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‎content/landing/_index.md

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## [Tutorials](/tutorials) are perfect for introducing yourself to a new topic.
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Some tutorials are offered as in-person and/or Zoom sessions regularly. Find the notes or slides and download materials [here](/tutorials).
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Some tutorials are offered as in-person and/or Zoom workshops regularly. Find the notes or slides and download materials [here](/tutorials).
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For a list of upcoming workshops, please see our [page](https://www.rc.virginia.edu/education/workshops/) at the UVARC Web site.
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‎content/notes/hpc-intro/_index.md

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UVA's primary resource for high\-performance computing provides a platform for computationally-intensive research across a variety of disciplines.
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{{< figure src="/notes/hpc-intro/img/rivanna_racks.png" caption="The Rivanna cluster" >}}
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‎content/notes/hpc-intro/connecting_to_the_system/connecting_fastx.md

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parent: Connecting to The System
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FastX is a Web-based desktop environment for HPC. It is accessible either through the [Open OnDemand Interactive Apps](/notes/rivanna-intro/ood_interactive_apps) menu, or directly at [rivanna-desktop.hpc.virginia.edu](https://rivanna-desktop.hpc.virginia.edu).
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FastX is a Web-based desktop environment for HPC. It is accessible either through the [Open OnDemand Interactive Apps](/notes/hpc-intro/ood_interactive_apps) menu, or directly at [rivanna-desktop.hpc.virginia.edu](https://rivanna-desktop.hpc.virginia.edu).
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FastX requires the VPN. If the VPN is not active, the start page _will not_ load.
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Always use either the OOD link or the `rivanna-desktop` URL. The underlying name of the host may change from time to time.
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{{< figure src="/notes/rivanna-intro/img/FastX_splash_screen.png" caption="Logging in to FastX" >}}
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{{< figure src="/notes/hpc-intro/img/FastX_splash_screen.png" caption="Logging in to FastX" >}}
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‎content/notes/hpc-intro/connecting_to_the_system/connecting_fastx_desktop.md

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A MATE desktop looks a little like an older Windows desktop. In the ribbon at the top are `Caja`, a file manager; a `Terminal` application, and the Firefox Web browser.
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{{< figure src="/notes/rivanna-intro/img/FastX_desktop.png" caption="The MATE Desktop" >}}
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{{< figure src="/notes/hpc-intro/img/FastX_desktop.png" caption="The MATE Desktop" >}}
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‎content/notes/hpc-intro/connecting_to_the_system/connecting_fastx_kill_restart.md

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You can also terminate -- or restart -- a session from the My Sessions tab. To terminate, click the `x` in the upper right of the session, or use the menu.
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To restart instead of terminating, click the arrow for "run".
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{{< figure src="/notes/rivanna-intro/img/FastX_kill_session.png" caption="Terminating or restarting a session." >}}
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{{< figure src="/notes/hpc-intro/img/FastX_kill_session.png" caption="Terminating or restarting a session." >}}
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‎content/notes/hpc-intro/connecting_to_the_system/connecting_fastx_logout.md

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If you simply close your session browser tab, FastX _suspends_ your session rather than terminates it. It is generally preferable to terminate rather than suspend so you will not accidentally have multiple sessions running.
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One way to terminate is to log out. Go to the System menu in the top ribbon and select `Log Out mst3k` (with your ID).
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{{< figure src="/notes/rivanna-intro/img/FastX_logout.png" caption="Logging out of the desktop." >}}
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{{< figure src="/notes/hpc-intro/img/FastX_logout.png" caption="Logging out of the desktop." >}}
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‎content/notes/hpc-intro/connecting_to_the_system/connecting_fastx_session_launch.md

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Most users should chose the MATE session.
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{{< figure src="/notes/rivanna-intro/img/FastX_session_launch.png" caption="Starting a MATE session" >}}
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{{< figure src="/notes/hpc-intro/img/FastX_session_launch.png" caption="Starting a MATE session" >}}
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Click the icon, then click the play button on the MATE session under "Disconnected Sessions" on the page. This will open a new window with two options: Browser Client, and Desktop Client.
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{{< figure src="/notes/rivanna-intro/img/FastX_connect_options.png" caption="Browser or Desktop Client" >}}
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{{< figure src="/notes/hpc-intro/img/FastX_connect_options.png" caption="Browser or Desktop Client" >}}
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Select the Browser Client to connect to your session.

‎content/notes/hpc-intro/connecting_to_the_system/connecting_fastx_session_page.md

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FastX starts a _session_ on a frontend. A new session is started by selecting either the _MATE_ or _Terminal_ icon under Applications on the right side of the page.
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{{< figure src="/notes/rivanna-intro/img/FastX_session_page.png" caption="Starting a new session" >}}
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{{< figure src="/notes/hpc-intro/img/FastX_session_page.png" caption="Starting a new session" >}}
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‎content/notes/hpc-intro/connecting_to_the_system/connecting_logging_on.md

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‎content/notes/hpc-intro/connecting_to_the_system/connecting_ood.md

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‎content/notes/hpc-intro/connecting_to_the_system/connecting_ood_dashboard.md

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The Open OnDemand home page is the Dashboard.
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{{< figure src="/notes/rivanna-intro/img/OOD_Dashboard.png" caption="OOD Dashboard" >}}
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{{< figure src="/notes/hpc-intro/img/OOD_Dashboard.png" caption="OOD Dashboard" >}}
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‎content/notes/hpc-intro/features_of_ood/features.md

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# Add menu entry to sidebar.
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name: Features of Open OnDemand
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Open OnDemand has many features accessible directly from the menu bar.
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{{< figure src="/notes/rivanna-intro/img/OOD_File_Menu.png" caption="Open OnDemand Menu Options" >}}
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{{< figure src="/notes/hpc-intro/img/OOD_File_Menu.png" caption="Open OnDemand Menu Options" >}}
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‎content/notes/hpc-intro/features_of_ood/features_exercise2.md

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‎content/notes/hpc-intro/features_of_ood/features_files_tab.md

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The "Files" tab on the menu bar gives access to all files in home or project (if applicable) directories.
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{{< figure src="/notes/rivanna-intro/img/OOD_files_tab.png" caption="OOD Files Menu" >}}
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{{< figure src="/notes/hpc-intro/img/OOD_files_tab.png" caption="OOD Files Menu" >}}
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Here, you can upload and download small files to and from the cluster from your local computer. You can also create and delete new files and directories in addition to copying or renaming them. The Filter search bar searches for files or directories in the file system.

‎content/notes/hpc-intro/features_of_ood/features_interactive_sessions.md

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This tab will show you running, pending or completed interactive sessions from the OOD interface.
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{{< figure src="/notes/rivanna-intro/img/features_interactive.png" caption="Interactive Sessions" >}}
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{{< figure src="/notes/hpc-intro/img/features_interactive.png" caption="Interactive Sessions" >}}

‎content/notes/hpc-intro/features_of_ood/features_job_composer.md

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The job composer tab allows you to create and submit a job to run on the cluster.
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{{< figure src="/notes/rivanna-intro/img/Features_job_composer.png" caption="OOD Job Composer" >}}
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{{< figure src="/notes/hpc-intro/img/Features_job_composer.png" caption="OOD Job Composer" >}}
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Selecting the default template will automatically create a submission script called ```demo_hello_world.slurm``` located in ```/home/computingID/Rivanna/data/sys/myjobs/projects/default/1``` on the file system:
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{{< figure src="/notes/rivanna-intro/img/featues_template_job.png" caption="Default Template Job" >}}
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{{< figure src="/notes/hpc-intro/img/featues_template_job.png" caption="Default Template Job" >}}
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Before submitting the job, ```your_allocation``` on the ```#SBATCH --account=your_allocation``` line must be replaced with the name of the allocation you're a member of. We will review editing files later. Once the correct allocation name is edited in, you can click "Submit" to queue your job. It will be given a corresponding Job ID, and once it's completed, the Folder contents will now contain a corresponding output file that contains the instructions from the submission script:
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{{< figure src="/notes/rivanna-intro/img/features_job_output.png" caption="Default Template Output" >}}
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{{< figure src="/notes/hpc-intro/img/features_job_output.png" caption="Default Template Output" >}}
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There are several different job templates that can be run in addition to the default hello world option under New Job > From Template:
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{{< figure src="/notes/rivanna-intro/img/features_templates.png" caption="Template Options" >}}
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{{< figure src="/notes/hpc-intro/img/features_templates.png" caption="Template Options" >}}

‎content/notes/hpc-intro/features_of_ood/features_job_stats.md

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In the OOD Job Viewer, clicking on the right arrow for a particular job will show details of the job if it is queued or running. Completed jobs will have no information available. Be patient as it can take a few moments for the information to be loaded. In this illustration the selected job is PENDING. The reason given is Resources, which means that no resources are available yet for this job.
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{{< figure src="/notes/rivanna-intro/img/OOD_job_status.png" caption="Viewing only my jobs." >}}
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{{< figure src="/notes/hpc-intro/img/OOD_job_status.png" caption="Viewing only my jobs." >}}
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Completed jobs will be visible only for a short while as they are wrapping up and exiting.
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‎content/notes/hpc-intro/features_of_ood/features_job_viewer.md

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Open OnDemand allows you to check the status of your jobs easily. Open the Jobs tab and go to Active Jobs. The default view is All Jobs.
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{{< figure src="/notes/rivanna-intro/img/OOD_squeue_viewer.png" caption="Job status viewer in OOD." >}}
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{{< figure src="/notes/hpc-intro/img/OOD_squeue_viewer.png" caption="Job status viewer in OOD." >}}
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You can filter to select subsets of the jobs, for example you can view only jobs in the `gpu` partition.
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{{< figure src="/notes/rivanna-intro/img/OOD_squeue_filter.png" caption="Viewing only the GPU partition." >}}
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{{< figure src="/notes/hpc-intro/img/OOD_squeue_filter.png" caption="Viewing only the GPU partition." >}}
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You can also look at the status of only your own jobs by switching from All Jobs to My Jobs.
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{{< figure src="/notes/rivanna-intro/img/OOD_squeue_myjobs.png" caption="Viewing only my jobs." >}}
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{{< figure src="/notes/hpc-intro/img/OOD_squeue_myjobs.png" caption="Viewing only my jobs." >}}

‎content/notes/hpc-intro/features_of_ood/features_jobs_tab.md

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The "Jobs" tab on the menu bar allows you to submit and search for jobs on the cluster.
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{{< figure src="/notes/rivanna-intro/img/OOD_jobs_tab.png" caption="OOD Jobs Menu" >}}
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{{< figure src="/notes/hpc-intro/img/OOD_jobs_tab.png" caption="OOD Jobs Menu" >}}
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The "Active Jobs" tab shows all jobs currently running or queues on all partitions for all users. The Filter search bar allows you to narrow jobs by either user, queue, job name, job ID, or job status (running, queued, completed, etc).
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‎content/notes/hpc-intro/features_of_ood/features_shell_access.md

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The "Clusters" tab on the menu bar open a new browser tab with a Linux command line interface for shell access:
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{{< figure src="/notes/rivanna-intro/img/features_shell_access.png" caption="Command line Shell Access" >}}
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{{< figure src="/notes/hpc-intro/img/features_shell_access.png" caption="Command line Shell Access" >}}
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Here, you are able to upload and download small files to and from the cluster from your local computer. You can also create and delete new files and directories in addition to copying or renaming them. The Filter search bar searches for files or directories in the file system.

‎content/notes/hpc-intro/features_of_ood/features_useful_commands.md

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Sometimes it's useful to check how many SUs are still available on your allocation. The ```allocations``` command displays information on your allocations and how many SUs are associated with them:
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{{< figure src="/notes/rivanna-intro/img/features_allocations.png" caption="Allocations" >}}
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{{< figure src="/notes/hpc-intro/img/features_allocations.png" caption="Allocations" >}}
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running ```allocations -a <allocation_name>``` provides even more detail on when the allocation was last renewed and its members.
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One way to check your storage utilization is with the ```hdquota``` command. This command will show you how much of your home, scratch, and project (if applicable) storage are being utilized. Below is the sample output for ```hdquota```:
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{{< figure src="/notes/rivanna-intro/img/features_hdquota.png" caption="Disk Usage" >}}
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{{< figure src="/notes/hpc-intro/img/features_hdquota.png" caption="Disk Usage" >}}
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This is a useful command to check whether or not you're running out of storage space or to see where files need to be cleaned up. For more detailed information on disk utilization you may also use the ```du``` command to investiage specific directories.
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To gain information on the different queues you can type ```qlist``` on the command line:
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{{< figure src="/notes/rivanna-intro/img/features_qlist.png" caption="Queues" >}}
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{{< figure src="/notes/hpc-intro/img/features_qlist.png" caption="Queues" >}}
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This will show the list of paritions, their occupancy, and the SU charge rate. You can type ```qlimits``` for information on each queue's limits:
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{{< figure src="/notes/rivanna-intro/img/features_qlimits.png" caption="Queue Limits" >}}
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{{< figure src="/notes/hpc-intro/img/features_qlimits.png" caption="Queue Limits" >}}
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Finally, the ```sinfo``` command will provide some more detailed information on the health of each queue and the number of active nodes available. These commands can be useful in diagnosing why a job may not be running, or in better understanding queue usage for more efficient job throughput. More information on hardware specifications and queue information can be found on our [website](https://www.rc.virginia.edu/userinfo/rivanna/overview/#system-details).
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‎content/notes/hpc-intro/files/file.md

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‎content/notes/hpc-intro/files/file_actions_create_delete.md

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‎content/notes/hpc-intro/files/file_actions_mv_cp.md

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‎content/notes/hpc-intro/files/file_editing.md

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* The built-in editor in Open OnDemand. Click on Files on the Dashboard, highlight the file that you want to edit. From the dropdown menu next to the file name, select Edit. A simple editor will open. To create a file, navigate to the desired location, click the New File button, then edit that file.
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* If logged in through FastX, you can use the `pluma` editor, which is accessible through the Applications->Accessories menu. You can also start it from a terminal with either its name `pluma` or as `gedit` (those are the same program).
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* The MATE desktop in FastX also provides the semi-graphical editors `Emacs` and `GVim` in the same menu.
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* In FastX, you can also use a programmer's interface such as VSCode, Spyder, or Rstudio. For extensive editing or running programs through environments such as VSCode, use the Open OnDemand [interactive app](notes/rivanna-intro/interactive).
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* In FastX, you can also use a programmer's interface such as VSCode, Spyder, or Rstudio. For extensive editing or running programs through environments such as VSCode, use the Open OnDemand [interactive app](notes/hpc-intro/interactive).

‎content/notes/hpc-intro/files/file_exercise3.md

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