FASSE Environment

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To request a new account, fill out the online Account Request form.

When you enter your PI’s name, it should auto-fill. This should also provide the options for the Approver drop-down menu.

If you select a PI that is for FASSE, the last page should say that NCF (the old cluster) compute resource access has automatically been included. If for some reason it doesn’t, please email RC (rchelp@fas.harvard.edu) and let them know.

If you are an outside user, select Users without a Harvard Key (or with a key if you have one).

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We use two-factor authentication, which requires users to use their username and password as well as second factor, which is an openauth token, in order to gain entry to FASSE infrastructure.

1. Get your token

When you requested your account, you should have received an email with instructions for setting up the vpn. If you can’t find this, you can go to https://docs.rc.fas.harvard.edu/kb/openauth/ for instructions.

On that page, click on the https://two-factor.rc.fas.harvard.edu link.

The instructions include two main ways to get this, either from your phone or from a desktop application. Keep in mind that this software creates a token that is specific to you, so if you use a different computer, you will need to set it up again, or use the token from your phone. Therefore, if you plan on VPNing to the cluster from multiple locations it is highly recommended to install the phone app also.

Tips for desktop app: Use the .dmg or .exe apps version.

Tips for the phone app: Use the Duo Mobile version, since this is the same thing you might have already installed for the regular Harvard VPN.

However you do it, you will need the 6 digit number it generates to log into the VPN. If you have a new Mac, you might get an error message when you launch the desktop app telling you to download the Java Developer Kit. This means you will need to install java (link) to get the program to run.

See here for the instructions written by RC.

2. Get the VPN client

Now that you have the openauth token generator, you will need the actual VPN client. These steps will only need to be followed once per machine you want to log in from, and this application is not specific to a user, so if you find it already installed on a machine you can use it if you have your own personal openauth token. It is also the same one you use to VPN more generally to Harvard, you just need to change the address as listed below. To get the VPN client (if you don’t already have it) go to https://vpn.rc.fas.harvard.edu/, for the username use username@fasse. Again, you will only have to do this step once, as this will install the Cisco AnyConnect VPN Client onto your system.

The web based installation of the client almost always fails. However, after it fails, it gives you the option to download the disk-image. Go ahead and do that. When you try and open the installer package, it may give you an error that it is broken and can’t run. This is usually due to your security preferences in your web browser.

On a Mac:

• Go to System Preferences -> Security & Privacy
• Click on the General tab
• Click on the lock to allow changes
• Under the heading “Allow applications downloaded from:” chose Anywhere

Then double lick on the vpn.pkg and the installation should work. Afterwards, you can go back and set the “Allow applications downloaded from:” to be Mac App Store and identified developers.

For instructions written by RC, see here.

3. Connect!

Once you launch the VPN client, make sure the “Connect to” path name at the top is vpn.rc.fas.harvard.edu

Next you will be prompted for your username, make sure to follow it with your domain: @ncf i.e. hgranger@fasse, DON’T FORGET THE @fasse!! Next you will be prompted for your password and the Two-Step Verification Code. The password should be what ever you set your account up with, if you need to change it see here. The Verification Code field is for the 6 digit passcode from your openauth app. Once you enter this information, you should be able to connect.

Occasionally, you may have to try logging in once or twice, particularly if the token is getting ready to expire right as you put it in. Once you are connected, you want to start a VNC session by following these directions.

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There are several choices to be made for your remote desktop.

First, you can choose the FAS-RC Remote Desktop or the Containerized FAS-RC Remote Desktop. You must choose the FAS-RC Remote Desktop (NOT containerized) if you plan to use Docker/Singularity containers during your session.

You can also choose three choices of partitions:

1. test
2. fasse,
3. fasse_bigmem,
4. fasse_ultramem,
5. fasse_gpu, and
6. remoteviz.

Which you choose depends on what you want to do, but when in doubt, use test. Also, keep in mind that you can directly ssh to the cluster via fasselogin if you don’t like the remote desktop option, or if it is full or down for any reason. You might also want to read the FAQ on submitting your jobs, because the descriptions below refer to the different queues.

test: These are limited to 8 hours, so works well for a remote desktop session.

fasse: This is just like test, but has a 7 day time limit.

fasse_bigmem and fasse_ultramem: This are for the rare case where you need a bunch of memory (greater than 30 gigs) but also need a graphics window. In general, given the different hardware of bigmem (which is also a queue you can submit jobs to via sbatch), the numbers returned could be slightly different than the ncf_holy queue. fasse_bigmem has 6 nodes with 500 gigs, and fasse_ultramem has 1 node with 2 TB. Note that batch jobs on these partitions will fail if you request < 30 gigs.

fasse_gpu: This one includes 4 V100 GPUs.

remoteviz: This one is for graphics intensive work, such as looking at your brain data and possibly editing scripts if you like the remote desktop. If you do any number crunching on here, which should generally not be done, the numbers could be slightly different than running it via sbatch to fasse_holy. If you are doing super intensive graphics like 3D brains, you should see the first tip below.

If the remote desktop seems slow, the biggest thing you can do to speed things up is GET A WIRED CONNECTION!!! The wireless network is much slower, and while convenient, is not great for remotely working with the cluster. We also now have the ability to take advantage of virtual GL which speeds up graphic intensive programs. To connect via ethernet you need to register your computer: nice instructions from SEAS.

Open On-demand Remote Desktop (VNC)

From Chrome (preferred) or Firefox while on the VPN, go to: https://fasseood.rc.fas.harvard.edu and login with your RC credentials.

Research Computing has written a nice FAQ on their website about this: (link to RC virtual desktop documentation). This covers the interactive apps, including the remote desktop session, Jupyter notebook, and Rstudio.

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Graphics intensive programs: If you are running a graphics intensive program like Freeview or FSLeyes, you can vglrun before the name of the process:

vglrun freeview -v mysubj/mri/T1.mgz

Note that vglrun MUST be used with connectome workbench(wb_view) or wb_view will not work!

Copy and Paste between local machine: Remember that the command to Copy is Control + C (as opposed to Command + C if you use a Mac) and Paste is Control + V.

If the keyboard shortcuts aren’t working, you can also use the clipboard, on the far right. To open it, click the little arrow on the left side of the desktop.

Then click on the image that looks like a clipboard. The window it opens is a place to copy and paste things back and forth, always with your laptops copy/paste commands. To get something from the cluster to show up there, highlight and middle click, or copy with your remote desktop copy commands.

Text editor: The default text editor is EMacs. However, for programming, we suggest using Sublime Text. To load it, first type module load ncf sublime_text into a Terminal. Then to open the application, type sublime_text

How to make text look nicer: To make the text look a little ‘smoother’. From within your remote desktop session, go to the top left corner to Applications ->Settings -> Appearance -> Fonts and change Hinting to None.

Edit keyboard shortcuts To change the command combinations for copy and paste: From within your remote desktop session, go to the top left corner to Applications ->Settings -> Appearance -> Settings and check Enable editable accelerators. Then go to a terminal window, click on Edit, and hover over Copy or Paste with your mouse. Then perform the key combination you would like to use. You should see the key combination listed on the right change. For reference, you can use ctrl-c for copy, and the system will smartly figure out when you want to copy something or kill a running process, for which the UNIX command is ctrl-c.

How to get your terminal windows (and directories) back when you start a new session:

The key is to ‘log out’ from the session you want to save. This won’t save your matlab session or reload modules, but it will open all your terminal windows back up in the same directory they were when you logged out. To logout:

Go to the top menu bar Applications-> Log out, its all the way at the bottom in green.

Then click on the green logout button that appears.

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To ssh to FASSE you must be on the VPN. You can then ssh to a login node. From a mac you can use Terminal. From a PC see here. This is a great place to submit scripts from, or edit files, but you shouldn’t be doing any number crunching. Especially as the hardware differs from the cluster, so if you do number crunching here and on the cluster the numbers could differ slightly.

ssh -YC fasseusername@fasselogin.rc.fas.harvard.edu

where fasseusername is your RC username (e.g., hgranger@fasselogin.rc.fas.harvard.edu) You will prompted first for you password, and then for your “verification code” (aka the 2 factor authentication code via Duo Mobile).

The hostname “fasselogin” will redirect to one of several specific nodes, e.g., fasselogin2, whichever is least busy. You can also choose a specific one if you prefer.

You can also access a shell from the VNC server site, on the cluster tab.

Also keep in mind, if you need to do an analysis (aka number crunching) but also need graphics or if you just like a nice graphical interface you can use a remote desktop.

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If you are working in bash, which is the default on the FASSE cluster, you should have a file in your user directory called .bashrc. You can open/create this file using your favorite text editor, such as sublime. Our current default bashrc can be found at https://ncfcode.rc.fas.harvard.edu/nrg/default_bashrc or directly on the cluster as /ncf/mri/01/users/shared/default_bashrc/bashrc.

If you have questions about setting up your environment, contact rchelp@fas.harvard.edu. See below for how to change versions of software via modules.

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The process is the same if you want to use the Open On-Demand remote desktop client. If you want to ssh to one of the login nodes like described here. To enable X11 forwarding in PuTTY you need to configure your settings.  

RC has some nice instructions here, see below for some basic steps.

Start up PuTTY.  In the configuration box you need to give it the Host Name of the vncserver. The hostname should be fasselogin.rc.fas.harvard.edu for centOS7. You can also save these settings by giving your session a name in the Saved Sessions box and then click Save.  You should save it again once you set the X11 forwarding.

Next, under the Connection Category, expand SSH (click where red arrow pointing) and choose X11.  Click on the Enable X11 Forwarding checkbox.  

Then, click on the Session Category, and save your settings again.  Next time when you open this program, you can Load the saved settings.

Finally, click on Open.  You should then be prompted for your username and password.  When you are done, make sure you end your SSH session by typing exit at the command prompt before you X out of the PuTTY program.

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The openauth token code required for the two-factor authentication is specific to your username. Therefore, if you want to VPN from a different machine, you will have to set this up again. An alternative is to get the openauth app for your iphone, blackberry, or android. The instructions for doing so are here.

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To reset or change your password, use the Research Computing website https://portal.rc.fas.harvard.edu/pwreset/