Thursday, December 04, 2008

Installing Ubuntu on HP Pavilion dv 4 1114nr

I got a new HP Pavilion dv4 1114nr in this holiday season. It has Windows Vista Home Edition pre-installled. Here is a log on how I install ubuntu on this laptop

1. Create Windows Vista recovery disk
Boot into Window s Vista. First, since HP does not provide recovery disk with new laptops any longer, you need to create your own recovery disks in case you need Windows Vista in the future. Start -> Recovery Disk Creation and follow the instructions.

2. Re-participation the hard drive
Windows Vista comes with hand drive resizing and re-participation utilities. That's cool! It saves our trouble to search for a 3rd party software.
Follow the instructions in the following documents:
1. Screenshot Tour: Repartition your hard drive in Windows Vista
2. Can I repartition my hard disk?

3. Download
Don't bother to download ubuntu installation iso and create your own installation CD. If you have internet access (a fair weak condition, isn't it?), you can use Unetbootin (http://en.wikipedia.org/wiki/UNetbootin).

I am not exactly sure. There seems a bug with Unetbootin.
I participated my hard drive into three particitions: C: windows system partition; D: HP recovery partition; F: unformated free partition, which is intended for Linux installation.

But when I select mode as Hard Drive, only C: partition is displayed; I have to select USB Live mode and select F: partition there. I am not sure what this implies, still waiting for the result.

5. sound issues
After the installation, the speaker and the microphone does not work. Particularly, I could not use skype :-(.

Solution to "no sound problem"
Open
sudo vi /etc/modprobe.d/alsa-base
Add the following line to the end of the file
options options snd-hda-intel model=laptop enable_msi=1

Solution to microphone problem:
It is possible due to the mic is muted.
Open Volume Control by double clicking the icon at top-right corner. Select preference and select the device for recording and playback. And cancel the mutation option.

Solution to skype "Audio playback" problem
Excute the following command in a terminal

killall pulseaudio
sudo apt-get remove pulseaudio # this seems not necessary
sudo apt-get install esound
sudo rm /etc/X11/Xsession.d/70pulseaudio
refer to http://www.econowics.com/news-from-the-net/170/skype-problem-with-audio-playback-ubuntu-810-intrepid-ibex/

refer to
https://bugs.launchpad.net/ubuntu/+bug/269586
https://help.ubuntu.com/community/HdaIntelSoundHowto


6. install skype
7. install songbird
8. install Java Runtime Environment
9. install Open Office 3.0
10. install Mac4lin
11. install VLC and other codecs
12 install sopcast and gsopcast (online TV channel)
13 install fcitx Chinese input
First remove default scim framework and install fcitx
sudo apt-get autoremove scim
sudo apt-get install fcitx
next modify Xsession to automatically start fictx for all users. Open
sudo gedit /etc/X11/Xsession.d/95xinput
and chang it to
export XMODIFIERS=@im=fcitx
export XIM=fcitx
export XIM_PROGRAM=fcitx
export GTK_IM_MODULE=fcitx
export QT_IM_MODULE=XIM
fcitx
Open
sudo vim /usr/lib/gtk-2.0/2.10.0/immodule-files.d/libgtk2.0-0.immodules
Change the line about xim to
"xim" "X Input Method" "gtk20" "/usr/share/locale" "en:ko:ja:th:zh"
======
Well, I come back to update this post. I just returned this hp laptop. This was the first time I bought a laptop from HP, unfortunately it was an disappointing experience. I have two issues to complain. The cpu fan is too noise. Even after I disabled the feature "Keep fan running" in BIOS, the fan still makes too much noise. The CD -ROM drive is not quiet either; it feels earthquake when the CD drive is working.

The recovery too is also annoying. I could not recovery my laptop to factory configuration, either via harddrive recovery tool or via recovery CDs. It failed with the "error 1002"; and the HP customer service can not provide any useful help (they outsource custume serive to India, as a result we have to adapt to Indian English).

Anyway, I will blacklist this model from HP: HP Pavilion dv4.

Reference:
1. Screenshot Tour: Repartition your hard drive in Windows Vista
2. Can I repartition my hard disk?
3. Unetbootin http://unetbootin.sourceforge.net/
4. Tutorial: Ubuntu Linux on HP Pavilion
http://aldeby.org/blog/index.php/howto-ubuntu-linux-on-hp-pavilion-dv2000-dv6000-dv9000-series-laptops
5. http://www.dailygyan.com/2008/11/10-things-you-should-do-immediately.html
6. Top 10 Ubuntu downloads http://lifehacker.com/5227309/top-10-ubuntu-downloads
7. http://theindexer.wordpress.com/2009/04/24/to-do-list-after-installing-ubuntu-904-aka-jaunty-jackalope/
8. Install Microsoft YaHei font http://hi.baidu.com/zzy011/blog/item/6651e3ed44a9c62f63d09f37.html

Saturday, November 08, 2008

<R>andom Notes

1. how to estimate the running time of a R function?

R has a function proc.time() http://rweb.stat.umn.edu/R/library/base/html/proc.time.html
sample code
## a way to time an R expression: system.time is preferred
> ptm <- proc.time()
> for (i in 1:50) mad(stats::runif(500))
> proc.time() - ptm
user system elapsed 
0.039 0.001 0.052 
## End(Not run)

2. string manipulation in R

define a string
> s = "some characters"

convert other type into a string
> s = as.character(some_variable_in_other_type)

Convert a string into numbers
> pi = as.numeric("3.14159")


string length
>nchar(s)

string concatenation
> s1 = "string1"
> s2 = "string2"
> paste(s1, s2, sep = "")

given a vector of strings, vs, return a string that is the concatenation of vs's elements
> vs = c("song", "qiang")
> paste(vs, collapse = "")
 "song qiang"

string splicing
suppose s is a string, how do we slice a substring of the s given starting position and ending position?
we use the following function. there is no default value for stop. it the value of stop is larger the the total
length of string, it is truncated to the length of the string
> substr(s, first = 1, stop = 12)

string split

> strsplit("song qiang", split=" ")
[1] "song" "qiang"


3. when making figures with legend box, the text expand out of legend box when we use dev.copy2eps()  to convert  the figure image to a eps file

This problem comes from the different specification of font sizes in difference devices. A ugly way to solve this problem is to specify text.width=strwidth("some string"),
where "some string"  refers to the longest legend text plus some extra characters. The optimal number of extra characters should be determined by trial and error.

4. How to handle exceptions in R?
Read about two functions try and tryCatch (R FAQ 7.32). An example with try is shown below:
for(i in 1:16)
{
   result <- try(nonlinear_modeling(i));
   if(class(result) == "try-error") next;
}

GNU/Linux Notes

GNU/Linux Notes

1. How to speed up my Linux booting?
See Bootchart http://www.bootchart.org/index.html
and remove unnecessary services in the booting process


2. One important thing to remember when creating a SVN repository
In Subversion 1.1, a repository is created with a Berkeley
DB back-end by default. This behavior may change in future
releases. Regardless, the type can be explicitly chosen with
the --fs-type argument:
$ svnadmin create --fs-type fsfs /path/to/repos
$ svnadmin create --fs-type bdb /path/to/other/repos

Do not create a Berkeley DB repository on a network
share—it cannot exist on a remote
filesystem such as NFS, AFS, or Windows SMB. Berkeley DB
requires that the underlying filesystem implement strict POSIX
locking semantics, and more importantly, the ability to map
files directly into process memory. Almost no network
filesystems provide these features. If you attempt to use
Berkeley DB on a network share, the results are
unpredictable—you may see mysterious errors right away,
or it may be months before you discover that your repository
database is subtly corrupted.
If you need multiple computers to access the repository,
you create an FSFS repository on the network share, not a
Berkeley DB repository. Or better yet, set up a real server
process (such as Apache or svnserve), store
the repository on a local filesystem which the server can
access, and make the repository available over a network.
Chapter 6, Server Configuration covers this process in
detail.
3. count file numbers in a directory and its directory

total number of files
find . some_directory|wc -l

list number of files in each directory in detail
#! /usr/bin/python

import os
import sys

def count(p):
if not os.path.isdir(p):
print "%s\t%d" % (p, 1)
return 1

pls = os.listdir(p)
s = 0
for d in pls:
if os.path.isdir(d):
s += count(d)
else:
s += 1

print "%s\t%d " % (p, s)
return s

p = sys.argv[1]
count(p)


4.  Ubuntu DNS Server Problem
Problem Description:  I run Ubuntu 9.04 on my computer and use Wicd (Wired and Wireless Network Manager) to configure network settings. However, sometimes when I use wireless network, Wicd is able to connect to routers (pingable), but it fails to parse domain names. There is something wrong with DNS server.


Tentative Solution: 1) First disable all settings related to DNS inside Wicd, i.e. do not use either static or global DNS server; 2) edit /etc/resolv.conf, add available DNS servers; 3) restart computer. 4) [Optional] sometimes if we configure wicd to automatically connect and use static DNS server, Wicd freezes while setting static server. In this case, we can edit /etc/wireless-settings.conf to disable automatic connection and static DNS server.


5. How to rename files or directories in order to remove white spaces in the filename?
for i in $(ls -1 *|grep " "); do
     mv "$i" $(echo $i|sed 's/ /-/g');
done

6. How to backup files (or directories) with tar and 7-zip?
First we create tar balls with the tar utility and then compress the tar balls with the 7z program.  If the content of the file is sensitive, you can encrypt it with the internal encryption option in 7z or with GPG. The code is as following:
for i in *; do
     tar cfv "$i.tar" "$i" && \
     7z a "$i.tar.7z" "$i.tar" && \
     # rm -rf "$i" && \
     # rm -rf "$i.tar"; done
done

7. how do I output the matching regex pattern in a line?
use grep -o PATTERN.

Wednesday, May 07, 2008

Connecting USC VPN Network in Ubuntu

[Update 2013-02-12]
Surprisingly, this old post still receive visitors occasionally. Right now, If you just want to browse the internet and download some papers, you may try the web svn service: sslvpn1.usc.edu.

[Original Post:]
At USC, when you use computers on campus, you can use directly electronic resources, databases, electronic journals because you are in USC private network. Now suppose that you go back to your apartment off campus or you travel away from USC, how can you get access to those electronic resources that USC pays for? That's where VPN come into place. VPN, also called IP tunneling, is a secure method to access computer resources in a private network. VPN stands for "virtual private network". Generally speaking, USC runs a VPN server which listens to your call in and access request. You need to run a VPN client on your own computer, which connects to the server and offer you access to USC resources as you are in USC private network.

However, ITS only provieds official support of VPN clients for Windows (link)and Mac OS (link). Here we give a VPN solution for linux users (take Ubuntu 8.04 for example).

1. Install Network Manager Applet through the Add/Remove in the Ubuntu menu. (Most time, this applet should be installed defautly; if so, just skip to step 2);

2. Install the VPN plug-in network-manager-vpnc. Open Synaptic Package Manager, search for package network-manager-vpnc and install;

3. Left click the network manager applet (usually in the top right corner of your screen) and select VPN Connections->Configure VPN->Add. Type a name in the Connection Name box, USC VPN for example; In Gateway field, type ; In vpn3k.usc.edu; In Group Name field, type USC. Click the Optional tab, select Override user name, type in your USC account (the same as your USC email) in the textbox below. Click Apply. Close the window titled VPN Connections


4. Left click the network manager applet and select VPN Connections then click on USC connection (USC VPN) to connect. In the above password box, type in your password associated with your USC account; in the below Group password, type GoTrojan. OK, we are done!


This tutorial is based on Ubuntu. I think you can also configure VPN client in Debian, Fedora, OpenSuse and other Linux distrobutions.

References:
1.VPN Client on Ubuntu https://help.ubuntu.com/community/VPNClient
2. Configuring the Cisco VPN 3000 Client (Windows 2000/XP/Vista) http://www.usc.edu/its/vpn/vpn3k47win.html#help

Saturday, May 03, 2008

Fixing Resolution Problem of Ubuntu On Paralles Desktop

Problem

After installing Ubuntu 8.04 Hardy Heron in Parallels Desktop on my Macbook Pro, the default resolution is 1024*768. I want to use my Macbook pro's 1440*900 full resolution. I tried to use System->Preference->Screen Resolution, but there are not 1440*900 at all.

Solution

Basic idea: The problem arises because Ubuntu fails to detect the settings of my monitor automatically. Then can I mannually modify xorg.conf to set the right resolution? Let's go!

Open up a terminal. First Backup the original xorg.conf

sudo cp /etc/X11/xorg.conf  /etc/X11/xorg.conf.backup

Next open, open xorg.conf with your favorite editor

sudo vi /etc/X11/xorg.conf

Search the section "Screen" like below.

Section "Screen"
Identifier "Default Screen"
Device "Generic Video Card"
Monitor "Generic Monitor"
EndSection

Probabably your file contains more lines similar to the following

SubSection "Display"
Depth 24
Modes "1024x768" "800x600" "640x480"
EndSubSection

Note the line "Modes "1024x768" "800x600" "640x480"". It says that there are three different kinds resolutions, but our desired resolution 1440x900 is omitted. So we can simply add this resolution option. It is like the following after modification

SubSection "Display"
Depth 24
Modes "1440x900" "1024x768" "800x600" "640x480"
EndSubSection

It’ll appear several times throughout the file. Each time you see it, just add your desired resolution (in your case, 1440×900).

If your file doesn't contain a similar Subsection "Display" inside the Section "Screen" (as shown above), you just add the Subsection "Display" yourself. And th final result looks like

Section "Screen"
Identifier "Default Screen"
Device "Generic Video Card"
Monitor "Generic Monitor"
DefaultDepth 24
SubSection "Display"
Depth 1
Modes "1440x900" "1024x768" "800x600" "640x480"
EndSubSection
SubSection "Display"
Depth 4
Modes "1440x900" "1024x768" "800x600" "640x480"
EndSubSection
SubSection "Display"
Depth 8
Modes "1440x900" "1024x768" "800x600" "640x480"
EndSubSection
SubSection "Display"
Depth 15
Modes "1440x900" "1024x768" "800x600" "640x480"
EndSubSection
SubSection "Display"
Depth 16
Modes "1440x900" "1024x768" "800x600" "640x480"
EndSubSection
SubSection "Display"
Depth 24
Modes "1440x900" "1024x768" "800x600" "640x480"
EndSubSection
EndSection

Finally save the above modifications. Restart your X session by pressing Ctrl-Atl-Breakspace (or reboot your ubuntu), it just works!

If you encounter total messy after this modificaion, don't panic because you still have the backup of the original xorg.conf!

Reference
1. http://gonz.wordpress.com/2007/09/22/fixing-screen-resolution-on-ubuntu-linux-in-parallels-desktop/
2. http://www.simplehelp.net/2007/04/30/how-to-increase-the-screen-resolutions-available-to-ubuntu-while-running-in-parallels-for-os-x/

Thursday, April 17, 2008

Installing R in Suse SLED 10.1

Some one comments:"R is a nightmare in ANY distribution." I agree with him in regards to SUSE Linux Enterprise Edition version 10.1. I am using a x86_64 machine running SUSE SLED 10.1. I wrote in a letter about my bad experience when installing R.
"At first I tried SUSE's install software application, but it can't find R in its repository. Then I downloaded the rpm package of R for SUSE 10.1 from CRAN mirrors, and tried install software application again. But it can not resolve dependencies. At last I ran rpm -i R-base-2.6.1-3.1.x86_64.rpm from terminal. It said it needs libgfortran.

OK, I downloaded and installed libgfortran package, and then tried rpm -i R-base-2.6.1-3.1.x86_64.rpm again. This time it needed base. I downloaded base package and try to install it by running rpm -i base-1.3.6-1mdv2008.0.noarch.rpm (I am not sure this is the right package for my computer), butit needs apache-mod_php, apache-mod_ssl, php-mysql, etc. I have to give up."

Also it seems difficult to me to compile R from source code because the package dependency is so complex.

Finally I figured out a trick: we can run windows version R in a linux with Wine. First go to http://www.winehq.org/. download and install wine. And then grab a Windows installer of R and install it. It works, either basic computation or graphic display. But there is a little problem as shown in the following graph: the cursor overlaps with the text.




ps: Another by-product is that I can play starcraft on that Linux machine with a big display.

Reference:
1. Stuff I've learned about Wine

Saturday, April 05, 2008

Anti RSI Software

RSI stands for Repetitive Strain Injury. It results from repetitive motion of hands, wrist and long time incorrect posture that keeps specific muscles tense all the time. It is commonly seen in people who use computers a lot.

It is helpful to use more human-friendly mouse and keyboard, comfortable chairs and desks and pleasant work space; however we easily forget how long we use a computer when entirely concertrating on the work. Anti-RSI software can reminds us regular breaks and micropause .

Yun Fang recommended Workpace software to me yesterday. It offers a 30-day trial version, but charges a fee after that period. I found two alternative free anti-RSI software: Workrave for Windows and Linux and AntiRSI for Mac OS.






http://www.workrave.org/welcome/












http://tech.inhelsinki.nl/antirsi/

Reference:
Alleviate RSI the Hacker Way

Saturday, March 01, 2008

Synchronization Between Linux, Mac & Windows

Sooner or later after you begin to have more than one computer, you will face the problem of synchronization files between them. Of course the easiest solution is to sell n-1 computers; but it is not reasonable since we must have stronger reason to have n computers at first .

Let me do the research.

My situation is as following:
I run SUSE Linux on the desktop in my lab, which is supposed to running all the time; Also I have a desktop at home running windows xp and finally my macbook laptop. My first priority is to sync between mac and linux for I usc them heavily; and second between mac and windows. Also since I use computer

References


Sync folders between a Mac and PC?


2.

How to mount a Windows shared folder on your Mac


Geek to Live: Mirror files across systems with rsync

http://lifehacker.com/software/mac-os-x/how-to-access-a-macs-files-on-your-pc-247541.php

How to set up a home FTP server

http://ceitl.zanestate.edu/blog/archives/2005/10/synchronizing-files-across-computers-and-platforms/

Geek to Live: Automatically back up your hard drive

http://everythinglinux.org/rsync/

Passwordless SSH Login
http://www.hackinglinuxexposed.com/articles/20021226.html


http://linuxmafia.com/%7Erick/linux-info/filesync.html

Monday, January 14, 2008

Synthetic Biology

Drew Endy Foundations for engineering biology

the four challenges that greatly limit engineering biology today are 1)biological complexity; 2)the tedious and unreliable construction and characterization of synthetic biological systems; 3)the spontaneous variation of biological systems; and 4) evolution.

Lessons from the past
standardization
Registry of Standard Biological Parts: http://parts.mit.edu/registry/index.php/Main_Page

decoupling;
separation of deign and implementation
for example, one group design useful DNA sequences and another group synthesize the piece of DNA chemically. (it seems possible now)

abstraction

design of reproducing machines
reliable computing with unreliable components
error detection & correction mechanism
self-replicating automata

additional reading:
Elowitz, M. B. & Leibler, S. A synthetic oscillatory network of transcriptional
regulators. Nature 403, 335–-338 (2000)

Sprinzak, D. & Elowitz, M. B. Reconstruction of genetic circuits. Nature
doi:10.1038/nature04335