Doc: tweak +pemap offset description #140

Workflow file for this run

	name: CI

	on: [pull_request, merge_group]

	# Cancel in progress CI runs when a new run targeting the same PR or branch/tag is triggered.
	# https://stackoverflow.com/questions/66335225/how-to-cancel-previous-runs-in-the-pr-when-you-push-new-commitsupdate-the-curre
	concurrency:
	group: ${{ github.workflow }}-${{ github.event.pull_request.number \|\| github.ref }}
	cancel-in-progress: true

	jobs:
	buildold_netlrts-linux-x86_64:
	timeout-minutes: 90
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Run build
	run: ./buildold all-test netlrts-linux-x86_64 -g -j4 --with-production
	- name: test
	run: make -C netlrts-linux-x86_64/tmp test TESTOPTS="++local"
	- name: testp P=2
	run: make -C netlrts-linux-x86_64/tmp testp TESTOPTS="++local" P=2
	- name: testp P=3
	run: make -C netlrts-linux-x86_64/tmp testp TESTOPTS="++local" P=3

	changa_netlrts-linux-x86_64:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: build-charm++
	run: ./build ChaNGa netlrts-linux-x86_64 -g -j4 --with-production
	- name: build-changa
	run: \|
	git clone https://github.com/N-bodyshop/utility
	git clone https://github.com/N-bodyshop/changa
	cd changa
	./configure
	make -j4
	- name: test-changa
	run: \|
	cd changa/teststep
	make test

	charm4py_netlrts-linux-x86_64_tcp:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: build-charm++
	run: \|
	git fetch --unshallow # Need full repo for 'git describe' used by charm4py
	./build charm4py netlrts-linux-x86_64 tcp -g -j4 --with-production
	- name: build-charm4py
	run: \|
	pip3 install setuptools cython cffi greenlet numpy torch torchvision
	git clone https://github.com/UIUC-PPL/charm4py
	export PYTHONPATH="$PWD/charm4py"

	mkdir -p charm4py/charm_src/charm/bin && cp bin/charmrun charm4py/charm_src/charm/bin
	mkdir -p charm4py/charm_src/charm/lib && cp lib/libcharm.so charm4py/charm_src/charm/lib
	mkdir -p charm4py/charm_src/charm/include && cp -r -L include/* charm4py/charm_src/charm/include

	cd charm4py
	export CHARM4PY_BUILD_CFFI=1
	python3 setup.py build_ext --inplace
	- name: test-charm4py
	run: \|
	export PYTHONPATH="$PWD/charm4py"
	export CHARM4PY_TEST_NUM_PROCESSES=2
	cd charm4py
	python3 auto_test.py

	cuda_netlrts-linux-x86_64_buildonly:
	# Buildonly test, as CUDA needs an actual device to run.
	timeout-minutes: 45
	runs-on: ubuntu-20.04 # FIXME: ubuntu-latest does not work
	steps:
	- uses: actions/checkout@v4
	- name: build
	run: \|
	sudo apt-get update
	sudo apt-get -y install nvidia-cuda-toolkit
	./build all-test netlrts-linux-x86_64 cuda -j4 -g
	export CUDATOOLKIT_HOME=/usr # TODO: make this unnecessary
	make -j4 -C netlrts-linux-x86_64-cuda/examples/charm++/cuda OPTS="-g"
	make -j4 -C netlrts-linux-x86_64-cuda/examples/ampi/cuda OPTS="-g"

	doc:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	-
	uses: actions/setup-python@v4
	with:
	python-version: '3.x'
	- name: Install prerequisites
	run: pip3 install sphinx sphinx_rtd_theme
	- name: Run sphinx
	run: \|
	cd doc
	make html

	mpi-linux-x86_64:
	timeout-minutes: 90
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: install-prerequisites
	run: sudo apt-get update && sudo apt-get install -y mpich libmpich-dev
	- name: build
	run: ./build all-test mpi-linux-x86_64 smp --build-shared --with-production --enable-error-checking --enable-lbuserdata -j3 -g -Werror=vla
	# TODO: this should build tests with "-charm-shared". See #2735 on why this is not done currently.
	- name: test
	run: make -C mpi-linux-x86_64-smp/tmp test TESTOPTS="+setcpuaffinity"
	# Disabled due to several hangs and segfaults.
	#- name: testp
	# run: make -C mpi-linux-x86_64-smp/tmp testp P=4 TESTOPTS="+setcpuaffinity ++ppn 2"

	mpi-linux-x86_64_syncft:
	timeout-minutes: 90
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: install-prerequisites
	run: sudo apt-get update && sudo apt-get install -y mpich libmpich-dev
	- name: build
	run: ./build all-test mpi-linux-x86_64 syncft -j2 -g
	- name: test
	run: make -C mpi-linux-x86_64-syncft/tmp mpisyncfttest

	multicore-darwin-x86_64_projections:
	timeout-minutes: 60
	runs-on: macos-12
	steps:
	- uses: actions/checkout@v4
	- name: build
	run: ./build LIBS multicore-darwin-x86_64 -g -j3 --with-production --enable-tracing
	- name: test
	run: \|
	make -C multicore-darwin-x86_64/tmp all-test -j3 OPTS="-g -tracemode projections"
	make -C multicore-darwin-x86_64/tmp test
	- name: projections
	run: \|
	git clone https://github.com/UIUC-PPL/projections
	cd projections
	make
	proj=$PWD/bin/projections
	cd ..
	files=$(find . -name *.sts)
	for f in $files; do echo $f; pushd .; cd $(dirname $f); $proj --exit $(basename $f); popd; done

	# FIXME: disabled since tests don't pass
	# multicore-darwin-arm8_projections:
	# timeout-minutes: 60
	# runs-on: macos-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: build
	# run: ./build LIBS multicore-darwin-arm8 -g -j3 --with-production --enable-tracing
	# - name: test
	# run: \|
	# make -C multicore-darwin-arm8/tmp all-test -j3 OPTS="-g -tracemode projections"
	# make -C multicore-darwin-arm8/tmp test
	# - name: projections
	# run: \|
	# git clone https://github.com/UIUC-PPL/projections
	# cd projections
	# make
	# proj=$PWD/bin/projections
	# cd ..
	# files=$(find . -name *.sts)
	# for f in $files; do echo $f; pushd .; cd $(dirname $f); $proj --exit $(basename $f); popd; done

	namd_netlrts-linux-x86_64:
	# Since NAMD requires a secret to download its source from Gitlab, CI builds from outside PPL
	# always fail in this test since the secret is not available.
	env:
	namd_secret: ${{ secrets.NAMD_CI_USERNAME_TOKEN }}
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v4
	- name: install-prerequisites
	if: ${{ env.namd_secret != '' }}
	run: \|
	sudo apt-get update
	sudo apt-get -y install sfftw-dev
	# test build without Fortran support
	sudo apt-get -y remove gfortran
	- name: build-charm++
	if: ${{ env.namd_secret != '' }}
	run: ./build LIBS netlrts-linux-x86_64 -g -j4 --with-production
	- name: build-namd
	if: ${{ env.namd_secret != '' }}
	run: \|
	cd ..
	git clone https://${{ secrets.NAMD_CI_USERNAME_TOKEN }}@gitlab.com/tcbgUIUC/namd.git
	cd namd
	./config Linux-x86_64-g++ --charm-base ../charm --charm-arch netlrts-linux-x86_64 --without-tcl
	cd Linux-x86_64-g++
	make -j4
	- name: test-namd-alanin
	if: ${{ env.namd_secret != '' }}
	run: \|
	cd ../namd/Linux-x86_64-g++
	./charmrun ++local +p2 ./namd3 src/alanin

	- name: Cache apoa1 files
	if: ${{ env.namd_secret != '' }}
	id: cache-apoa1-files
	uses: actions/cache@v3
	with:
	path: ~/namddata/apoa1
	key: namd-apoa1-files
	- name: Download apoa1 files
	if: steps.cache-apoa1-files.outputs.cache-hit != 'true'
	run: \|
	mkdir -p ~/namddata
	cd ~/namddata
	wget http://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz
	tar xzf apoa1.tar.gz
	sed -i 's,500,250,' apoa1/apoa1.namd # Reduce number of steps
	sed -i 's,/usr/tmp,/tmp,' apoa1/apoa1.namd # Change output prefix
	rm apoa1.tar.gz

	- name: test-namd-apoa1
	if: ${{ env.namd_secret != '' }}
	run: \|
	cd ../namd/Linux-x86_64-g++
	./charmrun ++local +p4 ./namd3 ~/namddata/apoa1/apoa1.namd

	netlrts-darwin-x86_64:
	timeout-minutes: 60
	runs-on: macos-12
	steps:
	- uses: actions/checkout@v4
	- name: build
	run: ./build all-test netlrts-darwin-x86_64 --build-shared --with-production --enable-error-checking --enable-lbuserdata -j3 -g -Werror=vla
	# TODO: this should build tests with "-charm-shared". See #2735 on why this is not done currently.
	- name: test
	run: make -C netlrts-darwin-x86_64/tmp test TESTOPTS="++local"
	- name: testp P=2
	run: make -C netlrts-darwin-x86_64/tmp testp P=2 TESTOPTS="++local"

	# FIXME: disabled since tests don't pass
	# netlrts-darwin-arm8:
	# timeout-minutes: 60
	# runs-on: macos-latest
	# steps:
	# - uses: actions/checkout@v4
	# - name: build
	# run: ./build all-test netlrts-darwin-arm8 --build-shared --with-production --enable-error-checking --enable-lbuserdata -j3 -g -Werror=vla
	# # TODO: this should build tests with "-charm-shared". See #2735 on why this is not done currently.
	# - name: test
	# run: make -C netlrts-darwin-arm8/tmp test TESTOPTS="++local"
	# - name: testp P=2
	# run: make -C netlrts-darwin-arm8/tmp testp P=2 TESTOPTS="++local"

	netlrts-linux-i386:
	timeout-minutes: 60
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: install-prerequisites
	run: \|
	sudo dpkg --add-architecture i386
	sudo apt-get update
	sudo apt-get install -y gcc-multilib g++-multilib gfortran-multilib zlib1g-dev:i386 libjpeg-dev:i386
	- name: build
	run: ./build all-test netlrts-linux-i386 --build-shared --with-production --enable-error-checking --enable-lbuserdata -j3 -g -Werror=vla
	# TODO: this should build tests with "-charm-shared". See #2735 on why this is not done currently.
	- name: test
	run: make -C netlrts-linux-i386/tmp test TESTOPTS="++local"
	- name: testp P=2
	run: make -C netlrts-linux-i386/tmp testp P=2 TESTOPTS="++local"

	netlrts-linux-x86_64:
	timeout-minutes: 60
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: build
	run: ./build all-test netlrts-linux-x86_64 --with-production --enable-error-checking --enable-lbuserdata -j3 -g -Werror=vla
	# TODO: this should build tests with "-charm-shared". See #2735 on why this is not done currently.
	- name: test
	run: make -C netlrts-linux-x86_64/tmp test TESTOPTS="++local"
	- name: testp P=2
	run: make -C netlrts-linux-x86_64/tmp testp P=2 TESTOPTS="++local"

	netlrts-linux-x86_64_smp:
	timeout-minutes: 60
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: build
	run: ./build all-test netlrts-linux-x86_64 smp --with-production --enable-error-checking --enable-lbuserdata -j3 -g -Werror=vla
	# TODO: this should build tests with "-charm-shared". See #2735 on why this is not done currently.
	- name: test
	run: make -C netlrts-linux-x86_64-smp/tmp test TESTOPTS="++local +setcpuaffinity +CmiSleepOnIdle"
	- name: testp P=4 PPN=2
	run: make -C netlrts-linux-x86_64-smp/tmp testp P=4 TESTOPTS="++local +setcpuaffinity +CmiSleepOnIdle ++ppn 2"

	netlrts-linux-x86_64_syncft:
	timeout-minutes: 90
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: build
	run: ./build all-test netlrts-linux-x86_64 syncft -j2 -g
	- name: test
	run: make -C netlrts-linux-x86_64-syncft/tmp syncfttest TESTOPTS="++local"

	shellcheck:
	# See https://github.com/koalaman/shellcheck/wiki
	# for explanations of ShellCheck error codes
	timeout-minutes: 10
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: ShellCheck
	run: \|
	# TODO: add more scripts
	shellcheck \
	build \
	buildcmake \
	package-tarball.sh \
	relink.script \
	src/scripts/commitid.sh \
	src/scripts/testrun \
	src/arch/multicore/charmrun \
	src/arch/mpi-win-x86_64/charmrun \

	spack:
	name: spack_${{ matrix.os }}
	runs-on: ${{ matrix.os }}

	strategy:
	fail-fast: false
	matrix:
	os: [ubuntu-latest, macos-12]

	steps:
	- uses: actions/checkout@v4
	- name: Install Spack
	run: \|
	cd ..
	git clone --depth 1 https://github.com/spack/spack
	cd spack
	[[ $(uname) == "Linux" ]] && sudo apt-get install -y gfortran

	# Use this branch for testing, not main
	sed -i -e 's,="main",="${{ github.head_ref }}",' var/spack/repos/builtin/packages/charmpp/package.py

	# Use a fork, not the main repo
	# If in merge_group mode, the branch should be created in the main repo
	if [[ ${{ github.event_name }} == 'pull_request' ]]; then
	sed -i -e 's,charmplusplus/charm.git,${{github.event.pull_request.head.repo.full_name}},' var/spack/repos/builtin/packages/charmpp/package.py
	fi

	# Compile with debug symbols
	sed -i -e 's,build(target,options.append("-g"); build(target,' var/spack/repos/builtin/packages/charmpp/package.py

	# Add +setcpuaffinity option to TESTOPTS
	sed -i -e 's,\+\+local,++local +setcpuaffinity,' var/spack/repos/builtin/packages/charmpp/package.py

	# No need for automake/autoconf
	sed -i -e '/automake/d' var/spack/repos/builtin/packages/charmpp/package.py
	sed -i -e '/autoconf/d' var/spack/repos/builtin/packages/charmpp/package.py

	- name: Build Charm++
	run: \|
	cd ../spack
	source share/spack/setup-env.sh
	spack compiler find
	spack compiler list
	spack spec charmpp@main
	spack install --test root charmpp@main

	ucx-linux-x86_64_openpmix:
	timeout-minutes: 60
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v1
	# Uncomment the lines below to set up a tmate session for debugging.
	# See https://github.com/marketplace/actions/debugging-with-tmate for details.
	# This can't be enabled all the time as the tmate session will wait for a user to connect before running
	# the build.
	#- name: Tmate session for debugging
	# uses: mxschmitt/action-tmate@v2
	- name: install-prerequisites
	run: \|
	sudo apt-get update
	sudo apt-get install libucx-dev libevent-dev libhwloc-dev
	- name: build-openpmix
	run: \|
	wget https://github.com/openpmix/openpmix/releases/download/v3.1.5/pmix-3.1.5.tar.gz
	tar -xf pmix-3.1.5.tar.gz
	cd pmix-3.1.5
	./configure
	make -j4
	sudo make install
	# OpenMPI is needed to launch Charm++ programs with the UCX backend
	- name: build-ompi
	run: \|
	wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.5.tar.gz
	tar -xf openmpi-4.0.5.tar.gz
	cd openmpi-4.0.5
	./configure --enable-mca-no-build=btl-uct --with-pmix=/usr/local
	make -j4
	sudo make install
	- name: build
	run: ./build all-test ucx-linux-x86_64 openpmix -g -j4 --with-production
	- name: test
	run: \|
	export PATH=/usr/local/bin:$PATH
	export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
	export OMPI_MCA_rmaps_base_oversubscribe=1
	make -C ucx-linux-x86_64-openpmix/tests test
	make -C ucx-linux-x86_64-openpmix/examples test

	verbs-linux-x86_64_smp:
	# Buildonly test, as the machine layer needs an actual device to run.
	# Also test packaging a tarball and building from it.
	# Since it is buildonly, test both build and buildold with the tarball.
	timeout-minutes: 45
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: install-prerequisites
	run: \|
	sudo apt-get update
	sudo apt-get -y install libibverbs-dev
	- name: package-tarball
	run: \|
	./package-tarball.sh
	cd ..
	tar -xzf charm/charm-*.tar.gz
	- name: build-smp
	run: \|
	cd ../charm-*
	# TODO: this should build tests with "-charm-shared". See #2735 on why this is not done currently.
	./build all-test verbs-linux-x86_64 smp -j4 -g --build-shared
	- name: buildold-nonsmp
	run: \|
	cd ../charm-*
	# TODO: this should build tests with "-charm-shared". See #2735 on why this is not done currently.
	./buildold all-test verbs-linux-x86_64 -j4 -g --build-shared

	netlrts-win-x86_64_mingw64:
	timeout-minutes: 90

	runs-on: windows-latest
	defaults:
	run:
	shell: msys2 {0}

	steps:
	- uses: actions/checkout@v4
	- uses: msys2/setup-msys2@v2
	with:
	msystem: MINGW64
	update: true
	install: git mingw-w64-x86_64-toolchain mingw-w64-x86_64-libtool mingw-w64-x86_64-cmake make libtool autoconf automake
	- name: build
	run: \|
	. src/arch/win/vsenv.sh
	./build AMPI netlrts-win-x86_64 --with-production -j2
	make -C netlrts-win-x86_64/tests -j2
	- name: test
	run: \|
	make -C netlrts-win-x86_64/tests test TESTOPTS="++local"

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Doc: tweak +pemap offset description #140

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