Kungl. Tekniska Högskolan Royal Institute of Technology
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Frequently Asked Questions about the computer system

Documentation

Other sources: Installed programs | NQS | Our WWW | File access privileges |

  1. How is the computer system organized?
  2. How to print?
  3. How to handle PDF files?
  4. How to send and read e-mail?
  5. How to access our system from remote computer (FTP, telnet)?
  6. How to access PDC computers convinently?
  7. How to download whole directory tree?
  8. Data safety (backup)?
  9. How to restore files that were accidentally deleted?
  10. Which computers can I use for computations?
  11. What directory can I use for a computation's scratch space?
  12. Where I can found a documentation for different LaTeX packages?
  13. Where I can find DEC Fortran online docs?
  14. How can I add my publication to the data base?
  15. What has happened to xmgr? How can I create plots?

How is the computer system organized?

Our computer system consists of three main parts:

  1. Main file-,mail-,web-server. This is the core of our system.
  2. Two (990716) Alpha servers. For computations.
  3. A number of PC-based Linux-powered desktop computers.

All the computers have shared accounts (passwords, user information) as well as files in the /home directory.


How to print?

Information about printing and scanning is maintained in the file printingandscanning.html!


How to handle PDF files

  • To view and print PDF files
    • Use acroread for browsing PDF files. If this does not work, use xpdf command
      Print the file also using acroread or xpdf

    • In order to print PDF file safely
      type acroread -toPostScript [-fast] filename.pdf | lpr
      Use -fast option when you experience problems without it. Option -shrink shrinks to fit the page.

  • To create PDF file from .tex LaTex document
    • Use command pdflatex filename.tex.
      Works well.

    • Failsafe way:
      To convert .dvi file to suitable .ps file
      use command dvips -Ppdf -G0 filename.dvi -o filename.ps
      Then convert obtained .ps file to PDF file,
      use command ps2pdf -sPAPERSIZE=a4 -dMaxSubsetPct=100 -dCompatibilityLevel=1.2 -dSubsetFonts=true -dEmbedAllFonts=true filename.ps

How to send and read e-mail

  • Your e-mail address is <user>@theochem.kth.se
  • The recommended way to access your email is via IMAP.
  • Good IMAP clients include: thunderbird, balsa, pine*, evolution.
    *) pine is replaced by alpine on some new machines.

    How to access our system from remote computers (FTP, telnet)?

    The preferred method of accessing our system from outside is ssh and scp (read respective man pages, RTFM shortly). Never use telnet or ftp. You have to add -X flag to run window applications remotely (check the ssh man page for details), alternatively add ForwardX11 yes to your ~/.ssh/config file as described on the ssh_config man page. Remember about the security implications!

    • Use scp or sftp for file transfer.

    How to access PDC system convinently?

    In the same way as the lenngren system.


    How to download whole directory tree?

    Use a GNOME program gftp. Just type gftp& at the command prompt or find it in the right button mouse menu. It is a very convenient program -- particularly for GUI-oriented users.

    Another option is to use wget (it is installed only on beta due to my laziness and the rare need for such a tool). Example (check wget --help for more help):

    wget -r ftp://pawsa:password@hostname//full/path/to/the/directory

    Data safety (backup)

    Due to lack of man power only /home directory is backed up to the tape. The incoming mail folder is NOT backed up - move important e-mails to folders in your home directory.

    Full backup (0 level backup) of the /home directory is done once every 6 weeks on a 12/24GB magnetic tape streamer. Every week (weekend) we intend to do incremental backup on the 2GB tapes. In this incremental backup of certain level only new files or those that changed from the last backup of the same or lower level are copied to tape. Currently the scheme for backup levels is 0 - 5 - 4 - 7 - 6 - 9 - 8 - 0.

    Backup can be done only by root on elf. Read the file README.backup in the root directory there for more details. See also manual pages for dump and mt.


    How to restore files that were accidentally deleted?

    We intend to do regular incremental backup of /home directory every week (see Data safety (backup)). Thus all the files older than week, or the files created before last backup (usually on weekends) should in principle be possible to restore. It is however necessary to find the right tape on which the file should be copied (look on the backup level scheme, and also to the file backup.history). Restoring files is done by command restore - again it has to be done by root on elf. See file README.backup and man restore for more details.

    Ask Viktor or Pawel if you need to restore your files.

    Currently we are not doing a backup of mail folder. Please move important mails to the folders in your home directory.

    Magnetic tape is a slow medium. Restoring of the files take therefore relatively long time (more than half hour).


    What directory can I use for a computation's scratch space?

    Use /scratch (if it exists) or /tmp directory. On computers where /scratch exists it is optimized for high performance IO and much faster than /tmp.

    If performance is a factor never use the shared directory (/home and subdirectories). This disk is 20-80 times slower than local /tmp space - it is actually the network which is the bottleneck. If you run out of space, consider rather direct computations.

    Observe that files in /tmp not touched for one month are automatically removed by the system.


    Documentation for different LaTeX packages

    1. /usr/doc directory
    2. LaTeX home page at IFM, Linköping.

    What has happened to xmgr? How can I create plots?

    xmgr was not developed or supported for many years. It has been replaced by xmGrace which comes with an excellent online help (look in the menu).


    Send your questions to webmaster-at-theochem (or just walk to the right room, that's much simpler, isn't it?) Your feedback is most welcome!

    | Theoretical Chemistry home page > Documentation.

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    Select SSL access (with pine specify {mint.biotech.kth.se/ssl})
    In thunderbird, you have to manually edit server settings after account creation.
    Outgoing SMTP serversmtp.kth.se
    User nameyour central KTH login name
    Passwordyour central KTH login password

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