SOF-7810: tutorial on building containerized applications

lang/en/docs/cli/actions/add-software.md

@@ -4,15 +4,18 @@
 Users can compile their own software via the
 [Command Line Interface](../overview.md) (CLI). This is helpful if users need
 to run a specific version of an application that is not installed "globally".
-The globally installed applications are currently distributed as
-Apptainer[^1] (Singularity[^2]) containers, bundled with all required
-dependencies. This ensures that each application is isolated and avoids
-dependency conflicts.
-
-When planning to run an application that is not installed in
-our cluster, we encourage packaging code and its dependencies as an
-Apptainer/<wbr/>Singularity container. Existing Docker images
-can be converted into an Apptainer/<wbr/>Singularity images.
+The globally installed applications are currently distributed as Apptainer[^1]
+(Singularity[^2]) containers, bundled with all required dependencies. This
+ensures that each application is isolated and avoids dependency conflicts.
+
+When planning to run an application that is not installed in our cluster, we
+encourage packaging code and its dependencies as an Apptainer/<wbr/>Singularity
+container. Existing Docker images can be converted into an
+Apptainer/<wbr/>Singularity images.
+
+<div class="video-wrapper">
+<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/G1hfW_kS8oY?controls=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+</div>
 
 ## Using Sandbox mode
 Apptainer's sandbox mode is helpful for testing and fine-tuning the build steps

lang/en/docs/cli/actions/apptainer-tutorial.json

@@ -0,0 +1,221 @@
+{
+    "descriptionLinks": [
+        "Build containerized applications with GPU support: https://docs.mat3ra.com/cli/actions/add-software/"
+    ],
+    "description": "How to build containerized applications with GPU support using Apptainer.",
+    "tags": [
+        {
+            "...": "../../metadata/general.json#/tags"
+        },
+        "apptainer",
+        "container",
+        "containerization",
+        "gpu",
+        "nvidia",
+        "singularity"
+    ],
+    "title": "Mat3ra Tutorial: Build containerized applications with GPU support",
+    "youTubeCaptions": [
+        {
+            "text": "In this tutorial, <break time='0.15'/> we will learn, how we can build containerized applications with Apptainer.",
+            "startTime": "00:00:00.150",
+            "endTime": "00:00:06.000"
+        },
+        {
+            "text": "We will also discuss how you can enable GPU support for such containers.",
+            "startTime": "00:00:06.500",
+            "endTime": "00:00:15.000"
+        },
+        {
+            "text": "The detailed steps of this tutorial are available on our documentation site.",
+            "startTime": "00:00:16.000",
+            "endTime": "00:00:21.000"
+        },
+        {
+            "text": "The documentation link can be found in the description below.",
+            "startTime": "00:00:21.500",
+            "endTime": "00:00:25.000"
+        },
+        {
+            "text": "Now, let's head over to platform dot matera dot com and launch the web terminal.",
+            "startTime": "00:00:25.500",
+            "endTime": "00:00:30.000"
+        },
+        {
+            "text": "Alternatively, you can connect to the login node using SSH.",
+            "startTime": "00:00:30.500",
+            "endTime": "00:00:34.000"
+        },
+        {
+            "text": "Let's verify that the Apptainer is installed, and check its version.",
+            "startTime": "00:00:34.500",
+            "endTime": "00:00:39.000"
+        },
+        {
+            "text": "First, <break time='0.15'/> we can use the Apptainer sandbox mode to test and fine tune the build steps interactively.",
+            "startTime": "00:00:39.500",
+            "endTime": "00:00:45.000"
+        },
+        {
+            "text": "Once the build steps are finalized, we can package the sandbox folder into a final image.",
+            "startTime": "00:00:45.500",
+            "endTime": "00:00:51.000"
+        },
+        {
+            "text": "Or, <break time='0.15'/> we can create a definition file with finalized build steps and build the container from it.",
+            "startTime": "00:00:51.500",
+            "endTime": "00:00:55.000"
+        },
+        {
+            "text": "Let's call our sandbox folder GCC sandbox.",
+            "startTime": "00:00:55.500",
+            "endTime": "00:01:00.000"
+        },
+        {
+            "text": "And initialize the sandbox with Alma Linux 9 base-image from the Docker registry.",
+            "startTime": "00:01:00.500",
+            "endTime": "00:01:06.000"
+        },
+        {
+            "text": "Notice the warning messages, we first need to set appropriate file permissions for the sandbox folder to be able to delete it later.",
+            "startTime": "00:01:06.500",
+            "endTime": "00:01:13.000"
+        },
+        {
+            "text": "Next, we can enter the sandbox container in the shell mode with write permission and as root user.",
+            "startTime": "00:01:13.500",
+            "endTime": "00:01:19.000"
+        },
+        {
+            "text": "Now, we can install packages in the sandbox container as you would normally do.",
+            "startTime": "00:01:19.500",
+            "endTime": "00:01:24.000"
+        },
+        {
+            "text": "Once the installation is complete, we can exit the sandbox container.",
+            "startTime": "00:01:24.500",
+            "endTime": "00:01:28.000"
+        },
+        {
+            "text": "We can package the sandbox folder into a final image with the build command.",
+            "startTime": "00:01:28.500",
+            "endTime": "00:01:33.000"
+        },
+        {
+            "text": "Now, we can verify that the container is working by running the GCC compiler.",
+            "startTime": "00:01:33.500",
+            "endTime": "00:01:38.000"
+        },
+        {
+            "text": "There is a second way to build the container, by creating a definition file with the build steps.",
+            "startTime": "00:01:38.500",
+            "endTime": "00:01:45.000"
+        },
+        {
+            "text": "An example definition file is available in our documentation site, let's copy it to clipboard.",
+            "startTime": "00:01:45.500",
+            "endTime": "00:01:51.000"
+        },
+        {
+            "text": "To transfer the clipboard content from the host machine to the web terminal, we can open the Remote-connection Sidebar by pressing Control Alt Shift <break time='0.15'/> in Windows and Linux <break time='0.15'/> or Control Option Shift in Mac.",
+            "startTime": "00:01:51.500",
+            "endTime": "00:02:03.000"
+        },
+        {
+            "text": "We can open vim editor, press i to enter insert mode, and right click to paste the clipboard content.",
+            "startTime": "00:02:03.500",
+            "endTime": "00:02:08.000"
+        },
+        {
+            "text": "Press the escape key, and type colon <break time='0.15'/> w q to save and exit the file.",
+            "startTime": "00:02:08.500",
+            "endTime": "00:02:14.000"
+        },
+        {
+            "text": "Now, we can run apptainer build command <break time='0.15'/> with the image name followed by the definition file name.",
+            "startTime": "00:02:14.500",
+            "endTime": "00:02:19.000"
+        },
+        {
+            "text": "However note that computationally intensive builds should not be directly run on the login node.",
+            "startTime": "00:02:19.500",
+            "endTime": "00:02:25.000"
+        },
+        {
+            "text": "Instead they should be submitted as a job to the batch system as described in our documentation.",
+            "startTime": "00:02:25.500",
+            "endTime": "00:02:30.000"
+        },
+        {
+            "text": "If you need GPU support, please use the dash dash NV flag with apptainer exec command.",
+            "startTime": "00:02:30.500",
+            "endTime": "00:02:37.000"
+        },
+        {
+            "text": "This will map the necessary drivers from the host to the container and set the necessary environment variables.",
+            "startTime": "00:02:37.500",
+            "endTime": "00:02:44.000"
+        },
+        {
+            "text": "Note that it is not necessary to install all dependencies inside the container.",
+            "startTime": "00:02:44.500",
+            "endTime": "00:02:49.000"
+        },
+        {
+            "text": "Especially large libraries like NVIDIA HPC SDK or Intel OneAPI.",
+            "startTime": "00:02:49.500",
+            "endTime": "00:02:55.000"
+        },
+        {
+            "text": "Instead, you can map such libraries from the host to the container using the bind directive.",
+            "startTime": "00:02:55.500",
+            "endTime": "00:03:01.000"
+        },
+        {
+            "text": "Commonly used libraries are available in our clusters under /export or /cluster-share directories.",
+            "startTime": "00:03:01.500",
+            "endTime": "00:03:06.000"
+        },
+        {
+            "text": "You may visit our open source container registry at GitHub to inspect the definition files.",
+            "startTime": "00:03:06.500",
+            "endTime": "00:03:11.000"
+        },
+        {
+            "text": "You are also welcome to contribute to our container registry by submitting a pull request.",
+            "startTime": "00:03:11.500",
+            "endTime": "00:03:16.000"
+        },
+        {
+            "text": "And build containers automatically via GitHub Actions workflow.",
+            "startTime": "00:03:16.500",
+            "endTime": "00:03:22.000"
+        },
+        {
+            "text": "Once the images are built, they are listed under the packages.",
+            "startTime": "00:03:022.500",
+            "endTime": "00:03:27.000"
+        },
+        {
+            "text": "First select the application name, then select appropriate image tag and copy its URL.",
+            "startTime": "00:03:27.500",
+            "endTime": "00:03:32.000"
+        },
+        {
+            "text": "We can go back to the web terminal and download the image using apptainer pull command.",
+            "startTime": "00:03:32.500",
+            "endTime": "00:03:38.000"
+        },
+        {
+            "text": "Now, visit platform dot matera dot com and try building your own containers.",
+            "startTime": "00:03:38.500",
+            "endTime": "00:03:44.000"
+        },
+        {
+            "text": "Thank you for watching this tutorial and using our platform.",
+            "startTime": "00:03:44.500",
+            "endTime": "00:03:46.000"
+        }
+    ],
+    "youTubeId": "G1hfW_kS8oY"
+}

lang/en/docs/getting-started/run-first-simulation/web-interface.md

@@ -13,7 +13,7 @@ various UI components of Mat3ra web platform.
 <iframe class="gifffer"
     width="100%"
     height="100%"
-    src="https://www.youtube.com/embed/hT1VBFH7HHo"
+    src="https://www.youtube.com/embed/hT1VBFH7HHo?controls=0"
     frameborder="0"
     allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture"
     allowfullscreen>

lang/en/docs/jobs/overview.md

@@ -64,5 +64,5 @@ Below we present a short video demonstrating how to create jobs in Mat3ra
 platform.
 
 <div class="video-wrapper">
-<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/hT1VBFH7HHo" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/hT1VBFH7HHo?controls=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 </div>

lang/en/docs/jupyterlite/accessing-jupyterlite.md

@@ -33,5 +33,5 @@ In the below tutorial, we present how we can use JupyterLite session in Mat3ra
 platform to postprocess or analyze data.
 
 <div class="video-wrapper">
-<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/PXosTghiAzs" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/PXosTghiAzs?controls=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 </div>

lang/en/docs/tutorials/dft/electronic/hubbard.md

@@ -99,7 +99,7 @@ Once the job is finished, the Hubbard U values are shown in the **Results** tab.
 In the below animation, we go through an example calculation.
 
 <div class="video-wrapper">
-<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/33PykNO8QlQ" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/33PykNO8QlQ?controls=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 </div>
 
 

lang/en/docs/tutorials/dft/electronic/spin-magnetic-qe.md

@@ -104,5 +104,5 @@ down spin components, respectively.
 In the below video, we go through an example calculation.
 
 <div class="video-wrapper">
-<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/-FVgw46gh3w" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/-FVgw46gh3w?controls=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 </div>

lang/en/docs/tutorials/dft/electronic/spin-orbit-coupling-qe.md

@@ -102,5 +102,5 @@ topological Dirac states clearly.
 In the below video, we go through an example calculation.
 
 <div class="video-wrapper">
-<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/Zr1jcalLYPU" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/Zr1jcalLYPU?controls=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 </div>

lang/en/docs/tutorials/dft/optical/epsilon-optimal-basis.md

@@ -127,5 +127,5 @@ plotting program for visualization.
 In the below tutorial, we go through the whole process.
 
 <div class="video-wrapper">
-<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/v7c52D4p1gs" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/v7c52D4p1gs?controls=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 </div>

lang/en/docs/tutorials/jobs-cli/qe-gpu.md

@@ -86,5 +86,5 @@ and find what gives you the best performance.
 ## Step-by-step screenshare video
 
 <div class="video-wrapper">
-<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/trLDEwWc3ho" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/trLDEwWc3ho?controls=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 </div>

lang/en/docs/tutorials/ml/deepmd-mlff-with-espresso-cp-and-lammps.md

@@ -126,5 +126,5 @@ Jupyter Notebook session in our platform to further analyze output files.
 In the below animation, we walk you through the whole workflow process.
 
 <div class="video-wrapper">
-<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/daTwJyMPIvE" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/daTwJyMPIvE?controls=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 </div>

lang/en/docs/tutorials/platform-access.md

@@ -1,16 +1,16 @@
 # Accessing the Platform
 
-There are three main modes of accessing the Mat3ra platform: 
+There are three main modes of accessing the Mat3ra platform:
 
-- (1) Web/browser interface 
-- (2) [Command line interface](../cli/overview.md) (CLI), and 
+- (1) Web/browser interface
+- (2) [Command line interface](../cli/overview.md) (CLI), and
 - (3) [REST API](../rest-api).
 
 - Below we present a short video demonstrating various ways of accessing the Mat3ra platform. It covers:
 
 - 00:54 Web platform overview
 - 01:42 Materials designer
-- 02:26 Command Line Interface 
+- 02:26 Command Line Interface
 - 02:57 SSH to login node
 - 04:01 Web terminal
 - 04:13 API access
@@ -20,5 +20,5 @@ There are three main modes of accessing the Mat3ra platform:
 ## The Video
 
 <div class="video-wrapper">
-<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/vERldqp77bU" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+<iframe class="gifffer" width="100%" height="100%" src="https://www.youtube.com/embed/vERldqp77bU?controls=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 </div>

mkdocs.yml

@@ -30,7 +30,7 @@ extra_javascript:
 copyright: <a target="_blank" href="https://mat3ra.com">Exabyte Inc</a>. All rights reserved. | <a target="_blank" href="https://platform.mat3ra.com">Back to platform</a>
 
 extra:
-    version: "2025.12.25"
+    version: "2026.1.22"
     preload_javascript:
         - /extra/js/preload_hotjar.js
         - /extra/js/preload.js