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NCF VDI Apps

The NCF VDI portal is available at the address https://ncfood.rc.fas.harvard.edu 

NOTE: you need to be on the NCF VPN to reach the portal. 
NOTE: if you are not a NCF user, you are on the wrong page. Please refer to this page for further information on how to connect to the Odyssey VDI portal 

The Interactive Apps currently supported on the NCF VDI portal ( https://ncfood.rc.fas.harvard.edu )  are :

  • Remote Desktop 
    This app allows the user to schedule a Remote Desktop slurm job on one of the nodes in the ncf_vdi partition and opens a browser based viewer to connect to it

  • Jupyter notebook
    The app schedules a notebook session on one of the compute nodes in the centos7 NCF partition and open a connection to it in a new tab.

  • RStudio Server 
    The app schedules a rstudio server session on one of the compute nodes in the centos7 NCF partition and open a connection to it in a new tab.

Remote Desktop 

The Remote Desktop app will schedule a job on one of the nodes in ncf_vdi partition, start a vnc server and provide a link to connect to in via a browser based app. No client is needed to connect to it. 

To launch the session, select the "Odyssey Remote Desktop" entry from the "Interactive Apps" menu, and fill in the following form. 
In the form you will be able to select the memory allocated for the job (Max 8GB) and the allocated time (Max 12hrs).
If you want to be notified by email when the job starts select the checkbox and include a valid email address in the form.

When you made your selection press the "Launch" button.  
Allow a few seconds for the portal to process your submission form, and you will be redirected to the "My Interactive Sessions" page.

You will be able to click on "Launch noVNC in new Tab" to open the connection to the Remote Desktop directly in your browser. 
The Remote Desktop  runs the lightweight "Xfce" desktop.  Please see here (link to doc provided shortly) a few tips and tricks on how to customize some aspect of the looks of your session.

Note: If you close the noVNC tab or the connection times out due to long inactivity, you will be always able to reconnect to your session clicking again on the "Launch noVNC in new Tab" in the "My Interactive Sessions" page . Your job is controlled by Slurm and will keep running until the allocated time, or until you cancel the job.

Note: If you want to terminate your job and your Remote Desktop session, you can simply click the "Delete" button on the "My Interactive Sessions"  in the section corresponding to that particular job.

 

Jupyter Notebook

This App allows you to submit a job which starts a Jupyter notebook on a compute node and provides a link to connect to it on a new browser tab.

To launch the notebook, select the "Jupyter notebook" entry from the "Interactive Apps" menu, and fill in the following form. 
In the form you will be able to select the memory allocated for the job (<= 120GB) , the number of cores (<=32 cores)  and the allocated time (Max 12hrs).
If you want to be notified by email when the job starts select the checkbox and include a valid email address in the form.
The "Slurm Account" can be use to specify which lab account you want to charge in terms of FairShare for tis particular job.
If you only are affiliated to one lab you can ignore that entry as it will default to your primary group.

When you made your selection press the "Launch" button.  
Allow a few seconds for the portal to process your submission form, and you will be redirected to the "My Interactive Sessions" page.

You will be able to use the "Connect to Jupyter" button to open the notebook in a new tab on your browser.

Note: If you want to learn more about how to customize the execution kernels available in your Jupyter Notebook sessions please follow instructions here (documentation link will be provided shortly).

Note: When you are done running your computation you can delete the job using the "Delete" button in the section for that particular job in the  "My Interactive Sessions" page.

 

RStudio Server

This App allows you to submit a job which starts a Rstudio session  on a compute node and provides a link to connect to it on a new browser tab.

To launch the notebook, select the "Rstudio Server " entry from the "Interactive Apps" menu, and fill in the following form. 
In the form you will be able to select the memory allocated for the job (<= 120GB) , the number of cores (<=32 cores)  and the allocated time (Max 12hrs).

You can then select the version of R you want to run in your Rsession in RStudio, chasing from the modules available on the Odyssey Cluster ( for example R/3.5.1-fasrc01 Core).

You can also specify the location of the folder where your personally installed R packages will be installed. (for example ~/apps/R_3.5.1_Core ). The folder will be created if it does not already exist. 

If you want to be notified by email when the job starts select the checkbox and include a valid email address in the form.
The "Slurm Account" can be use to specify which lab account you want to charge in terms of FairShare for tis particular job.
If you only are affiliated to one lab you can ignore that entry as it will default to your primary group.

When you made your selection press the "Launch" button.  
Allow a few seconds for the portal to process your submission form, and you will be redirected to the "My Interactive Sessions" page.

You will be able to use the "Connect to RStudio Server" button to open the RStudio session in a new tab on your browser.

Note: When you are done running your computation you can delete the job using the "Delete" button in the section related to that particular job in the  "My Interactive Sessions" page.

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