Access the NMRFAM network

Accessing 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 - google it) and commercial products (SecureCRT- available freely for UW faculty, staff, and students). There are many websites showing how to use these programs. 

Linux/Mac:

Gateway computers: login1.nmrfam.wisc.edu or login2.nmrfam.wisc.edu.

To login:

Your_home_computer_prompt> ssh -Y <username>@login1.nmrfam.wisc.edu

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.

Windows:

Use putty to login to the NMRFAM network (google putty.exe). I recommend searching for putty tutorial windows. http://support.suso.com/supki/SSH_Tutorial_for_Windows

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

cd .ssh

rm known_hosts


NMRFAM e-mail account

Along with your NMRFAM account you will be given an e-mail <username>@nmrfam.wisc.edu.

ssh herens, and type " maildirmake ~/Maildir " (without the quotes)

Create new "account" in your e-mail software.

Type is IMAP, incoming server is mail.nmrfam.wisc.edu, outgoing server is mail.nmrfam.wisc.edu. (To read mail from home, check "SSL" box in incoming server setup.

Your software will complain about SSL certificate on the first connection, ignore it: the certificate is OK.)

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>@hotmail.com).

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

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>@login1.nmrfam.wisc.edu

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 & other instrumentation

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 Linux/Mac: Remote operating instructions or Windows: Remote operating instructions).

Spectrometer Computer name /home directory Probe
Agilent VNMRS 900 fleckvieh /fleckvieh/home/ c-tr
Agilent VNMRS 800 gelbvieh /gelbvieh/home/ c-tr
Bruker AVIII 750 telemark /telemark/home/ c-tr
Bruker AVIII 700 rotvieh /rotvieh/home/ c-tr(sc)
Bruker AVIII 600 dexter /dexter/home/ c-tr(sc)
Agilent VNMRS 600 jaulan /jaulan/home/ c-tr(sc)
Agilent VNMRS 600 vosges /vosges/home/ c-tr
Bruker AVIII 600 kurgan /kurgan/home/ c-tr(sc)
Bruker AVIII 500 kerry /kerry/home c-tr(sc)
Bruker AVIII 500 devon /devon/home/ c-tr/bb/HRMAS/CPMAS
Bruker DMX 400 pisa /home (global) rt-QNP (1H,13C,15N,31P)

KEY: rt - room temperature; c - cryogenic; tr -1H{13C,15N} triple 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 (except pisa, which has a global home directory). Data is saved within the users local home directory.

Bruker DMX 400 (pisa):   /pisa/data/<username>/nmr/ Bruker

 (note: this directory is local to pisa, it is not the home directory, which is global on pisa)

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

 

Bruker AVIII 500II (devon): /devon/home/<username>/nmr/

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

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

Varian VNS 600III (vosges): /vosges/home/<username>/vnmrsys 

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

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

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

Varian VNS 900 (fleckvieh): /fleckvieh/home/<username>/vnmrsys

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

The raw and processed data is periodically deleted from these disks. Copy the data off the spectrometer disks as soon as possible.

 

Compute servers

 Gateways, file servers, and compute servers:

Computer name Purpose Data storage (local) Selected features
login1.nmrfam.wisc.edu gateway;login none /home;/nmrfam_data; spectrometers; compute servers-mounted
login2.nmrfam.wisc.edu 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

2 GPU

3 TB RAID GPU ready Amber 12
gaur

4X6 CPU

8 GPU

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 login1.nmrfam.wisc.edu and login2.nmrfam.wisc.edu.

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.

TIP:

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

For a complete list of computer names and IP addresses at NMRFAM, type at a Linux/Unix prompt: Linux_prompt> dig axfr nmrfam.wisc.edu

Compute servers:

Please look at the screen when you login to see the installed software packages.


Remote spectrometer access – Linux/Mac

NMRFAM policy for secure remote access to facility spectrometers.

To enter the NMRFAM computer network you must ssh to login1.nmrfam.wisc.edu (or login2.nmrfam.wisc.edu) and only then will you be able to access other facility computers. To run the spectrometers you will need to tunnel VNC through ssh (see below)

Logging in to a spectrometer (or other NMRFAM) computer

From your Unix, Linux, MacOSX, etc. computer open a terminal:

ssh <username>@ login1.nmrfam.wisc.edu

(replace <username> with your user name, e.g. jsmith)

The first time that you login in a question about authenticity will appear. Answer yes.
The computer will respond with a request for your password. Type in your password.

You are now inside the NMRFAM network. You can connect to any computer (including spectrometers) using ssh.

 

For example, if you want to connect to the 900 MHz spectrometer use:

ssh fleckvieh

Use the table below for other spectrometers:

Spectrometer

computer cow name

Agilent 900

fleckvieh

Agilent 800

gelbvieh

Bruker 750

telemark

Bruker 600I

dexter

Agilent 600II

jaulan

Agilent 600III

vosges

Bruker 600IV

kurgan

Bruker 500I

kerry

Bruker 500II

devon

DMX Bruker 400

pisa


Starting a VNC server (first time user, if not skip to vncserver command)

Use the following commands (on fleckvieh in this case):

ssh -Y <username>@ login1.nmrfam.wisc.edu

ssh fleckvieh

cd

mkdir .vnc

cd .vnc

rm xstartup

gedit xstartup

paste the following into xstartup and then exit:

#!/bin/sh

xrdb $HOME/.Xresources
xsetroot -solid grey
#x-terminal-emulator -geometry 80×24+10+10 -ls -title “$VNCDESKTOP Desktop” &
#x-window-manager &
exec gnome-session

 

 VERY IMPORTANT:

The file xstartup must be made executable. This is done from the command line:

chmod +x xstartup

vncserver

or

vncserver -geometry 2048×1024  (you can adjust the geometry to fit your screen)

++++++++++

For xwinnmr (on DMX 400 (pisa) only) you MUST start the VNC server as:

vncserver -depth 8 -cc 3 -geometry 2048×1024

(chose a geometry close to the resolution of your monitor)

++++++++++

The computer will respond with something like:

New ‘fleckvieh:4 (username)’ desktop is fleckvieh:4

Remember the new display (desktop) number (here it is 4).

exit (from fleckvieh)

exit (from login1)

Note. The first time you start a VNC server on any spectrometer, the computer will request you to set a VNC password. This password can be set to anything and doesn’t have to be the same as the login password. To reset the VNC password, login to the spectrometer computer as shown above and type vncpasswd.

To access a VNC session (assuming that you have started a VNC server on fleckvieh and was assigned display number 4)

A) From a linux computer with Tightvnc installed

vncviewer -via <username>@login1.nmrfam.wisc.edu fleckvieh:4

B) On an Apple computer running Mac OS X 10.4 (Tiger) through 5.12 (Yosemite) (no solution yet for El Capitain as of Nov. 2015).

Connect to VNC server using Chicken (not Chicken of the  VNC!). Chicken is a VNC client for Mac OS X that allows remote access to another computer over the network. Chicken is based on Chicken of the VNC (NOTE WELL: only Chicken offers the 'Tunnel over SSH' option needed below, Chicken of the VNC doesn't!).

The download link for Chicken 2.2b2 as of Nov. 2015 is:
  • Download, install, and start the Chicken 2.2b2 program
  • From the top menu bar, click on Connection > New Connection or Connection > Open Connection window and you'll get:

Chicken Of The VNC Screenshot 1

  • Fill in the information in the VNC login window (or Connect window, the information is the same) as shown above. The password requested in this window is the VNC password (that you set up on fleckvieh when you started the VNC server the first time).
  • For the Tunnel over SSH you need to fill your NMRFAM login name, followed by '@', and the name of one of the NMRFAM gateway computers: login1.nmrfam.wisc.edu or login2.nmrfam.wisc.edu, as shown above.

and then click on Connect. Another window will pop-up requesting you NMRFAM password (this is the ssh password you used when you connected to login1.nmrfam.wisc.edu). Once you type it, a new window will appear with the graphical desktop(s) of the spectrometer computer. You can now see (or start) your topspin, vnmrj, or xwinnmr session.

 

Stopping a VNCserver

If you are finished using a NMRFAM spectrometer and are logging out, then remember to exit the NMR software (topspin, vnmrj, or xwinnmr) or else you will continue to be charged.

When you are finished accessing a NMRFAM computer via vnc, you can kill the vncserver by logging on to the computer that is running the vncserver and typing:

vncserver -kill :#             where #n is the number of the vnc session that you want to kill.

Remote spectrometer access – Windows

NMRFAM policy for secure remote access to facility spectrometers.

To enter the NMRFAM computer network you must ssh to login1.nmrfam.wisc.edu (or login2.nmrfam.wisc.edu) and only then will you be able to access other facility computers. To run the spectrometers you will need to tunnel VNC through ssh. The easiest way to do that (especially from Windows) is by using SSVNC.

SSVNC is a standalone Java VNC viewer with a clean and easy to use interface for Windows, Mac OS X, and Unix that automatically starts up a tunnel for SSH/SSL connections to any VNC server, and then launches the VNC Viewer to use the encrypted tunnel:

http://www.karlrunge.com/x11vnc/ssvnc.html

Download it from here:

http://www.math.stonybrook.edu/~scott/mat331.spr08/ssvnc/

Logging in to a spectrometer or other NMRFAM computer from Windows

Download and use putty.exe (google it) to connect securely (through SSH) to login1.nmrfam.wisc.edu (or login2)

http://en.wikipedia.org/wiki/PuTTY

Once you successfully logged in to the NMRFAM gateway (i.e. login1 or login2 computers) using putty you can connect to any computer (including spectrometers) using ssh. For example, if you want to connect to the 900 MHz spectrometer type in your putty window:

ssh fleckvieh

For other spectrometers use the table below:

Spectrometer

computer cow name

Agilent 900

fleckvieh

Agilent 800

gelbvieh

Bruker 750

telemark

Bruker 600I

dexter

Agilent 600II

jaulan

Agilent 600III

vosges

Bruker 600IV

kurgan

Bruker 500I

kerry

Bruker 500II

devon

DMX Bruker 400

pisa


The first time that you login in a question about authenticity will appear. Answer yes.
The computer will respond with a request for your password. Type in your NMRFAM password.

Starting a VNC server (first time user, if not skip to vncserver command)

ssh -Y <username>@ login1.nmrfam.wisc.edu

cd

mkdir .vnc

cd .vnc

rm xstartup

gedit xstartup

paste the following into xstartup and then exit:

#!/bin/sh

xrdb $HOME/.Xresources
xsetroot -solid grey
#x-terminal-emulator -geometry 80×24+10+10 -ls -title “$VNCDESKTOP Desktop” &
#x-window-manager &
exec gnome-session

 VERY IMPORTANT:

The file xstartup must be made executable. This is done from the command line:

chmod +x xstartup

Use the following commands (on fleckvieh in this case):

vncserver

or

vncserver -geometry 2048×1024 (you can adjust the geometry to fit your screen)

++++++++++

For xwinnmr (on DMX 400 (pisa) only) you MUST start the VNC server as:

vncserver -depth 8 -cc 3 -geometry 2048×1024

(chose a geometry close to the resolution of your monitor)

 

++++++++++

The computer will respond with something like:

New ‘fleckvieh:4 (username)’ desktop is fleckvieh:4

Remember the new desktop number (here it is 4)

exit (from fleckvieh)

exit (from login1)

Starting a VNC viewer

Download and extract SSVNC (for windows only). Create a desktop shortcut/icon for “sshvnc.bat” found in the ssvnc/windows installation folder and double click on it to start the program. A window will appear:

ssvnc1.PNG

Enter fleckvieh:4 in the VNC Host:Display Name field.

Enter <username>@login1.nmrfam.wisc.edu in the the Proxy/Gateway field. (Alternatively, login2.nmrfam.wisc.edu can be used).

If you want to save what you just typed click on Save and name it for example fleckvieh. Next time you can use the Load button and the fields above will be pre-filled. If needed, you will change only the display number allocated to the vncserver.

Click Connect.

In the black pop-up window type your NMRFAM password:

ssvnc2.PNG

In the new pop-up window type your vncpasswd (the one that you entered when you started your first vnc session):

ssvnc3.PNG 

If you have forgotten the vncpasswd then ssh login1.nmrfam.wisc.edu and then ssh fleckvieh and type vncpasswd. You do not need to know the old vncpasswd to change it.

The vncviewer will provide you with a graphical desktop of the spectrometer computer. You can start vnmrj or topspin or xwinnmr from a shell (terminal window) in that desktop:

ssvnc4.PNG

Stopping a VNCserver

When you are finished accessing a NMRFAM computer via vnc, you can kill the vncserver by logging on to the computer that is running the vncserver and typing:

vncserver -kill :# where #n is the number of the vnc session that you want to kill

 

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. It is left to the user to backup his/her own data. Raw data collected on the spectrometers is backed up nightly, but is not available to the user on demand (contact the facility staff). There are no RAID systems on the instrumentation computers.

There is no safe data storage.

If the building burns your data will help fuel the fire; make a copy of your data and take it home!

 

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).

Linux/Mac

Open a terminal.

 

Linux_prompt> ssh <username>@login1.nmrfam.wisc.edu

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).

 

 

Windows

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. http://support.suso.com/supki/SSH_Tutorial_for_Windows

 

 

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

 

Linux/Mac

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

Terminal:

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>@login1.nmrfam.wisc.edu:/nmrfam_data/<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 login1.nmrfam.wisc.edu or login2.nmrfam.wisc.edu.

Change directory to whatever computer and directory you want to copy data from then drag&drop. I recommend searching for winscp tutorial windows.
http://www.siteground.com/tutorials/ssh/ssh_winscp.htm

 

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 milo@login1.nmrfam.wisc.edu:/nmrfam_data/milo/nmr/snase/bestdata.pdf .

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. 
 

Data from other instrumentation :

The LC-MS-SPE, SAXS instruments, and the Daedalus high pressure equipment are not accessible from outside the facility. Please contact the facility about their use.

 


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2017 NMRFAM Introductory Structure Determination Workshop (6/4-9, 2017), Madison WI

2017 NMRFAM ADVANCED Structure Refinement Workshop ( 8/6-9, 2017), Madison WI 

"The Future of NMR-Based Metabolomics, Current Opinion in Biotechnology (2017), pp. 34-40

Telluride School on Biomolecular Structure and Dynamics;Theory and Experiment (July 24-31, 2017) 

AMPERE NMR School (June 25th - July 1, 2017: Zakopane, Poland)

Documents on the use of the Bruker-Axs Nanostar,SAXS instrument and analysis of SAXS data are now available.

NMRFAM-SPARKY Distribution - the popular NMR analysis program SPARKY recompiled (including updated python and Tcl/Tk) with incorporation of PINE-Sparky, enhancements to import/export to the structural analysis program CYANA, and other useful python extensions.

ADAPT-NMR Enhancer: Complete Package for Reduced Dimensionality in Protein NMR Spectroscopy

RNA-PAIRS: RNA Probabilistic Assignment of Imino Resonance Shifts

PACSY, a Relational Database Management System for Protein Structure and Chemical Shift Analysis 

 

Donate to NMRFAM. US tax-deductible donation can be made to NMRFAM
Please write check payable to "UW Foundation, Account 112152802"  
And mail to: 
Attn: Sarah Lynn Traver Saunders
Associate Administrative Program Specialist 
University of Wisconsin-Madison 
433 Babcock Drive 
Madison, WI 53706 
Tel: 608-265-2507 or email 

 

1st: Lai Bergeman 
Rm 171; Phone 262-3173

2nd: Milo Westler
Rm B160; Phone 263-9599

3rd: Mark Anderson
Rm B224; Phone 265-3303

4th: Marco Tonelli
Rm B160; Phone 263-9493

5th: John Markley
Rm 171A; Phone 263-9349

We welcome your questions and feedback!

NMRFAM Established 1987