipy py-pandas py-seaborn py-matplotlib arbor nest@3.0 neuron py-pynn tvb-data tvb-library meta-brainscales %gcc@10.3.0 >> $LAB_KERNEL_PATH/bin/env.sh - # append the necessary env variables for spack env and tools -cd /opt/app-root/src -diff before.txt after.txt|grep ">"|cut -c 3- |awk '$0="export "$0' >> $LAB_KERNEL_PATH/bin/env.sh +diff /tmp/before.txt /tmp/after.txt|grep ">"|cut -c 3- |awk '$0="export "$0' >> $KERNEL_PATH/bin/env.sh # end of env creation -cat <<EOF >>$LAB_KERNEL_PATH/bin/env.sh +cat <<EOF >>$KERNEL_PATH/bin/env.sh python -m ipykernel_launcher -f \$@ EOF -chmod +x $LAB_KERNEL_PATH/bin/env.sh +chmod +x $KERNEL_PATH/bin/env.sh + # create the new kernel's configuration file -mkdir $LAB_KERNEL_PATH/spack_python_kernel_release_202112 -cat <<EOF >$LAB_KERNEL_PATH/spack_python_kernel_release_202112/kernel.json +mkdir -p $KERNEL_PATH/$KERNEL_NAME +cat <<EOF >$KERNEL_PATH/$KERNEL_NAME/kernel.json { - "argv": ["$LAB_KERNEL_PATH/bin/env.sh", "{connection_file}", "--profile=default"], - "display_name": "EBRAINS_release_v0.2_202112", - "name": "spack_python_kernel_release_202112", - "language": "python" + "argv": ["$KERNEL_PATH/bin/env.sh", "{connection_file}", "--profile=default"], + "display_name": "$RELEASE_NAME", + "name": "$KERNEL_NAME", + "language": "python", + "env": { "LAB_KERNEL_NAME": "$RELEASE_NAME", "LAB_KERNEL_RELEASE_DATE": "$(date +"%Y-%m-%d")" } } EOF + +# add EBRAINS logo to kernel +cp $LAB_KERNEL_ROOT/../logo/logo-64x64.png $KERNEL_PATH/$KERNEL_NAME/ diff --git a/create_job.sh b/create_job.sh index 906e1ba37bc6a6adccd61bfabf2cdac5843e0bf2..e8bc5fca02ef692b4d68aa13d503b6389b564c41 100644 --- a/create_job.sh +++ b/create_job.sh @@ -1,13 +1,21 @@ #!/bin/bash -INSTALLATION_ROOT=$1 -SPACKIFIED_ENV=$2 +# =========================================================================================================== +# title : create_job.sh +# usage : ./create_job.sh $OC_JOB_ID $BUILD_ENV_DOCKER_IMAGE $OP $INSTALLATION_ROOT $SPACK_VERSION +# $SPACK_ENV $BRANCH $RELEASE_NAME $LAB_KERNEL_ROOT +# description : creates OKD job yaml file that builds/updates spack environment and creates Lab kernel +# =========================================================================================================== + +OC_JOB_ID=$1 +BUILD_ENV_DOCKER_IMAGE=$2 OP=$3 -SPACK_ENV_TAR_FILE=$4 -OC_JOB_ID=$5 -BUILD_ENV_DOCKER_IMAGE=$6 -LAB_KERNEL_PATH=$7 -OKD_CLUSTER_UID=$8 +INSTALLATION_ROOT=$4 +SPACK_VERSION=$5 +SPACK_ENV=$6 +BRANCH=$7 +RELEASE_NAME=$8 +LAB_KERNEL_ROOT=$9 cat <<EOT >> simplejob.yml apiVersion: batch/v1 @@ -15,32 +23,35 @@ kind: Job metadata: name: simplejob${OC_JOB_ID} spec: - parallelism: 1 + parallelism: 1 completions: 1 - backoffLimit: 0 - template: + backoffLimit: 0 + template: metadata: name: testjob spec: - #securityContext: - # supplementalGroups: [1000410000] - # seLinuxOptions: - # level: s0:c25,c10 containers: - name: simplejob image: ${BUILD_ENV_DOCKER_IMAGE} imagePullPolicy: Always - securityContext: - runAsUser: ${OKD_CLUSTER_UID} volumeMounts: - name: sharedbin mountPath: /srv - command: ["/usr/local/bin/deploy-build-env.sh", "$INSTALLATION_ROOT", "$SPACKIFIED_ENV", "$OP", "$SPACK_ENV_TAR_FILE", "$LAB_KERNEL_PATH"] + command: ["/usr/local/bin/deploy-build-env.sh", "$OP", "$INSTALLATION_ROOT", "$SPACK_VERSION", "$SPACK_ENV", "$BRANCH", "$RELEASE_NAME", "$LAB_KERNEL_ROOT"] + env: + - name: GITLAB_USER + valueFrom: + secretKeyRef: + name: spack-repo-gitlab-token + key: username + - name: GITLAB_TOKEN + valueFrom: + secretKeyRef: + name: spack-repo-gitlab-token + key: password volumes: - name: sharedbin persistentVolumeClaim: claimName: shared-binaries restartPolicy: Never - #nodeSelector: - # kubernetes.io/hostname: okd-worker-3.dev.hbp.eu EOT diff --git a/install_spack_env.sh b/install_spack_env.sh new file mode 100644 index 0000000000000000000000000000000000000000..e2808820fbd607e7cac7bb0b672f20c292235961 --- /dev/null +++ b/install_spack_env.sh @@ -0,0 +1,63 @@ +#!/bin/bash + +# =========================================================================================================== +# title : install_spack_env.sh +# usage : ./install_spack_env.sh $INSTALLATION_ROOT $SPACK_VERSION $EBRAINS_REPO $EBRAINS_SPACK_ENV +# description : installs or updates the spack environment defined in the EBRAINS spack repo +# (if the specified spack instance doesn't exist, it also creates it) +# =========================================================================================================== + +INSTALLATION_ROOT=$1 +SPACK_VERSION=$2 +EBRAINS_REPO=$3 +EBRAINS_SPACK_ENV=$4 + +# specify location of .spack dir (by default in ~) +export SPACK_USER_CACHE_PATH=$INSTALLATION_ROOT/spack/.spack +export SPACK_USER_CONFIG_PATH=$INSTALLATION_ROOT/spack/.spack + +# initial setup: if spack dir doesn't already exist, clone it and install gcc and python +if [ ! -d $INSTALLATION_ROOT/spack ] +then + # clone spack repo, import packages.yaml config file and activate + git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch $SPACK_VERSION https://github.com/spack/spack $INSTALLATION_ROOT/spack + cp $EBRAINS_REPO/packages.yaml $INSTALLATION_ROOT/spack/etc/spack/packages.yaml + source $INSTALLATION_ROOT/spack/share/spack/setup-env.sh + # install platform compiler and python (extract versions from packages.yaml) + EBRAINS_SPACK_COMPILER=$(grep 'compiler' $EBRAINS_REPO/packages.yaml | awk -F'[][]' '{ print $2 }') + EBRAINS_SPACK_PYTHON=python@$(grep -A1 'python' $EBRAINS_REPO/packages.yaml | tail -n1 | awk -F'[][]' '{ print $2 }') + spack compiler find + spack install $EBRAINS_SPACK_COMPILER + spack load $EBRAINS_SPACK_COMPILER + spack compiler find + spack install $EBRAINS_SPACK_PYTHON %$EBRAINS_SPACK_COMPILER +else + source $INSTALLATION_ROOT/spack/share/spack/setup-env.sh +fi + +# add repo if it does not exist +if [[ ! $(spack repo list | grep $EBRAINS_REPO) ]] +then + spack repo add $EBRAINS_REPO +fi + +# create environment if it does not exist +if [ ! -d "$SPACK_ROOT/var/spack/environments/$EBRAINS_SPACK_ENV" ] +then + spack env create $EBRAINS_SPACK_ENV +fi + +# activate environment +cp $EBRAINS_REPO/spack.yaml $SPACK_ROOT/var/spack/environments/$EBRAINS_SPACK_ENV/spack.yaml +spack env activate $EBRAINS_SPACK_ENV +# remove any existing concrete specs from spack.lock and re-concretize everything +spack concretize --fresh --force +# install the environment, use 2 jobs to reduce the amount of required RAM +spack install --fresh --no-check-signature -y -j2 + +# create modules files with spack +spack module tcl refresh -y +# rebuild spack's database +spack reindex +# create loads script that when sourced activates and loads the installed spack environment +spack env loads -r diff --git a/packages/hxtorch/package.py b/packages/hxtorch/package.py index 30d79712f0702f80a8f130bbe7ce9bc2d8677cd2..6ac13f5d225ae135030e5b794deae5bb5de8609e 100644 --- a/packages/hxtorch/package.py +++ b/packages/hxtorch/package.py @@ -3,6 +3,7 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +from spack.pkg.builtin.boost import Boost import os @@ -21,6 +22,7 @@ class Hxtorch(WafPackage): # host software dependencies depends_on('bitsery', type=('build', 'link', 'run')) depends_on('binutils+gold+ld+plugins', type=('build', 'link', 'run')) # specialize + depends_on(Boost.with_default_variants) depends_on('boost@1.69.0: +graph+icu+mpi+python+numpy+coroutine+context cxxstd=17', type=('build', 'link', 'run')) # specialize boost (non-clingo, type=('build', 'link', 'run')) depends_on('cereal', type=('build', 'link', 'run')) depends_on('cppcheck', type=('build', 'link', 'run')) diff --git a/packages/llvm/package.py b/packages/llvm/package.py index 4d0226b73eadec1074649cc1c671aa32f2cace15..a12a7760917b3a7d33acf9e7d12297b34f8c9aa5 100644 --- a/packages/llvm/package.py +++ b/packages/llvm/package.py @@ -771,7 +771,7 @@ class Llvm(CMakePackage, CudaPackage): return ret # ECM: might be not needed anymore? - def add_files_to_view(self, view, merge_map): + def add_files_to_view(self, view, merge_map, skip_if_exists=True): # we remove libgomp-related files from views as they conflict with # gcc-ones ignore_file_paths = [ @@ -783,7 +783,7 @@ class Llvm(CMakePackage, CudaPackage): if path in merge_map: del merge_map[path] - super(Llvm, self).add_files_to_view(view, merge_map) + super(Llvm, self).add_files_to_view(view, merge_map, skip_if_exists=True) def get_llvm_targets_to_build(spec): targets = spec.variants['targets'].value diff --git a/packages/py-scipy/package.py b/packages/py-scipy/package.py new file mode 100644 index 0000000000000000000000000000000000000000..f3290e6ed221939dd6c45a66df3a190bb7632f05 --- /dev/null +++ b/packages/py-scipy/package.py @@ -0,0 +1,124 @@ +# this package was slightly adapted from the spack v0.18.1 upstream because with py-pybind11@2.10.1 +# available, the concretizer selected py-scipy@1.5:1.6.1 +# depends_on('py-pybind11@2.4.3:2.8', when='@1.8:', type=('build', 'link')) +# was changed to +# depends_on('py-pybind11@2.4.3:', when='@1.8:', type=('build', 'link')) + +# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +class PyScipy(PythonPackage): + """SciPy (pronounced "Sigh Pie") is a Scientific Library for Python. + It provides many user-friendly and efficient numerical routines such + as routines for numerical integration and optimization.""" + + homepage = "https://www.scipy.org/" + pypi = "scipy/scipy-1.5.4.tar.gz" + git = "https://github.com/scipy/scipy.git" + + maintainers = ['adamjstewart', 'rgommers'] + + version('master', branch='master') + version('1.8.1', sha256='9e3fb1b0e896f14a85aa9a28d5f755daaeeb54c897b746df7a55ccb02b340f33') + version('1.8.0', sha256='31d4f2d6b724bc9a98e527b5849b8a7e589bf1ea630c33aa563eda912c9ff0bd') + version('1.7.3', sha256='ab5875facfdef77e0a47d5fd39ea178b58e60e454a4c85aa1e52fcb80db7babf') + version('1.7.2', sha256='fa2dbabaaecdb502641b0b3c00dec05fb475ae48655c66da16c9ed24eda1e711') + version('1.7.1', sha256='6b47d5fa7ea651054362561a28b1ccc8da9368a39514c1bbf6c0977a1c376764') + version('1.7.0', sha256='998c5e6ea649489302de2c0bc026ed34284f531df89d2bdc8df3a0d44d165739') + version('1.6.3', sha256='a75b014d3294fce26852a9d04ea27b5671d86736beb34acdfc05859246260707') + version('1.6.2', sha256='e9da33e21c9bc1b92c20b5328adb13e5f193b924c9b969cd700c8908f315aa59') + version('1.6.1', sha256='c4fceb864890b6168e79b0e714c585dbe2fd4222768ee90bc1aa0f8218691b11') + version('1.6.0', sha256='cb6dc9f82dfd95f6b9032a8d7ea70efeeb15d5b5fd6ed4e8537bb3c673580566') + version('1.5.4', sha256='4a453d5e5689de62e5d38edf40af3f17560bfd63c9c5bd228c18c1f99afa155b') + version('1.5.3', sha256='ddae76784574cc4c172f3d5edd7308be16078dd3b977e8746860c76c195fa707') + version('1.5.2', sha256='066c513d90eb3fd7567a9e150828d39111ebd88d3e924cdfc9f8ce19ab6f90c9') + version('1.5.1', sha256='039572f0ca9578a466683558c5bf1e65d442860ec6e13307d528749cfe6d07b8') + version('1.5.0', sha256='4ff72877d19b295ee7f7727615ea8238f2d59159df0bdd98f91754be4a2767f0') + version('1.4.1', sha256='dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59') + version('1.4.0', sha256='31f7cfa93b01507c935c12b535e24812594002a02a56803d7cd063e9920d25e8') + version('1.3.3', sha256='64bf4e8ae0db2d42b58477817f648d81e77f0b381d0ea4427385bba3f959380a') + version('1.3.2', sha256='a03939b431994289f39373c57bbe452974a7da724ae7f9620a1beee575434da4') + version('1.3.1', sha256='2643cfb46d97b7797d1dbdb6f3c23fe3402904e3c90e6facfe6a9b98d808c1b5') + version('1.3.0', sha256='c3bb4bd2aca82fb498247deeac12265921fe231502a6bc6edea3ee7fe6c40a7a') + version('1.2.3', sha256='ecbe6413ca90b8e19f8475bfa303ac001e81b04ec600d17fa7f816271f7cca57') + version('1.2.2', sha256='a4331e0b8dab1ff75d2c67b5158a8bb9a83c799d7140094dda936d876c7cfbb1') + version('1.2.1', sha256='e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c') + version('1.1.0', sha256='878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1') + version('1.0.0', sha256='87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10') + version('0.19.1', sha256='a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6') + version('0.18.1', sha256='8ab6e9c808bf2fb3e8576cd8cf07226d9cdc18b012c06d9708429a821ac6634e') + version('0.17.0', sha256='f600b755fb69437d0f70361f9e560ab4d304b1b66987ed5a28bdd9dd7793e089') + version('0.15.1', sha256='a212cbc3b79e9a563aa45fc5c517b3499198bd7eb7e7be1e047568a5f48c259a') + version('0.15.0', sha256='0c74e31e08acc8bf9b6ceb9bced73df2ae0cc76003e0366350bc7b26292bf8b1') + + # pyproject.toml + depends_on('py-wheel@:0.37', type='build') + depends_on('py-setuptools', type='build') + depends_on('py-setuptools@:51.0.0', when='@1.6', type='build') + depends_on('py-setuptools@:57', when='@1.7', type='build') + depends_on('py-setuptools@:59', when='@1.8:', type='build') + depends_on('py-cython@0.29.18:2', when='@1.7:', type='build') + depends_on('py-pybind11@2.2.4:', when='@1.4.0', type=('build', 'link')) + depends_on('py-pybind11@2.4.0:', when='@1.4.1:1.4', type=('build', 'link')) + depends_on('py-pybind11@2.4.3:', when='@1.5:1.6.1', type=('build', 'link')) + depends_on('py-pybind11@2.4.3:2.6', when='@1.6.2:1.7.1', type=('build', 'link')) + depends_on('py-pybind11@2.4.3:2.7', when='@1.7.2:1.7', type=('build', 'link')) + depends_on('py-pybind11@2.4.3:', when='@1.8:', type=('build', 'link')) + depends_on('py-pythran@0.9.11', when='@1.7.0:1.7.1', type=('build', 'link')) + depends_on('py-pythran@0.9.12:0.9', when='@1.7.2:1.7', type=('build', 'link')) + depends_on('py-pythran@0.10:', when='@1.8:', type=('build', 'link')) + # setup.py + depends_on('py-numpy@1.5.1:+blas+lapack', when='@:0.15', type=('build', 'link', 'run')) + depends_on('py-numpy@1.6.2:+blas+lapack', when='@0.16:0.17', type=('build', 'link', 'run')) + depends_on('py-numpy@1.7.1:+blas+lapack', when='@0.18.0:0.18', type=('build', 'link', 'run')) + depends_on('py-numpy@1.8.2:+blas+lapack', when='@0.19:1.2', type=('build', 'link', 'run')) + depends_on('py-numpy@1.13.3:+blas+lapack', when='@1.3:1.4', type=('build', 'link', 'run')) + depends_on('py-numpy@1.14.5:+blas+lapack', when='@1.5.0:1.5', type=('build', 'link', 'run')) + depends_on('py-numpy@1.16.5:+blas+lapack', when='@1.6:1.6.1', type=('build', 'link', 'run')) + depends_on('py-numpy@1.16.5:1.22+blas+lapack', when='@1.6.2:1.7', type=('build', 'link', 'run')) + depends_on('py-numpy@1.17.3:1.24+blas+lapack', when='@1.8:', type=('build', 'link', 'run')) + depends_on('python@2.6:2.8,3.2:', when='@:0.17', type=('build', 'link', 'run')) + depends_on('python@2.7:2.8,3.4:', when='@0.18:1.2', type=('build', 'link', 'run')) + depends_on('python@3.5:', when='@1.3:1.4', type=('build', 'link', 'run')) + depends_on('python@3.6:', when='@1.5.0:1.5', type=('build', 'link', 'run')) + depends_on('python@3.7:', when='@1.6:1.6.1', type=('build', 'link', 'run')) + depends_on('python@3.7:3.9', when='@1.6.2:1.7.1', type=('build', 'link', 'run')) + depends_on('python@3.7:3.10', when='@1.7.2:1.7', type=('build', 'link', 'run')) + depends_on('python@3.8:3.10', when='@1.8:', type=('build', 'link', 'run')) + depends_on('py-pytest', type='test') + + # NOTE: scipy picks up Blas/Lapack from numpy, see + # http://www.scipy.org/scipylib/building/linux.html#step-4-build-numpy-1-5-0 + depends_on('blas') + depends_on('lapack') + # https://github.com/scipy/scipy/wiki/Dropping-support-for-Accelerate + depends_on('lapack@3.4.1:', when='@1.2:') + + # https://github.com/scipy/scipy/issues/12860 + patch('https://git.sagemath.org/sage.git/plain/build/pkgs/scipy/patches/extern_decls.patch?id=711fe05025795e44b84233e065d240859ccae5bd', + sha256='5433f60831cb554101520a8f8871ac5a32c95f7a971ccd68b69049535b106780', when='@1.2:1.5.3') + + patch('scipy-clang.patch', when='@1.5.0:1.6.3 %clang') + + def setup_build_environment(self, env): + # https://github.com/scipy/scipy/issues/9080 + env.set('F90', spack_fc) + + # https://github.com/scipy/scipy/issues/11611 + if self.spec.satisfies('@:1.4 %gcc@10:'): + env.set('FFLAGS', '-fallow-argument-mismatch') + + def install_options(self, spec, prefix): + args = [] + if spec.satisfies('%fj'): + args.extend(['config_fc', '--fcompiler=fujitsu']) + return args + + @run_after('install') + @on_package_attributes(run_tests=True) + def install_test(self): + with working_dir('spack-test', create=True): + python('-c', 'import scipy; scipy.test("full", verbose=2)') + diff --git a/packages/py-scipy/scipy-clang.patch b/packages/py-scipy/scipy-clang.patch new file mode 100644 index 0000000000000000000000000000000000000000..5dc19faeab93a31ea0162ea89d4d9093e64339cd --- /dev/null +++ b/packages/py-scipy/scipy-clang.patch @@ -0,0 +1,14 @@ +diff --git a/scipy/special/_faddeeva.cxx b/scipy/special/_faddeeva.cxx +index 9134516..159122c 100644 +--- a/scipy/special/_faddeeva.cxx ++++ b/scipy/special/_faddeeva.cxx +@@ -130,7 +130,7 @@ double faddeeva_voigt_profile(double x, double sigma, double gamma) + + if(sigma == 0){ + if (gamma == 0){ +- if (isnan(x)) ++ if (std::isnan(x)) + return x; + if (x == 0) + return NPY_INFINITY; + diff --git a/packages/pynn-brainscales/package.py b/packages/pynn-brainscales/package.py index aa53b8cc47ab9faee36e2af40f6005da62db1f6d..95e0d97a9e46c99867daac395add7a52b0d8f903 100644 --- a/packages/pynn-brainscales/package.py +++ b/packages/pynn-brainscales/package.py @@ -3,6 +3,7 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +from spack.pkg.builtin.boost import Boost class PynnBrainscales(WafPackage): @@ -19,6 +20,7 @@ class PynnBrainscales(WafPackage): # host software dependencies depends_on('bitsery', type=('build', 'link', 'run')) depends_on('binutils+gold+ld+plugins', type=('build', 'link', 'run')) # specialize + depends_on(Boost.with_default_variants) depends_on('boost@1.69.0: +graph+icu+mpi+python+numpy+coroutine+context cxxstd=17', type=('build', 'link', 'run')) # specialize boost (non-clingo, type=('build', 'link', 'run')) depends_on('cereal', type=('build', 'link', 'run')) depends_on('cppcheck', type=('build', 'link', 'run')) diff --git a/spack.yaml b/spack.yaml index 9f97800e61a36d9acd4346f82952e6f018df7d86..c507f2e320ef05496dcc0cb611d2c2645f86be3f 100644 --- a/spack.yaml +++ b/spack.yaml @@ -68,4 +68,5 @@ spack: #- sda # demo for codejam12 #- funniest1022 - concretization: together + concretizer: + unify: true