ESM Changes (#43)

Updated readme for docker with proxy instructions.
Minor code changes to enable docker with proxy

Author: arunvelliyangiri18

applications/esm/Dockerfile.esm

@@ -14,8 +14,7 @@ RUN bash -c "source ${HOME}/conda/etc/profile.d/conda.sh && \
 source ${HOME}/conda/etc/profile.d/mamba.sh && \
 mamba activate esm_py11 && \
 pip install . &&\
-pip install torch==2.4.0+cpu torchvision==0.19.0+cpu torchaudio==2.4.0+cpu --index-url https://download.pytorch.org/whl/cpu  && \
-pip install intel-extension-for-pytorch==2.4.0"
+pip install torch==2.4.0+cpu torchvision==0.19.0+cpu torchaudio==2.4.0+cpu --index-url https://download.pytorch.org/whl/cpu"
 
 RUN echo "#!/bin/bash" >> /app/init.sh && \
 echo "source ${HOME}/conda/etc/profile.d/conda.sh" >> /app/init.sh && \

applications/esm/README.md

@@ -4,12 +4,24 @@
 Open-Omics-ESM is an optimized version of the Evolutionary Scale Modeling (ESM) toolkit, tailored for modern CPUs. It enhances the performance of key ESM modules—such as ESM-embeddings, LM-Design, InverseFolding, and ESMFold—by leveraging the Intel Extension for PyTorch (IPEX), the latest version of PyTorch, and lower-precision (bf16) computations.
 
 ## Installation
-### Step 1: Run the script to create the Docker images
-Execute the script using the following command:
+### Step 1: 🛠️ Building the Docker Image
+Run the following command to build the Docker image:
 
 ```bash
- ./build_docker_images.sh
+./build_docker_images.sh
 ```
+#### 🌐 Building Behind a Proxy
+If you're working in a corporate or institutional environment, your internet access may be routed through a proxy server. In such cases, Docker may not be able to download dependencies during the build process unless you explicitly configure proxy settings.
+
+To build the Docker image with proxy settings, you can use the --build-arg option to pass your proxy configuration:
+
+```bash
+./build_docker_images.sh --http_proxy=$http_proxy --https_proxy=$https_proxy --no_proxy=$no_proxy
+```
+🔒 Note: Make sure the environment variables http_proxy, https_proxy, and no_proxy are correctly set in your shell before running this command.
+
+For more details, refer to the official Docker documentation:
+[Docker behind proxy](https://docs.docker.com/engine/cli/proxy/)
 ### Step 2: Choose the ESM image to install
 Select the ESM image you want to build based on your specific needs
 

applications/esm/build_docker_images.sh

@@ -16,6 +16,25 @@ image_exists() {
   $runtime images -q "$image_name" | grep -q .
 }
 
+# Parse optional proxy args from command-line
+for arg in "$@"; do
+  case $arg in
+    --http_proxy=*)
+      http_proxy="${arg#*=}"
+      ;;
+    --https_proxy=*)
+      https_proxy="${arg#*=}"
+      ;;
+    --no_proxy=*)
+      no_proxy="${arg#*=}"
+      ;;
+    *)
+      echo "Unknown option: $arg"
+      exit 1
+      ;;
+  esac
+done
+
 runtime=docker
 if ! command_exists "$runtime"; then
   echo "$runtime is not installed on your system. Please install it first."
@@ -33,65 +52,44 @@ echo "3 Both esm and esm_fold"
 read -r task_option
 
 case $task_option in
-    1)
-        build_esm=true
-        ;;
-    2)
-        build_esmfold=true
-        ;;
-    3)
-        build_esm=true
-        build_esmfold=true
-        ;;
-    *)
-        echo "Invalid option selected. Please choose 1, 2, or 3."
-        exit 1
-        ;;
+    1) build_esm=true ;;
+    2) build_esmfold=true ;;
+    3) build_esm=true; build_esmfold=true ;;
+    *) echo "Invalid option selected. Please choose 1, 2, or 3."; exit 1 ;;
 esac
 
 echo "build_esm = ${build_esm}"
 echo "build_esmfold = ${build_esmfold}"
 
-# Function to build a Docker image with optional proxy arguments
+# Function to build Docker image
 build_image() {
-    local image_name="$1"
-    local dockerfile="$2"
-    local args=()
-
-    # Add proxy arguments if set
-    if [[ -n "$http_proxy" ]]; then
-        args+=(--build-arg http_proxy=$http_proxy)
-    fi
-    if [[ -n "$https_proxy" ]]; then
-        args+=(--build-arg https_proxy=$https_proxy)
-    fi
-    if [[ -n "$no_proxy" ]]; then
-        args+=(--build-arg no_proxy=$no_proxy)
-    fi
-
-    # Add the BASE_IMAGE argument
-    args+=(--build-arg BASE_IMAGE=$BASE_IMAGE)
-
-    # Execute the build command
-    $runtime build "${args[@]}" -f "$dockerfile" -t "$image_name" .
+  local image_name="$1"
+  local dockerfile="$2"
+  local args=(--build-arg BASE_IMAGE=$BASE_IMAGE)
+
+  [[ -n "$http_proxy" ]] && args+=(--build-arg http_proxy=$http_proxy)
+  [[ -n "$https_proxy" ]] && args+=(--build-arg https_proxy=$https_proxy)
+  [[ -n "$no_proxy" ]] && args+=(--build-arg no_proxy=$no_proxy)
+
+  $runtime build "${args[@]}" -f "$dockerfile" -t "$image_name" .
 }
 
-# Build base image with optional proxy arguments
+# Build base image
 if ! image_exists "$BASE_IMAGE"; then
-    echo "Building base image..."
-    build_image "$BASE_IMAGE" "Dockerfile.base"
+  echo "Building base image..."
+  build_image "$BASE_IMAGE" "Dockerfile.base"
 fi
 
-# Build image for esm
+# Build esm image
 if $build_esm && ! image_exists "$ESM_IMAGE"; then
-    echo "Building image for esm..."
-    build_image "$ESM_IMAGE" "Dockerfile.esm"
+  echo "Building image for esm..."
+  build_image "$ESM_IMAGE" "Dockerfile.esm"
 fi
 
-# Build image for esm_fold
+# Build esm_fold image
 if $build_esmfold && ! image_exists "$ESMFOLD_IMAGE"; then
-    echo "Building image for esm_fold..."
-    build_image "$ESMFOLD_IMAGE" "Dockerfile.esmfold"
+  echo "Building image for esm_fold..."
+  build_image "$ESMFOLD_IMAGE" "Dockerfile.esmfold"
 fi
 
 echo "Build process completed."