Merge branch 'master' into nodelist_test

neuronsimulator · Jun 20, 2023 · 7ce1b2a · 7ce1b2a
2 parents ff111c1 + 7197b37
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diff --git a/.github/ISSUE_TEMPLATE/release-patch.md b/.github/ISSUE_TEMPLATE/release-patch.md
@@ -13,8 +13,7 @@ Action items
 Pre-release
 ---
 - [ ] Create a cherrypicks branch where all commits go into new release and open a PR against `release/x.y` branch
-- [ ] Create CoreNEURON tag on the `release/x.y` branch after cherrypicking required commits, update semantic version in its `CMakeLists.txt`, tag it & update submodule in cherrypicks PR
-- [ ] Look out for ModelDB regressions by manually submitting and analyzing [nrn-modeldb-ci](https://github.com/neuronsimulator/nrn-modeldb-ci/actions/workflows/nrn-modeldb-ci.yaml?query=event%3Aschedule++) for the cherrypicks branch vs previous version
+- [ ] Make sure to look out for ModelDB regressions by manually submitting and analyzing [nrn-modeldb-ci](https://github.com/neuronsimulator/nrn-modeldb-ci/actions/workflows/nrn-modeldb-ci.yaml?query=event%3Aschedule++) for the cherrypicks branch vs previous version
 - [ ] Update cherrypicks PR:
   - [ ] Update semantic version in `CMakeLists.txt`
   - [ ] Update changelog below and agree on it with everyone; then commit it to `docs/changelog` in the cherrypicks PR (copy structure as-is)
@@ -25,20 +24,20 @@ Sanity checks
 - [ ] After cherrypicks PR is merged, make sure GitHub, Azure and CircleCI builds pass for `release/x.y` branch
 - [ ] Run [nrn-build-ci](https://github.com/neuronsimulator/nrn-build-ci/actions/workflows/build-neuron.yml) for the `release/x.y` branch; see [nrn-build-ci guide](https://github.com/neuronsimulator/nrn-build-ci#azure-wheels-testing---manual-workflow) 
 - [ ] Activate ReadTheDocs build for `release/x.y` & make it hidden. Check docs are fine after build is done.
-- [ ] Run BBP Simulation Stack, CoreNEURON CI & other relevant tests
+- [ ] Run BBP Simulation Stack & other relevant tests
 - [ ] Build release wheels but WITHOUT upload ([see details](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure))
 
 
 Releasing
 ---
-- [ ] Create new release+tag on GitHub via [release workflow](https://github.com/neuronsimulator/nrn/actions/workflows/release.yml?query=workflow%3A%22NEURON+Release%22). Note that the GitHub release will be marked as pre-release.
+- [ ] Create new release+tag on GitHub via [release workflow](https://github.com/neuronsimulator/nrn/actions/workflows/release.yml?query=workflow%3A%22NEURON+Release%22). Note that the GitHub release will be marked as pre-release and  will contain the full-src-package and the Windows installer at the end of the release workflow.
 - [ ] Create, test and upload manual artifacts 
   - [ ] MacOS package installer (manual task, ask Michael)
   - [ ] arm64 wheels (manual task, check with Alex or Pramod)
   - [ ] aarch64 wheels (use existing `release/x.y-aarch64` branch for this, see [guide](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-circleci))
 - [ ] Publish the `x.y.z` wheels on PyPI; see [wheel publishing instructions](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure)
 - [ ] Once wheels are published, activate the `x.y.z` tag on ReadTheDocs
-- [ ] Upload Windows installer from the wheels publishing Azure run (to get correct tag)
+- [ ] Rename the Windows installer in the GitHub release to match the new version and the supported python versions (i.e. `nrn-8.2.2.w64-mingw-py-37-38-39-310-311-setup.exe`)
 - [ ] Publish release on GitHub (edit https://github.com/neuronsimulator/nrn/releases/tag/x.y.z and un-tick the pre-release checkbox) 
 
 

diff --git a/.github/ISSUE_TEMPLATE/release.md b/.github/ISSUE_TEMPLATE/release.md
@@ -12,15 +12,14 @@ Action items
 
 Pre-release
 ---
-- [ ] Look out for ModelDB regressions by analyzing [nrn-modeldb-ci last version vs nightly reports](https://github.com/neuronsimulator/nrn-modeldb-ci/actions/workflows/nrn-modeldb-ci.yaml?query=event%3Aschedule++)
-- [ ] Create CoreNEURON release branch, update semantic version in `CMakeLists.txt`, tag it & update submodule in NEURON
+- [ ] Make sur to look out for ModelDB regressions by launching analyzing [nrn-modeldb-ci last version vs nightly reports](https://github.com/neuronsimulator/nrn-modeldb-ci/actions/workflows/nrn-modeldb-ci.yaml?query=event%3Aschedule++)
 
 Sanity checks
 ---
 - [ ] Create `release/x.y` branch and make sure GitHub, Azure and CircleCI builds pass
 - [ ] Run [nrn-build-ci](https://github.com/neuronsimulator/nrn-build-ci/actions/workflows/build-neuron.yml) for the respective Azure build; see [Azure drop guide](https://github.com/neuronsimulator/nrn-build-ci#azure-wheels-testing---manual-workflow) 
 - [ ] Activate ReadTheDocs build for `release/x.y` & make it hidden. Check docs are fine after build is done.
-- [ ] Run BBP Simulation Stack, CoreNEURON CI & other relevant tests
+- [ ] Run BBP Simulation Stack & other relevant tests
 - [ ] Build release wheels but WITHOUT upload ([see details](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure))
 
 
@@ -30,14 +29,15 @@ Releasing
 - [ ] Update changelog below and agree on it with everyone; then commit it to `docs/changelog` (copy structure as-is)
 - [ ] Update `docs/index.rst` accordingly with the new `.pkg` and `.exe` links for `PKG installer` and `Windows Installer`
 - [ ] Run the ReadTheDocs build again for `release-x.y`, make sure the build passes and inspect the Changelog page.
-- [ ] Create new release+tag on GitHub via [release workflow](https://github.com/neuronsimulator/nrn/actions/workflows/release.yml?query=workflow%3A%22NEURON+Release%22). Note that the GitHub release will be marked as pre-release.
-- [ ] Create, test and upload manual artifacts 
+- [ ] Create new release+tag on GitHub via [release workflow](https://github.com/neuronsimulator/nrn/actions/workflows/release.yml?query=workflow%3A%22NEURON+Release%22). Note that the GitHub release will be marked as pre-release and  will contain the full-src-package and the Windows installer at the end of the release workflow.
+- [ ] Create, test and upload manual artifacts
   - [ ] MacOS package installer (manual task, ask Michael)
   - [ ] arm64 wheels (manual task, check with Alex or Pramod)
   - [ ] aarch64 wheels (create a `release/x.y-aarch64` branch for this, see [guide](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-circleci))
 - [ ] Publish the `x.y.z` wheels on Pypi; see [wheel publishing instructions](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure)
 - [ ] Once wheels are published, activate the `x.y.z` tag on ReadTheDocs
-- [ ] Upload Windows installer from the wheels publishing Azure run (to get correct tag)
+- [ ] Rename the Windows installer in the GitHub release to match the new version and the supported python versions (i.e. `nrn-8.2.2.w64-mingw-py-37-38-39-310-311-setup.exe`
+)
 - [ ] Publish release on GitHub (edit https://github.com/neuronsimulator/nrn/releases/tag/x.y.z and un-tick the pre-release checkbox)
 
 

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -41,7 +41,7 @@ jobs:
 
       - name: Install apt packages
         run: |
-          sudo apt-get install xfonts-100dpi build-essential doxygen lcov libboost-all-dev libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin patchelf gpg ninja-build flex bison libfl-dev
+          sudo apt-get install xfonts-100dpi build-essential doxygen lcov libboost-all-dev libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin gpg ninja-build flex bison libfl-dev
         shell: bash
 
       - name: Setup Caliper profiler

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -30,7 +30,7 @@ jobs:
       - name: Install apt packages
         run: |
           sudo apt-get update --fix-missing
-          sudo apt-get install build-essential libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin patchelf
+          sudo apt-get install build-essential libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin
           sudo apt-get install ffmpeg doxygen pandoc
         shell: bash
 

diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
@@ -104,7 +104,7 @@ jobs:
         run: |
           sudo apt-get install build-essential ccache libopenmpi-dev \
             libmpich-dev libx11-dev libxcomposite-dev mpich ninja-build \
-            openmpi-bin patchelf flex libfl-dev bison
+            openmpi-bin flex libfl-dev bison
           # The sanitizer builds use ubuntu 22.04
           if [[ "${{matrix.os}}" == "ubuntu-20.04" ]]; then
             sudo apt-get install g++-7 g++-8

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -23,6 +23,7 @@ jobs:
     name: tag-n-release ${{ github.event.inputs.rel_tag }} (${{ github.event.inputs.rel_branch }})
     outputs:
       release_url: ${{ steps.create_release.outputs.upload_url }}
+      rel_tag: ${{ env.REL_TAG }}
     steps:
       - uses: actions/checkout@v3
         name: Checkout branch ${{ env.REL_BRANCH }}
@@ -74,15 +75,17 @@ jobs:
     - name: Create full-src-package
       id: tar
       run: |
-        tar -czvf ${REL_TAG}.tar.gz nrn
-        echo "asset_file=${REL_TAG}.tar.gz" >> $GITHUB_OUTPUT
+        tar -czvf full-src-package-${REL_TAG}.tar.gz nrn
+        echo "asset_file=full-src-package-${REL_TAG}.tar.gz" >> $GITHUB_OUTPUT
 
     - name: Upload full-src-package to release
-      uses: actions/upload-release-asset@v1
-      with:
-        upload_url: ${{ needs.tag-n-release.outputs.release_url }}
-        asset_name: ${{ github.job }}-${{ steps.tar.outputs.asset_file }}
-        asset_content_type: application/gzip
-        asset_path: ${{ steps.tar.outputs.asset_file }}
+      run: |
+        gh release upload ${{ needs.tag-n-release.outputs.rel_tag }} ${{ steps.tar.outputs.asset_file }}
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  windows-installer:
+    needs: tag-n-release
+    uses: neuronsimulator/nrn/.github/workflows/windows.yml@master
+    with:
+      tag: ${{ needs.tag-n-release.outputs.rel_tag }}
diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
@@ -5,8 +5,16 @@ concurrency:
   cancel-in-progress: true  
 
 on:
+  workflow_call:
+    inputs:
+      tag:
+        description: 'Release version (tag name)'
+        default: ''
+        required: true
+        type: string
   push:
     branches: 
+      - master
       - release/**
   pull_request:
     branches:
@@ -28,7 +36,7 @@ jobs:
     steps:
     - uses: actions/checkout@v3
       with:
-        fetch-depth: 0
+        ref: ${{ inputs.tag }}
 
     - name: Retrieve rxd test data
       run: |
@@ -84,3 +92,11 @@ jobs:
       run: .\ci\win_test_installer.cmd
       shell: cmd
       working-directory: ${{runner.workspace}}\nrn
+
+    - name: Publish Release Installer
+      working-directory: ${{runner.workspace}}\nrn
+      if: inputs.tag != ''
+      run: |
+        gh release upload ${{ inputs.tag }} nrn-nightly-AMD64.exe
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -567,6 +567,7 @@ endif()
 # =============================================================================
 # Add project directories AFTER CMake modules
 # =============================================================================
+add_subdirectory(src/gnu)
 add_subdirectory(src/nrniv)
 
 # Collect the environment variables that are needed to execute NEURON from the build directory. This
@@ -676,7 +677,7 @@ if(NRN_ENABLE_DOCS)
     sphinx
     COMMAND ${NRN_DOCS_COMMAND_PREFIX} ${SPHINX_EXECUTABLE} -j auto -b html
             "${PROJECT_SOURCE_DIR}/docs" "${PROJECT_SOURCE_DIR}/docs/_build"
-    COMMAND echo "Copy/Paste to Browser ${PROJECT_SOURCE_DIR}/docs/_build/index.html"
+    COMMAND echo "Copy/Paste to Browser file://${PROJECT_SOURCE_DIR}/docs/_build/index.html"
     WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/docs
     COMMENT "Generating documentation with Sphinx")
 

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -67,7 +67,7 @@ stages:
             -e NRN_RELEASE_UPLOAD \
             -e SETUPTOOLS_SCM_PRETEND_VERSION \
             -e NRN_BUILD_FOR_UPLOAD=1 \
-            'neuronsimulator/neuron_wheel:latest-gcc9-x86_64' \
+            'neuronsimulator/neuron_wheel:latest-x86_64' \
             packaging/python/build_wheels.bash linux $(python.version) coreneuron
         displayName: 'Building ManyLinux Wheel'
 
@@ -79,58 +79,6 @@ stages:
       - template: ci/azure-wheel-test-upload.yml
 
 
-    - job: 'ManyLinuxGPUWheels'
-      timeoutInMinutes: 45
-      pool:
-        vmImage: 'ubuntu-20.04'
-      variables:
-        GPU_BUILD: 'true'
-      strategy:
-        matrix:
-          Python38:
-            python.version: '3.8'
-          Python39:
-            python.version: '3.9'
-          Python310:
-            python.version: '3.10'
-          Python311:
-            python.version: '3.11'
-      steps:
-
-      # Secure files documentation:
-      #   https://docs.microsoft.com/en-us/azure/devops/pipelines/library/secure-files?view=azure-devops
-      #   NOTE: when uploading new secure files, access must be permitted from the Azure pipeline interface (check message there)
-      - task: DownloadSecureFile@1
-        name: mpt_headersSF
-        displayName: 'Download mpt_headers secure file'
-        inputs:
-          secureFile: 'mpt_headears.2.21.tar.gz'
-
-      # Note that mpt headers must be mounted in the docker imager under `/nrnwheel/mpt`
-      # This path is checked by `packaging/python/build_wheels.bash` when run in the image.
-      - script: |
-          sudo mkdir -p /opt/nrnwheel/mpt
-          sudo tar -zxf $(mpt_headersSF.secureFilePath) --directory /opt/nrnwheel/mpt
-          docker run --rm \
-            -w /root/nrn \
-            -v $PWD:/root/nrn \
-            -v /opt/nrnwheel/mpt:/nrnwheel/mpt \
-            -e NEURON_NIGHTLY_TAG \
-            -e NRN_NIGHTLY_UPLOAD \
-            -e NRN_RELEASE_UPLOAD \
-            -e SETUPTOOLS_SCM_PRETEND_VERSION \
-            -e NRN_BUILD_FOR_UPLOAD=1 \
-            'neuronsimulator/neuron_wheel_gpu:nvhpc-22.1-cuda-11.5-gcc9' \
-            packaging/python/build_wheels.bash linux $(python.version) coreneuron-gpu
-        displayName: 'Building ManyLinux Wheel'
-
-      - script: |
-          sudo apt update
-          sudo apt install -y mpich openmpi-bin libopenmpi-dev libmpich-dev
-        displayName: 'Install Test System Depdendencies'
-
-      - template: ci/azure-wheel-test-upload.yml
-
     # Jobs to build OSX wheels natively
     - job: 'MacOSWheels'
       timeoutInMinutes: 45
@@ -202,42 +150,6 @@ stages:
       - template: ci/azure-wheel-test-upload.yml
 
 
-    # Jobs to build NEURON installer natively
-    - job: 'WindowsInstaller'
-      timeoutInMinutes: 45
-      pool:
-        vmImage: windows-latest
-      variables:
-        MSYS2_ROOT: C:\msys64
-
-      steps:
-      - checkout: self
-        submodules: 'true'
-        clean: 'true'
-
-      - task: BatchScript@1
-        inputs:
-          filename: ci/win_download_deps.cmd
-        displayName: "Download Dependencies"
-        condition: succeeded()
-
-      - task: BatchScript@1
-        inputs:
-          filename: ci/win_install_deps.cmd
-        displayName: "Install Dependencies"
-        condition: succeeded()
-
-      # WSL is enabled by default in the image, with no installed linux distribution.
-      # WSL creates an unusable `bash.EXE` that can be resolved first from the environment.
-      # This is why we remove that file.
-      - script: |
-          rm.exe "C:/WINDOWS/system32/bash.EXE"
-          %MSYS2_ROOT%\usr\bin\bash -lc "$BUILD_SOURCESDIRECTORY/ci/win_build_cmake.sh"
-        displayName: "Build and Create Installer"
-        condition: succeeded()
-
-      - template: ci/azure-win-installer-upload.yml
-
   - stage: Final
     jobs:
       - job: AzureDropURL

diff --git a/bin/nrnivmodl_core_makefile.in b/bin/nrnivmodl_core_makefile.in
@@ -52,16 +52,6 @@ ifeq ($(origin CXX), default)
     CXX = @CMAKE_CXX_COMPILER@
 endif
 
-ifeq (@CORENRN_ENABLE_GPU@, ON)
-  ifneq ($(shell $(CXX) --version | grep -o nvc++), nvc++)
-    $(error GPU wheels are only compatible with the NVIDIA C++ compiler nvc++, but CXX=$(CXX) and --version gives $(shell $(CXX) --version))
-  endif
-  # nvc++ -dumpversion is simpler, but only available from 22.2
-  ifeq ($(findstring nvc++ @CORENRN_NVHPC_MAJOR_MINOR_VERSION@, $(shell $(CXX) --version)),)
-    $(error GPU wheels are currently not compatible across NVIDIA HPC SDK versions. You have $(shell $(CXX) -V | grep nvc++) but this wheel was built with @CORENRN_NVHPC_MAJOR_MINOR_VERSION@.)
-  endif
-endif
-
 # In case of wheel, python and perl exe paths are from the build machine.
 # First prefer env variables set by neuron's nrnivmodl wrapper then check
 # binary used during build. If they don't exist then simply use python and

diff --git a/bin/nrnivmodl_makefile_cmake.in b/bin/nrnivmodl_makefile_cmake.in
@@ -40,29 +40,8 @@ endif
 # - @NRN_LINK_DEFS
 LDFLAGS = $(IV_LINK) $(READLINE_LINK) $(LINKFLAGS) $(UserLDFLAGS) @NRN_LINK_DEFS@
 
-# In GPU wheel distributions then the shipped libnrniv.so is linked against
-# some NVIDIA runtime libraries that are shipped with the wheel. If we use
-# nrnivmodl on the user machine then the NVIDIA compilers will link the local
-# versions of these libraries too, causing duplication.
-libnrniv_without_nvidia: $(libdir)/libnrniv.so
-	cp -v $(libdir)/libnrniv.so $(OUTPUT)/libnrniv-without-nvidia.so
-	patchelf $(OUTPUT)/libnrniv-without-nvidia.so --print-needed | grep '^libnv\(hpcatm\|omp\|cpumath\|cpumath-avx2\|c\)-[a-f0-9]\{8\}\.so' | xargs -t -r -n 1 patchelf $(OUTPUT)/libnrniv-without-nvidia.so --remove-needed
-	patchelf $(OUTPUT)/libnrniv-without-nvidia.so --set-soname libnrniv-without-nvidia.so
-	patchelf $(OUTPUT)/libnrniv-without-nvidia.so --print-rpath
-	ldd $(OUTPUT)/libnrniv-without-nvidia.so
-
-# In a GPU wheel build then we need to fudge libnrniv.so before linking to it.
-# NEURONDEMO should be set when we run this as part of the wheel build, in
-# which case we do *not* want this hack.
-ifeq (@NRN_ENABLE_CORENEURON@@NRN_WHEEL_BUILD@@CORENRN_ENABLE_GPU@$(if $(NRNDEMO),OFF,ON), ONONONON)
-  NRNLIB_FLAGS = -L$(OUTPUT) -lnrniv-without-nvidia
-  NRNLIB_RPATH_FLAGS = -Wl,-rpath,\$$ORIGIN -Wl,-rpath,\$$ORIGIN/..
-  nrn_lib = libnrniv_without_nvidia
-else
-  NRNLIB_FLAGS = -L$(libdir) -lnrniv
-  NRNLIB_RPATH_FLAGS = -Wl,-rpath,$(libdir)
-  nrn_lib =
-endif
+NRNLIB_FLAGS = -L$(libdir) -lnrniv
+NRNLIB_RPATH_FLAGS = -Wl,-rpath,$(libdir)
 
 OS_NAME := $(shell uname)
 _cm =,
@@ -142,13 +121,13 @@ special: $(mech_lib)
 
 $(mech_lib): $(mech_lib_type)
 
-mech_lib_shared: mod_func.o $(mod_objs) $(nrn_lib) build_always
+mech_lib_shared: mod_func.o $(mod_objs) build_always
 	@printf " => $(C_GREEN)LINKING$(C_RESET) shared library $(mech_lib)\n"
 	$(CXX_LINK_SHARED) -I $(incdir) -o ${mech_lib} ${_SONAME} \
 	  $(mod_func_o) $(mod_objs) $(NRNLIB_FLAGS) $(NRNLIB_RPATH_FLAGS) $(LDFLAGS)
 	rm -f $(OBJS_DIR)/.libs/libnrnmech.so ; mkdir -p $(OBJS_DIR)/.libs ; cp $(mech_lib) $(OBJS_DIR)/.libs/libnrnmech.so
 
-mech_lib_static: mod_func.o $(mod_objs) $(nrn_lib) build_always
+mech_lib_static: mod_func.o $(mod_objs) build_always
 	@printf " => $(C_GREEN)LINKING$(C_RESET) static library $(mech_lib)\n"
 	ar cq ${mech_lib} $(mod_func_o) $(mod_objs) $(cobjs);