JISAO computer helps

Please contribute to this list. The html file is /home/disk/tao/data/mosaic/computer_helps/index.html and everyone has write permission for this file. Keep your write-up short, and include your name and the date of your contribution.

Harry Edmon and David Warren of UW Atmospheric Sciences maintain the computer network, and questions having to do with the network should be sent to support@atmos.washington.edu. Harry and David will also answer other questions, but the groups within JISAO have chosen not to fund them to provide general software support, so keep that in mind if you write to them.

Cannot print from the Macintoshes
Work your way down the following list until you are able to print again.
  1. make sure that the printer is selected with the chooser.
  2. turn your Mac off and on
  3. turn the printer off, wait five seconds, and turn it on
  4. an ethernet hub sits on the printer table. It has eight little lights on it. Unplug the power from this device and plug it in again.
  5. On your Macintosh, go to the "apple" menu (upper left corner), select "chooser," select "apple talk," select "local network," and then select "apple talk".
Todd Mitchell, February 1999.
How to force a Macintosh to reboot

If a Macintosh does not respond to keyboard input, simultaneously depress the "control", "apple" (it's an apple logo), and "triangle that is tipped up on one corner" (upper right part of keyboard) keys.

Todd Mitchell, July 2000.
Copying a file from a UNIX machine to your Apple computer

From the terminal of your Apple computer, type

scp username@unixmachinename:filename target_directoryname

to copy file "filename" from "username"s acccount on the "unixmachine" machine to "target_directory" on the Apple computer. For example,

scp mitchell@ecfc:work.pdf ~/Desktop

will copy "work.pdf" from the "mitchell" home directory on "ecfc.atmos.washington.edu" (a UNIX machine) to the Desktop directory on Todd Mitchell's Apple computer. Doing the copy from the Apple computer avoids having to set up an ssh server.

Todd Mitchell, August 2009.
Copying a file from your Apple computer to a workstation You will need to have "FileZilla" software on your computer, and also to have "acitivate Web Publishing" on your account with the University of Washington. https://uwnetid.washington.edu/manage/?service

Filezilla generates a GUI, and you should type the following into "Host" box: "sftp://username:password@machinename" (no quotes) followed by a "return"
where username and password are your username and password on the workstation
machinename will be something like "piura.atmos.washington.edu".
You will then see your Apple directories on the left side of the GUI, and your workstation home directory on the right side of the GUI. Drag the file / directory (?) of interest from the left to the right.

Todd Mitchell, November 2012.

Import an ecapsulated PostScript file that resides on a workstation into a Word document (with Word running on an IBM).

David Warren recommends that you run Word on the IBM but save the Word document on a workstation. The workstation files are backed up, but the IBM files are not.

  1. Generate an ecapsulated PostScript file:
    From the SUN computers, type ps2epsi filename.ps filename.epsi.
The remainder of the commands are on the IBM:
  1. To start Word: Click on the "Start" menu at the lower left corner of the screen, select "programs", and then select "Microsoft Word."
  2. Moving an encapsulated PostScript file from a workstation to the IBM:
    Click on the "Start" menu at the lower left corner of the screen, select "find", select "computer", enter "dry" as the computer name, double click on the small "dry" icon that appears, enter the login name and password that you use for the workstations. Click on the small icon labeled with your login name, and you will get your home directory. For reasons known only to Bill Gates, the icon labels for files do not include suffixes (so the icon labels for "filename.ps" and "filename.epsi" are both "filename"). If you select an icon, the full filename, creation date, and size are shown on the left side of the window.
  3. So now you are in the Word document, click on the bar at the bottom of the screen that is labeled with your login name "on dry," for example, "mitchell on dry". This will cause the window of your home directory to come up. Click on the encapsulated PostScript file of interest and drag it into the word document.
Todd Mitchell, June 1999
File compression (reading files whose filenames end in .Z, .gz, .pdf)

Files are commonly compressed so that they take up less room on a disk and so that they are easier to send on the internet. Consider a PostScript for a figure, "sfctempudg.nam.ps". This file, and several versions of this file under different compressions take up the following amounts of bytes:

    bytes    filename             kind of compression
  1470815  sfctempudg.nam.ps      original, uncompressed file
   340378  sfctempudg.nam.pdf     Portable Document Format -- good for papers
   469995  sfctempudg.nam.ps.Z    UNIX compression
   359608  sfctempudg.nam.ps.gz   gzip -- UNIX-, IBM-, Apple-compatible
For a figure PostScript file, the 3 compressions are similar in efficiency. PDF should be more efficient for files with lots of text. I don't think that you can recover data from a file that has been turned into a PDF file. In general you want to use PDF for papers, and gzip otherwise.

How to create compressed files:

  • PDF: "ps2pdf filename filename.pdf" produces "filename.pdf". Do not convert a data file into a PDF file. I'm not sure that you can or how you can recover the data.
  • UNIX-compression: "compress filename" produces "filename.Z".
  • gzip: "gzip file_or_directoryname" produces "file_or_directoryname.gz".
  • For more information, type "man compress" or "man gzip".

    How to uncompress or read:

  • PDF: "acroread filename.pdf".
  • UNIX-compression: "uncompress filename.Z" produces "filename".
  • gzip: "gzip -d file_or_directoryname.gz" produces "file_or_directoryname".
  • For more information, type "man compress" or "man gzip".

    Todd Mitchell - February 2002
    Original contribution by Imke Durre.

    Reading PowerPoint, Word, or Excel documents on the UNIX machines.
    On the SUN machines, type soffice and this will start the "Star Office" software that will open all of these file formats. The first tim you use soffice it will ask a bunch of questions. You should select the default "standard workstation installation" (or something like that) where it downloads software from the network everytime you use soffice. I encourage someone to edit this WWW page with more specific information on the wording of the above option.

    Todd Mitchell - February 2000

    February 2004:
    ssh flake
    oowriter filename.doc

    Write permissions on the UNIX machines.

    Each file and directory has with it information on who is able to read, write, or use a file. This is a basic UNIX idea, and typing man chmod will provide a description of this concept. To change the write permission on a directory, its subdirectories, and all files therein, type chmod -R g+w directoryname.

    Todd Mitchell - May 2000

    JPEG files: how to create, print, and convert to other formats.

    Pictures on WWW pages are files in either GIF or JPEG image formats. Up to this point we have used only GIF files on the JISAO WWW pages, but apparently JPEG files are of higher quality and future WWW pages will be written with JPEG images. One of the key differences between GIF and JPEG is that JPEG files can resolve much finer gradations in color.

  • The XV utility will convert GIF or TIFF files into JPEG.
  • In MATLAB "print -jpegNN filename.jpeg" (no double quotes) where NN is the "quality level". The default quality level is 75. A higher quality level would be 90, e.g., -jpeg90 .
  • PostScript files can be converted to JPEG on the SUN computers with pstoppm filename.ps | cjpeg > filename.jpg
  • To produce a PostScript file from a jpeg file: djpeg -pnm filename.jpg | pnmtops > filename.ps
  • To print a jpeg file: djpeg -pnm filename.jpg | pnmtops | lpr -Pprintername

    Todd Mitchell - January 2002

    How to scan images and print them.
    In the south computer room there is a workstation ("muggy") that
    has a color scanner attached to it.  The following are the 
    steps to scan an image.
    1) You must sit at the "muggy" console and log in.
    2) The utilities "xscanimage" and "gimp" are available for 
    scanning images.  "Gimp" is the fancier utility.
      a) xscanimage produces files in "portable anymap" format, for which
         filenames end in ".pnm".  The command 
         "pnmtops filename.pnm > filename.ps" (no double quotes) converts
         from pnm to PostScript.
      b) type "gimp" (no double quotes).
         You will get a little schematic menu, select the 
         "Xtns" menu, select "acquire image", "epson", and then
         you will get the same graphical user interface as with 
         xscanimage.  To convert the image into a PostScript file, place
         the cursor over the image, depress the right button, and
         select "save as".  You will get a window, and, under
         "Save Options, Determine file type", depress the "By extension"
         menu, and select Postscript.

    Todd Mitchell - October 2001

    Graphics and word processing software
    Graphics and word processing software are only maintained on the SUN
    machines at JISAO.


  • "gs filename.ps" and "ghostview filename.ps" to view PostScript files on your screen. I believe that "gs" is a stripped down version of ghostview.
  • "xv filename.image_format" to view any of numerous image formats on your screen (TIFF, GIF, JPG, XPM, BMP, ...).
  • "gimp filename" will read PostScript, JPG, or images and does some image manipulation.
  • "tgif filename" will read encapsulated PostScript, JPG, or images and does some image manipulation and annotation.
  • Numerous filters exist on the SUNs to convert from one format to another, for example, ps2pdf, giftoppm, cjpeg, ... Ask me about them or type "apropos 'image suffix of interest'", for example, "apropos ppm", and see what you find. You may have to convert a file to an intermediate file format to get to the format that you want, for example, giftopnm filename.gif | pnmtops > filename.ps

    Word processing

  • "soffice filename" to read word documents (and other formats), and also to write text (input graphics?)
  • "ileaf6" is interleaf. Reportedly, there is a steep learning curve to using this software.
  • "xwp" is word perfect.

    Please add to this list.

    Todd Mitchell - February 2002

    Viewing CDROM html files with a WWW browser
    If you have a CDROM that has html files, you can view these files one
    of the two following ways.

    Put the CDROM into the CDROM-reader of a machine, let's call the computer "machineA".
    Method 1: The URL for the WWW browser (running on machineA) should be: "file:/cdrom/" (no quotes)
    Method 2: What should be an equivalent way to do this is to go to the JISAO WWW page directory, /home/disk/tao/data/mosaic/, and write symbolic link to the cdrom-reader (ln -s /home/cdrom/cdrom0/ somename. The URL for the browser (running on machineA) should be "http://jisao.washington.edu/somename" (no double quotes). This method does not quite work right now.

    Todd Mitchell - February 2002

    Finding errors in your HTML files (WWW pages)
    On the SUN machines, there is a utility called "htmltidy" which will
    find errors in your HTML files, and even provide you with a clean file
    if you like:  "htmltidy filename.html > output.html" (no quotes).

    There are lots of options for this utility: "htmltidy -h" (no quotes)

    Todd Mitchell - May 2002

    How to make a pretty, XHTML cross linked version of a matlab directory.
    The matlab2html script is a perl script that will create a nicely formatted, cross-referencing, syntax-highlighted series of HTML documents based on a directory of matlab (.m) files. It's a hack of the best features of a pair of scripts I found on the web, so there are probably lots of things that I've broken in the process. For the most part it works pretty well. An example of the what gets created when you run the script on Dan Vimont's voluminous matlab directory, posted completely without permission while he's in NZ, is available here .

    The script currently only works on linux boxes, so you should run it from muggy.

    To run the script on a matlab directory (e.g. ~/matlab) and put the HTML files under my web directory ~/public_html/matlab, you would do the following:

    ssh muggy
    ~rennert/bin/noarch/matlab2html -dirmfiles ~/matlab  -dirhtml ~/public_html/matlab/
    Make sure the call to matlab2html has all of the options on one line. There may be some error output, but things seem to work anyway. If you followed the above example, then your web pages are available at http://www.atmos.washington.edu/~your_username/matlab/

    It should also be noted that, if you're not interested in having your matlab scripts visible for the world to see, you can put the web files in a local directory and look at them there. For example, if I'd like to keep the matlab html files in my home directory under the subdirectory matlab_html_files , I would do:

    ssh muggy
    ~rennert/bin/noarch/matlab2html -dirmfiles ~/matlab  -dirhtml ~/matlab_html_files/
    and point my browser at the local files by going to the file URL: file:///home/disk/atmos/rennert/matlab_html_files

    There are lots of options, try using just the

    option for a list of the main ones. The author credits for the initial two scripts that have been hacked are located in the script source code.

    Kevin Rennert - May 2003

    Determining disk usage stratified by directory
    du -sk /home/disk/diskname/* | sort -rn
    produces a list of usernames and disk usage in kilobytes, sorted by directory.

    Todd Mitchell - December 2008

    Determining the time a file was last read ("accessed")
    ls -ul

    Todd Mitchell - March 2009

    Putting large numbers of files on the WWW for others to retrieve.
    It is common to have a large number of files that you want to transfer
     to someone at another institution.  This is can be done in two
    1) Have Harry or David set up an account for you on /home/disk/user_www
    Copy your many files to a subdirectory, subdirectoryname, on that directory.
    2) The contents of the directory can be pulled over with
    wget -r -nd --no-parent http://www.atmos.washington.edu/~your_login_name/subdirectoryname

    Todd Mitchell - August 2010

    Moving directory trees
    I obtained the following information from David Warren and used the first method with
    partial success.
    to move /a/c and everything in it to /b/c :
    Method 1: 
    cd /a
    tar cf - c | (cd /b; tar xvfp -)
    c will be copied from under /a to under /b and the dates should be preserved.
    Check that this method moves all of the files, by using "du -k" before
    and after.  It wasn't moving all of the files for me, and I thought
    that write permissions had something to do with this.  David Warren
    ended up moving the directories for me.
    Method 2: 
    It looks like cp has an option for this as well so
    cp -r -p c /b
    will recursively copy c into /b and preserve dates.
    The one thing tar does that cp doesn't is it also preserves links
    Todd Mitchell - October 2010

    Todd Mitchell <mitchell@atmos.washington.edu>
    November 2012