How to back up your NMR data

10/15/2004, IU NMR Facility, prepared by JWT, DEB, and XFG

To transfer your data and back them up, you can use different options, depending on the storage media used, and whether you want to transfer your data for archiving or for working with individual files. Your different goals may dictate whether you want to copy the data in the regular structure or concatenate them with tar. Procedures and media covered here include:

Backing-up or Archiving Data onto CDs
Backing-up or Archiving Data onto USB Key Drives
Backing-up or Archiving Data onto Remote computers and their peripheries (hard drives, key drives, remote zip drives, etc.)

I Backing-up or Archiving Data onto CD

There is a CD writer in one of the PCs in the NMR Facility as well as one on the NMRSUN4 workstation. The writer on NMRSUN4 is faster but it's a little more difficult to use.

On MAGRES in the NMR Facility (or any Windows XP PC in the indiana.edu domain):
1. Copy the files to be burned onto CD:
  1. To backup/archive files from a spectrometer:
    1. Open up a SFTP (Secure File Transfer Protocol) file transfer window with the icon on the desktop.
    2. Hit Enter and, in the "Connect to Remote Host" window, type in the name of the specrometer to which you want to connect and your username (see image below).
    3. Hit Enter again and fill in your password when prompted.
    4. In the left hand pane, go to C:\User Files and click on the "New Local Folder" icon to create a new folder with your username.
    5. From there simply drag and drop the files you want from the spectrometer to C:\User Files\xxx, where xxx is the folder you just created.
  2. To backup/archive files from an archive CD:
    1. Put the CD in the CDR (if you're doing this in your lab or office you'll need to check out the necessary CDs from the NMR facility first).
    2. In Explorer, navigate to C:\User Files and in the menu bar go to File/New/Folder to create a new folder with your username.
    3. From there either copy and paste the files you want from the CD to this new folder or drag and drop from a second Explorer window. [Unfortunately, this will only work with archive CDs made from the end of 2003 to the present as the older ones have a file in each directory called <translation table> (brackets included) which Windows Explorer doesn't like.
2. Burn the CD:
  1. In Windows Explorer, go to the folder you've created containing either, all your files, or the folders with the spectrometer names that contain all the files.
  2. Select all using the mouse or Ctrl+A.
  3. Right-click on the selections and choose "Properties" in the popup context menu.
  4. Look at the "Size" value. If it's greater than about 600MB than the files will require more than one CD and you have to choose subsets of files and create more than one CD. Close the "Properties" window by clicking on either "OK" or "Cancel".
  5. Insert a blank CDR(W) into the CDRW drive.
  6. With the desired files or folders selected choose "Write these files to CD".
On NMRSUN4:
1. Copy the files to be burned onto CD:
  1. To backup/archive files from the spectrometers:
    1. Log in and change to the temp_archive folder (directory) by typing "cd /sun4b/temp_archive".
    2. Create a temporary folder with the command "mkdir username" where username is your 3 letter username.
    3. Type "cd username" to change to this folder.
    4. If you will be archiving data from more than one spectrometer, create directories for each of the spectrometers with "mkdir spec_name" where spec_name is gem300, vxr400, i400, and/or i500.
      - If you've created sub-folders for each spectrometer, cd to the one you want to get first.
    5. Use the command "cp -Rp /nmr/spec_name/username/filename ./" to copy just one file, or "cp -Rp /nmr/spec_name/username/*.fid ./" to copy all the files from that spectrometer to the current folder.
    6. If you've created sub-folders for each spectrometer type "cd ../spec_name" to go to the next empty folder and repeat step 4 using the new spectromater name.
  2. To backup/archive files from archive CDs:
    1. Log in and change to the temp_archive folder (directory) by typing "cd /sun4b/temp_archive".
    2. Create a temporary folder with the command "mkdir username" where username is your 3 letter username.
    3. Type "cd username" to change to this folder.
    4. If you will be archiving data from more than one spectrometer, create directories for each of the spectrometers with "mkdir spec_name" where spec_name is gem300, vxr400, i400, and/or i500.
      - If you've created sub-folders for each spectrometer, cd to the one you want to collect first (ie. "cd i400").
    5. Insert the (first) CDROM in the CDROM drive.
    6. Type "pwd" to make sure you're in the correct directory (it should return /sun4b/temp_archive/username, or /sun4b/temp_archive/username/i400 as in the example above).
    7. Use the command "cp -Rp /cdrom/cdrom0/username/filename ./" to copy just one file, or "cp -Rp /cdrom/cdrom0/username/*.fid ./" to copy all the spectrum files for you, or any other user, from that archive CD to the current folder.
    8. If you have more than one CD from which you want to copy files:
      - Type "eject" to eject the current CD.
      - Insert the next archive CD.
      - Repeat steps 6 and 7 for each CD (hint: you can use the up arrow on the keyboard to bring previous commands and eliminate a lot of typing an/or typos).
    9. If you've created sub-folders for each spectrometer type "cd ../spec_name" to go to the next empty folder and repeat steps 5-7. After you've ejected your last CD, type "cd ../".
    10. Type "pwd" to make sure you're in the correct directory (it should return /sun4b/temp_archive/username).
2. Burn the CD
  1. Type du -sh. If it returns a value larger than 600M (K=kilobytes, M=Megabytes, and G=gigabytes), you'll have to back the data up to more than one CDR(W) disk. If this is not a trivial matter for you, ask for help.
  2. Put a blank CDR or CDRW in the Plextor drive attached to nmrsun4.
  3. Type "burncd" (burncd is a C shell script located in /usr/bin in case you want or need to know for any reason). This will first create a .iso (CDROM format) file and then burn it to a CDR(W).

II Backing-up or Archiving Data onto USB Key Drives

There are two available USB ports on the back of MAGRES which can be used for backing-up data to a USB Key Drive. To do so, follow the instructions above in 1.-(a)-i. on how to collect files into a folder on MAGRES, from one or more spectrometers and/or one or more archive CDs, then:

Copy to Key Drive:
1. In Windows Explorer, go to the folder you've created containing either, all your files, or the folders with the spectrometer names that contain all the files.
2. Select all using the mouse or Ctrl+A.
3. Open the Key Drive in another Explorer Window (Doucle-click “My Computer” on the desktop, then double-click on the Key Drive.
4. Right-click in the Key Drive Explorer window and choose “Paste”.

III Backing-up or Archiving Data to Remote Computers and their Peripherals

Remote computers are those, for which you have to use the SFTP program instead of simply copying files between filesystems. This is basically the same as was described above in part 1.-(a)-i. If you don't have an SSH(SFTP) client on your computer you can obtain one at: http://www.ssh.com among others.

Transferring your data to the host computer.
Go to the host computer that contains the drive you want to back up the data on (hard drive, key drive, zip drive, floppy drive, etc.). Transfer the data with SFTP to the drive at your machine. The login and file transfer windows for SSHs Secure File Transfer are shown below. If you are backing up to a Key, Zip, Hard, or Floppy drive, you can select it in the left hand pane and save it directly. If you are putting the files on CD, you'll have to copy them first to the hard drive, and from there follow the instructions in 1.(b).

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Last updated: October 19, 2004
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