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.gitlab-ci.yml

+245 −128
Original line number Diff line number Diff line
@@ -3,27 +3,40 @@ stages: 
  - test



variables:

  BUILD_ENV_DOCKER_IMAGE: docker-registry.ebrains.eu/tc/ebrains-spack-build-env/okd:okd_23.06

  GITLAB_BUILD_ENV_DOCKER_IMAGE: docker-registry.ebrains.eu/tc/ebrains-spack-build-env/gitlab_runners_nfs:gitlab_runners_nfs_23.06

  SPACK_VERSION: v0.21.1

  SPACK_PATH_GITLAB: /mnt/spack_v0.21.1

  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: 20m



# start an OpenShift Job that will build the Spack environment

# ===================================================================

# 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:

    - apk add kubectl

  script:

    # login and select project in openshift

    - oc login "$OPENSHIFT_SERVER" --token="$OPENSHIFT_TOKEN"

    - oc project $OC_PROJECT

    # 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 $CI_PIPELINE_ID $BUILD_ENV_DOCKER_IMAGE update $INSTALLATION_ROOT $SPACK_VERSION $SPACK_ENV $CI_COMMIT_BRANCH $RELEASE_NAME $LAB_KERNEL_ROOT

    - 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

    # start the deploy job

    - oc create -f simplejob.yml

    - kubectl create -f simplejob.yml

    # 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 

    - 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
@@ -32,159 +45,200 @@ variables: 
    # - 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

    - oc logs jobs/simplejob${CI_PIPELINE_ID} | tee log.txt

    - 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:

    - shell-runner

    - 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



# Deploy in the lab-int environment the version of the tools to be

# tested before released to production (push pipeline)

# deploy on the dev environment of the okd dev cluster at CSCS

# runs on protected branches only as the token variable is protected

deploy-int-release-dev-cscs:

# -------------------------------------------------------------------

# Lab deployment target environments: dev and prod Lab instances

# -------------------------------------------------------------------



# deploy to a dev lab environment

.deploy-dev-server:

  extends: .deploy-build-environment

  variables:

    OPENSHIFT_SERVER: $CSCS_OPENSHIFT_DEV_SERVER

    OPENSHIFT_TOKEN: $CSCS_OPENSHIFT_DEV_TOKEN

    OC_PROJECT: jupyterhub-int

    LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/int

    INSTALLATION_ROOT: /srv/test-build-2402

    SPACK_ENV: test

    RELEASE_NAME: EBRAINS-test

  resource_group: shared-NFS-mount-dev-cscs

  rules:

    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH && $CI_PROJECT_NAMESPACE =~ /platform\/esd/ && $CI_PIPELINE_SOURCE != "schedule"

    INSTALLATION_ROOT: /srv/test-build-2502



# 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

deploy-prod-release-prod-cscs:

# deploy to a prod lab environment

.deploy-prod-server:

  extends: .deploy-build-environment

  variables:

    OPENSHIFT_SERVER: $CSCS_OPENSHIFT_PROD_SERVER

    OPENSHIFT_TOKEN: $CSCS_OPENSHIFT_PROD_TOKEN

    OC_PROJECT: jupyterhub

    LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/prod

    INSTALLATION_ROOT: /srv/main-spack-instance-2402

    SPACK_ENV: ebrains-24-04

    RELEASE_NAME: EBRAINS-24.04

  resource_group: shared-NFS-mount-prod-cscs

  rules:

    - if: $CI_COMMIT_BRANCH =~ /^ebrains/

      when: manual

    INSTALLATION_ROOT: /srv/main-spack-instance-2502



# Deploy the production release of tools (manual pipeline)

# deploy on the production environment of the okd prod cluster at JSC

# runs on protected branches only as the token variable is protected

deploy-prod-release-prod-jsc:

  extends: .deploy-build-environment

# deploy to the dev lab environment at CINECA

.deploy-dev-server-cineca:

  extends: .deploy-dev-server

  variables:

    OPENSHIFT_SERVER: $JSC_OPENSHIFT_PROD_SERVER

    OPENSHIFT_TOKEN: $JSC_OPENSHIFT_PROD_TOKEN

    OC_PROJECT: jupyterhub

    LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/prod

    INSTALLATION_ROOT: /srv/main-spack-instance-2402

    SPACK_ENV: ebrains-24-04

    RELEASE_NAME: EBRAINS-24.04

    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

# (the master branch and any branch starting with "lab-" is deployed to a dedicated kernel)

.deploy-int-release:

  variables:

    SPACK_ENV: $CI_COMMIT_BRANCH

    RELEASE_NAME: $CI_COMMIT_BRANCH

  rules:

    - if: '($CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH || $CI_COMMIT_BRANCH =~ /^lab-/) && $CI_PROJECT_NAMESPACE =~ /platform\/esd/ && $CI_PIPELINE_SOURCE == "push"'



# deploy a pre-production environment first, to avoid directly modifying the experimental or official release environments

.deploy-ppd-release:

  variables:

    SPACK_ENV: ppd

    RELEASE_NAME: EBRAINS-ppd

  allow_failure: false

  rules:

    - if: $CI_PIPELINE_SOURCE == "schedule"  && $DEPLOYMENT == "prod"

    - if: $CI_COMMIT_BRANCH =~ /^ebrains/

      when: manual



# Deploy the experimental release of tools (sheduled pipeline)

# once a week from latest working version of integration release 

# (branch=experimental_release) to an experimental JupyterLab kernel

# deploy on the dev environment of the okd dev cluster at CSCS

# runs on protected branches only as the token variable is protected

deploy-exp-release-dev-cscs:

  extends: .deploy-build-environment

# deploy the experimental release of tools once a week from latest working version of int release 

.deploy-exp-release:

  variables:

    OPENSHIFT_SERVER: $CSCS_OPENSHIFT_DEV_SERVER

    OPENSHIFT_TOKEN: $CSCS_OPENSHIFT_DEV_TOKEN

    OC_PROJECT: jupyterhub-int

    LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/int

    INSTALLATION_ROOT: /srv/test-build-2402

    SPACK_ENV: experimental

    RELEASE_NAME: EBRAINS-experimental

  resource_group: shared-NFS-mount-dev-cscs



# 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 of tools (sheduled pipeline)

# once a week from latest working version of integration release 

# (branch=experimental_release) to an experimental JupyterLab kernel

# deploy on the prod environment of the okd prod cluster at CSCS

# runs on protected branches only as the token variable is protected

deploy-exp-release-prod-cscs:

  extends: .deploy-build-environment

  variables:

    OPENSHIFT_SERVER: $CSCS_OPENSHIFT_PROD_SERVER

    OPENSHIFT_TOKEN: $CSCS_OPENSHIFT_PROD_TOKEN

    OC_PROJECT: jupyterhub

    LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/prod

    INSTALLATION_ROOT: /srv/main-spack-instance-2402

    SPACK_ENV: experimental

    RELEASE_NAME: EBRAINS-experimental

  resource_group: shared-NFS-mount-prod-cscs

  tags:             # this is just to ensure that the two jobs will run on different runners

    - read-write    # to avoid issues with common environment variables

    - shell-runner

# 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 experimental release of tools (sheduled pipeline)

# once a week from latest working version of integration release 

# (branch=experimental_release) to an experimental JupyterLab kernel

# deploy on the prod environment of the okd prod cluster at JSC

# runs on protected branches only as the token variable is protected

deploy-exp-release-prod-jsc:

  extends: .deploy-build-environment

# deploy the production release of tools

.deploy-prod-release:

  variables:

    OPENSHIFT_SERVER: $JSC_OPENSHIFT_PROD_SERVER

    OPENSHIFT_TOKEN: $JSC_OPENSHIFT_PROD_TOKEN

    OC_PROJECT: jupyterhub

    LAB_KERNEL_ROOT: /srv/jupyterlab_kernels/prod

    INSTALLATION_ROOT: /srv/main-spack-instance-2402

    SPACK_ENV: experimental

    RELEASE_NAME: EBRAINS-experimental

  resource_group: shared-NFS-mount-prod-jsc

  tags:             # this is just to ensure that the two jobs will run on different runners

    - read-only     # to avoid issues with common environment variables

    - shell-runner

    SPACK_ENV: ebrains-25-02

    RELEASE_NAME: EBRAINS-25.02

  rules:

    - if: $CI_PIPELINE_SOURCE == "schedule"  && $DEPLOYMENT == "prod"

      when: never

    - 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 ppd release to prod environment at JSC

deploy-ppd-release-prod-jsc:

  extends:

    - .deploy-ppd-release

    - .deploy-prod-server-jsc



# deploy ppd release to prod environment at CINECA

deploy-ppd-release-prod-cineca:

  extends:

    - .deploy-ppd-release

    - .deploy-prod-server-cineca



# deploy exp release to prod environment at JSC

deploy-exp-release-prod-jsc:

  needs: [deploy-ppd-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:

  needs: [deploy-ppd-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:

  needs: [deploy-ppd-release-prod-jsc]

  extends:

    - .deploy-prod-release

    - .deploy-prod-server-jsc



# deploy prod release to prod environment at CINECA

deploy-prod-release-prod-cineca:

  needs: [deploy-ppd-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:

    - docker-runner

    - read-only

  image: $GITLAB_BUILD_ENV_DOCKER_IMAGE

  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

    - . install_spack_env.sh $CI_PROJECT_DIR $SPACK_VERSION $CI_PROJECT_DIR $SPACK_DEV_ENV $SPACK_PATH_GITLAB

    # re-activate envionment and run tests

    - spack env activate $SPACK_DEV_ENV

    # TODO: run all tests when test dependency issue is fixed

    # - spack test run -x wf-brainscales2-demos wf-multi-area-model

    - 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

    - PKG_DIR=$CI_PROJECT_DIR/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0

    - if cd $PKG_DIR; then find . \( -name ".spack" -o -name ".build" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/installed \;; fi

    - . $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
@@ -195,33 +249,95 @@ build-spack-env-on-runner: 
    when: always

  timeout: 2 days

  rules:

    - if: $CI_PIPELINE_SOURCE != "schedule" && $CI_PIPELINE_SOURCE != "merge_request_event"

    - 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: $GITLAB_BUILD_ENV_DOCKER_IMAGE

  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

    - rm -rf $SPACK_REPO_PATH && cp -r $CI_PROJECT_DIR $SPACK_REPO_PATH

    - 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

    - . install_spack_env.sh $SPACK_PATH_GITLAB $SPACK_VERSION $SPACK_REPO_PATH $SPACK_NFS_ENV

    - 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);

    - . create_JupyterLab_kernel.sh $SPACK_PATH_GITLAB $SPACK_NFS_ENV $RELEASE_NAME /mnt/ebrains_env

    - 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)

    - PKG_DIR=$SPACK_PATH_GITLAB/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0

    - if cd $PKG_DIR; then find . -newer $SPACK_REPO_PATH/repo.yaml \( -name ".spack" -o -name ".build" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/installed \;; fi

    - . $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:
@@ -229,15 +345,17 @@ sync-gitlab-spack-instance: 
      - spack_logs

    when: always

  rules:

    - if: ($CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH || $CI_COMMIT_BRANCH == "experimental_rel" || $CI_COMMIT_BRANCH =~ /^ebrains/) && $CI_PROJECT_NAMESPACE =~ /platform\/esd/ && $CI_PIPELINE_SOURCE != "schedule"

    # 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: $GITLAB_BUILD_ENV_DOCKER_IMAGE

  image: $BUILD_ENV_DOCKER_IMAGE

  variables:

    SPACK_REPO_PATH: $SPACK_PATH_GITLAB/ebrains-spack-builds

    SPACK_USER_CACHE_PATH: $SPACK_PATH_GITLAB/spack/.spack
@@ -256,4 +374,3 @@ test-gitlab-spack-instance: 
    when: always

  rules:

    - if: $CI_PIPELINE_SOURCE == "schedule" && $TEST_DEPLOYMENT == "true"

.gitlab/merge_request_templates/new-package.md

0 → 100644
+17 −0
Original line number Diff line number Diff line 
### Summary



|               |                                        |

|---------------|----------------------------------------|

| Package       | <!-- Spack package name -->            |

| Contact point | <!-- maintainer GitLab handle -->      |

| KG entry      | <!-- insert link -->                   |





### Checks



<!-- please read the EBRAINS Software Quality Guidelines and fill out the checklist, and attach/replace the file below -->

* [ ] Software Follows [EBRAINS Software Quality Guidelines](https://drive.ebrains.eu/d/6061531326d048308823/files/?p=%2FSQ-Guideline.pdf) and reaches level: <!-- passing, silver, gold -->

   > *fill the [SQ-Checklist.pdf](https://drive.ebrains.eu/d/6061531326d048308823/files/?p=%2FSQ-Checklist.pdf) and attach below*

* [ ] 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
+18 −0
Original line number Diff line number Diff line 
### Summary



|               |                                        |

|---------------|----------------------------------------|

| Package       | <!-- Spack package name -->            |

| Version added | <!-- version number -->                |

| Contact point | <!-- maintainer GitLab handle -->      |

| KG entry      | <!-- insert link -->                   |





### Checks



<!-- please read the EBRAINS Software Quality Guidelines and fill out the checklist, and attach/replace the file below -->

* [ ] Software Follows [EBRAINS Software Quality Guidelines](https://drive.ebrains.eu/d/6061531326d048308823/files/?p=%2FSQ-Guideline.pdf) and reaches level: <!-- passing, silver, gold -->

   > *fill the [SQ-Checklist.pdf](https://drive.ebrains.eu/d/6061531326d048308823/files/?p=%2FSQ-Checklist.pdf) and attach below*

* [ ] 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
+8 −0
Original line number Diff line number Diff line 
[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

README.md

+2 −7
Original line number Diff line number Diff line
@@ -38,9 +38,9 @@ Clone this repository. You can use the `ebrains-yy-mm` branches to install the E 
git clone --branch {branch-name} https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/ebrains-spack-builds.git

```



Clone Spack. We currently use version v0.21.1:

Clone Spack. We currently use version v0.23.1:

```

git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch v0.20.0 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

```



Activate Spack:
@@ -53,11 +53,6 @@ Add the project repository to your Spack environment: 
spack repo add ebrains-spack-builds

```



Create the environment:

```

spack env create -d ebrains-spack-builds/

```



Define your site-specific configurations:

```

export SYSTEMNAME=<your-system-name>

create_JupyterLab_kernel.sh

+8 −1
Original line number Diff line number Diff line
@@ -7,6 +7,8 @@ 
#                 loaded by all users.

# ===========================================================================================================



set -euo pipefail



INSTALLATION_ROOT=$1

EBRAINS_SPACK_ENV=$2

RELEASE_NAME=$3
@@ -35,12 +37,17 @@ cp $INSTALLATION_ROOT/spack/var/spack/environments/$EBRAINS_SPACK_ENV/load_env.s 
# 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/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

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

create_job.sh

+73 −20
Original line number Diff line number Diff line
@@ -2,20 +2,20 @@ 


# ===========================================================================================================

# 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

# 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

OP=$3

INSTALLATION_ROOT=$4

SPACK_VERSION=$5

SPACK_ENV=$6

BRANCH=$7

RELEASE_NAME=$8

LAB_KERNEL_ROOT=$9

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
@@ -34,26 +34,79 @@ spec: 
      - name: simplejob

        image: ${BUILD_ENV_DOCKER_IMAGE}

        imagePullPolicy: Always

        resources:

          limits:

            cpu: '8'

            memory: '32Gi'

            ephemeral-storage: '10Gi'

          requests:

            cpu: '4'

            memory: '20Gi'

            ephemeral-storage: '256Mi'

        volumeMounts:

          - name: sharedbin

            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:

          - name: SYSTEMNAME

            value: ebrainslab

          - name: GITLAB_USER

            valueFrom:

              secretKeyRef:

                name: spack-repo-gitlab-token

                key: username

          - name: GITLAB_TOKEN

            valueFrom:

              secretKeyRef:

                name: spack-repo-gitlab-token

                key: password

          - 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

        - name: tmp

          emptyDir: {}

      restartPolicy: Never

EOT

create_job_widget_script.sh

0 → 100644
+68 −0
Original line number Diff line number Diff line 
#!/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 --first clb-nb-utils py-pip 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

install_spack_env.sh

+136 −39
Original line number Diff line number Diff line 
#!/bin/bash



# ===============================================================================================================================

# =========================================================================================================================================

# title         : install_spack_env.sh

# usage         : ./install_spack_env.sh $INSTALLATION_ROOT $SPACK_VERSION $EBRAINS_REPO $EBRAINS_SPACK_ENV $UPSTREAM_INSTANCE

# 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)

# ===============================================================================================================================

# =========================================================================================================================================



INSTALLATION_ROOT=$1  # where to set up the installation

SPACK_VERSION=$2      # which spack version to use

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



SPACK_REPO=https://gitlab.ebrains.eu/ri/tech-hub/platform/esd/spack.git

SPACK_VERSION_EBRAINS=${SPACK_VERSION}_ebrains24.04

# make sure spack uses the symlinked folder as path

export CI_SPACK_ROOT=${INSTALLATION_ROOT}/spack



# specify location of .spack dir (by default in ~)

# this is where cache and configuration settings are stored

export SPACK_USER_CACHE_PATH=$INSTALLATION_ROOT/spack/.spack

export SPACK_USER_CONFIG_PATH=$INSTALLATION_ROOT/spack/.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}}



# initial setup: clone spack if spack dir doesn't already exist

if [ ! -d $INSTALLATION_ROOT/spack ]

then

  git clone --depth 1 -c advice.detachedHead=false -c feature.manyFiles=true --branch $SPACK_VERSION_EBRAINS $SPACK_REPO $INSTALLATION_ROOT/spack

  # SPACK PATCH: the post-build logs on install-time-test-logs.txt gets ovewritten by the post-install logs.

  # quick fix for that: (TODO: investigate more and open PR)

  sed -i "s/self.file_like, \"w\"/self.file_like, \"a\"/g" $INSTALLATION_ROOT/spack/lib/spack/llnl/util/tty/log.py

# 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



if [[ $UPSTREAM_INSTANCE ]]

then

  cat <<EOF > $INSTALLATION_ROOT/spack/etc/spack/defaults/upstreams.yaml

upstreams:

  upstream-spack-instance:

    install_tree: $UPSTREAM_INSTANCE/spack/opt/spack

EOF

# 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 $INSTALLATION_ROOT/spack/share/spack/setup-env.sh

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 [[ ! $(spack repo list | grep ebrains-spack-builds$) ]]
@@ -51,37 +66,119 @@ then 
  spack repo add $EBRAINS_REPO

fi



# install platform compiler (extract version from packages.yaml)

if [ $SYSTEMNAME == ebrainslab ]

then

  EBRAINS_SPACK_COMPILER=$(grep 'compiler' $EBRAINS_REPO/site-config/$SYSTEMNAME/packages.yaml | awk -F'[][]' '{ print $2 }')

  spack compiler find

  spack load $EBRAINS_SPACK_COMPILER || { spack install $EBRAINS_SPACK_COMPILER; spack load $EBRAINS_SPACK_COMPILER; }

# 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 "$SPACK_ROOT/var/spack/environments/$EBRAINS_SPACK_ENV" ]

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 $SPACK_ROOT/var/spack/environments/$EBRAINS_SPACK_ENV/site-config && cp -r $EBRAINS_REPO/site-config $SPACK_ROOT/var/spack/environments/$EBRAINS_SPACK_ENV

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 $SPACK_ROOT/var/spack/environments/$EBRAINS_SPACK_ENV/

cp /tmp/spack.yaml ${CI_SPACK_ROOT}/var/spack/environments/$EBRAINS_SPACK_ENV/



# activate environment

spack env activate --without-view $EBRAINS_SPACK_ENV



# fetch all sources

spack concretize --force --fresh --test root

spack-python -c "exit(not len(spack.environment.active_environment().uninstalled_specs()))" && spack fetch --dependencies --missing



# 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

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

spack reindex
@@ -90,7 +187,7 @@ spack reindex 
# this needs deactivating the environment first:

spack env deactivate

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

# spack module tcl refresh -y

packages/acpype/package.py

+1 −1
Original line number Diff line number Diff line
@@ -3,7 +3,7 @@ 
#

# SPDX-License-Identifier: (Apache-2.0 OR MIT)



from spack import *

from spack.package import *



class Acpype(PythonPackage):

    """A tool based in Python to use Antechamber to generate topologies for chemical

packages/ambertools/package.py

+55 −39
Original line number Diff line number Diff line
@@ -3,28 +3,31 @@ 
#

# SPDX-License-Identifier: (Apache-2.0 OR MIT)



from spack import *

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."""

    """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."""



    # Set the homepage and download url

    homepage = "http://ambermd.org/AmberTools.php"

    url      = "http://ambermd.org/downloads/AmberTools22jlmrcc.tar.bz2"

    homepage = "https://ambermd.org/AmberTools.php"

    url = "https://ambermd.org/downloads/AmberTools22jlmrcc.tar.bz2"



    # Set the gitlab accounts of this package maintainers

    maintainers = ['dbeltran', 'elmath']

    maintainers("d-beltran")



    version('22jlmrcc', sha256='1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121')

    # begin EBRAINS (added): add version

    version("23_rc6", sha256="debb52e6ef2e1b4eaa917a8b4d4934bd2388659c660501a81ea044903bf9ee9d")

    # end EBRAINS

    version("22jlmrcc", sha256="1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121")



    # Dependencies

    depends_on("flex",                      type="build") # This is necessary for sure (experimentally tested)

    depends_on("bison",                     type="build") # This is necessary for sure (experimentally tested)

    depends_on("flex", type="build")

    depends_on("bison", type="build")

    depends_on("tcsh", type="build")

    depends_on("zlib",                      type=("build", "link", "run"))

    depends_on("zlib", type=("build", "run"))

    depends_on("bzip2", type=("build", "run"))

    depends_on("blas", type=("build", "run"))

    depends_on("lapack", type=("build", "run"))
@@ -34,21 +37,24 @@ class Ambertools (CMakePackage): 
    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 - from the build log "Could NOT find Boost (missing: thread system program_options iostreams regex timer chrono filesystem graph)"

    depends_on("boost+thread+system+program_options+iostreams+regex+timer+chrono+filesystem+graph", 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

    # WARNING: If a python 3.8 version is already installed in spack then the '+tkinter' variant makes spack ignore the version

    # WARNING: Spack may try to install the preferred python version (i.e. python 3.10.8)

    # WARNING: The soultion is uninstall python and reinstall with this variant

    depends_on('python@3.8: +tkinter',      type=('build', 'run'))

    # 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 that is mentioned in the ambertools CMake guide

        # 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"),
@@ -58,9 +64,9 @@ class Ambertools (CMakePackage): 
            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:

            # 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)

            self.define("BUILD_GUI", False),

        ]

        return args
@@ -72,7 +78,17 @@ class Ambertools (CMakePackage): 
        env.set("AMBER_PREFIX", self.prefix)

        env.set("AMBERHOME", self.prefix)



    @run_after('install')

    @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],

        )

packages/apbs/package.py

+3 −3
Original line number Diff line number Diff line
@@ -3,7 +3,7 @@ 
#

# SPDX-License-Identifier: (Apache-2.0 OR MIT)



from spack import *

from spack.package import *





class Apbs(CMakePackage):
@@ -38,9 +38,9 @@ class Apbs(CMakePackage): 
    depends_on('boost',             type=('build', 'run'))

    depends_on('blas',              type=('build', 'run'))

    depends_on('arpack-ng',         type=('build', 'run'))

    depends_on('suite-sparse+tbb',  type=('build', 'run'))

    depends_on('suite-sparse',      type=('build', 'run'))

    depends_on('maloc',             type=('build', 'run'))

    depends_on('python@3.8:3.10',   type=('build', 'run'))

    depends_on('python@3.8:3.11',   type=('build', 'run'))



    def cmake_args(self):

        # Min and max Python versions need to be set as variables to pass tests.

packages/arbor/package.py

+38 −14
Original line number Diff line number Diff line
@@ -13,10 +13,15 @@ class Arbor(CMakePackage, CudaPackage): 
    homepage = "https://arbor-sim.org"

    git = "https://github.com/arbor-sim/arbor.git"

    url = "https://github.com/arbor-sim/arbor/releases/download/v0.9.0/arbor-v0.9.0-full.tar.gz"

    maintainers = ["thorstenhater", "brenthuisman", "haampie"]

    maintainers = ("thorstenhater", "ErbB4", "haampie")



    version("master", branch="master")

    version("develop")

    version("master", branch="master", submodules=True)

    version("develop", branch="master", submodules=True)

    version(

        "0.10.0",

        sha256="72966b7a2f45ce259b8ba167ca3e4f5ab9f212136a300267aaac0c04ed3fe3fc",

        url="https://github.com/arbor-sim/arbor/releases/download/v0.10.1/arbor-v0.10.0-full.tar.gz",

    )

    version(

        "0.9.0",

        sha256="5f9740955c821aca81e23298c17ad64f33f635756ad9b4a0c1444710f564306a",
@@ -75,36 +80,50 @@ class Arbor(CMakePackage, CudaPackage): 
    conflicts("%cce@:9.1")

    conflicts("%intel")



    # begin EBRAINS (modified: added run dep)

    depends_on("cmake@3.19:", type=("build", "run"))

    # end EBRAINS



    # misc dependencies

    depends_on("fmt@7.1:", when="@0.5.3:")  # required by the modcc compiler

    depends_on("fmt@9.1:", when="@0.7.1:")

    depends_on("googletest@1.12.1", when="@0.7.1:")

    # begin EBRAINS (modified: relaxed (upstream gave no info about update))

    # upstream adds: depends_on("fmt@10.1:", when="@0.9.1:")

    depends_on("googletest@1.12.1:", when="@0.7.1:")

    depends_on("pugixml@1.11:", when="@0.7.1:")

    depends_on("nlohmann-json@3.11.2")

    # upstream adds: depends_on("pugixml@1.13:", when="@0.9.1:")

    depends_on("nlohmann-json@3.11.2:")

    depends_on("random123")

    #upstream adds: depends_on("random123@1.14.0:", when="@0.10:")

    # end EBRAINS (modified)

    with when("+cuda"):

        depends_on("cuda@10:")

        depends_on("cuda@11:", when="@0.7.1:")

        depends_on("cuda@12:", when="@0.9.1:")



    # mpi

    # begin EBRAINS (modified: added run dep)

    depends_on("mpi", when="+mpi", type=("build", "run"))

    # end EBRAINS (modified)

    depends_on("py-mpi4py", when="+mpi+python", type=("build", "run"))



    # python (bindings)

    extends("python", when="+python")

    depends_on("python@3.7:", when="+python", type=("build", "run"))

    depends_on("py-numpy", when="+python", type=("build", "run"))

    with when("+python"):

        extends("python")

        depends_on("python@3.7:", type=("build", "run"))

        depends_on("python@3.9:", when="@0.9.1:", type=("build", "run"))

        depends_on("py-numpy", type=("build", "run"))

        depends_on("py-pybind11@2.6:", type="build")

        depends_on("py-pybind11@2.8.1:", when="@0.5.3:", type="build")

        depends_on("py-pybind11@2.10.1:", when="@0.7.1:", type="build")

        depends_on("py-pandas", type="test")

        depends_on("py-seaborn", type="test")



    # sphinx based documentation

    depends_on("python@3.7:", when="+doc", type="build")

    depends_on("py-sphinx", when="+doc", type="build")

    depends_on("py-svgwrite", when="+doc", type="build")

    with when("+doc"):

        depends_on("python@3.10:", type="build")

        depends_on("py-sphinx", type="build")

        depends_on("py-svgwrite", type="build")



    @property

    def build_targets(self):
@@ -124,10 +143,14 @@ class Arbor(CMakePackage, CudaPackage): 


        # query spack for the architecture-specific compiler flags set by its wrapper

        args.append("-DARB_ARCH=none")

        opt_flags = self.spec.target.optimization_flags(

            self.spec.compiler.name, self.spec.compiler.version

        opt_flags = spack.build_environment.optimization_flags(

            self.compiler, self.spec.target

        )

        # Might return nothing

        if opt_flags:

            args.append("-DARB_CXX_FLAGS_TARGET=" + opt_flags)

        # Needed, spack has no units package

        args.append("-DARB_USE_BUNDLED_UNITS=ON")



        return args
@@ -135,3 +158,4 @@ class Arbor(CMakePackage, CudaPackage): 
    @on_package_attributes(run_tests=True)

    def install_test(self):

        python("-c", "import arbor")

        python("python/example/single_cell_model.py")

packages/bazel/bazelconfiguration-0.3.patch

deleted100644 → 0
+0 −16
Original line number Diff line number Diff line 
--- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java

+++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java

@@ -150,6 +150,13 @@

       builder.put("PATH", null);

       builder.put("LD_LIBRARY_PATH", null);

     }

+

+    Map<String, String> spackEnv = System.getenv();

+    for (String envName : spackEnv.keySet()) {

+      if (envName.startsWith("SPACK_")) {

+        builder.put(envName, spackEnv.get(envName));

+      }

+    }

   }

 

   private static PathFragment determineShellExecutable(OS os, PathFragment fromOption) {

packages/bazel/bazelruleclassprovider-0.14.patch

deleted100644 → 0
+0 −16
Original line number Diff line number Diff line 
--- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java

+++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java

@@ -168,6 +168,13 @@ public class BazelRuleClassProvider {

       env.put("PATH", null);

     }

 

+    Map<String, String> spackEnv = System.getenv();

+    for (String envName : spackEnv.keySet()) {

+      if (envName.startsWith("SPACK_")) {

+        env.put(envName, spackEnv.get(envName));

+      }

+    }

+

     // Shell environment variables specified via options take precedence over the

     // ones inherited from the fragments. In the long run, these fragments will

     // be replaced by appropriate default rc files anyway.

packages/bazel/build-0.29.1.patch

deleted100644 → 0
+0 −61
Original line number Diff line number Diff line 
From 9c9d27561780bc56d9f0867e325c7421a94ee1cb Mon Sep 17 00:00:00 2001

From: Harsh Bhatia <bhatia4@llnl.gov>

Date: Tue, 15 Dec 2020 15:56:10 -0800

Subject: [PATCH] https://github.com/bazelbuild/bazel/commit/ab62a6e097590dac5ec946ad7a796ea0e8593ae0 



---

 src/conditions/BUILD | 6 ++++++

 third_party/BUILD    | 8 ++++++--

 2 files changed, 12 insertions(+), 2 deletions(-)



diff --git a/src/conditions/BUILD b/src/conditions/BUILD

index 2b28e28057..faa41a439d 100644

--- a/src/conditions/BUILD

+++ b/src/conditions/BUILD

@@ -10,6 +10,12 @@ filegroup(

     visibility = ["//src:__pkg__"],

 )

 

+config_setting(

+    name = "linux_ppc",

+    values = {"cpu": "ppc"},

+    visibility = ["//visibility:public"],

+)

+

 config_setting(

     name = "linux_x86_64",

     values = {"cpu": "k8"},

diff --git a/third_party/BUILD b/third_party/BUILD

index 159006d741..4fcae54c00 100644

--- a/third_party/BUILD

+++ b/third_party/BUILD

@@ -523,12 +523,13 @@ UNNECESSARY_DYNAMIC_LIBRARIES = select({

     "//src/conditions:darwin": "*.so *.dll",

     "//src/conditions:darwin_x86_64": "*.so *.dll",

     "//src/conditions:linux_x86_64": "*.jnilib *.dll",

+    "//src/conditions:linux_ppc": "*.so *.jnilib *.dll",

     # The .so file is an x86 one, so we can just remove it if the CPU is not x86

     "//src/conditions:arm": "*.so *.jnilib *.dll",

     "//src/conditions:linux_aarch64": "*.so *.jnilib *.dll",

     # Play it safe -- better have a big binary than a slow binary

     # zip -d does require an argument. Supply something bogus.

-    "//conditions:default": "*.bogusextension",

+    "//conditions:default": "",

 })

 

 # Remove native libraries that are for a platform different from the one we are

@@ -537,7 +538,10 @@ genrule(

     name = "filter_netty_dynamic_libs",

     srcs = ["netty_tcnative/netty-tcnative-boringssl-static-2.0.24.Final.jar"],

     outs = ["netty_tcnative/netty-tcnative-filtered.jar"],

-    cmd = "cp $< $@ && zip -qd $@ " + UNNECESSARY_DYNAMIC_LIBRARIES,

+    cmd = "cp $< $@ && " +

+      # End successfully if there is nothing to be deleted from the archive

+      "if [ -n '" + UNNECESSARY_DYNAMIC_LIBRARIES + "' ]; then " +

+      "zip -qd $@ " + UNNECESSARY_DYNAMIC_LIBRARIES + "; fi",

 )

 

 java_import(

-- 

2.21.0 (Apple Git-122.2)

packages/bazel/cc_configure-0.3.0.patch

deleted100644 → 0
+0 −24
Original line number Diff line number Diff line 
--- a/tools/cpp/cc_configure.bzl

+++ b/tools/cpp/cc_configure.bzl

@@ -173,8 +173,19 @@

   else:

     inc_dirs = result.stderr[index1 + 1:index2].strip()

 

-  return [repository_ctx.path(_cxx_inc_convert(p))

-          for p in inc_dirs.split("\n")]

+  default_inc_directories = [

+    repository_ctx.path(_cxx_inc_convert(p))

+    for p in inc_dirs.split("\n")

+  ]

+

+  env = repository_ctx.os.environ

+  if "SPACK_INCLUDE_DIRS" in env:

+    for path in env["SPACK_INCLUDE_DIRS"].split(":"):

+      default_inc_directories.append(

+        repository_ctx.path(_cxx_inc_convert(path))

+      )

+

+  return default_inc_directories

 

 def _add_option_if_supported(repository_ctx, cc, option):

   """Checks that `option` is supported by the C compiler."""

packages/bazel/cc_configure-0.5.0.patch

deleted100644 → 0
+0 −24
Original line number Diff line number Diff line 
--- a/tools/cpp/cc_configure.bzl

+++ b/tools/cpp/cc_configure.bzl

@@ -200,8 +200,19 @@

   else:

     inc_dirs = result.stderr[index1 + 1:index2].strip()

 

-  return [_escape_string(repository_ctx.path(_cxx_inc_convert(p)))

-          for p in inc_dirs.split("\n")]

+  default_inc_directories = [

+    _escape_string(repository_ctx.path(_cxx_inc_convert(p)))

+    for p in inc_dirs.split("\n")

+  ]

+

+  env = repository_ctx.os.environ

+  if "SPACK_INCLUDE_DIRS" in env:

+    for path in env["SPACK_INCLUDE_DIRS"].split(":"):

+      default_inc_directories.append(

+        repository_ctx.path(_cxx_inc_convert(path))

+      )

+

+  return default_inc_directories

 

 

 def _add_option_if_supported(repository_ctx, cc, option):

packages/bazel/compile-0.13.patch

deleted100644 → 0
+0 −11
Original line number Diff line number Diff line 
--- a/compile.sh

+++ b/compile.sh

@@ -92,7 +92,7 @@

 log "Building output/bazel"

 # We set host and target platform directly since the defaults in @bazel_tools

 # have not yet been generated.

-bazel_build "src:bazel${EXE_EXT}" \

+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}" \

   --host_platform=@bazel_tools//platforms:host_platform \

   --platforms=@bazel_tools//platforms:target_platform \

   || fail "Could not build Bazel"

packages/bazel/compile-0.16.patch

deleted100644 → 0
+0 −11
Original line number Diff line number Diff line 
--- a/compile.sh

+++ b/compile.sh

@@ -92,7 +92,7 @@ display "."

 log "Building output/bazel"

 # We set host and target platform directly since the defaults in @bazel_tools

 # have not yet been generated.

-bazel_build "src:bazel_nojdk${EXE_EXT}" \

+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel_nojdk${EXE_EXT}" \

   --host_platform=@bazel_tools//platforms:host_platform \

   --platforms=@bazel_tools//platforms:target_platform \

   || fail "Could not build Bazel"

packages/bazel/compile-0.21.patch

deleted100644 → 0
+0 −11
Original line number Diff line number Diff line 
--- a/compile.sh

+++ b/compile.sh

@@ -92,7 +92,7 @@ display "."

 log "Building output/bazel"

 # We set host and target platform directly since the defaults in @bazel_tools

 # have not yet been generated.

-bazel_build "src:bazel_nojdk${EXE_EXT}" \

+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel_nojdk${EXE_EXT}" \

   --action_env=PATH \

   --host_platform=@bazel_tools//platforms:host_platform \

   --platforms=@bazel_tools//platforms:target_platform \

packages/bazel/compile-0.3.patch

deleted100644 → 0
+0 −11
Original line number Diff line number Diff line 
--- a/compile.sh

+++ b/compile.sh

@@ -99,7 +99,7 @@

   new_step 'Building Bazel with Bazel'

   display "."

   log "Building output/bazel"

-  bazel_build "src:bazel${EXE_EXT}"

+  CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}"

   cp -f "bazel-bin/src/bazel${EXE_EXT}" "output/bazel${EXE_EXT}"

   chmod 0755 "output/bazel${EXE_EXT}"

   BAZEL="$(pwd)/output/bazel${EXE_EXT}"

packages/bazel/compile-0.9.patch

deleted100644 → 0
+0 −11
Original line number Diff line number Diff line 
--- a/compile.sh

+++ b/compile.sh

@@ -92,7 +92,7 @@

 log "Building output/bazel"

 # We set host and target platform directly since the defaults in @bazel_tools

 # have not yet been generated.

-bazel_build "src:bazel${EXE_EXT}" \

+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}" \

   --host_platform=//tools/platforms:host_platform \

   --platforms=//tools/platforms:target_platform \

   || fail "Could not build Bazel"

packages/bazel/cppcompileaction-0.3.0.patch

deleted100644 → 0
+0 −11
Original line number Diff line number Diff line 
--- a/src/main/java/com/google/devtools/build/lib/rules/cpp/CppCompileAction.java.orig    2020-06-08 13:42:14.035342560 -0400

+++ b/src/main/java/com/google/devtools/build/lib/rules/cpp/CppCompileAction.java 2020-06-08 13:42:25.149375458 -0400

@@ -963,7 +963,7 @@

           // are, it's probably due to a non-hermetic #include, & we should stop

           // the build with an error.

           if (execPath.startsWith(execRoot)) {

-            execPathFragment = execPath.relativeTo(execRoot); // funky but tolerable path

+             //  execPathFragment = execPath.relativeTo(execRoot); // funky but tolerable path

           } else {

             problems.add(execPathFragment.getPathString());

             continue;

packages/bazel/cppcompileaction-7.0.0.patch

0 → 100644
+12 −0
Original line number Diff line number Diff line 
diff --color=auto --color=auto -Naur a/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java b/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java

--- a/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java	1980-01-01 00:00:00

+++ b/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java	2024-02-15 13:36:37

@@ -143,7 +143,7 @@

               LabelConstants.EXPERIMENTAL_EXTERNAL_PATH_PREFIX.getRelative(

                   execPath.relativeTo(execRoot.getParentDirectory()));

         } else {

-          absolutePathProblems.add(execPathFragment.getPathString());

+          // absolutePathProblems.add(execPathFragment.getPathString());

           continue;

         }

       }

packages/bazel/unix_cc_configure-0.10.patch

deleted100644 → 0
+0 −22
Original line number Diff line number Diff line 
--- a/tools/cpp/unix_cc_configure.bzl

+++ b/tools/cpp/unix_cc_configure.bzl

@@ -147,9 +147,18 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc, additional_flags = []):

   else:

     inc_dirs = result.stderr[index1 + 1:index2].strip()

 

-  return [_prepare_include_path(repository_ctx, _cxx_inc_convert(p))

-          for p in inc_dirs.split("\n")]

+  default_inc_directories = [

+    _prepare_include_path(repository_ctx, _cxx_inc_convert(p))

+      for p in inc_dirs.split("\n")

+  ]

+ 

+  env = repository_ctx.os.environ

+  if "SPACK_INCLUDE_DIRS" in env:

+    for path in env["SPACK_INCLUDE_DIRS"].split(":"):

+      default_inc_directories.append(path)

+

+  return default_inc_directories

 



 def _is_option_supported(repository_ctx, cc, option):

packages/bazel/unix_cc_configure-0.5.3.patch

deleted100644 → 0
+0 −24
Original line number Diff line number Diff line 
--- a/tools/cpp/unix_cc_configure.bzl

+++ b/tools/cpp/unix_cc_configure.bzl

@@ -117,9 +117,19 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc):

   else:

     inc_dirs = result.stderr[index1 + 1:index2].strip()

 

-  return [escape_string(repository_ctx.path(_cxx_inc_convert(p)))

-          for p in inc_dirs.split("\n")]

+  default_inc_directories = [

+    escape_string(repository_ctx.path(_cxx_inc_convert(p)))

+          for p in inc_dirs.split("\n")

+  ]

 

+  env = repository_ctx.os.environ

+  if "SPACK_INCLUDE_DIRS" in env:

+    for path in env["SPACK_INCLUDE_DIRS"].split(":"):

+      default_inc_directories.append(

+        repository_ctx.path(_cxx_inc_convert(path))

+      )

+

+  return default_inc_directories

 

 def _add_option_if_supported(repository_ctx, cc, option):

   """Checks that `option` is supported by the C compiler. Doesn't %-escape the option."""

packages/biobb-common/package.py

deleted100644 → 0
+0 −38
Original line number Diff line number Diff line 
# 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 import *



class BiobbCommon(PythonPackage):

    """Biobb_common is the base package required to use the biobb packages"""



    # Homepage and download url

    homepage = "https://github.com/bioexcel/biobb_common"

    git = 'https://github.com/bioexcel/biobb_common.git'

    url = 'https://github.com/bioexcel/biobb_common/archive/refs/tags/v4.0.0.tar.gz'



    # Set the gitlab accounts of this package maintainers

    maintainers = ['dbeltran']



    # Versions

    version('master', branch='master')

    version('4.0.0', sha256='fff990dce42ded2af3d587567dbf5321b1498f12f24d04d62003f9869d6eb8fe')



    # Dependencies

    depends_on('py-setuptools')

    depends_on('python@3.8:', type=('build', 'run'))

    depends_on('py-pyyaml', type=('build', 'run'))

    depends_on('py-requests', type=('build', 'run'))

    depends_on('py-biopython@1.78:1.80', type=('build', 'run'))



    # Custom patch to enable python 3.10.8 for this package

    def patch(self):

        filter_file("    python_requires='>=3.7,<=3.10',", "    python_requires='>=3.7,<3.11',", "setup.py")



    # Test

    @run_after('install')

    @on_package_attributes(run_tests=True)

    def check_install (self):

        python("-c", 'import biobb_common')

packages/biobb-gromacs/package.py

deleted100644 → 0
+0 −37
Original line number Diff line number Diff line 
# 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 import *



class BiobbGromacs(PythonPackage):

    """Biobb_gromacs is the Biobb module collection to perform molecular

    dynamics simulations using Gromacs"""



    # Homepage and download url

    homepage = "https://github.com/bioexcel/biobb_gromacs"

    git = 'https://github.com/bioexcel/biobb_gromacs.git'

    url = 'https://github.com/bioexcel/biobb_gromacs/archive/refs/tags/v4.0.0.tar.gz'



    # Set the gitlab accounts of this package maintainers

    maintainers = ['dbeltran']



    # Versions

    version('master', branch='master')

    version('4.0.0', sha256='87f9079ec8b72ff43cd1b388a06fee5b1f64bb4080ffab110941f3c6d155ef0b')



    # Dependencies

    depends_on('python@3.8:', type=('build', 'run'))

    depends_on('biobb-common')

    depends_on('gromacs')



    # Patching to enable python 3.10 (not official, might not be stable)

    def patch(self):

        filter_file("    python_requires='>=3.7,<=3.10',", "    python_requires='>=3.7,<3.11',", "setup.py")



    # Test

    @run_after('install')

    @on_package_attributes(run_tests=True)

    def check_install (self):

        python("-c", 'import biobb_gromacs')

packages/biobb-io/package.py

deleted100644 → 0
+0 −42
Original line number Diff line number Diff line 
# 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 import *



class BiobbIo(PythonPackage):

    """Biobb_io is the Biobb module collection to fetch data to be

    consumed by the rest of the Biobb building blocks"""



    # Homepage and download url

    homepage = "https://github.com/bioexcel/biobb_io"

    git = 'https://github.com/bioexcel/biobb_io.git'

    url = 'https://github.com/bioexcel/biobb_io/archive/refs/tags/v4.0.0.tar.gz'



    # Set the gitlab accounts of this package maintainers

    maintainers = ['dbeltran']



    # Versions

    version('master', branch='master')

    version('4.0.0', sha256='600a30f14b1a0e21f57775ba1be695e1595f5702237415fe90d7c531b5a0408a')



    # Dependencies

    depends_on('biobb-common')

    depends_on('python@3.8:', type=('build', 'run'))



    # Patching to enable python 3.10 (not official, might not be stable)

    def patch(self):

        filter_file("    python_requires='>=3.7,<3.10',", "    python_requires='>=3.7,<3.11',", "setup.py")

        filter_file(

            "'Programming Language :: Python :: 3.9'",

            "'Programming Language :: Python :: 3.9',\r\n        "

            "'Programming Language :: Python :: 3.10'",

            "setup.py",

        )



    # Test

    @run_after('install')

    @on_package_attributes(run_tests=True)

    def check_install (self):

        python("-c", 'import biobb_io')

packages/biobb-model/package.py

deleted100644 → 0
+0 −43
Original line number Diff line number Diff line 
# 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 import *



class BiobbModel(PythonPackage):

    """Biobb_model is the Biobb module collection to check and model 3d structures,

    create mutations or reconstruct missing atoms"""



    # Homepage and download url

    homepage = "https://github.com/bioexcel/biobb_model"

    git = 'https://github.com/bioexcel/biobb_model.git'

    url = 'https://github.com/bioexcel/biobb_model/archive/refs/tags/v4.0.0.tar.gz'



    # Set the gitlab accounts of this package maintainers

    maintainers = ['dbeltran']



    # Versions

    version('master', branch='master')

    version('4.0.0', sha256='92387725b7ccd3f40d18c1d3e30a6169ca4204ba498ac72e25c9e701b1a89d91')



    # Dependencies

    depends_on('python@3.8:', type=('build', 'run'))

    depends_on('biobb-common')

    depends_on('biobb-structure-checking')



    # Patching to enable python 3.10 (not official, might not be stable)

    def patch(self):

        filter_file("    python_requires='>=3.7,<=3.10',", "    python_requires='>=3.7,<3.11',", "setup.py")

        filter_file(

            "'Programming Language :: Python :: 3.9'",

            "'Programming Language :: Python :: 3.9',\r\n        "

            "'Programming Language :: Python :: 3.10'",

            "setup.py",

        )



    # Test

    @run_after('install')

    @on_package_attributes(run_tests=True)

    def check_install (self):

        python("-c", 'import biobb_model')

packages/biobb-structure-checking/package.py

deleted100644 → 0
+0 −36
Original line number Diff line number Diff line 
# 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 import *



class BiobbStructureChecking(PythonPackage):

    """Biobb_structure_checking performs a checking of the quality of a 

    3D structure intended to facilitate the setup of molecular dynamics 

    simulation of protein or nucleic acids systems"""



    # Homepage and download url

    homepage = "https://github.com/bioexcel/biobb_structure_checking"

    git = 'https://github.com/bioexcel/biobb_structure_checking.git'

    url = 'https://github.com/bioexcel/biobb_structure_checking/archive/refs/tags/v3.12.1.tar.gz'



    # Set the gitlab accounts of this package maintainers

    maintainers = ['dbeltran']



    # Versions

    version('master', branch='master')

    version('3.12.1', sha256='ef3e6fe5f7763e534c91fac00bf873c3d88bcca18be7a63c63608dceb36f3d40')



    # Dependencies

    depends_on('py-setuptools')

    depends_on('python@3.8:', type=('build', 'run'))

    depends_on('py-psutil', type=('build', 'run'))

    depends_on('py-numpy', type=('build', 'run'))

    depends_on('py-biopython@1.78:1.80', type=('build', 'run'))



    # Test

    @run_after('install')

    @on_package_attributes(run_tests=True)

    def check_install (self):

        python("-c", 'import biobb_structure_checking')

packages/biobb-structure-utils/package.py

deleted100644 → 0
+0 −43
Original line number Diff line number Diff line 
# 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 import *



class BiobbStructureUtils(PythonPackage):

    """Biobb_structure_utils is the Biobb module collection to modify 

    or extract information from a PDB structure file."""



    # Homepage and download url

    homepage = "https://github.com/bioexcel/biobb_structure_utils"

    git = 'https://github.com/bioexcel/biobb_structure_utils.git'

    url = 'https://github.com/bioexcel/biobb_structure_utils/archive/refs/tags/v4.0.0.tar.gz'



    # Set the gitlab accounts of this package maintainers

    maintainers = ['dbeltran']



    # Versions

    version('master', branch='master')

    version('4.0.0', sha256='f328eee2166631e1cc514118eb41187620c358c8024431ce2a0b0e4547692c47')



    # Dependencies

    depends_on('python@3.8:', type=('build', 'run'))

    depends_on('biobb-common')

    depends_on('biobb-structure-checking')



    # Patching to enable python 3.10 (not official, might not be stable)

    def patch(self):

        filter_file("    python_requires='>=3.7,<=3.10',", "    python_requires='>=3.7,<3.11',", "setup.py")

        filter_file(

            "'Programming Language :: Python :: 3.9'",

            "'Programming Language :: Python :: 3.9',\r\n        "

            "'Programming Language :: Python :: 3.10'",

            "setup.py",

        )



    # Test

    @run_after('install')

    @on_package_attributes(run_tests=True)

    def check_install (self):

        python("-c", 'import biobb_structure_utils')

packages/build-brainscales/package.py

+106 −1
Original line number Diff line number Diff line
@@ -7,7 +7,7 @@ import os 
import unittest.mock

import xml.etree.ElementTree as ET



from spack import *

from spack.package import *

from spack.util.environment import EnvironmentModifications

import spack.build_environment
@@ -15,10 +15,93 @@ import spack.build_environment 
class BuildBrainscales(WafPackage):

    """Common stuff for BrainScaleS packages..."""



    version(

        "11.0-a3",

        git="https://github.com/electronicvisions/releases-ebrains",

        tag="ebrains-11.0-a3",

        commit="4f27672655f57f41d13b44520e315398887d29ff",

        submodules=True,

    )

    version(

        "11.0-a2",

        git="https://github.com/electronicvisions/releases-ebrains",

        tag="ebrains-11.0-a2",

        commit="65abdc96d737415af853a524e8c5177381a7845c",

        submodules=True,

    )

    version(

        "11.0-a1",

        git="https://github.com/electronicvisions/releases-ebrains",

        tag="ebrains-11.0-a1",

        commit="1bf0f6d3c7da681d3db9401bfe0681f95d0baed1",

        submodules=True,

    )

    version(

        "10.0-a1",

        git="https://github.com/electronicvisions/releases-ebrains",

        tag="ebrains-10.0-a1",

        commit="d9bd675b446be8f313972aef2d6657ffbbb91ed2",

        submodules=True,

    )

    version(

        "9.0-a9",

        git="https://github.com/electronicvisions/releases-ebrains",

        tag="ebrains-9.0-a9",

        commit="41d2597bd6c1c20aee4d538c42c248195a133680",

        submodules=True,

    )

    version(

        "9.0-a8",

        git="https://github.com/electronicvisions/releases-ebrains",

        tag="ebrains-9.0-a8",

        commit="44323be431da4b4b43890815f453c27207dee0b2",

        submodules=True,

    )

    version(

        "9.0-a7",

        git="https://github.com/electronicvisions/releases-ebrains",

        tag="ebrains-9.0-a7",

        commit="2337adc6a33f907900d2b8be5d9f0b15872a200a",

        submodules=True,

    )

    version(

        "9.0-a6",

        git="https://github.com/electronicvisions/releases-ebrains",

        tag="ebrains-9.0-a6",

        commit="e9b6746edb5e8465ae2848556b70e4edd555182e",

        submodules=True,

    )

    version(

        "9.0-a5",

        git="https://github.com/electronicvisions/releases-ebrains",

        tag="ebrains-9.0-a5",

        commit="5fcb0682626d83c089e016aaf433e0938e921634",

        submodules=True,

    )

    version(

        "9.0-a4",

        git="https://github.com/electronicvisions/releases-ebrains",

        tag="ebrains-9.0-a4",

        commit="8d5be2a23ac1eb0129bdf1f83fb0a1c5193c4c85",

        submodules=True,

    )



    # common dependencies of BuildBrainscales-derived packages

    depends_on('oppulance@9.0-a9', when='@10.0-a1:', type=('build', 'link', 'run', 'test')) # keep the old one for now

    depends_on('oppulance@9.0-a9', when='@9.0-a9', type=('build', 'link', 'run', 'test'))

    depends_on('oppulance@9.0-a8', when='@9.0-a8', type=('build', 'link', 'run', 'test'))

    depends_on('oppulance@9.0-a7', when='@9.0-a7', type=('build', 'link', 'run', 'test'))

    depends_on('oppulance@9.0-a6', when='@9.0-a6', type=('build', 'link', 'run', 'test'))

    depends_on('oppulance@9.0-a5', when='@9.0-a5', type=('build', 'link', 'run', 'test'))

    depends_on('oppulance@9.0-a4', when='@9.0-a4', type=('build', 'link', 'run', 'test'))



    # waf setup performs git clone and might query gerrit

    depends_on('git', type=('build', 'link'))

    depends_on('py-git-review', type=('build', 'link'))



    # old BrainScaleS EBRAINS releases used `waf setup --project=X` to download

    # sources of the dependent repositories

    @when("@:8")

    def do_fetch(self, mirror_only=False):

        """Setup the project."""
@@ -56,6 +139,16 @@ class BuildBrainscales(WafPackage): 
        with unittest.mock.patch('spack.fetch_strategy.GitFetchStrategy.archive', new=custom_archive):

            self.stage.cache_local()



    # new BrainScaleS EBRAINS releases use git submodules to download sources;

    # we still need to keep the `.git/` folders of the submodules in the source cache though

    @when("@9:")

    def do_fetch(self, mirror_only=False):

        # in the configure step, we need access to all archived .git folders

        def custom_archive(self, destination):

            super(spack.fetch_strategy.GitFetchStrategy, self).archive(destination)

        with unittest.mock.patch('spack.fetch_strategy.GitFetchStrategy.archive', new=custom_archive):

            super(BuildBrainscales, self).do_fetch(mirror_only)



    def _setup_common_env(self, env):

        # grenade needs to find some libraries for the JIT-compilation of

        # programs for BrainScaleS-2's embedded processor.
@@ -84,10 +177,18 @@ class BuildBrainscales(WafPackage): 
        # spack tries to find headers and libraries by itself (i.e. it's not

        # relying on the compiler to find it); we explicitly expose the

        # spack-provided env vars that contain include and library paths

        if 'SPACK_STORE_INCLUDE_DIRS' in my_env:

            for dir in reversed(get_path(my_env, "SPACK_STORE_INCLUDE_DIRS")):

                env.prepend_path("C_INCLUDE_PATH", dir)

                env.prepend_path("CPLUS_INCLUDE_PATH", dir)

        if 'SPACK_INCLUDE_DIRS' in my_env:

            for dir in reversed(get_path(my_env, "SPACK_INCLUDE_DIRS")):

                env.prepend_path("C_INCLUDE_PATH", dir)

                env.prepend_path("CPLUS_INCLUDE_PATH", dir)

        if 'SPACK_STORE_LINK_DIRS' in my_env:

            for dir in reversed(get_path(my_env, "SPACK_STORE_LINK_DIRS")):

                env.prepend_path("LIBRARY_PATH", dir)

                env.prepend_path("LD_LIBRARY_PATH", dir)

        if 'SPACK_LINK_DIRS' in my_env:

            for dir in reversed(get_path(my_env, "SPACK_LINK_DIRS")):

                env.prepend_path("LIBRARY_PATH", dir)
@@ -112,6 +213,9 @@ class BuildBrainscales(WafPackage): 


        args = ['--prefix={0}'.format(self.prefix)]

        args += self.configure_args()



        if spec.version >= Version("9"):

            self.waf('setup', '--directory=' + str(spec.name), '--repo-db-url=https://github.com/electronicvisions/projects')

        self.waf('configure', '--build-profile=release', '--disable-doxygen', *args)



    def build_args(self):
@@ -133,6 +237,7 @@ class BuildBrainscales(WafPackage): 
                    if (elem.tag == 'failure') and not (

                            elem.get('message').startswith("pylint:") or

                            elem.get('message').startswith("pycodestyle:") or

                            "catchsegv: not found" in elem.get('message') or

                            ("OK" in elem.get('message') and "Segmentation fault" in elem.get('message'))):

                        raise RuntimeError("Failed test found: {}".format(testcase.get('name')))

packages/build-jupyter-notebook/package.py

0 → 100644
+59 −0
Original line number Diff line number Diff line 
from spack.package import *

import os



class BuildJupyterNotebook(Package):



    depends_on('py-notebook', type='test')



    def execute_notebook(self, input_nb, output_nb, timeout=None):

        """

        Execute a Jupyter notebook and save the executed copy.



        Args:

            input_nb (str): Path to the input notebook.

            output_nb (str): Path to the executed notebook.

            timeout (int | None): Cell execution timeout in seconds. If None, no timeout.

        """

        jupyter = Executable("jupyter")

        cmd = [

            "nbconvert",

            "--ExecutePreprocessor.kernel_name=python3",

            "--execute",

            "--to", "notebook",

            input_nb,

            "--output", output_nb,

        ]

        if timeout:

            cmd.append(f"--ExecutePreprocessor.timeout={timeout}")



        try:

            # Run notebook and save output

            jupyter(*cmd, output=str.split, error=str.split)

        except Exception as err:

            # If execution fails, re-run with --allow-errors (except on timeout)

            if "CellTimeoutError" not in str(err):

                jupyter(*cmd, "--allow-errors")

            raise



    def batch_execute_notebooks(self, notebooks, output_dir, timeout=None):

        """

        Execute a batch of Jupyter notebooks, saving outputs in the given directory.



        Args:

            notebooks (list[str]): List of notebook file paths to execute.

            output_dir (str): Directory where executed notebooks are saved.

            timeout (int | None): Execution timeout for each notebook.

        """

        mkdirp(output_dir)

        failures: list[Exception] = []



        for notebook in notebooks:

            output_path = join_path(output_dir, os.path.basename(notebook))

            try:

                self.execute_notebook(notebook, output_path, timeout=timeout)

            except Exception as err:

                failures.append(err)



        if failures:

            raise Exception(f"Notebook execution failed for {len(failures)} file(s).")

packages/clb-nb-utils/package.py

+1 −1
Original line number Diff line number Diff line
@@ -3,7 +3,7 @@ 
#

# SPDX-License-Identifier: (Apache-2.0 OR MIT)



from spack import *

from spack.package import *



# Usage

# from clb_nb_utils import oauth

packages/cmdstan/package.py

0 → 100644
+92 −0
Original line number Diff line number Diff line 
# 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 Cmdstan(MakefilePackage):

    """CmdStan is the command line interface to Stan."""



    homepage = "https://mc-stan.org/users/interfaces/cmdstan"

    url = "https://github.com/stan-dev/cmdstan/releases/download/v2.30.1/cmdstan-2.30.1.tar.gz"



    license("BSD-3-Clause")



    # begin EBRAINS (added)

    version("2.37.0", sha256="635e2e1cf9c4774c9019001325354d3610bae2adc4ed5af2fed87872dfc671fc")

    # end EBRAINS

    version("2.30.1", sha256="bab76dcefa7f4c955595c0bf0496770507fc6ab0df5896e8cf8c2db0a17eedb9")



    depends_on("c", type="build")  # generated

    depends_on("cxx", type="build")  # generated

    depends_on("fortran", type="build")  # generated



    variant("threads", default=True, description="enable thread support")

    variant("opencl", default=False, description="enable OpenCl support")

    variant("mpi", default=False, description="enable MPI support")



    depends_on("opencl", when="+opencl")

    depends_on("mpi", when="+mpi")



    build_targets = ["build"]



    filter_compiler_wrappers("local", relative_root="make")



    def edit(self, spec, prefix):

        if spec.satisfies("%intel"):

            cxx_type = "icc"

        else:

            cxx_type = spec.compiler.name



        if spec.satisfies("+mpi"):

            cxx = spec["mpi"].mpicxx

        else:

            cxx = spack_cxx



        make_options = [

            "CXX={0}\n".format(cxx),

            "CXXFLAGS+= -O2 -funroll-loops\n",

            "LDFLAGS+={0}{1}\n".format(

                self.compiler.cc_rpath_arg,

                join_path(prefix, "stan", "lib", "stan_math", "lib", "tbb"),

            ),

            "STANCFLAGS+= --warn-pedantic\n",

            "TBB_CXX_TYPE={0}\n".format(cxx_type),

        ]



        if spec.satisfies("+threads"):

            make_options.append("STAN_THREADS=true\n")



        if spec.satisfies("+opencl"):

            make_options.append("STAN_OPENCL=true\n")



        if spec.satisfies("+mpi"):

            make_options.append("STAN_MPI=true\n")



        filepath = join_path(self.stage.source_path, "make", "local")

        with open(filepath, "w") as make_file:

            make_file.writelines(make_options)



    def install(self, spec, prefix):

        make(join_path("examples", "bernoulli", "bernoulli"))



        mkdir(prefix.bin)



        with working_dir(self.build_directory):

            copy("makefile", prefix)

            copy_tree("make", prefix.make)

            copy_tree("examples", prefix.examples)

            copy_tree("lib", prefix.lib)

            copy_tree("src", prefix.src)

            copy_tree("stan", prefix.stan)



        with working_dir(join_path(self.build_directory, "bin")):

            install("diagnose", prefix.bin)

            install("print", prefix.bin)

            install("stanc", prefix.bin)

            install("stansummary", prefix.bin)



    def setup_run_environment(self, env):

        env.set("CMDSTAN", self.prefix)

packages/cudnn/package.py

0 → 100644
+409 −0
Original line number Diff line number Diff line 
# 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)



import os

import platform



from spack.package import *



_versions = {

    # cuDNN 9.8.0

    "9.8.0.87-12": {

        "Linux-x86_64": "321b9b33bb1287404d93d5672d352f16feabc4b220ac6ae0b86e4b27f257dcf4",

        "Linux-aarch64": "f03ece3ff07d1719f06218973a8797cec1be387cc317baab5bb118dc988199e7",

    },

    "9.8.0.87-11": {

        "Linux-x86_64": "cf4dfaef8311d987d640a322f668cd5240ac3e5302abe9617dd991b5b2532758"

    },

    # cuDNN 9.2.0

    "9.2.0.82-12": {

        "Linux-x86_64": "1362b4d437e37e92c9814c3b4065db5106c2e03268e22275a5869e968cee7aa8",

        "Linux-aarch64": "24cc2a0308dfe412c02c7d41d4b07ec12dacb021ebf8c719de38eb77d22f68c1",

    },

    "9.2.0.82-11": {

        "Linux-x86_64": "99dcb3fa2bf7eed7f35b0f8e58e7d1f04d9a52e01e382efc1de16fed230d3b26"

    },

    # cuDNN 8.9.7

    "8.9.7.29-12": {

        "Linux-x86_64": "475333625c7e42a7af3ca0b2f7506a106e30c93b1aa0081cd9c13efb6e21e3bb",

        "Linux-ppc64le": "8574d291b299f9cc0134304473c9933bd098cc717e8d0876f4aba9f9eebe1b76",

    },

    "8.9.7.29-11": {

        "Linux-x86_64": "a3e2509028cecda0117ce5a0f42106346e82e86d390f4bb9475afc976c77402e",

        "Linux-ppc64le": "f23fd7d59f9d4f743fa926f317dab0d37f6ea21edb2726ceb607bea45b0f9f36",

    },

    # cuDNN 8.9.5

    "8.9.5.30-12": {

        "Linux-x86_64": "2a2eb89a2ab51071151c6082f1e816c702167a711a9372f9f73a7b5c4b06e01a",

        "Linux-ppc64le": "38388ec3c99c6646aaf5c707985cd35e25c67f653d780c4081c2df5557ab665f",

        "Linux-aarch64": "0491f7b02f55c22077eb678bf314c1f917524bd507cf5b658239bf98a47233a1",

    },

    "8.9.5.30-11": {

        "Linux-x86_64": "bbe10e3c08cd7e4aea1012213781e4fe270e1c908263444f567cafefb2cc6525",

        "Linux-ppc64le": "d678f8b2903b95de7eeaef38890c5674705864ea049b2b63e90565f2c0ea682f",

    },

    # cuDNN 8.9.0

    "8.9.0.131-12": {

        "Linux-x86_64": "477631002be61022b60961cba0a501271507a93f81d6b08384bc320cb8706c98",

        "Linux-ppc64le": "ff239e4cbbf21fa18104b62a887686e2197f820ad58817d62e509c735a331829",

        "Linux-aarch64": "fab70f4fb3b933ff502200a1d954d2c6fc205ff9c9b1d271ea4c41e980a66596",

    },

    "8.9.0.131-11": {

        "Linux-x86_64": "3cb82c50723f14b41d43523f222cd52cc9d50b3ad67c380f4be51bd1133daa2d",

        "Linux-ppc64le": "18778de490550c5b584e96560208e5e37678397037946e10a1c2824174c69725",

    },

    # cuDNN 8.8.1

    "8.8.1.3-12": {

        "Linux-x86_64": "79d77a769c7e7175abc7b5c2ed5c494148c0618a864138722c887f95c623777c",

        "Linux-ppc64le": "b0e89021a846952cad8cfc674edce2883f6e344ebd47a2394f706b1136715bc7",

    },

    "8.8.1.3-11": {

        "Linux-x86_64": "af7584cae0cc5524b5913ef08c29ba6154113c60eb0a37a0590a91b515a8a8f9",

        "Linux-ppc64le": "d086003d09d5388aa42142f07483a773aa74b602478b0933e24fc63f56f1658f",

    },

    # cuDNN 8.7.0

    "8.7.0.84-11.8": {

        "Linux-x86_64": "976c4cba7233c97ae74006afab5172976300ba40f5b250a21f8cf71f59c9f76d",

        "Linux-ppc64le": "0433d6d8b6841298e049e8a542750aa330a6e046a52ad95fae0c2f75dabe5575",

        "Linux-aarch64": "cf967f78dbf6c075243cc83aa18759e370db3754aa15b12a0a14e8bf67a3a9d4",

    },

    # cuDNN 8.6.0

    "8.6.0.163-11.8": {

        "Linux-x86_64": "bbc396df47294c657edc09c600674d608cb1bfc80b82dcf4547060c21711159e",

        "Linux-ppc64le": "c8a25e7e3df1bb9c4e18a4f24dd5f25cfd4bbe8b7054e34008e53b2be4f58a80",

        "Linux-aarch64": "a0202278d3cbd4f3adc3f7816bff6071621cb042b0903698b477acac8928ac06",

    },

    # cuDNN 8.5.0

    "8.5.0.96-11.7": {

        "Linux-x86_64": "5454a6fd94f008728caae9adad993c4e85ef36302e26bce43bea7d458a5e7b6d",

        "Linux-ppc64le": "00373c3d5e0b536a5557d0d0eb50706777f213a222b4030e1b71b1bec43d205f",

        "Linux-aarch64": "86780abbecd4634e7363fad1d000ae23b7905a5f8383bddbf7332c6934791dde",

    },

    # cuDNN 8.4.0

    "8.4.0.27-11.6": {

        "Linux-x86_64": "d19bdafd9800c79d29e6f6fffa9f9e2c10d1132d6c2ff10b1593e057e74dd050",

        "Linux-ppc64le": "7ef72353331cf42b357f53cb4a4971fb07e2f0b2ae66e03d54933df52de411c8",

        "Linux-aarch64": "3972ab37b6f0271274931f69c5675c3b61d16f8f5a2dedd422a5efd7b0f358e5",

    },

    "8.4.0.27-10.2": {

        "Linux-x86_64": "14c5e3ca4258271996d1fd959c42d17c582ce4d9aff451f84524469e784fd154"

    },

    # cuDNN 8.3.3

    "8.3.3.40-11.5": {

        "Linux-x86_64": "eabe96c75cf03ea4f5379894d914f1f8ae14ceab121989e84b0836d927fb7731",

        "Linux-ppc64le": "eaedc8dea675767f9445c11d96e6b472110d2fed728db4179153ca7da6503083",

        "Linux-aarch64": "83b1d21b0f6495dfdc2316e6d53489db8ab1b752e4e4d21caca0a08fb2136cdc",

    },

    "8.3.3.40-10.2": {

        "Linux-x86_64": "d8554f2b32e6295d5fc8f3ac25e68f94058b018c801dab9c143e36812f8926ab"

    },

    # cuDNN 8.3.2

    "8.3.2.44-11.5": {

        "Linux-x86_64": "5500953c08c5e5d1dddcfda234f9efbddcdbe43a53b26dc0a82c723fa170c457",

        "Linux-ppc64le": "0581bce48023a3ee71c3a819aaefcabe693eca18b61e2521dc5f8e6e71567b1b",

        "Linux-aarch64": "7eb8c96bfeec98e8aa7cea1e95633d2a9481fc99040eb0311d31bf137a7aa6ea",

    },

    # cuDNN 8.3.1

    "8.3.1.22-11.5": {

        "Linux-x86_64": "f5ff3c69b6a8a9454289b42eca1dd41c3527f70fcf49428eb80502bcf6b02f6e",

        "Linux-ppc64le": "1d2419a20ee193dc6a3a0ba87e79f408286d3d317c9831cbc1f0b7a268c100b0",

        "Linux-aarch64": "ff23a881366c0ee79b973a8921c6dd400628a321557550ad4e0a26a21caad263",

    },

    # cuDNN 8.2.4

    "8.2.4.15-11.4": {

        "Linux-x86_64": "0e5d2df890b9967efa6619da421310d97323565a79f05a1a8cb9b7165baad0d7",

        "Linux-ppc64le": "af8749ca83fd6bba117c8bee31b787b7f204946e864294030ee0091eb7d3577e",

        "Linux-aarch64": "48b11f19e9cd3414ec3c6c357ad228aebbd43282aae372d42cab2af67c32a08b",

    },

    # cuDNN 8.2.0

    "8.2.0.53-11.3": {

        "Linux-x86_64": "7a195dc93a7cda2bdd4d9b73958d259c784be422cd941a9a625aab75309f19dc",

        "Linux-ppc64le": "cfe06735671a41a5e25fc7542d740177ac8eab1ab146bd30f19e0fa836895611",

        "Linux-aarch64": "0f44af94eef7826dc7b41f92aade3d5210891cdb10858bc0a28ba7167909ab7c",

    },

    "8.2.0.53-10.2": {

        "Linux-x86_64": "6ecbc98b3795e940ce0831ffb7cd2c0781830fdd6b1911f950bcaf6d569f807c"

    },

    # cuDNN 8.1.1

    "8.1.1.33-11.2": {

        "Linux-x86_64": "98a8784e92862f20018d20c281b30d4a0cd951f93694f6433ccf4ae9c502ba6a",

        "Linux-ppc64le": "c3e535a5d633ad8f4d50be0b6f8efd084c6c6ed3525c07cbd89fc508b1d76c7a",

        "Linux-aarch64": "4f7e4f5698539659d51f28dff0da11e5445a5ae58439af1d8a8e9f2d93535245",

    },

    "8.1.1.33-10.2": {

        "Linux-x86_64": "2a4a7b99a6e9bfa690eb19bb41e49553f2a7a491a5b3abfcae900e166c5b6ebd"

    },

    # cuDNN 8.1.0

    "8.1.0.77-11.2": {

        "Linux-x86_64": "dbe82faf071d91ba9bcf00480146ad33f462482dfee56caf4479c1b8dabe3ecb",

        "Linux-ppc64le": "0d3f8fa21959e9f94889841cc8445aecf41d2f3c557091b447313afb43034037",

        "Linux-aarch64": "ba16ff486b68a8b50b69b32702612634954de529f39cfff68c12b8bfc1958499",

    },

    "8.1.0.77-10.2": {

        "Linux-x86_64": "c5bc617d89198b0fbe485156446be15a08aee37f7aff41c797b120912f2b14b4"

    },

    # cuDNN 8.0.5

    "8.0.5.39-11.1": {

        "Linux-x86_64": "1d046bfa79399dabcc6f6cb1507918754439442ea0ca9e0fbecdd446f9b00cce",

        "Linux-aarch64": "0c3542c51b42131247cd9f839d0ebefe4e02bb46d1716be1682cb2919278085a",

    },

    "8.0.5.39-11.0": {

        "Linux-x86_64": "4e16ee7895deb4a8b1c194b812ba49586ef7d26902051401d3717511898a9b73",

        "Linux-ppc64le": "05207a02c0b4f22464dbb0ee646693df4a70ae557640ba576ba8678c26393004",

    },

    "8.0.5.39-10.2": {

        "Linux-x86_64": "21f84c05c67bf1ec859e77c38ccd5bf154964fa1c308f449959be4c356e382f3",

        "Linux-ppc64le": "ce128ea090b05e36d00ffe921e45982ca10e8207e40cfc2e0067d0f62d9b36f9",

    },

    "8.0.5.39-10.1": {

        "Linux-x86_64": "90908495298896b33aa95063a3471f93c36627d7ac01c17dc36d75c65eea4a00",

        "Linux-ppc64le": "e43b10bb3932d5e7a598dcc726d16dc9938dd99dd319cd74b3420f3ed65fe5e0",

    },

    # cuDNN 8.0.4

    "8.0.4.30-11.1": {

        "Linux-x86_64": "8f4c662343afce5998ce963500fe3bb167e9a508c1a1a949d821a4b80fa9beab",

        "Linux-ppc64le": "b4ddb51610cbae806017616698635a9914c3e1eb14259f3a39ee5c84e7106712",

    },

    "8.0.4.30-11.0": {

        "Linux-x86_64": "38a81a28952e314e21577432b0bab68357ef9de7f6c8858f721f78df9ee60c35",

        "Linux-ppc64le": "8da8ed689b1a348182ddd3f59b6758a502e11dc6708c33f96e3b4a40e033d2e1",

    },

    "8.0.4.30-10.2": {

        "Linux-x86_64": "c12c69eb16698eacac40aa46b9ce399d4cd86efb6ff0c105142f8a28fcfb980e",

        "Linux-ppc64le": "32a5b92f9e1ef2be90e10f220c4ab144ca59d215eb6a386e93597f447aa6507e",

    },

    "8.0.4.30-10.1": {

        "Linux-x86_64": "eb4b888e61715168f57a0a0a21c281ada6856b728e5112618ed15f8637487715",

        "Linux-ppc64le": "690811bbf04adef635f4a6f480575fc2a558c4a2c98c85c7090a3a8c60dacea9",

    },

    # cuDNN 8.0.3

    "8.0.3.33-11.0": {

        "Linux-x86_64": "8924bcc4f833734bdd0009050d110ad0c8419d3796010cf7bc515df654f6065a",

        "Linux-ppc64le": "c2d0519831137b43d0eebe07522edb4ef5d62320e65e5d5fa840a9856f25923d",

    },

    "8.0.3.33-10.2": {

        "Linux-x86_64": "b3d487c621e24b5711983b89bb8ad34f0378bdbf8a1a4b86eefaa23b19956dcc",

        "Linux-ppc64le": "ff22c9c37af191c9104989d784427cde744cdde879bfebf3e4e55ca6a9634a11",

    },

    "8.0.3.33-10.1": {

        "Linux-x86_64": "4752ac6aea4e4d2226061610d6843da6338ef75a93518aa9ce50d0f58df5fb07",

        "Linux-ppc64le": "c546175f6ec86a11ee8fb9ab5526fa8d854322545769a87d35b1a505992f89c3",

    },

    # cuDNN 8.0.2

    "8.0.2.39-11.0": {

        "Linux-x86_64": "672f46288b8edd98f8d156a4f1ff518201ca6de0cff67915ceaa37f6d6d86345",

        "Linux-ppc64le": "b7c1ce5b1191eb007ba3455ea5f497fdce293a646545d8a6ed93e9bb06d7f057",

    },

    "8.0.2.39-10.2": {

        "Linux-x86_64": "c9cbe5c211360f3cfbc0fb104f0e9096b37e53f89392525679f049276b2f701f",

        "Linux-ppc64le": "c32325ff84a8123491f2e58b3694885a9a672005bc21764b38874688c0e43262",

    },

    "8.0.2.39-10.1": {

        "Linux-x86_64": "82148a68bd6bdaab93af5e05bb1842b8ccb3ab7de7bed41f609a7616c102213d",

        "Linux-ppc64le": "8196ec4f031356317baeccefbc4f61c8fccb2cf0bdef0a6431438918ddf68fb9",

    },

    # cuDNN 8.0

    "8.0.0.180-11.0": {

        "Linux-x86_64": "9e75ea70280a77de815e0bdc85d08b67e081bc99a708b574092142344d2ba07e",

        "Linux-ppc64le": "1229e94731bbca63ee7f5a239f4e1838a51a301d896f3097fbf7377d74704060",

    },

    "8.0.0.180-10.2": {

        "Linux-x86_64": "0c87c12358ee2b99d57c2a8c7560e3bb93e54bb929f5f8bec4964a72a2bb261d",

        "Linux-ppc64le": "59e4ad6db15fcc374976e8052fe39e3f30f34079710fb3c7751a64c853d9243f",

    },

    # cuDNN 7.6.5

    "7.6.5.32-10.2": {

        "Linux-x86_64": "600267f2caaed2fd58eb214ba669d8ea35f396a7d19b94822e6b36f9f7088c20",

        "Linux-ppc64le": "7dc08b6ab9331bfd12207d4802c61db1ad7cace7395b67a6e7b16efa0335668b",

    },

    "7.6.5.32-10.1": {

        "Linux-x86_64": "7eaec8039a2c30ab0bc758d303588767693def6bf49b22485a2c00bf2e136cb3",

        "Darwin-x86_64": "8ecce28a5ed388a2b9b2d239e08d7c550f53b79288e6d9e5eb4c152bfc711aff",

        "Linux-ppc64le": "97b2faf73eedfc128f2f5762784d21467a95b2d5ba719825419c058f427cbf56",

    },

    "7.6.5.32-10.0": {

        "Linux-x86_64": "28355e395f0b2b93ac2c83b61360b35ba6cd0377e44e78be197b6b61b4b492ba",

        "Darwin-x86_64": "6fa0b819374da49102e285ecf7fcb8879df4d0b3cc430cc8b781cdeb41009b47",

        "Linux-ppc64le": "b1717f4570083bbfc6b8b59f280bae4e4197cc1cb50e9d873c05adf670084c5b",

    },

    "7.6.5.32-9.2": {

        "Linux-x86_64": "a2a2c7a8ba7b16d323b651766ee37dcfdbc2b50d920f73f8fde85005424960e4",

        "Linux-ppc64le": "a11f44f9a827b7e69f527a9d260f1637694ff7c1674a3e46bd9ec054a08f9a76",

    },

    "7.6.5.32-9.0": {

        "Linux-x86_64": "bd0a4c0090d5b02feec3f195738968690cc2470b9bc6026e6fe8ff245cd261c8"

    },

    # cuDNN 7.6.4

    "7.6.4.38-10.1": {

        "Linux-x86_64": "32091d115c0373027418620a09ebec3658a6bc467d011de7cdd0eb07d644b099",

        "Darwin-x86_64": "bfced062c3689ced2c1fb49c7d5052e6bc3da6974c1eb707e4dcf8cd209d4236",

        "Linux-ppc64le": "f3615fea50986a4dfd05d7a0cf83396dfdceefa9c209e8bf9691e20a48e420ce",

    },

    "7.6.4.38-10.0": {

        "Linux-x86_64": "417bb5daf51377037eb2f5c87649000ca1b9cec0acb16cfe07cb1d3e9a961dbf",

        "Darwin-x86_64": "af01ab841caec25087776a6b8fc7782883da12e590e24825ad1031f9ae0ed4b1",

        "Linux-ppc64le": "c1725ad6bd7d7741e080a1e6da4b62eac027a94ac55c606cce261e3f829400bb",

    },

    "7.6.4.38-9.2": {

        "Linux-x86_64": "c79156531e641289b6a6952888b9637059ef30defd43c3cf82acf38d67f60a27",

        "Linux-ppc64le": "98d8aae2dcd851558397a9a30b73242f257e1556be17c83650e63a0685969884",

    },

    "7.6.4.38-9.0": {

        "Linux-x86_64": "8db78c3623c192d4f03f3087b41c32cb0baac95e13408b5d9dabe626cb4aab5d"

    },

    # cuDNN 7.6.3

    "7.6.3.30-10.1": {

        "Linux-x86_64": "352557346d8111e2f954c494be1a90207103d316b8777c33e62b3a7f7b708961",

        "Linux-ppc64le": "f274735a8fc31923d3623b1c3d2b1d0d35bb176687077c6a4d4353c6b900d8ee",

    },

    # cuDNN 7.5.1

    "7.5.1.10-10.1": {

        "Linux-x86_64": "2c833f43c9147d9a25a20947a4c5a5f5c33b2443240fd767f63b330c482e68e0",

        "Linux-ppc64le": "a9e23bc83c970daec20874ccd1d8d80b648adf15440ecd0164818b330b1e2663",

    },

    "7.5.1.10-10.0": {

        "Linux-x86_64": "c0a4ec438920aa581dd567117b9c316745b4a451ac739b1e04939a3d8b229985",

        "Linux-ppc64le": "d9205718da5fbab85433476f9ff61fcf4b889d216d6eea26753bbc24d115dd70",

    },

    # cuDNN 7.5.0

    "7.5.0.56-10.1": {

        "Linux-x86_64": "c31697d6b71afe62838ad2e57da3c3c9419c4e9f5635d14b683ebe63f904fbc8",

        "Linux-ppc64le": "15415eb714ab86ab6c7531f2cac6474b5dafd989479b062776c670b190e43638",

    },

    "7.5.0.56-10.0": {

        "Linux-x86_64": "701097882cb745d4683bb7ff6c33b8a35c7c81be31bac78f05bad130e7e0b781",

        "Linux-ppc64le": "f0c1cbd9de553c8e2a3893915bd5fff57b30e368ef4c964d783b6a877869e93a",

    },

    # cuDNN 7.3.0

    "7.3.0.29-9.0": {

        "Linux-x86_64": "403f9043ff2c7b2c5967454872275d07bca11fd41dfc7b21995eadcad6dbe49b"

    },

    # cuDNN 7.2.1

    "7.2.1.38-9.0": {

        "Linux-x86_64": "cf007437b9ac6250ec63b89c25f248d2597fdd01369c80146567f78e75ce4e37"

    },

    # cuDNN 7.1.3

    "7.1.3-9.1": {

        "Linux-x86_64": "dd616d3794167ceb923d706bf73e8d6acdda770751492b921ee6827cdf190228",

        "Linux-ppc64le": "e3b4837f711b98a52faacc872a68b332c833917ef3cf87c0108f1d01af9b2931",

    },

    # cuDNN 6.0

    "6.0-8.0": {

        "Linux-x86_64": "9b09110af48c9a4d7b6344eb4b3e344daa84987ed6177d5c44319732f3bb7f9c"

    },

    # cuDNN 5.1

    "5.1-8.0": {

        "Linux-x86_64": "c10719b36f2dd6e9ddc63e3189affaa1a94d7d027e63b71c3f64d449ab0645ce"

    },

}





class Cudnn(Package):

    """NVIDIA cuDNN is a GPU-accelerated library of primitives for deep

    neural networks"""



    homepage = "https://developer.nvidia.com/cudnn"



    # Latest versions available at:

    #     https://developer.nvidia.com/rdp/cudnn-download

    # Archived versions available at:

    #     https://developer.nvidia.com/rdp/cudnn-archive

    # Note that download links don't work from command line,

    # need to use modified URLs like in url_for_version.

    maintainers("adamjstewart", "bvanessen")



    skip_version_audit = ["platform=darwin", "platform=windows"]



    license("MIT")



    for ver, packages in _versions.items():

        key = "{0}-{1}".format(platform.system(), platform.machine())

        pkg = packages.get(key)

        cudnn_ver, cuda_ver = ver.split("-")

        long_ver = "{0}-{1}".format(cudnn_ver, cuda_ver)

        if pkg:

            version(long_ver, sha256=pkg)

            # Add constraints matching CUDA version to cuDNN version

            # cuDNN builds for CUDA 11.x are compatible with all CUDA 11.x:

            # https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#fntarg_2

            if Version(cuda_ver) >= Version("11"):

                cuda_ver = Version(cuda_ver).up_to(1)

            depends_on("cuda@{}".format(cuda_ver), when="@{}".format(long_ver))



    def url_for_version(self, version):

        # Get the system and machine arch for building the file path

        sys = "{0}-{1}".format(platform.system(), platform.machine())

        # Munge it to match Nvidia's naming scheme

        sys_key = sys.lower()

        if version < Version("8.3.1"):

            sys_key = (

                sys_key.replace("x86_64", "x64")

                .replace("darwin", "osx")

                .replace("aarch64", "aarch64sbsa")

            )

        elif version < Version("8.8.0"):

            sys_key = sys_key.replace("aarch64", "sbsa")



        if version >= Version("8.3.1"):

            # NOTE: upload layout changed for 8.3.1, they include a 10.2

            # artifact for cuda@10.2 x86_64, but the runtime is only supported

            # for cuda@11.  See

            # https://docs.nvidia.com/deeplearning/cudnn/release-notes/rel_8.html

            # As such, hacking the `directory` to include the extra

            # local_installers/11.5 is included as this may not happen again.

            directory = version[:3]

            ver = version[:4]

            cuda = version[4:]

            directory = "{0}/local_installers/{1}".format(directory, cuda)

        elif version >= Version("7.2"):

            directory = version[:3]

            ver = version[:4]

            cuda = version[4:]

        elif version >= Version("7.1"):

            directory = version[:3]

            ver = version[:2]

            cuda = version[3:]

        elif version >= Version("7.0"):

            directory = version[:3]

            ver = version[0]

            cuda = version[3:]

        else:

            directory = version[:2]

            ver = version[:2]

            cuda = version[2:]



        # 8.8.0 changed the base url again

        if version >= Version("8.8.0"):

            url = "https://developer.download.nvidia.com/compute/cudnn/redist/cudnn/{0}/cudnn-{0}-{1}_cuda{2}-archive.tar.xz"

            return url.format(sys_key, ver, cuda.up_to(1))

        # 8.5.0 removed minor from cuda version

        elif version >= Version("8.5.0"):

            url = "https://developer.download.nvidia.com/compute/redist/cudnn/v{0}/cudnn-{1}-{2}_cuda{3}-archive.tar.xz"

            return url.format(directory, sys_key, ver, cuda.up_to(1))

        # 8.3.1 switched to xzip tarballs and reordered url parts.

        elif version >= Version("8.3.1"):

            url = "https://developer.download.nvidia.com/compute/redist/cudnn/v{0}/cudnn-{1}-{2}_cuda{3}-archive.tar.xz"

            return url.format(directory, sys_key, ver, cuda)

        else:

            url = "https://developer.download.nvidia.com/compute/redist/cudnn/v{0}/cudnn-{1}-{2}-v{3}.tgz"

            return url.format(directory, cuda, sys_key, ver)



    def setup_run_environment(self, env):

        # Package is not compiled, and does not work unless LD_LIBRARY_PATH is set

        env.prepend_path("LD_LIBRARY_PATH", self.prefix.lib)



        if self.spec.satisfies("target=ppc64le: platform=linux"):

            env.set("cuDNN_ROOT", os.path.join(self.prefix, "targets", "ppc64le-linux"))



    def install(self, spec, prefix):

        install_tree(".", prefix)



        if spec.satisfies("target=ppc64le: platform=linux"):

            target_lib = os.path.join(prefix, "targets", "ppc64le-linux", "lib")

            if os.path.isdir(target_lib) and not os.path.isdir(prefix.lib):

                symlink(target_lib, prefix.lib)

            target_include = os.path.join(prefix, "targets", "ppc64le-linux", "include")

            if os.path.isdir(target_include) and not os.path.isdir(prefix.include):

                symlink(target_include, prefix.include)

packages/gcc/darwin/apfs.patch

deleted100644 → 0
+0 −12
Original line number Diff line number Diff line 
diff -uNr gcc-7.2.0.orig/libstdc++-v3/include/Makefile.in gcc-7.2.0/libstdc++-v3/include/Makefile.in

--- gcc-7.2.0.orig/libstdc++-v3/include/Makefile.in     2017-07-25 14:05:07.000000000 -0400

+++ gcc-7.2.0/libstdc++-v3/include/Makefile.in  2017-09-02 12:22:08.000000000 -0400

@@ -1764,6 +1764,8 @@

 @GLIBCXX_HOSTED_TRUE@install-data-local: install-headers

 @GLIBCXX_HOSTED_FALSE@install-data-local: install-freestanding-headers

 

+.NOTPARALLEL: install-headers

+

 # This is a subset of the full install-headers rule.  We only need <ciso646>,

 # <cstddef>, <cfloat>, <limits>, <climits>, <cstdint>, <cstdlib>, <new>,

 # <typeinfo>, <exception>, <initializer_list>, <cstdalign>, <cstdarg>,

packages/gcc/darwin/clang13.patch

deleted100644 → 0
+0 −32
Original line number Diff line number Diff line 
--- a/gcc/genconditions.c	2019-01-01 12:37:19.064943662 +0100

+++ b/gcc/genconditions.c	2019-10-11 10:57:11.464595789 +0200

@@ -57,8 +57,9 @@ write_header (void)

 \n\

 /* It is necessary, but not entirely safe, to include the headers below\n\

    in a generator program.  As a defensive measure, don't do so when the\n\

-   table isn't going to have anything in it.  */\n\

-#if GCC_VERSION >= 3001\n\

+   table isn't going to have anything in it.\n\

+   Clang 9 is buggy and doesn't handle __builtin_constant_p correctly.  */\n\

+#if GCC_VERSION >= 3001 && __clang_major__ < 9\n\

 \n\

 /* Do not allow checking to confuse the issue.  */\n\

 #undef CHECKING_P\n\

@@ -170,7 +171,7 @@ struct c_test\n\

    vary at run time.  It works in 3.0.1 and later; 3.0 only when not\n\

    optimizing.  */\n\

 \n\

-#if GCC_VERSION >= 3001\n\

+#if GCC_VERSION >= 3001 && __clang_major__ < 9\n\

 static const struct c_test insn_conditions[] = {\n");

 

   traverse_c_tests (write_one_condition, 0);

@@ -191,7 +192,7 @@ write_writer (void)

 	"  unsigned int i;\n"

         "  const char *p;\n"

         "  puts (\"(define_conditions [\");\n"

-	"#if GCC_VERSION >= 3001\n"

+	"#if GCC_VERSION >= 3001 && __clang_major__ < 9\n"

 	"  for (i = 0; i < ARRAY_SIZE (insn_conditions); i++)\n"

 	"    {\n"

 	"      printf (\"  (%d \\\"\", insn_conditions[i].value);\n"

packages/gcc/darwin/gcc-4.9.patch1

deleted100644 → 0
+0 −42
Original line number Diff line number Diff line 
diff --git a/gcc/configure b/gcc/configure

index 9523773..52b0bf7 100755

--- a/gcc/configure

+++ b/gcc/configure

@@ -24884,7 +24884,7 @@ if test "${gcc_cv_as_ix86_filds+set}" = set; then :

 else

   gcc_cv_as_ix86_filds=no

   if test x$gcc_cv_as != x; then

-    $as_echo 'filds mem; fists mem' > conftest.s

+    $as_echo 'filds (%ebp); fists (%ebp)' > conftest.s

     if { ac_try='$gcc_cv_as $gcc_cv_as_flags  -o conftest.o conftest.s >&5'

   { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5

   (eval $ac_try) 2>&5

@@ -24915,7 +24915,7 @@ if test "${gcc_cv_as_ix86_fildq+set}" = set; then :

 else

   gcc_cv_as_ix86_fildq=no

   if test x$gcc_cv_as != x; then

-    $as_echo 'fildq mem; fistpq mem' > conftest.s

+    $as_echo 'fildq (%ebp); fistpq (%ebp)' > conftest.s

     if { ac_try='$gcc_cv_as $gcc_cv_as_flags  -o conftest.o conftest.s >&5'

   { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_try\""; } >&5

   (eval $ac_try) 2>&5

diff --git a/gcc/configure.ac b/gcc/configure.ac

index 68b0ee8..bd53978 100644

--- a/gcc/configure.ac

+++ b/gcc/configure.ac

@@ -3869,13 +3869,13 @@ foo:	nop

 

     gcc_GAS_CHECK_FEATURE([filds and fists mnemonics],

        gcc_cv_as_ix86_filds,,,

-       [filds mem; fists mem],,

+       [filds (%ebp); fists (%ebp)],,

        [AC_DEFINE(HAVE_AS_IX86_FILDS, 1,

          [Define if your assembler uses filds and fists mnemonics.])])

 

     gcc_GAS_CHECK_FEATURE([fildq and fistpq mnemonics],

        gcc_cv_as_ix86_fildq,,,

-       [fildq mem; fistpq mem],,

+       [fildq (%ebp); fistpq (%ebp)],,

        [AC_DEFINE(HAVE_AS_IX86_FILDQ, 1,

          [Define if your assembler uses fildq and fistq mnemonics.])])

packages/gcc/darwin/gcc-4.9.patch2

deleted100644 → 0
+0 −28
Original line number Diff line number Diff line 
From 82f81877458ea372176eabb5de36329431dce99b Mon Sep 17 00:00:00 2001

From: Iain Sandoe <iain@codesourcery.com>

Date: Sat, 21 Dec 2013 00:30:18 +0000

Subject: [PATCH] don't try to mark local symbols as no-dead-strip



---

 gcc/config/darwin.c | 5 +++++

 1 file changed, 5 insertions(+)



diff --git a/gcc/config/darwin.c b/gcc/config/darwin.c

index 40804b8..0080299 100644

--- a/gcc/config/darwin.c

+++ b/gcc/config/darwin.c

@@ -1259,6 +1259,11 @@ darwin_encode_section_info (tree decl, rtx rtl, int first ATTRIBUTE_UNUSED)

 void

 darwin_mark_decl_preserved (const char *name)

 {

+  /* Actually we shouldn't mark any local symbol this way, but for now

+     this only happens with ObjC meta-data.  */

+  if (darwin_label_is_anonymous_local_objc_name (name))

+    return;

+

   fprintf (asm_out_file, "\t.no_dead_strip ");

   assemble_name (asm_out_file, name);

   fputc ('\n', asm_out_file);

-- 

2.2.1

packages/gcc/darwin/gcc-6.1.0-jit.patch

deleted100644 → 0
+0 −21
Original line number Diff line number Diff line 
# Fix for libgccjit.so linkage on Darwin

# https://gcc.gnu.org/bugzilla/show_bug.cgi?id=64089

# https://github.com/Homebrew/homebrew-core/issues/1872#issuecomment-225625332

# https://github.com/Homebrew/homebrew-core/issues/1872#issuecomment-225626490



# Stolen from Homebrew:

# https://raw.githubusercontent.com/Homebrew/formula-patches/e9e0ee09389a54cc4c8fe1c24ebca3cd765ed0ba/gcc/6.1.0-jit.patch

diff --git a/gcc/jit/Make-lang.in b/gcc/jit/Make-lang.in

index 44d0750..4df2a9c 100644

--- a/gcc/jit/Make-lang.in

+++ b/gcc/jit/Make-lang.in

@@ -85,8 +85,7 @@ $(LIBGCCJIT_FILENAME): $(jit_OBJS) \

	     $(jit_OBJS) libbackend.a libcommon-target.a libcommon.a \

	     $(CPPLIB) $(LIBDECNUMBER) $(LIBS) $(BACKENDLIBS) \

	     $(EXTRA_GCC_OBJS) \

-	     -Wl,--version-script=$(srcdir)/jit/libgccjit.map \

-	     -Wl,-soname,$(LIBGCCJIT_SONAME)

+	     -Wl,-install_name,$(LIBGCCJIT_SONAME)



 $(LIBGCCJIT_SONAME_SYMLINK): $(LIBGCCJIT_FILENAME)

	ln -sf $(LIBGCCJIT_FILENAME) $(LIBGCCJIT_SONAME_SYMLINK)

packages/gcc/darwin/gcc-7.1.0-headerpad.patch

deleted100644 → 0
+0 −19
Original line number Diff line number Diff line 
# Use -headerpad_max_install_names in the build,

# otherwise lto1 load commands cannot be edited on El Capitan



# Stolen from Homebrew:

# https://raw.githubusercontent.com/Homebrew/formula-patches/32cf103/gcc/7.1.0-headerpad.patch



diff --git a/config/mh-darwin b/config/mh-darwin

index 148b730..c2318b5 100644

--- a/config/mh-darwin

+++ b/config/mh-darwin

@@ -16,7 +16,7 @@ DARWIN_GCC_MDYNAMIC_NO_PIC := \

 DARWIN_NO_PIE := `case ${host} in *-*-darwin[1][1-9]*) echo -Wl,-no_pie ;; esac;`

 

 BOOT_CFLAGS += $(DARWIN_MDYNAMIC_NO_PIC)

-BOOT_LDFLAGS += $(DARWIN_NO_PIE)

+BOOT_LDFLAGS += $(DARWIN_NO_PIE) -Wl,-headerpad_max_install_names

 

 # Similarly, for cross-compilation.

 STAGE1_CFLAGS += $(DARWIN_MDYNAMIC_NO_PIC)

packages/gcc/darwin/headers-10.13-fix.patch

deleted100644 → 0
+0 −127
Original line number Diff line number Diff line 
diff -pur fixincludes/fixincl.x gcc-5.5.0/fixincludes/fixincl.x

--- a/fixincludes/fixincl.x	2017-01-30 17:08:42.000000000 +0100

+++ b/fixincludes/fixincl.x	2017-12-21 14:34:35.000000000 +0100

@@ -1,12 +1,12 @@

 /*  -*- buffer-read-only: t -*- vi: set ro:

- * 

+ *

  * DO NOT EDIT THIS FILE   (fixincl.x)

- * 

- * It has been AutoGen-ed  January  5, 2017 at 06:05:06 PM by AutoGen 5.16.2

+ *

+ * It has been AutoGen-ed  December 21, 2017 at 02:34:35 PM by AutoGen 5.18.7

  * From the definitions    inclhack.def

  * and the template file   fixincl

  */

-/* DO NOT SVN-MERGE THIS FILE, EITHER Thu Jan  5 18:05:06 CET 2017

+/* DO NOT SVN-MERGE THIS FILE, EITHER Thu Dec 21 14:34:35 CET 2017

  *

  * You must regenerate it.  Use the ./genfixes script.

  *

@@ -15,7 +15,7 @@

  * certain ANSI-incompatible system header files which are fixed to work

  * correctly with ANSI C and placed in a directory that GNU C will search.

  *

- * This file contains 240 fixup descriptions.

+ * This file contains 241 fixup descriptions.

  *

  * See README for more information.

  *

@@ -2579,6 +2579,43 @@ extern \"C\" {\n\

 

 /* * * * * * * * * * * * * * * * * * * * * * * * * *

  *

+ *  Description of Darwin_Osavailability fix

+ */

+tSCC zDarwin_OsavailabilityName[] =

+     "darwin_osavailability";

+

+/*

+ *  File name selection pattern

+ */

+tSCC zDarwin_OsavailabilityList[] =

+  "os/availability.h\0";

+/*

+ *  Machine/OS name selection pattern

+ */

+tSCC* apzDarwin_OsavailabilityMachs[] = {

+        "*-*-darwin*",

+        (const char*)NULL };

+

+/*

+ *  content selection pattern - do fix if pattern found

+ */

+tSCC zDarwin_OsavailabilitySelect0[] =

+       "#define[ \t]+__(API_[A-Z_]*)\\(\\.\\.\\.\\)";

+

+#define    DARWIN_OSAVAILABILITY_TEST_CT  1

+static tTestDesc aDarwin_OsavailabilityTests[] = {

+  { TT_EGREP,    zDarwin_OsavailabilitySelect0, (regex_t*)NULL }, };

+

+/*

+ *  Fix Command Arguments for Darwin_Osavailability

+ */

+static const char* apzDarwin_OsavailabilityPatch[] = {

+    "format",

+    "#define %1(...)",

+    (char*)NULL };

+

+/* * * * * * * * * * * * * * * * * * * * * * * * * *

+ *

  *  Description of Darwin_9_Long_Double_Funcs_2 fix

  */

 tSCC zDarwin_9_Long_Double_Funcs_2Name[] =

@@ -9818,9 +9855,9 @@ static const char* apzX11_SprintfPatch[]

  *

  *  List of all fixes

  */

-#define REGEX_COUNT          276

+#define REGEX_COUNT          277

 #define MACH_LIST_SIZE_LIMIT 187

-#define FIX_COUNT            240

+#define FIX_COUNT            241

 

 /*

  *  Enumerate the fixes

@@ -9885,6 +9922,7 @@ typedef enum {

     CTRL_QUOTES_DEF_FIXIDX,

     CTRL_QUOTES_USE_FIXIDX,

     CXX_UNREADY_FIXIDX,

+    DARWIN_OSAVAILABILITY_FIXIDX,

     DARWIN_9_LONG_DOUBLE_FUNCS_2_FIXIDX,

     DARWIN_EXTERNC_FIXIDX,

     DARWIN_GCC4_BREAKAGE_FIXIDX,

@@ -10364,6 +10402,11 @@ tFixDesc fixDescList[ FIX_COUNT ] = {

      CXX_UNREADY_TEST_CT, FD_MACH_ONLY | FD_SUBROUTINE,

      aCxx_UnreadyTests,   apzCxx_UnreadyPatch, 0 },

 

+  {  zDarwin_OsavailabilityName,    zDarwin_OsavailabilityList,

+     apzDarwin_OsavailabilityMachs,

+     DARWIN_OSAVAILABILITY_TEST_CT, FD_MACH_ONLY | FD_SUBROUTINE,

+     aDarwin_OsavailabilityTests,   apzDarwin_OsavailabilityPatch, 0 },

+

   {  zDarwin_9_Long_Double_Funcs_2Name,    zDarwin_9_Long_Double_Funcs_2List,

      apzDarwin_9_Long_Double_Funcs_2Machs,

      DARWIN_9_LONG_DOUBLE_FUNCS_2_TEST_CT, FD_MACH_ONLY | FD_SUBROUTINE,

diff -pur fixincludes/inclhack.def gcc-5.5.0/fixincludes/inclhack.def

--- a/fixincludes/inclhack.def	2017-01-30 17:08:42.000000000 +0100

+++ b/fixincludes/inclhack.def	2017-12-21 14:34:28.000000000 +0100

@@ -1337,6 +1337,18 @@ fix = {

     test_text = "extern void* malloc( size_t );";

 };

 

+fix = {

+    hackname  = darwin_osavailability;

+    mach      = "*-*-darwin*";

+    files     = os/availability.h;

+    select    = "#define[ \t]+__(API_[A-Z_]*)\\(\\.\\.\\.\\)";

+    c_fix     = format;

+    c_fix_arg = "#define %1(...)";

+

+    test_text = "#define __API_AVAILABLE(...)\n"

+		"#define API_AVAILABLE(...)\n";

+};

+

 /*

  *  For the AAB_darwin7_9_long_double_funcs fix to be useful,

  *  you have to not use "" includes.

packages/gcc/detection_test.yaml

deleted100644 → 0
+0 −38
Original line number Diff line number Diff line 
paths:

  # Ubuntu 18.04, system compilers without Fortran

  - layout:

      - executables:

        - "bin/gcc"

        - "bin/g++"

        script: "echo 7.5.0"

    results:

      - spec: "gcc@7.5.0 languages=c,c++"

  # Mock a version < 7 of GCC that requires -dumpversion and

  # errors with -dumpfullversion

  - layout:

      - executables:

        - "bin/gcc-5"

        - "bin/g++-5"

        - "bin/gfortran-5"

        script: |

          if [[ "$1" == "-dumpversion" ]] ; then

            echo "5.5.0"

          else

            echo "gcc-5: fatal error: no input files"

            echo "compilation terminated."

            exit 1

          fi

    results:

      - spec: "gcc@5.5.0 languages=c,c++,fortran"

  # Multiple compilers present at the same time

  - layout:

      - executables:

        - "bin/x86_64-linux-gnu-gcc-6"

        script: 'echo 6.5.0'

      - executables:

        - "bin/x86_64-linux-gnu-gcc-10"

        - "bin/x86_64-linux-gnu-g++-10"

        script: "echo 10.1.0"

    results:

      - spec: "gcc@6.5.0 languages=c"

      - spec: "gcc@10.1.0 languages=c,c++"
 
 No newline at end of file

packages/gcc/gcc-backport.patch

deleted100644 → 0
+0 −138
Original line number Diff line number Diff line 
2016-02-20  Bernd Edlinger  <bernd.edlinger@hotmail.de>



	Backported from mainline

	2016-02-19  Jakub Jelinek  <jakub@redhat.com>

		    Bernd Edlinger  <bernd.edlinger@hotmail.de>



	* Make-lang.in: Invoke gperf with -L C++.

 	* cfns.gperf: Remove prototypes for hash and libc_name_p

 	inlines.

 	* cfns.h: Regenerated.

	* except.c (nothrow_libfn_p): Adjust.



Index: gcc/cp/Make-lang.in

===================================================================

--- a/gcc/cp/Make-lang.in	(revision 233574)

+++ b/gcc/cp/Make-lang.in	(working copy)

@@ -111,7 +111,7 @@ else

 # deleting the $(srcdir)/cp/cfns.h file.

 $(srcdir)/cp/cfns.h:

 endif

-	gperf -o -C -E -k '1-6,$$' -j1 -D -N 'libc_name_p' -L ANSI-C \

+	gperf -o -C -E -k '1-6,$$' -j1 -D -N 'libc_name_p' -L C++ \

 		$(srcdir)/cp/cfns.gperf --output-file $(srcdir)/cp/cfns.h

 

 #

Index: gcc/cp/cfns.gperf

===================================================================

--- a/gcc/cp/cfns.gperf	(revision 233574)

+++ b/gcc/cp/cfns.gperf	(working copy)

@@ -1,3 +1,5 @@

+%language=C++

+%define class-name libc_name

 %{

 /* Copyright (C) 2000-2015 Free Software Foundation, Inc.

 

@@ -16,14 +18,6 @@ for more details.

 You should have received a copy of the GNU General Public License

 along with GCC; see the file COPYING3.  If not see

 <http://www.gnu.org/licenses/>.  */

-#ifdef __GNUC__

-__inline

-#endif

-static unsigned int hash (const char *, unsigned int);

-#ifdef __GNUC__

-__inline

-#endif

-const char * libc_name_p (const char *, unsigned int);

 %}

 %%

 # The standard C library functions, for feeding to gperf; the result is used

Index: gcc/cp/cfns.h

===================================================================

--- a/gcc/cp/cfns.h	(revision 233574)

+++ b/gcc/cp/cfns.h	(working copy)

@@ -1,5 +1,5 @@

-/* ANSI-C code produced by gperf version 3.0.3 */

-/* Command-line: gperf -o -C -E -k '1-6,$' -j1 -D -N libc_name_p -L ANSI-C cfns.gperf  */

+/* C++ code produced by gperf version 3.0.4 */

+/* Command-line: gperf -o -C -E -k '1-6,$' -j1 -D -N libc_name_p -L C++ --output-file cfns.h cfns.gperf  */

 

 #if !((' ' == 32) && ('!' == 33) && ('"' == 34) && ('#' == 35) \

       && ('%' == 37) && ('&' == 38) && ('\'' == 39) && ('(' == 40) \

@@ -28,7 +28,7 @@

 #error "gperf generated tables don't work with this execution character set. Please report a bug to <bug-gnu-gperf@gnu.org>."

 #endif

 

-#line 1 "cfns.gperf"

+#line 3 "cfns.gperf"

 

 /* Copyright (C) 2000-2015 Free Software Foundation, Inc.

 

@@ -47,26 +47,19 @@ for more details.

 You should have received a copy of the GNU General Public License

 along with GCC; see the file COPYING3.  If not see

 <http://www.gnu.org/licenses/>.  */

-#ifdef __GNUC__

-__inline

-#endif

-static unsigned int hash (const char *, unsigned int);

-#ifdef __GNUC__

-__inline

-#endif

-const char * libc_name_p (const char *, unsigned int);

 /* maximum key range = 391, duplicates = 0 */

 

-#ifdef __GNUC__

-__inline

-#else

-#ifdef __cplusplus

-inline

-#endif

-#endif

-static unsigned int

-hash (register const char *str, register unsigned int len)

+class libc_name

 {

+private:

+  static inline unsigned int hash (const char *str, unsigned int len);

+public:

+  static const char *libc_name_p (const char *str, unsigned int len);

+};

+

+inline unsigned int

+libc_name::hash (register const char *str, register unsigned int len)

+{

   static const unsigned short asso_values[] =

     {

       400, 400, 400, 400, 400, 400, 400, 400, 400, 400,

@@ -122,14 +115,8 @@ along with GCC; see the file COPYING3.  If not see

   return hval + asso_values[(unsigned char)str[len - 1]];

 }

 

-#ifdef __GNUC__

-__inline

-#ifdef __GNUC_STDC_INLINE__

-__attribute__ ((__gnu_inline__))

-#endif

-#endif

 const char *

-libc_name_p (register const char *str, register unsigned int len)

+libc_name::libc_name_p (register const char *str, register unsigned int len)

 {

   enum

     {

Index: gcc/cp/except.c

===================================================================

--- a/gcc/cp/except.c	(revision 233574)

+++ b/gcc/cp/except.c	(working copy)

@@ -1040,7 +1040,8 @@ nothrow_libfn_p (const_tree fn)

      unless the system headers are playing rename tricks, and if

      they are, we don't want to be confused by them.  */

   id = DECL_NAME (fn);

-  return !!libc_name_p (IDENTIFIER_POINTER (id), IDENTIFIER_LENGTH (id));

+  return !!libc_name::libc_name_p (IDENTIFIER_POINTER (id),

+				   IDENTIFIER_LENGTH (id));

 }

 

 /* Returns nonzero if an exception of type FROM will be caught by a

packages/gcc/glibc-2.31-libsanitizer-1-gcc-6.patch

deleted100644 → 0
+0 −39
Original line number Diff line number Diff line 
From ce9568e9e9cf6094be30e748821421e703754ffc Mon Sep 17 00:00:00 2001

From: Jakub Jelinek <jakub@redhat.com>

Date: Fri, 8 Nov 2019 19:53:18 +0100

Subject: [PATCH] backport: re PR sanitizer/92154 (new glibc breaks arm

 bootstrap due to libsanitizer)



	Backported from mainline

	2019-10-22  Tamar Christina  <tamar.christina@arm.com>

	Backported for version 5.3.0 <= gcc <= 6.5.0

	2020-06-05  John L. Jolly  <john.jolly@gmail.com>



	PR sanitizer/92154

	* sanitizer_common/sanitizer_platform_limits_posix.cc:

	Cherry-pick compiler-rt revision r375220.



From-SVN: r277981

---

 libsanitizer/ChangeLog                                   | 9 +++++++++

 .../sanitizer_common/sanitizer_platform_limits_posix.cc  | 6 +++++-

 2 files changed, 14 insertions(+), 1 deletion(-)



diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

index 6cd4a5bac8b0..06a605ff4670 100644

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

@@ -1130,8 +1130,12 @@ CHECK_SIZE_AND_OFFSET(ipc_perm, uid);

 #ifndef __GLIBC_PREREQ

 #define __GLIBC_PREREQ(x, y) 0

 #endif

-#if !defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)

+#if (!defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)) && \

+    !defined(__arm__)

 /* On aarch64 glibc 2.20 and earlier provided incorrect mode field.  */

+/* On Arm glibc 2.31 and later provide a different mode field, this field is

+   never used by libsanitizer so we can simply ignore this assert for all glibc

+   versions.  */

 CHECK_SIZE_AND_OFFSET(ipc_perm, mode);

 #endif

packages/gcc/glibc-2.31-libsanitizer-1.patch

deleted100644 → 0
+0 −37
Original line number Diff line number Diff line 
From ce9568e9e9cf6094be30e748821421e703754ffc Mon Sep 17 00:00:00 2001

From: Jakub Jelinek <jakub@redhat.com>

Date: Fri, 8 Nov 2019 19:53:18 +0100

Subject: [PATCH] backport: re PR sanitizer/92154 (new glibc breaks arm

 bootstrap due to libsanitizer)



	Backported from mainline

	2019-10-22  Tamar Christina  <tamar.christina@arm.com>



	PR sanitizer/92154

	* sanitizer_common/sanitizer_platform_limits_posix.cc:

	Cherry-pick compiler-rt revision r375220.



From-SVN: r277981

---

 libsanitizer/ChangeLog                                   | 9 +++++++++

 .../sanitizer_common/sanitizer_platform_limits_posix.cc  | 6 +++++-

 2 files changed, 14 insertions(+), 1 deletion(-)



diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

index 6cd4a5bac8b0..06a605ff4670 100644

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

@@ -1156,8 +1156,12 @@ CHECK_SIZE_AND_OFFSET(ipc_perm, uid);

 CHECK_SIZE_AND_OFFSET(ipc_perm, gid);

 CHECK_SIZE_AND_OFFSET(ipc_perm, cuid);

 CHECK_SIZE_AND_OFFSET(ipc_perm, cgid);

-#if !defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)

+#if (!defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)) && \

+    !defined(__arm__)

 /* On aarch64 glibc 2.20 and earlier provided incorrect mode field.  */

+/* On Arm glibc 2.31 and later provide a different mode field, this field is

+   never used by libsanitizer so we can simply ignore this assert for all glibc

+   versions.  */

 CHECK_SIZE_AND_OFFSET(ipc_perm, mode);

 #endif

packages/gcc/glibc-2.31-libsanitizer-2-gcc-6.patch

deleted100644 → 0
+0 −69
Original line number Diff line number Diff line 
From 75003cdd23c310ec385344e8040d490e8dd6d2be Mon Sep 17 00:00:00 2001

From: Jakub Jelinek <jakub@redhat.com>

Date: Fri, 20 Dec 2019 17:58:35 +0100

Subject: [PATCH] backport: re PR sanitizer/92154 (new glibc breaks arm

 bootstrap due to libsanitizer)



	Backported from mainline

	2019-11-26  Jakub Jelinek  <jakub@redhat.com>

	Backported for version 5.3.0 <= gcc <= 6.5.0

	2020-06-05  John L. Jolly  <john.jolly@gmail.com>



	PR sanitizer/92154

	* sanitizer_common/sanitizer_platform_limits_posix.h: Cherry-pick

	llvm-project revision 947f9692440836dcb8d88b74b69dd379d85974ce.

	* sanitizer_common/sanitizer_platform_limits_posix.cc: Likewise.



From-SVN: r279653

---

 libsanitizer/ChangeLog                            | 10 ++++++++++

 .../sanitizer_platform_limits_posix.cc            |  9 +++------

 .../sanitizer_platform_limits_posix.h             | 15 +--------------

 3 files changed, 14 insertions(+), 20 deletions(-)



diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

index 06a605ff4670..d823a12190c0 100644

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

@@ -1130,12 +1130,9 @@ CHECK_SIZE_AND_OFFSET(ipc_perm, uid);

 #ifndef __GLIBC_PREREQ

 #define __GLIBC_PREREQ(x, y) 0

 #endif

-#if (!defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)) && \

-    !defined(__arm__)

-/* On aarch64 glibc 2.20 and earlier provided incorrect mode field.  */

-/* On Arm glibc 2.31 and later provide a different mode field, this field is

-   never used by libsanitizer so we can simply ignore this assert for all glibc

-   versions.  */

+#if !SANITIZER_LINUX || __GLIBC_PREREQ (2, 31)

+/* glibc 2.30 and earlier provided 16-bit mode field instead of 32-bit

+   on many architectures.  */

 CHECK_SIZE_AND_OFFSET(ipc_perm, mode);

 #endif

 

diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

index 73af92af1e8f..6a673a7c9959 100644

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

@@ -211,20 +211,13 @@ namespace __sanitizer {

     unsigned long __unused1;

     unsigned long __unused2;

 #elif defined(__sparc__)

-# if defined(__arch64__)

     unsigned mode;

-    unsigned short __pad1;

-# else

-    unsigned short __pad1;

-    unsigned short mode;

     unsigned short __pad2;

-# endif

     unsigned short __seq;

     unsigned long long __unused1;

     unsigned long long __unused2;

 #else

-    unsigned short mode;

-    unsigned short __pad1;

+    unsigned int mode;

     unsigned short __seq;

     unsigned short __pad2;

 #if defined(__x86_64__) && !defined(_LP64)

packages/gcc/glibc-2.31-libsanitizer-2-gcc-7.patch

deleted100644 → 0
+0 −69
Original line number Diff line number Diff line 
From 75003cdd23c310ec385344e8040d490e8dd6d2be Mon Sep 17 00:00:00 2001

From: Jakub Jelinek <jakub@redhat.com>

Date: Fri, 20 Dec 2019 17:58:35 +0100

Subject: [PATCH] backport: re PR sanitizer/92154 (new glibc breaks arm

 bootstrap due to libsanitizer)



	Backported from mainline

	2019-11-26  Jakub Jelinek  <jakub@redhat.com>

	Backported for version 7.1.0 <= gcc <= 7.4.0

	2020-06-05  John L. Jolly  <john.jolly@gmail.com>



	PR sanitizer/92154

	* sanitizer_common/sanitizer_platform_limits_posix.h: Cherry-pick

	llvm-project revision 947f9692440836dcb8d88b74b69dd379d85974ce.

	* sanitizer_common/sanitizer_platform_limits_posix.cc: Likewise.



From-SVN: r279653

---

 libsanitizer/ChangeLog                            | 10 ++++++++++

 .../sanitizer_platform_limits_posix.cc            |  9 +++------

 .../sanitizer_platform_limits_posix.h             | 15 +--------------

 3 files changed, 14 insertions(+), 20 deletions(-)



diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

index 06a605ff4670..d823a12190c0 100644

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

@@ -1156,12 +1156,9 @@ CHECK_SIZE_AND_OFFSET(ipc_perm, uid);

 CHECK_SIZE_AND_OFFSET(ipc_perm, gid);

 CHECK_SIZE_AND_OFFSET(ipc_perm, cuid);

 CHECK_SIZE_AND_OFFSET(ipc_perm, cgid);

-#if (!defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)) && \

-    !defined(__arm__)

-/* On aarch64 glibc 2.20 and earlier provided incorrect mode field.  */

-/* On Arm glibc 2.31 and later provide a different mode field, this field is

-   never used by libsanitizer so we can simply ignore this assert for all glibc

-   versions.  */

+#if !SANITIZER_LINUX || __GLIBC_PREREQ (2, 31)

+/* glibc 2.30 and earlier provided 16-bit mode field instead of 32-bit

+   on many architectures.  */

 CHECK_SIZE_AND_OFFSET(ipc_perm, mode);

 #endif

 

diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

index 73af92af1e8f..6a673a7c9959 100644

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

@@ -211,20 +211,13 @@ namespace __sanitizer {

     unsigned long __unused1;

     unsigned long __unused2;

 #elif defined(__sparc__)

-# if defined(__arch64__)

     unsigned mode;

-    unsigned short __pad1;

-# else

-    unsigned short __pad1;

-    unsigned short mode;

     unsigned short __pad2;

-# endif

     unsigned short __seq;

     unsigned long long __unused1;

     unsigned long long __unused2;

 #else

-    unsigned short mode;

-    unsigned short __pad1;

+    unsigned int mode;

     unsigned short __seq;

     unsigned short __pad2;

 #if defined(__x86_64__) && !defined(_LP64)

packages/gcc/glibc-2.31-libsanitizer-2.patch

deleted100644 → 0
+0 −73
Original line number Diff line number Diff line 
From 75003cdd23c310ec385344e8040d490e8dd6d2be Mon Sep 17 00:00:00 2001

From: Jakub Jelinek <jakub@redhat.com>

Date: Fri, 20 Dec 2019 17:58:35 +0100

Subject: [PATCH] backport: re PR sanitizer/92154 (new glibc breaks arm

 bootstrap due to libsanitizer)



	Backported from mainline

	2019-11-26  Jakub Jelinek  <jakub@redhat.com>



	PR sanitizer/92154

	* sanitizer_common/sanitizer_platform_limits_posix.h: Cherry-pick

	llvm-project revision 947f9692440836dcb8d88b74b69dd379d85974ce.

	* sanitizer_common/sanitizer_platform_limits_posix.cc: Likewise.



From-SVN: r279653

---

 libsanitizer/ChangeLog                            | 10 ++++++++++

 .../sanitizer_platform_limits_posix.cc            |  9 +++------

 .../sanitizer_platform_limits_posix.h             | 15 +--------------

 3 files changed, 14 insertions(+), 20 deletions(-)



diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

index 06a605ff4670..d823a12190c0 100644

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

@@ -1156,12 +1156,9 @@ CHECK_SIZE_AND_OFFSET(ipc_perm, uid);

 CHECK_SIZE_AND_OFFSET(ipc_perm, gid);

 CHECK_SIZE_AND_OFFSET(ipc_perm, cuid);

 CHECK_SIZE_AND_OFFSET(ipc_perm, cgid);

-#if (!defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)) && \

-    !defined(__arm__)

-/* On aarch64 glibc 2.20 and earlier provided incorrect mode field.  */

-/* On Arm glibc 2.31 and later provide a different mode field, this field is

-   never used by libsanitizer so we can simply ignore this assert for all glibc

-   versions.  */

+#if !SANITIZER_LINUX || __GLIBC_PREREQ (2, 31)

+/* glibc 2.30 and earlier provided 16-bit mode field instead of 32-bit

+   on many architectures.  */

 CHECK_SIZE_AND_OFFSET(ipc_perm, mode);

 #endif

 

diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

index 73af92af1e8f..6a673a7c9959 100644

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

@@ -211,26 +211,13 @@ namespace __sanitizer {

     u64 __unused1;

     u64 __unused2;

 #elif defined(__sparc__)

-#if defined(__arch64__)

     unsigned mode;

-    unsigned short __pad1;

-#else

-    unsigned short __pad1;

-    unsigned short mode;

     unsigned short __pad2;

-#endif

     unsigned short __seq;

     unsigned long long __unused1;

     unsigned long long __unused2;

-#elif defined(__mips__) || defined(__aarch64__) || defined(__s390x__)

-    unsigned int mode;

-    unsigned short __seq;

-    unsigned short __pad1;

-    unsigned long __unused1;

-    unsigned long __unused2;

 #else

-    unsigned short mode;

-    unsigned short __pad1;

+    unsigned int mode;

     unsigned short __seq;

     unsigned short __pad2;

 #if defined(__x86_64__) && !defined(_LP64)

packages/gcc/glibc-2.31-libsanitizer-3-gcc-5.patch

deleted100644 → 0
+0 −81
Original line number Diff line number Diff line 
diff -ru a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc

--- a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc	2014-09-23 17:59:53.000000000 +0000

+++ b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc	2021-10-30 19:48:38.690007561 +0000

@@ -358,15 +358,6 @@

 

 #if SANITIZER_LINUX && !SANITIZER_ANDROID

   // _(SIOCDEVPLIP, WRITE, struct_ifreq_sz); // the same as EQL_ENSLAVE

-  _(CYGETDEFTHRESH, WRITE, sizeof(int));

-  _(CYGETDEFTIMEOUT, WRITE, sizeof(int));

-  _(CYGETMON, WRITE, struct_cyclades_monitor_sz);

-  _(CYGETTHRESH, WRITE, sizeof(int));

-  _(CYGETTIMEOUT, WRITE, sizeof(int));

-  _(CYSETDEFTHRESH, NONE, 0);

-  _(CYSETDEFTIMEOUT, NONE, 0);

-  _(CYSETTHRESH, NONE, 0);

-  _(CYSETTIMEOUT, NONE, 0);

   _(EQL_EMANCIPATE, WRITE, struct_ifreq_sz);

   _(EQL_ENSLAVE, WRITE, struct_ifreq_sz);

   _(EQL_GETMASTRCFG, WRITE, struct_ifreq_sz);

diff -ru a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc	2021-10-30 19:40:51.805824323 +0000

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc	2021-10-30 19:51:13.640403192 +0000

@@ -143,7 +143,6 @@

 #include <sys/statvfs.h>

 #include <sys/timex.h>

 #include <sys/user.h>

-#include <linux/cyclades.h>

 #include <linux/if_eql.h>

 #include <linux/if_plip.h>

 #include <linux/lp.h>

@@ -392,7 +391,6 @@

 

 #if SANITIZER_LINUX && !SANITIZER_ANDROID

   unsigned struct_ax25_parms_struct_sz = sizeof(struct ax25_parms_struct);

-  unsigned struct_cyclades_monitor_sz = sizeof(struct cyclades_monitor);

 #if EV_VERSION > (0x010000)

   unsigned struct_input_keymap_entry_sz = sizeof(struct input_keymap_entry);

 #else

@@ -759,15 +757,6 @@

 #endif  // SANITIZER_LINUX || SANITIZER_FREEBSD

 

 #if SANITIZER_LINUX && !SANITIZER_ANDROID

-  unsigned IOCTL_CYGETDEFTHRESH = CYGETDEFTHRESH;

-  unsigned IOCTL_CYGETDEFTIMEOUT = CYGETDEFTIMEOUT;

-  unsigned IOCTL_CYGETMON = CYGETMON;

-  unsigned IOCTL_CYGETTHRESH = CYGETTHRESH;

-  unsigned IOCTL_CYGETTIMEOUT = CYGETTIMEOUT;

-  unsigned IOCTL_CYSETDEFTHRESH = CYSETDEFTHRESH;

-  unsigned IOCTL_CYSETDEFTIMEOUT = CYSETDEFTIMEOUT;

-  unsigned IOCTL_CYSETTHRESH = CYSETTHRESH;

-  unsigned IOCTL_CYSETTIMEOUT = CYSETTIMEOUT;

   unsigned IOCTL_EQL_EMANCIPATE = EQL_EMANCIPATE;

   unsigned IOCTL_EQL_ENSLAVE = EQL_ENSLAVE;

   unsigned IOCTL_EQL_GETMASTRCFG = EQL_GETMASTRCFG;

diff -ru a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h	2021-10-30 19:40:51.698824053 +0000

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h	2021-10-30 19:51:39.680469814 +0000

@@ -875,7 +875,6 @@

 

 #if SANITIZER_LINUX && !SANITIZER_ANDROID

   extern unsigned struct_ax25_parms_struct_sz;

-  extern unsigned struct_cyclades_monitor_sz;

   extern unsigned struct_input_keymap_entry_sz;

   extern unsigned struct_ipx_config_data_sz;

   extern unsigned struct_kbdiacrs_sz;

@@ -1220,15 +1219,6 @@

 #endif  // SANITIZER_LINUX || SANITIZER_FREEBSD

 

 #if SANITIZER_LINUX && !SANITIZER_ANDROID

-  extern unsigned IOCTL_CYGETDEFTHRESH;

-  extern unsigned IOCTL_CYGETDEFTIMEOUT;

-  extern unsigned IOCTL_CYGETMON;

-  extern unsigned IOCTL_CYGETTHRESH;

-  extern unsigned IOCTL_CYGETTIMEOUT;

-  extern unsigned IOCTL_CYSETDEFTHRESH;

-  extern unsigned IOCTL_CYSETDEFTIMEOUT;

-  extern unsigned IOCTL_CYSETTHRESH;

-  extern unsigned IOCTL_CYSETTIMEOUT;

   extern unsigned IOCTL_EQL_EMANCIPATE;

   extern unsigned IOCTL_EQL_ENSLAVE;

   extern unsigned IOCTL_EQL_GETMASTRCFG;

packages/gcc/glibc-2.36-libsanitizer-gcc-10-12.patch

deleted100644 → 0
+0 −27
Original line number Diff line number Diff line 
diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp

index badf6a401cc..b43733033a6 100644

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp

@@ -72,7 +72,6 @@

 #include <sys/vt.h>

 #include <linux/cdrom.h>

 #include <linux/fd.h>

-#include <linux/fs.h>

 #include <linux/hdreg.h>

 #include <linux/input.h>

 #include <linux/ioctl.h>

@@ -822,10 +821,10 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr);

   unsigned IOCTL_EVIOCGPROP = IOCTL_NOT_PRESENT;

   unsigned IOCTL_EVIOCSKEYCODE_V2 = IOCTL_NOT_PRESENT;

 #endif

-  unsigned IOCTL_FS_IOC_GETFLAGS = FS_IOC_GETFLAGS;

-  unsigned IOCTL_FS_IOC_GETVERSION = FS_IOC_GETVERSION;

-  unsigned IOCTL_FS_IOC_SETFLAGS = FS_IOC_SETFLAGS;

-  unsigned IOCTL_FS_IOC_SETVERSION = FS_IOC_SETVERSION;

+  unsigned IOCTL_FS_IOC_GETFLAGS = _IOR('f', 1, long);

+  unsigned IOCTL_FS_IOC_GETVERSION = _IOR('v', 1, long);

+  unsigned IOCTL_FS_IOC_SETFLAGS = _IOW('f', 2, long);

+  unsigned IOCTL_FS_IOC_SETVERSION = _IOW('v', 2, long);

   unsigned IOCTL_GIO_CMAP = GIO_CMAP;

   unsigned IOCTL_GIO_FONT = GIO_FONT;

   unsigned IOCTL_GIO_UNIMAP = GIO_UNIMAP;

packages/gcc/glibc-2.36-libsanitizer-gcc-5-9.patch

deleted100644 → 0
+0 −27
Original line number Diff line number Diff line 
diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

index e8fce8a02..5122baa46 100644

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

@@ -65,7 +65,6 @@

 #include <sys/vt.h>

 #include <linux/cdrom.h>

 #include <linux/fd.h>

-#include <linux/fs.h>

 #include <linux/hdreg.h>

 #include <linux/input.h>

 #include <linux/ioctl.h>

@@ -846,10 +845,10 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr);

   unsigned IOCTL_EVIOCGPROP = IOCTL_NOT_PRESENT;

   unsigned IOCTL_EVIOCSKEYCODE_V2 = IOCTL_NOT_PRESENT;

 #endif

-  unsigned IOCTL_FS_IOC_GETFLAGS = FS_IOC_GETFLAGS;

-  unsigned IOCTL_FS_IOC_GETVERSION = FS_IOC_GETVERSION;

-  unsigned IOCTL_FS_IOC_SETFLAGS = FS_IOC_SETFLAGS;

-  unsigned IOCTL_FS_IOC_SETVERSION = FS_IOC_SETVERSION;

+  unsigned IOCTL_FS_IOC_GETFLAGS = _IOR('f', 1, long);

+  unsigned IOCTL_FS_IOC_GETVERSION = _IOR('v', 1, long);

+  unsigned IOCTL_FS_IOC_SETFLAGS = _IOW('f', 2, long);

+  unsigned IOCTL_FS_IOC_SETVERSION = _IOW('v', 2, long);

   unsigned IOCTL_GIO_CMAP = GIO_CMAP;

   unsigned IOCTL_GIO_FONT = GIO_FONT;

   unsigned IOCTL_GIO_UNIMAP = GIO_UNIMAP;

packages/gcc/package.py

deleted100644 → 0
+0 −1114

File deleted.

Preview size limit exceeded, changes collapsed.

packages/gcc/patch-2b40941d23b1570cdd90083b58fa0f66aa58c86e.patch

deleted100644 → 0
+0 −121
Original line number Diff line number Diff line 
From 2b40941d23b1570cdd90083b58fa0f66aa58c86e Mon Sep 17 00:00:00 2001

From: Tamar Christina <tamar.christina@arm.com>

Date: Fri, 21 May 2021 12:16:56 +0100

Subject: [PATCH] libsanitizer: Remove cyclades from libsanitizer



The Linux kernel has removed the interface to cyclades from

the latest kernel headers[1] due to them being orphaned for the

past 13 years.



libsanitizer uses this header when compiling against glibc, but

glibcs itself doesn't seem to have any references to cyclades.



Further more it seems that the driver is broken in the kernel and

the firmware doesn't seem to be available anymore.



As such since this is breaking the build of libsanitizer (and so the

GCC bootstrap[2]) I propose to remove this.



[1] https://lkml.org/lkml/2021/3/2/153

[2] https://gcc.gnu.org/bugzilla/show_bug.cgi?id=100379



libsanitizer/ChangeLog:



	PR sanitizer/100379

	* sanitizer_common/sanitizer_common_interceptors_ioctl.inc: Cherry-pick

	llvm-project revision f7c5351552387bd43f6ca3631016d7f0dfe0f135.

	* sanitizer_common/sanitizer_platform_limits_posix.cc: Likewise.

	* sanitizer_common/sanitizer_platform_limits_posix.h: Likewise.

---

 .../sanitizer_common_interceptors_ioctl.inc           |  9 ---------

 .../sanitizer_platform_limits_posix.cc                | 11 -----------

 .../sanitizer_platform_limits_posix.h                 | 10 ----------

 3 files changed, 30 deletions(-)



diff --git a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc

index 5408ea17c59..7a9cd3f5968 100644

--- a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc

+++ b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc

@@ -365,15 +365,6 @@ static void ioctl_table_fill() {

 

 #if SANITIZER_LINUX && !SANITIZER_ANDROID

   // _(SIOCDEVPLIP, WRITE, struct_ifreq_sz); // the same as EQL_ENSLAVE

-  _(CYGETDEFTHRESH, WRITE, sizeof(int));

-  _(CYGETDEFTIMEOUT, WRITE, sizeof(int));

-  _(CYGETMON, WRITE, struct_cyclades_monitor_sz);

-  _(CYGETTHRESH, WRITE, sizeof(int));

-  _(CYGETTIMEOUT, WRITE, sizeof(int));

-  _(CYSETDEFTHRESH, NONE, 0);

-  _(CYSETDEFTIMEOUT, NONE, 0);

-  _(CYSETTHRESH, NONE, 0);

-  _(CYSETTIMEOUT, NONE, 0);

   _(EQL_EMANCIPATE, WRITE, struct_ifreq_sz);

   _(EQL_ENSLAVE, WRITE, struct_ifreq_sz);

   _(EQL_GETMASTRCFG, WRITE, struct_ifreq_sz);

diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

index d823a12190c..e8fce8a0287 100644

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

@@ -157,7 +157,6 @@ typedef struct user_fpregs elf_fpregset_t;

 # include <sys/procfs.h>

 #endif

 #include <sys/user.h>

-#include <linux/cyclades.h>

 #include <linux/if_eql.h>

 #include <linux/if_plip.h>

 #include <linux/lp.h>

@@ -466,7 +465,6 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr);

 

 #if SANITIZER_LINUX && !SANITIZER_ANDROID

   unsigned struct_ax25_parms_struct_sz = sizeof(struct ax25_parms_struct);

-  unsigned struct_cyclades_monitor_sz = sizeof(struct cyclades_monitor);

 #if EV_VERSION > (0x010000)

   unsigned struct_input_keymap_entry_sz = sizeof(struct input_keymap_entry);

 #else

@@ -833,15 +831,6 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr);

 #endif // SANITIZER_LINUX || SANITIZER_FREEBSD

 

 #if SANITIZER_LINUX && !SANITIZER_ANDROID

-  unsigned IOCTL_CYGETDEFTHRESH = CYGETDEFTHRESH;

-  unsigned IOCTL_CYGETDEFTIMEOUT = CYGETDEFTIMEOUT;

-  unsigned IOCTL_CYGETMON = CYGETMON;

-  unsigned IOCTL_CYGETTHRESH = CYGETTHRESH;

-  unsigned IOCTL_CYGETTIMEOUT = CYGETTIMEOUT;

-  unsigned IOCTL_CYSETDEFTHRESH = CYSETDEFTHRESH;

-  unsigned IOCTL_CYSETDEFTIMEOUT = CYSETDEFTIMEOUT;

-  unsigned IOCTL_CYSETTHRESH = CYSETTHRESH;

-  unsigned IOCTL_CYSETTIMEOUT = CYSETTIMEOUT;

   unsigned IOCTL_EQL_EMANCIPATE = EQL_EMANCIPATE;

   unsigned IOCTL_EQL_ENSLAVE = EQL_ENSLAVE;

   unsigned IOCTL_EQL_GETMASTRCFG = EQL_GETMASTRCFG;

diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

index 6a673a7c995..f921bf2b5b5 100644

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

@@ -1040,7 +1040,6 @@ struct __sanitizer_cookie_io_functions_t {

 

 #if SANITIZER_LINUX && !SANITIZER_ANDROID

   extern unsigned struct_ax25_parms_struct_sz;

-  extern unsigned struct_cyclades_monitor_sz;

   extern unsigned struct_input_keymap_entry_sz;

   extern unsigned struct_ipx_config_data_sz;

   extern unsigned struct_kbdiacrs_sz;

@@ -1385,15 +1384,6 @@ struct __sanitizer_cookie_io_functions_t {

 #endif  // SANITIZER_LINUX || SANITIZER_FREEBSD

 

 #if SANITIZER_LINUX && !SANITIZER_ANDROID

-  extern unsigned IOCTL_CYGETDEFTHRESH;

-  extern unsigned IOCTL_CYGETDEFTIMEOUT;

-  extern unsigned IOCTL_CYGETMON;

-  extern unsigned IOCTL_CYGETTHRESH;

-  extern unsigned IOCTL_CYGETTIMEOUT;

-  extern unsigned IOCTL_CYSETDEFTHRESH;

-  extern unsigned IOCTL_CYSETDEFTIMEOUT;

-  extern unsigned IOCTL_CYSETTHRESH;

-  extern unsigned IOCTL_CYSETTIMEOUT;

   extern unsigned IOCTL_EQL_EMANCIPATE;

   extern unsigned IOCTL_EQL_ENSLAVE;

   extern unsigned IOCTL_EQL_GETMASTRCFG;

-- 

2.31.1

packages/gcc/patch-745dae5923aba02982563481d75a21595df22ff8.patch

deleted100644 → 0
+0 −123
Original line number Diff line number Diff line 
From 745dae5923aba02982563481d75a21595df22ff8 Mon Sep 17 00:00:00 2001

From: Tamar Christina <tamar.christina@arm.com>

Date: Fri, 21 May 2021 10:30:59 +0100

Subject: [PATCH] libsanitizer: Remove cyclades from libsanitizer



The Linux kernel has removed the interface to cyclades from

the latest kernel headers[1] due to them being orphaned for the

past 13 years.



libsanitizer uses this header when compiling against glibc, but

glibcs itself doesn't seem to have any references to cyclades.



Further more it seems that the driver is broken in the kernel and

the firmware doesn't seem to be available anymore.



As such since this is breaking the build of libsanitizer (and so the

GCC bootstrap[2]) I propose to remove this.



[1] https://lkml.org/lkml/2021/3/2/153

[2] https://gcc.gnu.org/bugzilla/show_bug.cgi?id=100379



(cherry picked from commit f7c5351552387bd43f6ca3631016d7f0dfe0f135)



libsanitizer/ChangeLog:



	PR sanitizer/100379

	* sanitizer_common/sanitizer_common_interceptors_ioctl.inc: Cherry-pick

	llvm-project revision f7c5351552387bd43f6ca3631016d7f0dfe0f135.

	* sanitizer_common/sanitizer_platform_limits_posix.cpp: Likewise.

	* sanitizer_common/sanitizer_platform_limits_posix.h: Likewise.

---

 .../sanitizer_common_interceptors_ioctl.inc           |  9 ---------

 .../sanitizer_platform_limits_posix.cpp               | 11 -----------

 .../sanitizer_platform_limits_posix.h                 | 10 ----------

 3 files changed, 30 deletions(-)



diff --git a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc

index 7f181258eab..b7da6598755 100644

--- a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc

+++ b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc

@@ -370,15 +370,6 @@ static void ioctl_table_fill() {

 

 #if SANITIZER_GLIBC

   // _(SIOCDEVPLIP, WRITE, struct_ifreq_sz); // the same as EQL_ENSLAVE

-  _(CYGETDEFTHRESH, WRITE, sizeof(int));

-  _(CYGETDEFTIMEOUT, WRITE, sizeof(int));

-  _(CYGETMON, WRITE, struct_cyclades_monitor_sz);

-  _(CYGETTHRESH, WRITE, sizeof(int));

-  _(CYGETTIMEOUT, WRITE, sizeof(int));

-  _(CYSETDEFTHRESH, NONE, 0);

-  _(CYSETDEFTIMEOUT, NONE, 0);

-  _(CYSETTHRESH, NONE, 0);

-  _(CYSETTIMEOUT, NONE, 0);

   _(EQL_EMANCIPATE, WRITE, struct_ifreq_sz);

   _(EQL_ENSLAVE, WRITE, struct_ifreq_sz);

   _(EQL_GETMASTRCFG, WRITE, struct_ifreq_sz);

diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp

index 35a690cba5c..6e5c330b98e 100644

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp

@@ -143,7 +143,6 @@ typedef struct user_fpregs elf_fpregset_t;

 # include <sys/procfs.h>

 #endif

 #include <sys/user.h>

-#include <linux/cyclades.h>

 #include <linux/if_eql.h>

 #include <linux/if_plip.h>

 #include <linux/lp.h>

@@ -460,7 +459,6 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr);

 

 #if SANITIZER_GLIBC

   unsigned struct_ax25_parms_struct_sz = sizeof(struct ax25_parms_struct);

-  unsigned struct_cyclades_monitor_sz = sizeof(struct cyclades_monitor);

 #if EV_VERSION > (0x010000)

   unsigned struct_input_keymap_entry_sz = sizeof(struct input_keymap_entry);

 #else

@@ -824,15 +822,6 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr);

 #endif // SANITIZER_LINUX

 

 #if SANITIZER_LINUX && !SANITIZER_ANDROID

-  unsigned IOCTL_CYGETDEFTHRESH = CYGETDEFTHRESH;

-  unsigned IOCTL_CYGETDEFTIMEOUT = CYGETDEFTIMEOUT;

-  unsigned IOCTL_CYGETMON = CYGETMON;

-  unsigned IOCTL_CYGETTHRESH = CYGETTHRESH;

-  unsigned IOCTL_CYGETTIMEOUT = CYGETTIMEOUT;

-  unsigned IOCTL_CYSETDEFTHRESH = CYSETDEFTHRESH;

-  unsigned IOCTL_CYSETDEFTIMEOUT = CYSETDEFTIMEOUT;

-  unsigned IOCTL_CYSETTHRESH = CYSETTHRESH;

-  unsigned IOCTL_CYSETTIMEOUT = CYSETTIMEOUT;

   unsigned IOCTL_EQL_EMANCIPATE = EQL_EMANCIPATE;

   unsigned IOCTL_EQL_ENSLAVE = EQL_ENSLAVE;

   unsigned IOCTL_EQL_GETMASTRCFG = EQL_GETMASTRCFG;

diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

index ad358eef8b7..cba41ba5494 100644

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h

@@ -983,7 +983,6 @@ extern unsigned struct_vt_mode_sz;

 

 #if SANITIZER_LINUX && !SANITIZER_ANDROID

 extern unsigned struct_ax25_parms_struct_sz;

-extern unsigned struct_cyclades_monitor_sz;

 extern unsigned struct_input_keymap_entry_sz;

 extern unsigned struct_ipx_config_data_sz;

 extern unsigned struct_kbdiacrs_sz;

@@ -1328,15 +1327,6 @@ extern unsigned IOCTL_VT_WAITACTIVE;

 #endif  // SANITIZER_LINUX

 

 #if SANITIZER_LINUX && !SANITIZER_ANDROID

-extern unsigned IOCTL_CYGETDEFTHRESH;

-extern unsigned IOCTL_CYGETDEFTIMEOUT;

-extern unsigned IOCTL_CYGETMON;

-extern unsigned IOCTL_CYGETTHRESH;

-extern unsigned IOCTL_CYGETTIMEOUT;

-extern unsigned IOCTL_CYSETDEFTHRESH;

-extern unsigned IOCTL_CYSETDEFTIMEOUT;

-extern unsigned IOCTL_CYSETTHRESH;

-extern unsigned IOCTL_CYSETTIMEOUT;

 extern unsigned IOCTL_EQL_EMANCIPATE;

 extern unsigned IOCTL_EQL_ENSLAVE;

 extern unsigned IOCTL_EQL_GETMASTRCFG;

-- 

2.31.1

packages/gcc/patch-f1feb74046e0feb0596b93bbb822fae02940a90e.patch

deleted100644 → 0
+0 −133
Original line number Diff line number Diff line 
From f1feb74046e0feb0596b93bbb822fae02940a90e Mon Sep 17 00:00:00 2001

From: Patrick Palka <ppalka@redhat.com>

Date: Fri, 4 Jun 2021 13:46:53 -0400

Subject: [PATCH] c++: tsubst_function_decl and excess arg levels [PR100102]



Here, when instantiating the dependent alias template

duration::__is_harmonic with args={{T,U},{int}}, we find ourselves

substituting the function decl _S_gcd.  Since we have more arg levels

than _S_gcd has parm levels, an old special case in tsubst_function_decl

causes us to unwantedly reduce args to its innermost level, yielding

args={int}, which leads to a nonsensical substitution into the decl

context and eventually a crash.



The comment for this special case refers to three examples for which we

ought to see more arg levels than parm levels here, but none of the

examples actually demonstrate this.  In the first example, when

defining S<int>::f(U) parms_depth is 2 and args_depth is 1, and

later when instantiating say S<int>::f<char> both depths are 2.  In the

second example, when substituting the template friend declaration

parms_depth is 2 and args_depth is 1, and later when instantiating f

both depths are 1.  Finally, the third example is invalid since we can't

specialize a member template of an unspecialized class template like

that.



Given that this reduction code seems no longer relevant for its

documented purpose and that it causes problems as in the PR, this patch

just removes it.  Note that as far as bootstrap/regtest is concerned,

this code is dead; the below two tests would be the first to reach it.



	PR c++/100102



gcc/cp/ChangeLog:



	* pt.c (tsubst_function_decl): Remove old code for reducing

	args when it has excess levels.



gcc/testsuite/ChangeLog:



	* g++.dg/cpp0x/alias-decl-72.C: New test.

	* g++.dg/cpp0x/alias-decl-72a.C: New test.



(cherry picked from commit 5357ab75dedef403b0eebf9277d61d1cbeb5898f)

---

 gcc/cp/pt.c                                 | 39 ---------------------

 gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C  |  9 +++++

 gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C |  9 +++++

 3 files changed, 18 insertions(+), 39 deletions(-)

 create mode 100644 gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C

 create mode 100644 gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C



diff --git a/gcc/cp/pt.c b/gcc/cp/pt.c

index 1434beb80f4..1761a902218 100644

--- a/gcc/cp/pt.c

+++ b/gcc/cp/pt.c

@@ -13954,45 +13954,6 @@ tsubst_function_decl (tree t, tree args, tsubst_flags_t complain,

 	  if (tree spec = retrieve_specialization (gen_tmpl, argvec, hash))

 	    return spec;

 	}

-

-      /* We can see more levels of arguments than parameters if

-	 there was a specialization of a member template, like

-	 this:

-

-	 template <class T> struct S { template <class U> void f(); }

-	 template <> template <class U> void S<int>::f(U);

-

-	 Here, we'll be substituting into the specialization,

-	 because that's where we can find the code we actually

-	 want to generate, but we'll have enough arguments for

-	 the most general template.

-

-	 We also deal with the peculiar case:

-

-	 template <class T> struct S {

-	   template <class U> friend void f();

-	 };

-	 template <class U> void f() {}

-	 template S<int>;

-	 template void f<double>();

-

-	 Here, the ARGS for the instantiation of will be {int,

-	 double}.  But, we only need as many ARGS as there are

-	 levels of template parameters in CODE_PATTERN.  We are

-	 careful not to get fooled into reducing the ARGS in

-	 situations like:

-

-	 template <class T> struct S { template <class U> void f(U); }

-	 template <class T> template <> void S<T>::f(int) {}

-

-	 which we can spot because the pattern will be a

-	 specialization in this case.  */

-      int args_depth = TMPL_ARGS_DEPTH (args);

-      int parms_depth =

-	TMPL_PARMS_DEPTH (DECL_TEMPLATE_PARMS (DECL_TI_TEMPLATE (t)));

-

-      if (args_depth > parms_depth && !DECL_TEMPLATE_SPECIALIZATION (t))

-	args = get_innermost_template_args (args, parms_depth);

     }

   else

     {

diff --git a/gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C

new file mode 100644

index 00000000000..8009756dcba

--- /dev/null

+++ b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C

@@ -0,0 +1,9 @@

+// PR c++/100102

+// { dg-do compile { target c++11 } }

+

+template<int()> struct ratio;

+template<class T, class U> struct duration {

+  static constexpr int _S_gcd();

+  template<class> using __is_harmonic = ratio<_S_gcd>;

+  using type = __is_harmonic<int>;

+};

diff --git a/gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C

new file mode 100644

index 00000000000..a4443e18f9d

--- /dev/null

+++ b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C

@@ -0,0 +1,9 @@

+// PR c++/100102

+// { dg-do compile { target c++11 } }

+

+template<int> struct ratio;

+template<class T> struct duration {

+  static constexpr int _S_gcd();

+  template<class> using __is_harmonic = ratio<(duration::_S_gcd)()>;

+  using type = __is_harmonic<int>;

+};

-- 

2.31.1

packages/gcc/patch-fc930b3010bd0de899a3da3209eab20664ddb703.patch

deleted100644 → 0
+0 −133
Original line number Diff line number Diff line 
From fc930b3010bd0de899a3da3209eab20664ddb703 Mon Sep 17 00:00:00 2001

From: Patrick Palka <ppalka@redhat.com>

Date: Fri, 4 Jun 2021 13:46:53 -0400

Subject: [PATCH] c++: tsubst_function_decl and excess arg levels [PR100102]



Here, when instantiating the dependent alias template

duration::__is_harmonic with args={{T,U},{int}}, we find ourselves

substituting the function decl _S_gcd.  Since we have more arg levels

than _S_gcd has parm levels, an old special case in tsubst_function_decl

causes us to unwantedly reduce args to its innermost level, yielding

args={int}, which leads to a nonsensical substitution into the decl

context and eventually a crash.



The comment for this special case refers to three examples for which we

ought to see more arg levels than parm levels here, but none of the

examples actually demonstrate this.  In the first example, when

defining S<int>::f(U) parms_depth is 2 and args_depth is 1, and

later when instantiating say S<int>::f<char> both depths are 2.  In the

second example, when substituting the template friend declaration

parms_depth is 2 and args_depth is 1, and later when instantiating f

both depths are 1.  Finally, the third example is invalid since we can't

specialize a member template of an unspecialized class template like

that.



Given that this reduction code seems no longer relevant for its

documented purpose and that it causes problems as in the PR, this patch

just removes it.  Note that as far as bootstrap/regtest is concerned,

this code is dead; the below two tests would be the first to reach it.



	PR c++/100102



gcc/cp/ChangeLog:



	* pt.c (tsubst_function_decl): Remove old code for reducing

	args when it has excess levels.



gcc/testsuite/ChangeLog:



	* g++.dg/cpp0x/alias-decl-72.C: New test.

	* g++.dg/cpp0x/alias-decl-72a.C: New test.



(cherry picked from commit 5357ab75dedef403b0eebf9277d61d1cbeb5898f)

---

 gcc/cp/pt.c                                 | 39 ---------------------

 gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C  |  9 +++++

 gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C |  9 +++++

 3 files changed, 18 insertions(+), 39 deletions(-)

 create mode 100644 gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C

 create mode 100644 gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C



diff --git a/gcc/cp/pt.c b/gcc/cp/pt.c

index 5a957141ba3..7ce9ac234f8 100644

--- a/gcc/cp/pt.c

+++ b/gcc/cp/pt.c

@@ -13811,45 +13811,6 @@ tsubst_function_decl (tree t, tree args, tsubst_flags_t complain,

 	  if (tree spec = retrieve_specialization (gen_tmpl, argvec, hash))

 	    return spec;

 	}

-

-      /* We can see more levels of arguments than parameters if

-	 there was a specialization of a member template, like

-	 this:

-

-	 template <class T> struct S { template <class U> void f(); }

-	 template <> template <class U> void S<int>::f(U);

-

-	 Here, we'll be substituting into the specialization,

-	 because that's where we can find the code we actually

-	 want to generate, but we'll have enough arguments for

-	 the most general template.

-

-	 We also deal with the peculiar case:

-

-	 template <class T> struct S {

-	   template <class U> friend void f();

-	 };

-	 template <class U> void f() {}

-	 template S<int>;

-	 template void f<double>();

-

-	 Here, the ARGS for the instantiation of will be {int,

-	 double}.  But, we only need as many ARGS as there are

-	 levels of template parameters in CODE_PATTERN.  We are

-	 careful not to get fooled into reducing the ARGS in

-	 situations like:

-

-	 template <class T> struct S { template <class U> void f(U); }

-	 template <class T> template <> void S<T>::f(int) {}

-

-	 which we can spot because the pattern will be a

-	 specialization in this case.  */

-      int args_depth = TMPL_ARGS_DEPTH (args);

-      int parms_depth =

-	TMPL_PARMS_DEPTH (DECL_TEMPLATE_PARMS (DECL_TI_TEMPLATE (t)));

-

-      if (args_depth > parms_depth && !DECL_TEMPLATE_SPECIALIZATION (t))

-	args = get_innermost_template_args (args, parms_depth);

     }

   else

     {

diff --git a/gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C

new file mode 100644

index 00000000000..8009756dcba

--- /dev/null

+++ b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72.C

@@ -0,0 +1,9 @@

+// PR c++/100102

+// { dg-do compile { target c++11 } }

+

+template<int()> struct ratio;

+template<class T, class U> struct duration {

+  static constexpr int _S_gcd();

+  template<class> using __is_harmonic = ratio<_S_gcd>;

+  using type = __is_harmonic<int>;

+};

diff --git a/gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C

new file mode 100644

index 00000000000..a4443e18f9d

--- /dev/null

+++ b/gcc/testsuite/g++.dg/cpp0x/alias-decl-72a.C

@@ -0,0 +1,9 @@

+// PR c++/100102

+// { dg-do compile { target c++11 } }

+

+template<int> struct ratio;

+template<class T> struct duration {

+  static constexpr int _S_gcd();

+  template<class> using __is_harmonic = ratio<(duration::_S_gcd)()>;

+  using type = __is_harmonic<int>;

+};

-- 

2.31.1

packages/gcc/piclibs.patch

deleted100644 → 0
+0 −62
Original line number Diff line number Diff line 
diff --git a/libgfortran/Makefile.in b/libgfortran/Makefile.in

index 62b9f7a..7666fdb 100644

--- a/libgfortran/Makefile.in

+++ b/libgfortran/Makefile.in

@@ -357,11 +357,11 @@ AUTOMAKE = @AUTOMAKE@

 AWK = @AWK@

 CC = @CC@

 CCDEPMODE = @CCDEPMODE@

-CFLAGS = @CFLAGS@

+CFLAGS = @CFLAGS@ -fPIC

 CPP = @CPP@

-CPPFLAGS = @CPPFLAGS@

+CPPFLAGS = @CPPFLAGS@ -fPIC

 CYGPATH_W = @CYGPATH_W@

-DEFS = @DEFS@

+DEFS = @DEFS@ -fPIC

 DEPDIR = @DEPDIR@

 DSYMUTIL = @DSYMUTIL@

 DUMPBIN = @DUMPBIN@

@@ -371,7 +371,7 @@ ECHO_T = @ECHO_T@

 EGREP = @EGREP@

 EXEEXT = @EXEEXT@

 FC = @FC@

-FCFLAGS = @FCFLAGS@

+FCFLAGS = @FCFLAGS@ -fPIC

 FGREP = @FGREP@

 FPU_HOST_HEADER = @FPU_HOST_HEADER@

 GREP = @GREP@

diff --git a/libstdc++-v3/Makefile.in b/libstdc++-v3/Makefile.in

index bede542..9b3e442 100644

--- a/libstdc++-v3/Makefile.in

+++ b/libstdc++-v3/Makefile.in

@@ -115,7 +115,7 @@ CC = @CC@

 CCODECVT_CC = @CCODECVT_CC@

 CCOLLATE_CC = @CCOLLATE_CC@

 CCTYPE_CC = @CCTYPE_CC@

-CFLAGS = @CFLAGS@

+CFLAGS = @CFLAGS@ -fPIC

 CLOCALE_CC = @CLOCALE_CC@

 CLOCALE_H = @CLOCALE_H@

 CLOCALE_INTERNAL_H = @CLOCALE_INTERNAL_H@

@@ -124,7 +124,7 @@ CMESSAGES_H = @CMESSAGES_H@

 CMONEY_CC = @CMONEY_CC@

 CNUMERIC_CC = @CNUMERIC_CC@

 CPP = @CPP@

-CPPFLAGS = @CPPFLAGS@

+CPPFLAGS = @CPPFLAGS@ -fPIC

 CPU_DEFINES_SRCDIR = @CPU_DEFINES_SRCDIR@

 CPU_OPT_BITS_RANDOM = @CPU_OPT_BITS_RANDOM@

 CPU_OPT_EXT_RANDOM = @CPU_OPT_EXT_RANDOM@

@@ -139,7 +139,7 @@ CYGPATH_W = @CYGPATH_W@

 C_INCLUDE_DIR = @C_INCLUDE_DIR@

 DBLATEX = @DBLATEX@

 DEBUG_FLAGS = @DEBUG_FLAGS@

-DEFS = @DEFS@

+DEFS = @DEFS@ -fPIC

 DOT = @DOT@

 DOXYGEN = @DOXYGEN@

 DSYMUTIL = @DSYMUTIL@

-- 

2.8.3

packages/gcc/signal.patch

deleted100644 → 0
+0 −28
Original line number Diff line number Diff line 
From 6c709b6262e8b6441b1e94526d6d65d4ce7a7dec Mon Sep 17 00:00:00 2001

From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>

Date: Thu, 7 Sep 2017 07:18:57 +0000

Subject: [PATCH] 2017-09-07  Matthias Klose  <doko@ubuntu.com>



        * asan/asan_linux.cc: Include <signal.h>





git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251830 138bc75d-0d04-0410-961f-82ee72b054a4

---

 libsanitizer/asan/asan_linux.cc | 1 +

 2 files changed, 5 insertions(+)



diff --git a/libsanitizer/asan/asan_linux.cc b/libsanitizer/asan/asan_linux.cc

index c504168..59087b9 100644

--- a/libsanitizer/asan/asan_linux.cc

+++ b/libsanitizer/asan/asan_linux.cc

@@ -29,6 +29,7 @@

 #include <dlfcn.h>

 #include <fcntl.h>

 #include <pthread.h>

+#include <signal.h>

 #include <stdio.h>

 #include <unistd.h>

 #include <unwind.h>

-- 

2.9.3

packages/gcc/stack_t-4.9.patch

deleted100644 → 0
+0 −80
Original line number Diff line number Diff line 
From 833e00c01e96f61e24cd7ec97b93fad212dc914b Mon Sep 17 00:00:00 2001

From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>

Date: Thu, 7 Sep 2017 07:17:17 +0000

Subject: [PATCH] 2017-09-07  Matthias Klose  <doko@ubuntu.com>



        Backported from mainline

        2017-07-14  Jakub Jelinek  <jakub@redhat.com>



        PR sanitizer/81066

        * sanitizer_common/sanitizer_linux.h: Cherry-pick upstream r307969.

        * sanitizer_common/sanitizer_linux.cc: Likewise.

        * sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc: Likewise.

        * tsan/tsan_platform_linux.cc: Likewise.





git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251829 138bc75d-0d04-0410-961f-82ee72b054a4

---

 libsanitizer/sanitizer_common/sanitizer_linux.cc              |  3 +--

 libsanitizer/sanitizer_common/sanitizer_linux.h               |  4 +---

 .../sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc  |  2 +-

 libsanitizer/tsan/tsan_platform_linux.cc                      |  2 +-

 5 files changed, 15 insertions(+), 7 deletions(-)



diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.cc b/libsanitizer/sanitizer_common/sanitizer_linux.cc

index 9feb307..821b26d 100644

--- a/libsanitizer/sanitizer_common/sanitizer_linux.cc

+++ b/libsanitizer/sanitizer_common/sanitizer_linux.cc

@@ -514,8 +514,7 @@ uptr internal_prctl(int option, uptr arg2, uptr arg3, uptr arg4, uptr arg5) {

 }

 #endif

 

-uptr internal_sigaltstack(const struct sigaltstack *ss,

-                         struct sigaltstack *oss) {

+uptr internal_sigaltstack(const void *ss, void *oss) {

   return internal_syscall(__NR_sigaltstack, (uptr)ss, (uptr)oss);

 }

 

diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.h b/libsanitizer/sanitizer_common/sanitizer_linux.h

index 086834c..3a6f4cd 100644

--- a/libsanitizer/sanitizer_common/sanitizer_linux.h

+++ b/libsanitizer/sanitizer_common/sanitizer_linux.h

@@ -27,8 +26,7 @@ struct linux_dirent;

 // Syscall wrappers.

 uptr internal_getdents(fd_t fd, struct linux_dirent *dirp, unsigned int count);

 uptr internal_prctl(int option, uptr arg2, uptr arg3, uptr arg4, uptr arg5);

-uptr internal_sigaltstack(const struct sigaltstack* ss,

-                          struct sigaltstack* oss);

+uptr internal_sigaltstack(const void* ss, void* oss);

 uptr internal_sigaction(int signum, const __sanitizer_kernel_sigaction_t *act,

     __sanitizer_kernel_sigaction_t *oldact);

 uptr internal_sigprocmask(int how, __sanitizer_kernel_sigset_t *set,

diff --git a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc

index 5881202..c54894d 100644

--- a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc

+++ b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc

@@ -234,7 +234,7 @@ static int TracerThread(void* argument) {

 

   // Alternate stack for signal handling.

   InternalScopedBuffer<char> handler_stack_memory(kHandlerStackSize);

-  struct sigaltstack handler_stack;

+  stack_t handler_stack;

   internal_memset(&handler_stack, 0, sizeof(handler_stack));

   handler_stack.ss_sp = handler_stack_memory.data();

   handler_stack.ss_size = kHandlerStackSize;

diff --git a/libsanitizer/tsan/tsan_platform_linux.cc b/libsanitizer/tsan/tsan_platform_linux.cc

index 3259131..b8e9078 100644

--- a/libsanitizer/tsan/tsan_platform_linux.cc

+++ b/libsanitizer/tsan/tsan_platform_linux.cc

@@ -377,7 +377,7 @@ bool IsGlobalVar(uptr addr) {

 int ExtractResolvFDs(void *state, int *fds, int nfd) {

 #if SANITIZER_LINUX

   int cnt = 0;

-  __res_state *statp = (__res_state*)state;

+  struct __res_state *statp = (struct __res_state*)state;

   for (int i = 0; i < MAXNS && cnt < nfd; i++) {

     if (statp->_u._ext.nsaddrs[i] && statp->_u._ext.nssocks[i] != -1)

       fds[cnt++] = statp->_u._ext.nssocks[i];

-- 

2.9.3

packages/gcc/stack_t.patch

deleted100644 → 0
+0 −88
Original line number Diff line number Diff line 
From 833e00c01e96f61e24cd7ec97b93fad212dc914b Mon Sep 17 00:00:00 2001

From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>

Date: Thu, 7 Sep 2017 07:17:17 +0000

Subject: [PATCH] 2017-09-07  Matthias Klose  <doko@ubuntu.com>



        Backported from mainline

        2017-07-14  Jakub Jelinek  <jakub@redhat.com>



        PR sanitizer/81066

        * sanitizer_common/sanitizer_linux.h: Cherry-pick upstream r307969.

        * sanitizer_common/sanitizer_linux.cc: Likewise.

        * sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc: Likewise.

        * tsan/tsan_platform_linux.cc: Likewise.





git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251829 138bc75d-0d04-0410-961f-82ee72b054a4

---

 libsanitizer/sanitizer_common/sanitizer_linux.cc              |  3 +--

 libsanitizer/sanitizer_common/sanitizer_linux.h               |  4 +---

 .../sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc  |  2 +-

 libsanitizer/tsan/tsan_platform_linux.cc                      |  2 +-

 5 files changed, 15 insertions(+), 7 deletions(-)



diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.cc b/libsanitizer/sanitizer_common/sanitizer_linux.cc

index 9feb307..821b26d 100644

--- a/libsanitizer/sanitizer_common/sanitizer_linux.cc

+++ b/libsanitizer/sanitizer_common/sanitizer_linux.cc

@@ -514,8 +514,7 @@ uptr internal_prctl(int option, uptr arg2, uptr arg3, uptr arg4, uptr arg5) {

 }

 #endif

 

-uptr internal_sigaltstack(const struct sigaltstack *ss,

-                         struct sigaltstack *oss) {

+uptr internal_sigaltstack(const void *ss, void *oss) {

   return internal_syscall(SYSCALL(sigaltstack), (uptr)ss, (uptr)oss);

 }

 

diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.h b/libsanitizer/sanitizer_common/sanitizer_linux.h

index 086834c..3a6f4cd 100644

--- a/libsanitizer/sanitizer_common/sanitizer_linux.h

+++ b/libsanitizer/sanitizer_common/sanitizer_linux.h

@@ -18,7 +18,6 @@

 #include "sanitizer_platform_limits_posix.h"

 

 struct link_map;  // Opaque type returned by dlopen().

-struct sigaltstack;

 

 namespace __sanitizer {

 // Dirent structure for getdents(). Note that this structure is different from

@@ -27,8 +26,7 @@ struct linux_dirent;

 

 // Syscall wrappers.

 uptr internal_getdents(fd_t fd, struct linux_dirent *dirp, unsigned int count);

-uptr internal_sigaltstack(const struct sigaltstack* ss,

-                          struct sigaltstack* oss);

+uptr internal_sigaltstack(const void* ss, void* oss);

 uptr internal_sigprocmask(int how, __sanitizer_sigset_t *set,

     __sanitizer_sigset_t *oldset);

 void internal_sigfillset(__sanitizer_sigset_t *set);

diff --git a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc

index 5881202..c54894d 100644

--- a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc

+++ b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc

@@ -234,7 +234,7 @@ static int TracerThread(void* argument) {

 

   // Alternate stack for signal handling.

   InternalScopedBuffer<char> handler_stack_memory(kHandlerStackSize);

-  struct sigaltstack handler_stack;

+  stack_t handler_stack;

   internal_memset(&handler_stack, 0, sizeof(handler_stack));

   handler_stack.ss_sp = handler_stack_memory.data();

   handler_stack.ss_size = kHandlerStackSize;

diff --git a/libsanitizer/tsan/tsan_platform_linux.cc b/libsanitizer/tsan/tsan_platform_linux.cc

index 3259131..b8e9078 100644

--- a/libsanitizer/tsan/tsan_platform_linux.cc

+++ b/libsanitizer/tsan/tsan_platform_linux.cc

@@ -377,7 +377,7 @@ bool IsGlobalVar(uptr addr) {

 int ExtractResolvFDs(void *state, int *fds, int nfd) {

 #if SANITIZER_LINUX

   int cnt = 0;

-  __res_state *statp = (__res_state*)state;

+  struct __res_state *statp = (struct __res_state*)state;

   for (int i = 0; i < MAXNS && cnt < nfd; i++) {

     if (statp->_u._ext.nsaddrs[i] && statp->_u._ext.nssocks[i] != -1)

       fds[cnt++] = statp->_u._ext.nssocks[i];

-- 

2.9.3

packages/gcc/sys_ustat-4.9.patch

deleted100644 → 0
+0 −34
Original line number Diff line number Diff line 
The sys_ustat.h patch modified for gcc 4.9.x.



diff -Naurb gcc-4.9.4.orig/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc gcc-4.9.4/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

--- gcc-4.9.4.orig/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc	2013-12-19 06:54:11.000000000 -0600

+++ gcc-4.9.4/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc	2018-12-11 15:57:46.901800462 -0600

@@ -81,7 +81,6 @@

 #include <sys/statvfs.h>

 #include <sys/timex.h>

 #include <sys/user.h>

-#include <sys/ustat.h>

 #include <linux/cyclades.h>

 #include <linux/if_eql.h>

 #include <linux/if_plip.h>

@@ -163,7 +162,19 @@

   unsigned struct_old_utsname_sz = sizeof(struct old_utsname);

   unsigned struct_oldold_utsname_sz = sizeof(struct oldold_utsname);

   unsigned struct_itimerspec_sz = sizeof(struct itimerspec);

-  unsigned struct_ustat_sz = sizeof(struct ustat);

+  // Use pre-computed size of struct ustat to avoid <sys/ustat.h> which

+  // has been removed from glibc 2.28.

+#if defined(__aarch64__) || defined(__s390x__) || defined (__mips64) \

+  || defined(__powerpc64__) || defined(__arch64__) || defined(__sparcv9) \

+  || defined(__x86_64__)

+#define SIZEOF_STRUCT_USTAT 32

+#elif defined(__arm__) || defined(__i386__) || defined(__mips__) \

+  || defined(__powerpc__) || defined(__s390__)

+#define SIZEOF_STRUCT_USTAT 20

+#else

+#error Unknown size of struct ustat

+#endif

+  unsigned struct_ustat_sz = SIZEOF_STRUCT_USTAT;

 #endif // SANITIZER_LINUX

 

 #if SANITIZER_LINUX && !SANITIZER_ANDROID

packages/gcc/sys_ustat.h.patch

deleted100644 → 0
+0 −63
Original line number Diff line number Diff line 
From 9569b61168b963a6cea7b782fd350dee489ad42c Mon Sep 17 00:00:00 2001

From: "H.J. Lu" <hjl.tools@gmail.com>

Date: Mon, 21 May 2018 13:17:55 -0700

Subject: [PATCH] libsanitizer: Use pre-computed size of struct ustat for Linux



Cherry-pick compiler-rt revision 333213:



<sys/ustat.h> has been removed from glibc 2.28 by:



commit cf2478d53ad7071e84c724a986b56fe17f4f4ca7

Author: Adhemerval Zanella <adhemerval.zanella@linaro.org>

Date:   Sun Mar 18 11:28:59 2018 +0800



    Deprecate ustat syscall interface



This patch uses pre-computed size of struct ustat for Linux.



	PR sanitizer/85835

	* sanitizer_common/sanitizer_platform_limits_posix.cc: Don't

	include <sys/ustat.h> for Linux.

	(SIZEOF_STRUCT_USTAT): New.

	(struct_ustat_sz): Use SIZEOF_STRUCT_USTAT for Linux.

---

 .../sanitizer_platform_limits_posix.cc            | 15 +++++++++++++--

 1 file changed, 13 insertions(+), 2 deletions(-)



diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

index 858bb218450..de18e56d11c 100644

--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

+++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc

@@ -157,7 +157,6 @@ typedef struct user_fpregs elf_fpregset_t;

 # include <sys/procfs.h>

 #endif

 #include <sys/user.h>

-#include <sys/ustat.h>

 #include <linux/cyclades.h>

 #include <linux/if_eql.h>

 #include <linux/if_plip.h>

@@ -250,7 +249,19 @@ namespace __sanitizer {

 #endif // SANITIZER_LINUX || SANITIZER_FREEBSD

 

 #if SANITIZER_LINUX && !SANITIZER_ANDROID

-  unsigned struct_ustat_sz = sizeof(struct ustat);

+  // Use pre-computed size of struct ustat to avoid <sys/ustat.h> which

+  // has been removed from glibc 2.28.

+#if defined(__aarch64__) || defined(__s390x__) || defined (__mips64) \

+  || defined(__powerpc64__) || defined(__arch64__) || defined(__sparcv9) \

+  || defined(__x86_64__)

+#define SIZEOF_STRUCT_USTAT 32

+#elif defined(__arm__) || defined(__i386__) || defined(__mips__) \

+  || defined(__powerpc__) || defined(__s390__)

+#define SIZEOF_STRUCT_USTAT 20

+#else

+#error Unknown size of struct ustat

+#endif

+  unsigned struct_ustat_sz = SIZEOF_STRUCT_USTAT;

   unsigned struct_rlimit64_sz = sizeof(struct rlimit64);

   unsigned struct_statvfs64_sz = sizeof(struct statvfs64);

 #endif // SANITIZER_LINUX && !SANITIZER_ANDROID

-- 

2.17.0

packages/gcc/ucontext_t-java.patch

deleted100644 → 0
+0 −60
Original line number Diff line number Diff line 
From 9b9287cde20ea57578cf07efb2a96ed4cc0da36f Mon Sep 17 00:00:00 2001

From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>

Date: Thu, 7 Sep 2017 07:22:07 +0000

Subject: [PATCH] 2017-09-07  Matthias Klose  <doko@ubuntu.com>



        * include/x86_64-signal.h (HANDLE_DIVIDE_OVERFLOW): Replace

        'struct ucontext' with ucontext_t.

        * include/i386-signal.h (HANDLE_DIVIDE_OVERFLOW): Likewise.

        * include/s390-signal.h (HANDLE_DIVIDE_OVERFLOW): Likewise.





git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251832 138bc75d-0d04-0410-961f-82ee72b054a4

---

 libjava/include/i386-signal.h   | 2 +-

 libjava/include/s390-signal.h   | 2 +-

 libjava/include/x86_64-signal.h | 2 +-

 4 files changed, 10 insertions(+), 3 deletions(-)



diff --git a/libjava/include/i386-signal.h b/libjava/include/i386-signal.h

index c2409b0..ef77e7e 100644

--- a/libjava/include/i386-signal.h

+++ b/libjava/include/i386-signal.h

@@ -29,7 +29,7 @@ static void _Jv_##_name (int, siginfo_t *,			\

 #define HANDLE_DIVIDE_OVERFLOW						\

 do									\

 {									\

-  struct ucontext *_uc = (struct ucontext *)_p;				\

+  ucontext_t *_uc = (ucontext_t *)_p;					\

   gregset_t &_gregs = _uc->uc_mcontext.gregs;				\

   unsigned char *_eip = (unsigned char *)_gregs[REG_EIP];		\

 									\

diff --git a/libjava/include/s390-signal.h b/libjava/include/s390-signal.h

index 4ca4c10..9261b52 100644

--- a/libjava/include/s390-signal.h

+++ b/libjava/include/s390-signal.h

@@ -51,7 +51,7 @@ do									\

   struct                                                                \

   {                                                                     \

     unsigned long int uc_flags;                                         \

-    struct ucontext *uc_link;                                           \

+    ucontext_t *uc_link;                                                \

     stack_t uc_stack;                                                   \

     mcontext_t uc_mcontext;                                             \

     unsigned long sigmask[2];                                           \

diff --git a/libjava/include/x86_64-signal.h b/libjava/include/x86_64-signal.h

index 12383b5..e36c5a3 100644

--- a/libjava/include/x86_64-signal.h

+++ b/libjava/include/x86_64-signal.h

@@ -28,7 +28,7 @@ static void _Jv_##_name (int, siginfo_t *,			\

 #define HANDLE_DIVIDE_OVERFLOW						\

 do									\

 {									\

-  struct ucontext *_uc = (struct ucontext *)_p;				\

+  ucontext_t *_uc = (ucontext_t *)_p;					\

   gregset_t &_gregs = _uc->uc_mcontext.gregs;				\

   unsigned char *_rip = (unsigned char *)_gregs[REG_RIP];		\

 									\

-- 

2.9.3

packages/gcc/zstd.patch

deleted100644 → 0
+0 −43
Original line number Diff line number Diff line 
--- a/gcc/Makefile.in

+++ b/gcc/Makefile.in

@@ -1075,7 +1075,8 @@ GNATMAKE = @GNATMAKE@

 # Libs needed (at present) just for jcf-dump.

 LDEXP_LIB = @LDEXP_LIB@

 

-ZSTD_LIB = @ZSTD_LIB@

+ZSTD_INC = @ZSTD_CPPFLAGS@

+ZSTD_LIB = @ZSTD_LDFLAGS@ @ZSTD_LIB@

 

 # Likewise, for use in the tools that must run on this machine

 # even if we are cross-building GCC.

@@ -2275,7 +2276,7 @@ CFLAGS-version.o += -DBASEVER=$(BASEVER_s) -DDATESTAMP=$(DATESTAMP_s) \

 version.o: $(REVISION) $(DATESTAMP) $(BASEVER) $(DEVPHASE)

 

 # lto-compress.o needs $(ZLIBINC) added to the include flags.

-CFLAGS-lto-compress.o += $(ZLIBINC)

+CFLAGS-lto-compress.o += $(ZLIBINC) $(ZSTD_INC)

 

 CFLAGS-lto-streamer-in.o += -DTARGET_MACHINE=\"$(target_noncanonical)\"

 

--- a/gcc/configure

+++ b/gcc/configure

@@ -786,6 +786,8 @@ LTLIBICONV

 LIBICONV

 ZSTD_LIB

 ZSTD_INCLUDE

+ZSTD_LDFLAGS

+ZSTD_CPPFLAGS

 DL_LIB

 LDEXP_LIB

 EXTRA_GCC_LIBS

--- a/gcc/configure.ac

+++ b/gcc/configure.ac

@@ -1339,6 +1339,8 @@ AC_SUBST(ZSTD_INCLUDE)

 AC_SUBST(ZSTD_LIB)

 ZSTD_CPPFLAGS=

 ZSTD_LDFLAGS=

+AC_SUBST(ZSTD_CPPFLAGS)

+AC_SUBST(ZSTD_LDFLAGS)

 AC_ARG_WITH(zstd,

 	[AS_HELP_STRING([--with-zstd=PATH],

 		[specify prefix directory for installed zstd library.

packages/genpybind/package.py

+3 −1
Original line number Diff line number Diff line
@@ -3,7 +3,7 @@ 
#

# SPDX-License-Identifier: (Apache-2.0 OR MIT)



from spack import *

from spack.package import *





class Genpybind(WafPackage):
@@ -21,6 +21,8 @@ class Genpybind(WafPackage): 
    version('develop', branch='develop')



    version('visions', branch='master', git='https://github.com/electronicvisions/genpybind')

    # good for ebrains-10.0 too…

    version('ebrains-llvm15', tag='ebrains-9.0-a9', git='https://github.com/electronicvisions/genpybind')

    version('ebrains', tag='ebrains_release-1-rc1', git='https://github.com/electronicvisions/genpybind')



    depends_on(

packages/glfw/package.py

0 → 100644
+61 −0
Original line number Diff line number Diff line 
# 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 Glfw(CMakePackage):

    """GLFW is an Open Source, multi-platform library for

    OpenGL, OpenGL ES and Vulkan development on the desktop. It

    provides a simple API for creating windows, contexts and

    surfaces, receiving input and events."""



    homepage = "https://www.glfw.org/"

    url = "https://github.com/glfw/glfw/archive/3.3.2.tar.gz"



    license("Zlib")



    # begin EBRAINS (added): new version

    version("3.4", sha256="c038d34200234d071fae9345bc455e4a8f2f544ab60150765d7704e08f3dac01")

    # end EBRAINS

    version("3.3.8", sha256="f30f42e05f11e5fc62483e513b0488d5bceeab7d9c5da0ffe2252ad81816c713")

    version("3.3.2", sha256="98768e12e615fbe9f3386f5bbfeb91b5a3b45a8c4c77159cef06b1f6ff749537")

    version("3.3.1", sha256="6bca16e69361798817a4b62a5239a77253c29577fcd5d52ae8b85096e514177f")

    version("3.3", sha256="81bf5fde487676a8af55cb317830703086bb534c53968d71936e7b48ee5a0f3e")

    version("3.2.1", sha256="e10f0de1384d75e6fc210c53e91843f6110d6c4f3afbfb588130713c2f9d8fe8")

    version("3.2", sha256="cb3aab46757981a39ae108e5207a1ecc4378e68949433a2b040ce2e17d8f6aa6")

    version("3.1.2", sha256="6ac642087682aaf7f8397761a41a99042b2c656498217a1c63ba9706d1eef122")

    version("3.1.1", sha256="4de311ec9bf43bfdc8423ddf93b91dc54dc73dcfbedfb0991b6fbb3a9baf245f")

    version("3.1", sha256="2140f4c532e7ce4c84cb7e4c419d0979d5954fa1ce204b7646491bd2cc5bf308")

    version("3.0.4", sha256="a4e7c57db2086803de4fc853bd472ff8b6d2639b9aa16e6ac6b19ffb53958caf")

    version("3.0.3", sha256="7a182047ba6b1fdcda778b79aac249bb2328b6d141188cb5df29560715d01693")



    depends_on("c", type="build")  # generated



    variant("doc", default=False, description="Build documentation")

    variant("shared", default=False, description="Builds a shared version of the library")



    # dependencies

    depends_on("doxygen", type="build", when="+doc")



    # linux only dependencies

    depends_on("libxrandr", when="platform=linux")

    depends_on("libxinerama", when="platform=linux")

    depends_on("libxcursor", when="platform=linux")

    depends_on("libxdamage", when="platform=linux")

    depends_on("libxft", when="platform=linux")

    depends_on("libxi", when="platform=linux")

    depends_on("libxmu", when="platform=linux")

    depends_on("freetype", when="platform=linux")

    depends_on("fontconfig", when="platform=linux")

    depends_on("pkgconfig", type="build", when="platform=linux")



    # begin EBRAINS (added): missing dependency

    depends_on("wayland", when="platform=linux")

    depends_on("libxkbcommon", when="platform=linux")

    # end EBRAINS



    def cmake_args(self):

        return [self.define_from_variant("BUILD_SHARED_LIBS", "shared")]

packages/hxtorch/fix-multi-site-packages.patch

0 → 100644
+30 −0
Original line number Diff line number Diff line 
diff --git a/src/hxtorch/wscript b/src/hxtorch/wscript

index aaf670f..39322c8 100644

--- a/hxtorch/wscript

+++ b/hxtorch/wscript



@@ -45,13 +45,19 @@

     )

 

     site_packages = site.getsitepackages()

-    assert isinstance(site_packages, list) and len(site_packages) == 1

-    includes_torch = [os.path.join(x, 'torch/include') for x in site_packages]

-    includes_torch_csrc_api = [os.path.join(x, 'torch/include/torch/csrc/api/include') for x in site_packages]

+    includes_torch = []

+    includes_torch_csrc_api = []

+    for x in site_packages:

+        torch_inc = os.path.join(x, 'torch/include')

+        if os.path.exists(torch_inc):

+            includes_torch.append(torch_inc)

+        torch_csrc_inc = os.path.join(x, 'torch/include/torch/csrc/api/include')

+        if os.path.exists(torch_csrc_inc):

+            includes_torch_csrc_api.append(torch_csrc_inc)

     libpath_torch = [os.path.join(x, 'torch/lib') for x in site_packages]

     libnames = []

     # if torch isn't available via site-packages, try sys.path/PYTHONPATH

-    if not os.path.exists(libpath_torch[0]):

+    if not any([os.path.exists(x) for x in libpath_torch]):

         # find other possible paths

         libpath_torch = [os.path.join(x, 'torch/lib') for x in sys.path if 'torch' in x]

         # filter on existance of path

packages/inja/package.py

+1 −1
Original line number Diff line number Diff line
@@ -3,7 +3,7 @@ 
#

# SPDX-License-Identifier: (Apache-2.0 OR MIT)



from spack import *

from spack.package import *





class Inja(CMakePackage):

packages/sleef/package.py

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+0 −63

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spack.yaml

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