Merge branch 'main' into vchang/ucx_ett_rmm_settings

Author: mocsharp

applications/adv_networking_bench/Dockerfile

@@ -14,8 +14,10 @@
 # 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.
+
+# Note: duplicate of ../../operators/advanced_network to facilitate
+# the use of ./dev_container build_and_run adv_networking_bench
 ARG BASE_IMAGE
-ARG GPU_TYPE
 
 FROM ${BASE_IMAGE} AS base
 ARG UBUNTU_VERSION=22.04
@@ -24,30 +26,27 @@ ARG CACHEBUST=1
 ARG TARGETARCH
 RUN echo "Using architecture ${TARGETARCH}"
 
-
 RUN apt update && apt install -y python3-pyelftools ninja-build meson libyaml-cpp-dev
 RUN pip3 install scipy loguru attrs
 WORKDIR /opt
 
 ARG DEBIAN_FRONTEND=noninteractive
-ARG DOCA_REPO_LINK=https://linux.mellanox.com/public/repo/doca/2.8.0/ubuntu22.04/x86_64
 
 RUN if [ "${TARGETARCH}" = "amd64" ]; then \
         DOCA_REPO_LINK=https://linux.mellanox.com/public/repo/doca/2.8.0/ubuntu22.04/x86_64; \
     elif [ "$TARGETARCH" = "arm64" ]; then \
-        DOCA_REPO_LINK=https://linux.mellanox.com/public/repo/doca/2.8.0/ubuntu22.04/arm64; \
+        DOCA_REPO_LINK=https://linux.mellanox.com/public/repo/doca/2.8.0/ubuntu22.04/arm64-sbsa; \
     else \
         echo "Unknown architecture: $TARGETARCH"; \
         exit 1; \
     fi \
     && echo "Using DOCA_REPO_LINK=${DOCA_REPO_LINK}" \
-    && apt install -y --no-install-recommends wget software-properties-common gpg-agent \
-    && wget -qO - ${DOCA_REPO_LINK}/GPG-KEY-Mellanox.pub | apt-key add - \
-    && add-apt-repository "deb [trusted=yes] ${DOCA_REPO_LINK} ./" \
+    && LOCAL_GPG_KEY_PATH="/usr/share/keyrings/mellanox-archive-keyring.gpg" \
+    && curl -fsSL ${DOCA_REPO_LINK}/GPG-KEY-Mellanox.pub | gpg --dearmor | tee ${LOCAL_GPG_KEY_PATH} \
+    && echo "deb [signed-by=${LOCAL_GPG_KEY_PATH}] ${DOCA_REPO_LINK} ./" | tee /etc/apt/sources.list.d/mellanox.list \
     && apt update -y \
     && apt install -y --no-install-recommends doca-sdk-aes-gcm doca-sdk-apsh doca-sdk-argp doca-sdk-comch doca-sdk-comm-channel doca-sdk-common doca-sdk-compress doca-sdk-devemu doca-sdk-dma doca-sdk-dpa doca-sdk-dpdk-bridge doca-sdk-erasure-coding doca-sdk-eth doca-sdk-flow doca-sdk-pcc doca-sdk-rdma doca-sdk-sha doca-sdk-telemetry-exporter doca-sdk-urom doca-apsh-config doca-bench doca-caps doca-comm-channel-admin doca-pcc-counters doca-sha-offload-engine doca-socket-relay doca-all doca-sdk-gpunetio libdoca-sdk-gpunetio-dev rdma-core flexio libyara8
 
-
 # ==============================
 # DOCA Target (inherits from base)
 # This stage is only built when --target doca is specified. It contains any DOCA-specific configurations.

applications/sam2/Dockerfile

@@ -16,30 +16,32 @@
 # limitations under the License.
 
 
-FROM nvcr.io/nvidia/pytorch:24.06-py3 as pytorch
+FROM nvcr.io/nvidia/pytorch:24.06-py3 AS pytorch
 
 
 # Install dependencies
 RUN apt-get update && apt-get install -y \
-    git \
+    git \   
     git-lfs \ 
     x11-apps \
     && rm -rf /var/lib/apt/lists/*
 
 # Set up Git LFS
 RUN git lfs install
 
+
 # Clone sam2
 WORKDIR /workspace
 ARG COMPUTE_CAPACITY
-RUN git clone https://github.com/facebookresearch/segment-anything-2.git \
-    && cd segment-anything-2 \
+RUN git clone https://github.com/facebookresearch/sam2.git \
+    && cd sam2 \
     && python3 -m pip install --no-cache-dir -e . \
     && python3 -m pip install --no-cache-dir -e ".[demo]" \
     && cd checkpoints \
     && ./download_ckpts.sh
 WORKDIR /workspace
 
+
 # Check the architecture and download the CUDA keyring
 RUN if [ $(uname -m) = "aarch64" ]; then ARCH=arm64 \
     wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/sbsa/cuda-keyring_1.1-1_all.deb \
@@ -48,8 +50,8 @@ RUN if [ $(uname -m) = "aarch64" ]; then ARCH=arm64 \
     ; else echo "Unsupported architecture"; fi
 RUN dpkg -i cuda-keyring_1.1-1_all.deb \
     && apt-get update \
-    && apt-get -y install holoscan \
-    && export PYTHONPATH="/opt/nvidia/holoscan/python/lib"
+    && apt-get -y install holoscan
+
 
 # Setup Docker & NVIDIA Container Toolkit's apt repositories to enable DooD
 # for packaging & running applications with the CLI

applications/sam2/README.md

@@ -46,18 +46,18 @@ Determine your desired video device and edit the source device in [segment_one_t
 This application uses a custom Dockerfile based on a pytorch container.
 Build and run the application using
 ```sh
- ./dev_container build_and_run sam2 --docker_file applications/sam2/Dockerfile --img holohub:sam2
+ ./dev_container build_and_run sam2 --docker_file applications/sam2/Dockerfile --img holohub:sam2.1
 ``` 
 Or first build the container, then launch it and run.
 
 ```sh
- ./dev_container build --docker_file applications/sam2/Dockerfile --img holohub:sam2
+ ./dev_container build --docker_file applications/sam2/Dockerfile --img holohub:sam2.1
 ```
 ```sh
-./dev_container launch --img holohub:sam
+./dev_container launch --img holohub:sam2.1
 ```
 ```sh
-python holohub/applications/sam2/segment_one_thing.py
+./run launch sam2
 ```
 
 ### x86 only

applications/sam2/metadata.json

@@ -35,7 +35,7 @@
 		},
 
 		"run": {
-			"command": "python  '<holohub_app_source>/segment_one_thing.py'",
+			"command": "<holohub_app_source>/start.sh",
 			"workdir": "holohub_bin"
 		}
 	}

applications/sam2/segment_one_thing.yaml

@@ -30,23 +30,23 @@ preprocessor:
 point_publisher:
   point_mover:
     - "width" : 1024
-      "height": 1024
+      "height": 1024 
       "radius": 100
       "center_x": 512
       "center_y": 512
       "frequency": 0.2
 
 sam2:
-  checkpoint_path: "/workspace/segment-anything-2/checkpoints/sam2_hiera_large.pt"
-  model_cfg: "sam2_hiera_l.yaml"
+  checkpoint_path: "/workspace/sam2/checkpoints/sam2.1_hiera_large.pt"
+  model_cfg: "configs/sam2.1/sam2.1_hiera_l.yaml"
 
 # sam2:
-#   checkpoint_path: "/workspace/segment-anything-2/checkpoints/sam2_hiera_small.pt"
-#   model_cfg: "sam2_hiera_s.yaml"
+#   checkpoint_path: "/workspace/sam2/checkpoints/sam2.1_hiera_small.pt"
+#   model_cfg: "configs/sam2.1/sam2.1_hiera_s.yaml"
 
 # sam2:
-#   checkpoint_path: "/workspace/segment-anything-2/checkpoints/sam2_hiera_tiny.pt"
-#   model_cfg: "sam2_hiera_t.yaml"
+#   checkpoint_path: "/workspace/sam2/checkpoints/sam2.1_hiera_tiny.pt"
+#   model_cfg: "configs/sam2.1/sam2.1_hiera_t.yaml"
 
 postprocessor:
   slice_dim: 0
@@ -72,5 +72,3 @@ holoviz:
   #   # [0.3, 0.3, 0.9, 0.75], #Blue RGB for SELLA with alpha=0.5
   #   # [0.9, 0.9, 0.3, 0.75], #Yellow RGB for CLIVAL RECESS alpha=0.5 #https://rgbcolorpicker.com/0-1
   #   ]
-
-

applications/sam2/start.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# change the pythonpath
+export PYTHONPATH="${PYTHONPATH}:/workspace/sam2"
+export PYTHONPATH="${PYTHONPATH}:/opt/nvidia/holoscan/python/lib"
+
+# launch the application
+python /workspace/holohub/applications/sam2/segment_one_thing.py

dev_container

@@ -874,6 +874,7 @@ build_and_run_desc() { c_echo 'Build and run a requested application in a Docker
         --run_args : Run the app with additional args
         --verbose : Print extra output to console
         --dryrun : View build and run commands without doing anything
+        --parallel_jobs: Set the # of parallel build jobs, e.g. $(($(nproc)-1))
     '
 }
 
@@ -892,6 +893,7 @@ build_and_run() {
     local run_app=1
     local install=""
     local configure_args=""
+    local parallel_jobs=""
 
     # Parse CLI arguments next
     while [[ $# -gt 0 ]]; do
@@ -1014,6 +1016,16 @@ build_and_run() {
                 exit 1
             fi
             ;;
+        --parallel_jobs)
+            if [[ -n "$2" ]]; then
+                parallel_jobs="--parallel '$2'"
+                shift 2
+            else
+                echo "Error: --parallel_jobs requires a value"
+                build_and_run_desc
+                exit 1
+            fi
+            ;;
         *)
             if [[ -z "$app_name" ]]; then
                 app_name="$1"
@@ -1057,7 +1069,7 @@ build_and_run() {
     run_command  ${SCRIPT_DIR}/dev_container build "${container_build_args[@]}"
     if [[ $build_app == 1 ]]; then
         c_echo "Building application..."
-        run_command ${SCRIPT_DIR}/dev_container launch $container_launch_args --docker_opts "$docker_opts" -- -c "./run build $app_name $install $extra_build_with $extra_build_args"
+        run_command ${SCRIPT_DIR}/dev_container launch $container_launch_args --docker_opts "$docker_opts" -- -c "./run build $app_name $install $parallel_jobs $extra_build_with $extra_build_args"
     fi
 
     if [[ $run_app == 1 ]]; then

gxf_extensions/emergent_source/CMakeLists.txt

@@ -28,6 +28,7 @@ target_link_libraries(gxf_emergent_source_lib
   CUDA::cuda_driver
   GXF::multimedia
   GXF::std
+  holoscan::core
   yaml-cpp
   EmergentCamera
 )

operators/advanced_network/Dockerfile

@@ -24,30 +24,27 @@ ARG CACHEBUST=1
 ARG TARGETARCH
 RUN echo "Using architecture ${TARGETARCH}"
 
-
 RUN apt update && apt install -y python3-pyelftools ninja-build meson libyaml-cpp-dev
 RUN pip3 install scipy loguru attrs
 WORKDIR /opt
 
 ARG DEBIAN_FRONTEND=noninteractive
-ARG DOCA_REPO_LINK=https://linux.mellanox.com/public/repo/doca/2.8.0/ubuntu22.04/x86_64
 
 RUN if [ "${TARGETARCH}" = "amd64" ]; then \
         DOCA_REPO_LINK=https://linux.mellanox.com/public/repo/doca/2.8.0/ubuntu22.04/x86_64; \
     elif [ "$TARGETARCH" = "arm64" ]; then \
-        DOCA_REPO_LINK=https://linux.mellanox.com/public/repo/doca/2.8.0/ubuntu22.04/arm64-ssba; \
+        DOCA_REPO_LINK=https://linux.mellanox.com/public/repo/doca/2.8.0/ubuntu22.04/arm64-sbsa; \
     else \
         echo "Unknown architecture: $TARGETARCH"; \
         exit 1; \
     fi \
     && echo "Using DOCA_REPO_LINK=${DOCA_REPO_LINK}" \
-    && apt install -y --no-install-recommends wget software-properties-common gpg-agent \
-    && wget -qO - ${DOCA_REPO_LINK}/GPG-KEY-Mellanox.pub | apt-key add - \
-    && add-apt-repository "deb [trusted=yes] ${DOCA_REPO_LINK} ./" \
+    && LOCAL_GPG_KEY_PATH="/usr/share/keyrings/mellanox-archive-keyring.gpg" \
+    && curl -fsSL ${DOCA_REPO_LINK}/GPG-KEY-Mellanox.pub | gpg --dearmor | tee ${LOCAL_GPG_KEY_PATH} \
+    && echo "deb [signed-by=${LOCAL_GPG_KEY_PATH}] ${DOCA_REPO_LINK} ./" | tee /etc/apt/sources.list.d/mellanox.list \
     && apt update -y \
     && apt install -y --no-install-recommends doca-sdk-aes-gcm doca-sdk-apsh doca-sdk-argp doca-sdk-comch doca-sdk-comm-channel doca-sdk-common doca-sdk-compress doca-sdk-devemu doca-sdk-dma doca-sdk-dpa doca-sdk-dpdk-bridge doca-sdk-erasure-coding doca-sdk-eth doca-sdk-flow doca-sdk-pcc doca-sdk-rdma doca-sdk-sha doca-sdk-telemetry-exporter doca-sdk-urom doca-apsh-config doca-bench doca-caps doca-comm-channel-admin doca-pcc-counters doca-sha-offload-engine doca-socket-relay doca-all doca-sdk-gpunetio libdoca-sdk-gpunetio-dev rdma-core flexio libyara8
 
-
 # ==============================
 # DOCA Target (inherits from base)
 # This stage is only built when --target doca is specified. It contains any DOCA-specific configurations.

run

@@ -557,6 +557,9 @@ build_desc() {
   echo "   --configure-args <extra_args>        : Additional configuration arguments"
   echo "                                          multiple arguments can be passed between quotes"
   echo "                                          or using several --configure-args in the command line"
+  echo "   --parallel <jobs>                    : Build in parallel using the given number of jobs."
+  echo "                                          Only needed to override the native build tool's default."
+  echo "                                          Example: --parallel $(($(nproc)-1))"
   echo ""
   echo "Prior to the first build use './run setup' to install the required dependencies"
   echo ""
@@ -619,6 +622,7 @@ build() {
   local build_path="${CMAKE_BUILD_PATH}"
   local benchmark=false
   local install=false
+  local parallel_jobs=""
 
   for i in "${!ARGS[@]}"; do
       arg="${ARGS[i]}"
@@ -650,6 +654,10 @@ build() {
       elif [ "$arg" = "--buildpath" ]; then
          build_path="${ARGS[i+1]}"
          skipnext=1
+      elif [ "$arg" = "--parallel" ]; then
+         parallel_jobs="${ARGS[i+1]}"
+         echo "Setting the number of parallel build jobs: ${ARGS[i+1]}"
+         skipnext=1
       elif [[ $arg = -* ]]; then
         print_error "Unknown option $arg"
         exit 1
@@ -692,7 +700,8 @@ build() {
   run_command cmake -S . -B ${build_path} ${cmake_extra_args} -DCMAKE_BUILD_TYPE=${build_type} ${holoscan_sdk} ${application}
   ret=$?
   check_exit_code $ret "Error building application."
-  run_command cmake --build ${build_path} -j
+  # Job concurrency determined by the underlying build tool unless a number is specified
+  run_command cmake --build ${build_path} -j ${parallel_jobs}
   ret=$?
   check_exit_code $ret "Error building application."