Remove GPU wheels.

neuronsimulator · Jun 8, 2023 · f64173a · f64173a
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commit f64173a
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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/azure-pipelines.yml b/azure-pipelines.yml
@@ -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

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);
 

diff --git a/docs/coreneuron/installation.rst b/docs/coreneuron/installation.rst
@@ -13,22 +13,17 @@ release, or ``pip install neuron-nightly`` to install a snapshot of the
 development branch.
 You may want to use ``virtualenv`` to manage your Python package installations.
 
-If you want to use the GPU-enabled wheel then you should run
-``pip install neuron-gpu``, for the latest release, or
-``pip install neuron-gpu-nightly`` to install a snapshot of the
-development branch.
-This binary wheel does not include all the NVIDIA dependencies that are
-required to build and execute GPU code, so you should install the
-`NVIDIA HPC SDK <https://developer.nvidia.com/hpc-sdk>`_ on your
-machine.
-
 .. warning::
-   It is currently necessary to use the same version of the HPC SDK as
-   was used to build the binary wheels.
-   This is currently defined
-   `in this file <https://github.com/neuronsimulator/nrn/blob/master/packaging/python/Dockerfile_gpu>`_
-   in the NEURON repository, at the time of writing this is version
-   22.1
+
+   Between versions 8.1 and 8.2.2 a GPU-enabled wheel was available via ``pip install neuron-gpu``
+   and ``pip install neuron-gpu-nightly``.
+   Due to ease-of-use and maintainability concerns, this has been removed in nrn#XXX until
+   person-power is available to pursue a more robust solution.
+   Using the released GPU wheels with custom mechanism files (``nrnivmodl``) requires that you have
+   the same version of the `NVIDIA HPC SDK <https://developer.nvidia.com/hpc-sdk>`_ installed on
+   your system as was used to build the wheels.
+   For example, in 8.2.2 this was version 22.1, as can be seen `in this file
+   <https://github.com/neuronsimulator/nrn/blob/8.2.2/packaging/python/Dockerfile_gpu#L14>`_.
 
 
 Installing from source

diff --git a/docs/install/python_wheels.md b/docs/install/python_wheels.md
@@ -30,7 +30,6 @@ All wheels built on Azure are:
 * Published to `Pypi.org` as
   * `neuron-nightly` -> when the pipeline is launched in CRON mode
   * `neuron-x.y.z` -> when the pipeline is manually triggered for release `x.y.z`
-  * additionally, for Linux only: `neuron-gpu-nightly` and `neuron-gpu-x.y.z`
 * Stored as `Azure artifacts` in the Azure pipeline for every run.
 
 Refer to the following image for the NEURON Docker Image workflow: 
@@ -139,18 +138,11 @@ You can build the wheel for a specific python version:
 bash packaging/python/build_wheels.bash linux 38    # 38 for Python v3.8
 ```
 
-To build wheels with GPU support you have to pass an additional argument:
-* `coreneuron` : build wheel with `CoreNEURON` support
-* `coreneuron-gpu` : build wheel with `CoreNEURON` and `GPU` support
-
+To build wheels with CoreNEURON support you have to pass an additional argument: `coreneuron`.
 ```
-bash packaging/python/build_wheels.bash linux 38 coreneuron-gpu
-
-# or
-
 bash packaging/python/build_wheels.bash linux 3* coreneuron
 ```
-In the last example we are passing `3*` to build the wheels with `CoreNEURON` support for all python 3 versions.
+Where we are passing `3*` to build the wheels with `CoreNEURON` support for all python 3 versions.
 
 ### macOS
 As mentioned above, for macOS all dependencies have to be available on a system. You have to then clone NEURON repository and execute:

diff --git a/packaging/python/Dockerfile_gpu b/packaging/python/Dockerfile_gpu
diff --git a/packaging/python/build_wheels.bash b/packaging/python/build_wheels.bash
@@ -97,19 +97,6 @@ build_wheel_linux() {
         setup_args="--enable-coreneuron"
         clone_install_nmodl_requirements
         CMAKE_DEFS="${CMAKE_DEFS},LINK_AGAINST_PYTHON=OFF"
-    elif [ "$2" == "coreneuron-gpu" ]; then
-        setup_args="--enable-coreneuron --enable-gpu"
-        # nvhpc is required for GPU support but make sure
-        # CC and CXX are unset for building python extensions
-        source ~/.bashrc
-        module load nvhpc
-        unset CC CXX
-        # make the NVIDIA compilers default to targeting haswell CPUs
-        # the default is currently 70;80, partly because NVHPC does not
-        # support OpenMP target offload with 60. Wheels use mod2c and
-        # OpenACC for now, so we can be a little more generic.
-        CMAKE_DEFS="${CMAKE_DEFS},CMAKE_CUDA_ARCHITECTURES=60;70;80,CMAKE_C_FLAGS=-tp=haswell,CMAKE_CXX_FLAGS=-tp=haswell,CORENRN_ENABLE_OPENMP_OFFLOAD=OFF,LINK_AGAINST_PYTHON=OFF"
-        clone_install_nmodl_requirements
     fi
 
     # Workaround for https://github.com/pypa/manylinux/issues/1309
@@ -156,9 +143,6 @@ build_wheel_osx() {
     if [ "$2" == "coreneuron" ]; then
         setup_args="--enable-coreneuron"
         clone_install_nmodl_requirements
-    elif [ "$2" == "coreneuron-gpu" ]; then
-        echo "Error: GPU support on MacOS is not available!"
-        exit 1
     fi
 
     CMAKE_DEFS="NRN_MPI_DYNAMIC=$3"
@@ -207,7 +191,7 @@ if [ ! -z "$2" ]; then
   python_wheel_version=$2
 fi
 
-# enable coreneuron support: "coreneuron" or "coreneuron-gpu"
+# enable coreneuron support: "coreneuron"
 # this should be removed/improved once wheel is stable
 coreneuron=$3
 
@@ -251,7 +235,7 @@ case "$1" in
     ;;
 
   *)
-    echo "Usage: $(basename $0) < linux | osx > [python version 36|37|38|39|3*]  [coreneuron | coreneuron-gpu]"
+    echo "Usage: $(basename $0) < linux | osx > [python version 36|37|38|39|3*]  [coreneuron]"
     exit 1
     ;;
 

diff --git a/packaging/python/fix_target_processor_in_makefiles.sh b/packaging/python/fix_target_processor_in_makefiles.sh
diff --git a/packaging/python/test_wheels.sh b/packaging/python/test_wheels.sh
@@ -301,10 +301,7 @@ $python_exe -m pip install --upgrade pip
 # install numpy, pytest and neuron
 $python_exe -m pip install numpy pytest
 $python_exe -m pip install $python_wheel
-$python_exe -m pip show neuron \
-    || $python_exe -m pip show neuron-nightly \
-    || $python_exe -m pip show neuron-gpu \
-    || $python_exe -m pip show neuron-gpu-nightly
+$python_exe -m pip show neuron || $python_exe -m pip show neuron-nightly
 
 
 # check the existence of coreneuron support

diff --git a/setup.py b/setup.py
@@ -20,7 +20,6 @@ class Components:
     MPI = True
     MUSIC = False  # still early support
     CORENRN = False  # still early support
-    GPU = False  # still early support
 
 
 # Check if we've got --cmake-build-dir path that will be used to build extensions only
@@ -93,10 +92,6 @@ class Components:
     Components.CORENRN = True
     sys.argv.remove("--enable-coreneuron")
 
-if "--enable-gpu" in sys.argv:
-    Components.GPU = True
-    sys.argv.remove("--enable-gpu")
-
 if "--enable-music" in sys.argv:
     Components.MUSIC = True
     sys.argv.remove("--enable-music")
@@ -320,16 +315,6 @@ def _run_cmake(self, ext):
                     cwd=self.build_temp,
                     env=env,
                 )
-                if Components.GPU:
-                    subprocess.check_call(
-                        [
-                            ext.sourcedir
-                            + "/packaging/python/fix_target_processor_in_makefiles.sh",
-                            ext.cmake_install_prefix,
-                        ],
-                        cwd=self.build_temp,
-                        env=env,
-                    )
 
         except subprocess.CalledProcessError as exc:
             logging.error("Status : FAIL. Logging.\n%s", exc.output)
@@ -427,16 +412,6 @@ def setup_package():
                 ]
                 if Components.CORENRN
                 else []
-            )
-            + (
-                [
-                    "-DCORENRN_ENABLE_GPU=ON",
-                    "-DCMAKE_C_COMPILER=nvc",  # use nvc and nvc++ for GPU support
-                    "-DCMAKE_CXX_COMPILER=nvc++",
-                    "-DCMAKE_CUDA_COMPILER=nvcc",
-                ]
-                if Components.GPU
-                else []
             ),
             include_dirs=[
                 "src",
@@ -512,15 +487,11 @@ def setup_package():
     logging.info("RX3D is %s", "ENABLED" if Components.RX3D else "DISABLED")
 
     # package name
-    package_name = "NEURON-gpu" if Components.GPU else "NEURON"
+    package_name = "NEURON"
 
     # For CI, we want to build separate wheel with "-nightly" suffix
     package_name += os.environ.get("NEURON_NIGHTLY_TAG", "-nightly")
 
-    # GPU wheels use patchelf to avoid duplicating NVIDIA runtime libraries when
-    # using nrnivmodl.
-    maybe_patchelf = ["patchelf"] if Components.GPU else []
-
     setup(
         name=package_name,
         package_dir={"": NRN_PY_ROOT},
@@ -538,8 +509,7 @@ def setup_package():
             else "node-and-date"
         },
         cmdclass=dict(build_ext=CMakeAugmentedBuilder, docs=Docs),
-        install_requires=["numpy>=1.9.3", "packaging", "find_libpython"]
-        + maybe_patchelf,
+        install_requires=["numpy>=1.9.3", "packaging", "find_libpython"],
         tests_require=["flake8", "pytest"],
         setup_requires=["wheel", "setuptools_scm"]
         + maybe_docs

diff --git a/share/lib/python/scripts/_binwrapper.py b/share/lib/python/scripts/_binwrapper.py
@@ -67,13 +67,7 @@ def _config_exe(exe_name):
     package_name = "neuron"
 
     # determine package to find the install location
-    if "neuron-gpu-nightly" in working_set.by_key:
-        print("INFO : Using neuron-gpu-nightly Package (Alpha Developer Version)")
-        package_name = "neuron-gpu-nightly"
-    elif "neuron-gpu" in working_set.by_key:
-        print("INFO : Using neuron-gpu Package (Alpha Version)")
-        package_name = "neuron-gpu"
-    elif "neuron-nightly" in working_set.by_key:
+    if "neuron-nightly" in working_set.by_key:
         print("INFO : Using neuron-nightly Package (Developer Version)")
         package_name = "neuron-nightly"
     elif "neuron" in working_set.by_key: