From 21c51d2fe016493d2f814ce18ad1e46fd028c662 Mon Sep 17 00:00:00 2001
From: Stefan Kesselheim <s.kesselheim@fz-juelich.de>
Date: Thu, 17 Feb 2022 23:20:19 +0100
Subject: [PATCH] added code
---
create_kernel.sh | 3 +++
example_submission_script.sh | 13 +++++++++++++
jupyter-jsc/kernel.json | 9 +++++++++
jupyter-jsc/kernel.sh | 5 +++++
src/hello_world.py | 5 +++++
5 files changed, 35 insertions(+)
create mode 100755 create_kernel.sh
create mode 100644 example_submission_script.sh
create mode 100644 jupyter-jsc/kernel.json
create mode 100755 jupyter-jsc/kernel.sh
create mode 100644 src/hello_world.py
diff --git a/create_kernel.sh b/create_kernel.sh
new file mode 100755
index 0000000..a741e3c
--- /dev/null
+++ b/create_kernel.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+mkdir -p ~/.local/share/jupyter/kernels/singularity_docker_jupyter
+sed -e "s|/path/to|$PWD|" ./jupyter-jsc/kernel.json > ~/.local/share/jupyter/kernels/singularity_docker_jupyter/kernel.json
diff --git a/example_submission_script.sh b/example_submission_script.sh
new file mode 100644
index 0000000..d8aa296
--- /dev/null
+++ b/example_submission_script.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=00:01:00
+#SBATCH --partition=batch
+#SBATCH --account=atmlaml
+
+module load Singularity-Tools
+echo "-------- Outside of the container -----------"
+python src/hello_world.py
+echo "-------- Inside of the container ------------"
+singularity run singularity_docker_jupyter.sif python3 src/hello_world.py
+echo "--------------------------------------------"
diff --git a/jupyter-jsc/kernel.json b/jupyter-jsc/kernel.json
new file mode 100644
index 0000000..b4d6e82
--- /dev/null
+++ b/jupyter-jsc/kernel.json
@@ -0,0 +1,9 @@
+{
+ "argv": [
+ "/path/to/jupyter-jsc/kernel.sh",
+ "-f",
+ "{connection_file}"
+ ],
+ "display_name": "singularity_docker_jupyter",
+ "language": "python"
+}
diff --git a/jupyter-jsc/kernel.sh b/jupyter-jsc/kernel.sh
new file mode 100755
index 0000000..d4a5095
--- /dev/null
+++ b/jupyter-jsc/kernel.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+SOURCE_PATH=`dirname ${BASH_SOURCE}`
+module purge
+module load Singularity-Tools
+exec singularity run ${SOURCE_PATH}/../singularity_docker_jupyter.sif python3 -m ipykernel "$@"
diff --git a/src/hello_world.py b/src/hello_world.py
new file mode 100644
index 0000000..24a9c83
--- /dev/null
+++ b/src/hello_world.py
@@ -0,0 +1,5 @@
+
+import sys
+print("Hello world. This is my Python version:")
+print(sys.version)
+
--
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