From 1990a407eb9d28f3d33377535218756c6a79331b Mon Sep 17 00:00:00 2001
From: Ravi Tripathi <ravi89@uab.edu>
Date: Tue, 7 May 2019 15:14:21 -0500
Subject: [PATCH] Modified the heading of Example 3 and removed NGC section
---
singularity_container.ipynb | 47 ++++---------------------------------
1 file changed, 5 insertions(+), 42 deletions(-)
diff --git a/singularity_container.ipynb b/singularity_container.ipynb
index 99539cb..74c115b 100644
--- a/singularity_container.ipynb
+++ b/singularity_container.ipynb
@@ -297,7 +297,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## Example 2:\n",
+ "## Pulling a Docker Image\n",
"\n",
"In this example we are going to be pulling a singularity image from [dockerhub](https://hub.docker.com/). This singularity image contains [google-cloud-sdk tools](https://cloud.google.com/sdk/).\n",
"\n",
@@ -319,58 +319,21 @@
"metadata": {},
"outputs": [],
"source": [
- "!singularity exec -B /data gcloud.simg gsutil"
+ "!singularity exec -B /data/user/$USER gcloud.simg gsutil"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "To clean your directory of all the container images, you can run the command below"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "!rm *.simg"
+ "## Clean your directory:"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "## Example 3:\n",
- "\n",
- "[NVIDIA GPU Cloud](https://www.nvidia.com/en-us/gpu-cloud/) (NGC) offers a container registry of Docker images with over 35 HPC, HPC visualization, deep learning, and data analytics containers optimized for GPUs and delivering accelerated performance (figure 3). The registry includes some of the most popular applications including GROMACS, NAMD, ParaView, VMD, and TensorFlow.\n",
- "\n",
- "For this example you would have to start a new Jupyter Notebook session on the 'pascalnodes' partition. Most of the settings are similar to the ones that you had in the [Git repo](https://gitlab.rc.uab.edu/rc-training-sessions/singularity_containers) for this session. you just need to add/modify the following things.\n",
- "\n",
- "In the Environment parameter add\n",
- "```\n",
- "module load cuda92/toolkit/9.2.88\n",
- "module load CUDA/9.2.88-GCC-7.3.0-2.30\n",
- "module load Singularity/2.5.2-GCC-5.4.0-2.26\n",
- "module load Anaconda3\n",
- "```\n",
- "\n",
- "And in the partition choose:\n",
- "```\n",
- "pascalnodes\n",
- "```\n",
- "\n",
- "You will need to create a new account on Nvidia GPU Cloud, to pull down these conatiners."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "!singularity build vmc_gpu.simg docker://nvcr.io/hpc/vmd:cuda9-ubuntu1604-egl-1.9.4a17"
+ "To clean your directory of all the container images, you can run the command below"
]
},
{
@@ -379,7 +342,7 @@
"metadata": {},
"outputs": [],
"source": [
- "!singularity exec --nv vmc_gpu.simg /opt/vmd/bin/vmd -dispdev openglpbuffer -e hiv-simple-egloptix-test.vmd"
+ "!rm *.simg"
]
},
{
--
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