Geekee Way

Tuesday, April 27, 2010

Writing: Keywords

This article shows a collection of terms that are usually erroneously used (by myself).

computation time instead of computational time
a large percentage of
a 5% error
3-D instead of 3D

Saturday, December 26, 2009

Ubuntu 9.04, 9.10, 10.04 Installation Tweaks

MATLAB

sudo apt-get install sun-java6-jre

sudo aptitude install network-manager-vpnc
Panel --> VPN connections --> Configure VPN --> Import the .pcf file
IPv4 Tab --> click Routes --> uncheck "Use this connection only..."
click OK, Apply, Close
Reboot
Panel --> VPN connections --> MITnet VPN Connection

MATLAB

tar -xvf thefile
cd thefolder
sudo ./install...sh

Eclipse

download: http://www.eclipse.org/downloads/download.php?file=/technology/epp/downloads/release/galileo/SR1/eclipse-cpp-galileo-SR1-linux-gtk.tar.gz
tar -xvf thefile

Microsoft Office

WineHQ

wget -q http://wine.budgetdedicated.com/apt/387EE263.gpg -O- | sudo apt-key add -
sudo wget http://wine.budgetdedicated.com/apt/sources.list.d/jaunty.list -O /etc/apt/sources.list.d/winehq.list
sudo apt-get update
sudo apt-get install wine
(some steps may be redundant. need further checks.)

WineHQ (for 10.04)

Just go to Ubuntu Software Center. Search for it and install it.

Windows Programs

Right click on "setup.exe --> Open with "Wine Windows Program Loader"

Latex

TexLive

sudo apt-get install texlive (~200 MB) or
sudo apt-get install texlive-full (~700 MB)

TexMaker
An Latex IDE with fewer KDE library dependencies
Pros: smaller (~200 MB), looks nice, intuitive configuration
Cons: not very good auto completion, no block indent

sudo apt-get install texmaker

Kile
An Latex IDE with huge KDE library dependencies
Pros: looks nicer (much better than the screenshots in its official website) and many utilities
Cons: fat (~500 MB)

sudo apt-get install kile

Input Method (also works for 9.10 and 10.04)

noseeing

sudo apt-get install gcin
set up default input method manager:
im-switch -s gcin
download the mapping table
wget http://edt1023.sayya.org/gcin/noseeing-12.tar.gz
move the table to the gcin folder
mv noseeing.gtab ~/.gcin
Reboot and right click gcin-setup

Numerical Libraries

Lapack (share)

sudo apt-get install liblapack3gf
sudo ln -s /usr/lib/liblapack.so.3gf /usr/lib/liblapack.so

Blas (share)

sudo apt-get install libblas3gf
sudo ln -s /usr/lib/libblas.so.3gf /usr/lib/libblas.so

GotoBlas (static)

download http://www.tacc.utexas.edu/tacc-projects/
tar -xvf thefile
cd thefolder
./quickbuild.32bit or
gedit Makefile.rule
make
mkdir temp --> cp libgoto2_penryn-r1.09p3.a ./temp --> cd temp
unarchive: ar x libgoto2_penryn-r1.09p3.a
recompile into a shared library:
gfortran -shared -Wl,-soname,libgoto2.so -o libgoto2.so.1.09p3 *.o
See here for the knowledge of shared libraries.
sudo cp libgoto2.so.1.09p3 /usr/lib
sudo ldconfig

Misc.

Turn off the terminal beep (9.04 only)

Terminal --> Profiles --> Edit --> General Tab --> uncheck Terminal bell

RAR Archiver

sudo apt-get install rar
sudo ln -fs /usr/bin/rar /usr/bin/unrar

7z Archiver

sudo apt-get install p7zip-full

Skype (works well for 9.04, 9.10, 10.04)

http://www.skype.com/intl/zh-Hant/download/skype/linux/choose/
8.10+ 32-bit works fine on 9.04 32-bit

Printer (D-Link DI-707p)

System --> Administration --> Printing --> Devices --> Network Printer --> LPD/LPR Host or Printer --> Host: 192.168.0.1 Queue: lp
Select your printer driver

Codec (obsolete)

sudo apt-get install ubuntu-restricted-extras

Battery management (Thinkpad)

not yet done....

CPU hiss "CPU Whine" (from ThinkWiki)
(for grub2, applicable to ubuntu 9.10 and after)

sudo joe /etc/default/grub
Search for the line GURB_CMDLINE_LINUX=""
Replace "" with "processor.max_cstate=2"
If the original "" is not empty inside the double quote, simply add processor.max_cstate=2 before the closing quote mark, e.g. replace
GRUB_CMDLINE_LINUX="acpi_osi="Linux"" with
GRUB_CMDLINE_LINUX="acpi_osi="Linux" processor.max_cstate=2"
sudo update-grub
sudo reboot

Install restricted codec and more

Launch Amarok
Choose to install all recommended packages

Thursday, December 24, 2009

Installation List

Windows 7:

7-zip
Anti-vir
Dr. eye
cwtex
Eclipse
GIMP
Google Desktop
Logitech driver
MATLAB
Microsoft Office
Microsoft Visio
FireFox

AutoPager, Video DownloadHelper, DownThemAll!, Forecastfox, Personal Menu,

Chromifox, Foxdie: neat and configurable

NX Client
PC Man
PDF Creator
PDF Xchange Viewer
RealPlayer
Secure CRT/FX
Skype
WinDjView
Windows Live
X-Win32
紫微論斷

Ubuntu:
Wine
Microsoft Office, Visio
MATLAB
Firefox and its add-ons
Fastcap
GotoBLAS, libblas, liblapack
Eclipse
Nx server/client

Ubuntu server:
OpenSSH
FTP

Thursday, November 19, 2009

Scientific Computing / Linear Algebra Library Survey

This is my 101st times surveying linear algebra libraries for C++. Originally I tried to google the performance comparison from one to the other, but unexpectedly this is the most fruitful survey I have ever had since three months ago.

Linear Algebra Libraries by Claire Mouton, March 2009.
Detailed comparison btw CPPLapack, Eigen, Flens, Gmm++, GNU Scientific Library, IT++, Lapack++, MTL, PETSc, Seldon, SparseLib++, TNT, Trilinos, uBlas, and others by listing developers, license, interface, performance description, portability, dependencies, and some limitations. A very clear and useful document.
On the Reusability and Numeric Efficiency of C++ Packages in Scientific Computing
http://www.linuxclustersinstitute.org/conferences/archive/2003/PDF/Mello_U.pdf
by Ulisses Mello and Ildar Khabibrakhmanov, IBM T.J. Watson Research Center, Yorktown, NY, USA

Performance comparison by plots in different Blas level 1, 2, 3 experiments. It compares ATLAS, Goto Blas, Blitz, uBlas, STL implementation, Fortran 77 code, C code, bsm, MTL, and A++. It's more like pure performance comparison regardless its interface or whether there is OO wrapper or not. It also provides some observations and reasons why one beats another.
Help choosing a C++ matrix library
http://old.nabble.com/Help-choosing-a-C%2B%2B-matrix-library-td18857631.html
In-depth forum discussion. Point out several requirements for a good matrix library.

Some webpages regarding specific libraries:

Goto Blas
http://www.utexas.edu/features/2006/goto/
The author's story. Goto is the author's Japanese last name. GotoBlas is known to be the fastest Blas library in the world. It is handcrafted down to assembly code for different specific architectures.
Discussion about the adoption of either uBlas or MTL4
http://stackoverflow.com/questions/1067821/ublas-vs-matrix-template-library-mtl4
One mentioned Eigen.
Eigen benchmark
http://eigen.tuxfamily.org/index.php?title=Benchmark
OO abstract, though it provides readable and maintainable code, is always a penalty for performance consideration. Eigen is one of the actively developing libraries which claims its performance. Others as I know are MTL and armadillo. One reason of not claiming performance of their C++ code is because although they provide OO interface, many of them are "wrappers" of Blas and Lapack, like IT++, Lapack++, in order to provide Fortran level performance instead of C++ implementations. It is interesting to note that Eigen claims their code is at a similar speed as ATLAS (Automatically Tuned Linear Algebra Software) and Goto Blas (critically parts are written in assembly). The other thing that is worth noting is that the FLOPS drops when performing vector-vector additions over a certain vector size, while in the IBM report above it happens in matrix-vector multiplication instead. By the way, the performance results are all about Blas level 1, 2, 3. None of them compare solving linear systems or some other advanced decomposition method, like SVD, Cholesky, eigenvalue, etc.

Short conclusion: My criteria are OO wraper, namespace, performance, and actively developing or not. I used to be pro MTL4 before I look closer Eigen. Though their is no direct comparison between MTL4 and Eigen (there is a comparison btw MTL2 and Eigen where MTL2 is very slow in Eigen benchmark). MTL4 in their performance report does not beat Goto Blas but the Eigen authors claim they do. Though there is no way to convince myself the comparison is fair, Eigen does provide several "lazy" shortcut and comfortable coding interface compared with MTL4. The other candidate is Boost::uBlas. The advantage of uBlas is it is part of Boost project. That seems to imply more users and better maintenance at the first glance. However, comparing those three, MTL4 seems much more updated than uBlas, and Eigen is more actively updated on its website than the rest two. Eigen also seems more willing to provide other decomposition methods like SVD, eigenvalues.

The last thing: license. LGPL vs. GPL used to be a very big drawback of Qt before version 4.5 since GPL means using the library is equivalent to open your source code to everyone who have access to GPL code (virtually every human being), while LGPL provides flexibility for commercial software and closed code is permitted. Eigen is either GPL or LGPL. It depends on your choice. MTL4 seems not that liberal.

Saturday, October 24, 2009

MTL4: MinGW + Eclipse Installation

TDM-MinGW
Eclipse
boost
mtl4

Monday, October 12, 2009

LATEX: Good reference

NUM: Finite Difference Method readings

Good tutorial, especially for boundary conditions.

Finite Di erence Methods for Di erential Equations
Randall J. LeVeque
UW, 2006

which is first discovered from wikipedia.