Fix Cosmos Installation

tools/env_setup/install_cosmos_transfer1.sh

@@ -21,15 +21,13 @@ set -e
 # Assuming this script is in tools/env_setup/
 PROJECT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && cd ../.. && pwd)"
 
-# Source utility functions
-source "$PROJECT_ROOT/tools/env_setup/bash_utils.sh"
+# Allow setting the python in PYTHON_EXECUTABLE
+PYTHON_EXECUTABLE=${PYTHON_EXECUTABLE:-python}
 
-check_project_root
-check_conda_env
+# Install cuDNN
+bash "$PROJECT_ROOT/tools/env_setup/install_cudnn.sh"
 
-conda install -c conda-forge ninja libgl ffmpeg gcc=12.4.0 gxx=12.4.0 -y
-
-COSMOS_TRANSFER_DIR="$PROJECT_ROOT/third_party/cosmos-transfer1"
+COSMOS_TRANSFER_DIR=${1:-$$PROJECT_ROOT/third_party/cosmos-transfer1}
 
 if [ -d "$COSMOS_TRANSFER_DIR" ]; then
     echo "Cosmos Transfer directory already exists at $COSMOS_TRANSFER_DIR. Skipping clone."
@@ -41,13 +39,11 @@ fi
 pushd "$COSMOS_TRANSFER_DIR"
 git checkout bf54a70a8c44d615620728c493ee26b4376ccfd6
 git submodule update --init --recursive
-pip install -r requirements.txt
-# Patch Transformer engine linking issues in conda environments.
-ln -sf $CONDA_PREFIX/lib/python3.10/site-packages/nvidia/*/include/* $CONDA_PREFIX/include/
-ln -sf $CONDA_PREFIX/lib/python3.10/site-packages/nvidia/*/include/* $CONDA_PREFIX/include/python3.10
-pip install transformer-engine[pytorch]==1.12.0
+$PYTHON_EXECUTABLE -m pip install -r requirements.txt
+MAX_JOBS=2 $PYTHON_EXECUTABLE -m pip install transformer-engine[pytorch]==1.12.0
+$PYTHON_EXECUTABLE -m pip install tensorstore==0.1.74
 
-CUDA_HOME=$CONDA_PREFIX PYTHONPATH=$(pwd) python scripts/test_environment.py
+$PYTHON_EXECUTABLE scripts/test_environment.py
 popd
 
 echo "Cosmos Transfer Dependencies Installation Finished"

tools/env_setup/install_cudnn.sh

@@ -0,0 +1,63 @@
+#!/bin/bash
+
+# SPDX-FileCopyrightText: Copyright (c) 2025 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+# SPDX-License-Identifier: Apache-2.0
+
+# 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.
+
+set -e
+
+# Check if CUDNN_PATH and CUDNN_INCLUDE_PATH are set. If so, skip the installation.
+if [ -d "$CUDNN_PATH" ] && [ -d "$CUDNN_INCLUDE_PATH" ]; then
+    echo "CUDNN_PATH and CUDNN_INCLUDE_PATH are set. Skipping CUDNN installation."
+    exit 0
+fi
+
+# Check if CUDA_HOME is set. If not, set it to /usr/local/cuda.
+if [ -z "$CUDA_HOME" ]; then
+    echo "CUDA_HOME is not set. Setting it to /usr/local/cuda."
+    export CUDA_HOME=/usr/local/cuda
+fi
+
+# Get the cuDNN version and see if it is 8.9.7. If it is, skip the installation.
+if [ -f "$CUDA_HOME/include/cudnn_version.h" ]; then
+    CUDNN_VERSION="$(grep -oP '#define CUDNN_MAJOR \K\d+' $CUDA_HOME/include/cudnn_version.h).$(grep -oP '#define CUDNN_MINOR \K\d+' $CUDA_HOME/include/cudnn_version.h).$(grep -oP '#define CUDNN_PATCHLEVEL \K\d+' $CUDA_HOME/include/cudnn_version.h)"
+    if [ "$CUDNN_VERSION" == "8.9.7" ]; then
+        echo "cuDNN version is 8.9.7. Skipping CUDNN installation."
+        exit 0
+    fi
+fi
+
+
+# Install CUDNN
+echo "Install cuDNN 8.9.7..."
+
+mkdir -p /tmp/cudnn
+
+wget https://developer.download.nvidia.com/compute/cudnn/redist/cudnn/linux-x86_64/cudnn-linux-x86_64-8.9.7.29_cuda12-archive.tar.xz \
+    -O /tmp/cudnn/cudnn-linux-x86_64-8.9.7.29_cuda12-archive.tar.xz
+tar -xvf /tmp/cudnn/cudnn-linux-x86_64-8.9.7.29_cuda12-archive.tar.xz -C /tmp/cudnn/
+
+if [ "$EUID" -ne 0 ]; then
+    sudo cp /tmp/cudnn/cudnn-linux-x86_64-8.9.7.29_cuda12-archive/lib/libcudnn* $CUDA_HOME/lib64/
+    sudo cp /tmp/cudnn/cudnn-linux-x86_64-8.9.7.29_cuda12-archive/include/cudnn*.h $CUDA_HOME/include/
+    sudo ldconfig $CUDA_HOME/lib64
+else
+    cp /tmp/cudnn/cudnn-linux-x86_64-8.9.7.29_cuda12-archive/lib/libcudnn* $CUDA_HOME/lib64/
+    cp /tmp/cudnn/cudnn-linux-x86_64-8.9.7.29_cuda12-archive/include/cudnn*.h $CUDA_HOME/include/
+    ldconfig $CUDA_HOME/lib64
+fi
+
+rm -rf /tmp/cudnn
+
+echo "cuDNN is installed to $CUDA_HOME/lib64 and headers are in $CUDA_HOME/include"

tools/env_setup/install_holoscan.sh

@@ -21,17 +21,16 @@ set -e
 # Assuming this script is in tools/env_setup/
 PROJECT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && cd ../.. && pwd)"
 
-# Assuming bash_utils.sh is in $PROJECT_ROOT/tools/env_setup/bash_utils.sh
-source "$PROJECT_ROOT/tools/env_setup/bash_utils.sh"
+# Allow setting the python in PYTHON_EXECUTABLE
+PYTHON_EXECUTABLE=${PYTHON_EXECUTABLE:-python}
 
-check_project_root
-check_conda_env
+HOLOSCAN_DIR=${1:-$PROJECT_ROOT/workflows/robotic_ultrasound/scripts/holoscan_apps/}
 
-conda install -c conda-forge gcc=13.3.0 -y
-pip install holoscan==2.9.0
-
-HOLOSCAN_DIR=$PROJECT_ROOT/workflows/robotic_ultrasound/scripts/holoscan_apps/
+# ---- Install Holoscan ----
+$PYTHON_EXECUTABLE -m pip install holoscan==2.9.0
+echo "Holoscan installed successfully!"
 
+# ---- Install Holoscan Apps ----
 echo "Building Holoscan Apps..."
 pushd $HOLOSCAN_DIR
 

tools/env_setup/install_isaac.sh

@@ -52,8 +52,4 @@ echo "Installing IsaacLab ..."
 yes Yes | ./isaaclab.sh --install
 popd
 
-# ---- Install libstdcxx-ng for mesa ----
-echo "Installing libstdcxx-ng..."
-conda install -c conda-forge libstdcxx-ng=13.2.0 -y
-
 echo "IsaacSim and dependencies installed successfully!"

tools/env_setup_robot_us.sh

@@ -122,12 +122,18 @@ if [[ "$INSTALL_WITH_POLICY" == "gr00tn1" ]]; then
 fi
 
 
+# for holoscan and cosmos transfer1, we need to install the following conda packages:
+conda install -c conda-forge ninja libgl ffmpeg pybind11 gcc=12.4.0 gxx=12.4.0 libstdcxx-ng=12.4.0 -y
+
+
 # ---- Install Holoscan (Common) ----
 echo "Installing Holoscan..."
 bash "$PROJECT_ROOT/tools/env_setup/install_holoscan.sh"
 
+# ---- Install Cosmos (Common) ----
+echo "Installing Cosmos..."
+bash "$PROJECT_ROOT/tools/env_setup/install_cosmos_transfer1.sh"
 
 echo "=========================================="
 echo "Environment setup script finished."
-echo "Selected policy dependencies ($INSTALL_WITH_POLICY) should be installed along with base components."
 echo "=========================================="

workflows/robotic_ultrasound/README.md

@@ -104,7 +104,7 @@ The main script `tools/env_setup_robot_us.sh` installs all necessary dependencie
 The script supports installing additional policy-specific dependencies using the `--policy` flag:
 - **`--policy pi0` (Default)**: Installs PI0 policy dependencies (e.g., OpenPI)
 - **`--policy gr00tn1`**: Installs GR00T N1 policy dependencies (e.g., Isaac-GR00T)
-- **`--policy base`**: Installs only common base dependencies
+- **`--policy none`**: Installs only common base dependencies
 
 Run the script from the repository root:
 ```bash