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habrok:connecting_to_the_system:web_portal [2023/07/12 07:58] – [Jupyter Notebook] fokkehabrok:connecting_to_the_system:web_portal [2023/11/08 08:50] (current) – [Jupyter Notebook] fokke
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 ** **
-''The Web Portal for Hábrók is now available, but some functionality is still lacking. For instance, the interactive apps for remote desktop, MATLAB, COMSOL, TensorFlow, and PyTorch are not available yet.''+''The Web Portal for Hábrók is now available, but some functionality is still lacking. For instance, the interactive apps for TensorFlow and PyTorch are not available yet.''
 ** **
  
 ====== Web Portal ====== ====== Web Portal ======
  
-We have implemented a new web portal for Hábrók, based on software developed at the [[https://www.osc.edu/|Ohio Supercomputer Center]], called [[http://openondemand.org/|OpenOnDemand]] (affectionately known as [[https://en.wikipedia.org/wiki/Ood|OOD]]). Using your username and password just as you would do on Hábrók, you can login to this portal at the following address:+We have implemented a new web portal for Hábrók, based on software developed at the [[https://www.osc.edu/|Ohio Supercomputer Center]], called [[http://openondemand.org/|OpenOnDemand]] (affectionately known as [[https://en.wikipedia.org/wiki/Ood|OOD]]). Using your username and password, just as you would do on Hábrók, you can log in to this portal at the following address:
  
 https://portal.hb.hpc.rug.nl https://portal.hb.hpc.rug.nl
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 ===== Logging in ===== ===== Logging in =====
-  - If you already have a Hábrók account, you can just go to [[https://portal.hb.hpc.rug.nl]] and click on the <html><span class="glyphicon glyphicon-log-in hidden-sm"></span></html> Login button at the top-right corner. You will be prompted to enter your username, password and MFA token, using the RUG single sign on page, after which you will be logged in to the Web Portal.+  - If you already have a Hábrók account, you can just go to [[https://portal.hb.hpc.rug.nl]] and click on the <html><span class="glyphicon glyphicon-log-in hidden-sm"></span></html> Login button at the top-right corner. You will be prompted to enter your username, password, and MFA token, using the RUG single sign-on page, after which you will be logged in to the Web Portal.
   - If you don't have a Hábrók account, then go the [[https://iris.service.rug.nl|IRIS]] support system to request an account (more information at the [[..:introduction/policies|"Accounts and policies"]] page). Once your account has been added to Hábrók, follow from step 1 here to login.   - If you don't have a Hábrók account, then go the [[https://iris.service.rug.nl|IRIS]] support system to request an account (more information at the [[..:introduction/policies|"Accounts and policies"]] page). Once your account has been added to Hábrók, follow from step 1 here to login.
 ===== The Dashboard ===== ===== The Dashboard =====
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 {{dashboard.png|}} {{dashboard.png|}}
  
-Here, in addition the “Message of the Day” that you see when you ''ssh'' into Hábrók, we will also display messages relevant only to the web portal (such as any planned maintenance of the portal).+Here, in addition to the “Message of the Day” that you see when you ''ssh'' into Hábrók, we will also display messages relevant only to the web portal (such as any planned maintenance of the portal).
  
 The menu has several items, the most useful ones being: The menu has several items, the most useful ones being:
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 ===== The Files menu ===== ===== The Files menu =====
  
-In the ''%%Files%%'' menu you have access to your home, ''%%/projects%%'' and ''%%/scratch%%'' folders, as well as any group folders in ''%%/scratch%%'' for groups you belong to, and which are names as ''%%hb-<group-name>%%''. When accessing any of the submenus in ''%%Files%%'', the corresponding folder will be opened in a file explorer in a new browser tab. From here you can navigate, perform file operations (copy, delete, etc.), view and even edit files (the file editor has syntax highlighting for a large number of text file formats).+In the ''%%Files%%'' menu you have access to your home, ''%%/projects%%'' and ''%%/scratch%%'' folders, as well as any group folders in ''%%/scratch%%'' for groups you belong to, and which are named as ''%%hb-<group-name>%%''. When accessing any of the submenus in ''%%Files%%'', the corresponding folder will be opened in a file explorer in a new browser tab. From here you can navigate, perform file operations (copy, delete, etc.), view and even edit files (the file editor has syntax highlighting for a large number of text file formats).
  
 ===== The Jobs menu ===== ===== The Jobs menu =====
  
-In the ''%%Jobs%%'' menu, there are two subitems: ''%%Active Jobs%%'' and ''%%Job Composer%%''. The ''%%Job Composer%%'' allows you to define a submit a job directly from the web portal, but at the moment it is a bit cumbersome and counter-intuitive in our opinion, so we do not recommend using it just yet. The ''%%Active Jobs%%'' provides and overview of jobs on the cluster, either for yourself or all users. It is similar to the ''%%squeue%%'' from the command line.+In the ''%%Jobs%%'' menu, there are two subitems: ''%%Active Jobs%%'' and ''%%Job Composer%%''. The ''%%Job Composer%%'' allows you to define a submit a job directly from the web portal, but at the moment it is a bit cumbersome and counter-intuitive in our opinion, so we do not recommend using it just yet. The ''%%Active Jobs%%'' provides an overview of jobs on the cluster, either for yourself or all users. It is similar to the ''%%squeue%%'' from the command line.
  
 ===== The Clusters menu ===== ===== The Clusters menu =====
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   * ''<ipython_version> = IPython/8.5.0-GCCcore-11.3.0'' for ''Python 3.10.4''   * ''<ipython_version> = IPython/8.5.0-GCCcore-11.3.0'' for ''Python 3.10.4''
 +  * ''<ipython_version> = IPython/7.26.0-GCCcore-11.2.0'' for ''Python 3.8.16''
  
 Now build a virtual environment in ''$HOME/venvs'': Now build a virtual environment in ''$HOME/venvs'':
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 source $HOME/venvs/my_env/bin/activate source $HOME/venvs/my_env/bin/activate
 </code> </code>
- +It is advisable to upgrade the version of pip for you new virtual environment, to suppress the warning that you will get anytime you install a new package. Also installing or updating the ''wheels'' and ''setuptools'' modules is required.
-Optionally, you can upgrade the version of pip for you new virtual environment, to suppress the warning that you will get anytime you install a new package. Also installing and updating setuptools is required.+
 <code> <code>
 pip install --upgrade pip wheel setuptools pip install --upgrade pip wheel setuptools
 </code> </code>
  
-Before your are able to build a Jupyter Notebook kernel for your new virtual environment, there are a few additional packages that you need to install. +Before you are able to build a Jupyter Notebook kernel for your new virtual environment, there are a few additional packages that you need to install:
 <code> <code>
-pip install pip install tomlkit jupyter-contrib-core+pip install tomlkit jupyter-contrib-core
 </code> </code>
  
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 </code> </code>
  
-You can check that the kernel has been properly generated by having a look at its file, which is usually in ''$HOME/.local/share/jupyter/kernels/my_env/kernel.json''. If you see a reference to your virtual environment in this file, something like ''/data/$USER/.envs/my_env/bin/python'', this means that everything is properly setup.+You can check that the kernel has been properly generated by having a look at its file, which is usually in ''$HOME/.local/share/jupyter/kernels/my_env/kernel.json''. If you see a reference to your virtual environment in this file, something like ''$HOME/venvs/my_env/bin/python'', this means that everything is properly set up.
  
-That's it! You have now access to the virtual environment you just built from the Jupyter Notebook (note that you may need to reload the Jupyter web page), through a kernel named ''my_env'' (You can, of course, use any name you please).+That's it! You now have access to the virtual environment you've just built from the Jupyter Notebook (note that you may need to reload the Jupyter web page), through a kernel named ''my_env'' (You can, of course, use any name you please).
  
 Any packages you install in this virtual environment will be available from the Jupyter Notebook immediately. We suggest you use a ''requirements.txt'' file to keep track of the packages you've installed. Any packages you install in this virtual environment will be available from the Jupyter Notebook immediately. We suggest you use a ''requirements.txt'' file to keep track of the packages you've installed.
  
 +==== Hábrók Remote Desktop ====
 +
 +The Remote Desktop app will launch a graphical desktop environment (based on ([[https://mate-desktop.org/|MATE]]) on a compute node, allowing you to interactively run tools with a graphical user interface with some more resources than what's available on the login/interactive nodes. By submitting to the ''gpu'' partition, you can even make use of a GPU and do OpenGL hardware rendering. The desktop environment itself has some tools like a web browser, text editors, and terminal available, but in a terminal you can also make use of all the modules. This would allow you to run tools like MATLAB, Mathematica, ParaView, or VMD. 
 +
 +{{portal_remote_desktop.png?1600|}}
 ===== Testing ===== ===== Testing =====