EH: CS-1125 Provide a NVIDIA enroot Clara Parabricks container example using GPUs

source/dist/CMakeLists.txt

@@ -30,6 +30,7 @@ if (INSTALL_SGE_COMMON)
          hadoop
          mpi
          util
+         containerruntimes
          DESTINATION .
          USE_SOURCE_PERMISSIONS)
 endif ()

source/dist/containerruntimes/enroot/parabricks_job.sh

@@ -0,0 +1,99 @@
+#!/bin/bash
+#___INFO__MARK_BEGIN_NEW__
+###########################################################################
+#
+#  Copyright 2025 HPC-Gridware GmbH
+#
+#  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.
+#
+###########################################################################
+#___INFO__MARK_END_NEW__
+#$ -S /bin/bash
+#$ -V
+#$ -l h_rt=1:00:00
+#$ -l h_vmem=16G
+#$ -l NVIDIA_GPUS=1
+#$ -q gpu.q
+#$ -j y
+#$ -N enrootTest
+
+set -euo pipefail
+set -x
+
+# ------------------------------------------------------------------------------
+# This job script runs NVIDIA's Clara Parabricks in an enroot container.
+# It requires a gpu.q which setup the NVIDIA_VISIBLE_DEVICES env variable
+# and configures the NVIDIA_GPUS RSMAP. This is typically setup by 
+# Gridware Cluster Scheduler's qgpu utility.
+# ------------------------------------------------------------------------------
+
+# ------------------------------------------------------------------------------
+# User-configurable settings
+# ------------------------------------------------------------------------------
+CONTAINER_NAME="parabricks450"
+# By default, look for the image in the user's home directory
+IMAGE_FILE="$HOME/parabricks4501.sqsh"
+IMAGE_SOURCE="docker://nvcr.io#nvidia/clara/clara-parabricks:4.5.0-1"
+
+# (Optional) If $TMPDIR or a scratch path is preferred, change IMAGE_FILE as needed.
+# e.g., IMAGE_FILE="$TMPDIR/parabricks4501.sqsh"
+# ------------------------------------------------------------------------------
+
+# Ensure XDG_RUNTIME_DIR is set (some sites require this for enroot)
+export XDG_RUNTIME_DIR="/tmp"
+
+echo "Starting the job script..."
+echo "Host: $(hostname)"
+echo "Working directory: $(pwd)"
+echo "Date: $(date)"
+echo "----------------------------------------"
+
+# 1) Check if the container is already listed
+if enroot list | grep -q "^${CONTAINER_NAME}\$"; then
+  echo "Container '${CONTAINER_NAME}' already exists."
+else
+  echo "Container '${CONTAINER_NAME}' not found."
+
+  # 2) Check if the image file is already downloaded
+  if [[ -f "${IMAGE_FILE}" ]]; then
+    echo "Using existing local image file '${IMAGE_FILE}'."
+  else
+    echo "Local image file '${IMAGE_FILE}' not found. Importing from Docker registry..."
+    enroot import -o "${IMAGE_FILE}" "${IMAGE_SOURCE}"
+  fi
+
+  # 3) Double-check that the image file now exists
+  if [[ -f "${IMAGE_FILE}" ]]; then
+    echo "Confirmed image file exists: ${IMAGE_FILE}"
+  else
+    echo "ERROR: Image file '${IMAGE_FILE}' was not found or failed to import."
+    exit 1
+  fi
+
+  # 4) Create the container from the image
+  echo "Creating enroot container '${CONTAINER_NAME}'..."
+  enroot create --name "${CONTAINER_NAME}" "${IMAGE_FILE}"
+fi
+
+echo "----------------------------------------"
+echo "Current enroot container list:"
+enroot list
+echo "----------------------------------------"
+
+# 5) Start the container and run nvidia-smi (example command)
+echo "Launching '${CONTAINER_NAME}' container..."
+enroot start --rw "${CONTAINER_NAME}" nvidia-smi
+
+echo "----------------------------------------"
+echo "Job script completed."
+