Charles L. Mayne and Dennis Edwards
Notes on the use of floppy disks, recordable CD's and NSF-mounted file systems
for the archiving of data.
This is the first in a series of application notes concerning the use of University of Utah Department of Chemistry NMR Laboratory spectrometers and equipment. Additional notes will be published from time to time to supplement the material in the vendor supplied manuals and to make researchers aware of new developments in the NMR Laboratory. Suggestions for topics to be treated are welcome. Articles for publication in this series are also solicited. Researchers who have a technique they wish to share with others may contact Charles Mayne to have their material considered for publication.
This note treats the use of floppy disks with the Sun Sparcstations, transfer of data to the Department of Chemistry Sun 4/670 server, and archiving of data using the Macintosh recordable CD system. This note presumes that the reader is familiar with the basic operation of Varian NMR spectrometer systems using Sun workstations as hosts and with basic operation of Macintosh computers.
1.0 Policies for Disk Usage
Researchers are required to use CD's or floppy disks rather
than local hard disk files for long term storage of data because the size of the local
hard disks is not enough to store many FID's for each of the hundred or so users of
the NMR's. However, local fidlib directories should be left in place to be used for
temporary storage. The archive directory on atlas can also be used for this purpose.
Files in the atlas:/data/archive directory will no longer be migrated to 8 mm tape
as in the past. All the existing 8 mm archive tapes will be kept indefinitely, and
files may be retrieved from this archive as before. For now we will not impose disk
quotas or other restrictive measures. As long as everyone cooperates to keep the volume
of data in the file systems reasonable, it will not be necessary to do so.
One source of high disk consumption is unneeded experiment files especially with large 2D FID's and the corresponding transformed spectra in them. Please delete all unneeded experiments after the data in them has been saved.
Use of large amounts of disk space on /data other than in the archive is also a potential problem. Again we will make no restrictive policies for the moment, but just encourage everyone to be considerate.
2.0 Use of Floppy Disks
Use of floppy disks is still possible but no longer encouraged;
other more efficient and reliable methods are available as described below. Under
the Sun Solaris operating system, one must use the file manager tool to handle floppy
disks. See the Solaris documentation for details.
3.0 Archiving to Recordable CD's
As an alternative to saving FID's on floppy disks, one can
write data on a recordable compact disk (CD-R). A Macintosh computer located in room
1204 HEB is dedicated for this purpose. This is the currently recommended method especially
for large data sets.
CD-R is a write once read many (WORM) file system.This means that once files are written, they cannot be erased or modified. New (blank) CD-R disks cost about $8.00 each and have a capacity of 650 MB. This will hold about 1200 128 K double precision FID's. The current software produces a CD with a Macintosh file system.
CD's created with this system can be read on any Macintosh CD drive but only after the directory on the CD is finalized. The first time the CD is finalized will consume 25 MB of the disk; subsequent finalized sessions will consume 14 MB each. Because of this, it is not recommended to finalize each time you add spectra to your CD. Since the data is for archival purposes, one can put off finalizing for quite a while. When the CD is full, it must be finalized. After this, no more data may be written to the disk. Only finalized files can be read on another CD drive.
CD's can be damaged with improper handling. You may want to make two copies of important data and store them in different locations. However, the CD's are not affected by magnetic fields as floppy disks and tapes are; and, as long as CD's are not physically damaged, they will be readable for at least 30 years. Magnetic media, on the other hand, have an expected lifetime of only a few years.
3.2 Writing Data to a CD-R
Note: It is assumed that the user is familiar with operating a Macintosh computer.
3.2.1 Formatting a New Disk
1. Get a new disk. The Chemistry Stockroom should have a supply. The CD surface should be free of all dust. Put the disk in the disk caddy with the label side up. Use care when handling the disk. Hold it by the edges so as not to get fingerprints on the disk surface.
2. Place the caddy into the CD-R drive. The clear window is on top and the end with the arrow goes in first.
- 3. After the disk is scanned, a dialog box appears allowing you to initialize the disk. Enter a title of your choice for the volume label, then select ``initialize'' from the menu.
- 5. The CD may now be accessed just like a regular hard disk. You can create folders and drag & drop folders or files into them. You can delete files and folders, but this only causes them to disappear from the directories - the space they occupy is not recovered as with a regular hard disk.
3.2.2 Adding Items to a Previously Formatted Disk
1. Place the disk in the caddy as described above and insert it into the CD-R drive. If a dialog box appears indicating that the disk is not initialized, click initialize, then when the ``all files will be erased...'' box appears, click continue. Don't worry, your files will not be erased.
2. An icon for the CD will then appear on the desktop. The CD may now be accessed as usual.
3.2.3 Copying NMR Data Files to a CD
1. Run the FETCH program by double clicking the FETCH icon on the Mac desktop or by selecting FETCH from the apple menu.
2. If a new connection dialog box does not appear, select NEW CONNECTION from the FILE menu. A dialog box should appear with a default connection to atlas.chem.utah.edu. This may be changed as needed to retrieve data from other systems. Use the TAB key or the mouse to select fields in the dialog box. Enter your name and password as indicated and click OK. After connection occurs, you will be looking at files in your home directory.
3. Point the directory browser to the desired directory, e.g., /data/archive/your_user_name.
4. Select BINARY at the bottom of the FETCH window. This is very important! Your data may appear to be copied successfully, but you will not be able to restore it if BINARY is not selected.
5. Select an FID or other file or directory that is to be copied and, under the REMOTE menu, select ``GET DIRECTORIES AND FILES''. When the destination dialog box opens, select the CD volume or one of its subdirectories and click the SAVE button. Repeat this process until all desired items have been copied to the CD.
6. Quit the FETCH program and double click on the CD icon to verify that all the items were copied. When the CD volume is opened, the size of the stored data is displayed at the top of the directory window.
7. To eject the CD, drag its icon to the trash on the desktop. A dialog box will ask you if you want to finalize the directory or eject. In general, you will NOT want to finalize each time you copy files as this consumes 14Mb of your CD.
8. Carefully label the CD and store it in its case. A disk can become unreadable if scratched, so handle it carefully.1. Place the disk in the caddy as described above and insert it into the CD-R drive. If a dialog box appears indicating that the disk is not initialized, click initialize, then when the ``all files will be erased...'' box appears, click continue. Don't worry, your files will not be erased.
2. An icon for the CD will then appear on the desktop. The CD may now be accessed as usual.
3. Run the FETCH program by double clicking the FETCH icon on the Mac desktop or by selecting FETCH from the apple menu.
4. If a new connection dialog box does not appear, select NEW CONNECTION from the FILE menu. A dialog box should appear with a default connection to atlas.chem.utah.edu. This may be changed as needed to restore data to other systems. Use the TAB key or the mouse to select fields in the dialog box. Enter your name and password as indicated and click OK. After connection occurs, you will be looking at files in your home directory.
5. Point the directory browser to the directory where you want the retrieved files to be placed, e.g., /data/archive/your_user_name.
6. From the REMOTE menu, select PUT DIRECTORIES AND FILES. When the dialog box opens, go to the desired directory on the CD and select the directory or FID to be retrieved. Click the ADD button. Repeat, adding items as desired. When all desired items have been added, click the DONE button. The files will then be copied from the CD to the workstation disk.
7. Quit the FETCH program.
8. To eject the CD, drag its icon to the trash on the desktop. If the CD directory has not been previously finalized, a dialog box will ask you if you want to finalize the directory or eject. Click EJECT.
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