Access to the NMRFAM network and spectrometers
NMRFAM network of computers and spectrometers
- SSH required
- Accessing the NMRFAM network
- Change your password
- NMRFAM E-mail account (updated)
- NMRFAM spectrometers
- NMRFAM Computers
- infrastructure computers
- Where should I login to do something?
- Data backup
- To copy data from the spectrometers (within the NMRFAM network)
- To copy files to or from NMRFAM computers from outside the NMRFAM network
- Software on the compute servers
- To use NMRFAM computers from home or another lab
- Remote spectrometer and computer access via VNC (Linux/Mac)
- Remote spectrometer and computer access via VNC (Windows using putty)
- Extranet
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. Open a terminal.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. [return to top]
Accessing the NMRFAM network from outside
login1.nmrfam.wisc.edu (or login2.nmrfam.wisc.edu) gateway computer(s) to access NMRFAM from the outside.
To login:
Your_home_computer_prompt> ssh -X @login1.nmrfam.wisc.edu
login:
password: your password (not visible when entered)
Linux_prompt_for_login1>
From login1 (aka hereford - login2 is also hereland) you can login to any other NMRFAM computer. All spectrometers and compute servers are accessible from the net. [return to top]
This must be done on angus but 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.
Linux_prompt> ssh angus.nmrfam.wisc.edu
Linux_prompt> login: <username>
Linux_prompt> password: (enter your 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>
We are in the process of changing mail servers and this may cause some disruption in service. If it does try the following. (09/10/09)
1. Logon to herens, run
maildirmake ~/Maildir
2. 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.)
3. See the above page for spam filtering setup.
4. Let Milo or Dimitri know you’ve set it all up and are ready to switch.
Along with your NMRFAM account you will be given an e-mail <username>@nmrfam.wisc.edu. If you want to receive the emails at another account then you should login and create a new file named “.forward” (note the prepended “.“). In that file enter the email account name (e.g. <username>@hotmail.com).
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 related 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 Remote operating instructions).
| Spectrometer | Computer name | Shortcut name | Probea |
| Varian VNS 900 | fleckvieh | vns900 | c-tr |
| Varian VNS 800 | gelbvieh | vns800 | c-tr |
| Bruker DMX 750 | telemark | dmx750 | c-tr |
| Bruker DMX 600 | dexter | dmx600I | c-tr |
| Varian VNS 600 | jaulan | vns600II | c-tr |
| Varian VNS 600 | vosges | vns600III | c-tr |
| Bruker Avance 500 | kerry | dmx500I | multiple/sample changer |
| Bruker DMX 500 | devon | dmx500II | c-tr |
| Bruker DMX 400 | pisa | dmx400 | multiple |
| a rt - room temperature; c - cryogenic; tr -1H{13C,15N} triple resonance; multiple - multiple probes; VNS- Varian Direct Drive console; DMX- Bruker; Avance- Bruker Avance III. You can use either the Computer name or the Shortcut name (inside NMRFAM) to login to the spectrometers | |||
NMRFAM Computers (.nmrfam.wisc.edu)
hereford (login1) – gateway computer to login into the NMRFAM network
hereland (login2) – gateway computer to login into the NMRFAM network
chianina – 12 processor compute server
data drive- /chianina/data – 1TB
charolais – 12 processor compute server
data drive- /charolais/data – 1TB
watusi – 16 processor compute server
data drive- /watusi/data – 1TB
jenubi – 16 processor compute server
data drive- /jenubi/data – 1TB
angoni – 24 processor compute server
data drive- /angoni/data – 1TB
rendena – global home and data directories (5 TB)
/usr1;/usr3;/usr4;/banyo;/banyo2
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Other infrastructure computers
chiangus – PINE server (pine.nmrfam.wisc.edu)
tortona – vnmrj offline computer
angus – computer used to change passwords
herens - administrative/compute server
nimari – restricted backup (not for users)
nelore – restricted backup (not for users)
banyo – old server for SGI computers
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
Where should I login to do something?
If you are using the spectrometer, then login to the spectrometer.
If you are processing, flip a coin for one of the compute servers, but make sure your favorite software is installed.
you may want to use the command “top” to see how many jobs are running on the computer that you chose.
If you are moving data around, it shouldn’t matter. The use of the spectrometer computers for this is not recommended since they have enough to do already.
Global home directories:
/usr1/people
/usr3/people
/usr4/people
When you login into any NMRFAM linux or Unix computer these are the directories that you go to. (except on the Varian spectrometers, Avance Bruker spectrometers, chianina, and charolais)
Home directories that are local to the computer
/chianina/home/<username>
/charolais/home/<username>
/jaulan/home/<username> Varian 600II
/vosges/home/<username> Varian 600III
/gelbvieh/home/<username> Varian 800
/fleckvieh/home/<username> Varian 900
Data directories:
/banyo/data (not local to any compute server)
/banyo2/data (not local to any compute server)
/chianina/data/ (local to chianina)
/charolais/data/ (local to charolais)
/watusi/data/ (local to watusi)
/jenubi/data/ (local to jenubi)
Spectrometer data directories
| /pisa/data/<username>/nmr/ | Bruker 400 |
| /kerry/data/<username>/nmr/ | Bruker 500I |
| /devon/data/<username>/nmr/ | Bruker 500II |
| /dexter/data/<username>/nmr/ | Bruker 600I |
| /telemark/data/<username>/nmr/ | Bruker 750 |
| /jaulan/home/<username>/vnmrsys | Varian 600II |
| /vosges/home/<username>/vnmrsys | Varian 600III |
| /gelbvieh/home/<username>/vnmrsys | Varian 800 |
| /fleckvieh/home/<username>/vnmrsys | Varian 900 |
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.
You can create your own directory in any of the above data directories (please use you username “mkdir <username>”). These directories
are for work space and old data may be deleted without notice. No home or data directories are backed up.
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.
Data backups
The data directories (except for /chianina/data and /charolais/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.
Data collected on the spectrometers is backed up, but (currently) is not available to the user on demand (tapes must be manually loaded).
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 within the NMRFAM network
e.g. You (<username>) have collected a series of data on the Bruker 750 (dmx750- see table of spectrometers above) in a directory named /great_data and you want to save it to /banyo2/data.
login to any unix or linux NMRFAM computer (here rendena, which is the server running the 5TB RAID 10 disk system)
Linux_prompt> ssh <username>@rendena
username@rendena’s password:
Linux_prompt> cd /banyo2/data
if you have not created a directory on this disk (/banyo2/data) then
Linux_prompt> mkdir <username> (please use your login name for <username>)
Linux_prompt> cd /banyo2/data/<username>
Linux_prompt> cp –r /dmx750/data/<username>/nmr/great_data .
(note the “.” at the end, this stands for the current directry and in this case replaces “/banyo2/data/<username>/”. You can always use the full path as well.
“cp -r” copies all files and directories in the great_data/ directory).
Remote scp (To copy files to or from NMRFAM computers from outside the NMRFAM network)
For Windows use Winscp (freeware) or secureFX from Doit - login to login1 or login2
Linux
- For scp to/from a directory that IS MOUNTED on login1 (or login2) use standard scp syntax:
Here <username> wishes to copy file_name to the local current directory on his home computer.
Home_computer_prompt> scp <username>@login1.nmrfam.wisc.edu:/chianina/data/<username>/file_name .
Password:
(note “.” at the end to copy to the current directory)
For windows machines use WinSCP, FileZilla or the like and login to login1 or login2.
- For scp from/to a directory that is NOT MOUNTED on login1 (or login2) use scp through an ssh tunnel:
Here <username> wishes to copy file_name to the local current directory on his home computer.
Home_computer_prompt> ssh -L 2345:charolais:22 <username>@login1.nmrfam.wisc.edu
Password:
login1_prompt>
leave this session open and start new terminal
Home_computer_prompt> scp -P 2345 <username>@localhost:/charolais/home/<username>/file_name .
Password:
(note “.” at the end to copy to the current directory)
Software on the compute servers
Please look at the screen when you login to see the installed software packages.
chianina and charolais – 12 processor SGI Altix (Redhat)
– these computers have local home directories
Available software (08/2009):
• nmrPipe 2.4 (nmrPipe)
• amber9 (sander, gibbs, antechamber, etc.)
• Gaussian 03 (g03) (NBO5)
• Gaussview (gv)
• UNIO_08 (ExecuteAtnosCandid only)
• CARA 1.5.4 (cara)
• CYANA 3.0 (cyana)
• CNS
• dock (/usr2/Dock/bin/dock5.linux)
• octave
• XPLOR-NIH 2.19 (xplor)
• gromacs
jenubi and watusi – 16 processor Supermicro 4 X quadcore AMD (CentOS 5.2)
Available software (08/2009):
• NMRPipe System Version 3.0
• cyana-3.0
• UNIO_08 (ExecuteAtnosCandid only)
• xplor-nih-2.21
• vmd-xplor-1.5
• cns_solve_1.21
• PQS (Parallel Quantum Systems) version 3.3
• Octave 3
angoni - 24 processor Supermicro 4 X 6 core Xeon (centos)
Available software (08/2009):
• NMRPipe System Version 3.0
To specifically run on one of the compute servers login to that machine. e.g. to run on chianina type “ssh –X chianina”. Using the –X option in ssh will allow X types graphics to be displayed. Do NOT run the nmr spectrometers using this method!
To use NMRFAM computers from home or another lab (Linux/Unix/OSX):
Home_computer_prompt> ssh <username>@login1.nmrfam.wisc.edu
Password:
login1_prompt>
At this point you can ssh to any other computer on the NMRFAM network. Alternatively, you can ssh to login2.nmrfam.wisc.edu.
For interactive X graphics (not for use with remote spectrometer operation):
Home_computer_prompt> ssh -X <username>@login1.nmrfam.wisc.edu
Password:
login1_prompt>
Windows users can use putty.exe or another windows compatible ssh client.
The extranet is a location within the NMRFAM net that holds information specific to facility operations. It has limited accessibility from remote sites because of copyrighted materials located there. Any NMRFAM account owners can access the extranet.
To gain access to the NMRFAM extranet through your web browser, you can use ssh dynamic port forwarding. This allows you to run your
browser as if you were attached directly to the NMRFAM network, (e.g. extranet is accessible among other things)
ssh -D3456 <username>@login1.nmrfam.wisc.edu
3456 is an example, choose a 4 digit number greater than 1024
leave this connection open and set the manual proxy port in your browser to this number (3456 in this case).
Setting manual proxy
Firefox:
Options->Advanced->Settings
click on manual proxy configuration
SOCKS host 127.0.01 port 3456 (or whatever number you chose)
For internet explorer, google: “proxy settings internet explorer”
try: www.proxyway.com/www/set-proxy-configuration/configure-proxy-settings.html
Windows use putty:
google: “putty” and download putty.exe
google: “putty dynamic port forward” for instructions
For other browsers I also recommend google for instructions.