H C I - D C o m p u t e r A d m i n i s t r a t i o n

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1 Guide to Informatik Facilities (D39) Document Overview Data and Data Storage MS Windows Emulation Printing Software and Software Documentation Research Computations Data and Data Storage 1) Your Home Directory a) Mounting your Home Directory On under me services->nas-dfs you can find a guide how to mount your home directory. If you exceed your quota on this home directory you may no longer be able to logon at public work-stations (Unix or Windows) at the ETH and you won't be able to write to the disk if you exceed the limit. Then you must contact the Helpdesk. For this reason it is best to sporadically check your memory balance. To see how much disk space you are using, use on Linux the command du. Delete unused files or move files out to the local disk before you reach the limit. You may want to use data compression (gzip, tar ) for files that you don't need often. b) Security You can change your nethz-password on Your password should contain numbers, punctuation marks, or unusual uppercase/lowercase letters and should not consist of a single word out of a dictionary. Do not grant write access to your home directory to anyone else. You may consider restricting read access too. c) Electronic Mail Use your address provided by ETH. Open it in a Web browser via Go to Outlook Web Access. Log on with your nethzpassword and -username. 2) Your local Disk Space There is no local disk space available any more.

2 3) Data backups To backup data, a gzipped tar archive ("tar" = "tape archive") is often of use. Common operations using the tar utility are described below. (The man pages for the tar utility should be consulted for details of more advanced uses.) a) To create an archive: a) Place the data for which a backup is to be made into a temporary directory. For example, suppose we are located in the home directory of user hanswurst, the following commands might be entered: $> whoami; hanswurst $> pwd ; /home/hanswurst $> mkdir tar_backup ; $> mv *data.to.backup tar_backup ; b) Make sure you are located one directory above the directory to be archived. c) Type tar cfvz < name_of_target_tarfile > source_directory. In the present example the command would be: $> tar cfvz tar_backup.tar.gz tar_backup This creates the archive in your current directory. So, we would have the file tar_backup.tar.gz in directory /home/hanswurst. Note that this file has been automatically compressed by gzip during the archive process, because we used the "z" option. d) Copy the compressed archive to your CD or DVD. b) To check an archive Type tar tfvz <file_path_of_archive> c) To extract files form an archive Type tar xfvz <file_path_of_archive> For user hanswurst, located in its home directory, the command tar xfvz ~/tar_backup.tar.gz would make a directory ~/tar_backup (and would overwrite any directory of that name at that location), where ~ means the home of hanswurst, which is equal to /home/hanswurst.

3 4) Removable Media: CD and DVD Drive a) Using the devices All machines are equipped with a CD RW/DVD±RW drive. To use them: 1) Put your CD/DVD disk in the drive. 2) On your desktop, an icon for your CD/DVD disk should pop up. You should also find the media under Places Computer CD-RW/DVD±RW Drive:<name of your disk> on the top toolbar on the desktop. 3) Double-click on the icon of the disk. A CD/DVD Creator is opened. Copy the data to be stored on the disk to this CD/DVD Creator Folder. 4) Press Write to Disk and your CD/DVD will be written. 5) Eject your disk by right-clicking on the icon for your disk and choosing Eject in the pop-up menu. Printing Printing works best via Select Send VPP Job for ps-files, Send PDF VPP Job for pdf-files. You have to give at least the following information: Destination: HCID267 Device: PTS Username: <your username> File to print: <your filename> At the end press Send Print Job. To convert a text file test.txt to a ps-file test.ps use a2ps o test.ps test.txt. Use ps2pdf o test.pdf test.ps to convert a ps-file test.ps into a pdf-file test.pdf. For more information about the vpp-service of the ETH see There is also a vpp command which one can execute from the console, but it doesn t always work. The command to print a ps-file is: vpp dest=hcid267 -dev=pts file.ps. See the vpp man page for more details. Software and Software Documentation In the following section, some software is described. The list may not be complete and may change.

4 1) Manual Pages Thorough descriptions of any command, with its behavior and options, are found in the so-called man pages. To get manual pages of a certain command, type man command. For an overview of commands according to a keyword, use apropos keyword or whatis keyword. 2) Text Editors a) Emacs emacs is a powerful editor with unlimited functionality. It is especially suited for programming and supports various modes for different programming languages and multiple buffers. It is controlled via menu or key sequences. C-s or M-x for example mean: Hold control key and press s key, or hold meta key (equal to Alt key) and press x. Some useful commands: b) Other editors C-h t invoke a tutorial, useful before first use C-x C-f load a file C-x C-s save a buffer C-x C-w save a buffer under a different name C-g cancel command (type also if something does not operate as expected) C-x b switch between buffers C-s search for a string C-w kill marked region C-y yank (paste) region (previously killed or marked) C-x C-c exit emacs M-x cmd execute emacs command cmd gedit is a simple editor with menu control. vi is an old-style line-editor, but is quite powerful and (when one is familiar with it) fast. 3) Word-Processing/Typesetting a) LaTeX Especially useful for reports containing many formulae and for people that don't want to spend time worrying about the layout: it always produces nice documents.

5 Source code and compile concept: write your latex source with.tex extension, e.g. report.tex. The command latex report.tex will compile the latex source into a dvi file (report.dvi) which can be viewed by xdvi report. dvi. Use dvips -o report.ps report.dvi to transform the dvi file into a PostScript file for printing. Latex source files may also be converted to PDF format using, in this case: pdflatex report.tex. b) Lyx LyX (type lyx ) is a graphical front end to LaTeX. It has the look and feel of standard WYSIWYG word-processors and shares their ease of use. However, it uses a meta language which it translates into regular LaTeX for post-processing. LyX is what we recommend to everybody who wants to use LaTeX but prefers intuitive user interfaces over complex formatting commands. Most of the commonly used LaTeX commands are integrated as buttons, pull-down menus, and keyboard shortcuts. Unavailable LaTeX commands can still be entered explicitly (in TeX mode). Even though development is still in its early stages, the product has matured considerably recently. The large memory requirements are a downside, however. Long documents (tens or even hundreds of pages) can still be handled, however, we recommend to use LyX only for editing. You should export files in LaTeX format, and use the normal command line sequence (latex report.tex; dvips -o report.ps report.dvi ) to produce a PostScript file. For short documents (a few pages) you can easily use the built-in functions for generating, viewing and printing the resulting PostScript file. You will find all of these in the file menu. For further information, contact the LyX home page and the online documentation which consists of several extensive documents written in LyX. c) Interactive spell-checker ispell checks ascii and tex texts, english only. It provides suggestions for unknown words and learns new words using a personal dictionary. See man page for more details. d) PostScript and Portable-Data-Format (PDF) Viewers PostScript: Evince Document viewer, (evince) can be used to display PostScript files. PDF: Acrobat Reader, (acroread ) version is installed to view PDF files. You could also use the Evince Document viewer (evince). 4) Graphical Software gnuplot is an interactive plotting program. See the man page and the online help, type help at the gnuplot prompt. Other quite useful information is available at

6 The big advantages of this plotting package are its ease of use and its 3D abilities. xmgr is much more powerful, but this comes at the expense of a more complex user interface. Note, however, that the development of xmgr has been discontinued in favor of a more user-friendly package, called xmgrace. On the computers only xmgrace is installed. Note that neither xmgr nor xmgrace can handle 3D plots. Information is available from the online help and from (for xmgrace) plasma-gate.weizmann.ac.il/grace/doc/usersguide.html. Other programs who allow you to look at graphs are xfig GIMP (gimp), Dia Diagram Editor (dia). Please read their help pages for more information. 5) Software Development Tools a) GNU software gcc g++ g09 gdb b) Scripting Languages Unix Shells: sh csh bash tcsh Other scripting languages: awk sed perl python tcl (tclsh) tk (wish) 6) Mathematical Software maple is a powerful symbolic mathematics program. It can solve nearly any problem analytically. xmaple provides a nice graphical user interface. See the help menu for more information. matlab is especially strong for matrix calculations and high-end visualization. Mathematica is also available. You can open it via Applications on the top toolbar. See the help menu for more information. It can also be started by typing mathematica.

7 There is also a statistical tool called R (type R). You can learn more about in on 7) Chemical and Molecular modeling Software a) Packages for computation Gaussian: an extensive quantum chemistry package. In order to use the programs in the package one must create input files in the correct format. This may be done manually or with GaussView. Jobs may be run using GaussView, or using shellscripts. See for further information. Type g09 to start. NOTE: The two following programs are not yet installed but should be by the start of the spring semester (path may be different): TURBOMOLE: Program package for ab initio electronic structure calculations. You can find it in the directory /usr/supp/bin/turbomole. ADF: The Amsterdam Density Functional (ADF) package is software for firstprinciples electronic structure calculations. The binaries are in /usr/share/adf2007/bin. There you can also find adfview to start it. b) Programs to edit computational chemistry input files NOTE: The following program is not installed on the machines. MOLDEN: A pre- and post-processing program of molecular and electronic structure. Type gmolden. MOLDEN is a package for displaying molecular density from the ab initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the semi-empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format. More information about it you will find on c) Programs to display chemical graphics Please note: The graphics software mentioned here should not be used remotely as this would disturb the operation of the network. Large molecules vmd: powerful molecular viewing program. Can handle several coordinate formats. For information consult the VMD user guide /usr/local/lib/vmd/doc/ug.pdf, or the VMD home page at