[REVIEW] FEA SciPy sparse matrix input support for WCC, SCC, SSSP, and BFS

CHANGELOG.md

@@ -8,6 +8,7 @@
 - PR #1265 Implement Hungarian Algorithm
 - PR #1274 Add generic from_edgelist() and from_adjlist() APIs
 - PR #1279 Add self loop check variable in graph
+- PR #1277 SciPy sparse matrix input support for WCC, SCC, SSSP, and BFS
 
 ## Improvements
 - PR #1227 Pin cmake policies to cmake 3.17 version

build.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (c) 2019, NVIDIA CORPORATION.
+# Copyright (c) 2019-2020, NVIDIA CORPORATION.
 
 # cugraph build script
 
@@ -17,6 +17,7 @@ ARGS=$*
 # NOTE: ensure all dir changes are relative to the location of this
 # script, and that this script resides in the repo dir!
 REPODIR=$(cd $(dirname $0); pwd)
+LIBCUGRAPH_BUILD_DIR=${LIBCUGRAPH_BUILD_DIR:=${REPODIR}/cpp/build}
 
 VALIDARGS="clean libcugraph cugraph docs -v -g -n --allgpuarch --show_depr_warn -h --help"
 HELP="$0 [<target> ...] [<flag> ...]
@@ -33,19 +34,21 @@ HELP="$0 [<target> ...] [<flag> ...]
  --show_depr_warn - show cmake deprecation warnings
  -h - print this text
 
- default action (no args) is to build and install 'libcugraph' then 'cugraph' targets and then docs
+ default action (no args) is to build and install 'libcugraph' then 'cugraph' then 'docs' targets
+
+ libcugraph build dir is: ${LIBCUGRAPH_BUILD_DIR}
+
+ Set env var LIBCUGRAPH_BUILD_DIR to override libcugraph build dir.
 "
-LIBCUGRAPH_BUILD_DIR=${LIBCUGRAPH_BUILD_DIR:=${REPODIR}/cpp/build}
 CUGRAPH_BUILD_DIR=${REPODIR}/python/build
 BUILD_DIRS="${LIBCUGRAPH_BUILD_DIR} ${CUGRAPH_BUILD_DIR}"
 
 # Set defaults for vars modified by flags to this script
-ARG_COUNT=${NUMARGS}
 VERBOSE=""
 BUILD_TYPE=Release
 INSTALL_TARGET=install
 BUILD_DISABLE_DEPRECATION_WARNING=ON
-BUILD_ALL_GPU_ARCH=0
+GPU_ARCH=""
 
 # Set defaults for vars that may not have been defined externally
 # FIXME: if PREFIX is not set, check CONDA_PREFIX, but there is no fallback
@@ -58,6 +61,10 @@ function hasArg {
  (( ${NUMARGS} != 0 )) && (echo " ${ARGS} " | grep -q " $1 ")
 }
 
+function buildAll {
+ (( ${NUMARGS} == 0 )) || !(echo " ${ARGS} " | grep -q " [^-]\+ ")
+}
+
 if hasArg -h || hasArg --help; then
  echo "${HELP}"
  exit 0
@@ -76,30 +83,31 @@ fi
 # Process flags
 if hasArg -v; then
  VERBOSE=1
- ARG_COUNT=$((ARG_COUNT -1))
 fi
 if hasArg -g; then
  BUILD_TYPE=Debug
- ARG_COUNT=$((ARG_COUNT -1))
 fi
 if hasArg -n; then
  INSTALL_TARGET=""
- ARG_COUNT=$((ARG_COUNT -1))
 fi
 if hasArg --allgpuarch; then
- BUILD_ALL_GPU_ARCH=1
+ GPU_ARCH="-DGPU_ARCHS=ALL"
 fi
 if hasArg --show_depr_warn; then
  BUILD_DISABLE_DEPRECATION_WARNING=OFF
- ARG_COUNT=$((ARG_COUNT -1))
 fi
 
 # If clean given, run it prior to any other steps
 if hasArg clean; then
- # If the dirs to clean are mounted dirs in a container, the
- # contents should be removed but the mounted dirs will remain.
- # The find removes all contents but leaves the dirs, the rmdir
- # attempts to remove the dirs but can fail safely.
+ # FIXME: ideally the "setup.py clean" command below would also be run to
+ # remove all the "inplace" python build artifacts, but currently, running
+ # any setup.py command has side effects (eg. cloning repos).
+ #(cd ${REPODIR}/python && python setup.py clean)
+
+ # If the dirs to clean are mounted dirs in a container, the contents should
+ # be removed but the mounted dirs will remain. The find removes all
+ # contents but leaves the dirs, the rmdir attempts to remove the dirs but
+ # can fail safely.
  for bd in ${BUILD_DIRS}; do
  if [ -d ${bd} ]; then
  find ${bd} -mindepth 1 -delete
@@ -110,53 +118,44 @@ fi
 
 ################################################################################
 # Configure, build, and install libcugraph
-if (( ${ARG_COUNT} == 0 )) || hasArg libcugraph; then
- if (( ${BUILD_ALL_GPU_ARCH} == 0 )); then
- GPU_ARCH=""
+if buildAll || hasArg libcugraph; then
+ if [[ ${GPU_ARCH} == "" ]]; then
  echo "Building for the architecture of the GPU in the system..."
  else
- GPU_ARCH="-DGPU_ARCHS=ALL"
  echo "Building for *ALL* supported GPU architectures..."
  fi
-
  mkdir -p ${LIBCUGRAPH_BUILD_DIR}
  cd ${LIBCUGRAPH_BUILD_DIR}
  cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
-  ${GPU_ARCH} \
-  -DDISABLE_DEPRECATION_WARNING=${BUILD_DISABLE_DEPRECATION_WARNING} \
-  -DCMAKE_BUILD_TYPE=${BUILD_TYPE} ..
+ ${GPU_ARCH} \
+  -DDISABLE_DEPRECATION_WARNING=${BUILD_DISABLE_DEPRECATION_WARNING} \
+ -DCMAKE_BUILD_TYPE=${BUILD_TYPE} ${REPODIR}/cpp
  make -j${PARALLEL_LEVEL} VERBOSE=${VERBOSE} ${INSTALL_TARGET}
 fi
 
 # Build and install the cugraph Python package
-if (( ${ARG_COUNT} == 0 )) || hasArg cugraph; then
-
+if buildAll || hasArg cugraph; then
  cd ${REPODIR}/python
+ # setup.py references an env var CUGRAPH_BUILD_PATH to find the libcugraph
+ # build. If not set by the user, set it to LIBCUGRAPH_BUILD_DIR
+ CUGRAPH_BUILD_PATH=${CUGRAPH_BUILD_PATH:=${LIBCUGRAPH_BUILD_DIR}}
+ env CUGRAPH_BUILD_PATH=${CUGRAPH_BUILD_PATH} python setup.py build_ext --inplace --library-dir=${LIBCUGRAPH_BUILD_DIR}
  if [[ ${INSTALL_TARGET} != "" ]]; then
- python setup.py build_ext --inplace --library-dir=${LIBCUGRAPH_BUILD_DIR}
- python setup.py install
- else
- python setup.py build_ext --inplace --library-dir=${LIBCUGRAPH_BUILD_DIR}
+ env CUGRAPH_BUILD_PATH=${CUGRAPH_BUILD_PATH} python setup.py install
  fi
 fi
 
-################################################################################
 # Build the docs
-if (( ${ARG_COUNT} == 0 )) || hasArg docs; then
-
+if buildAll || hasArg docs; then
  if [ ! -d ${LIBCUGRAPH_BUILD_DIR} ]; then
  mkdir -p ${LIBCUGRAPH_BUILD_DIR}
  cd ${LIBCUGRAPH_BUILD_DIR}
  cmake -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
  -DDISABLE_DEPRECATION_WARNING=${BUILD_DISABLE_DEPRECATION_WARNING} \
- -DCMAKE_BUILD_TYPE=${BUILD_TYPE} ..
+ -DCMAKE_BUILD_TYPE=${BUILD_TYPE} ${REPODIR}/cpp
  fi
-
  cd ${LIBCUGRAPH_BUILD_DIR}
-
  make -j${PARALLEL_LEVEL} VERBOSE=${VERBOSE} docs_cugraph
-
  cd ${REPODIR}/docs
  make html
-
 fi

python/cugraph/__init__.py

@@ -55,6 +55,7 @@
 from cugraph.cores import core_number, k_core
 
 from cugraph.components import (
+ connected_components,
  weakly_connected_components,
  strongly_connected_components,
 )

python/cugraph/components/__init__.py

@@ -11,5 +11,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from cugraph.components.connectivity import connected_components
 from cugraph.components.connectivity import weakly_connected_components
 from cugraph.components.connectivity import strongly_connected_components