diff --git a/README.md b/README.md
index ba8bf6c8..39ede523 100644
--- a/README.md
+++ b/README.md
@@ -52,17 +52,21 @@ This is not a product. Use it at your own risk and discretion.
 
 We provide both Apptainer and Docker images for easy setup:
 
-#### Using Apptainer
-```bash
-./apptainer/build.sh
-./apptainer/run.sh
-```
-#### Using Docker
-```bash
-./docker/build.sh
-./docker/run.sh
+```console
+$ ./containers/run.sh 
+Must specify either --docker or --apptainer.
+Usage: ./containers/run.sh [--docker|-d] [--apptainer|-a]
+  --docker      Run using Docker container
+  --apptainer   Run using Apptainer container
 ```
 
+That's it! The run script will:
+
+- ✅ Automatically build the container if it doesn't exist
+- ✅ Mount your project directory to the container
+- ✅ Start an interactive session where you can run IntelliPerf
+- ✅ Persist all output files to your host machine
+
 Or use our prebuilt Docker image:
 ```bash
 docker pull audacioussw/intelliperf:latest
diff --git a/VERSION b/VERSION
new file mode 100644
index 00000000..6c6aa7cb
--- /dev/null
+++ b/VERSION
@@ -0,0 +1 @@
+0.1.0
\ No newline at end of file
diff --git a/apptainer/build.sh b/apptainer/build.sh
deleted file mode 100755
index 6fc89cca..00000000
--- a/apptainer/build.sh
+++ /dev/null
@@ -1,69 +0,0 @@
-#!/bin/bash
-################################################################################
-# MIT License
-
-# Copyright (c) 2025 Advanced Micro Devices, Inc. All Rights Reserved.
-
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
-
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-# SOFTWARE.
-################################################################################
-
-debug=0
-
-while [[ $# -gt 0 ]]; do
-    case $1 in
-        -d|--debug)
-            debug=1
-            shift
-            ;;
-        *)
-            echo "Usage: $0 [-d|--debug]"
-            exit 1
-            ;;
-    esac
-done
-
-
-# Auto config SSH agent
-if [ ! -S ~/.ssh/ssh_auth_sock ]; then
-    eval `ssh-agent` > /dev/null
-    ln -sf "$SSH_AUTH_SOCK" ~/.ssh/ssh_auth_sock
-fi
-export SSH_AUTH_SOCK=~/.ssh/ssh_auth_sock
-[ -f ~/.ssh/id_rsa ] && ssh-add ~/.ssh/id_rsa
-[ -f ~/.ssh/id_ed25519 ] && ssh-add ~/.ssh/id_ed25519
-
-ssh_auth_sock_path=$(readlink -f "$SSH_AUTH_SOCK")
-# Build the Singularity container
-#   --build-arg SSH_AUTH_SOCK=$SSH_AUTH_SOCK is used to pass the SSH agent socket to the container
-#   (advantage of this method is that the key is at no point copied to the container image.)
-#   If your SSH_AUTH_SOCK will not already bound to the container, and is available at /run/..., add `--bind /run` to the build command
-definition="apptainer/intelliperf.def"
-
-if [[ $debug -eq 1 ]]; then
-    image="apptainer/intelliperf_debug.sif"
-    cmake_build_type="Debug"
-else
-    image="apptainer/intelliperf.sif"
-    cmake_build_type="Release"
-fi
-
-apptainer build \
-    --build-arg SSH_AUTH_SOCK=${ssh_auth_sock_path} \
-    --build-arg CMAKE_BUILD_TYPE=${cmake_build_type}\
-     $image $definition
\ No newline at end of file
diff --git a/apptainer/intelliperf.def b/apptainer/intelliperf.def
deleted file mode 100644
index 28c6d4af..00000000
--- a/apptainer/intelliperf.def
+++ /dev/null
@@ -1,98 +0,0 @@
-Bootstrap: docker
-From: ubuntu:22.04
-
-%environment
-    # Locale
-    export LANG=en_US.UTF-8
-
-    # ROCm globals
-    export PATH=/opt/rocm/bin:$PATH
-    export LD_LIBRARY_PATH=/opt/rocm/lib:$LD_LIBRARY_PATH
-    export ROCM_PATH=/opt/rocm
-
-    # Misc globals
-    export GT_TUNING=/root/guided-tuning
-    export PATH=/opt/omniprobe/bin/logDuration:$PATH
-    export PATH=/root/rocprofiler-compute/src:$PATH
-
-%files
-    examples/bank_conflict/llm.c/requirements.txt /examples/bank_conflict/llm.c/requirements.txt
-
-%post
-    # Set locale
-    apt-get -y update
-    apt-get install -y locales
-    locale-gen en_US.UTF-8
-    export LANG=en_US.UTF-8
-
-    # Install dependencies
-    apt-get -y update
-    apt-get install -y software-properties-common
-    apt-get upgrade -y
-    apt-get install -y build-essential python3 python3-pip python3-setuptools python3-wheel git wget clang lld libzstd-dev libomp-dev vim libdwarf-dev
-    apt-get install -y locales
-    locale-gen en_US.UTF-8
-    python3 -m pip install --upgrade pip
-    python3 -m pip install 'cmake==3.22'
-
-    # Add GitHub trusted host
-    mkdir -p ~/.ssh
-    touch ~/.ssh/known_hosts
-    ssh-keyscan github.com >> ~/.ssh/known_hosts
-    chmod 700 ~/.ssh
-    chmod 644 ~/.ssh/known_hosts
-
-    # Install ROCm
-    apt-get -y update
-    wget https://repo.radeon.com/amdgpu-install/6.3.3/ubuntu/jammy/amdgpu-install_6.3.60303-1_all.deb
-    apt-get -y install ./amdgpu-install_6.3.60303-1_all.deb
-    apt-get -y update
-    apt-get install -y rocm-dev rocm-llvm-dev rocm-hip-runtime-dev rocm-smi-lib rocminfo rocthrust-dev rocprofiler-compute rocblas rocm-gdb gdb tmux
-    export PATH=/opt/rocm/bin:$PATH
-    export LD_LIBRARY_PATH=/opt/rocm/lib:$LD_LIBRARY_PATH
-    export ROCM_PATH=/opt/rocm
-
-    # Install rocprof-compute (via package manager)
-    # python3 -m pip install --ignore-installed blinker
-    # python3 -m pip install -r /opt/rocm/libexec/rocprofiler-compute/requirements.txt
-    # Install rocprof-compute (from feature branch)
-    export SSH_AUTH_SOCK={{ SSH_AUTH_SOCK }}
-    cd /root
-    git clone -v https://github.com/ROCm/rocprofiler-compute.git
-    cd rocprofiler-compute
-    git checkout 41e73650d5cfc3dbd98e007d6279235578f8529a
-    python3 -m pip install --ignore-installed blinker
-    python3 -m pip install -r requirements.txt
-    cd src
-    export PATH=$PWD:$PATH
-
-    # Install Triton (version pinned)
-    cd /root
-    export TRITON_HOME=/root
-    git clone -v https://github.com/triton-lang/triton.git
-    cd triton
-    git checkout 6fa33ef1eecc97348d056688df84845db7d22507
-    python3 -m pip install ninja wheel pybind11
-    python3 -m pip install -e python
-
-    # Install omniprobe
-    echo "Building with CMAKE_BUILD_TYPE={{ CMAKE_BUILD_TYPE }}"
-    cd /root
-    git clone -v git@github.com:AARInternal/omniprobe.git
-    cd omniprobe
-    git checkout 9083730ab0da50114c767773df49cb1d2165ba7f
-    git submodule update --init --recursive
-    mkdir -p build 
-    cmake -DCMAKE_INSTALL_PREFIX=/opt/omniprobe\
-            -DCMAKE_PREFIX_PATH=${ROCM_PATH}\
-            -DTRITON_LLVM=/root/.triton/llvm/llvm-ubuntu-x64\
-            -DCMAKE_BUILD_TYPE={{ CMAKE_BUILD_TYPE }}\
-            -DCMAKE_VERBOSE_MAKEFILE=ON -S . -B build
-    cmake --build build --target install
-    export PATH=/opt/omniprobe/bin/logDuration:$PATH
-
-    # Install agents dependencies
-    python3 -m pip install openai
-
-    # Install examples dependencies
-    pip3 install --no-cache-dir -r /examples/bank_conflict/llm.c/requirements.txt
diff --git a/apptainer/run.sh b/apptainer/run.sh
deleted file mode 100755
index 9eb9f0d7..00000000
--- a/apptainer/run.sh
+++ /dev/null
@@ -1,67 +0,0 @@
-#!/bin/bash
-################################################################################
-# MIT License
-
-# Copyright (c) 2025 Advanced Micro Devices, Inc. All Rights Reserved.
-
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
-
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-# SOFTWARE.
-################################################################################
-
-script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-parent_dir="$(dirname "$script_dir")"
-working_dir=$(pwd)
-
-cd $parent_dir
-
-size=2048
-debug=0
-
-while [[ $# -gt 0 ]]; do
-    case $1 in
-        -s)
-            size=$2
-            shift 2
-            ;;
-        -d|--debug)
-            debug=1
-            shift
-            ;;
-        *)
-            echo "Usage: $0 [-s size] [-d|--debug]"
-            exit 1
-            ;;
-    esac
-done
-workload=$(date +"%Y%m%d%H%M%S")
-overlay="/tmp/intelliperf_overlay_$(whoami)_$workload.img"
-if [ ! -f $overlay ]; then
-    echo "[Log] Overlay image ${overlay} does not exist. Creating overlay of ${size} MiB..."
-    apptainer overlay create --size ${size} --create-dir /var/cache/intelliperf ${overlay}
-else
-    echo "[Log] Overlay image ${overlay} already exists. Using this one."
-fi
-echo "[Log] Utilize the directory /var/cache/intelliperf as a sandbox to store data you'd like to persist between container runs."
-
-# Run the container
-if [[ $debug -eq 1 ]]; then
-    image="apptainer/intelliperf_debug.sif"
-else
-    image="apptainer/intelliperf.sif"
-fi
-apptainer exec --bind $HOME/.ssh:/root/.ssh:ro --overlay ${overlay} --pwd "$working_dir" --cleanenv --env OPENAI_API_KEY=$OPENAI_API_KEY $image bash --rcfile /etc/bash.bashrc
diff --git a/apptainer/run_cmd.sh b/apptainer/run_cmd.sh
deleted file mode 100755
index 928eab38..00000000
--- a/apptainer/run_cmd.sh
+++ /dev/null
@@ -1,78 +0,0 @@
-#!/bin/bash
-################################################################################
-# MIT License
-
-# Copyright (c) 2025 Advanced Micro Devices, Inc. All Rights Reserved.
-
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
-
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-# SOFTWARE.
-################################################################################
-
-script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-parent_dir="$(dirname "$script_dir")"
-
-cd $parent_dir
-
-size=2048
-cmd=""
-debug=0
-
-while [[ $# -gt 0 ]]; do
-    case $1 in
-        -s)
-            size=$2
-            shift 2
-            ;;
-        --cmd)
-            cmd=$2
-            shift 2
-            ;;
-        -d|--debug)
-            debug=1
-            shift
-            ;;
-        *)
-            echo "Usage: $0 [-s size] --cmd '<command>' [-d|--debug]"
-            exit 1
-            ;;
-    esac
-done
-
-workload=$(date +"%Y%m%d%H%M%S")
-
-# Create filesystem image overlay, if it doesn't exist
-overlay="/tmp/intelliperf_overlay_$(whoami)_$workload.img"
-if [ ! -f $overlay ]; then
-    echo "[Log] Overlay image ${overlay} does not exist. Creating overlay of ${size} MiB..."
-    apptainer overlay create --size ${size} --create-dir /var/cache/intelliperf ${overlay}
-else
-    echo "[Log] Overlay image ${overlay} already exists. Using this one."
-fi
-echo "[Log] Utilize the directory /var/cache/intelliperf as a sandbox to store data you'd like to persist between container runs."
-
-# Run the container
-if [[ $debug -eq 1 ]]; then
-    image="apptainer/intelliperf_debug.sif"
-else
-    image="apptainer/intelliperf.sif"
-fi
-echo "cmd: $cmd"
-apptainer exec --overlay "${overlay}"\
-            --cleanenv --env OPENAI_API_KEY="$OPENAI_API_KEY"\
-            "$image" bash --rcfile /etc/bash.bashrc\
-            -c "cd src && eval \"$cmd\""
\ No newline at end of file
diff --git a/containers/build.sh b/containers/build.sh
new file mode 100755
index 00000000..0a614c61
--- /dev/null
+++ b/containers/build.sh
@@ -0,0 +1,74 @@
+#!/bin/bash
+
+# Container name
+name="intelliperf"
+
+# Script directories
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+parent_dir="$(dirname "$script_dir")"
+cur_dir=$(pwd)
+
+# Parse arguments
+build_docker=false
+build_apptainer=false
+
+while [[ $# -gt 0 ]]; do
+  case $1 in
+    --docker|-d)
+      build_docker=true
+      shift
+      ;;
+    --apptainer|-a)
+      build_apptainer=true
+      shift
+      ;;
+    *)
+      echo "Unknown option: $1"
+      echo "Usage: $0 [--docker|-d] [--apptainer|-a] -- Exactly one option is required."
+      exit 1
+      ;;
+  esac
+done
+
+if [ "$build_docker" = false ] && [ "$build_apptainer" = false ]; then
+    echo "Error: At least one of the options --docker or --apptainer is required."
+    echo "Usage: $0 [--docker] [--apptainer]"
+    echo "  --docker      Build Docker container"
+    echo "  --apptainer   Build Apptainer container"
+    exit 1
+fi
+
+pushd "$parent_dir"
+
+if [ "$build_docker" = true ]; then
+    echo "Building Docker container..."
+
+    # Enable BuildKit and build the Docker image
+    export DOCKER_BUILDKIT=1
+    docker build \
+        -t "$name:$(cat "$parent_dir/VERSION")" \
+        -f "$script_dir/intelliperf.Dockerfile" \
+        .
+
+    echo "Docker build complete!"
+fi
+
+if [ "$build_apptainer" = true ]; then
+    echo "Building Apptainer container..."
+
+    # Check if apptainer is installed
+    if ! command -v apptainer &> /dev/null; then
+        echo "Error: Apptainer is not installed or not in PATH"
+        echo "Please install Apptainer first: https://apptainer.org/docs/admin/main/installation.html"
+        exit 1
+    fi
+
+    # Build the Apptainer container with ROCm version
+    export ROCM_VERSION="$rocm_version"
+    apptainer build \
+      "${script_dir}/${name}_$(cat "$parent_dir/VERSION").sif" "$script_dir/intelliperf.def"
+
+    echo "Apptainer build complete!"
+fi
+  
+popd
\ No newline at end of file
diff --git a/docker/intelliperf.Dockerfile b/containers/intelliperf.Dockerfile
similarity index 51%
rename from docker/intelliperf.Dockerfile
rename to containers/intelliperf.Dockerfile
index b7a3adc2..1a596cdc 100644
--- a/docker/intelliperf.Dockerfile
+++ b/containers/intelliperf.Dockerfile
@@ -19,19 +19,10 @@ RUN apt-get update && apt-get install -y \
     gdb \
     && locale-gen en_US.UTF-8
 
-# Add GitHub trusted host
-RUN mkdir -p ~/.ssh && \
-    touch ~/.ssh/known_hosts && \
-    ssh-keyscan github.com >> ~/.ssh/known_hosts && \
-    chmod 700 ~/.ssh && \
-    chmod 644 ~/.ssh/known_hosts
-
 # Set the working directory
 WORKDIR $INTELLIPERF_HOME
+COPY ../ $INTELLIPERF_HOME
 
-# Clone IntelliPerf only in non-dev mode
-RUN --mount=type=ssh bash -c 'if [ "$DEV_MODE" = "false" ]; then \
-    git clone git@github.com:AMDResearch/intelliperf.git . ; \
-    pip install -e .; \
-    python3 scripts/install_tool.py --all; \
-    fi'
+# Install tool
+RUN pip install -e . && \
+    python3 scripts/install_tool.py --all
diff --git a/containers/intelliperf.def b/containers/intelliperf.def
new file mode 100644
index 00000000..077a2cdb
--- /dev/null
+++ b/containers/intelliperf.def
@@ -0,0 +1,37 @@
+Bootstrap: docker
+From: rocm/vllm-dev:nightly_aiter_integration_final_20250325
+
+%arguments
+    INTELLIPERF_HOME=/intelliperf
+
+%environment
+    # Runtime environment inside the finished SIF
+    export LANG=en_US.UTF-8
+    export PATH=/opt/rocm/bin:$PATH
+    export INTELLIPERF_HOME={{ INTELLIPERF_HOME }}
+
+%files
+    . /intelliperf
+
+%post
+    PATH=/opt/rocm/bin:$PATH
+    INTELLIPERF_HOME={{ INTELLIPERF_HOME }}
+
+    mkdir -p "${INTELLIPERF_HOME}"
+
+    apt-get update
+    apt-get install -y --no-install-recommends \
+        libzstd-dev \
+        python3-setuptools \
+        python3-wheel \
+        libdwarf-dev \
+        rocm-llvm-dev \
+        locales \
+        gdb \
+        ssh
+    locale-gen en_US.UTF-8 
+    rm -rf /var/lib/apt/lists/*
+    
+    cd "${INTELLIPERF_HOME}"
+    pip install -e .
+    python3 scripts/install_tool.py --all
\ No newline at end of file
diff --git a/containers/run.sh b/containers/run.sh
new file mode 100755
index 00000000..39bee16d
--- /dev/null
+++ b/containers/run.sh
@@ -0,0 +1,146 @@
+#!/bin/bash
+
+# Supports both Docker and Apptainer with automatic building
+
+# Container name
+name="intelliperf"
+
+# Script directories
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+parent_dir="$(dirname "$script_dir")"
+
+# Parse arguments
+use_docker=false
+use_apptainer=false
+overlay_size=2048
+
+while [[ $# -gt 0 ]]; do
+  case $1 in
+    --docker|-d)
+      use_docker=true
+      shift
+      ;;
+    --apptainer|-a)
+      use_apptainer=true
+      shift
+      ;;
+    -s|--overlay-size)
+      overlay_size=$2
+      shift 2
+      ;;
+    *)
+      echo "Unknown option: $1"
+      echo "Usage: $0 [--docker|-d] [--apptainer|-a] [-s|--overlay-size SIZE] -- Exactly one option is required."
+      echo "  -s, --overlay-size SIZE   Size of overlay filesystem in MiB (default: 2048, Apptainer only)"
+      exit 1
+      ;;
+  esac
+done
+
+# Validate arguments
+if [ "$use_docker" = true ] && [ "$use_apptainer" = true ]; then
+    echo "Error: Cannot use both --docker and --apptainer simultaneously."
+    echo "Usage: $0 [--docker] [--apptainer]"
+    exit 1
+elif [ "$use_docker" = false ] && [ "$use_apptainer" = false ]; then
+    echo "Error: Must specify either --docker or --apptainer."
+    echo "Usage: $0 [--docker] [--apptainer]"
+    echo "  --docker      Run using Docker container"
+    echo "  --apptainer   Run using Apptainer container"
+    exit 1
+fi
+
+echo "Starting intelliperf container..."
+echo "Project directory will be mounted at $(pwd)"
+echo "Any files you create/modify will persist after the container closes."
+echo ""
+
+if [ "$use_docker" = true ]; then
+    echo "Using Docker containerization..."
+    
+    # Check if the Docker image exists
+    if ! docker image inspect "$name:$(cat "$parent_dir/VERSION")" > /dev/null 2>&1; then
+        echo "Docker image $name:$(cat "$parent_dir/VERSION") not found."
+        echo "Building Docker image..."
+        echo ""
+        
+        if ! "$script_dir/build.sh" --docker; then
+            echo "Error: Failed to build Docker image."
+            exit 1
+        fi
+        
+        echo ""
+        echo "Docker image built successfully!"
+    else
+        echo "Docker image found."
+    fi
+    
+    # Run the Docker container
+    echo "Running Docker container with project directory mounted..."
+    docker run -it --rm \
+        --device=/dev/kfd \
+        --device=/dev/dri \
+        --group-add video \
+        --cap-add=SYS_PTRACE \
+        --security-opt seccomp=unconfined \
+        -e LLM_GATEWAY_KEY="$LLM_GATEWAY_KEY" \
+        -v $(pwd):$(pwd) \
+        -w $(pwd) \
+        "$name:$(cat "$parent_dir/VERSION")"
+
+elif [ "$use_apptainer" = true ]; then
+    echo "Using Apptainer containerization..."
+    
+    # Check if apptainer is installed
+    if ! command -v apptainer &> /dev/null; then
+        echo "Error: Apptainer is not installed or not in PATH"
+        echo "Please install Apptainer first: https://apptainer.org/docs/admin/main/installation.html"
+        exit 1
+    fi
+    
+    # Apptainer image filename
+    apptainer_image="$script_dir/${name}_$(cat "$parent_dir/VERSION").sif"
+    
+    # Check if the Apptainer image exists
+    if [ ! -f "$apptainer_image" ]; then
+        echo "Apptainer image $apptainer_image not found."
+        echo "Building Apptainer image automatically..."
+        echo ""
+        
+        if ! "$script_dir/build.sh" --apptainer; then
+            echo "Error: Failed to build Apptainer image."
+            exit 1
+        fi
+        
+        echo ""
+        echo "Apptainer image built successfully!"
+    else
+        echo "Apptainer image found."
+    fi
+
+    # Create overlay filesystem for writable areas
+    workload=$(date +"%Y%m%d%H%M%S")
+    overlay="/tmp/intelliperf_overlay_$(whoami)_$workload.img"
+    if [ ! -f "$overlay" ]; then
+        echo "[Log] Overlay image ${overlay} does not exist. Creating overlay of ${overlay_size} MiB..."
+        apptainer overlay create --size ${overlay_size} --create-dir /var/cache/intelliperf ${overlay}
+    else
+        echo "[Log] Overlay image ${overlay} already exists. Using this one."
+    fi
+    echo "[Log] Overlay filesystem provides writable areas for profiling tools."
+    echo "[Log] Use /var/cache/intelliperf as a sandbox for persistent data between container runs."
+    
+    # Run the Apptainer container
+    echo "Running Apptainer container with project directory mounted..."
+    cd "$parent_dir"
+    apptainer exec \
+        --cleanenv \
+        --pwd $(pwd) \
+        --overlay ${overlay} \
+        --env LLM_GATEWAY_KEY=$LLM_GATEWAY_KEY \
+        "$apptainer_image" \
+        /bin/bash \
+        --rcfile /etc/bashrc
+fi
+
+echo "Container session ended." 
\ No newline at end of file
diff --git a/docker/build.sh b/docker/build.sh
deleted file mode 100755
index c91ac2cd..00000000
--- a/docker/build.sh
+++ /dev/null
@@ -1,80 +0,0 @@
-#!/bin/bash
-################################################################################
-# MIT License
-
-# Copyright (c) 2025 Advanced Micro Devices, Inc. All Rights Reserved.
-
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
-
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-# SOFTWARE.
-################################################################################
-
-# Parse command line arguments
-dev_mode=false
-while [[ $# -gt 0 ]]; do
-    case $1 in
-        --dev|-d)
-            dev_mode=true
-            shift
-            ;;
-        *)
-            echo "Unknown option: $1"
-            exit 1
-            ;;
-    esac
-done
-
-# Container name
-name="intelliperf"
-
-# Script directories
-script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-parent_dir="$(dirname "$script_dir")"
-cur_dir=$(pwd)
-
-# Set INTELLIPERF_HOME based on dev mode
-if [ "$dev_mode" = true ]; then
-    intelliperf_home="$cur_dir"
-else
-    intelliperf_home="/intelliperf"
-fi
-
-pushd "$script_dir"
-
-# Auto-configure SSH agent
-if [ ! -S ~/.ssh/ssh_auth_sock ]; then
-    eval "$(ssh-agent)" > /dev/null
-    ln -sf "$SSH_AUTH_SOCK" ~/.ssh/ssh_auth_sock
-fi
-export SSH_AUTH_SOCK=~/.ssh/ssh_auth_sock
-
-# Add default keys if they exist
-[ -f ~/.ssh/id_rsa ] && ssh-add ~/.ssh/id_rsa
-[ -f ~/.ssh/id_ed25519 ] && ssh-add ~/.ssh/id_ed25519
-[ -f ~/.ssh/id_github ] && ssh-add ~/.ssh/id_github
-
-# Enable BuildKit and build the Docker image
-export DOCKER_BUILDKIT=1
-docker build \
-    --ssh default \
-    -t "$name" \
-    --build-arg DEV_MODE="$dev_mode" \
-    --build-arg INTELLIPERF_HOME="$intelliperf_home" \
-    -f "$script_dir/intelliperf.Dockerfile" \
-    .
-
-popd
diff --git a/docker/run.sh b/docker/run.sh
deleted file mode 100755
index 4f4ecdae..00000000
--- a/docker/run.sh
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/bin/bash
-################################################################################
-# MIT License
-
-# Copyright (c) 2025 Advanced Micro Devices, Inc. All Rights Reserved.
-
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
-
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-# SOFTWARE.
-################################################################################
-
-name="intelliperf"
-
-docker run -it --rm \
-    --name "$name" \
-    --device=/dev/kfd \
-    --device=/dev/dri \
-    --group-add video \
-    -v $HOME/.ssh:/tmp/ssh:ro \
-    -v $(pwd):$(pwd) \
-    -w $(pwd) \
-    -e LLM_GATEWAY_KEY="$LLM_GATEWAY_KEY" \
-    -e SSH_AUTH_SOCK="$SSH_AUTH_SOCK" \
-    -v $SSH_AUTH_SOCK:$SSH_AUTH_SOCK \
-    "$name" \
-    bash -c "cp -r /tmp/ssh/* /root/.ssh/ 2>/dev/null || true && chown -R root:root /root/.ssh && chmod 700 /root/.ssh && chmod 600 /root/.ssh/config /root/.ssh/id_* /root/.ssh/known_hosts 2>/dev/null || true; exec bash"
diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md
index f47f1d2d..f92eb12c 100644
--- a/docs/CONTRIBUTING.md
+++ b/docs/CONTRIBUTING.md
@@ -35,14 +35,12 @@ We provide both Apptainer and Docker images containing all the dependencies. To
 #### Using Apptainer
 
 ```bash
-./apptainer/build.sh
-./apptainer/run.sh
+./containers/run.sh --apptainer
 ```
 
 #### Using Docker
 ```bash
-./docker/build.sh
-./docker/run.sh
+./containers/run.sh --docker
 ```
 
 ### Setting Up Development Environment
diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
index 16a0d784..0ab44fb6 100644
--- a/examples/CMakeLists.txt
+++ b/examples/CMakeLists.txt
@@ -31,7 +31,10 @@ function(add_example name source_file)
     add_executable(${name} ${source_file})
     # CMake instrumentation integration example
     if(INSTRUMENT)
-        set(OMNIPROBE_PATH ${CMAKE_SOURCE_DIR}/../external/omniprobe/install)
+        # Use provided OMNIPROBE_PATH or default to the standard location
+        if(NOT DEFINED OMNIPROBE_PATH)
+            set(OMNIPROBE_PATH ${CMAKE_SOURCE_DIR}/../external/omniprobe/install)
+        endif()
         # Only use omniprobe if the path exists
         if(EXISTS ${OMNIPROBE_PATH}/lib/libAMDGCNSubmitAddressMessages-rocm.so)
             # Use the plugin to instrument the code
diff --git a/examples/scripts/build_examples.sh b/examples/scripts/build_examples.sh
index 8cdb1aca..a5dae7c3 100755
--- a/examples/scripts/build_examples.sh
+++ b/examples/scripts/build_examples.sh
@@ -32,14 +32,16 @@ parallel=8
 build_dir=build
 verbose=false
 instrument=false
+omniprobe_path=""
 
 print_usage() {
     echo "Usage: $0 [options]"
     echo "Options:"
-    echo "  -c, --clean       Clean build directory"
-    echo "  -v, --verbose     Print verbose output"
-    echo "  -i, --instrument  Instrument the code with Omniprobe"
-    echo "  -j, --jobs <num>  Set number of parallel jobs"
+    echo "  -c, --clean             Clean build directory"
+    echo "  -v, --verbose           Print verbose output"
+    echo "  -i, --instrument        Instrument the code with Omniprobe"
+    echo "  -o, --omniprobe <path>  Specify path to omniprobe tool"
+    echo "  -j, --jobs <num>        Set number of parallel jobs"
 }
 
 # Parse arguments
@@ -57,6 +59,16 @@ while [[ $# -gt 0 ]]; do
             instrument=true
             shift
             ;;
+        -o|--omniprobe)
+            if [[ -n "$2" ]]; then
+                omniprobe_path="$2"
+                shift 2
+            else
+                echo "Error: --omniprobe requires a path argument"
+                print_usage
+                exit 1
+            fi
+            ;;
         -j|--jobs)
             if [[ -n "$2" && "$2" =~ ^[0-9]+$ ]]; then
                 parallel="$2"
@@ -88,6 +100,9 @@ if [ "$instrument" = true ]; then
     cmake_config_args+=(-DINSTRUMENT=ON)
 fi
 
+if [ -n "$omniprobe_path" ]; then
+    cmake_config_args+=(-DOMNIPROBE_PATH="$omniprobe_path")
+fi
 
 
 config_command="cmake -B "$build_dir"\
diff --git a/pyproject.toml b/pyproject.toml
index f066944d..c6ccae4f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,8 +38,31 @@ python3 -m pip install -r requirements.txt
 """
 
 
+
+[tool.omniprobe]
+git = "https://github.com/AMDResearch/omniprobe.git"
+branch = "4eb1b3d49b83f2d50823525e073eea356661e871"
+build_command = """
+export CC=${ROCM_PATH}/bin/hipcc
+export CXX=${ROCM_PATH}/bin/hipcc
+git submodule update --init --recursive
+python3 -m pip install -r omniprobe/requirements.txt
+#TODO: search for a Triton LLVM.
+if [ -d "/root/.triton/llvm/llvm-ubuntu-x64" ]; then
+    export TRITON_LLVM_PATH="/root/.triton/llvm/llvm-ubuntu-x64"
+else
+    export TRITON_LLVM_PATH="${ROCM_PATH}/llvm/"
+fi
+cmake -DCMAKE_PREFIX_PATH=${ROCM_PATH} \
+      -DCMAKE_BUILD_TYPE=Release \
+      -DCMAKE_INSTALL_PREFIX=install \
+      -DCMAKE_VERBOSE_MAKEFILE=ON -S . -B build &&
+cmake --build build --parallel 1 &&
+cmake --install build
+"""
+
 [tool.nexus]
-git = "git@github.com:AMDResearch/nexus.git"
+git = "https://github.com/AMDResearch/nexus"
 branch = "main"
 build_command = """
 export CC=${ROCM_PATH}/bin/hipcc
@@ -59,6 +82,9 @@ dev = [
 [tool.ruff]
 line-length = 120
 target-version = "py38"
+exclude = [
+    "external/guided-tuning/"
+]
 
 [tool.ruff.lint]
 select = [
diff --git a/scripts/build_examples.sh b/scripts/build_examples.sh
index 9962aa52..8f41c88e 100755
--- a/scripts/build_examples.sh
+++ b/scripts/build_examples.sh
@@ -32,14 +32,16 @@ parallel=8
 build_dir=build
 verbose=false
 instrument=false
+omniprobe_path=""
 
 print_usage() {
     echo "Usage: $0 [options]"
     echo "Options:"
-    echo "  -c, --clean       Clean build directory"
-    echo "  -v, --verbose     Print verbose output"
-    echo "  -i, --instrument  Instrument the code with Omniprobe"
-    echo "  -j, --jobs <num>  Set number of parallel jobs"
+    echo "  -c, --clean             Clean build directory"
+    echo "  -v, --verbose           Print verbose output"
+    echo "  -i, --instrument        Instrument the code with Omniprobe"
+    echo "  -o, --omniprobe <path>  Specify path to omniprobe tool"
+    echo "  -j, --jobs <num>        Set number of parallel jobs"
 }
 
 # Parse arguments
@@ -57,6 +59,16 @@ while [[ $# -gt 0 ]]; do
             instrument=true
             shift
             ;;
+        -o|--omniprobe)
+            if [[ -n "$2" ]]; then
+                omniprobe_path="$2"
+                shift 2
+            else
+                echo "Error: --omniprobe requires a path argument"
+                print_usage
+                exit 1
+            fi
+            ;;
         -j|--jobs)
             if [[ -n "$2" && "$2" =~ ^[0-9]+$ ]]; then
                 parallel="$2"
@@ -88,6 +100,9 @@ if [ "$instrument" = true ]; then
     cmake_config_args+=(-DINSTRUMENT=ON)
 fi
 
+if [ -n "$omniprobe_path" ]; then
+    cmake_config_args+=(-DOMNIPROBE_PATH="$omniprobe_path")
+fi
 
 
 config_command="cmake -B "$build_dir"\
diff --git a/src/intelliperf/core/application.py b/src/intelliperf/core/application.py
index 7accae92..4a763fac 100644
--- a/src/intelliperf/core/application.py
+++ b/src/intelliperf/core/application.py
@@ -160,7 +160,7 @@ def profile(self, top_n: int):
 				"-w",
 				str(last_matching_id),
 				"-k",
-				f"{'|'.join(top_n_kernels)}",
+				f'"{"|".join(top_n_kernels)}"',
 				"--separate",
 				"--save",
 				f"{get_guided_tuning_path()}/intelliperf_report_card.json",
diff --git a/src/intelliperf/formulas/bank_conflict.py b/src/intelliperf/formulas/bank_conflict.py
index 57ff6bbe..f87f9a33 100644
--- a/src/intelliperf/formulas/bank_conflict.py
+++ b/src/intelliperf/formulas/bank_conflict.py
@@ -22,11 +22,9 @@
 # SOFTWARE.
 ################################################################################
 
-import glob
 import json
 import logging
 import os
-import shutil
 
 from intelliperf.core.llm import LLM
 from intelliperf.formulas.formula_base import (
@@ -35,7 +33,10 @@
 	filter_json_field,
 	get_kernel_name,
 )
-from intelliperf.utils.env import get_llm_api_key
+from intelliperf.utils.env import (
+	get_llm_api_key,
+	get_omniprobe_path,
+)
 from intelliperf.utils.process import capture_subprocess_output
 from intelliperf.utils.regex import generate_ecma_regex_from_list
 
@@ -131,17 +132,6 @@ def instrument_pass(self) -> Result:
 		"""
 		super().instrument_pass()
 
-		# Log instrumentation completion
-		self.get_logger().record(
-			"instrument_pass_complete", {"success": True, "note": "Instrumentation pass completed via parent class"}
-		)
-
-		return Result(
-			success=False,
-			asset=self._instrumentation_results,
-			error_report="Instrumentation pass not implemented for bank conflict.",
-		)
-
 		# Always instrument the first kernel
 		kernel_to_instrument = self.get_top_kernel()
 		if kernel_to_instrument is None:
@@ -150,11 +140,11 @@ def instrument_pass(self) -> Result:
 				error_report="No source code found. Please compile your code with -g.",
 			)
 
-		omniprobe_output_dir = os.path.join(self._application.get_project_directory(), "memory_analysis_output")
+		omniprobe_output_file = os.path.join(self._application.get_project_directory(), "memory_analysis_output.json")
 
-		# Remove directory if it exists and create a new one
-		if os.path.exists(omniprobe_output_dir):
-			shutil.rmtree(omniprobe_output_dir)
+		# Remove file if it exists before running omniprobe
+		if os.path.exists(omniprobe_output_file):
+			os.remove(omniprobe_output_file)
 
 		ecma_regex = generate_ecma_regex_from_list([kernel_to_instrument])
 		logging.debug(f"ECMA Regex for kernel names: {ecma_regex}")
@@ -162,12 +152,16 @@ def instrument_pass(self) -> Result:
 		logging.debug(f"Omniprobe profiling command is: {cmd}")
 		success, output = capture_subprocess_output(
 			[
-				"omniprobe",
+				str(get_omniprobe_path()),
 				"--instrumented",
 				"--analyzers",
 				"MemoryAnalysis",
 				"--kernels",
-				ecma_regex,
+				f'"{ecma_regex}"',
+				"--log-format",
+				"json",
+				"--log-location",
+				omniprobe_output_file,
 				"--",
 				" ".join(self._application.get_app_cmd()),
 			],
@@ -182,10 +176,9 @@ def instrument_pass(self) -> Result:
 
 		# Try loading the memory analysis output
 		# Find all files in the memory_analysis_output directory
-		output_files = glob.glob(os.path.join(omniprobe_output_dir, "memory_analysis_*.json"))
-		if len(output_files) == 0:
-			return Result(success=False, error_report="No memory analysis output files found.")
-		output_file = output_files[0]
+		output_file = omniprobe_output_file
+		if not os.path.exists(output_file):
+			return Result(success=False, error_report="Memory analysis output file not found.")
 		try:
 			with open(output_file, "r") as f:
 				self._instrumentation_results = json.load(f)
@@ -230,13 +223,6 @@ def optimize_pass(self, temperature: float = 0.0, max_tokens: int = 3000) -> Res
 			api_key=llm_key, system_prompt=system_prompt, model=model, provider=provider, logger=self.get_logger()
 		)
 
-		kernel_to_optimize = self.get_top_kernel()
-		if kernel_to_optimize is None:
-			return Result(
-				success=False,
-				error_report="No source code or bank conflicts found. Please compile your code with -g.",
-			)
-
 		kernel = None
 		kernel_file = None
 
@@ -301,7 +287,52 @@ def optimize_pass(self, temperature: float = 0.0, max_tokens: int = 3000) -> Res
 					f"access the same memory bank simultaneously, causing serialization and performance degradation."
 				)
 		else:
-			pass
+			kernel = self._instrumentation_results[0]["kernel_analysis"]["kernel_info"]["name"]
+			kernel_name = get_kernel_name(kernel)
+			files = {}  # supposed to be a dict of file_path -> list of line numbers
+			line_numbers = []
+
+			# Extract files from bank conflict accesses
+			bank_conflicts = self._instrumentation_results[0]["kernel_analysis"]["bank_conflicts"]["accesses"]
+			for access in bank_conflicts:
+				file_path = access["source_location"]["file"]
+				line_number = access["source_location"]["line"]
+				if file_path not in files:
+					files[file_path] = []
+				files[file_path].append(line_number)
+
+			kernel_file = None
+			for file in files.keys():
+				if os.path.exists(file):
+					with open(file, "r") as f:
+						unoptimized_file_content = f.read()
+						if kernel_name in unoptimized_file_content:
+							kernel_file = file
+							line_numbers.append(files[file])
+							break
+			if kernel_file is None:
+				return Result(success=False, error_report="Kernel file not found.")
+
+			# Create user prompt and required reports
+			user_prompt = (
+				f"There is a bank conflict in the kernel {kernel} at line(s) numbered {line_numbers} in the source code {unoptimized_file_content}."
+				f" Please fix the conflict but do not change the semantics of the program."
+				" Do not remove any comments or licenses."
+				" Do not include any markdown code blocks or text other than the code."
+			)
+			if self.current_summary is not None:
+				user_prompt += f"\n\nThe current summary is: {self.current_summary}"
+				cur_diff = self.compute_diff([kernel_file])
+				user_prompt += f"\nThe diff between the current and initial code is: {cur_diff}"
+
+			self.previous_source_code = unoptimized_file_content
+
+			args = kernel.split("(")[1].split(")")[0]
+			self.bottleneck_report = (
+				f"Bank Conflict Detection: IntelliPerf identified shared memory bank conflicts in kernel "
+				f"`{kernel_name}` with arguments `{args}`. Bank conflicts occur when multiple threads "
+				f"access the same memory bank simultaneously, causing serialization and performance degradation."
+			)
 
 		if kernel is None:
 			return Result(success=False, error_report="Failed to extract the kernel name.")
@@ -363,10 +394,13 @@ def correctness_validation_pass(self, accordo_absolute_tolerance: float = 1e-6)
 		return result
 
 	def performance_validation_pass(self) -> Result:
+		# Currently, Omniprobe appends the '[clone .kd]' suffix to the kernel name
+		# this needs to me adjusted to reflect the actual kernel name
+		kernel_signature_non_cloned = self.current_kernel_signature.split(" [clone .kd]")[0]
 		unoptimized_results = filter_json_field(
 			self._initial_profiler_results,
 			field="kernel",
-			comparison_func=lambda x: x == self.current_kernel_signature,
+			comparison_func=lambda x: x == kernel_signature_non_cloned,
 		)
 
 		unoptimized_time = unoptimized_results[0]["durations"]["ns"]
@@ -378,7 +412,7 @@ def performance_validation_pass(self) -> Result:
 		optimized_results = filter_json_field(
 			self._optimization_results,
 			field="kernel",
-			comparison_func=lambda x: x == self.current_kernel_signature,
+			comparison_func=lambda x: x == kernel_signature_non_cloned,
 		)
 
 		optimized_time = optimized_results[0]["durations"]["ns"]
diff --git a/src/intelliperf/utils/env.py b/src/intelliperf/utils/env.py
index 996d21ed..f728e855 100644
--- a/src/intelliperf/utils/env.py
+++ b/src/intelliperf/utils/env.py
@@ -28,6 +28,12 @@
 from intelliperf.utils.process import exit_on_fail
 
 
+def get_omniprobe_path():
+	if os.environ.get("OMNIPROBE_PATH"):
+		return Path(os.environ["OMNIPROBE_PATH"]).resolve()
+	return (Path(__file__).resolve().parent / "../../../external/omniprobe/install/bin/logDuration/omniprobe").resolve()
+
+
 def get_guided_tuning_path():
 	if os.environ.get("GT_TUNING"):
 		return Path(os.environ["GT_TUNING"]).resolve()
diff --git a/src/intelliperf/utils/process.py b/src/intelliperf/utils/process.py
index ae4befa4..2bcdb32b 100644
--- a/src/intelliperf/utils/process.py
+++ b/src/intelliperf/utils/process.py
@@ -45,7 +45,7 @@ def capture_subprocess_output(
 	"""
 	verbose = logging.getLogger().getEffectiveLevel() <= logging.DEBUG
 
-	logging.debug(f"Running the command: {' '.join(subprocess_args)}")
+	# logging.debug(f"Running the command: {' '.join(subprocess_args)}")
 
 	if working_directory is not None:
 		logging.debug(f"Working directory: {working_directory}")
@@ -58,7 +58,15 @@ def capture_subprocess_output(
 	if additional_path is not None:
 		env["PATH"] = str(additional_path) + ":" + env["PATH"]
 
+	if working_directory is not None:
+		# Convert to absolute path to be safe
+		abs_working_dir = os.path.abspath(working_directory)
+		shell_cmd = f'cd "{abs_working_dir}" && {" ".join(subprocess_args)}'
+		subprocess_args = ["bash", "-c", shell_cmd]
+		working_directory = None  # Let shell handle it
+
 	logging.debug(f"PATH: {env['PATH']}")
+	logging.debug(f"Running the command: {' '.join(subprocess_args)}")
 
 	# Run the process and wait for completion
 	try:
diff --git a/src/intelliperf/utils/regex.py b/src/intelliperf/utils/regex.py
index 30fc8bf9..25fb9633 100644
--- a/src/intelliperf/utils/regex.py
+++ b/src/intelliperf/utils/regex.py
@@ -38,11 +38,10 @@ def generate_ecma_regex_from_list(kernel_names: set) -> str:
 		# Note: Temporary fix, but until bug in omniprobe is fixed we need to also
 		# add the name of the instrumented kernel clone to the regex, otherwise we'll skip it
 		# and exclude it from the memory analysis report
-		# duplicate_kernel_str = f"__amd_crk_{i.replace(')', ', void*)', 1)}"
-		# duplicate_kernel_str = f"__amd_crk_{i.replace(")", ", void*)", 1)}"
-		# escaped_string = re.escape(duplicate_kernel_str)
-		# regex_string = r"^" + escaped_string + r"$"
-		# res.append(regex_string)
+		duplicate_kernel_str = f"__amd_crk_{i.replace(')', ', void*)', 1)}"
+		escaped_string = re.escape(duplicate_kernel_str)
+		regex_string = r"^" + escaped_string + r"$"
+		res.append(regex_string)
 
 	regex = f"({'|'.join(res)})"
 	return regex