ETH
H C I - D 2 6 7 C o m p u t e r A d m i n i s t r a t i o n
Chemie
Biologie
Physik
Informatikgestützte Chemie (igc)
HCI G241
ETH Hönggerberg
8093 Zürich
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 www.passwort.ethz.ch 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 www.password.ethz.ch. 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 e-mail address provided by ETH. Open it in a Web browser via
www.mail.ethz.ch
. Go to “Outlook Web Access”. Log on with your nethz-
password and -username.
2)
Your “local” Disk Space
There is no local disk space available any more.
ETH
H C I - D 2 6 7 C o m p u t e r A d m i n i s t r a t i o n
Chemie
Biologie
Physik
Informatikgestützte Chemie (igc)
HCI G241
ETH Hönggerberg
8093 Zürich
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
c)
To extract files form an archive
Type tar xfvz
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
.
ETH
H C I - D 2 6 7 C o m p u t e r A d m i n i s t r a t i o n
Chemie
Biologie
Physik
Informatikgestützte Chemie (igc)
HCI G241
ETH Hönggerberg
8093 Zürich
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:” 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 www.vpp.ethz.ch. 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:
File to print:
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 www.vpp.ethz.ch.
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.
ETH
H C I - D 2 6 7 C o m p u t e r A d m i n i s t r a t i o n
Chemie
Biologie
Physik
Informatikgestützte Chemie (igc)
HCI G241
ETH Hönggerberg
8093 Zürich
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:
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
b)
Other editors
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.
ETH
H C I - D 2 6 7 C o m p u t e r A d m i n i s t r a t i o n
Chemie
Biologie
Physik
Informatikgestützte Chemie (igc)
HCI G241
ETH Hönggerberg
8093 Zürich
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 www.lyx.org 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 8.1.2 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
ETH
H C I - D 2 6 7 C o m p u t e r A d m i n i s t r a t i o n
Chemie
Biologie
Physik
Informatikgestützte Chemie (igc)
HCI G241
ETH Hönggerberg
8093 Zürich
www.gnuplot.info
. 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
.
ETH
H C I - D 2 6 7 C o m p u t e r A d m i n i s t r a t i o n
Chemie
Biologie
Physik
Informatikgestützte Chemie (igc)
HCI G241
ETH Hönggerberg
8093 Zürich
There is also a statistical tool called R (type R). You can learn more about in on
www.r-project.org
.
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 shell-
scripts. See www.gaussian.com 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 first-
principles 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
www.cmbi.ru.nl/molden/molden.html
.
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
http://www.ks.uiuc.edu/Research/vmd
.
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