Jetstream2 Deployment

hands-on/session II/Materials/build_jetstream_environment.sh

@@ -0,0 +1,191 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# ----------------------------------------
+# Pretty printing helpers (same style)
+# ----------------------------------------
+
+function generate_separator {
+  local max_len=0
+  for arg in "$@"; do
+    ((${#arg} > max_len)) && max_len=${#arg}
+  done
+
+  local spaces
+  printf -v spaces "%${max_len}s" ""
+  echo "${spaces// /=}"
+}
+
+function print_separated_message {
+  local sep
+  sep=$(generate_separator "$@")
+
+  echo "$sep"
+  for line in "$@"; do
+    echo "$line"
+  done
+  echo "$sep"
+}
+
+function die {
+  echo "ERROR: $*" >&2
+  exit 1
+}
+
+function step {
+  # Usage: step "1/7" "Message"
+  print_separated_message "[${1}] ${2}"
+}
+
+# ----------------------------------------
+# Static settings (change only if needed)
+# ----------------------------------------
+
+ENV_NAME="NSDF-Tutorial"
+KERNEL_NAME="nsdf-tutorial"
+KERNEL_DISPLAY='Python (NSDF-Tutorial)'
+
+# ----------------------------------------
+# Derived paths
+# ----------------------------------------
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+cd "$SCRIPT_DIR"
+
+# ----------------------------------------
+# 0) Ensure conda is available
+# ----------------------------------------
+
+step "0/7" "Checking conda availability"
+
+if command -v module >/dev/null 2>&1; then
+  # Jetstream module environment
+  module purge >/dev/null 2>&1 || true
+  module load miniforge >/dev/null 2>&1 || true
+fi
+
+command -v conda >/dev/null 2>&1 || die "conda not found. Did you 'module load miniforge'?"
+
+# Make conda activate work in scripts
+# shellcheck disable=SC1090
+source "$(conda info --base)/etc/profile.d/conda.sh"
+
+# ----------------------------------------
+# 1) Create env from environment.yml (replace if exists)
+# ----------------------------------------
+
+step "1/7" "Create env from environment.yml (name: ${ENV_NAME})"
+
+if conda env list | awk '{print $1}' | grep -qx "$ENV_NAME"; then
+  echo "Removing existing env: ${ENV_NAME}"
+  conda env remove -n "$ENV_NAME" -y >/dev/null
+fi
+
+conda env create -f environment.yml >/dev/null
+
+# ----------------------------------------
+# 2) Activate environment
+# ----------------------------------------
+
+step "2/7" "Activate env: ${ENV_NAME}"
+
+conda activate "$ENV_NAME"
+hash -r
+
+# ----------------------------------------
+# 3) Verify activation (hard fail if wrong)
+# ----------------------------------------
+
+step "3/7" "Verify activation"
+
+python - <<PY
+import os, sys
+env = os.environ.get("CONDA_DEFAULT_ENV")
+prefix = os.environ.get("CONDA_PREFIX")
+print("CONDA_DEFAULT_ENV:", env)
+print("CONDA_PREFIX:", prefix)
+print("sys.executable:", sys.executable)
+if env != "$ENV_NAME":
+    raise SystemExit(f"ERROR: expected CONDA_DEFAULT_ENV=$ENV_NAME but got {env}")
+PY
+
+# ----------------------------------------
+# 4) Install GEOtiled/geotiled editable
+# ----------------------------------------
+
+step "4/7" "Install GEOtiled/geotiled editable"
+
+GEOTILED_DIR="$SCRIPT_DIR/GEOtiled/geotiled"
+[[ -d "$GEOTILED_DIR" ]] || die "GEOtiled/geotiled dir not found: $GEOTILED_DIR"
+
+python -m pip install -e "$GEOTILED_DIR" >/dev/null
+
+# ----------------------------------------
+# 5) Configure Openvisuspy environment variables
+# ----------------------------------------
+
+step "5/7" "Configure Openvisuspy env vars (~/.bashrc)"
+
+OPENVISUSPY_SRC="$SCRIPT_DIR/openvisuspy/src"
+[[ -d "$OPENVISUSPY_SRC" ]] || die "openvisuspy/src not found: $OPENVISUSPY_SRC"
+
+# Append only if not already present (idempotent-ish)
+append_if_missing () {
+  local line="$1"
+  local file="$2"
+  grep -Fqx "$line" "$file" 2>/dev/null || echo "$line" >> "$file"
+}
+
+BASHRC="$HOME/.bashrc"
+
+append_if_missing "export PATH=\"\$PATH:${OPENVISUSPY_SRC}\"" "$BASHRC"
+append_if_missing "export PYTHONPATH=\"\$PYTHONPATH:${OPENVISUSPY_SRC}\"" "$BASHRC"
+append_if_missing "export BOKEH_ALLOW_WS_ORIGIN='*'" "$BASHRC"
+append_if_missing "export BOKEH_RESOURCES='cdn'" "$BASHRC"
+append_if_missing "export VISUS_CACHE=/tmp/visus-cache/nsdf-services/somospie" "$BASHRC"
+append_if_missing "export VISUS_CPP_VERBOSE=1" "$BASHRC"
+append_if_missing "export VISUS_NETSERVICE_VERBOSE=1" "$BASHRC"
+append_if_missing "export VISUS_VERBOSE_DISKACCESS=1" "$BASHRC"
+
+# Load into current shell too
+# shellcheck disable=SC1090
+source "$BASHRC"
+
+# ----------------------------------------
+# 6) Install openvisuspy editable
+# ----------------------------------------
+
+step "6/7" "Install openvisuspy editable"
+
+OPENVISUSPY_DIR="$SCRIPT_DIR/openvisuspy"
+[[ -d "$OPENVISUSPY_DIR" ]] || die "openvisuspy dir not found: $OPENVISUSPY_DIR"
+
+python -m pip install -e "$OPENVISUSPY_DIR" >/dev/null
+
+# ----------------------------------------
+# 7) Install ipykernel + register kernel
+# ----------------------------------------
+
+step "7/7" "Install Jupyter kernel + extras"
+
+# keep these visible enough to diagnose, but not too noisy
+ENV_BIN_DIR="$CONDA_PREFIX/bin"
+
+python -m ipykernel install --user \
+  --name "$KERNEL_NAME" \
+  --display-name "$KERNEL_DISPLAY" \
+  --env PATH "$ENV_BIN_DIR:$OPENVISUSPY_SRC:$PATH" \
+  --env LD_LIBRARY_PATH "$CONDA_PREFIX/lib:$CONDA_PREFIX/lib/gdalplugins" \
+  --env PROJ_LIB "$CONDA_PREFIX/share/proj" \
+  --env GDAL_DATA "$CONDA_PREFIX/share/gdal" \
+  --env PROJ_NETWORK "ON" 
+
+print_separated_message \
+  "DONE" \
+  "" \
+  "Environment:" \
+  "  conda activate ${ENV_NAME}" \
+  "" \
+  "Kernel:" \
+  "  jupyter kernelspec list" \
+  "  (look for '${KERNEL_DISPLAY}')"

hands-on/session II/Materials/environment.yml

@@ -21,4 +21,4 @@ dependencies:
   - pip
   - pip:
       - panel==1.3.8
-      - OpenVisusNoGui==2.2.128
+      - OpenVisusNoGui==2.2.149

hands-on/session II/README.md

@@ -49,8 +49,9 @@ You can download the introductory slides [here](https://drive.google.com/file/d/
 1. [Running the Tutorial](#running-the-tutorial)
 2. [Option 1: GitHub Codespaces (Recommended)](#option-1-GitHub-codespaces-recommended)
 3. [Option 2: Docker](#0ption-2-docker)
-4. [APPENDIX: Prerequities for Docker](#appendix-prerequities-for-docker)
-5. [Community and Resources](#community-and-resources)
+4. [Option 3: Jetstream2](#option-3-jetstream2)
+5. [APPENDIX: Prerequities for Docker](#appendix-prerequities-for-docker)
+6. [Community and Resources](#community-and-resources)
 7. [Publications](#publications)
 8. [Copyright and License](#copyright-and-license)
 9. [Authors](#authors)
@@ -118,6 +119,77 @@ docker-compose up -d</code></pre>
     </li>
   </ol>
 
+## Option 3: Jetstream2
+<p><strong>Requirements:</strong> Access to a Jetstream2 instance via SSH.</p>
+
+<h4>Initial Setup (First Time Only)</h4>
+<ol>
+  <li>
+    If you do not already have a Jetstream2 instance, follow the
+    <a href="Materials/jetstream2_manual.pdf" target="_blank">
+    Jetstream2 Setup Manual
+    </a>
+    to create and connect to one.
+  </li>
+
+  <li>Connect to your Jetstream2 instance via SSH.</li>
+
+<li>
+  Clone the tutorial repository:
+  <pre><code>git clone https://github.com/TauferLab/NSDF-Tutorial-2025.git</code></pre>
+</li>
+
+  <li>
+    Navigate to the session materials directory and build the environment:
+    <pre><code>cd NSDF-Tutorial-2025/hands-on/session\ II/Materials/
+module load miniforge
+./build_jetstream_environment.sh</code></pre>
+  </li>
+
+  <li>
+    Start Jupyter Lab:
+    <pre><code>cd ..
+jupyter-ip.sh</code></pre>
+  </li>
+
+  <li>Open the Jupyter Lab URL printed in the terminal in your web browser.</li>
+
+  <li>
+    In Jupyter Lab, select the kernel named
+    <strong>NSDF-Tutorial</strong>.
+  </li>
+</ol>
+
+<h4>Starting the Environment (After Installation)</h4>
+<ol>
+  <li>
+    Load Conda:
+    <pre><code>module load miniforge
+</code></pre>
+  </li>
+
+  <li>
+    Navigate to the tutorial directory and start Jupyter:
+    <pre><code>cd hands-on/session\ II
+jupyter-ip.sh</code></pre>
+  </li>
+
+  <li>Open the Jupyter Lab URL printed in the terminal in your browser.</li>
+</ol>
+
+<h4>Accessing OpenVisuspy Dashboards</h4>
+<ol>
+  <li>
+    From your local machine, create an SSH tunnel to forward the dashboard port:
+    <pre><code>ssh -L 8989:127.0.0.1:8989 &lt;Jetstream Native SSH&gt;</code></pre>
+  </li>
+
+  <li>
+    After executing the corresponding dashboard cell in Jupyter, open your browser and navigate to:
+    <pre><code>http://localhost:8989</code></pre>
+  </li>
+</ol>
+
 
 ## APPENDIX: Prerequisites
 

hands-on/session III/environment.yml

@@ -4,6 +4,7 @@ channels:
   - defaults
 dependencies:
   - python=3.10
+  - ipykernel==6.29.2
   - pip
   - pip:
     - numpy