NMR Computer Network and Data Server

The purpose of the network is to allow NMR users access the NMR data from their own computers. All the data acquired from each NMR instruments can be saved directly on the data server without using FTP or other means to transfer the data. i.e.  an imaginary disk has been mounted to each host computer that controls the NMR instrument.  The server will equipped with a RAID disk system and a secondary back system.

All NMR users can download the NMR data and process their data on their own computers. We recommend MNOVA (PC or MAC) for off-line processing.


  • Computer software:
  •  Linux: RED HAT Enterprise Linux version 4 – for 64 bit AMD 64 or INTEL EM64T
  • Sun Solaris 8 or 9
  • NMR  VNMRJ 2.3A, 2.1B, 1.1D and VNMR6.1C.
  • Computer Harware:
  • Dell Precision 380 with two Ethernet cards (eth0 and eth1)
  • Sun Microsystem Blade 150, Blade 1500, Ultr 10 with two Ethernet cards.
  • Router CentrCOM MR820TR
  • Data Server Dell Precision 470, it is replaced by much powerful server DELL T310.


Install Ubuntu (Linux) on Dell PowerEdge T310 Server: (Service Tag: 7HJ6HQ1, purchased (6/5/2011)
Updated: 8/19/2011 swu

When Power up there are few keys F2, F10,  F11, you can press before boot up. It can get into the BIOS setup. In this case, we just need to boot on CDROM. 
On the DELL CD, there is a utility to configure the RAID. We want to configure it as RAID 10 that will be mirroring and stripping for best redundancy and performance. But we have to use all four disks (it is minimum requirement).
Detailed setup for RAID, see the document on line: support.dell.com

  • Insert the CD that is provided by DELL (System Management Tools and Documentation version 6.5.0; P/N FCCFT Rev A00 april 2011)
  • After boot up on CD. It takes about several minutes.  A window (System Build and Update Utility Home page) will show up. Select the first line to build up the system.
  • There are three options: Server OS Installation; Hardware Configuration; and Firmware Update. Select Hardware Configuration to configure the RAID. Click Hardware Configuration.
  •  In the new page, Click RAID ----- not Configured à a new page à click Create Virtual disk.
  • Select: slot 1 – PERC 6/I Adaper (RAID card installed); all (four of them installed); RAID 10.  Then click save settings.  Now you will see    RAID ---- Configured.
  • Back to home page. Click Appy/Export configuration. Check on Apply configuration to current system, and exit on failure.
  • Click apply/export. After save and exporting…. Few minutes,  it will reboot.  Take the CD out, before it booton the CD, otherwise, it will start it again. The configuration will be erased.

Note: Before reboot, push the CD eject bottom, the CD cannot be ejected. So force the computer power down by press the power on botton for few seconds, after the power down, then turn on the power again, press the CD eject bottom, the CD is ejected. Then rebooted the system.   How  to  check  the RAID  setup?

  •  Insert the Ubuntu server CD and reboot on it.
  • After boot up on the CD. A language page comes up. Choose English. Select install Ubuntu Server. ----- If it is a new system, do the test first before install the server.

After the test, it will start again from boot.don’t test the memory, it takes too much time.

  • Select English.  United States.  Keyboard select USA. Then the computer will start install the OS.
  • Use eth0 to connect the internet. (You have to connect internet to install the OS!)
  • Hostname: nmr-server   ---- cannot use “_”!
  • It takes a little longer, then you expected to setup the time zoon. Select Eastern
  • Partition disks:   ---select Manual.
  • Select: SCSI5 (2.0,0,) sad    --- 999.1 GB Dell Perc 6/I adapter ------ we are using this one.
  • YES. Next page. Select pri/log 999.1 GB   free space.
  • Select YES, to create a new partition:

On the next page, select pri/log 999.1GB free space, then press return
Select Create a new partition.
Type the parameters as following, to partition the disk.
400MB   primary  beginning      and use ext2 file system for boot. Mount point /boot
Bootable flag on.    ----- done setting up the partition, it will go back to setup more partition.
100 GB primary beginning   and use ext4 jounaling file system for /root. Mount point /root bootable flag on.
1 GB primary beginning  and use swap area,  /swap    bootable flag on
Rest of the space(897.7GB), ext4 mount point: /media/nmr_data  bootable flag on
Use manual to change the mounting point.

Finish partitioning and write change to disk.
Show the partition table:
/boot            400Mb
/                  100 GB
/swap     1 GB
/media/nmr-data    897.7 GB

Then press “finish partitioning and write change to dick”
Computer will start to install the base system.

  •  Full name for the user: Shaoxiong Wu,  swu  passwd ;  encrypt home directory NO.
  • HTTP proxy information: leave it blank --- press return
  • Update on the system?   No automatic updates
  • Use space bar to select options: Open SSH server and Samba file server.  Then press Enter
  • Install the GRUB boot loader to the master boot record: YES
  • Automatically eject the CD and then reboot.

After reboot: login as vnmr1/swu
Now it is time to install Linux (Ubuntu)---- get files online.
$sudo apt-get update, it will ask for the root passwd.
Lots files will be loaded
$sudo apt-get upgrade
$sudo apt-get install xorg
$sudo apt-get install gnome
Lots lots files will be loaded.

$sudo reboot

After reboot:
At  the Ubuntu login screen: login
$sudo apt-get install ubuntu-desktop
$sudo apt-get install gnome-network-admin
Useful commands:
$sudo /etc/init.d/networking restart

$sudo ifconfig eth0 netmask



The OS works. Works as 64 bits   (not for i386----- install MNOVA 7.0 for Ubuntu 11.04, wrong architecture ‘i386’ ----- ????
Need to work on it

After above installation the internet is working,  but we want to use a static IP address for the server.

  • $sudo apt-get install gnome-network-admin
  • $sudo apt-get install ubuntu-desktop

############ after install all, we cannot setup the network (automatically installed), cannot setup the static IP etc. So try install the Ubuntu desttop instead of the server OS:
Install Ubuntu Desktop OS:

  • Boot on the CD (downloaded).  -----
  • After bootup, click install Ubuntu.
  • There are three green check, leave them on then click forward.
  • Select Erase Ubuntu 11.04 and reinstall. The forward
  • 999.1GB /dev/sda(ext4), click forward.
  • Select time zoon: NY. Forward
  • Keyboard: USA
  • Shaoxiong Wu, T310 swu  nmr4me
  • Copying files to the disk …….
  • After completed, take the CD out and Restart:
  • There is are two arrows at right-up corner. Click it to open the network editing.

Edit Connectionsàin the new window, click auto eth0 (you can change the name). then click edità Method; Manual à type into the IP address, netmask, gateway etc. à save.
Use ifconfig command to find the MAC number, that is required by editing the network card. Use eth0 for outside use eth1 for inside

  • In the terminal, type ifconfig. The new IP address should take over.
  • $sudo apt-get update, it will ask for the root passwd.
  • $sudo apt-get upgrade
  • $sudo apt-get install xorg --à already installed itself.
  • $sudo apt-get install gnome
  • $sudo apt-get install ubuntu-desktop ---- Already installed
  • $sudo reboot
  • $sudo apt-get install apache2

The network is working properly:
Next  step: install the server connect to NMRs.
Click the network icon, à Edit Connections  àwired  à  outside  àedit àIPv4àmanualà
Select require IPv4 addressing for this connection to complete.  Click save
For the  inside:
After complete the setting. Turn on the network. Then check by ping command:
Eth0  for outside,Eth1 is for inside.
Use ifconfig to check the connectivity

If install correctly, ping both networks, it should return 64 bytes from IP  ……….   123 ms

Since it is started from the Ubuntu desktop CD I386: so we have to install the nfs kernel.
If not installed, there is no file: /etc/exports

sudo apt-get install nfs-kernel-server 

After installed nfs server, there is a file /etc/exports. Edit it as following:
Note:  /media/nmr_server/400_inova     is a folder on the server. Make it rwx for everyone. is the IP for the client --- i.e. the inova400. Edit it for all instruments.

sudo /etc/init.d/nfs-kernel-server start 


Install the SSH server.
# sudo apt-get install openssh-server


Use ifconfig command to get the MAC  code (HWaddr) then insert it in the Edit Connections à select inside à Editàdevice MAC addressà select Connect automatically à selected Available to all users. à save.
These two network cards have different MAC #.



  • Add new user on the data server (Red Hat):

Application àsystem settings à User and Group

  • Add new user on the data server (Ubunto)

System à Administration à User and Group

  • Files on the V400:  

User login: computer à /media/data_server/groups/individual_files
The groups should be added by the computer on the machine. Under the groups, user can make their own directories as they wish. The groups-name must match the login name. The files are saved in this folder, the files will be show up on the server.

  • Files on the Sun (inova400, inova600, unity600 and Mercury300)

User login and load the vnmr software. Click the main à directory à parent, parent à data_server;  create a new directory of the group, and then individual user directory. The files are saved in this folder, the files will be show up on the server.


  • Files on the server (Red Hat): /media/nmr_data/400_inova

Under the nmr_data: there are a list of machine. Under the machine name, there are groups name. Under the groups’ name there are individual user name_folder.
The files are ready for SSH:

Find SSH for window: Tectia SSH 3.2.9, for Mac: CrossFTP-1.75a-mac
The IP for the server: port 22 for SSH and 21 for FTP.
After login find /media/nmr_data:  there are a list of instruments. Clcik the name of the instrument, then find your group name. your files will be there and ready to FTP.

Limitation: You are only allowed to use Emory network to download the data. (IP: 170.140.*.*





Install Ubuntu 11.04 Desktop is386

  • Use Dell disk to setup the Raid and reboot.
  • Insert the Ubunti disk, boot.
  • Select English, Install ubuntu
  • Select Forward
  • Erase disk and install Ubuntu
  • Entire disk will be used 999.1GB, forward
  • Time zoon NY, forward
  • Keyboard USA
  • Shaoxiong Wu, nmr-server, swu, nmr4me  ---- crashed!!!!


@@@@@@@@@@@@@@@Useful Commands
$sudo shutdown –h
************************************************************************************************************************************************************************************ For Users***************************

  • Open a group account on the server (same as login ID and passwd).
  • ON EACH MACHINE for each user group, make a directory as following:

Under each group_ID, they can make more directories for each user.

  • The can save files into the directory and access the file through the SSH FTP.


Download FTP from Emory website:
Software express to download FTP.

%%%%% On the Mercury 300

  • Move the mouse cursor at the background and hold the right mouse bottom. Select file manager, a new window will come up. In the window, double click the home, double click the data_server, to create a new folder for your group (group ID).   File à new folder à type the group ID as the folder name. ----(note: other than the group ID will be deleted).  Your group data directory  /export/home/data_server/your_groupID/your_data_folder
  • To save your NMR data on the server: cd(‘/export/home/data_server/your_groupID/your_dir’), then svf(‘NMR_data’)
  • You can access the data by FTP the data to your own computer.
  • You can download the FTP software from Emory website. After installed:

Use the following settings to get the data:
ID/host name:, port 22, your user ID
Set the director /media/data_server/group ID.
You can download the NMR file to your PC or Mac.


Setup Details:
Step One: ----- For the Server
Install the RedHAT linux software on the server:
Detailed instruction is on file (my note on the web). The screen problem can be resolved by using Varian CD to correct.

To configure the network.
Applications à Network the following screen will show up:redhat
If you have two Ethernet card installed, there are two lines.  If it is not active, click active first.
Double click the eth0: the following window will come up: the eth0  is used to connect the internet: 170.140.X.X.  configure it as your regular PC (but you have to setup the IP and gateway), do not use DHCP. After setup this, you can reboot it.  After it comes back, you should be able to surf the web. If not, you should check the hardware. And IP address and gateway (

Then double click the eth1 ---- this one is used to connect the router --- internal NMRs.
The IP can be any kind, but it must be same domain as the internal NMR computers. This one is 168.146.180.X  and the gateway (




In the Network Configure window, click DNS:
Input as the following to setup name server.


Then reboot the computer. After it comes up type the following in the terminal:
After that, this computer should be able to talk to both outside (internet) and inside router connections (internal NMR instruments). To test, use ping:
The first step is to ping all the computers: ping IP address. If it returns, then they communicate.
If not then there is a problem for the network.

Few things have to done on the server:
Hosts.allow ------ that file contains the IP address, this machine will allow to communicate:
Sshd: .chem.emory.edu
Sshd:      #this will allow my machine use SSH ftp to this server

Hosts.deny  ------ that file contains the IP address, it will not communicate.
ALL:ALL   -- deny all access, except specified in the hosts.allow.

Mount point:
Make a directories that will be mounted from different machines:  /media/nmr_data/400_inova  ------ this mount point is for inova 400 (/export/home/nmr_data). When an User login in inova400 (for example, davies),  the user is able to make a directory in /export/home/nmr_data/davies, even after /export/home/nmr_data/davies/john etc.  If the user change the current directory to /export/home/nmr_data/davies/john, then svf(‘file_name’) will save the data into the server /media/nmr_data/davies/john. The file are ready for their own PC to retrieve and process.
/etc/dfs/dfstab  (on the client)
Mount –F nfs  /export/home/nmr_data
Mount –F nfs  /export/home/data_server

/etc/exports (on the server)

To restart the server service:
/etc/init.d/nfs restart

To configure the SSH port (the default is 22)


On the client
A, on the Dell Linux computer (running VNMRJ)
Modify the hosts file:
Inside: 168.146.180.
Modify the hosts.allow and hosts. Deny
Make sure allow the IPs for communicating with the console. There are
Activate the service nfs à applications à server settings àservices à passwd à check the nfs to active it.



B. On the Sun Microsystem (running solaris 8 or 9)
Edit the file /etc/dfs/dfstab:
mount –F nfs  /export/home/data_server
mount –F nfs  /export/home/nmr_data

You can copy the line to mount the device manually. Then use df –k to check if it is mounted on.

For some reason, after restart the computer, the internet card (communication with the server) does not start automatically, have to go application à network à passwd then activated the card by click the network card and click activate.