From 89199a5dfdd57b5c9fbb43acf4bde5e3f50a6f7a Mon Sep 17 00:00:00 2001
From: mdefende <mdefende@uab.edu>
Date: Thu, 9 May 2024 19:36:11 -0500
Subject: [PATCH] add singularity options to the form and script
---
form.yml.erb | 25 +++++++++++++++++--------
template/script.sh.erb | 5 +++--
2 files changed, 20 insertions(+), 10 deletions(-)
diff --git a/form.yml.erb b/form.yml.erb
index 4b2fe3b..a29a0c3 100644
--- a/form.yml.erb
+++ b/form.yml.erb
@@ -14,12 +14,12 @@
cluster: "SLURM_CLUSTER"
# Title of the app displayed in the Dashboard
-title: "JupyterLab"
+title: "JupyterLab Singularity"
# Description of the app displayed in the Dashboard (can use multi-line string
# and Markdown syntax)
description: |
- This app will launch a JupyterLab server on one or more cores.
+ This app will launch a JupyterLab server on one or more cores from a given Singularity container.
# Define attribute values that aren't meant to be modified by the user within
# the Dashboard form
@@ -40,12 +40,9 @@ attributes:
widget: text_area
label: Environment Setup
value: |
- # The latest version of Anaconda3 with jupyter is loaded by default.
- # If you would like to load other modules
- # or use specific version of Anaconda please list below
- #
- # format:
- # module load example_module/VERSION example_module2
+ # load any other modules you may need here such as CUDA
+ # DO NOT LOAD Anaconda3 or Singularity, these are already
+ # taken care of
# Whether Conda extensions will be available within the JupyterLab
# server
@@ -59,6 +56,16 @@ attributes:
# @see https://docs.continuum.io/anaconda/user-guide/tasks/use-jupyter-notebook-extensions
conda_extensions: "1"
+ # User needs to set the path to the container
+ container_path:
+ widget: text_field
+ label: Path to Container File
+
+ # Any extra command line arguments to pass to `singularity exec ...`
+ extra_singularity_args:
+ widget: text_field
+ label: Extra Singularity arguments
+
# Any extra command line arguments to feed to the `jupyter-lab ...`
# command that launches the JupyterLab within the batch job
extra_jupyter_args:
@@ -112,6 +119,8 @@ attributes:
form:
- custom_environment
- conda_extensions
+ - container_path
+ - extra_singularity_args
- extra_jupyter_args
- bc_num_hours
- bc_partition
diff --git a/template/script.sh.erb b/template/script.sh.erb
index bfae0fe..8d9a755 100755
--- a/template/script.sh.erb
+++ b/template/script.sh.erb
@@ -6,8 +6,9 @@ module reset
#
# Start JupyterLab Server
#
-module load Anaconda3
<%= context.custom_environment.gsub(/\r\n?/, "\n") %>
unset XDG_RUNTIME_DIR
+export SINGULARITY_BINDPATH='/data,/scratch,/local,/share'
+
# Launch the JupyterLab Server
-jupyter-lab --config="${CONFIG_FILE}" <%= context.extra_jupyter_args %>
+singularity exec <%= context.extra_singularity_args %> <%= context.container_path %> jupyter-lab --config="${CONFIG_FILE}" <%= context.extra_jupyter_args %>
--
GitLab