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.gitignore
View file @ 83480fa1
__pycache__ __pycache__
*.pyc *.pyc
*.err
*.out
.spack-env/
spack.lock
.gitlab-ci.yml
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.gitlab/merge_request_templates/new-package.md 0 → 100644
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### 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
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LICENSE-MIT 0 → 100644
View file @ 83480fa1
MIT License
Copyright (c) 2013-2023 LLNS, LLC and other Spack Project Developers.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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SOFTWARE.
README.md
View file @ 83480fa1
...@@ -15,6 +15,7 @@ This repository is where the EBRAINS Spack packages are maintained. It contains: ...@@ -15,6 +15,7 @@ This repository is where the EBRAINS Spack packages are maintained. It contains:
- 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 - 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) - 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. - 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.
## Contributing ## Contributing
...@@ -34,17 +35,16 @@ To install the EBRAINS Spack environment on a new machine, it is recommended to ...@@ -34,17 +35,16 @@ To install the EBRAINS Spack environment on a new machine, it is recommended 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: 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:
``` ```
git clone --branch {branch-name} https://gitlab.ebrains.eu/technical-coordination/project-internal/devops/platform/ebrains-spack-builds.git git clone --branch {branch-name} https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds.git
``` ```
Clone Spack. We currently use version v0.18.1: Clone Spack. We currently use version v0.23.1:
``` ```
git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch v0.18.1 https://github.com/spack/spack git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch v0.23.1 https://github.com/spack/spack
``` ```
Modify (if needed) and copy the package.yaml file (that contains important package settings for Spack) and activate Spack: Activate Spack:
``` ```
cp ebrains-spack-builds/packages.yaml spack/etc/spack/packages.yaml
. spack/share/spack/setup-env.sh . spack/share/spack/setup-env.sh
``` ```
...@@ -53,17 +53,19 @@ Add the project repository to your Spack environment: ...@@ -53,17 +53,19 @@ Add the project repository to your Spack environment:
spack repo add ebrains-spack-builds spack repo add ebrains-spack-builds
``` ```
Create and activate the environment: Define your site-specific configurations:
``` ```
spack env create ebrains-env ebrains-spack-builds/spack.yaml export SYSTEMNAME=<your-system-name>
spack env activate ebrains-env mkdir ebrains-spack-builds/site-config/$SYSTEMNAME
# copy any site-specific .yaml files inside the new dir
``` ```
Install: Activate the environment and install:
``` ```
spack env activate ebrains-spack-builds
spack install --fresh spack install --fresh
``` ```
## Troubleshooting ## Troubleshooting
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/technical-coordination/project-internal/devops/platform/ebrains-spack-builds/-/issues/new) using the provided templates, or contact the Technical Coordination team directly. 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
View file @ 83480fa1
...@@ -7,6 +7,8 @@ ...@@ -7,6 +7,8 @@
# loaded by all users. # loaded by all users.
# =========================================================================================================== # ===========================================================================================================
set -euo pipefail
INSTALLATION_ROOT=$1 INSTALLATION_ROOT=$1
EBRAINS_SPACK_ENV=$2 EBRAINS_SPACK_ENV=$2
RELEASE_NAME=$3 RELEASE_NAME=$3
...@@ -28,17 +30,24 @@ EOF ...@@ -28,17 +30,24 @@ EOF
# (2) append the necessary env variables for spack env and tools # (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 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, # (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 # and the location of python modules installed in the base docker Collab image
cat <<EOF >> $KERNEL_PATH/bin/env.sh cat <<EOF >> $KERNEL_PATH/bin/env.sh
export PATH=\$PATH:/opt/app-root/src/.local/bin export PATH=\$PATH:/opt/app-root/src/.local/bin
export PYTHONPATH=\$PYTHONPATH:/opt/app-root/src/.local/lib/python3.8/site-packages:/usr/local/lib/python3.8/dist-packages export PYTHONPATH=\$PYTHONPATH:/opt/conda/lib/python3.11/site-packages
export R_LIBS_USER=/opt/app-root/src/.local/lib/R/site-library export R_LIBS_USER=/opt/app-root/src/.local/lib/R/site-library
mkdir -p \$R_LIBS_USER mkdir -p \$R_LIBS_USER
export R_LIBS=\$R_LIBS_USER:\$R_LIBS export R_LIBS=\$R_LIBS_USER:\$R_LIBS
EOF 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 # (4) create startup script for python kernel
cat $KERNEL_PATH/bin/env.sh > $KERNEL_PATH/bin/env_python.sh cat $KERNEL_PATH/bin/env.sh > $KERNEL_PATH/bin/env_python.sh
echo "python -m ipykernel_launcher -f \$@" >> $KERNEL_PATH/bin/env_python.sh echo "python -m ipykernel_launcher -f \$@" >> $KERNEL_PATH/bin/env_python.sh
...@@ -56,7 +65,7 @@ cat <<EOF > $KERNEL_PATH/$KERNEL_NAME/kernel.json ...@@ -56,7 +65,7 @@ cat <<EOF > $KERNEL_PATH/$KERNEL_NAME/kernel.json
EOF EOF
# ... and add EBRAINS logo to kernel # ... and add EBRAINS logo to kernel
cp $LAB_KERNEL_ROOT/../etc/logo-64x64-python.png $KERNEL_PATH/$KERNEL_NAME/logo-64x64.png cp $(dirname ${BASH_SOURCE[0]})/etc/logo-64x64-python.png $KERNEL_PATH/$KERNEL_NAME/logo-64x64.png
# (5) create startup script for R kernel # (5) create startup script for R kernel
cat $KERNEL_PATH/bin/env.sh > $KERNEL_PATH/bin/env_r.sh cat $KERNEL_PATH/bin/env.sh > $KERNEL_PATH/bin/env_r.sh
...@@ -75,5 +84,5 @@ cat <<EOF > $KERNEL_PATH/${KERNEL_NAME}-R/kernel.json ...@@ -75,5 +84,5 @@ cat <<EOF > $KERNEL_PATH/${KERNEL_NAME}-R/kernel.json
EOF EOF
# ... and add EBRAINS logo and kernel.js to kernel # ... and add EBRAINS logo and kernel.js to kernel
cp $LAB_KERNEL_ROOT/../etc/logo-64x64-R.png $KERNEL_PATH/${KERNEL_NAME}-R/logo-64x64.png cp $(dirname ${BASH_SOURCE[0]})/etc/logo-64x64-R.png $KERNEL_PATH/${KERNEL_NAME}-R/logo-64x64.png
cp $LAB_KERNEL_ROOT/../etc/kernel.js $KERNEL_PATH/${KERNEL_NAME}-R/ cp $(dirname ${BASH_SOURCE[0]})/etc/kernel.js $KERNEL_PATH/${KERNEL_NAME}-R/
create_job.sh
View file @ 83480fa1
...@@ -2,20 +2,20 @@ ...@@ -2,20 +2,20 @@
# =========================================================================================================== # ===========================================================================================================
# title : create_job.sh # title : create_job.sh
# usage : ./create_job.sh $OC_JOB_ID $BUILD_ENV_DOCKER_IMAGE $OP $INSTALLATION_ROOT $SPACK_VERSION # usage : ./create_job.sh $OC_JOB_ID $BUILD_ENV_DOCKER_IMAGE $INSTALLATION_ROOT
# $SPACK_ENV $BRANCH $RELEASE_NAME $LAB_KERNEL_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 # description : creates OKD job yaml file that builds/updates spack environment and creates Lab kernel
# =========================================================================================================== # ===========================================================================================================
OC_JOB_ID=$1 OC_JOB_ID=$1
BUILD_ENV_DOCKER_IMAGE=$2 BUILD_ENV_DOCKER_IMAGE=$2
OP=$3 INSTALLATION_ROOT=$3
INSTALLATION_ROOT=$4 EBRAINS_SPACK_ENV=$4
SPACK_VERSION=$5 COMMIT_SHA=$5
SPACK_ENV=$6 RELEASE_NAME=$6
BRANCH=$7 LAB_KERNEL_ROOT=$7
RELEASE_NAME=$8 UPDATE_SPACK_OCI_CACHES=$8
LAB_KERNEL_ROOT=$9 OCI_CACHE_PREFIX=$9
cat <<EOT >> simplejob.yml cat <<EOT >> simplejob.yml
apiVersion: batch/v1 apiVersion: batch/v1
...@@ -34,24 +34,77 @@ spec: ...@@ -34,24 +34,77 @@ spec:
- name: simplejob - name: simplejob
image: ${BUILD_ENV_DOCKER_IMAGE} image: ${BUILD_ENV_DOCKER_IMAGE}
imagePullPolicy: Always imagePullPolicy: Always
resources:
limits:
cpu: '8'
memory: '32Gi'
requests:
cpu: '4'
memory: '20Gi'
volumeMounts: volumeMounts:
- name: sharedbin - name: sharedbin
mountPath: /srv mountPath: /srv
command: ["/usr/local/bin/deploy-build-env.sh", "$OP", "$INSTALLATION_ROOT", "$SPACK_VERSION", "$SPACK_ENV", "$BRANCH", "$RELEASE_NAME", "$LAB_KERNEL_ROOT"] - 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: env:
- name: GITLAB_USER - name: SYSTEMNAME
valueFrom: value: ebrainslab
secretKeyRef: - name: INSTALLATION_ROOT
name: spack-repo-gitlab-token value: $INSTALLATION_ROOT
key: username - name: EBRAINS_SPACK_ENV
- name: GITLAB_TOKEN value: $EBRAINS_SPACK_ENV
valueFrom: - name: UPDATE_SPACK_OCI_CACHES
secretKeyRef: value: '$UPDATE_SPACK_OCI_CACHES'
name: spack-repo-gitlab-token - name: OCI_CACHE_PREFIX
key: password 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: volumes:
- name: sharedbin - name: sharedbin
persistentVolumeClaim: persistentVolumeClaim:
claimName: shared-binaries claimName: shared-binaries
- name: tmp
emptyDir: {}
restartPolicy: Never restartPolicy: Never
EOT 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
View file @ 83480fa1
#!/bin/bash #!/bin/bash
# =========================================================================================================== # =========================================================================================================================================
# title : install_spack_env.sh # title : install_spack_env.sh
# usage : ./install_spack_env.sh $INSTALLATION_ROOT $SPACK_VERSION $EBRAINS_REPO $EBRAINS_SPACK_ENV # 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 # 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) # (if the specified spack instance doesn't exist, it also creates it)
# =========================================================================================================== # =========================================================================================================================================
INSTALLATION_ROOT=$1 # where to set up the installation set -eo pipefail
SPACK_VERSION=$2 # which spack version to use
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_REPO=$3 # location of ebrains-spack-builds repository
EBRAINS_SPACK_ENV=$4 # name of EBRAINS Spack environment to be created/updated 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=$7
# specify location of .spack dir (by default in ~) # make sure spack uses the symlinked folder as path
# this is where cache and configuration settings are stored export CI_SPACK_ROOT=${INSTALLATION_ROOT}/spack
export SPACK_USER_CACHE_PATH=$INSTALLATION_ROOT/spack/.spack
export SPACK_USER_CONFIG_PATH=$INSTALLATION_ROOT/spack/.spack
# initial setup: clone spack if spack dir doesn't already exist # disable local configuration and cache directories
if [ ! -d $INSTALLATION_ROOT/spack ] export SPACK_DISABLE_LOCAL_CONFIG=true
then export SPACK_USER_CACHE_PATH=/tmp/spack
git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch $SPACK_VERSION https://github.com/spack/spack $INSTALLATION_ROOT/spack
# define SYSTEMNAME variable in sites where it's not already defined
export SYSTEMNAME=${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 fi
# SPACK PATCH: see https://github.com/spack/spack/pull/35290
sed -i 's/solver.solve(abstract_specs)/solver.solve(abstract_specs, tests=kwargs.get("tests", False))/g' $INSTALLATION_ROOT/spack/lib/spack/spack/concretize.py
# copy package settings (modify if necessary) and activate Spack # initial setup: use spack submodule if spack dir doesn't already exist
cp $EBRAINS_REPO/packages.yaml $INSTALLATION_ROOT/spack/etc/spack/packages.yaml SPACK_ROOT_EXISTED=1
source $INSTALLATION_ROOT/spack/share/spack/setup-env.sh if [ ! -d ${CI_SPACK_ROOT} ]; then
ln -s ${EBRAINS_REPO}/vendor/spack ${CI_SPACK_ROOT}
SPACK_ROOT_EXISTED=0
fi
# install platform compiler (extract version from packages.yaml) # activate Spack
EBRAINS_SPACK_COMPILER=$(grep 'compiler' $EBRAINS_REPO/packages.yaml | awk -F'[][]' '{ print $2 }') source ${CI_SPACK_ROOT}/share/spack/setup-env.sh
spack compiler find
spack install $EBRAINS_SPACK_COMPILER if [[ $UPSTREAM_INSTANCE ]]; then
spack load $EBRAINS_SPACK_COMPILER UPSTREAM_PREFIX=$(find $UPSTREAM_INSTANCE/spack/opt/spack/ -type d -name ".spack-db" 2>/dev/null | xargs -I {} dirname {})
spack compiler find spack config add upstreams:upstream-spack-instance:install_tree:$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 # add repo if it does not exist
if [[ ! $(spack repo list | grep $EBRAINS_REPO) ]] if [[ ! $(spack repo list | grep ebrains-spack-builds$) ]]
then then
spack repo add $EBRAINS_REPO spack repo add $EBRAINS_REPO
fi 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 ${SPACK_CACHE_BUILD}
fi
spack compiler find
# create environment if it does not exist # create environment if it does not exist
if [ ! -d "$SPACK_ROOT/var/spack/environments/$EBRAINS_SPACK_ENV" ] if [ ! -d "${CI_SPACK_ROOT}/var/spack/environments/$EBRAINS_SPACK_ENV" ]
then then
spack env create $EBRAINS_SPACK_ENV spack env create $EBRAINS_SPACK_ENV
fi fi
# update and activate environment # update environment site-configs
cp $EBRAINS_REPO/spack.yaml $SPACK_ROOT/var/spack/environments/$EBRAINS_SPACK_ENV/spack.yaml 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
spack env activate $EBRAINS_SPACK_ENV # update spack.yaml: merge top-level and site-specific spack.yaml files
# There is a known spack bug (https://github.com/spack/spack/issues/29447) in installing test dependencies spack-python $EBRAINS_REPO/site-config/ymerge.py $EBRAINS_REPO/spack.yaml $EBRAINS_REPO/site-config/$SYSTEMNAME/spack.yaml > /tmp/spack.yaml
# for installation tests. The workaround suggested in the issue is to NOT concretize separately, but simply cp /tmp/spack.yaml ${CI_SPACK_ROOT}/var/spack/environments/$EBRAINS_SPACK_ENV/
# remove the .lock file and let the enironment be concretized by the spack install command:
rm $SPACK_ROOT/var/spack/environments/$EBRAINS_SPACK_ENV/spack.lock || echo "No spack.lock file" # 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 ${CACHE_SPECFILE})
fi
# install the environment, use 2 jobs to reduce the amount of required RAM # install the environment, use 2 jobs to reduce the amount of required RAM
spack install -y -j2 --fresh --test root # delay exit code until we have updated the cache below
spack install --no-check-signature -y -j$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 # rebuild spack's database
spack reindex spack reindex
...@@ -65,7 +187,7 @@ spack reindex ...@@ -65,7 +187,7 @@ spack reindex
# this needs deactivating the environment first: # this needs deactivating the environment first:
spack env deactivate spack env deactivate
unset SPACK_LD_LIBRARY_PATH unset SPACK_LD_LIBRARY_PATH
spack env activate --sh $EBRAINS_SPACK_ENV > $SPACK_ROOT/var/spack/environments/$EBRAINS_SPACK_ENV/load_env.sh spack env activate --sh $EBRAINS_SPACK_ENV > ${CI_SPACK_ROOT}/var/spack/environments/$EBRAINS_SPACK_ENV/load_env.sh
# create modules files with spack # create modules files with spack
# spack module tcl refresh -y # spack module tcl refresh -y
......
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')
packages/.gitkeep deleted 100644 → 0
View file @ fd48dcd1
packages/acpype/package.py 0 → 100644
View file @ 83480fa1
# Copyright 2013-2024 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)
from spack.package import *
class Acpype(PythonPackage):
"""A tool based in Python to use Antechamber to generate topologies for chemical
compounds and to interface with others python applications like CCPN and ARIA"""
# Homepage and download url
homepage = "https://github.com/alanwilter/acpype"
git = 'https://github.com/alanwilter/acpype.git'
url = 'https://github.com/alanwilter/acpype/archive/refs/tags/2022.7.21.tar.gz'
# Set the gitlab accounts of this package maintainers
maintainers = ['dbeltran']
# Versions
version('master', branch='master')
version('2022.7.21', sha256='5f7e6162d9a0aed2f770b9ccf5617ac1398a423cca815ae37cbf66d4cd62ea2f')
# Dependencies
depends_on('python@3.8:', type=('build', 'run'))
depends_on('ambertools')
depends_on('openbabel')
depends_on('py-poetry-core')
# Test
@run_after('install')
@on_package_attributes(run_tests=True)
def check_install (self):
python("-c", 'import acpype')
packages/ambertools/package.py 0 → 100644
View file @ 83480fa1
# Copyright 2013-2024 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)
from spack.package import *
class Ambertools(CMakePackage):
"""AmberTools is a free, useful standalone package and a prerequisite
for installing Amber itself. The AmberTools suite is free of charge,
and its components are mostly released under the GNU General Public
License (GPL). A few components are included that are in the public
domain or which have other, open-source, licenses. The libsander and
libpbsa libraries use the LGPL license."""
homepage = "https://ambermd.org/AmberTools.php"
url = "https://ambermd.org/downloads/AmberTools22jlmrcc.tar.bz2"
maintainers("d-beltran")
# begin EBRAINS (added): add version
version("23_rc6", sha256="debb52e6ef2e1b4eaa917a8b4d4934bd2388659c660501a81ea044903bf9ee9d")
# end EBRAINS
version("22jlmrcc", sha256="1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121")
depends_on("flex", type="build")
depends_on("bison", type="build")
depends_on("tcsh", type="build")
depends_on("zlib", type=("build", "run"))
depends_on("bzip2", type=("build", "run"))
depends_on("blas", type=("build", "run"))
depends_on("lapack", type=("build", "run"))
depends_on("arpack-ng", type=("build", "run"))
depends_on("netcdf-c", type=("build", "run"))
depends_on("netcdf-fortran", type=("build", "run"))
depends_on("fftw", type=("build", "run"))
depends_on("readline", type=("build", "run"))
depends_on("netlib-xblas~plain_blas", type=("build", "run"))
# Specific variants needed for boost according to build logs
depends_on(
"boost+thread+system+program_options+iostreams+regex+timer+chrono+filesystem+graph",
type=("build", "run"),
)
# Python dependencies
# begin EBRAINS (modified): add version
depends_on("python@3.8:3.10 +tkinter", type=("build", "run"), when="@22jlmrcc")
depends_on("python@3.8: +tkinter", type=("build", "run"), when="@23_rc6")
# end EBRAINS
depends_on("py-setuptools", type="build")
depends_on("py-numpy", type=("build", "run"))
depends_on("py-matplotlib", type=("build", "run"))
depends_on("py-scipy", type=("build", "run"))
def cmake_args(self):
# Translated from ambertools build/run_cmake script
# We also add the TRUST_SYSTEM_LIBS argument mentioned in the ambertools guide
# https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Guide-to-Options
args = [
self.define("COMPILER", "GNU"),
self.define("MPI", False),
self.define("CUDA", False),
self.define("INSTALL_TESTS", True),
self.define("DOWNLOAD_MINICONDA", False),
self.define("TRUST_SYSTEM_LIBS", True),
# This is to avoid the x11 (X11_Xext_LIB) error
# It is equivalent to the "-noX11" flag accoridng to the docs:
# https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
self.define("BUILD_GUI", False),
]
return args
def setup_run_environment(self, env):
env.set("AMBER_PREFIX", self.prefix)
env.set("AMBERHOME", self.prefix)
def setup_build_environment(self, env):
env.set("AMBER_PREFIX", self.prefix)
env.set("AMBERHOME", self.prefix)
@run_after("install")
@on_package_attributes(run_tests=True)
def check_install(self):
make("test.serial")
# Temporarily copy netcdf.h header file to netcdf-fortran/include to pass the Ambertools
# cmake check (quickest fix, will probably cause problems, needs to change)
@run_before("cmake")
def fix_check(self):
cp = Executable("cp")
cp(
self.spec["netcdf-c"].headers.directories[0] + "/netcdf.h",
self.spec["netcdf-fortran"].headers.directories[0],
)