Remote Access

Accessing the NMRFAM network

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>@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 below: Remote spectrometer access – Linux/Mac or Remote spectrometer access – Windows).

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.

Gateways, file servers, and compute servers:

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:

Secure remote access to NMRFAM facility spectrometers and computers

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 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.

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 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. 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).

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.