Welcome! Here, you can find guides that are used by students and staff at TJHSST when interacting with services provided by or supported by the TJHSST Computer Systems Lab.

What is CASA?

CASA is a tool created by Google to allow students to access databases that TJ subscribes to while not on the TJ campus. Instead of using a proxy, CASA ties a token to your device when you access a database while on campus.

CASA Set Up

CASA Use

The next time that you use the same device to visit Google Scholar - on or off campus - it will automatically allow you to access any articles that are from databases that TJ subscribes to. In addition, if you are signed in to your gmail account on the device that originally generated the token, gmail can port that token to any other devices (laptop, tablet, mobile phone, desktop, etc.) that are signed into the same gmail account.

CASA Renewal

The off-campus access is valid for up to 120 days. To renew it, simply repeat the set up steps by visiting a database through Google Scholar while on campus again.

Printing is available in the library before school, at lunch if you are signed up for library lunch, in-between classes, and during 8th period if you are signed up for the library study hall.

There is no printing during instructional time.

Black & white printing is free; color printing is 50 cents per side.

Instructions for printing are posted by the library's Ricoh printer in the far corner of the library.

Sending Print Job

1. Download your document and save as a PDF.

2. Using FCPS Dell laptop or a library desktop: choose PRINT, use menu slider to choose FCPS CLOUDPRINT, then PRINT.

3. Using FCPS Chromebook: choose PRINT, then use menu slider to choose MOBILITY PRINTING, then PRINT.

Retrieving Print Job

1. Go to Ricoh printer in the corner of the library.

2. Log in using your FCPS student ID number.

3. Enter PIN. First time using the printer? Assign yourself a PIN using the NEED PIN button on the screen.

4. Log in with your FCPS student ID number and PIN.

5. Follow instructions on printer screen.

6. Log out.

Change or Reset a Forgotten Pin

2. Log in using your FCPS credentials.

3. Choose CHANGE DETAILS in the lower left corner of the screen.

4. Create a new PIN.

Information as of October 2024.

Clear Cache

You need to clear your browser cache for the proxy to work. Follow these instructions to do so.

1. Enter chrome://settings/clearBrowserData into your search bar

2. Go to the basic tab and select Cached images and files

3. Select the Clear Data button.

Configure Proxy

Follow the directions below to configure your proxy in Chrome.

1. Enter chrome://settings/system into your search bar

2. Select Open proxy settings and follow the specific instructions for your operating system.

Configure Proxy

Follow the screenshots below to configure your proxy on Mac OS X.

• Open "System Preferences"

• Click on "Network"

• Click on "Advanced"

• Choose the "Proxies" tab

• Select "Automatic Proxy Configuration"

• Enter https://pac.tjhsst.edu

• Click "OK"

Help

On all operating systems:

1. Make sure you've cleared your cache as per the instructions for your browser/operating system.

2. When you are prompted to enter your username and password, make sure to enter the password you use to login to Ion.

On Windows:

1. If you're using Chrome or Edge, try these steps:

   1. Open the Settings app.

   2. Navigate to Network & Internet > Proxy.

   3. Enable "Use setup script."

      1. Enter "https://pac.tjhsst.edu/" into the "Script address" box.

   4. Click "Save."

   5. Close Settings, reopen it, navigate back to the proxy settings, and make sure that the settings are still there.

   6. 1. Temporarily disabling Windows Defender (and any other antivirus software you have installed) while you access databases might work.

The criteria for announcement posting may be periodically revised, but it includes the following:

• The announcement must not violate any FCPS policy.

• The announcement must have a direct relationship to sanctioned school activities.

• It must not be inconsistent with the principal's directives.

• The announcement should not have typos.

• No announcement may be posted on behalf of a club not registered with the Eighth Period Office.

• The announcement's content must also:

  • be of good taste

  • promote respectful behavior

  • use proper spelling/grammar

  • avoid excessive use of bolding, capitalization, or italicization

  • avoid use of copyrighted material without proper attribution

  • remain in compliance with CSL policies

  • not violate the law

• Announcements should strive to avoid unnecessary repetition in the content being announced. For example, while it's okay for an eighth period club to advertise their existence once, announcements concerning a club should not be made every week.

• When linking to external content, the linked content should be controlled by a trusted source, of good taste, and generally consistent with a school environment. Links should also not be broken, and these links should link to the intended destination.

Ultimately, the decision on whether to post an announcement rests solely in the approving Intranet administrators, subject to the principal's supervision.

Clear Cache

Follow the instructions to clear your Edge cache.

• Open Edge.

• Click the menu button (three dots, horizontally).

• Click "Settings".

• Click "Choose what to clear".

• Make sure "Cached date and files" is checked. You may wish to uncheck the other unboxes.

• Click "Clear."

Configure Proxy

Follow the screenshots below to configure the database proxy on Windows.

• Click the Start menu icon. The Start menu appears

• In the search field, search "internet options" and click on the first result

• A window will open. Choose the "Connections" tab

• In the "Connections" tab, click on "LAN Settings.

• In the "LAN Settings" popup, check the box "Use automatic configuration script

• Click "OK" and then "OK" again.

Test It Out

• Open Edge

• Navigate to the Library Databases page and click "Access Science".

• You may be presented with a password prompt. If so, type the username and password you use to login to Ion.

• If you see the words "Thomas Jefferson High School", you have correctly set up the database proxy.

Help

Resetting Your Password

2. Log in with your FCPS Google account.

3. Follow the prompts to reset your password.

Possible Errors

If you see a page that informs you that you have an invalid Google login, one of two situations are possible:

1. If you attempt to authenticate with a Google account that is not your FCPS account, you will get a message like the one above. Please log in with your FCPS Google account.

Configure Proxy

Pull down the menu area and then long press the wifi symbol to access your wifi settings.

After that, long press the network you are connected to (Fairfax in this case) and then press manage network settings.

Press Show advanced options

Scroll down and then do the following:

1. Change the Proxy to Auto-config

2. Put in https://pac.tjhsst.edu in the PAC web address text field

3. Press connect

Testing out the Proxy

If you haven't logged in already, you will then see a login prompt like this.

If you have logged in successfully, you should see Thomas Jefferson High School after pressing the menu button.

For anyone wondering, yes, Firefox on Android is very different from desktop Firefox. This is especially true for setting up the proxy.

Clearing Cache

First, go to the menu by pressing the button with three vertical dots.

Then go to the settings.

On the settings page, select Clear private data.

Make sure that the cache option is checked and then select clear data.

Once you have cleared data, exit the settings screen and type in about:config in the address bar.

In this area, search for network.proxy.type and give it a value of 2. This lets Firefox know that you want to use a pac file for your proxy.

Then search for network.proxy.autoconfig_url and set it to be https://pac.tjhsst.edu.

Test it Out

To test this out, go to accessscience.com. You should see a prompt for a username and password pop up. When prompted, put in the login information you would use to access Ion.

When you reach Access Science, press the menu button or the three horizontal lines and you should see Thomas Jefferson High School

Updating Firefox

This guide uses Firefox Quantum (Firefox version 57.0 and above). Menu designs changed and look very different from every version below that, so the guide will not accurately describe the steps you should take if your version is lower.

Steps to checking what version you have

For Windows

1. Press Alt

2. Mouse over Help

3. Click About Firefox

For Macs

1. Click Firefox at the top left

2. Click About Firefox

If your About Firefox window shows Firefox Quantum, you have a late enough version. Otherwise, you will need to use this menu to restart and update Firefox until the About Firefox window shows Firefox Quantum.

Clearing Cache

Follow the instructions/screenshots below to setup your proxy:

Open the menu by clicking the three bars at the top-right and click on Options

Locate the search bar to the top right of the screen.

Search clear history and select the Clear History button.

1. Change the time range to Everything.

2. Make sure that Cache is selected under the History header

3. Select Clear Now.

Configure Proxy

Now, search Network Settings and select Settings.

1. Under the Configure Proxy Access to the Internet header, select Automatic proxy configuration URL.

2. Put https://pac.tjhsst.edu in the text field below.

3. Select Reload and then OK.

Test it Out

Once you have successfully authenticated, you should see Access via Thomas Jefferson High School at the top right of the site.

What is Ion OAuth?

Register an Application

• Name

  • Some descriptive name for your application.

• Client Type

  • Choose Confidential if your app has a backend component and your server can store the client ID and secret securely.

  • Choose Public if your app is purely client-side and a copy of the credentials will be distributed publicly.

• Authorization Grant Type

  • Choose Authorization code if your client type is Confidential.

  • Choose Implicit if your client type is Public.

• Redirect URIs

  • Enter one or more URLs that your application will redirect back to after the authorization is complete.

• Algorithm

  • If this option exists, leave it at the default No OIDC support. Ion doesn't support OpenID.

Requesting Authorization

Python

python-social-auth + Django

API Requests

For a Python client, use requests with requests-oauthlib. If running locally (without HTTPS), override the SSL requirement for OAuth2.

Create an OAuth2Session, with the CLIENT_ID and REDIRECT_URI you entered in the application form. Redirect the user to authorization_url.

The user authenticates, approves the request, and is redirected to the callback URL specified in redirect_uri, with a "code" GET parameter.

At this point, a valid access token has been gained, and you can request API resources.

After 36,000 seconds (1 hour), the token will expire; you need to renew it. This can be handled by putting API commands inside a try-except for a oauthlib.oauth2.TokenExpiredError, such as seen above. Alternatively, you can provide auto_refresh_url=refresh_url, auto_refresh_kwargs=args as additional arguments to OAuth2Session when it is created.

Node.js

Note: This code will not work out of the box. Read the comments carefully to determine how to integrate it into your application.

What is Mathematica?

Installing Mathematica at home

To install Mathematica on a personally-owned machine, please use the following instructions

2. After you submit the form, your activation key will be displayed and will also be sent to your TJ email.

3. To download the installers for Mathematica, follow the link on either the activation key page or in the email with your activation key.

4. Download the appropriate installer for your platform (Windows, OS X, or Linux) and install it as you would any other application for your platform.

5. After you launch Mathematica, you will be prompted to enter the activation key you received and accept the Mathematica EULA.

6. Congratulations, you now have Mathematica!

How do I use Mathematica?

Setting Up Forwarding

You should receive an email at the address you specified within 10 minutes. Follow the link in that email and enter the password that you use to log into Ion. Any emails sent to your @tjhsst.edu will be automatically forwarded to the specified address.

IMAP

You will need to use the following settings for IMAP (sometimes called incoming mail) and SMTP (sometimes called outgoing mail):

• IMAP

  • Server: imap.tjhsst.edu

  • Port: 993

  • Encryption Type: SSL

  • Username / Password: TJ Username and Password

• SMTP

  • Server: smtp.tjhsst.edu

  • Port: 465

  • Encryption Type: SSL

  • Requires Auth: YES

  • Username / Password: TJ Username and Password

POP3

Some clients do not support IMAP, but only support the older POP3 protocol. We do not support those clients, and we recommend you use an IMAP-capable client.

Setup

You should create a Google Form using your FCPS Google Drive. The form needs to follow the exact format pictured below and both questions should be required.

Click through the Google Form to open the spreadsheet of responses. Your students' responses will populate here. You must change the column headers to "Name" and "Email" as shown below. Capitalization is important and this process will not work if you do not change the column names.

During the Block

Post the link to the form you created. Make sure students know that they have to sign in with their FCPS emails to complete it and that they have to enter their first and last name as they appear in Ion. Additionally, emphasize that the email that they have to enter should be their @fcpsschools.net email.

After the Block

Go back to the spreadsheet of responses and click File -> Download -> Comma separated values. Save the file where you will be able to find it later.

Then, go into the page on Ion where you usually take attendance and click "Take Attendance with Google Meet CSV Report:" Upload the spreadsheet file that you downloaded.

Ion will do the rest of the work and will check off the students that it finds in the uploaded file. It will notify you of any students that were in the form, but couldn't be found as a signup. This is probably indicative of a formatting error in the students' submission. You will still be able to manually check off students to rectify these issues.

Printing

The Printing feature on Ion is a service that the CSL provides to students and staff member to be able to print to the 3 Syslab printers and to the 9 commons printers around the school. It's a service made available to students who don't use/have a school-provided laptop, use one of our 60+ workstations in the CSL, or needs to print something on-the-go.

Printers

We currently have 12 functioning printers around the school. Three of them are located in the Computer Systems Lab, with one in each room:

In the Syslab

• Room 202 Printer:

  • Model: HP LaserJet P3015

• Room 200c Printer:

  • Model: HP LaserJet P3015

• Room 200 Printer:

  • Model: HP LaserJet P3015

Around the School:

These printers were add to Ion in late 2023 as the demand for use of Ion printing has increased.

• Carver Commons Printer:

  • Model: HP LaserJet 4100

• Curie Commons Printer:

  • Model: HP LaserJet 4100

• Einstein Commons Printer:

  • Model: HP LaserJet 4100

• Faraday Commons Printer:

  • Model: HP LaserJet 4100

• Gandhi Commons Printer:

  • Model: HP LaserJet 4100

• Hopper Commons Printer:

  • Model: HP LaserJet 4100

• Newton Commons Printer:

  • Model: HP LaserJet 4100

• Tesla Commons Printer:

  • Model: HP LaserJet 4100

• Turing Commons Printer:

  • Model: HP LaserJet 4100

Ion Printing

To Print from Ion:

2. Select the file you want to print. Please make sure that the file type is supported as well. Here are the ones that currently are supported by Ion:

   1. .pdf: Adobe PDF

   2. .ps: Adobe PostScript

   3. .odt: OpenDocument Text Document

   4. .txt: Plain Text

   5. .doc and .docx (not recommended; format may come as off. Would recommend converting it to a PDF): Word Document

3. Select the printer you want to print to. Choosing the one close by you is highly recommended.

4. Check to see how many pages you are printing. The maximum amount of pages you can print at once is 16.

5. Check if you want your documents double-sided and/or fit-to-page.

6. Print.

Workstation Printing

Workstation Printing can be done by going to Ion, or printing directly from the command line. To Print from the command line:

1. Access the terminal.

2. Change directory to the file you want to print (not required but recommended).

3. Recommended: Check which printers are online and not disabled. You can use the command lpstat -p to see a list of printers and their status:

1. To print to a specific printer, you can use this command lp -d <PRINTER> <FILENAME>, where you replace the <PRINTER> with the printer of your choice, and the <FILENAME> to file you want to print.

Abuse Protection

Jobs are currently limited to 16 pages. Abuse of printing privileges may result in appropriate punishment as determined by the Faculty Sponsor and lead Sysadmins.

Best Practices

• Check to see if the printer contains ink or paper, if one of the two are low or missing, please contact a Sysadmin.

• If you sent to the printer a print job (you have hit the 'Print' button on Ion) and the printer seems not to work, please check the following:

  • The tray: This is where paper is stored. For the printers in the Syslab, pull the tray located at the bottom of the printer. DO NOT OPEN THE TRAY ON THE SIDE OF THE PRINTER! For the printers located in commons, pull the bottom tray. If there is paper there, ask a Sysadmin about the printer. Do not send another print job.

  • Disablement/Maintenance: There are in some cases where a printer may be disabled or temporarily down for maintenance and with that case can only be changed by a Printing Lead or current Lead Sysadmins.

  • Jammed: If a printer is jammed, do not attempt to unjam the printer! This will most likely cause the printer to be damaged. Instead, ask a Sysadmin or a nearby teacher to assist.

• Highly Recommend to be present at the printer when printing.

  • If in some circumstances where you printed from a different room/common than the printer is in, please pick up your documents. If this is not done, you may be subjected to a possible removal of printing privileges.

• Please avoid printing multiple times unless you have picked up your first copies.

What is JupyterHub?

How do I access JupyterHub?

• Default (4 CPUs, 8GB RAM)

• Compute (8 CPUs, 16GB RAM)

• 1 GPU (8 CPUs, 16 GB RAM, 1 GPU)

• 2 GPUs (8 CPUs, 16 GB RAM, 2 GPUs)

• 4 GPUs (8 CPUs, 16 GB RAM, 4 GPUs)

Please only choose what you need. Depending on usage, it may take longer to spawn instances for higher resource allocations, and others may be prevented from using resources allocated to you if you are not using them.

You will then be placed in a queue to wait for your own server to spawn. Our instance is configured such that your server may be spawned on one of 53 different machines. Even though your server is spawned on random machines, all your files are stored in a common location: /cluster/<username>.

Advanced Features

Python Interfaces

After logging in you may be greeted with a "Launcher" tab. This tab will have multiple options, including:

• Python Notebook

• Python Console

• Terminal

The Python Notebook and Python Console are two separate interfaces, and you may experiment with either of them.

Both of these Python interfaces are based in the "default" Python environment, meaning they have the default packages. In most cases the default packages will suffice, but if you need to install custom packages read the instructions below:

Creating Conda Environments

To create a personal custom Conda environment run the following:

On infocube or any cluster node run the following in your home dir (/cluster/<your_csl_username>)

conda create --name my_personal_environment ipykernel

The --name parameter can be anything you wish (in this case my_personal_environment). Additionally,ipykernel is REQUIRED at the end.

After creating the Conda environment, activate it:

conda activate my_personal_environment

Replace my_personal_environment with the environment name you previously chose.

Finally add the environment to JupyterHub:

python -m ipykernel install --user --name "my_env" --display-name "My Env"

The --name and --display-name parameters can be anything you wish.

After running the previous commands your launcher should now look like this:

Now you have created a personal environment you have total control of. You may use conda to install any custom packages you wish. Be sure to click on your new Python Notebook/Console option (not the default option) if you wish to access your custom environment.

Removing Environments

Removing the Conda environment is simple:

conda env remove -n my_personal_environment

Removing the entry is a little more involved:

rm -r /cluster/<username>/.local/share/jupyter/kernels/<name>

• The <name> parameter must match the --name parameter passed to the python -m ipykernel ... step, NOT --display-name! You may also ls around in this directory to find your matching environment and then rm -r the directory

• After removing the directory, reload JupyterHub and the entry will now be removed.

Purpose

The cluster was purchased by the Computer Systems Lab to serve the Parallel Computing and Computer Vision classes, but is available for usage by all TJ students and staff. Several senior research labs have expressed interest in using the cluster's resources for their own purposes. Academic jobs run on the cluster will receive priority allocation of resources, but non-academic jobs are accepted as well as long as they abide by the FCPS Acceptable Use Policy (Regulation 6410).

Specifications

The full cluster consists of 12 HPC cluster nodes, 40 Borg nodes, and 1 dedicated GPU node (zoidberg). This setup occupies almost 3 full racks in the server room. The CSL obtained the 40-node Borg cluster from NASA through an educational grant. The Borg nodes are named borg[1-40] consecutively and the HPC nodes are named hpc[1-12]. The login node is infocube

Cluster Nodes

All nodes on the cluster are directly accessible through ssh as well as Slurm. However, due to unfinished maintenance caused by COVID-19, some nodes are inaccessible indefinitely.

Available Cluster Nodes

Format: <prefix>[sequence]. (e.g borg[1-3] means borg1, borg2, and borg3 are available)

• borg[1-3], borg[6-31], borg40

• hpc[1-6], hpc[8-12], zoidberg

• snowy

Unavailable Cluster Nodes

• borg[4-5], borg[32-38]

• hpc7

• duke

An always up-to-date version of this list can be viewed by running sinfo on infocube or an available node.

SSH Access

You can directly access any available cluster node through ssh. To ssh into a cluster node:

1. ssh into remote.tjhsst.edu using your TJCSL username and password

   • ssh 2021abagali1@remote.tjhsst.edu

2. ssh into a cluster node

   • ssh borg1 (or any available node)

File Management

The login node and all cluster nodes use a file system that is separate from the ras1/ras2/workstation AFS directories. Instead all user files are stored in CephFS under the directory /cluster. For example the cluster files for 2021jdoe would be in the directory /cluster/2021jdoe.

When you log into infocube or any cluster node your cluster directory will be /cluster/<username>. In addition to the cluster nodes, you can access your cluster files on ras1/ras2, under the same directory.

Note: on ras your /cluster directory is not your default directory and is separate from your default directory files. You may use cp,mv, or another utility for moving files back and forth from anywhere on ras to your /cluster directory. This feature is currently unavailable on workstations. If you wish to copy files from a workstation over to your /cluster directory you may use sftp or scp to copy your files from the workstation over to the target cluster node.

It is safe to assume use of the keywords: "default directory", "home directory", "homedir", "cluster directory", etc while in the context of the Cluster refer to the directory at /cluster/<username>

Slurm

What is Slurm?

Slurm is a free, open-source job scheduler which provides tools and functionality for executing and monitoring parallel computing jobs. It ensures that any jobs which are run have exclusive usage of the requested amount of resources, and manages a queue if there are not enough resources available at the moment to run a job. Your processes won't be bothered by anybody else's processes; you'll have complete ownership of the resources that you request.

How do you use it?

The Login Node

To get started with running jobs on the Cluster you should connect to the login node, which is infocube in this case. Any of the following commands while on ras or TJ CSL computer will allow you to connect to infocube:

ssh infocube

After connecting to infocube you will be placed into your Cluster home directory (/cluster/<username>). infocube is a virtual machine and does not have nearly the amount of resources as the entire Cluster does, so do not run programs directly on infocube. Instead, you want to tell Slurm to launch a job

Jobs are how you can tell Slurm what processes you want run, and how many resources those processes should have. Slurm then goes out and launches your program on one or more of the actual HPC cluster nodes. This way, time consuming tasks can run in the background without requiring that you always be connected, and jobs can be queued to run at a later time.

Viewing information about the Cluster

Our Cluster is split into two partitions: compute and gpu. All nodes that are in the gpu partition are in the compute partition, but not vice versa. Nodes in the gpu partition have GPUs installed which can be accessed through Slurm.

To see information about the nodes of the cluster, you can run sinfo. You should get a table similar to this one:

PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
compute*     up   infinite      1    mix hpc9
compute*     up   infinite      8  alloc hpc[1-8]
compute*     up   infinite      3   idle hpc[10-12]
gpu          up   infinite      1  down* hpcgpu

• idle means that that block of nodes is not currently in use, and will be immediately allocated to any job that requests resources.

• alloc means that the node is busy and will not be available for any other jobs until the job is complete

• mix means that some of the cores within the node are allocated and others are free. Because this is annoying, it is good etiquette to allocate your jobs in multiples of full nodes (24 cores)

• down means that the node cannot currently be used.

• If a state ends with * that means those nodes cannot have jobs scheduled on them (useless nodes)

  • i.e if a node is in STATE idle*, no jobs will be scheduled onto that node, even though it is marked as idle.

To see which jobs are running and who started them, run squeue. You should see a table like this:

JOBID  PARTITION   NAME     USER    ST      TIME   NODES  NODELIST(REASON)
 882    compute   mpirun  2017ggol   R     44:56    12     hpc[1-12]
 884    compute    echo   2017ggol  PD      0:00     6     (Resources)

ST stands for state. The two common states are R, which means the job is currently running, and PD, which stands for pending. If the job is running, the rightmost column displays which nodes the job is running on. If the job is pending, the rightmost column displays why the job is not yet running. In this example, job 884 is waiting for six nodes worth of resources because job 882 is running on all 12 of the available nodes.

Creating Programs to Run of the HPC Cluster

When compiling your program, it's best to connect to infocube (the login node explained in the section above), so that your code is compiled in a similar environment to where it will be run. The login node should have all the necessary tools to do so, such as gcc, g++, and mpicc/mpixx. WARNING: compiling your program on a workstation/any other computer that is not part of the cluster and then transferring the generated executable over to the cluster WILL NOT WORK. This is called CROSS COMPILATION and it WILL NOT WORK. This is not a challenge, it is a statement of fact

Running a Job

And now the good stuff: running a job! Slurm provides 3 main methods of doing so:

salloc

Salloc allocates resources for a generic job and, by default, creates a shell with access to those resources. You can specify what resources you want to allocate with command line options (run man salloc to see them all), but the only one you need for most uses is -n [number] which specifies how many cores you want to allocate. You can also specify a command simply by placing it after all command line options (ex: salloc -n 4 echo "hello world"). This is currently the suggested way to run MPI jobs on the cluster. To run MPI jobs, first you must load the mpi module, as stated above (module load mpi). After that, simply run salloc -n [number of cores] mpiexec [your program]. Unfortunately, the displayed name of this job is, by default, just "mpiexec", which is not helpful for anyone. To give it a name, pass salloc (NOT mpirun) --job-name=[name]

$ salloc -n 4 bash # spawns a bash shell with access to 4 cores
$ salloc -n 4 mpiexec ./a.out # runs an mpi program (a.out) with 4 cores

srun

This is the simplest method, and is probably what you want to start out with. All you have to do is run srun -n (processes) (path_to_program), where (processes) is the number of instances of your program that you want to run, and (path_to_program) is, you guessed it, the path to the program you want to run. If your program is an MPI program, you should not use srun, and instead use the salloc method described above.

If your command is successful, you should see "srun: jobid (x) submitted". You can check on the status of your job by running sacct. You will receive any output of your program to the console. For more resource options, run man srun or use the official Slurm documentation.

sbatch

sbatch allows you to create batch files which specify a job and the resources required for the job and submit that directly to Slurm, instead of passing all the options to srun. Here's an example script, and assume you save it as test.sh:

#!/bin/bash
#SBATCH -n 4
#SBATCH --time=00:30:00
#SBATCH --ntasks-per-node=2

srun (path_to_program)

What is Matlab?

Installing Matlab at home

To install Matlab on a personally-owned machine, use the following instructions:

1. • Students must use their @tjhsst.edu email

   • Faculty must use their @fcps.edu email

2. Confirm your email and follow the link to the setup page

3. Select an appropriate Department

   • e.g Student

4. Associate with license number: 18332-25780-63027-21100-78245

   • Make sure to include the dashes

   • This will complete your account setup

5. Once your account is created, click on My Account, and go to My Downloads

6. Download one of the listed versions for your operating system and install!

   • In the installation process you will be required to log in and verify your account and installation

Disclaimer

Running Qiime2

Logging in

2. You will be placed into a queue until a computer is allocated to you (one of 40+ machines)

3. Once logged in select "File > New > Terminal" this will give you a terminal on the machine you are n

   • This is the same effect as Running ssh [Ion username]@remote.tjhsst.edu and then ssh [computer] from there.

Activating Conda

Conda is a package manager that has been installed on these servers. It creates environments in which you can run and install software. You need to initialize conda once for your user account before you can access the qiime2 installation.

• If you have never run conda before run: /opt/conda/bin/conda init bash && source ~/.bashrc

Activating qiime2

qiime2 and related packages are installed in the qiime2 conda environment. This environment can also be accessed through JupyterHub with the "Console" and "Notebook" options (Python only). To access qiime2 from the terminal run the following:

conda activate qiime2

The terminal prompt should now look something like this (noticed the (qiime2) preceding):

(qiime2) borg40 2021abagali $

Now you can run qiime to access Qiime2

Qiime2 Through JupyterHub

After logging into JupyterHub you should see the following on the JupyterHub "launcher":

The qiime2 options will spawn a Python Notebook or Console depending on what you choose. The R(qiime2) will spawn an R Notebook or Console depending on what you choose.

Connect to the FCPSonboard network. Go to http://www.neverssl.com and you should see the FCPS Wi-Fi sign in page.

Accept the terms, and click Start.

Select Staff and Students, and enter your FCPS Student ID as the username and your FCPS password (i.e. your Blackboard password) as the password.

You should see something like this. Select "Show all operating systems" at the bottom.

Scroll down and select Other Operating Systems.

Download both the CA certificate and the user certificate (step 1 and 2, respectively).

network={
ssid="Fairfax"
key_mgmt=WPA-EAP
eap=TLS
identity="guest@fcps.edu"
# or,
# identity="<FCPS STUDENT ID>@byod.fcps.edu"
ca_cert="/etc/wpa_supplicant/wifi_certs/FCPS.pem"
client_cert="/etc/wpa_supplicant/wifi_certs/user.crt"
private_key="/etc/wpa_supplicant/wifi_certs/user.key"
private_key_passwd="<guest password or FCPS password>"
}

Some desktop environments, GNOME below, allow you to configure this through built-in utilities. You can configure GNOME like this, with Identity being <FCPS ID>@byod.fcps.edu, the User Certificate and Private Key being the User CA you downloaded, the CA certificate being the CA certificate you downloaded, and the Private key password your FCPS password:

Note: As of somewhere around NetworkManager version 1.36.x (which ships by default in Ubuntu 22.04 LTS, Fedora 36, and probably some other major Linux distributions), NetworkManager will fail to connect if Domain is not properly set to xprsscnctvm.fcps.edu and will give NO helpful information about why.

What is Zoidberg

It can be used to run large machine learning projects that require a lot of power.

Accessing Zoidberg

First, ssh into TJ's remote access server, using your TJ Username (e.g. 2021jdoe)

Afterwards, ssh into zoidberg.

Conda

To run machine learning projects with python, it is recommended to set up virtual environments for each project (so each project can use different versions of python packages if needed).

To achieve this, it is best to use Conda on the Zoidberg environment.

How to use Conda

Creating a new environment

Activating a new environment

Deactivating a new environment

Installing a package

What is tmux

In other words, tmux allows you to start a session to run your job and then exit the terminal window without killing your process.

Creating a new tmux session

tmux new -s "name"

This will create (and open) a new tmux session with the given name. In the session, you can then run your job the way you normally would over ssh.

Detaching a tmux session

Detaching the session allows you to close your ssh connection (and then close the terminal) without killing the process running in the tmux session.

The session can be detached by clicking control-b and then typing a d.

Attaching a tmux session

After sshing back into the remote server, to "re-open" or attach a tmux session, use the following command. This can be used to see if your process finished running and/or the output of the process.

tmux attach-session -t "name"

Killing a tmux session

After your process finishes running in the tmux session, you can then kill it off with the following work.

tmux kill-session -t "name"

This will close off any process running in the session, so make sure that your job is done.

Listing all active sessions

tmux ls