Commit e13174c1 authored by Tim Kreuzer's avatar Tim Kreuzer
Browse files

update faq hdfcloud notebook

parent c6c321e8
......@@ -2,18 +2,15 @@
"cells": [
{
"cell_type": "markdown",
"metadata": {
"toc-hr-collapsed": false
},
"metadata": {},
"source": [
"# Welcome to the Jupyter@JSC Virtual Machine JupyterLab"
"# Welcome to the Jupyter-JSC Virtual Machine JupyterLab"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"---\n",
"## Where is this JupyterLab running?"
]
},
......@@ -24,21 +21,6 @@
"      This JupyterLab instance is running on a [virtual machine](https://www.techopedia.com/definition/4805/virtual-machine-vm) on the [HDF-Cloud](https://www.fz-juelich.de/ias/jsc/EN/Expertise/SciCloudServices/HDFCloud/_node.html). It is started as a [Docker Container](https://www.docker.com/resources/what-container). "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Is there any limitation?"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"      You can use a maximum of 4 GB of RAM. \n",
"      If you need more memory please start your JupyterLab on a HPC system."
]
},
{
"cell_type": "markdown",
"metadata": {},
......@@ -50,24 +32,8 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"      You can stop this JupyterLab in the Control Panel of Jupyter@JSC. \n",
"      You can reach the Control Panel [here](https://zam10116.zam.kfa-juelich.de/hub/start) or in the menu File -> Hub Control Panel."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Why is the memory usage so high?"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"      If you have the feeling that your used Memory in the top right corner is too high, ensure that your kernels were shutdown. \n",
"      Whenever a Tab of your Notebook is closed, the kernel is still running in the background. \n",
"      You can see all running kernels by clicking on this symbol ![Kernels](https://jupyter-jsc.fz-juelich.de/hub/static/images/kernels.png \"kernels\") on the left sidebar."
"      You can stop this JupyterLab in the Control Panel of Jupyter-JSC. \n",
"      You can reach the Control Panel [here](https://jupyter-jsc.fz-juelich.de/hub/start) or in the menu File -> Hub Control Panel."
]
},
{
......@@ -83,7 +49,7 @@
"source": [
"      You can use git or you upload files with this button in the top left corner: \n",
" \n",
"      ![Upload files](https://zam10183.zam.kfa-juelich.de/hub/static/images/upload.png \"Upload Files\")"
"      ![Upload files](https://jupyter-jsc.fz-juelich.de/hub/static/images/upload.png \"Upload Files\")"
]
},
{
......@@ -112,9 +78,8 @@
"metadata": {},
"source": [
"      You can select between [these eight](https://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-base-notebook) Images. \n",
"      We installed additionally a few JupyterLab [extensions](https://nbviewer.jupyter.org/github/kreuzert/Jupyter-JSC/blob/master/Extensions.ipynb). \n",
"      We installed additionally a few JupyterLab extensions. You can find a List of all installed extensions [here.](https://nbviewer.jupyter.org/github/kreuzert/Jupyter-JSC/blob/master/Extensions.ipynb) \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;If you want to add your own Docker Image to Jupyter@JSC please contact the <a href=\"mailto:ds-support@fz-juelich.de?subject=Jupyter@JSC Support&amp;body=Please describe your problem here. (english or german)\">Jupyter@JSC support</a>."
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;We installed additionally a few JupyterLab extensions. \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;If you want to add your own Docker Image to Jupyter-JSC please contact the <a href=\"mailto:ds-support@fz-juelich.de?subject=Jupyter-JSC Support&amp;body=Please describe your problem here. (english or german)\">Jupyter-JSC support</a>."
]
},
{
......@@ -130,33 +95,16 @@
"source": [
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;You can store 10 GB of data in /home/jovyan/work. \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<font color='red'>All files in the ~/work directory will be stored persistently.</font> \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<font color='red'>All files in the ~/work directory will be accessible in all of your HDF-Cloud JupyterLabs.</font> \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<font color='red'>Any other files or directories will be deleted if you stop this JupyterLab.</font> \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Under no circumstances are we liable for any lost data. "
]
},
{
"cell_type": "markdown",
"metadata": {
"toc-hr-collapsed": true
},
"source": [
"## How much memory do I have?"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;These JupyterLabs are limited to 4GB Ram."
]
},
{
"cell_type": "markdown",
"metadata": {
"toc-hr-collapsed": true
},
"source": [
"## Collaborative work\n",
"# Collaborative work\n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;We offer four different solutions to share your work with your colleagues. "
]
},
......@@ -173,7 +121,7 @@
"metadata": {},
"source": [
"### Projects\n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Projects are the best way, if you just want to share a few files (or notebooks) with your colleague, who is also using Jupyter@JSC. \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Projects are the best way, if you just want to share a few files (or notebooks) with your colleague, that is also using Jupyter-JSC. \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Projects are directories, that are generated on the [virtual machine](https://www.techopedia.com/definition/4805/virtual-machine-vm) where your JupyterLab is running. \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;If you add another user to your project this directory will be mounted into their [Docker Container](https://www.docker.com/resources/what-container) . \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;You can manage your projects with the following command:\n",
......@@ -190,7 +138,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"### B2DROP"
"#### B2DROP"
]
},
{
......@@ -198,23 +146,17 @@
"metadata": {},
"source": [
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;You can easily mount your [B2DROP](https://b2drop.eudat.eu) files into this JupyterLab. \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Just run the command \"$ mount B2DROP\" in a terminal and insert your [application credentials](https://eudat.eu/services/userdoc/b2drop#UserDocumentation-B2DROPUsage-WebDavclient)\\. \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Just run the command `mount B2DROP` in a terminal and insert your [application credentials](https://eudat.eu/services/userdoc/b2drop#UserDocumentation-B2DROPUsage-WebDavclient)\\. \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;If you want to store your [application credentials](https://eudat.eu/services/userdoc/b2drop#UserDocumentation-B2DROPUsage-WebDavclient) add the following line to /home/jovyan/work/.davfs2/secrets: \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;https://b2drop.eudat.eu/remote.php/webdav \\<USERNAME> \\<PASSWORD>"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### HPCMOUNT (experimental)"
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;https://b2drop.eudat.eu/remote.php/webdav \\<USERNAME> \\<PASSWORD> \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;To unmount it run `umount B2DROP`"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<span style=\"color:red\">Your groups are not mounted. So you have only access to files that are yours.</span>"
"### HPCMOUNT"
]
},
{
......@@ -231,7 +173,7 @@
"\n",
"### &nbsp;&nbsp;&nbsp; What will the script do?\n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;If you run it for the first time, it will create a private/public key pair for you. For your safety, a passphrase is required for this key. \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Afterward, it will upload the public key to your [JUDAC](https://www.fz-juelich.de/ias/jsc/EN/Expertise/Datamanagement/JUDAC/JUDAC_node.html) ~/.ssh/authorized_keys file. This will be done with [UNICORE](https://www.unicore.eu) and the [credentials](https://judoor.fz-juelich.de/login) you used to log in to Jupyter@JSC. \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Afterward, it will upload the public key to your [JUDAC](https://www.fz-juelich.de/ias/jsc/EN/Expertise/Datamanagement/JUDAC/JUDAC_node.html) ~/.ssh/authorized_keys file. This will be done with [UNICORE](https://www.unicore.eu) and the [credentials](https://judoor.fz-juelich.de/login) you used to log in to Jupyter-JSC. \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;If your key is uploaded (or you have already used this script before) it will run the sshfs command to mount your HPC files. \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;You have to enter your passphrase, that you chose in the first run, to use your generated private key.\n",
"### &nbsp;&nbsp;&nbsp; How can I unmount it?\n",
......@@ -241,7 +183,7 @@
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The folder will be automatically unmounted if you stop this JupyterLab. \n",
"### &nbsp;&nbsp;&nbsp; Where is my private key stored?\n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The private key will be stored, like your other files, in the /home/jovyan/work directory, on a [virtual machine](https://www.techopedia.com/definition/4805/virtual-machine-vm) on the [HDF-Cloud](https://www.fz-juelich.de/ias/jsc/EN/Expertise/SciCloudServices/HDFCloud/_node.html) . \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The access to this virtual machine is limited to the administrators of Jupyter@JSC. \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The access to this virtual machine is limited to the administrators of Jupyter-JSC. \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Since your private key is encrypted with a passphrase, even an administrator is not able to use your private key to connect to any HPC system. \n",
"### &nbsp;&nbsp;&nbsp; I want to mount another account\n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;If you have multiple accounts (connected to your [JSC webservice credentials](https://judoor.fz-juelich.de/login)) you can tell the script which one it should use. \n",
......@@ -250,7 +192,7 @@
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\\<SYSTEM> is the HPC system that is used to upload your public key. Please use one of these: JURECA, JUWELS, JURON. Your account must have an active project on the chosen system. \n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\\<ACCOUNT> is your HPC account on this system ( and on [JUDAC](https://www.fz-juelich.de/ias/jsc/EN/Expertise/Datamanagement/JUDAC/JUDAC_node.html)) . \n",
"### &nbsp;&nbsp;&nbsp; I want to delete the public key from my HPC account\n",
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Jupyter@JSC does not delete anything from your authorized_keys file. So if you want to remove the public key you have to log in to JUDAC and remove it manually. "
"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Jupyter-JSC does not delete anything from your authorized_keys file. So if you want to remove the public key you have to log in to JUDAC and remove it manually. "
]
}
],
......@@ -270,7 +212,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.8"
"version": "3.7.3"
}
},
"nbformat": 4,
......
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