Remote Access

Remote Access diagram

This is an accordion element with a series of buttons that open and close related content panels.

Access the NMRFAM network

To access the NMRFAM network, you must have an NMRFAM network account (different from your Sundial account). Please contact Milo Westler to obtain it.

Once you have an NMRFAM account, you can use it to access any spectrometer computer either directly (from the spectrometer console) or remotely, from any place on Earth with internet access. To access NMRFAM network from outside you need to log in to one of the NMRFAM gateway computers by using ssh (see below).

SSH – required login program

All of the procedures below require the program ssh to login. For Linux and MacOSX systems usually it is already installed.

For windows there are free (putty.exe, MobaXterm – google them) and commercial products (SecureCRT- available freely for UW faculty, staff, and students). There are many websites showing how to use these programs.


Gateway computers: or

To login:

Your_home_computer_prompt> ssh -Y <username>

login: <username>

password: your password (not visible when entered)

Linux_prompt_for_login1> From login1 (or login2) you can login to any other NMRFAM computer.


Use putty to login to the NMRFAM network (google putty.exe). I recommend searching for putty tutorial windows. MobaXterm can also be used (

All spectrometers and compute servers are accessible from the net through the gateway computers.

“Man in the middle attack”

If you ever encounter a scary looking message about a “Man in the middle attack” when you try to ssh to computer within NMRFAM, don’t panic. This (hopefully) means that the computer you are logging into has been recently rebuilt by us.

Type the following: (yes, it looks like gibberish)


cd .ssh

rm known_hosts

NMRFAM e-mail account

Along with your NMRFAM account you will be given an e-mail <username>

If you want to receive the emails at another account then you should login and create a new file in your home directory named “.forward” (note the prepended “.”). In that file enter the email account name (e.g. <username>

Control your spam with Spamassassin

Where should I login to do something?

If you are using a spectrometer, then login to the spectrometer. In order to run the spectrometer remotely you must use VNC. NOTE: PLEASE do not use the spectrometer computer to save, inspect, process or analyze data or to use vnmr or topspin! Your PI will be charged for it! You can do any of that on several compute servers. If you are processing data or computing, flip a coin for one of the compute servers, but make sure your favorite software is installed. Once you ssh to the computer, you may want to use the command “top” to see how busy is (how many jobs are running on) the computer that you chose. If you are moving data around, it shouldn’t matter which computer you use (login1 and login2 are good for this purpose).

Change your password

How to change your password (via the Angus node)

Periodically, you will be required to change your password. This must be done on the computer “angus”. Remote access (through login1 or login2 from outside) is ok, you do not need to physically sit at angus’ console to do this. If you cannot log in, probably you need to have your password reset by the systems administrator.

From outside the NMRFAM network you will need to login to one of the gateway computers to access angus. e.g.:

Linux_prompt> ssh <username>

Linux_prompt> password: (enter your current (old) password here)

Linux_prompt> ssh <username>@angus

Linux_prompt> password: (enter your current password here)

Linux_prompt> passwd

Changing password for <username> old password: (enter old password)

new password: (enter new password – at least 8 characters and not too simple)

repeat new password: (repeat new password) Linux_prompt>

The new password will usually be available within about 5 – 10 minutes.

NMR Spectrometers

NMRFAM Spectrometers

Trivia: The names of the computers at NMRFAM are cattle names (cow names). The number of characters in a spectrometer name times 100 is equal to the proton frequency in MHz (with apologies for the Bruker 750). To use the spectrometers remotely you will need to use VNC with ssh tunneling (See below: Remote spectrometer access – Linux/Mac or Remote spectrometer access – Windows).

Spectrometer Computer name /home directory Probe
Bruker AVIII-HD 900 fleckvieh /fleckvieh/home/ c-tr/SSNMR
Agilent VNMRS 800 gelbvieh /gelbvieh/home/ c-tr
Bruker AVIII 750 telemark /telemark/home/ c-tr
Bruker AVIII 600 dexter /dexter/home/ c-qr(31P)(sc)
Agilent VNMRS 600 jaulan /jaulan/home/ c-tr(sc)
Bruker AVIII-HD 600 vosges /vosges/home/ c-qr(19F)/SSNMR
Bruker AVIII 600 kurgan /kurgan/home/ c-tr(sc)
Varian Infinity Plus 600 ribeye SSNMR
Varian Infinity Plus 600 taurus SSNMR
Bruker AVIII 500 kerry /kerry/home c-tr(sc)

KEY: rt – room temperature; c – cryogenic; tr -1H{13C,15N} triple resonance; qr – 1H{13C,15N)(X) quadruple resonance;  multiple – multiple probes; sc – sample changer; VNMRS- Varian NMR system console; DMX- Bruker; AVIII- Bruker Avance III. Please use the “Computer name” to login to the spectrometers.

All spectrometer home directories are local to the spectrometer. Data is saved within the users local home directory.

Bruker AVIII 500I (kerry):   /kerry/home/<username>/nmr/

Bruker DMX 600I (dexter): /dexter/home/<username>/nmr/

Varian VNS 600II (jaulan): /jaulan/home/<username>/vnmrsys

Bruker AVIII-HD 600III (vosges): /vosges/home/<username>/nmr/

Bruker AVIIII 600IV (kurgan): /kurgan/home/<username>/vnmrsys

Bruker DMX 750 (telemark): /telemark/data/<username>/nmr/

Varian VNS 800 (gelbvieh): /gelbvieh/home/<username>/vnmrsys

Bruker AVIII-HD  900 (fleckvieh): /fleckvieh/home/<username>/nmr/

The spectrometer directories are where parameters and data are stored during NMR experiments.

Compute servers

Gateways, file servers, and compute servers:

Computer name Purpose Data storage (local) Selected features gateway;login none /home;/nmrfam_data; spectrometers; compute servers-mounted gateway;login none /home;/nmrfam_data; spectrometers; compute servers-mounted
zebu/pinchow file server backup 4.5 TB RAID /home;/nmrfam_data
holstein/rendena spectrometer raw data backup 30 TB RAID Spectrometers
watusi 4X4 CPU 2 TB RAID Topspin/VnmrJ/nmrPipe
jenubi 4X4 CPU 1 TB RAID Topspin/VnmrJ/nmrPipe
angoni 4X6 CPU 1 TB RAID nmrPipe;CYANA;XPLOR;g09
luing 4X12 CPU 2 TB RAID nmrPipe;CYANA;XPLOR;g09
aubrac 4X12 CPU 2 TB RAID nmrPipe;CYANA;XPLOR;g09
chianina 4X12 CPU 3 TB RAID nmrPipe;CYANA;XPLOR;g09
charolais 4X12 CPU 3 TB RAID nmrPipe;CYANA;XPLOR;g09
zavot 2X4 CPU 1 TB RAID NMRFAM software server. See the software page
banyo 4X6 CPU


3 TB RAID GPU ready Amber 12
gaur 4X6 CPU


2 TB RAID GPU ready Amber 12

All spectrometer and server data directories are globally mounted and can be accessed from any computer. This means that if you are outside the NMRFAM network, you will have access to all server and spectrometer data directories from and

To access a compute server:

e.g. to run on aubrac (from a computer on the NMRFAM network) type: “ssh -Y aubrac”.

Using the -Y option in ssh will allow X types graphics to be displayed.

Do NOT run the nmr spectrometers using this method!!

All compute server /home directories are global (except zavot, chianina, and charolais which have local home directories).All compute servers have local /<computer_name>/data data directories for local data storage (consistently always named /raid/data on the local computer) and can also access the global /nmrfam_data.You can create your own directory on any of the above data directories. e.g. create a global directory ssh <username>@watusi cd /nmrfam_data (this is a global directory) mkdir <username> These directories are for work space and old data may be deleted without notice. No home or data directories are backed up, although these RAID systems have 2 copies of all data.


Using a local directory usually allows for faster input/output (I/O). If your computation keeps crashing and you are sure that your input is good, try moving the data to a local data drive. e.g. create a local directory ssh <username>@watusi cd /watusi/data (this is a directory local to watusi; input/output will be faster than using a global directory) mkdir <username>  Infrastructure computers:

Computer name Purpose
angus changing password
herens mail server
shami;chiangus webserver
zebu;pinchow fileserver


Remote spectrometer/computer access – Mac/Linux/Windows

Secure remote access to NMRFAM facility spectrometers and computers

To enter the NMRFAM computer network you must ssh to (or and only then will you be able to access other facility computers. To run the spectrometers remotely or to connect to an NMRFAM computer for analyzing data you will need to use VNC and tunnel through login1 or login2.

There are two parts to using VNC to connect to a computer at NMRFAM:

  1. First, you need to start a VNC server on the NMRFAM computer you want to connect to
  2. Second, you need to use a VNC viewer program on your computer to connect to the VNC server that you started on the NMRFAM computer.

How you start the VNC server will depend on whether you are “physically” logged into the NMRFAM computer that you want to connect to or not. Here physically” means that you logged in while physically sitting at the computer that you will access remotely.

  • Use vncserver to start a VNC server if you are NOT “physically” logged into the NMRFAM computer. This is typically done to run experiments remotely if you were unable to “physically” login to the spectrometer computer, or to connect to NMRFAM data servers to process and/or analyze data.

Below is a list of spectrometer names:

Spectrometer computer cow name
Bruker 900 fleckvieh
Agilent 800 gelbvieh
Bruker 750 telemark
Bruker 600I dexter
Agilent 600II jaulan
Bruker 600III vosges
Bruker 600IV kurgan
Varian 600V ribeye
Varian 600VI taurus
Bruker 500I kerry


NMRFAM network structure

NMRFAM instrumentation and computers


Data storage and retrieval

Data backups

The data directories (/nmrfam_data, /home, /raid/data/) are located on RAID systems that give a level of protection against loss due to a single disk failure. We are developing more robust backup servers and in the future will backup all user data, but please also be sure to maintain a personal backup of your critical research data.  Raw data collected on the spectrometers is backed up nightly and can be provided by facility staff upon request.  The instrumentation workstations do not currently have RAID systems.

To copy data from the spectrometers to a storage directory within the NMRFAM network:

e.g. You (<username>) have collected a series of data on the 900 MHz spectrometer (fleckvieh) and saved it in a directory named /fleckvieh/home/<username>/great_data and you want to save it to /nmrfam_data (the directory that is accessible to all computers on the network).


Open a terminal.


Linux_prompt> ssh <username>

password: <your password>

Linux_prompt> cd /nmrfam_data


if you have not created a directory on this disk (/nmrfam_data) then

Linux_prompt> mkdir <username> (please use your login name for <username>)


Linux_prompt> cd /nmrfam_data/<username>

Linux_prompt> cp -r /fleckvieh/home/<username>/great_data .

(note the “.” at the end stands for the current directory and in this case replaces “/nmrfam_data/<username>/”. You can always use the full path as well. “cp -r” copies all files and directories in the great_data/ directory).




Use putty to login to the NMRFAM network (google putty.exe) and then follow the instructions for Linux/Mac above. I recommend searching for putty tutorial windows.



Remote scp (To copy files from/to NMRFAM computers to/from outside the NMRFAM network)



Open a terminal or use Cyberduck, a GUI sftp client for MAC, or gigolo, a GUI sftp client for Linux.


Here <username> wishes to copy file_name to the local current directory on his home computer from a data file located at /nmrfam_data/<username>/file_name. All computers can be reached from

Home_computer_prompt> scp <username><username>/file_name .

(note “.” at the end to copy to the current directory)

Password:<enter password>

For windows machines use WinSCP, CyberDuck, FileZilla or the like

login to or

Change directory to whatever computer and directory you want to copy data from then drag&drop. I recommend searching for winscp tutorial windows.


As an example:

I want to download my file bestdata.pdf that is located in the directory /nmrfam_data/milo/nmr/snase/

Then from my linux machine (same for MAC) at home, I would open a terminal and enter.

scp .

after supplying my password, the file would be transferred.

Using one of the GUI programs, it is simply a matter of logging in,  finding the file on the NMRFAM network, and then drag and drop.