Derevianko Group
Computers/Graphics/etc Notes
Parallel programming
- Elko help
- Medusa help
- OpenMP standard
Setting up Project under Visual Fortran so that it can read binary files generated on AIX system [all our binary files have to be compatible]
- Choose Project settings->All configurations
- Tab Fortran->
- Category Compatibility-> Big Endian
- Category Fortran Data -> Check-mark Use Bytes as RECL=...
- Stack complaints: option /F<n>, where n is the number of bytes; Default is just 1Mb
- Library complaints: add cxml.lib atom.lib to Link Tab, General Category, Object/Library Modules
Mathematica
- Collection of Mathematica packages
- path setup under Windows: add AppendTo[$Path, "c:\Lib\MyPacs"] to file c:\Program Files\Wolfram Research\Mathematica\4.1\Configuration\Kernel\init.m
- running Mmka from UNR library CITRIX server
- Crash-course in Mathematica (html, notebook).
Libraries
Benchmarks:
To combine Adobe Illustrator with latex
New (better) solution, see this link
- Copy all *.pfb files which came with your installation of latex into the Program Files/Common Files/Adobe/Fonts/type1 so that AI could see the fonts.
- Use latex and pdf distiller to produce pdf file from your tex file. (dvips -G -j0 options may be helpful). SW5.0 latex2pdf works just fine.
- Open the pdf file in AI. Edit. To eliminate the font dependence outline fonts may be useful.
- For displaying eps files in Scientific Word 5.0 save eps files in the older AI version 8 format.
MikTeX configuration file & BibTeX directories
- in c:\texmf\miktex\config\miktek.ini modify
Input Dirs=.;c:\MyBib\;c:\MyBib\Styles;%R\bibtex// - ;; 1. create an empty configuration file in the local config
;; directory, e.g.
;; echo ;; my miktex.ini> C:\localtexmf\miktex\config\miktex.ini
;; 2. start editing the file:
;; notepad C:\localtexmf\miktex\config\miktex.ini
;; 3. add configuration settings, then save the file
;; 4. update the file name database:
;; initexmf -u
;; Settings specified in the local configuration file take precedence
- Integrated editor/shell: WinEdt, in Yap set the reverse-searching to Winedt
- To convert ris to bib run ris2xml.exe risfname.ris | xml2bib.exe | tee tmp.bib
Fonts:
http://www.masterstech-home.com/TypefacePreviewsIntro.html
Fortran:
- on lithium F90 compliler command line:
fort -fast source.f -o exename -lcxml - on neon (see one-time set-up below) compliler command line for serial code:
pgf90 -fast source.f -o exename -lacml - The first index of the array is the fastest
- Profiling:
- use -pg flag during compilation
- Run your code as you normally would. This creates file gmon.out
- gprof program-name. The data accumulated in gmon.out is analyzed.
- Building library xxx :
- Compile the sources (fort -fast *.o)
- ar r libxxx.a x.o y.o z.o ...
- ranlib libxxx.a
Unix/Linux
- Useful MSWindows tools for interfacing with Unix systems: webDrive , winsshd, X-Win32, Cygwin, putty
- Creating symbolic link : ln -s existing_file link_name
- Creating tar-gzip file: tar -cvzf archive.tgz *
- Extracting from tar-gzip file: tar -xvzf archive.tgz
- tar -cvzhf option resolves (i.e., archives pointed to files) symbolic links.
- to find your dynamic IP address do who -l
- ps -au $USER lists all your processes
- view the running processes: top
- running jobs in the background (bash) exename < inpute_file >& output_and_err_file &
- Bash-Scripting Guide
Neon setup
- Neon is AMD 64bit Opteron server. It has 4 CPUs, 12 Gb of RAM, 250Gb disk space. Runs SUSE Linux. Use ssh for connection.
- Compiler: Portland Group Fortran: pgf90 and pgf77. Supports OpenMP and MPI.
- man pgf90 for help. See also online documentation here.
- add to .bashrc initialization file (do pico .bashrc)
# PGI compiler section
PATH=/usr/pgi/linux86-64/6.1/bin:$PATH
export PATH
MANPATH=$MANPATH:/usr/pgi/linux86-64/6.1/man
export MANPATH
LM_LICENSE_FILE=/usr/pgi/license.dat
export LM_LICENSE_FILE
export PGI=/usr/pgi - -mp switch to compile parallel codes with OpenMP pragmas
- -fastsse
- -mcmodel=medium is required for large (>2Gb) data
- Sample Fortran makefile
- CALL FLUSH(6) for PGF compiler to flush the output buffers (where WRITE output is stored; this is required when running "tee" pipes )
- Math library linking -lacml
X-win32 and lithium/neon
- Configure ssh: allow tunneling X11 connections
- start Xconfig. Window mode: single + full screen. Security: add lithium, neon, and also add 127.0.0.1.; Other: Last session terminate. click OK
- start XWin32; a full-screen grayish window opens. Go to ssh window, log in and type startkde. Done.
- If connecting from home: it is much faster to run Xwin-32 on the dept. PC computer and then use RDP on your windows box.
VNC on Neon
Initial setup (you need to do this once):
1. You will need a
ssh program and vnc viewer for your PC.
Here are the links: tunnelier
and real VNC; both are free.
Download and install these programs.
2.SSH to neon and execute vncserver
On the first start vnc server asks to set up access passwords. After that you
will see a few important output lines
>>>
New 'X' desktop is neon:2
Creating default startup script /home/xyz/.vnc/xstartup
Starting applications specified in /home/xyz/.vnc/xstartup
Log file is /home/xyz/.vnc/neon:2.log
>>>
Here home/xyz is your $HOME directory. Notice name of your server, in this example it is neon:2. This defines the VNC access port 5900+2 =5902
3. While on neon, you need to cd to the directory ~/.vnc and to edit xstartup by replacing the last line "twm &" by "startkde &". Neon setup is done.
4. PC setup: Start tunnelier. Fill in the
self-explanatory fields in the Login tab.
Click on the C2S Fwding tab. Click on the Add button. Fill in the fields
there so they read: enabled; 127.0.0.1; 5902; localhost;5902.
Save configuration to a file to your Desktop. Exit.
5. You are done with the initial setup. If you need to restart
vncserver, kill it first:
> vncserver -kill
Connecting:
1. PC: Click on the previously
saved tunnelier configuration file. Login.
2. PC: Start VNC viewer. In the server field type localhost:2 (2 comes
from the neon:2, it will differ in your case)
3. Now you will see on your pc the kde graphical environment that runs on neon.
Useful programs: kate is the editor.
4. Close the VNC connection (do not exit kde when done). Next time you run VNC
it will continue from the place you left off.
On Linux boxes: vncviewer -via neon -fullscreen neon:2 (
Press F8 to switch from the fullscreen mode)
