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#!/bin/bash
#
# Copyright (c) 2020-2021, NVIDIA CORPORATION.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
init_globals() {
if [ "$0" != "/bin/bash" ]; then
SCRIPT_DIR=$(dirname "$(readlink -f "$0")")
export RUN_SCRIPT_FILE="$(readlink -f "$0")"
else
export RUN_SCRIPT_FILE="$(readlink -f "${BASH_SOURCE[0]}")"
fi
export TOP=$(git rev-parse --show-toplevel || $(dirname "${RUN_SCRIPT_FILE}"))
}
################################################################################
# Utility functions
################################################################################
#######################################
# Get list of available commands from a given input file.
#
# Available commands and command summary are extracted by checking a pattern
# "_desc() { echo '".
# Section title is extracted by checking a pattern "# Section: ".
# This command is used for listing available commands in CLI.
#
# e.g.)
# "# Section: String/IO functions"
# => "# String/IO functions"
# "to_lower_desc() { echo 'Convert to lower case"
# => "to_lower ----------------- Convert to lower case"
#
# Arguments:
# $1 - input file that defines commands
# Returns:
# Print list of available commands from $1
#######################################
get_list_of_available_commands() {
local file_name="$1"
if [ ! -e "$1" ]; then
echo "$1 doesn't exist!"
fi
local line_str='--------------------------------'
local IFS= cmd_lines="$(IFS= cat "$1" | grep -E -e "^(([[:alpha:]_[:digit:]]+)_desc\(\)|# Section: )" | sed "s/_desc() *{ *echo '/ : /")"
local line
while IFS= read -r line; do
local cmd=$(echo "$line" | cut -d":" -f1)
local desc=$(echo "$line" | cut -d":" -f2-)
if [ "$cmd" = "# Section" ]; then
c_echo B "${desc}"
else
# there is no substring operation in 'sh' so use 'cut'
local dash_line="$(echo "${line_str}" | cut -c ${#cmd}-)" # = "${line_str:${#cmd}}"
c_echo Y " ${cmd}" w " ${dash_line} ${desc}"
fi
# use <<EOF, not '<<<"$cmd_lines"' to be executable in sh
done <<EOF
$cmd_lines
EOF
}
my_cat_prefix() {
local IFS
local prefix="$1"
local line
while IFS= read -r line; do
echo "${prefix}${line}" # -e option doesn't work in 'sh' so disallow escaped characters
done <&0
}
c_str() {
local old_color=39
local old_attr=0
local color=39
local attr=0
local text=""
#local no_change=0
for i in "$@"; do
case "$i" in
r|R)
color=31
;;
g|G)
color=32
;;
y|Y)
color=33
;;
b|B)
color=34
;;
p|P)
color=35
;;
c|C)
color=36
;;
w|W)
color=37
;;
z|Z)
color=0
;;
esac
case "$i" in
l|L|R|G|Y|B|P|C|W)
attr=1
;;
n|N|r|g|y|b|p|c|w)
attr=0
;;
z|Z)
attr=0
;;
*)
text="${text}$i"
esac
if [ ${old_color} -ne ${color} ] || [ ${old_attr} -ne ${attr} ]; then
text="${text}\033[${attr};${color}m"
old_color=$color
old_attr=$attr
fi
done
/bin/echo -en "$text"
}
c_echo() {
local old_opt="$(shopt -op xtrace)" # save old xtrace option
set +x # unset xtrace
local text="$(c_str "$@")"
/bin/echo -e "$text\033[0m"
eval "${old_opt}" # restore old xtrace option
}
echo_err() {
>&2 echo "$@"
}
c_echo_err() {
>&2 c_echo "$@"
}
printf_err() {
>&2 printf "$@"
}
get_item_ranges() {
local indexes="$1"
local list="$2"
echo -n "$(echo "${list}" | xargs | cut -d " " -f "${indexes}")"
return $?
}
get_unused_ports() {
local num_of_ports=${1:-1}
local start=${2:-49152}
local end=${3:-61000}
comm -23 \
<(seq ${start} ${end} | sort) \
<(ss -tan | awk '{print $4}' | while read line; do echo ${line##*\:}; done | grep '[0-9]\{1,5\}' | sort -u) \
| shuf | tail -n ${num_of_ports} # use tail instead head to avoid broken pipe in VSCode terminal
}
newline() {
echo
}
info() {
c_echo W "$(date -u '+%Y-%m-%d %H:%M:%S') [INFO] " Z "$@"
}
error() {
echo R "$(date -u '+%Y-%m-%d %H:%M:%S') [ERROR] " Z "$@"
}
fatal() {
echo R "$(date -u '+%Y-%m-%d %H:%M:%S') [FATAL] " Z "$@"
echo
if [ -n "${SCRIPT_DIR}" ]; then
exit 1
fi
}
run_command() {
local status=0
local cmd="$*"
c_echo B "$(date -u '+%Y-%m-%d %H:%M:%S') " W "\$ " G "${cmd}"
[ "$(echo -n "$@")" = "" ] && return 1 # return 1 if there is no command available
"$@"
status=$?
unset IFS
return $status
}
retry() {
local retries=$1
shift
local count=0
until run_command "$@"; do
exit=$?
wait=$((2 ** count))
count=$((count + 1))
if [ $count -lt $retries ]; then
info "Retry $count/$retries. Exit code=$exit, Retrying in $wait seconds..."
sleep $wait
else
fatal "Retry $count/$retries. Exit code=$exit, no more retries left."
return 1
fi
done
return 0
}
#==================================================================================
# Section: Build
#==================================================================================
build_manylinux2014_desc() { echo 'Build manylinux2014 image
Arguments:
$1 - cuda version (e.g., 110, 111)
'
}
build_manylinux2014() {
local cuda_version="${1:-110}"
run_command docker build -f ${TOP}/Dockerfile-cuda${cuda_version} -t gigony/manylinux2014-x64:cuda${cuda_version} ${TOP}
read -n 1 -r -p "$(c_str R "Do you want to update dockcross-manylinux2014-x64 with " G "cuda${cuda_version}" R " (y/n)?")"
echo
if [[ $REPLY =~ ^[Yy]$ ]]; then
sed -i -e "s/manylinux2014-x64:cuda.../manylinux2014-x64:cuda${cuda_version}/g" ${TOP}/dockcross-manylinux2014-x64
c_echo W "Done"
fi
}
build_local_libcucim_() {
local source_folder=${1:-${TOP}}
local build_type=${2:-debug}
local build_type_str=${3:-Debug}
local prefix=${4:-}
local build_folder=${source_folder}/build-${build_type}
local CMAKE_CMD=${CMAKE_CMD:-cmake}
pushd ${source_folder} > /dev/null
# Copy cufile SDK from host system to temp/cuda
copy_gds_files_ $source_folder
${CMAKE_CMD} -S ${source_folder} -B ${build_folder} -G "Unix Makefiles" \
-DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=TRUE \
-DCMAKE_PREFIX_PATH=${prefix} \
-DCMAKE_BUILD_TYPE=${build_type_str} \
-DCMAKE_INSTALL_PREFIX=${source_folder}/install
${CMAKE_CMD} --build ${build_folder} --config ${build_type_str} --target cucim -- -j $(nproc)
${CMAKE_CMD} --build ${build_folder} --config ${build_type_str} --target install -- -j $(nproc)
popd
}
build_local_cuslide_() {
local source_folder=${1:-${TOP}/cpp/plugins/cucim.kit.cuslide}
local build_type=${2:-debug}
local build_type_str=${3:-Debug}
local prefix=${4:-}
local build_folder=${source_folder}/build-${build_type}
local CMAKE_CMD=${CMAKE_CMD:-cmake}
pushd ${source_folder} > /dev/null
${CMAKE_CMD} -S ${source_folder} -B ${build_folder} -G "Unix Makefiles" \
-DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=TRUE \
-DCMAKE_BUILD_TYPE=${build_type_str} \
-DCMAKE_PREFIX_PATH=${prefix} \
-DCMAKE_INSTALL_PREFIX=${source_folder}/install
${CMAKE_CMD} --build ${build_folder} --config ${build_type_str} --target cucim.kit.cuslide -- -j $(nproc)
${CMAKE_CMD} --build ${build_folder} --config ${build_type_str} --target install -- -j $(nproc)
popd
}
build_local_cucim_() {
local source_folder=${1:-${TOP}/python}
local build_type=${2:-debug}
local build_type_str=${3:-Debug}
local prefix=${4:-}
local build_folder=${source_folder}/build-${build_type}
local CMAKE_CMD=${CMAKE_CMD:-cmake}
pushd ${source_folder} > /dev/null
local python_library=$(python3 -c "import distutils.sysconfig as sysconfig, os; print(os.path.join(sysconfig.get_config_var('LIBDIR'), sysconfig.get_config_var('LDLIBRARY')))")
local python_include_dir=$(python3 -c "from distutils.sysconfig import get_python_inc; print(get_python_inc())")
${CMAKE_CMD} -S ${source_folder} -B ${build_folder} -G "Unix Makefiles" \
-DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=TRUE \
-DCMAKE_BUILD_TYPE=${build_type_str} \
-DCMAKE_PREFIX_PATH=${prefix} \
-DCMAKE_INSTALL_PREFIX=${source_folder}/install \
-DPYTHON_EXECUTABLE=$(which python3) \
-DPYTHON_LIBRARY=${python_library} \
-DPYTHON_INCLUDE_DIR=${python_include_dir}
${CMAKE_CMD} --build ${build_folder} --config ${build_type_str} --target cucim -- -j $(nproc)
${CMAKE_CMD} --build ${build_folder} --config ${build_type_str} --target install -- -j $(nproc)
popd
}
build_local_desc() { echo 'Build locally
Compile binaries locally
Arguments:
$1 - subcommand [all|clean_cache|clean|libcucim|cuslide|cucim] (default: all)
$2 - build type [debug|release|rel-debug] (default: debug)
'
}
build_local() {
local subcommand="${1:-all}"
local build_type="${2:-debug}"
local build_type_str="Debug"
local prefix=${3:-}
local major_version="$(cat ${TOP}/VERSION | cut -d. -f1)" # major version number
[ "$build_type" = "debug" ] && build_type_str="Debug"
[ "$build_type" = "release" ] && build_type_str="Release"
[ "$build_type" = "rel-debug" ] && build_type_str="RelWithDebInfo"
local old_opt="$(shopt -op errexit);$(shopt -op nounset)" # save old shopts
set -eu
if [ "$subcommand" = "clean_cache" ]; then
rm -f ${TOP}/build-*/CMakeCache.txt
rm -f ${TOP}/cpp/plugins/cucim.kit.cuslide/build-*/CMakeCache.txt
rm -f ${TOP}/python/build-*/CMakeCache.txt
fi
if [ "$subcommand" = "clean" ]; then
rm -rf ${TOP}/build-*
rm -rf ${TOP}/install
rm -rf ${TOP}/cpp/plugins/cucim.kit.cuslide/build-*/
rm -rf ${TOP}/cpp/plugins/cucim.kit.cuslide/install
rm -rf ${TOP}/python/build-*
rm -rf ${TOP}/python/install
fi
if [ "$subcommand" = "all" ] || [ "$subcommand" = "libcucim" ]; then
build_local_libcucim_ ${TOP} ${build_type} ${build_type_str} ${prefix}
fi
if [ "$subcommand" = "all" ] || [ "$subcommand" = "cuslide" ]; then
build_local_cuslide_ ${TOP}/cpp/plugins/cucim.kit.cuslide ${build_type} ${build_type_str} ${prefix}
fi
if [ "$subcommand" = "all" ] || [ "$subcommand" = "cucim" ]; then
build_local_cucim_ ${TOP}/python ${build_type} ${build_type_str} ${prefix}
fi
# Remove existing library files at python/cucim/src/cucim/clara
rm -f ${TOP}/python/cucim/src/cucim/clara/*.so*
if [ "$subcommand" = "all" ] || [ "$subcommand" = "cucim" ]; then
# We don't need to copy binary if executed by conda-build
if [ "${CONDA_BUILD:-}" != "1" ]; then
# Copy .so files from libcucim & cuslide's build folders to cuCIM's Python source folder
# Since wheel file doesn't support symbolic link (https://github.com/pypa/wheel/issues/203),
# we don't need to copy symbolic links. Instead copy only libcucim.so.${major_version} (without symbolic link)
cp ${TOP}/build-$build_type/lib*/libcucim.so.${major_version} ${TOP}/python/cucim/src/cucim/clara/
cp -P ${TOP}/cpp/plugins/cucim.kit.cuslide/build-$build_type/lib*/cucim* ${TOP}/python/cucim/src/cucim/clara/
# Copy .so files from pybind's build folder to cuCIM's Python source folder
cp ${TOP}/python/build-$build_type/lib/cucim/_cucim.*.so ${TOP}/python/cucim/src/cucim/clara/
fi
fi
eval "${old_opt}" # restore old shopts
}
copy_gds_files_() {
local root_folder=${1:-${TOP}}
local cufile_search="${root_folder}/temp/cuda/include:${root_folder}/temp/cuda/lib64" #"/usr/local/cuda/include:/usr/local/cuda/lib64 ${PREFIX:-}/include:${PREFIX:-}/lib ${CONDA_PREFIX:-}/include:${CONDA_PREFIX:-}/lib ${root_folder}/temp/cuda/include:${root_folder}/temp/cuda/lib64"
local gds_version=1.0.0
local candidate
local cufile_include
local cufile_lib
for candidate in ${cufile_search}; do
cufile_include="$(echo $candidate | cut -d: -f1)"
cufile_lib="$(echo $candidate | cut -d: -f2)"
if [ -f ${cufile_include}/cufile.h ] && [ -f ${cufile_lib}/libcufile.so ]; then
c_echo W "GDS client library is available at '${cufile_include}/cufile.h' and '${cufile_lib}/libcufile.so'"
break
fi
cufile_include=""
cufile_lib=""
done
if [ ! -f ${cufile_include}/cufile.h ]; then
c_echo_err Y "GDS client library is not available! Downloading the redistributable package to get cufile.h and libraries."
run_command rm -rf ${root_folder}/temp/cuda
run_command mkdir -p ${root_folder}/temp/cuda/include ${root_folder}/temp/cuda/lib64
local temp_tgz_dir=$(mktemp -d)
pushd ${temp_tgz_dir}
run_command wget https://developer.download.nvidia.com/gds/redist/rel-${gds_version}/gds-redistrib-${gds_version}.tgz
run_command tar xzvf gds-redistrib-${gds_version}.tgz
run_command cp -P gds-redistrib-${gds_version}/targets/x86_64-linux/include/cufile.h ${root_folder}/temp/cuda/include/
run_command cp -P gds-redistrib-${gds_version}/targets/x86_64-linux/lib/* ${root_folder}/temp/cuda/lib64/
popd > /dev/null
run_command rm -r ${temp_tgz_dir}
else
run_command mkdir -p ${root_folder}/temp/cuda/include ${root_folder}/temp/cuda/lib64
if [ "${cufile_include}" != "${root_folder}/temp/cuda/include" ]; then
run_command cp -Pf ${cufile_include}/cufile.h ${root_folder}/temp/cuda/include/ || true
run_command cp -Pf ${cufile_lib}/libcufile* ${root_folder}/temp/cuda/lib64/ || true
fi
fi
}
build_python_package_desc() { echo 'Build Python package
Note: This command does not remove `dist` folder before building.
'
}
build_python_package() {
local ret=0
local old_opt="$(shopt -op errexit);$(shopt -op nounset)" # save old shopts
set -eu
# Copy cufile SDK from host system to temp/cuda
copy_gds_files_
run_command ${TOP}/dockcross-manylinux2014-x64 ./run build_python_package_
ret=$?
eval "${old_opt}" # restore old shopts
return ${ret}
}
repair_wheel_() {
local wheel="$1"
local dest="${2:-./}"
local PLAT="${3:-manylinux2014_x86_64}"
if ! auditwheel show "$wheel"; then
echo "Skipping non-platform wheel ${wheel}"
else
$(head -1 $(which auditwheel) | cut -d'!' -f2) $TOP/scripts/auditwheel_repair.py repair --plat "${PLAT}" -w ${dest} "${wheel}"
fi
}
build_python_package_() {
local SRC_ROOT=${1:-${TOP}}
local BUILD_ROOT=${2:-${TOP}/temp}
local DEST_ROOT=${3:-${TOP}/dist}
local CUCIM_SDK_PATH=${4:-${BUILD_ROOT}/libcucim}
local old_opt="$(shopt -op errexit);$(shopt -op nounset)" # save old shopts
local major_version="$(cat ${TOP}/VERSION | cut -d. -f1)" # major version number
set -eu
# Clear CMakeCache.txt to use the latest options
run_command rm -f ${BUILD_ROOT}/libcucim/CMakeCache.txt
run_command rm -f ${BUILD_ROOT}/cuslide/CMakeCache.txt
run_command rm -f ${BUILD_ROOT}/cucim/CMakeCache.txt
# Create a folder for .whl file that repair_wheel_ is not applied.
TEMP_PYPKG_DIR=${BUILD_ROOT}/py_pkg # $(mktemp -d)
c_echo b "TEMP_PYPKG_DIR=${TEMP_PYPKG_DIR}"
mkdir -p $TEMP_PYPKG_DIR
rm -rf $TEMP_PYPKG_DIR/*
# trap 'rm -rf ${TEMP_PYPKG_DIR}' EXIT
local CMAKE_CMD=${CMAKE_CMD:-cmake}
local CMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE:-Release}
local NUM_THREADS=${NUM_THREADS:-$(nproc)}
local PLAT=manylinux2014_x86_64
local pybins
mkdir -p ${DEST_ROOT}
# Remove existing library files at build root
rm -rf ${BUILD_ROOT}/libcucim/lib/*
rm -rf ${BUILD_ROOT}/libcucim/install/lib*/lib*
rm -rf ${BUILD_ROOT}/cuslide/lib/*
rm -rf ${BUILD_ROOT}/cuslide/install/lib*/cucim*
rm -rf ${BUILD_ROOT}/cucim/lib/cucim/*.so*
rm -rf ${BUILD_ROOT}/cucim/install/lib/*.so*
# Build libcucim
${CMAKE_CMD} -S ${SRC_ROOT} -B ${BUILD_ROOT}/libcucim \
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} \
-DCMAKE_INSTALL_PREFIX=${CUCIM_SDK_PATH}/install
${CMAKE_CMD} --build ${BUILD_ROOT}/libcucim --config ${CMAKE_BUILD_TYPE} --target cucim -- -j ${NUM_THREADS}
${CMAKE_CMD} --build ${BUILD_ROOT}/libcucim --config ${CMAKE_BUILD_TYPE} --target install -- -j ${NUM_THREADS}
# Build cuslide plugin
${CMAKE_CMD} -S ${SRC_ROOT}/cpp/plugins/cucim.kit.cuslide -B ${BUILD_ROOT}/cuslide \
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} \
-DCMAKE_INSTALL_PREFIX=${BUILD_ROOT}/cuslide/install \
-DCUCIM_SDK_PATH=${CUCIM_SDK_PATH}
${CMAKE_CMD} --build ${BUILD_ROOT}/cuslide --config ${CMAKE_BUILD_TYPE} --target cucim.kit.cuslide -- -j ${NUM_THREADS}
${CMAKE_CMD} --build ${BUILD_ROOT}/cuslide --config ${CMAKE_BUILD_TYPE} --target install -- -j ${NUM_THREADS}
# Build Python bind
pybins="$(echo /opt/python/*/bin)"
if [ "${pybins}" = "/opt/python/*/bin" ]; then
pybins="$(dirname $(which python3))" # for building at host
fi
for PYBIN in ${pybins}; do
local python_library=$(${PYBIN}/python3 -c "import distutils.sysconfig as sysconfig; import os; print(os.path.join(sysconfig.get_config_var('LIBDIR'), sysconfig.get_config_var('LDLIBRARY')))")
local python_include_dir=$(${PYBIN}/python3 -c "from distutils.sysconfig import get_python_inc; print(get_python_inc())")
${CMAKE_CMD} -S ${SRC_ROOT}/python -B ${BUILD_ROOT}/cucim \
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} \
-DCMAKE_INSTALL_PREFIX=${BUILD_ROOT}/cucim/install \
-DCUCIM_SDK_PATH=${CUCIM_SDK_PATH} \
-DPYTHON_EXECUTABLE=${PYBIN}/python3 \
-DPYTHON_LIBRARY=${python_library} \
-DPYTHON_INCLUDE_DIR=${python_include_dir}
${CMAKE_CMD} --build ${BUILD_ROOT}/cucim --config ${CMAKE_BUILD_TYPE} --target cucim -- -j ${NUM_THREADS}
${CMAKE_CMD} --build ${BUILD_ROOT}/cucim --config ${CMAKE_BUILD_TYPE} --target install -- -j ${NUM_THREADS}
done
# Remove existing library files at python/cucim/src/cucim/clara
rm -f ${SRC_ROOT}/python/cucim/src/cucim/clara/*.so*
# Copy .so files to pybind's build folder
# (it uses -P to copy symbolic links as they are)
cp -P ${BUILD_ROOT}/libcucim/install/lib*/lib* ${BUILD_ROOT}/cucim/install/lib/
cp -P ${BUILD_ROOT}/cuslide/install/lib*/cucim* ${BUILD_ROOT}/cucim/install/lib/
# Copy .so files from pybind's build folder to cucim Python source folder
# Since wheel file doesn't support symbolic link (https://github.com/pypa/wheel/issues/203),
# we don't need to copy symbolic links. Instead copy only libcucim.so.${major_version} (without symbolic link)
#find ${BUILD_ROOT}/cucim/install/lib -maxdepth 1 -type f -exec cp {} ${SRC_ROOT}/python/cucim/src/cucim/clara/ \;
cp ${BUILD_ROOT}/cucim/install/lib/_cucim.*.so ${SRC_ROOT}/python/cucim/src/cucim/clara/
cp ${BUILD_ROOT}/cucim/install/lib/cucim.*.so ${SRC_ROOT}/python/cucim/src/cucim/clara/
cp ${BUILD_ROOT}/cucim/install/lib/libcucim.so.${major_version} ${SRC_ROOT}/python/cucim/src/cucim/clara/
find ${BUILD_ROOT}/cucim/install/lib -maxdepth 1 -type f -name "lib*.so" -exec cp {} ${SRC_ROOT}/python/cucim/src/cucim/clara/ \;
cd ${SRC_ROOT}/python/cucim
# Remove build folder
rm -rf ${SRC_ROOT}/python/cucim/build
# Compile wheels (one python binary is enough)
pybins="$(echo /opt/python/*/bin)"
[ ! -e /opt/python/cp36-cp36m/bin ] && pybins="$(dirname $(which python3))" # for building at host
pybins="$(echo /opt/python/*/bin)"
if [ "${pybins}" = "/opt/python/*/bin" ]; then # if multiple python binaries not found
pybins="$(dirname $(which python3))" # for building at host
else
pybins=/opt/python/cp36-cp36m/bin # use Python 3.6 for executing setup.py
fi
for PYBIN in ${pybins}; do # /opt/python/*/bin
run_command "${PYBIN}/python3" setup.py bdist_wheel -p $PLAT -d ${TEMP_PYPKG_DIR}
done
# Do not bundle external shared libraries for now.
# (CUDA-related libraries cannot be redistributed without EULA messages confirmed by user)
# Here, we just copy to dist folder.
# cp ${TEMP_PYPKG_DIR}/*.whl ${DEST_ROOT}/
# Bundle external shared libraries into the wheels
for whl in ${TEMP_PYPKG_DIR}/*.whl; do
repair_wheel_ "$whl" "${DEST_ROOT}/" "${PLAT}"
done
# run_command rm -rf ${TEMP_PYPKG_DIR}
# trap -- EXIT
# Copy cpp packages and examples
mkdir -p ${DEST_ROOT}/examples/cpp
cp -P -r ${BUILD_ROOT}/libcucim/install ${DEST_ROOT}/
cp -P -r ${BUILD_ROOT}/cuslide/install/lib/*.so ${DEST_ROOT}/install/lib/
cp -r ${SRC_ROOT}/examples/cpp/tiff_image ${DEST_ROOT}/examples/cpp/
cp ${BUILD_ROOT}/libcucim/CMakeLists.txt.examples.release ${DEST_ROOT}/examples/cpp/CMakeLists.txt
# # Install packages and test
# for PYBIN in /opt/python/*/bin/; do
# "${PYBIN}/pip" install python-manylinux-demo --no-index -f /io/wheelhouse
# (cd "$HOME"; "${PYBIN}/nosetests" pymanylinuxdemo)
# done
# python setup.py bdist_wheel -p manylinux2014-x86_64
eval "${old_opt}" # restore old shopts
}
build_package_desc() { echo 'Build package for release (& gen_docs)
'
}
build_package() {
local SRC_ROOT=${1:-${TOP}}
local BUILD_ROOT=${2:-${TOP}/temp}
local DEST_ROOT=${3:-${TOP}/dist}
local CUCIM_SDK_PATH=${4:-${BUILD_ROOT}/libcucim}
# Clean dist folder
mkdir -p ${DEST_ROOT}
[ -n "${DEST_ROOT}" ] && run_command sudo rm -rf ${DEST_ROOT}/*
build_python_package ${SRC_ROOT} ${BUILD_ROOT} ${DEST_ROOT} ${CUCIM_SDK_PATH}
gen_docs ${DEST_ROOT}/docs
copy_data_ ${SRC_ROOT} ${BUILD_ROOT} ${DEST_ROOT}
# Copy the built wheel file into ${TOP}/notebooks
run_command cp ${DEST_ROOT}/*.whl ${TOP}/notebooks/
}
copy_data_() {
c_echo W "Copy necessary files for packaging..."
local SRC_ROOT=${1:-${TOP}}
local BUILD_ROOT=${2:-${TOP}/temp}
local DEST_ROOT=${3:-${TOP}/dist}
# Create notebooks folder (add notebooks and scripts)
run_command mkdir -p ${DEST_ROOT}/notebooks/static_images
run_command cp $(git ls-files ${SRC_ROOT}/notebooks/*.ipynb) ${DEST_ROOT}/notebooks/
run_command cp ${SRC_ROOT}/notebooks/static_images/*.png ${DEST_ROOT}/notebooks/static_images/
# Create docker folder
run_command mkdir -p ${DEST_ROOT}/docker
run_command cp ${SRC_ROOT}/docker/*-jupyter{,-gds,.txt} ${DEST_ROOT}/docker/
run_command cp ${SRC_ROOT}/docker/*-claratrain{,.txt} ${DEST_ROOT}/docker/
run_command cp ${SRC_ROOT}/docker/*-cmake ${DEST_ROOT}/docker/
run_command cp ${SRC_ROOT}/docker/cufile.json ${DEST_ROOT}/docker/ # Copy cufile.json
# Copy main script
run_command cp ${SRC_ROOT}/scripts/run-dist ${DEST_ROOT}/run
# Create .dockerignore to speed up docker run
echo "notebooks" > ${DEST_ROOT}/.dockerignore
# Copy license files
run_command cp -r ${SRC_ROOT}/3rdparty ${SRC_ROOT}/LICENSE* ${DEST_ROOT}/
}
#==================================================================================
# Section: Test
#==================================================================================
test_desc() { echo 'Execute test cases
Arguments:
$1 - subcommand [all|python|c++] (default: all)
$2 - test_type [all|unit|integration|system|performance] (default: all)
$3 - test_component [all|clara|skimage] (default: all)
'
}
test() {
local subcommand="${1:-all}"
local test_type="${2:-all}"
shift;
if [ "$subcommand" = "all" ] || [ "$subcommand" = "python" ]; then
test_python "$@"
fi
}
install_python_test_deps_() {
if [ -n "${CONDA_PREFIX}" ]; then
# Override openslide-python due to the following issue:
# https://github.com/conda-forge/openslide-python-feedstock/issues/4
run_command conda install -c conda-forge -y \
--file ${TOP}/python/cucim/requirements-test.txt \
conda-forge/linux-64::openslide-python
else
if [ -n "${VIRTUAL_ENV}" ]; then
run_command pip3 install -r ${TOP}/python/cucim/requirements-test.txt
else
run_command pip3 install --user -r ${TOP}/python/cucim/requirements-test.txt
fi
fi
hash -r
}
test_python_desc() { echo 'Execute Python test cases
Arguments:
$1 - test_type [all|unit|integration|system|performance] (default: all)
$2 - test_component [all|clara|skimage] (default: all)
'
}
test_python() {
local test_type="${1:-all}"
local test_component="${2:-all}"
local result=0
local testsuite=""
local testsuite_unit_skimage="src"
local testsuite_unit_clara="tests/unit"
local testsuite_performance="tests/performance"
install_python_test_deps_
if [ "$test_type" = "all" ] || [ "$test_type" = "unit" ]; then
local testsuite="${testsuite_unit_skimage} ${testsuite_unit_clara}"
[ "$test_component" = "skimage" ] && testsuite="${testsuite_unit_skimage}"
[ "$test_component" = "clara" ] && testsuite="${testsuite_unit_clara}"
fi
if [ "$test_type" = "all" ] || [ "$test_type" = "performance" ]; then
testsuite="${testsuite} ${testsuite_performance}"
fi
pushd $TOP/python/cucim
run_command py.test --cache-clear -vv \
--cov=cucim \
--junitxml="$TOP/junit-cucim.xml" \
--cov-config=$TOP/python/cucim/.coveragerc \
--cov-report=xml:"$TOP/cucim-coverage.xml" \
--cov-report term \
${testsuite}
result=$?
popd
return $result
}
#==================================================================================
# Section: Example
#==================================================================================
download_testdata_desc() { echo 'Download test data from Docker Hub
'
}
download_testdata() {
c_echo W "Downloading test data..."
run_command mkdir -p ${TOP}/notebooks/input
if [ ! -e ${TOP}/notebooks/input/image.tif ]; then
run_command rm -rf ${TOP}/notebooks/input
id=$(docker create gigony/svs-testdata:little-big)
run_command docker cp $id:/input ${TOP}/notebooks
run_command docker rm -v $id
c_echo G "Test data is downloaded to ${TOP}/notebooks/input!"
else
c_echo G "Test data already exists at ${TOP}/notebooks/input!"
fi
}
launch_notebooks_desc() { echo 'Launch jupyter notebooks
Arguments:
-p <port> - port number
-h <host> - hostname to serve documentation on (default: 0.0.0.0)
-g <path to NVMe device> - launch GDS-enabled container
'
}
launch_notebooks() {
local OPTIND
local port=$(get_unused_ports 1 10000 10030)
local host='0.0.0.0'
local gds_postfix=''
local gds_nvme_path=''
while getopts 'p:h:g:' option;
do
case "${option}" in
p)
port="$OPTARG"
;;
h)
host="$OPTARG"
;;
g)
gds_postfix='-gds'
[ -z "$OPTARG" ] && c_echo_err R "Please specify NVMe path!" && return 1
gds_nvme_path=$(readlink -f "$OPTARG")
[ ! -d "$gds_nvme_path" ] && c_echo_err R "Folder $gds_nvme_path doesn't exist!" && return 1
# Copy cufile SDK from host system to temp/cuda
copy_gds_files_
;;
*)
return 1
esac
done
shift $((OPTIND-1))
download_testdata
run_command cp ${TOP}/dist/*.whl ${TOP}/notebooks
run_command nvidia-docker build -t cucim-jupyter${gds_postfix} -f ${TOP}/docker/Dockerfile-jupyter${gds_postfix}-dev ${TOP}
[ $? -ne 0 ] && return 1
c_echo W "Port " G "$port" W " would be used...(" B "http://$(hostname -I | cut -d' ' -f 1):${port}" W ")"
if [ -z "${gds_postfix}" ]; then
run_command nvidia-docker run --gpus all -it --rm \
-v ${TOP}/notebooks:/notebooks \
-p ${port}:${port} \
cucim-jupyter \
-c "echo -n 'Enter New Password: '; jupyter lab --ServerApp.password=\"\$(python3 -u -c \"from jupyter_server.auth import passwd;pw=input();print(passwd(pw));\" | egrep 'sha|argon')\" --ServerApp.root_dir=/notebooks --allow-root --port=${port} --ip=${host} --no-browser"
else
local MNT_PATH=/nvme
local GDS_IMAGE=cucim-jupyter${gds_postfix}
local BUILD_VER=`uname -r`
local NV_DRIVER=`nvidia-smi -q -i 0 | sed -n 's/Driver Version.*: *\(.*\) *$/\1/p'`
echo "using nvidia driver version $NV_DRIVER on kernel $BUILD_VER"
local ofed_version=$(ofed_info -s | grep MLNX)
if [ $? -eq 0 ]; then
local rdma_core=$(dpkg -s libibverbs-dev | grep "Source: rdma-core")
if [ $? -eq 0 ]; then
local CONFIG_MOFED_VERSION=$(echo $ofed_version | cut -d '-' -f 2)
echo "Found MOFED version $CONFIG_MOFED_VERSION"
fi
local MLNX_SRCS="--volume /usr/src/mlnx-ofed-kernel-${CONFIG_MOFED_VERSION}:/usr/src/mlnx-ofed-kernel-${CONFIG_MOFED_VERSION}:ro"
local MOFED_DEVS="--net=host --volume /sys/class/infiniband_verbs:/sys/class/infiniband_verbs/ "
fi
docker run \
--ipc host \
-it \
--rm \
--gpus all \
-v ${TOP}/notebooks:/notebooks \
-p ${port}:${port} \
--volume /run/udev:/run/udev:ro \
--volume /sys/kernel/config:/sys/kernel/config/ \
--volume /usr/src/nvidia-$NV_DRIVER:/usr/src/nvidia-$NV_DRIVER:ro ${MLNX_SRCS}\
--volume /dev:/dev:ro \
--privileged \
--env NV_DRIVER=${NV_DRIVER} \
--volume /lib/modules/$BUILD_VER/:/lib/modules/$BUILD_VER \
--volume "${MNT_PATH}:/notebooks/nvme:rw" \
${MOFED_DEVS} \
${GDS_IMAGE} \
-c "echo -n 'Enter New Password: '; jupyter lab --ServerApp.password=\"\$(python3 -u -c \"from jupyter_server.auth import passwd;pw=input();print(passwd(pw));\" | egrep 'sha|argon')\" --ServerApp.root_dir=/notebooks --allow-root --port=${port} --ip=${host} --no-browser"
fi
}
#==================================================================================
# Section: Documentation
#==================================================================================
install_tox_() {
if ! command -v tox > /dev/null; then
c_echo G "tox" W " doesn't exists. Installing " G "tox" W "..."
if [ -n "${CONDA_PREFIX}" ]; then
run_command pip3 install tox
else
if [ -n "${VIRTUAL_ENV}" ]; then
run_command pip3 install tox
else
run_command pip3 install --user tox
fi
fi
hash -r
fi
}
gen_docs_desc() { echo 'Generate document
Generated docs would be avaialable at ${TOP}/dist/docs.
Returns:
None
Exit code:
exit code returned from generating document
'
}
gen_docs() {
local OUTPUT_FOLDER=${1:-${TOP}/dist/docs}
local ret=0
pushd ${TOP}/python/cucim > /dev/null
# Install prerequisites
install_tox_
# Remove existing files in dist/docs
run_command rm -rf ${OUTPUT_FOLDER}/*
# Copy notebook files to python/cucim/dist/docs/notebooks
run_command mkdir -p ${TOP}/python/cucim/docs/notebooks
run_command rm -rf ${TOP}/python/cucim/docs/notebooks/*
run_command mkdir -p ${TOP}/python/cucim/docs/notebooks/static_images
run_command cp -r $(git ls-files ${TOP}/notebooks/*.ipynb) ${TOP}/python/cucim/docs/notebooks/
run_command cp -r ${TOP}/notebooks/static_images/*.png ${TOP}/python/cucim/docs/notebooks/static_images/
tox -e docs -- ${OUTPUT_FOLDER}
ret=$?
# Remove jupyter_execute folder explicitly until the issue is solved
# https://github.com/executablebooks/MyST-NB/issues/129
rm -rf $(dirname ${OUTPUT_FOLDER})/jupyter_execute
popd > /dev/null
return $ret
}
gen_docs_dev_desc() { echo 'Generate document
Launch dev-server for sphinx.
Generated docs would be avaialable at ${TOP}/python/cucim/dist/docs.
Arguments:
-p <port> - port number
-h <host> - hostname to serve documentation on (default: 0.0.0.0)
Returns:
None
Exit code:
exit code returned from generating document
'
}
gen_docs_dev() {
local OPTIND
local port=9999
local host=0.0.0.0
while getopts 'p:h:' option;
do
case "${option}" in
p)
port="$OPTARG"
;;
h)
host="$OPTARG"
;;
*)
echo_err R "Invalid option!"
return 1
esac
done
pushd ${TOP}/python/cucim > /dev/null
# Install prerequisites
install_tox_
# Remove existing files in python/cucim/dist/docs
run_command rm -rf ${TOP}/python/cucim/dist/docs/*
# Copy notebook files to python/cucim/dist/docs/notebooks
run_command mkdir -p ${TOP}/python/cucim/docs/notebooks/static_images
run_command rm -rf ${TOP}/python/cucim/docs/notebooks/*
run_command cp -r $(git ls-files ${TOP}/notebooks/*.ipynb) ${TOP}/python/cucim/docs/notebooks/
run_command cp -r ${TOP}/notebooks/static_images/*.png ${TOP}/python/cucim/docs/notebooks/static_images/
run_command tox -e docs-dev -- --port ${port} --host ${host} docs dist/docs
popd > /dev/null
}
publish_docs_desc() { echo 'Publish generated documents to the server
Publish generated documents to $GITLAB_PUBLISH_PROJECT_URL
The web page is available at the followings:
- $GITLAB_PUBLISH_PROJECT_URL
Arguments:
$1 - If specified, force creating a tag with the specified tag name.
Use "latest" tag to make public documents up to date.
Returns:
None
Exit code:
exit code returned from publishing documents
'
}
publish_docs() {