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  • rshimoura/ebrains-spack-builds
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View file @ 83480fa1
__pycache__
*.pyc
*.err
*.out
.spack-env/
spack.lock
.gitlab-ci.yml
View file @ 83480fa1
stages:
- deploy
- build
- test
variables:
OPENSHIFT_SERVER: https://okd-dev.hbp.eu
BUILD_ENV: test-build
OP: update
#SPACK_ENV_TAR_FILE: ebrains-spack-builds${CI_PIPELINE_ID}.tar.gz
SPACK_ENV_TAR_FILE: ebrains-spack-builds.tar.gz
deploy-build-environment:
stage: deploy
BUILD_ENV_DOCKER_IMAGE: docker-registry.ebrains.eu/ebrains-spack-build-env/base:devel
RUN_ENV_DOCKER_IMAGE: docker-registry.ebrains.eu/clb-jupyter-image/ebrains:dev-a7ab31be
SPACK_PATH_GITLAB: /mnt/spack_v0.23.1
SYSTEMNAME: ebrainslab
GIT_SUBMODULE_STRATEGY: recursive
GIT_CLEAN_FLAGS: -ffdxq
RUNNER_AFTER_SCRIPT_TIMEOUT: 20
# ===================================================================
# LAB DEPLOYMENTS
# ===================================================================
# start a k8s Job that will build the Spack environment
.deploy-build-environment:
variables:
OCI_CACHE_PREFIX: ""
UPDATE_SPACK_OCI_CACHES: false
stage: build
tags:
- docker-runner
- read-only
image: alpine:3.21.0
before_script:
- oc login "$OPENSHIFT_SERVER" --token="$OPENSHIFT_TOKEN"
- tar czf ${SPACK_ENV_TAR_FILE} packages/ repo.yaml spack.yaml
- mkdir copy_folder
- mv ${SPACK_ENV_TAR_FILE} copy_folder
- apk add kubectl
script:
# use the site-specific kubectl context
- kubectl config use-context $KUBE_CONTEXT
# create job description file
- chmod a+x create_job.sh
- ./create_job.sh $BUILD_ENV $OP $SPACK_ENV_TAR_FILE $CI_PIPELINE_ID
- sh create_job.sh $CI_PIPELINE_ID $BUILD_ENV_DOCKER_IMAGE $INSTALLATION_ROOT $SPACK_ENV $CI_COMMIT_SHA $RELEASE_NAME $LAB_KERNEL_ROOT $UPDATE_SPACK_OCI_CACHES $OCI_CACHE_PREFIX
- cat simplejob.yml
# select the project in openshift
- oc project jupyterhub-int
# start the deploy job
- oc create -f simplejob.yml
## wait for job to finish https://stackoverflow.com/questions/5073453wait-for-kubernetes-job-to-complete-on-either-failure-success-using-command-line
- oc get job/simplejob${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 [ $x == "Running" ]; then break; fi; sleep 1; done
- pod=$(oc get pods |grep simplejob${CI_PIPELINE_ID}|awk '{ print $1}')
- oc rsync copy_folder $pod:/opt/app-root/src
# when build job finishes get the logs
- while true; do sleep 10; x=$(oc get pods |grep $pod|awk '{ print $3}');if [ $x != "Running" ]; then break; fi; done
- oc logs jobs/simplejob${CI_PIPELINE_ID} | tee log.txt
- kubectl create -f simplejob.yml
# wait for job to finish to get the logs
- while true; do sleep 300; x=$(kubectl get pods -l job-name=simplejob${CI_PIPELINE_ID} -o jsonpath='{.items[0].status.phase}'); if [ $x != "Running" ]; then break; fi; done
# # copy logs of failed packages locally, to keep as job artifacts
# - oc rsync $(oc get pods -l job-name=simplejob${CI_PIPELINE_ID} -o name):/tmp ./ --include="*/" --include="spack/spack-stage/*/*.txt" --exclude="*"
# - mv tmp/spack/spack-stage spack_logs
# # also copy the spec of the created kernel, to keep as job artifacts
# - LAB_KERNEL_PATH = $LAB_KERNEL_ROOT/$(echo "$RELEASE_NAME" | tr '[:upper:]' '[:lower:]')
# - oc rsync $(oc get pods -l job-name=simplejob${CI_PIPELINE_ID} -o name):$LAB_KERNEL_PATH ./
# - mv .$LAB_KERNEL_PATH kernel_specs
# if spack install has failed, fail the pipeline
- if [ $(cat log.txt |grep "Error:"|wc -l) -gt 0 ]; then exit 1;fi;
# delete the job from OpenShift as we have the logs here
- oc delete job simplejob${CI_PIPELINE_ID} || true
- kubectl logs jobs/simplejob${CI_PIPELINE_ID} | tee log.txt
- if [ $(kubectl get pods -l job-name=simplejob${CI_PIPELINE_ID} -o jsonpath='{.items[0].status.containerStatuses[0].state.terminated.exitCode}') -ne 0 ]; then exit 1; fi;
# delete the job, as we have the logs here
- kubectl delete job simplejob${CI_PIPELINE_ID} || true
after_script:
- kubectl config use-context $KUBE_CONTEXT
- sh create_job_widget_script.sh $CI_PIPELINE_ID $RUN_ENV_DOCKER_IMAGE $INSTALLATION_ROOT $SPACK_ENV $RELEASE_NAME $LAB_KERNEL_ROOT
- cat widget-script.yml
- kubectl create -f widget-script.yml
- while true; do sleep 300; x=$(kubectl get pods -l job-name=widget-script${CI_PIPELINE_ID} -o jsonpath='{.items[0].status.phase}'); if [ $x != "Running" ]; then break; fi; done
- kubectl logs jobs/widget-script${CI_PIPELINE_ID} | tee log.txt
- if [ $(kubectl get pods -l job-name=widget-script${CI_PIPELINE_ID} -o jsonpath='{.items[0].status.containerStatuses[0].state.terminated.exitCode}') -ne 0 ]; then exit 1; fi;
- kubectl delete job widget-script${CI_PIPELINE_ID} || true
# artifacts:
# paths:
# - spack_logs
# - kernel_specs
# when: always
# -------------------------------------------------------------------
# Lab deployment target environments: dev and prod Lab instances
# -------------------------------------------------------------------
# deploy to a dev lab environment
.deploy-dev-server:
extends: .deploy-build-environment
variables:
LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/int
INSTALLATION_ROOT: /srv/test-build-2502
# deploy to a prod lab environment
.deploy-prod-server:
extends: .deploy-build-environment
variables:
LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/prod
INSTALLATION_ROOT: /srv/main-spack-instance-2502
# deploy to the dev lab environment at CINECA
.deploy-dev-server-cineca:
extends: .deploy-dev-server
variables:
KUBE_CONTEXT: cineca-int
resource_group: shared-NFS-mount-dev-cineca
# deploy to the prod lab environment at JSC
.deploy-prod-server-jsc:
extends: .deploy-prod-server
variables:
KUBE_CONTEXT: jsc-prod
resource_group: shared-NFS-mount-prod-jsc
# deploy to the prod lab environment at CINECA
.deploy-prod-server-cineca:
extends: .deploy-prod-server
variables:
KUBE_CONTEXT: cineca-prod
resource_group: shared-NFS-mount-prod-cineca
# -------------------------------------------------------------------
# Release types: test, experimental and official releases
# -------------------------------------------------------------------
# deploy int release (latest changes) to dev env to be tested before release to production
.deploy-int-release:
variables:
SPACK_ENV: test
RELEASE_NAME: EBRAINS-test
rules:
- if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH && $CI_PROJECT_NAMESPACE =~ /platform\/esd/ && $CI_PIPELINE_SOURCE == "push"
# deploy the experimental release of tools once a week from latest working version of int release
.deploy-exp-release:
variables:
SPACK_ENV: experimental
RELEASE_NAME: EBRAINS-experimental
# deploy the experimental release to dev env
.deploy-exp-dev-release:
extends: .deploy-exp-release
rules:
- if: $CI_PIPELINE_SOURCE == "schedule" && $DEPLOYMENT == "dev"
# deploy the experimental release to prod env
.deploy-exp-prod-release:
extends: .deploy-exp-release
rules:
- if: $CI_PIPELINE_SOURCE == "schedule" && $DEPLOYMENT == "prod"
# deploy the production release of tools
.deploy-prod-release:
variables:
SPACK_ENV: ebrains-24-04
RELEASE_NAME: EBRAINS-24.04
rules:
- if: $CI_COMMIT_BRANCH =~ /^ebrains/
when: manual
# -------------------------------------------------------------------
# Lab deployment jobs
# -------------------------------------------------------------------
# deploy int release to dev environment at CINECA
deploy-int-release-dev-cineca:
extends:
- .deploy-int-release
- .deploy-dev-server-cineca
# deploy exp release to dev environment at CINECA
deploy-exp-release-dev-cineca:
extends:
- .deploy-exp-dev-release
- .deploy-dev-server-cineca
# deploy exp release to prod environment at JSC
deploy-exp-release-prod-jsc:
extends:
- .deploy-exp-prod-release
- .deploy-prod-server-jsc
# deploy exp release to prod environment at CINECA
deploy-exp-release-prod-cineca:
extends:
- .deploy-exp-prod-release
- .deploy-prod-server-cineca
# deploy prod release to prod environment at JSC
deploy-prod-release-prod-jsc:
extends:
- .deploy-prod-release
- .deploy-prod-server-jsc
# deploy prod release to prod environment at CINECA
deploy-prod-release-prod-cineca:
extends:
- .deploy-prod-release
- .deploy-prod-server-cineca
# ===================================================================
# GITLAB RUNNER DEPLOYMENTS
# ===================================================================
# run test build job on any gitlab runner, trying to build latest changes
# with persistent, read-only deployment as upstream
build-spack-env-on-runner:
stage: build
tags:
- shell-runner
- docker-runner
- read-only
image: $BUILD_ENV_DOCKER_IMAGE
variables:
SPACK_DEV_ENV: ebrains-dev
SPACK_JOBS: 2
OCI_CACHE_PREFIX: ""
UPDATE_SPACK_OCI_CACHES: false
script:
# deactivate environment views (we don't need them for the test build-job)
- >
echo " view: False" >> $CI_PROJECT_DIR/site-config/$SYSTEMNAME/spack.yaml
# run installation script
- bash install_spack_env.sh $SPACK_JOBS $CI_PROJECT_DIR $CI_PROJECT_DIR $SPACK_DEV_ENV $SPACK_PATH_GITLAB $UPDATE_SPACK_OCI_CACHES $OCI_CACHE_PREFIX
after_script:
- mkdir -p $CI_PROJECT_DIR/spack_logs/installed $CI_PROJECT_DIR/spack_logs/not_installed
# for succesfully installed packages: keep the spack logs for any package modified during this CI job
- . $CI_PROJECT_DIR/spack/share/spack/setup-env.sh
- cd $(spack-python -c "print(spack.store.parse_install_tree(spack.config.get('config'))[0])")
- find . -mindepth 4 -maxdepth 4 \( -name ".spack" -o -name ".build" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/installed \;
# for not succesfully installed packages: also keep the spack logs for any packages that failed
- if cd /tmp/$(whoami)/spack-stage/; then find . -maxdepth 2 \( -name "*.txt" -o -name ".install_time_tests" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/not_installed \;; fi
# - if [ -d /tmp/spack_tests ]; then mv /tmp/spack_tests $CI_PROJECT_DIR; fi
artifacts:
paths:
- spack_logs
# - spack_tests
when: always
timeout: 2 days
rules:
- if: $CI_PIPELINE_SOURCE == "push"
# this one fills the spack caches and updates the ESD (ebrainslab-variant) images on harbor
sync-esd-image:
stage: build
tags:
- esd_image
image: docker-registry.ebrains.eu/esd/tmp:latest
variables:
CI_SPACK_ENV: esd
SPACK_JOBS: 4
# we access the branch-specific cache here (and also update it!)
OCI_CACHE_PREFIX: ${HARBOR_HOST}/${HARBOR_PROJECT}/${CI_COMMIT_BRANCH}
UPDATE_SPACK_OCI_CACHES: true
OCI_IMAGE_PREFIX: ${HARBOR_HOST}/${HARBOR_PROJECT}/${CI_COMMIT_BRANCH}/image
INSTALLATION_ROOT: /esd
SANDBOX_ROOT_RELATIVE: esd_image
SANDBOX_ROOT: ${CI_PROJECT_DIR}/${SANDBOX_ROOT_RELATIVE}
script:
# create a sandbox/image for performing an spack install inside based on some base image/install
- apptainer build --fix-perms --sandbox ${SANDBOX_ROOT}/ docker://${BUILD_ENV_DOCKER_IMAGE}
# run installation script inside future container environment
# => DAG concretization, subsequent cache access + fetching and actual build should be separate steps
- mkdir --mode=0777 -p ${SANDBOX_ROOT}/${INSTALLATION_ROOT}
- apptainer exec --writable --bind ${CI_PROJECT_DIR}:${INSTALLATION_ROOT} --cwd ${INSTALLATION_ROOT} ${SANDBOX_ROOT} bash ./install_spack_env.sh $SPACK_JOBS $INSTALLATION_ROOT ${INSTALLATION_ROOT} $CI_SPACK_ENV "" $UPDATE_SPACK_OCI_CACHES $OCI_CACHE_PREFIX
- echo "export SYSTEMNAME=${SYSTEMNAME}" >> ${SANDBOX_ROOT}/.singularity.d/env/90-environment.sh
- echo ". ${INSTALLATION_ROOT}/vendor/spack/var/spack/environments/${CI_SPACK_ENV}/load_env.sh" >> ${SANDBOX_ROOT}/.singularity.d/env/90-environment.sh
# preparing to assemble the image: move in the CI project contents...
- shopt -s dotglob
- find . -maxdepth 1 -and -not -name "." -and -not -name "${SANDBOX_ROOT_RELATIVE}" -exec mv -t ${SANDBOX_ROOT}/${INSTALLATION_ROOT} {} \;
# convert to SIF image file
- apptainer build latest.sif "${SANDBOX_ROOT}"
# upload SIF image as an artifact to OCI repo
- oras push --username $HARBOR_USERNAME --password $HARBOR_PASSWORD ${OCI_IMAGE_PREFIX}:lab_latest.sif latest.sif && oras_ret=$? || oras_ret=$?
# convert SIF image to OCI format and upload to OCI repo
- skopeo --insecure-policy copy --dest-creds=${HARBOR_USERNAME}:${HARBOR_PASSWORD} sif:latest.sif docker://${OCI_IMAGE_PREFIX}:lab_latest.oci && skopeo_ret=$? || skopeo_ret=$?
- exit $(expr $oras_ret + $skopeo_ret)
after_script:
- mkdir -p $CI_PROJECT_DIR/spack_logs/installed $CI_PROJECT_DIR/spack_logs/not_installed
# for succesfully installed packages: keep the spack logs for any package modified during this CI job
- PKG_DIR=${SANDBOX_ROOT}/${INSTALLATION_ROOT}/spack/opt/spack/**/linux-*/gcc-13.3.0
- if cd $PKG_DIR; then find . \( -name ".spack" -o -name ".build" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/installed \;; fi
# for not succesfully installed packages: also keep the spack logs for any packages that failed
- if cd /tmp/$(whoami)/spack-stage/; then find . -maxdepth 2 \( -name "*.txt" -o -name ".install_time_tests" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/not_installed \;; fi
artifacts:
paths:
- spack_logs
when: always
timeout: 2 days
resource_group: registry-esd-master-image
rules:
# branches that update the gitlab-runner upstream (read-only) installation and the spack OCI caches
- if: ($CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH || $CI_COMMIT_BRANCH == "experimental_rel" || $CI_COMMIT_BRANCH =~ /^ebrains/) && $CI_PROJECT_PATH =~ /platform\/esd\/ebrains-spack-builds/ && $CI_PIPELINE_SOURCE == "push"
when: manual
# update gitlab-runner upstream (read-only) installation
sync-gitlab-spack-instance:
stage: build
tags:
- docker-runner
- read-write
image: $BUILD_ENV_DOCKER_IMAGE
variables:
SPACK_REPO_PATH: $SPACK_PATH_GITLAB/ebrains-spack-builds
SPACK_JOBS: 16
OCI_CACHE_PREFIX: ""
UPDATE_SPACK_OCI_CACHES: false
script:
- SPACK_NFS_ENV=${CI_COMMIT_BRANCH//./-}
# create spack dir if it doesn't exist
- mkdir -p $SPACK_PATH_GITLAB
# get latest state of EBRAINS repo
- if [ ! -d $SPACK_REPO_PATH ]; then git clone $CI_REPOSITORY_URL --recurse-submodules $SPACK_REPO_PATH; fi
- cd $SPACK_REPO_PATH
- git fetch origin
- git reset --hard $CI_COMMIT_SHA
- git submodule update --force
# run installation script
- bash install_spack_env.sh $SPACK_JOBS $SPACK_PATH_GITLAB $SPACK_REPO_PATH $SPACK_NFS_ENV "" $UPDATE_SPACK_OCI_CACHES $OCI_CACHE_PREFIX
# create kernel spec, so that the environment can be used in gitlab CI jobs
- RELEASE_NAME=$(case $CI_COMMIT_BRANCH in experimental_rel) echo ebrains-experimental;; ebrains*) echo ${CI_COMMIT_BRANCH:0:10}.${CI_COMMIT_BRANCH:11};; *) echo $CI_COMMIT_BRANCH;; esac);
- bash create_JupyterLab_kernel.sh $SPACK_PATH_GITLAB $SPACK_NFS_ENV $RELEASE_NAME /mnt/ebrains_env
after_script:
- mkdir -p $CI_PROJECT_DIR/spack_logs/installed $CI_PROJECT_DIR/spack_logs/not_installed
# for succesfully installed packages: keep the spack logs for any package modified during this CI job
# (we use repo.yaml, that is modified at each start of the pipeline, as a reference file)
- . $SPACK_PATH_GITLAB/spack/share/spack/setup-env.sh
- cd $(spack-python -c "print(spack.store.parse_install_tree(spack.config.get('config'))[0])")
- find . -mindepth 4 -maxdepth 4 -newer $SPACK_REPO_PATH/repo.yaml \( -name ".spack" -o -name ".build" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/installed \;
# for not succesfully installed packages: also keep the spack logs for any packages that failed
- if cd /tmp/$(whoami)/spack-stage/; then find . -maxdepth 2 \( -name "*.txt" -o -name ".install_time_tests" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/not_installed \;; fi
artifacts:
paths:
- spack_logs
when: always
rules:
# branches that update the gitlab-runner upstream (read-only) installation
- if: ($CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH || $CI_COMMIT_BRANCH == "experimental_rel" || $CI_COMMIT_BRANCH =~ /^ebrains/) && $CI_PROJECT_NAMESPACE =~ /platform\/esd/ && $CI_PIPELINE_SOURCE == "push"
when: manual
# run (scheduled) standalone tests for environment
test-gitlab-spack-instance:
stage: test
tags:
- docker-runner
- read-write
image: $BUILD_ENV_DOCKER_IMAGE
variables:
SPACK_REPO_PATH: $SPACK_PATH_GITLAB/ebrains-spack-builds
SPACK_USER_CACHE_PATH: $SPACK_PATH_GITLAB/spack/.spack
SPACK_USER_CONFIG_PATH: $SPACK_PATH_GITLAB/spack/.spack
script:
- SPACK_NFS_ENV=${CI_COMMIT_BRANCH//./-}
- source $SPACK_PATH_GITLAB/spack/share/spack/setup-env.sh
- spack env activate $SPACK_NFS_ENV
# TODO: run all tests when test dependency issue is fixed
- spack test run -x wf-brainscales2-demos wf-multi-area-model
after_script:
- if [ -d /tmp/spack_tests ]; then mv /tmp/spack_tests $CI_PROJECT_DIR; fi
artifacts:
paths:
- spack_tests
when: always
rules:
- if: $CI_PIPELINE_SOURCE == "schedule" && $TEST_DEPLOYMENT == "true"
.gitlab/issue_templates/build-error.md 0 → 100644
View file @ 83480fa1
<!-- Thanks for taking the time to report this build failure. To proceed with the report please:
1. Title the issue "Installation issue: <name-of-the-package>".
2. Provide the information required below.
We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively! -->
### Summary
| | |
|---------------|-----------------------------------------------|
| Summary | Spack package build failure |
| Package info | <!-- Spack package name or entire spec --> |
| System | <!-- HPC cluster name/Collab Lab/other --> |
| Related | <!-- Other related issues (if applicable) --> |
### Steps to reproduce the issue
<!-- Fill in the console output from the exact spec you are trying to build. -->
```console
$ spack spec -I <spec>
...
$ spack install <spec>
...
```
### Error message
<!-- Please post the error message from spack inside the <details> tag below: -->
<details><summary>Error message</summary><pre><code>
(add error logs here)
</code></pre></details>
### Information on your system
<!-- Please include the output of `spack debug report` -->
<!-- If you have any relevant configuration detail (custom `packages.yaml` or `modules.yaml`, etc.) you can add that here as well. -->
### Additional information
<!-- Please upload the following files. They should be present in the stage directory of the failing build. Also upload any config.log or similar file if one exists. -->
* [spack-build-out.txt]()
* [spack-build-env.txt]()
/label ~build-error
.gitlab/issue_templates/test-error.md 0 → 100644
View file @ 83480fa1
<!-- Thanks for taking the time to report this test failure. To proceed with the report please:
1. Title the issue "Testing issue: <name-of-the-package>".
2. Provide the information required below.
We encourage you to try, as much as possible, to reduce your problem to the minimal example that still reproduces the issue. That would help us a lot in fixing it quickly and effectively! -->
### Summary
| | |
|---------------|-----------------------------------------------|
| Summary | Spack package test failure |
| Package info | <!-- Spack package name or entire spec --> |
| System | <!-- HPC cluster name/Collab Lab/other --> |
| Related | <!-- Other related issues (if applicable) --> |
### Steps to reproduce the issue
<!-- Fill in the console output from the exact spec you are trying to build and test. -->
```console
$ spack spec -I <spec>
...
$ spack spack install --test root <spec>
...
```
### Error message
<!-- Please post the error message from install-time-test-log.txt inside the <details> tag below: -->
The test error message (first 1000 lines) from install-time-test-log.txt is the following:
<details><summary>Error message</summary><pre><code>
(add error logs here)
</code></pre></details>
### Information on your system
<!-- Please include the output of `spack debug report` -->
### Additional information
<!-- Please upload the following files. They should be present in the stage directory of the failing build. Also upload any config.log or similar file if one exists. -->
* [spack-build-out.txt]()
* [spack-build-env.txt]()
* [install-time-test-log.txt]()
/label ~test-error
.gitlab/merge_request_templates/new-package.md 0 → 100644
View file @ 83480fa1
### Summary
| | |
|---------------|----------------------------------------|
| Package | <!-- Spack package name --> |
| Contact point | <!-- maintainer GitLab handle --> |
| KG entry | <!-- insert link --> |
### Checks
<!-- please download the EBRAINS Software Quality checklist, fill it and replace the file below -->
* [ ] Software Quality Checklist: [SQ-Checklist.pdf](https://drive.ebrains.eu/d/6061531326d048308823/files/?p=%2FSQ-Checklist.pdf) (level: <!-- passing, silver, gold -->)
* [ ] Current maintainer is listed first in `package.py`
* [ ] No pinned dependency versions
* [ ] Post-installation tests are defined
\ No newline at end of file
.gitlab/merge_request_templates/new-version.md 0 → 100644
View file @ 83480fa1
### Summary
| | |
|---------------|----------------------------------------|
| Package | <!-- Spack package name --> |
| Version added | <!-- version number --> |
| Contact point | <!-- maintainer GitLab handle --> |
| KG entry | <!-- insert link --> |
### Checks
<!-- please download the EBRAINS Software Quality checklist, fill it and replace the file below -->
* [ ] Software Quality Checklist: [SQ-Checklist.pdf](https://drive.ebrains.eu/d/6061531326d048308823/files/?p=%2FSQ-Checklist.pdf) (level: <!-- passing, silver, gold -->)
* [ ] Current maintainer is listed first in `package.py`
* [ ] No pinned dependency versions
* [ ] Post-installation tests are defined
\ No newline at end of file
.gitmodules 0 → 100644
View file @ 83480fa1
[submodule "vendor/spack"]
path = vendor/spack
url = https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/spack.git
shallow = true
[submodule "vendor/yashchiki"]
path = vendor/yashchiki
url = https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/dedal
shallow = true
LICENSE-APACHE 0 → 100644
View file @ 83480fa1
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
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LICENSE-MIT 0 → 100644
View file @ 83480fa1
MIT License
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SOFTWARE.
README.md
View file @ 83480fa1
# ebrains-spack-builds
Build and distribute software with Spack
Build and distribute EBRAINS software tools with Spack.
**Quickstart**
- Open a terminal at a running Collaboratory Lab Container and execute the following:
```
git clone https://gitlab.ebrains.eu/akarmas/ebrains-spack-builds.git
cd ebrains-spack-builds
source ./load_sim_tools.sh
```
- Then you can start python and import the available tools
- Currently installed:
arbor
neuron
nest
## Introduction
Building and deploying EBRAINS tools to make them available for direct use in the Collaboratory Lab environment is a challenging task, mainly due to the number of tools and the increasing complexity of resolving their dependency conflicts. To efficiently solve this problem, we have implemented a delivery strategy based on [Spack](https://spack.io/), a package manager specifically designed to simplify the installation and management of scientific software (more information [here](https://drive.ebrains.eu/f/73bcfe5acf924cef83cc/)).
Spack is highly customizable and flexible, allowing developers to create their own packages and specify their dependencies and custom build configurations. It supports a wide range of programming languages (Python, R, C, C++, Fortran etc), different hardware architectures and operating systems. All an EBRAINS developer needs to do is create a Spack package (simple description of the build logic of their software). Then Spack automatically handles downloading, building, and installing the entire EBRAINS environment, managing all their dependencies and other requirements.
## Gitlab CI/CD Enviromental variables
## Repository
The following variable(s) must be set up if not or re-configured if tokens expire.
OPENSHIFT_TOKEN: Token to login to OpenShift cluster (with the "gitlab" service account)
## Copy spack .yaml files and packages to the Openshift job pod that does the build
This repository is where the EBRAINS Spack packages are maintained. It contains:
- the EBRAINS [Spack repository](https://spack.readthedocs.io/en/latest/repositories.html), that contains all available EBRAINS Spack packages ([packages/](packages))
- the latest EBRAINS [Spack environment](https://spack.readthedocs.io/en/latest/environments.html) ([spack.yaml](spack.yaml)), a list of the specific versions of EBRAINS tools that are part of the software release
- a script ([install_spack_env.sh](install_spack_env.sh)) that can be used to install the latest spack environment on any machine (either install from scratch or update an existing installation)
- CI/CD pipelines configured for (a) testing the installation of new packages and (b) deploying the environment to the EBRAINS Collaboratory Lab.
- (WIP) all the site-specific configurations that have been used to install the EBRAINS Spack environment in different systems, such as the EBRAINS Lab and the Fenix HPC systems.
The gitlab runner copies the spack .yaml files and packages to the OpenShift job pod.
- The runner waits until the job's pod is running to start copying the files
- The pod (built from tc/ebrains-spack-build-env:latest image) waits until the necessary file(s) has finished copying so that it can continue the build process
## Contributing
## Bulding software binaries with Spack
HBP's developers/component owners that want their EBRAINS tools to be included in the official EBRAINS releases and deployed for direct use from the Lab environment should follow those steps:
**ToDo: The current build path needs to be automated with CI (e.g. gitlab runners)**
- Fork this repository
- Clone the forked repository to local machine (or use the Gitlab Web IDE)
- Create a new Spack package for your tool. For instructions on how to do this, see [the Spack documentation](https://spack.readthedocs.io/en/latest/packaging_guide.html) and the developer's section of [our documentation](https://drive.ebrains.eu/f/73bcfe5acf924cef83cc/). **Add the new package** to the repository, by creating a directory inside [packages/](./packages/) and copying the package recipe there. Also don't forget to **add a spec** to [spack.yaml](spack.yaml)
- Commit the new package and push to a new branch, e.g. `add-packagename`
- Create a Merge Request to merge your changes into the master branch of the original repository
- Check the results of the automated test build job and solve any issues
- Once the tests pass, wait for TC to approve and merge. Once merged, the package will be automatically built and deployed to the integration environment of the Collaboratory Lab (lab-int).
- As a reference you can find [here](https://spack.readthedocs.io/en/latest/command_index.html) the Spack commands list
- We will need to have different Spack environments to test specs (and build packages) and when tests are passing release specs from testing environments to production environment
## Installing the EBRAINS official Software release
- First of all we need to create an appropriate build environment (at a dedicated VM or container image or gitlab runner). The build environment must run on the same OS as the Collaboratory base container image and fulfill all Spack's pre-requisites ( [1](https://ashki23.github.io/spack.html), [2](https://spack.readthedocs.io/en/latest/getting_started.html) )
- The Spack installation folder at build time must (currently) be:
To install the EBRAINS Spack environment on a new machine, it is recommended to follow exactly the steps from [install_spack_env.sh](install_spack_env.sh), that installs or updates and tests the spack environment defined in this repository. In general, you need to:
Clone this repository. You can use the `ebrains-yy-mm` branches to install the EBRAINS official releases, the `experimental-rel` branch for the experimental release, or the `master` branch for the latest state:
```
/opt/app-root/src
git clone --branch {branch-name} https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds.git
```
to match the Spack installation directory on the current Collab base container image
- At the build environment a recent version of gcc must be running. Install the most appropriate gcc version based on the OS of the build environment. Below you can find the instructions to install the appropriate gcc version for CentOS 7 (current OS of Collaboratory base image).
Instructions to install **"devtoolset-9"** [here](https://linuxize.com/post/how-to-install-gcc-compiler-on-centos-7/).
- Then we can start building and installing tools with Spack:
Clone Spack. We currently use version v0.23.1:
```
spack install arbor %gcc@9.3.1
spack install neuron %gcc@9.3.1
spack install nest %gcc@9.3.1 +python
git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch v0.23.1 https://github.com/spack/spack
```
and perform tests for the installations:
https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html
https://neuron.yale.edu/neuron/static/docs/neuronpython/firststeps.html
https://nest-simulator.readthedocs.io/en/nest-2.20.1/auto_examples/one_neuron.html
- (Potentially) fix any potential errors for shared libraries (info [1](https://github.com/cdr/code-server/issues/766), [2](https://gcc.gnu.org/onlinedocs/libstdc++/manual/abi.html), [3](https://serverkurma.com/linux/how-to-install-and-update-gcc-on-centos-7/))
Activate Spack:
```
. spack/share/spack/setup-env.sh
```
## Delivery of the software binaries
Add the project repository to your Spack environment:
```
spack repo add ebrains-spack-builds
```
**ToDo:This methodology will change, and the delivery will be be implemented via Gitlab CI and use of the shared NFS drive**
Define your site-specific configurations:
```
export SYSTEMNAME=<your-system-name>
mkdir ebrains-spack-builds/site-config/$SYSTEMNAME
# copy any site-specific .yaml files inside the new dir
```
- After build is complete, we move on to zip the **"$SPACK_ROOT"** and the **~/.spack** folders of the build environment and transfer them to CSCS Object Storage (currently, in the future it will be a shared NFS drive)
- The artifacts that were built can now be used from the Collaboratory running containers to load and run the available simulation tools
Activate the environment and install:
```
spack env activate ebrains-spack-builds
spack install --fresh
```
## Activating software in the Collaboratory Lab containers
## Troubleshooting
- Currently to load the pre-built simulation tools in the Collaboratory Lab containers refer to **Quickstart** at the beggining of this file (currently the Object Storage at CSCS is used to download the pre-built software as a stop-gap measure until a shared NFS drive is available).
- This process will change in the future as all simulation tools will be available in the Collaboratory running containers from a shared NFS drive
If you encounter any issues with installing, testing, or using the EBRAINS Spack environment or a specific package, please [open an issue](https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds/-/issues/new) using the provided templates, or contact the Technical Coordination team directly.
create_JupyterLab_kernel.sh 0 → 100644
View file @ 83480fa1
#!/bin/bash
# ===========================================================================================================
# 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.
# ===========================================================================================================
set -euo pipefail
INSTALLATION_ROOT=$1
EBRAINS_SPACK_ENV=$2
RELEASE_NAME=$3
LAB_KERNEL_ROOT=$4
# kernel name is lowercase release name
KERNEL_NAME=$(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 base env.sh script required for the JupyterLab kernels:
mkdir -p $KERNEL_PATH/bin
# (1) create env.sh bash script
cat <<EOF > $KERNEL_PATH/bin/env.sh
#!/usr/bin/env bash
set -euxo pipefail
EOF
# (2) append the necessary env variables for spack env and tools
cat $INSTALLATION_ROOT/spack/var/spack/environments/$EBRAINS_SPACK_ENV/load_env.sh >> $KERNEL_PATH/bin/env.sh
# also copy the script so that it can be used independently:
cp $INSTALLATION_ROOT/spack/var/spack/environments/$EBRAINS_SPACK_ENV/load_env.sh $KERNEL_PATH/bin/
# (3) also add the user's .local locations to allow package installation at runtime,
# and the location of python modules installed in the base docker Collab image
cat <<EOF >> $KERNEL_PATH/bin/env.sh
export PATH=\$PATH:/opt/app-root/src/.local/bin
export PYTHONPATH=\$PYTHONPATH:/opt/conda/lib/python3.11/site-packages
export R_LIBS_USER=/opt/app-root/src/.local/lib/R/site-library
mkdir -p \$R_LIBS_USER
export R_LIBS=\$R_LIBS_USER:\$R_LIBS
EOF
# ... and set the SYSTEMNAME env var, to use Spack commands inside the kernel
cat <<EOF >> $KERNEL_PATH/bin/env.sh
export SYSTEMNAME=ebrainslab
EOF
# (4) create startup script for python kernel
cat $KERNEL_PATH/bin/env.sh > $KERNEL_PATH/bin/env_python.sh
echo "python -m ipykernel_launcher -f \$@" >> $KERNEL_PATH/bin/env_python.sh
chmod +x $KERNEL_PATH/bin/env_python.sh
# ... and the new kernel's configuration file
mkdir -p $KERNEL_PATH/$KERNEL_NAME
cat <<EOF > $KERNEL_PATH/$KERNEL_NAME/kernel.json
{
"argv": ["$KERNEL_PATH/bin/env_python.sh", "{connection_file}", "--profile=default"],
"display_name": "$RELEASE_NAME",
"language": "python",
"env": { "LAB_KERNEL_NAME": "$RELEASE_NAME", "LAB_KERNEL_RELEASE_DATE": "$(date +"%Y-%m-%d")" }
}
EOF
# ... and add EBRAINS logo to kernel
cp $(dirname ${BASH_SOURCE[0]})/etc/logo-64x64-python.png $KERNEL_PATH/$KERNEL_NAME/logo-64x64.png
# (5) create startup script for R kernel
cat $KERNEL_PATH/bin/env.sh > $KERNEL_PATH/bin/env_r.sh
echo "R --slave -e \"IRkernel::main()\" --args \$@" >> $KERNEL_PATH/bin/env_r.sh
chmod +x $KERNEL_PATH/bin/env_r.sh
# ... and the new R kernel's configuration file
mkdir -p $KERNEL_PATH/${KERNEL_NAME}-R
cat <<EOF > $KERNEL_PATH/${KERNEL_NAME}-R/kernel.json
{
"argv": ["$KERNEL_PATH/bin/env_r.sh", "{connection_file}"],
"display_name": "R-$RELEASE_NAME",
"language": "R",
"env": { "LAB_KERNEL_NAME": "R-$RELEASE_NAME", "LAB_KERNEL_RELEASE_DATE": "$(date +"%Y-%m-%d")" }
}
EOF
# ... and add EBRAINS logo and kernel.js to kernel
cp $(dirname ${BASH_SOURCE[0]})/etc/logo-64x64-R.png $KERNEL_PATH/${KERNEL_NAME}-R/logo-64x64.png
cp $(dirname ${BASH_SOURCE[0]})/etc/kernel.js $KERNEL_PATH/${KERNEL_NAME}-R/
create_job.sh
View file @ 83480fa1
#!/bin/bash
BUILD_ENV=$1
OP=$2
SPACK_ENV_TAR_FILE=$3
OC_JOB_ID=$4
# ===========================================================================================================
# title : create_job.sh
# usage : ./create_job.sh $OC_JOB_ID $BUILD_ENV_DOCKER_IMAGE $INSTALLATION_ROOT
# $SPACK_ENV $COMMIT_SHA $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
INSTALLATION_ROOT=$3
EBRAINS_SPACK_ENV=$4
COMMIT_SHA=$5
RELEASE_NAME=$6
LAB_KERNEL_ROOT=$7
UPDATE_SPACK_OCI_CACHES=$8
OCI_CACHE_PREFIX=$9
cat <<EOT >> simplejob.yml
apiVersion: batch/v1
......@@ -11,29 +23,88 @@ kind: Job
metadata:
name: simplejob${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: docker-registry.ebrains.eu/tc/ebrains-spack-build-env:latest
securityContext:
runAsUser: 1000410000
image: ${BUILD_ENV_DOCKER_IMAGE}
imagePullPolicy: Always
resources:
limits:
cpu: '8'
memory: '32Gi'
requests:
cpu: '4'
memory: '20Gi'
volumeMounts:
- name: sharedbin
mountPath: /srv
command: ["/usr/local/bin/deploy-build-env.sh", "$BUILD_ENV", "$OP", "$SPACK_ENV_TAR_FILE"]
- name: tmp
mountPath: /tmp
command:
- /bin/bash
- -c
- |
# create root dir if it doesn't exist
mkdir -p \$INSTALLATION_ROOT
# reset spack repository dir by cloning the selected version
if [ ! -d \$EBRAINS_REPO_PATH ]; then git clone ${CI_PROJECT_URL} --recurse-submodules \$EBRAINS_REPO_PATH; fi
cd \$EBRAINS_REPO_PATH
git fetch origin
git reset --hard \$COMMIT_SHA
git submodule update --force
# reset build error log dir (delete previous logs to save space)
rm -rf \$BUILD_LOGS_DIR
mkdir -p \$BUILD_LOGS_DIR
cd \$BUILD_LOGS_DIR
# run installation script
bash \$EBRAINS_REPO_PATH/install_spack_env.sh \$SPACK_JOBS \$INSTALLATION_ROOT \$EBRAINS_REPO_PATH \$EBRAINS_SPACK_ENV "" \$UPDATE_SPACK_OCI_CACHES \$OCI_CACHE_PREFIX
if [ \$? -eq 0 ]
then
# build process succeeded - create or update kernel on the NFS based on the current spack environment
bash \$EBRAINS_REPO_PATH/create_JupyterLab_kernel.sh \$INSTALLATION_ROOT \$EBRAINS_SPACK_ENV \$RELEASE_NAME \$LAB_KERNEL_ROOT && exit 0
else
# build process failed - keep spack build logs and fail the pipeline
cp -r /tmp/spack/spack-stage/* \$BUILD_LOGS_DIR
exit 1
fi
env:
- name: SYSTEMNAME
value: ebrainslab
- name: INSTALLATION_ROOT
value: $INSTALLATION_ROOT
- name: EBRAINS_SPACK_ENV
value: $EBRAINS_SPACK_ENV
- name: UPDATE_SPACK_OCI_CACHES
value: '$UPDATE_SPACK_OCI_CACHES'
- name: OCI_CACHE_PREFIX
value: $OCI_CACHE_PREFIX
- name: COMMIT_SHA
value: $COMMIT_SHA
- name: RELEASE_NAME
value: $RELEASE_NAME
- name: LAB_KERNEL_ROOT
value: $LAB_KERNEL_ROOT
- name: BUILD_LOGS_DIR
value: /srv/build_logs/$EBRAINS_SPACK_ENV
- name: EBRAINS_REPO_PATH
value: $INSTALLATION_ROOT/ebrains-spack-builds
- name: SPACK_JOBS
value: '6'
volumes:
- name: sharedbin
persistentVolumeClaim:
claimName: shared-binaries
restartPolicy: Never
- name: tmp
emptyDir: {}
restartPolicy: Never
EOT
create_job_widget_script.sh 0 → 100644
View file @ 83480fa1
#!/bin/bash
# ===========================================================================================================
# title : create_job_widget_script.sh
# usage : ./create_job_widget_script.sh $OC_JOB_ID $RUN_ENV_DOCKER_IMAGE $INSTALLATION_ROOT
# $SPACK_ENV $RELEASE_NAME $LAB_KERNEL_ROOT
# description : creates job file that generates a script to load the jupyter extensions for a given env
# ===========================================================================================================
OC_JOB_ID=$1
RUN_ENV_DOCKER_IMAGE=$2
INSTALLATION_ROOT=$3
EBRAINS_SPACK_ENV=$4
RELEASE_NAME=$5
LAB_KERNEL_ROOT=$6
cat <<EOT >> widget-script.yml
apiVersion: batch/v1
kind: Job
metadata:
name: widget-script${OC_JOB_ID}
spec:
parallelism: 1
completions: 1
backoffLimit: 0
template:
spec:
containers:
- name: widget-script
image: ${RUN_ENV_DOCKER_IMAGE}
imagePullPolicy: Always
resources:
limits:
cpu: '1'
memory: '1Gi'
requests:
cpu: '0.5'
memory: '500Mi'
volumeMounts:
- name: sharedbin
mountPath: /srv
command:
- /bin/bash
- -c
- |
. \$INSTALLATION_ROOT/spack/share/spack/setup-env.sh
spack env activate --without-view \$EBRAINS_SPACK_ENV
KERNEL_PATH=\$LAB_KERNEL_ROOT/\$(echo "\$RELEASE_NAME" | tr '[:upper:]' '[:lower:]')
spack load --sh py-tvb-ext-bucket py-tvb-ext-unicore py-tvb-ext-xircuits > \$KERNEL_PATH/bin/widget_activation.sh
env:
- name: SYSTEMNAME
value: ebrainslab
- name: SPACK_DISABLE_LOCAL_CONFIG
value: "true"
- name: INSTALLATION_ROOT
value: "$INSTALLATION_ROOT"
- name: EBRAINS_SPACK_ENV
value: "$EBRAINS_SPACK_ENV"
- name: RELEASE_NAME
value: "$RELEASE_NAME"
- name: LAB_KERNEL_ROOT
value: "$LAB_KERNEL_ROOT"
volumes:
- name: sharedbin
persistentVolumeClaim:
claimName: shared-binaries
restartPolicy: Never
EOT
etc/kernel.js 0 → 100644
View file @ 83480fa1
const cmd_key = /Mac/.test(navigator.platform) ? 'Cmd' : 'Ctrl'const edit_actions = [
{
name: 'R Assign',
shortcut: 'Alt--',
icon: 'fa-long-arrow-left',
help: 'R: Inserts the left-assign operator (<-)',
handler(cm) {
cm.replaceSelection(' <- ')
},
},
{
name: 'R Pipe',
shortcut: `Shift-${cmd_key}-M`,
icon: 'fa-angle-right',
help: 'R: Inserts the magrittr pipe operator (%>%)',
handler(cm) {
cm.replaceSelection(' %>% ')
},
},
{
name: 'R Help',
shortcut: 'F1',
icon: 'fa-book',
help: 'R: Shows the manpage for the item under the cursor',
handler(cm, cell) {
const {anchor, head} = cm.findWordAt(cm.getCursor())
const word = cm.getRange(anchor, head)
const callbacks = cell.get_callbacks()
const options = {silent: false, store_history: false, stop_on_error: true}
cell.last_msg_id = cell.notebook.kernel.execute(`help(\`${word}\`)`, callbacks, options)
},
},
]
const prefix = 'irkernel'
function add_edit_shortcut(notebook, actions, keyboard_manager, edit_action) {
const {name, shortcut, icon, help, handler} = edit_action
const action = {
icon, help,
help_index : 'zz',
handler: () => {
const cell = notebook.get_selected_cell()
handler(cell.code_mirror, cell)
},
}
const full_name = actions.register(action, name, prefix)
Jupyter.keyboard_manager.edit_shortcuts.add_shortcut(shortcut, full_name)
}
function render_math(pager, html) {
if (!html) return
const $container = pager.pager_element.find('#pager-container')
$container.find('p[style="text-align: center;"]').map((i, e) =>
e.outerHTML = `\\[${e.querySelector('i').innerHTML}\\]`)
$container.find('i').map((i, e) =>
e.outerHTML = `\\(${e.innerHTML}\\)`)
MathJax.Hub.Queue(['Typeset', MathJax.Hub, $container[0]])
}
define(['base/js/namespace'], ({
notebook,
actions,
keyboard_manager,
pager,
}) => ({
onload() {
edit_actions.forEach(a => add_edit_shortcut(notebook, actions, keyboard_manager, a))
pager.events.on('open_with_text.Pager', (event, {data: {'text/html': html}}) =>
render_math(pager, html))
},
}))
etc/logo-64x64-R.png 0 → 100644
View file @ 83480fa1
etc/logo-64x64-R.png

14.4 KiB

etc/logo-64x64-python.png 0 → 100644
View file @ 83480fa1
etc/logo-64x64-python.png

14 KiB

etc/logo-64x64.png 0 → 100644
View file @ 83480fa1
etc/logo-64x64.png

12.3 KiB

install_spack_env.sh 0 → 100644
View file @ 83480fa1
#!/bin/bash
# =========================================================================================================================================
# title : install_spack_env.sh
# usage : ./install_spack_env.sh $SPACK_JOBS $INSTALLATION_ROOT $EBRAINS_REPO $EBRAINS_SPACK_ENV $UPSTREAM_INSTANCE \
# $UPDATE_SPACK_OCI_CACHES $OCI_CACHE_PREFIX
# 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)
# =========================================================================================================================================
set -eo pipefail
SPACK_JOBS=$1 # number of jobs
INSTALLATION_ROOT=$2 # where to set up the installation
EBRAINS_REPO=$3 # location of ebrains-spack-builds repository
EBRAINS_SPACK_ENV=$4 # name of EBRAINS Spack environment to be created/updated
UPSTREAM_INSTANCE=$5 # path to Spack instance to use as upstream (optional)
UPDATE_SPACK_OCI_CACHES=$6 # "true" enables updating the OCI cache for spack sources and build results
export OCI_CACHE_PREFIX=$7
# make sure spack uses the symlinked folder as path
export CI_SPACK_ROOT=${INSTALLATION_ROOT}/spack
# disable local configuration and cache directories
export SPACK_DISABLE_LOCAL_CONFIG=true
export SPACK_USER_CACHE_PATH=/tmp/spack
# define SYSTEMNAME variable in sites where it's not already defined
export SYSTEMNAME=${SYSTEMNAME:-${HPC_SYSTEM:-$BSC_MACHINE}}
# cache related variables
export CACHE_SPECFILE=${CACHE_SPECFILE:-"env_specfile.yaml"}
export YASHCHIKI_HOME=${EBRAINS_REPO}/vendor/yashchiki
export SPACK_CACHE_SOURCE=${SPACK_CACHE_SOURCE:-${CI_SPACK_ROOT}/var/spack/cache}
export SPACK_CACHE_BUILD=${SPACK_CACHE_BUILD:-${CI_SPACK_ROOT}/var/spack/cache}
if [ ! -d ${INSTALLATION_ROOT} ]; then
mkdir -p ${INSTALLATION_ROOT}
fi
# initial setup: use spack submodule if spack dir doesn't already exist
SPACK_ROOT_EXISTED=1
if [ ! -d ${CI_SPACK_ROOT} ]; then
ln -s ${EBRAINS_REPO}/vendor/spack ${CI_SPACK_ROOT}
SPACK_ROOT_EXISTED=0
fi
# activate Spack
source ${CI_SPACK_ROOT}/share/spack/setup-env.sh
if [[ $UPSTREAM_INSTANCE ]]; then
UPSTREAM_PREFIX=$(find $UPSTREAM_INSTANCE/spack/opt/spack/ -type d -name ".spack-db" 2>/dev/null | xargs -I {} dirname {})
spack config add upstreams:upstream-spack-instance:install_tree:$UPSTREAM_PREFIX
fi
if [ "${SPACK_ROOT_EXISTED}" -eq 0 ]; then
# for caching purposes it's nice if we can relocate into long paths, but we
# can't do that for existing installations -> else path
# ECM (2025-01-23) true seems to yield too large paths for some packages (e.g., gcc)
spack config add config:install_tree:padded_length:128
fi
# add repo if it does not exist
if [[ ! $(spack repo list | grep ebrains-spack-builds$) ]]
then
spack repo add $EBRAINS_REPO
fi
# make sure all fetching/clingo stuff happens before anything else
spack spec aida
# rebuild spack's database (could be an debugging session)
spack reindex
# add local mirror if it does not exist
if [[ ! $(spack mirror list | grep local_cache) ]]; then
# TODO for newer spack versions, add: --autopush --unsigned, drop create cache command below
# (Note: spack expects `build_cache/` below the folder we specify here
spack mirror add local_cache ${SPACK_CACHE_BUILD}
fi
spack compiler find
# create environment if it does not exist
if [ ! -d "${CI_SPACK_ROOT}/var/spack/environments/$EBRAINS_SPACK_ENV" ]
then
spack env create $EBRAINS_SPACK_ENV
fi
# update environment site-configs
rm -rf ${CI_SPACK_ROOT}/var/spack/environments/$EBRAINS_SPACK_ENV/site-config && cp -r $EBRAINS_REPO/site-config ${CI_SPACK_ROOT}/var/spack/environments/$EBRAINS_SPACK_ENV
# update spack.yaml: merge top-level and site-specific spack.yaml files
spack-python $EBRAINS_REPO/site-config/ymerge.py $EBRAINS_REPO/spack.yaml $EBRAINS_REPO/site-config/$SYSTEMNAME/spack.yaml > /tmp/spack.yaml
cp /tmp/spack.yaml ${CI_SPACK_ROOT}/var/spack/environments/$EBRAINS_SPACK_ENV/
# activate environment
spack env activate --without-view $EBRAINS_SPACK_ENV
spack concretize --force --fresh --test root
# dump dag to file
spack spec -y > "${CACHE_SPECFILE}"
if [ -n "${OCI_CACHE_PREFIX}" ]; then
# fetch missing sources (if packages not yet installed)
python3 ${YASHCHIKI_HOME}/fetch_cached_sources.py \
--local-cache=${SPACK_CACHE_SOURCE} \
--remote-cache-type=oci \
--remote-cache=${OCI_CACHE_PREFIX}/source_cache \
--yashchiki-home=${YASHCHIKI_HOME} \
/tmp/missing_paths_sources.dat ${CACHE_SPECFILE}
# fetch missing build results (if packages not yet installed)
python3 ${YASHCHIKI_HOME}/fetch_cached_buildresults.py \
--local-cache=${SPACK_CACHE_BUILD}/build_cache \
--remote-cache-type=oci \
--remote-cache=${OCI_CACHE_PREFIX}/build_cache \
--yashchiki-home=${YASHCHIKI_HOME} \
/tmp/missing_paths_buildresults.dat ${CACHE_SPECFILE}
fi
spack-python -c "exit(not len(spack.environment.active_environment().uninstalled_specs()))" && (
# fetch all sources but delay exit code handling
spack fetch --dependencies --missing && ret=$? || ret=$?;
if [ -n "${OCI_CACHE_PREFIX}" ] && [ "${UPDATE_SPACK_OCI_CACHES:-false}" = "true" ]; then
# push freshly fetched sources to remote cache
echo "Performing update of the source cache"
python3 ${YASHCHIKI_HOME}/update_cached_sources.py \
--local-cache=${SPACK_CACHE_SOURCE} \
--remote-cache-type=oci \
--remote-cache=${OCI_CACHE_PREFIX}/source_cache \
/tmp/missing_paths_sources.dat;
else
echo "Updating of the source cache disabled."
fi
if [ "$ret" -ne 0 ]; then
(exit $ret)
fi
)
if [ -n "${OCI_CACHE_PREFIX}" ]; then
# record the state of installed/uninstalled packages before actually installing them
dag_hashes_pre_install=$(spack-python ${YASHCHIKI_HOME}/specfile_dag_hash.py ${CACHE_SPECFILE})
fi
# install the environment, use 2 jobs to reduce the amount of required RAM
# delay exit code until we have updated the cache below
spack install --no-check-signature -y -j$SPACK_JOBS --fresh --test root && spack_install_ret=$? || spack_install_ret=$?
# no need to update the local cache nor the remote cache if we don't want to update
if [ -n "${OCI_CACHE_PREFIX}" ] && [ "${UPDATE_SPACK_OCI_CACHES:-false}" = "true" ]; then
# push previously missing (but now installed) packages to the local cache
for dag_hash in $dag_hashes_pre_install; do
spack buildcache create --unsigned --only package ${SPACK_CACHE_BUILD} /${dag_hash} && ret=$? || ret=$?
if [ $ret -ne 0 ]; then
echo "Failed to push ${dag_hash}, trying to call spack find on it:"
spack find -Lvp /${dag_hash} || true
fi
done
# upload packages from local to remote cache
echo "Performing update of the build cache"
python3 ${YASHCHIKI_HOME}/update_cached_buildresults.py \
--local-cache=${SPACK_CACHE_BUILD}/build_cache \
--remote-cache-type=oci \
--remote-cache=${OCI_CACHE_PREFIX}/build_cache \
/tmp/missing_paths_buildresults.dat
else
echo "Updating of the build cache disabled."
fi
# propagate spack install exit code
if [ $spack_install_ret -ne 0 ]; then
(exit "$spack_install_ret")
fi
# remove local cache content
if [ -d ${SPACK_CACHE_BUILD} ]; then
spack mirror destroy --mirror-name local_cache
fi
# TODO: when using spack remote OCI build caches require an index file
#spack mirror add ebrains oci://docker-registry.ebrains.eu/esd/build_cache
#spack buildcache list -a ebrains && ret=$? || ret=$?
# rebuild spack's database
spack reindex
# create load script that when sourced activates and loads the installed spack environment, using views
# this needs deactivating the environment first:
spack env deactivate
unset SPACK_LD_LIBRARY_PATH
spack env activate --sh $EBRAINS_SPACK_ENV > ${CI_SPACK_ROOT}/var/spack/environments/$EBRAINS_SPACK_ENV/load_env.sh
# create modules files with spack
# spack module tcl refresh -y
# create loads script that when sourced activates and loads the installed spack environment, using modules
# spack env loads -r
load_sim_tools.sh deleted 100644 → 0
View file @ 512df053
#!/bin/bash
#title :load_sim_tools.sh
#description :Script to load simulation software on the Collaboratory Lab containers from the Object Storage at CSCS.
#author :Athanasios Karmas
#date :20210601
#usage :source ./load_sim_tools.sh
#==============================================================================
echo "Setting up environment..."
cp -r /srv/test-build/spack/.spack ~
source /srv/test-build/spack/share/spack/setup-env.sh
cd /srv/test-build/
spack repo add ebrains-spack-builds
cd ~
echo "Loading packages..."
spack load -r python %gcc@10.3.0
spack load -r py-numpy %gcc@10.3.0
spack load -r py-pip %gcc@10.3.0
spack load -r arbor %gcc@10.3.0
spack load -r neuron %gcc@10.3.0
spack load -r nest@2.20.0 %gcc@10.3.0
spack load -r py-pynn %gcc@10.3.0
echo "Everything ready!"
#echo "Starting Python..."
#python
operations/cleanup_script.py 0 → 100644
View file @ 83480fa1
# ensure compatability with Spack v0.18.0
try:
from spack.package_base import PackageStillNeededError
except:
from spack.package import PackageStillNeededError
needed = set()
# keep packages that are part of an environment
for e in spack.environment.all_environments():
needed.update(e.all_hashes())
# also keep packages that provide compilers (and their dependencies)
for c in spack.compilers.all_compiler_specs():
pkg_spec = spack.compilers.pkg_spec_for_compiler(c)
needed.update([dep.dag_hash() for pkg in spack.store.db.query(pkg_spec) for dep in pkg.traverse()])
installed = {spec.dag_hash(): spec for spec in spack.store.db.query()}
to_remove = set(installed) - needed
# this will try to uninstall ANY package that is not part of an environment
# including test dependencies
# for a list of all the packages that will be uninstalled:
print('The following packages will be uninstalled:')
print('\n'.join(sorted([installed[h].short_spec+' ('+h+')' for h in to_remove])))
# iteratively uninstall packages with no dependents
while to_remove:
# print('New iteration')
for hash in to_remove.copy():
spec = installed[hash]
try:
spec.package.do_uninstall()
to_remove.discard(hash)
except PackageStillNeededError:
pass
# print('Not ready to remove', spec.short_spec, 'in this iteration')