Remote Access

Accessing the NMRFAM network

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.

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.

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.

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

Configuring a VNC server

(Note: you need to perform this configuration step only when you connect for the first time to a spectrometer’s computer, for subsequent connections just skip to the ‘vncserver‘ command below)

Use the following commands to configure the VNC server (for example on fleckvieh):

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

ssh fleckvieh

cd

• the command above will navigate to your /home/<your login name> folder

cd .vnc

• the command above will navigate in the .vnc directory (/home/<your login name>/.vnc), if existent, if not -> use:

mkdir .vnc

• the command above will create a folder named ‘.vnc’ if  /home/<your login name> folder

rm xstartup

• the command above delete the existing ‘xstartup’ VNC configuration file, if existent

gedit xstartup

• the command above opens the ‘gedit’ text editor and creates a new blank ‘xstartup’ file

paste the following into ‘xstartup’, save, then exit the text editor:

#!/bin/sh

[ -x /etc/vnc/xstartup ] && exec /etc/vnc/xstartup
[ -r $HOME/.Xresources ] && xrdb $HOME/.Xresources
xsetroot -solid grey
vncconfig -iconic &
xterm -geometry 80×24+10+10 -ls -title “$VNCDESKTOP Desktop” &
exec gnome-session

 

*** VERY IMPORTANT:

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

chmod +x xstartup

 

Finally, start the VNC server:

vncserver

or

vncserver -geometry 1366×768  (you can adjust the geometry to fit the resolution of your screen)

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)

*** VERY IMPORTANT:

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 (replace “username” with your NMRFAM username):

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

B) On an Apple computer running Mac OS X 10.6 (Snow Leopard) through 10.13 (High Sierra):

Download and install TigerVNC:

https://bintray.com/tigervnc/stable/download_file?file_path=TigerVNC-1.8.0.dmg

Then, in a terminal window, navigate to the MacOS subfolder of TightVNC:

cd /Applications/TigerVNC\ Viewer\ 1.8.0.app/Contents/MacOS

and start the program “TightVNC Viewer” with the ‘-via’ option (replace “username” with your NMRFAM username):

./TigerVNC\ Viewer -via username@login1.nmrfam.wisc.edu telemark:4

• you will be prompted (in the terminal) to use your NMRFAM password (this is the password you used when you connected by ssh to login1.nmrfam.wisc.edu)
• The next password requested (in a pop-up window) is the VNC password (that you set up on fleckvieh when you started the VNC server the first time).

Once you type it, a new window will appear with the graphical desktop(s) of the spectrometer computer. You can now start topspin or vnmrj (or any other application installed there).

 

Stopping a VNCserver

If you are finished using a NMRFAM spectrometer and are logging out, then remember to exit the NMR software (topspin or vnmrj) 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 # is the number of the vnc session that you want to kill (i.e. 4 in the example above).

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.

Configuring a VNC server

(Note: you need to perform this configuration step only when you connect for the first time to a spectometer’s computer, for subsequent connections just skip to the ‘vncserver‘ command below)

Use the following commands to configure the VNC server (for example on fleckvieh):

cd

• the command above will navigate to your /home/<your login name> folder

cd .vnc

• the command above will navigate in the .vnc directory (/home/<your login name>/.vnc), if existent, if not -> use:

mkdir .vnc

• the command above will create a folder named ‘.vnc’ if  /home/<your login name> folder

rm xstartup

• the command above delete the existing ‘xstartup’ VNC configuration file, if existent

gedit xstartup

• the command above opens the ‘gedit’ text editor and creates a new blank ‘xstartup’ file

paste the following into ‘xstartup’, save, then exit the text editor:

#!/bin/sh

[ -x /etc/vnc/xstartup ] && exec /etc/vnc/xstartup
[ -r $HOME/.Xresources ] && xrdb $HOME/.Xresources
xsetroot -solid grey
vncconfig -iconic &
xterm -geometry 80×24+10+10 -ls -title “$VNCDESKTOP Desktop” &
exec gnome-session

*** VERY IMPORTANT:

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

chmod +x xstartup

 

Finally, start the VNC server:

vncserver

or

vncserver -geometry 1366×768  (you can adjust the geometry to fit the resolution of your screen)

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)

*** VERY IMPORTANT:

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)

Download and extract the SSVNC (for windows only), which is a VNC Viewer program. 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:

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:

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

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:

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 (i.e. 4 in the example above).

NMRFAM instrumentation and computers

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.