Wesley @BerryLab

[LINUX] Gentoo Tips

2008-08-26T00:53:00.009+08:00

solve system packages blocking

[blocks B] pkg1 (is blocking pkg2)

$ emerge --buildpkgonly --nodeps pkg2 && emerge -C pkg1 && emerge --usepkgonly pkg2

from

傻蛋碎碎唸: Gentoo emerge 套件發現 blocking 時的安全解法: "emerge --buildpkgonly --nodeps util-linux && emerge -C setarch && emerge --usepkgonly util-linux"

[SYSLOG] manage system logging

2008-08-25T03:00:00.010+08:00

my syslog-ng.conf

# Syslog-ng default configuration file for Gentoo Linux
# contributed by Michael Sterrett

options {
        chain_hostnames(off);
        sync(0);

        # The default action of syslog-ng 1.6.0 is to log a STATS line
        # to the file every 10 minutes.  That's pretty ugly after a while.
        # Change it to every 12 hours so you get a nice daily update of
        # how many messages syslog-ng missed (0).
        stats(43200);
};

source src {
    unix-stream("/dev/log" max-connections(256));
    internal();
    file("/proc/kmsg");
};

# mcelog
filter mcelog { program(mcelog); };
destination mcelog{ file("/var/log/mcelog"); };
log { source(src); filter(mcelog); destination(mcelog); };

# dhcpd
filter dhcpd { program("dhcpd"); };
destination dhcpd { file("/var/log/dhcpd"); };
log { source(src); filter(dhcpd); destination(dhcpd); };

# postfix
#filter postfix { facility(mail) or match("postfix"); };
filter mail { facility(mail); };
destination mail { file("/var/log/maillog"); };
log { source(src); filter(mail); destination(mail); };

# cron
filter cron { facility(cron); };
destination cron { file("/var/log/cron"); };
log { source(src); filter(cron); destination(cron); };

# sshd, su
#filter secure { facility(auth,authpriv) or program("sshd"); };
filter secure { facility(auth,authpriv); };
destination secure { file("/var/log/secure"); };
log { source(src); filter(secure); destination(secure); };

# syslog-ng
filter syslog { facility(syslog); };
destination syslog { file("/var/log/syslog"); };
log { source(src); filter(syslog); destination(syslog); };

# message log
filter messages { not filter(cron) and not filter(mail)
        and not filter(dhcpd) and not filter(secure) and not filter(syslog); };
destination messages { file("/var/log/messages"); };
log { source(src); filter(messages); destination(messages); };

# By default messages are logged to tty12...
destination console_all { file("/dev/tty12"); };
# ...if you intend to use /dev/console for programs like xconsole
# you can comment out the destination line above that references /dev/tty12
# and uncomment the line below.
#destination console_all { file("/dev/console"); };
log { source(src); destination(console_all); };

iptables log to ulog

iptables: Getting full packets out of the kernel

syslog-ng howto

syslog-ng log server安裝說明

syslog-ng的特異功能
經常check system event一直是系統管理上很容易被忽略的重要細節，原因在於大部分的system logs傳達的資訊是不重要的，以至於將重要的警訊淹沒。
如同syslog-ng的名稱，它是用以取代syslogd的next generation版本，原來的syslog是只能夠依priority及facility作分類，syslog-ng可以根據log的內容，以 regular expression自訂分類及log的處理方式，並且支援以tcp/udp將log送到遠端的server，或是即時通知在線上的系統管理者，甚至能將 log值當成某個program的標準輸入字串，直接將log作加工及分析。

syslog-ng的應用與範例
Syslog-ng的message path全部在syslog-ng.conf作編輯。在syslog-ng的message path中，可以包括多個sources、多個filter rules及多個destinations的同步多工處理。一般來說，採用syslog-ng最大的用途除了運用它分類的功能外，就是運用它的網路功能。如前所提，syslog-ng可以透過tcp或是udp的協定將log送到遠端的server作集中式的監控。
現在我們先假設一個情境，我們希望將幾台提供網路服務的server的log集中到一台server作管理，我們希望能夠將log值中含有特定 facility code或特定priority的log儲存在本地端，並且將所有收集到的log值全部送到log server作分類以及儲存。原來的syslog做不到這麼多點，所以我們必須在每一台server安裝syslog-ng，各透過tcp送到log server，log server的syslog-ng.conf依server.conf的範例設定。詳細的syslog-ng config參數當然不只這些，實際設計系統時最好直接看看官方網站的reference manual (http://www.balabit.hu/static/syslog-ng/ ... book1.html) 。


server.conf

#設定options,語法為options { S1 ; S2 ; S3…};
#options主要是對整個configuration的共通設定

options { use_fqdn(yes); keep_hostname(yes); use_dns(yes); long_hostnames(off); sync(3); log_fifo_size(300); };

#設定input來源,語法為source source_ name {S1 ; S2 ; …};
#internal()表所有本機產生的log
# unix-stream("/dev/log")表來自本機的log檔,本機是Linux,若為BSD則需用
#unix-dgram，這是開啟一個AF_UNIX socket聽取目的檔案的message.
#收集本地端以及來自192.168.0.100 port 514這台server送來的log值,
#keep-alive(yes/no)決定是否保持連線直到收到sighup訊號

source src { unix-stream("/dev/log"); internal(); };
source remote { tcp(ip("127.0.0.100") port(514) keep-alive(yes)); };

#設定output目的地,語法為destination destination_ name {S1 ; S2 ; …};
#file(“path”):以檔案的方式存在local端
#usertty(“user_name”):即時通知特定的線上的使用者

destination lpr { file("/var/log/lpr.log"); };
destination mail { file("/var/log/mail.log"); };
destination messages { file("/var/log/messages"); };
destination console { usertty("root"); };

#設定filter條件,filter filter_name{expresson;}; expression為各條件以and or not
#連結
#facility(string1,string2):篩選出包含string1或string2其中之一個字串的log.
#level(S1..S2..S3) or priority(S1..S2..S3),篩選出包含其中之一level的log

filter f_lpr { facility(lpr); };
filter f_mail { facility(mail); };
filter f_messages { level(info..emerg) and not facility(mail,lpr); };
filter f_emergency { level(emerg); };

###############################################################
# 將設定好的source,filter,destination依需求作組合

log { source(src); filter(f_lpr); destination(lpr); };
log { source(src); filter(f_mail); destination(mail); };
log { source(src); filter(f_messages); destination(messages); };
log { source(src); filter(f_emergency); destination(console); };

###############################################################
#將收到的所有log依host分資料夾,再依該log的facility code分別儲存，
#並設定owner, group, permission, directory permission

destination hosts { file("/var/log/HOSTS/$HOST/$FACILITY" owner(root) group(root) perm(0600) dir_perm(0700) create_dirs(yes)); };

log { source(remote); destination(hosts); };
###############################################################
另外，我們必須將/etc/logrotate.d/syslog置換成以下syslog-ng:

/var/log/lpr.log {
postrotate
/bin/kill -HUP `cat /var/run/syslogd-ng.pid 2> /dev/null` 2> /dev/null ||
true
endscript
}

/var/log/mail.log {
postrotate
/bin/kill -HUP `cat /var/run/syslogd-ng.pid 2> /dev/null` 2> /dev/null ||
true
endscript
}

/var/log/messages {
postrotate
/bin/kill -HUP `cat /var/run/syslogd-ng.pid 2> /dev/null` 2> /dev/null ||
true
endscript
}

/var/log/lastlog {
postrotate
/bin/kill -HUP `cat /var/run/syslogd-ng.pid 2> /dev/null` 2> /dev/null ||
true
endscript
}
最後啟動syslog-ng！
#/etc/rc.d/init.d/syslog-ng start

結合database
(1)如果我們希望將log值存進資料庫的話，我們必須將先將database server建起來(這裡我們選擇mysql)，我們必須產生一個syslog.sql以建立資料庫及資料表:
CREATE DATABASE syslog;

USE syslog;

CREATE TABLE logs (
host varchar(32) default NULL,
facility varchar(10) default NULL,
priority varchar(10) default NULL,
level varchar(10) default NULL,
tag varchar(10) default NULL,
date date default NULL,
time time default NULL,
program varchar(15) default NULL,
msg text,
seq int(10) unsigned NOT NULL auto_increment,
PRIMARY KEY (seq),
KEY host (host),
KEY seq (seq),
KEY program (program),
KEY time (time),
KEY date (date),
KEY priority (priority),
KEY facility (facility)
) TYPE=MyISAM;
然後執行mysql -u root -p < syslog.sql。
(1) 執行mkfifo /tmp/mysql.pipe
(2) 執行mysql -u root --password=passwd syslog < /tmp/mysql.pipe
(3) 最後，我們必須在syslog-ng.conf增加一條command:
destination d_mysql {
pipe("/tmp/mysql.pipe"
template("INSERT INTO logs (host, facility, priority, level, tag, date, time, program, msg) VALUES ( '$HOST', '$FACILITY', '$PRIORITY', '$LEVEL', '$TAG', '$YEAR-$MONTH-$DAY', '$HOUR:$MIN:$SEC', '$PROGRAM', '$MSG' );\n") template-escape(yes));
};
log { source(net); destination(d_mysql);};
(4) 重開syslog-ng
/etc/init.d/syslog-ng stop # Stop syslog-ng
/etc/ini.d/syslog-ng start # Start syslog-ng

syslog(d) howto

syslog Overview

The standard UNIX syslog facilities are

    kern – kernel
    user – application or user processes (this is the default if the application sending a message does not specify the facility)
    mail/news/UUCP/cron – electronic mail/NNTP/UUCP/cron subsystems
    daemon – system daemons
    auth – authentication and authorization related commands
    lpr – line printer spooling subsystem
    mark – inserts timestamp into log data at regular intervals
    local0-local7 – 8 facilities for customized auditing
    syslog – internal messages generated by syslog itself
    authpriv – non-system authorization messages
    * -- on most versions of UNIX, refers to all facilities except mark

syslog levels are nominally defined as:

    emerg – system is or will be unusable if situation is not resolved
    alert – immediate action required
    crit – critical situations
    warning – recoverable errors
    notice – unusual situation that merits investigation; a significant event that is typically part of normal day-to-day operation
    info – informational messages
    debug – verbose data for debugging

[BENCHMARK] Memory Test

2008-08-23T13:46:00.006+08:00

memtester

$ memtester <MEMORY> [ITERATIONS]

MEMORY the amount of memory to allocate and test, in megabytes.
ITERATIONS (optional) number of loops to iterate through. Default is infinite.

Example == Linux: How do I find out causes for memory faults?

[SYSTEM] Memory Error on Tyan S2882 with AMD Opteron 248 + 8x 1GB Cosair ECC DDR400

2008-08-19T15:07:00.029+08:00

memtester result with ECC disable

memtester version 4.0.8 (64-bit)
Copyright (C) 2007 Charles Cazabon.
Licensed under the GNU General Public License version 2 (only).

pagesize is 4096
pagesizemask is 0xfffffffffffff000
want 7000MB (7340032000 bytes)
got  7000MB (7340032000 bytes), trying mlock ...locked.
Loop 1:
  Stuck Address       : ok
  Random Value        : ok
  Compare XOR         : ok
  Compare SUB         : ok
  Compare MUL         : ok
  Compare DIV         : ok
  Compare OR          : ok
  Compare AND         : ok
  Sequential Increment: ok
  Solid Bits          : ok
  Block Sequential    : testing 123FAILURE: 0x7b7b7b7b7b7b7b7b != 0x7a7b7b7b7b7b7b7b at offset 0x062b25e3.
  Checkerboard        : ok
  ....

on loading large amount of memory

EDAC k8 MC1: general bus error: participating processor(local node response), time-out(no timeout) memory transaction type(generic read), mem or i/o(mem access), cache level(generic)
EDAC MC0: CE page 0xfc5b, offset 0x7d0, grain 8, syndrome 0xf654, row 2, channel 1, label "": k8_edac
EDAC k8 MC1: extended error code: ECC chipkill x4 error
EDAC k8 MC0: general bus error: participating processor(local node response), time-out(no timeout) memory transaction type(generic read), mem or i/o(mem access), cache level(generic)
EDAC MC0: CE page 0x1cfc16, offset 0x6c0, grain 8, syndrome 0x4472, row 0, channel 1, label "": k8_edac
EDAC k8 MC0: extended error code: ECC chipkill x4 error
EDAC k8 MC1: general bus error: participating processor(local node response), time-out(no timeout) memory transaction type(generic read), mem or i/o(mem access), cache level(generic)
EDAC MC0: CE page 0xea59, offset 0x830, grain 8, syndrome 0xf654, row 2, channel 1, label "": k8_edac
EDAC k8 MC1: extended error code: ECC chipkill x4 error

identify the DIMM

Re: EDAC chipkill messages
Machine Check Exception

machine check events

what does it mean ?

to show the contents

$ /usr/sbin/mcelog

[x86_64] how worried should I be about MCEs?

EDAC options in kernel and bios

EDAC Project
Chipkill Advanced ECC - Overview of How It Works
Speed vs. Precision
BIOS and Kernel Developer's Guide for AMD Athlon 64 and AMD Opteron Processors

corrected ecc error

   --------------------     
  | An Overview of ECC | 
   --------------------
                              
    Introduction
    ------------
      The scope of this discussion is limited to soft and hard errors that
      occur in memory and how they are reported by Solaris.  It does not
      account for errors that occur while data travels through the E10000
      interconnect, CPU Module, or I/O.  For this discussion, soft errors 
      are transient or temporary errors in memory that can be corrected by
      rewriting the affected memory cell.  Hard errors occur when a cell
      is permanently damaged and cannot hold the correct information. With
      a hard error, the cell can be permanently stuck-at "0", or "1".

    ECC Concepts
    ------------
      Any volatile storage medium, whether it be the Dynamic Random Access
      Memory (DRAM) used on main memory DIMMs or Static Random Access Memory
      (SRAM) mainly used for caches, is subject to occasional natural
      incidences of data loss due to the impact of alpha particles or cosmic
      rays. This data loss manifests itself in the changing of the value
      stored in the memory cell affected by the collision.  Typically only a
      single bit is affected, but there is a small probability that multiple
      cells can be upset.

      When a bit flips due to this phenomenon, it is referred to as a soft
      error.  This is to distinguish it from a hard error resulting from a
      hardware failure.  These soft errors happen at a rate, called the soft
      error rate (SER), that can be predicted as a function of the memory
      density, the memory technology, and the altitude of the system in which
      the memory resides.

      ECC was invented to allow survival from these naturally occurring
      losses of data.  The ECC method used on the E10000 is called a Single
      Error Correcting, Double Error Detecting code (SEC-DED).  The concept is
      that every word of data is written to memory along with a number of
      extra check bits.  When the word is read back from memory, a fresh set
      of check bits are recomputed and compared with the check that was
      stored in memory.  The result of this comparison is called the syndrome.

      If the syndrome is zero, the comparison was identical, and thus the
      data is good.  A non-zero syndrome means the data is in error, and the
      syndrome is used to find a single bit in error and correct it.  A
      single bit error is called a Correctable Error (CE).  The syndrome can
      also detect if two bits are in error, but it does not have enough
      information to identify which two bits.  This type of error is called
      an Uncorrectable Error (UE).  UltraSPARC microprocessors use a SEC-DED
      variant called S4ED that also can detect, but not correct, three or
      four bit errors if they are clustered within a four bit nibble.

[CVS] note for CVS

2008-07-27T20:50:00.012+08:00

using CVS over different SSH port

in .ssh/config

Host SomeCvsServer
HostKeyAlias cvs.some.server.com
Hostname cvs.some.server.com
Port 12345

cvs usage

$ export CVS_RSH=ssh
$ export CVSROOT=":ext:user@SomeCvsServer:/cvsroot"
$ cvs co project

[Q-CHEM] Build Q-Chem

2008-07-23T14:04:00.011+08:00

add remkey without re-building whole q-chem

$ rm $QC/config/rem.conf
$ qcmake rem_config rem rem_input
$ rm -f $QC/qparser/*.o $QC/libgen*.o
$ qcmake qparser.a libgen.a
$ rm -f $QC/<probably program>/*.o
$ qcmake qcprogall

local copy of qcaux

As suggested in README.QCAUX: "It is recommended to store qcaux locally, especially drivers, as loading appears to be pretty intensive and puts a heavy tax on NFS, and may stall Q-CHEM when network is flaky."

[SGE] Parallel Environment

2008-07-23T09:04:00.009+08:00

allocation rule

<integer>          allocate exactly this many slots per host 
$pe_slots          allocate as many slots on single host as stated on command line: qsub -pe <pe name> <slot range>
$fill_up           fill up one host, move to another, continue until range filled 
$round_robin       do round-robin allocation over all suitable hosts until range filled

[VIM] coding fonts for gVim

2008-07-15T13:29:00.019+08:00

good programming font criteria

 * Crisp clear characters
 * Extended characterset.
 * Good use of whitespace.
 * 'l', '1' and 'i' are easily distinguished
 * '0', 'o' and 'O' are easily distinguished
 * forward quotes from back quotes are easily distinguished -prefer mirrored appearance
 * Clear punctuation characters, especially braces, parenthesis and brackets

install Monaco.ttf, Consolas.ttf and DejaVu Sans Mono

Linux

$ cp *.ttf $HOME/.fonts
$ fc-cache -v -f

Mac OS X
M$ Windows

.gvimrc

Linux
set gfn=Monaco\ 14,\ Consolas\ 14
Mac OS X

set nomacatsui anti guifont=Monaco:h14
set nomacatsui anti guifont=Consolas:h14
set nomacatsui anti guifont=DejaVu\ Sans\ Mono:h14

M$ Windows

others

Bitstream Vera

note for cluster

2008-07-03T23:31:00.003+08:00

network

Jumbo Frames

Jumbo frames are Ethernet frames with more than 1,500 bytes of payload (MTU).

[BENCHMARK] netperf

2008-07-03T13:21:00.005+08:00

run netperf

# netperf -l [length] -H [server_IP] -t TCP_STREAM

You should make sure that a client-server pair runs netperf in both directions at the same time. This guarantees that your network is operating well in full-duplex mode. If everything is good, netperf reports a throughput of about 80 MBit/s. For a unidirectional netperf test, you should get about 92-95 MBit/s. For longer tests, increase the -l  value.

# ethtool eth0
# mii-tool --help

[SSH] SSH Tunnel Proxy

2008-06-08T16:12:00.003+08:00

ssh command

$ ssh -L [listening_port_for_browser]:[proxy_ip]:[actuall_proxy_port] [user]@[ssh_server]

[X] set gtk2 fontconfig

2008-06-03T20:43:00.012+08:00

reference

windows manager

$HOME/.gtkrc-2.0

include "/usr/share/themes/Default/gtk-2.0/gtkrc"
include "/home/jungoyuo/.gtkrc.mine"

# -- THEME AUTO-WRITTEN DO NOT EDIT
style "gtk-default-zh-tw" {
        font_name = "Helvetica ,MingLiU 12"
}
style "default" {
#       font_name = "Sans 12"
        font_name = "sans-serif 12"
}
class "GtkWidget" style "default"

$HOME/.fonts.conf

<?xml version="1.0"?>
<!DOCTYPE fontconfig SYSTEM "fonts.dtd">
<!-- /etc/fonts/fonts.conf file to configure system font access -->
<fontconfig>

<dir>/usr/share/fonts/100dpi</dir>
<dir>/usr/share/fonts/75dpi</dir>
<dir>/usr/share/fonts/arphicfonts</dir>
<dir>/usr/share/fonts/artwiz</dir>
<dir>/usr/share/fonts/CID</dir>
<dir>/usr/share/fonts/corefonts</dir>
<dir>/usr/share/fonts/cyrillic</dir>
<dir>/usr/share/fonts/encodings</dir>
<dir>/usr/share/fonts/freefont</dir>
<dir>/usr/share/fonts/local</dir>
<dir>/usr/share/fonts/misc</dir>
<dir>/usr/share/fonts/sharefonts</dir>
<dir>/usr/share/fonts/terminus</dir>
<dir>/usr/share/fonts/TrueType</dir>
<dir>/usr/share/fonts/ttf</dir>
<dir>/usr/share/fonts/TTF</dir>
<dir>/usr/share/fonts/ttf-bitstream-vera</dir>
<dir>/usr/share/fonts/Type1</dir>
<dir>/usr/share/fonts/ukr</dir>
<dir>/usr/share/fonts/unifont</dir>
<dir>/usr/share/fonts/util</dir>
<dir>/usr/share/fonts/zh-kcfonts</dir>
        
        <match target="font">
                <test name="lang" compare="contains">
                        <string>zh</string>
                </test>
                <edit name="hinting" mode="assign">
                        <bool>true</bool>
                </edit>
        </match>
<!-- turn off anti-alias function for font-size smaller than 13

        <match target="pattern">
                <test qual="any" name="size" compare="less">
                        <int>13</int>
                </test>
                <edit name="antialias" mode="assign">
                        <bool>false</bool>
                </edit>
        </match>
-->
        <alias>
                <family>serif</family>
                <prefer>
                        <family>Bitstream Vera Serif</family>
                        <family>Times New Roman</family>
                        <family>Times</family>
                        <family>PMingLiU</family>
                        <family>MingLiU</family>
                </prefer>
        </alias>
        <alias>
                <family>sans-serif</family>
                <prefer>
                        <family>Bitstream Vera Sans</family>
                        <family>Helvetica</family>
                        <family>Verdana</family>
                        <family>Arial</family>
                        <family>PMingLiU</family>
                        <family>MingLiU</family>
                </prefer>
        </alias>
        <alias>
                <family>monospace</family>
                <prefer>
                        <family>Bitstream Vera Sans Mono</family>
                        <family>Courier</family>
                        <family>Courier New</family>
                        <family>PMingLiU</family>
                        <family>MingLiU</family>
                </prefer>
        </alias>
</fontconfig>

[FFX] mathfont missing

2008-06-01T13:28:00.006+08:00

install fonts for MathML

Following the links provide by Fonts for MathML-enabled Mozilla, there are two font-sets for MathML:

1. TeX's Computer Modern Fonts
2. Mathematica 4.1 TrueType Fonts

Extract all font files to the system font directory and modify ffx pref.js by adding:
user_pref("font.mathfont-family", "CMSY10, CMEX10, Math1, Math2, Math4, Symbol");

[Q-CHEM] Intel wrapped fftw

2008-06-01T02:17:00.002+08:00

wrapped fftw in Intel MKL

try it !!

[TEX] beamer theme gallery

2008-05-29T16:02:00.002+08:00

theme image (http://mike.depalatis.net/beamerthemes/)

[SECURE] group check and consisteny

2008-05-11T19:59:00.004+08:00

Checking groups and convert to shadow

$ grpck # checking groups
$ grpconv # convert to shadow

[PROG] note

2008-04-12T00:26:00.006+08:00

useful tools

nm - list symbols from object files
ldd - print shared library dependencies

readable one-array format in C or C++

#define jArray[x + NCol*y]   jArray(x,y)

[LOG] booting log of SCSI card on (old) twinberry

2008-04-11T11:32:00.004+08:00

Adaptec ASC-39320 U320

scsi0 : Adaptec AIC79XX PCI-X SCSI HBA DRIVER, Rev 1.3.11
        
        aic7902: Ultra320 Wide Channel A, SCSI Id=7, PCI-X 101-133Mhz, 512 SCBs

(scsi0:A:1): 320.000MB/s transfers (160.000MHz DT|IU|QAS, 16bit)
(scsi0:A:5): 320.000MB/s transfers (160.000MHz DT|IU|QAS, 16bit)
  Vendor: SEAGATE   Model: ST373307LC        Rev: 0007
  Type:   Direct-Access                      ANSI SCSI revision: 03
scsi0:A:1:0: Tagged Queuing enabled.  Depth 253
  Vendor: IBM       Model: IC35L073UCDY10-0  Rev: S23C
  Type:   Direct-Access                      ANSI SCSI revision: 03
scsi0:A:5:0: Tagged Queuing enabled.  Depth 253
scsi1 : Adaptec AIC79XX PCI-X SCSI HBA DRIVER, Rev 1.3.11
        
        aic7902: Ultra320 Wide Channel B, SCSI Id=7, PCI-X 101-133Mhz, 512 SCBs

scsi1:A:3:0: DV failed to configure device.  Please file a bug report against this driver.
(scsi1:A:3): 160.000MB/s transfers (80.000MHz DT, 16bit)
  Vendor: BROWNIE   Model: 8600U3            Rev: 0001
  Type:   Direct-Access                      ANSI SCSI revision: 03
scsi1:A:3:0: Tagged Queuing enabled.  Depth 253

[GADGET] dmidecode

2008-04-10T23:17:00.005+08:00

introduction

Quote from the official website:
"Dmidecode reports information about your system's hardware as
described in your system BIOS according to the SMBIOS/DMI standard"

[QCHEM] bursted SCF energy in a parallel job with heterogeneous CPUs

2008-03-03T15:52:00.005+08:00

on berry6 (opteron 280) and berry8 (core2 quad)

 SCF converges when DIIS error is below 1.0E-08
 ---------------------------------------
  Cycle       Energy         DIIS Error
 ---------------------------------------
    1   -3361.2591633686      5.79E-02
    2   -3751.3667331414      1.40E-01
    3   -3753.7216460829      1.38E-01
    4   -3729.9708610746      1.51E-01
    5   -3356.8584124714      1.99E-01
    6   -2360.4516761724      2.65E-01
    7   -1906.3181437427      2.91E-01
    8   -1865.0400872828      2.92E-01
    9   -1836.4085108264      2.92E-01

[SECURE] virus infection

2008-02-26T21:00:00.002+08:00

trojan.win32.pakes.k

notes for network security

2008-01-27T17:16:00.000+08:00

nmap usage

$ nmap -sT -sU -v -oX -P0 {host}

[TEX] template for beamer

2008-01-14T21:47:00.000+08:00

preamble

% Layout Options
%
% [slidestop] puts frame titles & contents on the top left corner (default = [slidescentered])
% [compress] makes all navigation bars as small as possible (bad for multi-line navigation bars)
% [red] changes navigation bars and title to reddish color (default = blue; others = red,brown,blackandwhite)
%
% Font options 
% 
% [mathserif] use serif fonts for representing formulas instead of sans serif (default = mathsans)
%
% Note options
% [notes] adds notes to PDF screen
% [notesonly] make only notes
\documentclass[notes,blue,mathserif]{beamer}
%\documentclass[slidestop,blue,mathserif]{beamer}

\usepackage{graphicx}
\usepackage{fancybox}

% This package enables us to use special letters (with accents, cedillas, etc).
% You can discard this command when the presentation is in English.
\usepackage[latin1]{inputenc}


% in \begin{document} .. \end{document}
%\mode{\usepackage{fullpage}}

% in \begin{frame} .. \end{frame}
\mode
{
%\usetheme{Warsaw}
\usetheme{Berlin}
%\usetheme{Malmoe}
%\usetheme{Antibes}
%\usetheme{Berkeley}
%\usetheme{Singapore}
%\usetheme{Szeged}

% The default font theme installs a sans serif for all text of the presentation
\usefonttheme{default}

% Using default block style
%\setbeamertemplate{blocks}[default]

% Background colors
% solid style
%\beamertemplatesolidbackgroundcolor{gray}
% gradient style
%\beamertemplateshadingbackground{blue!5}{yellow!10}
%\beamertemplateshadingbackground{blue!10}{yellow!5}
\beamertemplateshadingbackground{yellow!5}{blue!10}
% grid style
%\beamertemplategridbackground[0.5in]
}

\title{Title of Presentation}
\author{Name of Author}
\institute{Institute of Chemistry, Academia Sinica}
%\date{\today}
\date{December 12, 2007}

making title page

% Beamer 2.20 macro
%\frame{\titlepage} 
% Beamer 3.0 to make cover slide
\begin{frame}
 \titlepage
\end{frame}

layout of presentation

%\section[title name]{real name}
\section[title name shown in navigation bars ]{real name shown in context}
%\subsection[title name]{real name}
\subsection[title name]{real name}
\begin{frame}
\frametitle{Title shown in the page}
\end{frame}

making outline page

% To define a frame containing the layout of the presentation
\section[Outline]{}
\frame{\tableofcontents}

adding note for each frame

% appending to \end{frame}
%\note[options]{ .. }; options = itemize, enumerate 
\note[itemize]{\item Notes content}

[SSH] ssh_exchange_identification: Connection closed by remote host

2007-12-29T00:33:00.000+08:00

description

ssh_exchange_identification: Connection closed by remote host

solution

re-compile tcp-wrappers with USE flag "ipv6"

[TEX] notes

2007-12-25T10:48:00.000+08:00

after installing packages

$ texhash

make equation left-aligned (default is center-aligned)

\documentclass[fleqn]{class}

make newcommand with parameters

\newcommand{newcommand}[numberofparas]{detail}

packages

\usepackage{graphicx}
\usepackage{fancybox}
% to add varied underlines
\usepackage{ulem}

% This package enables us to use special letters (with accents, cedillas, etc).
% You can discard this command when the presentation is in English.
\usepackage[latin1]{inputenc}

[QM] Notes for spin density

2007-12-19T22:56:00.000+08:00

definition of the spin density

A spin density is defined by the difference between an alpha spin one-particle density and a beta spin one-particle density.

physical meaning of the spin density

A spin density describes the probability density of finding twice of the z-component of an N-electron system in real space. The trace of a spin density shows twice of the z-component of an N-electron system or the difference between the number of alpha and beta electrons of an N-electron system.

spin densities in the MO theory

Given a system with equal number of alpha and beta electrons, the spin density of a restricted Slater determinant (RSD) is definitely vanished but the spin density of an unrestricted Slater determinant (USD) is not necessarily zero. The trace (the z-component of total spin) for both densities are definitely zero due to the same number of alpha and beta electrons.

The multiplicity of the former wavefunction (RSD) is singlet and the later one (USD) is possibly not a eigenfunciton of total spin-moment operator (S^2).



[GNUPLOT] postscript note
2007-12-18T23:57:00.002+08:00
how to use Greek symbols and enhanced text mode in gnuplot

set term postscript enhanced eps "Times-Roman" 30
set encoding iso_8859_1 # to access ISO Latin-1 fonts


reference

ps_guide



[INTEL] Mixing Fortran and C/C++ by Using Intel Compiler
2007-12-14T23:10:00.000+08:00
linking Fortran subroutines in C/C++ 

LDFLAGS = -L/opt/intel/fce/9.1/lib -lifport -lifcore -limf




[VIM] notes
2007-12-14T16:34:00.001+08:00
find match of current parenthesis, brace, or bracket

%

on the fly spell checking (vim 7.0)

:set spell - Turns on the spell checking
:set nospell - Turns off the spell checking (can be achieved using GUI too).
]s - Move to the next mis-spelled word in the document.
[s - Same as above command but searches backwards.
z= - Shows a list of close matches to the mis-spelled word from which the user can pick the correct one.

folding by {{{ ... }}} marker

:set foldmethod=maker

set shiftwidth to 2 in C indent

:set cino=>2

automatically word wrap for tex

let s:extfname = expand("%:e")
if s:extfname == "tex"
  set textwidth=70
endif

free Fortran90 format

let s:extfname = expand("%:e")
if s:extfname == "f90" || s:extfname == "F"
  let fortran_free_source=1
  unlet! fortran_fixed_source
else
  let fortran_fixed_source=1
  unlet! fortran_free_source
endif



[TEX] compile beamer with EPS
2007-12-12T22:23:00.000+08:00
teTeX

$ latex  && latex  && dvipdf 

MikTeX + M$

$ latex  && latex  && dvips  && ps2pdf .ps



[TEX] missing eps in DVI
2007-12-10T14:39:00.000+08:00
error when opening xdvi: gs: Unknown device: x11

make sure compile ghostscript with X11



[FFX] play M$ video
2007-12-07T01:26:00.000+08:00
invoke WMP to player videos

1. turn off your ffx
2. open the following file in notepad: %APPDATA%\Mozilla\Firefox\pluginreg.dat
3. search for "Windows Media Player Plug-in Dynamic Link Library"
4. add or modify bold lines: 

Windows Media Player Plug-in Dynamic Link Library|$
10
0|application/asx|Media Files|*|$
1|video/x-ms-asf-plugin|Media Files|*|$
2|application/x-mplayer2|Media Files|*|$
3|video/x-ms-asf|Media Files|asf,asx,*|$
4|video/x-ms-wm|Media Files|wm,*|$
5|audio/x-ms-wma|Media Files|wma,*|$
6|audio/x-ms-wax|Media Files|wax,*|$
7|video/x-ms-wmv|Media Files|wmv,*|$
8|video/x-ms-wvx|Media Files|wvx,*|$
9|video/x-msvideo|Media Files|avi,*|$




[Q-CHEM] routines and remkey  s added for FED
2007-12-06T21:11:00.002+08:00
remkeys (in $QC/config/rem.list)

!ZQY: State to State one electron transformation
STS_DONOR
STS_ACCEPTOR
STS_MOM
STS_FED
STS_GMH
STS_DC
STS_DC_DONOR = [iState, nState, nOccA, nOccB, nOrb]
STS_DC_ACCEPTOR = [iState, nState, nOccA, nOccB, nOrb]
*STS_D_NSTATE
*STS_D_NALPHA
*STS_A_NSTATE
*STS_A_NALPHA

* old remkeys

routines added


setman/setman.F (mod)
setman/sts.F (add)
setman/stsDC.F (add)
setman/stsdfd.F (add, make detach. and attach. densities for state-to-state transition)
setman/sfdfd.F (add, make detach. and attach. densities for spin-flip transition)
setman/cisfchg.F (add)
setman/cismulmom.F (add)
qparser/read_rem.C (mod, special input for stsDC)



[Q-CHEM] qcaux update
2007-12-04T16:33:00.000+08:00
basis update - racc-pV[DTQ]Z


plot spin density using plots section
2007-11-02T00:49:00.000+08:00
relevant routines

qparser/ParseQInput.C: invoke 'read_plots' function
qparser/read_plots.C: parsing the input in plots section
anlman/pltinp.C - get plot inputs from disk
anlman/dnsanl.F - invoke PltInp to gain plot inputs
(anlman/espevl.F)
(ccman/interface_qchem.C)
anlman/anlman.F - invoke DnsAnl to plot densities and MOs if IANLTY is set to 200 



knowledge to windows security
2007-08-07T01:57:00.002+08:00
TCP connections limit

Due to the warm attacks, M$ limit the number of TCP connections (to 10).
Apply patch from http://www.lvllord.de/?lang=en&url=downloads and reboot.

TCP/UDP Port 135, 139, 445

 http://www.grc.com/port_135.htm
 http://www.grc.com/port_139.htm
 http://www.grc.com/port_445.htm
 http://www.20cn.net/ns/hk/hacker/data/20020819051358.htm

Block through NAT

 Since those ports are supposed not to be exposed to the Internet,
 we block immediately them in incoming packets.

Stop NetBIOS over TCP/IP

 In "Internet Protocol (TCP/IP)" -> "Properties -> "Advanced" 
 -> "WINS" -> "Stop NetBIOS over TCP/IP", it will stop using port 139 (tcp).



snmp request timeout
2007-08-05T14:46:00.000+08:00
descriptions

 Return "Timeout: No Response from localhost"
 when running snmpwalk -c my_community -v 1 localhost system

solutions

 1. check access control in snmpd.conf
 2. check tcpwrap (/etc/hosts.allow) for allowing snmpd



[MAC] port and make
2007-08-03T12:20:00.000+08:00
port usage

update outdated portname
$ port sync
$ port -c -R upgrade outdated
$ port -f -c uninstall inactive

Determines which port owns a given file
$ port provides /path/to/file

Lists the installed ports that depend on the port portname
$ port dependents 


error when upgrade: Error: Error executing darwin_8: invalid command name "configure.compiler"

$ port -c -v selfupdate
$ port sync

configure: error: this program cannot be compiled without X

The top directory of X11 is located in /Developer/SDKs/MacOSX10.4u.sdk/usr/X11R6.
A example for making xdvik
$ ./configure --prefix=/usr/local/ --x-includes=/Developer/SDKs/MacOSX10.4u.sdk/usr/X11R6/include --x-libraries=/Developer/SDKs/MacOSX10.4u.sdk/usr/X11R6/lib --datadir=/opt/local/share --with-xdvi-x-toolkit=xaw




a good saying
2007-08-03T02:48:00.000+08:00
I apologize for writing a long letter because I didn't have time to write a short one.


memory insufficient using qchem with mpich
2007-08-03T02:15:00.000+08:00
solutions

P4_GLOBMEMSIZE=33554432
export P4_GLOBMEMSIZE



Command-line error: invalid GNU version number: 412
2007-07-31T10:48:00.000+08:00
description

 error message "Command-line error: invalid GNU version number: 412"
 when running icc v8.1 under the environment of gcc-4.1 and glibc-2.5 

sources

 That version is incompatible with gcc-4.1

solutions

 1. use icc v9.1 above instead
 2. try to install compatible library ex: libstdc++5 etc.



select() to /dev/rtc to wait for clock tick timed out
2007-07-30T10:10:00.000+08:00
description

 error message "select() to /dev/rtc to wait for clock tick timed out" when using hwclock 

solutions

 1. pass a parameter "--directisa" to hwclock
 2. pick up one module among "rtc", "genrtc" and "rtc-dev"



Quick guide to install Gentoo
2007-07-19T20:21:00.000+08:00
quick installation

booting Live CD
set up network
partition disk (eg. /dev/sda)
/dev/sda1  /boot      100MB
/dev/sda2  swap       2.5*MEM
/dev/sda3  /          10GB
/dev/sda5  /scratch   

prepare installation directory
$ mount /dev/sda3 /mnt/gentoo
$ mkdir /mnt/gentoo/boot
$ mount boot /mnt/gentoo/boot
check date 
change current directory to /mnt/gentoo 
download stage3 (links http://ftp.isu.edu.tw)
untar dowloaded stage file
configure compile options in etc/make.conf
CHOST="x86_64-pc-linux-gnu"
CFLAGS="-O2 -march=opteron -pipe"
CXXFLAGS="${CFLAGS}"
MAKEOPTS="-j3"

change root
$ cp -L /etc/resolve.conf /mnt/gentoo/etc/resolv.conf
$ mount -t proc none /mnt/gentoo/proc
$ mount -o bind /dev /mnt/gentoo/dev
$ chroot /mnt/gentoo /bin/bash
$ env-update
$ source /etc/profile
$ emerge --sync


install utilities for configuration

$ emerge vim ntp gentoolkit pciutils
$ cp -f /usr/share/zoneinfo/Asia/Taipei /etc/localtime
$ ntpdate stdtime.sinica.edu.tw; hwclock {--directisa} -w

check or change profiles (ls -FGg /etc/make.profile)
$ edit /etc/locale.gen ; run 'locale-gen'

update system (emerge system)
$ emerge gentoo-sources genkernel

configure kernel options

install utilities for administration

$ emerge syslog-ng vixie-cron logrotate logwatch xxfsprog tcsh nmap screen
$ emerge grub
.....
$ umount /mnt/gentoo/boot /mnt/gentoo/dev /mnt/gentoo/proc /mnt/gentoo


add daily services

10 5 * * * /usr/sbin/ntpdate stdtime.sinica.edu.tw && /sbin/hwclock -w

local mail delievery

install relative packages
$ USE="mailwrapper" emerge postfix procmail

use /etc/procmailrc below
DEFAULT=/var/spool/mail/$LOGNAME
SHELL=/bin/sh

modify those options in /etc/postfix/main.cf
myhostname = xxxx
mydomain = xxxx
inet_interfaces = localhost  # only allow local mail delievery
home_mailbox = /var/spool/mail/$LOGNAME
mailbox_command = /usr/bin/procmail

build aliases.db in /etc/mail/
$ newaliases

send a test mail with subject "test" 
$ /etc/init.d/postfix start
$ mail -s "test" your.mail.com
.
Ctrl+D

add postfix to startup

$ rc-update add postfix default


integration with your cluster

install relative packages
$ emerge ypbind nfs-utils

modify system database and switch file /etc/nsswitch.conf
#passwd:      compat
#shadow:      compat
#group:       compat

passwd:    db files nis
shadow:    db files nis
group:     db files nis

enable ypbind service and add it to startup
$ /etc/init.d/ypbind start
$ rc-update add ypbind default




IP listing at berrylab
2007-07-19T17:52:00.000+08:00
231  blueberry
232  salmonberry (firewall)
233  strawberry
234  raspberry
235  blackberry
236  boysenberry (cherri's printer #1)
237  sugarberry (cherri's printer #2)
238  (returned)
239  coralberry (Lexmark T520)
240  snowberry (Xerox C1618)
 
 30  (returned)
 31  sheepberry
 32  salmonberry (sander)
 33  gooseberry (CCD)
 34  twinberry

215  (returned)
216  (returned)
217  jrhwu8 (huckleberry) 
218  (returned)



Backup for configuration
2007-07-19T15:48:00.000+08:00
huckleberry

/root/nat.script
/root/route.script
/etc/syslog-ng/syslog-ng.conf



Reference for NAT & Routing
2007-07-17T21:20:00.000+08:00
 Guide to IP Layer Network Administration with Linux
 Policy Routing With Linux
 Building NAT
 netfilter
 Linux 2.4 Packet Filtering HOWTO
 Linux 2.4 NAT HOWTO
 Linux 2.4 Advanced Routing HOWTO
 Linux NET-2/3-HOWTO
 Linux Advanced Routing & Traffic Control HOWTO
 iptables & netfilter - How to get started
 Private IP & NAT
 Linux Firewall & NAT Host
 Linux iptables
 Routing


Network bridge (?)




Commands for administration
2007-07-17T20:46:00.000+08:00
system log analysis

$ logwatch --detail level{10,5,0} --service service-name --print
 
iptable rules list

$ iptables -L -v -t nat

MAC address request

$ ping ip-address
$ arp -n

show/manipulate routing, devices, policy routing and tunnels

please man ip

set an entry to ARP cache

$ /sbin/arp -s host_or_ip_address local_mac_address

set ARP proxy for a host

$ arp -Ds host_ip_address ethX pub

remove a host from proxy ARP

$ /sbin/arp -i ethX -d host_or_ip_address pub

ARP conversation captured with tcpdump

$ tcpdump -ennqti eth0 \( arp or icmp \)

add/remove a rule to routing table via iproute2

$ ip route add/remove x.x.x.x/n dev ethX

logging via program name (with syslog-ng)

 # comment for log
filter name_for_filter { program("program_name"); };
destination name_for_destl { file("/var/log/dir_to_log/file_to_log"); };
log { source(src); filter(name_for_filter); destination(name_for_dest); };

logging via matching content (with syslog-ng)

# comment for log
filter name_for_filter { match("reexp_to_match_content"); };
destination name_for_destl { file("/var/log/dir_to_log/file_to_log"); };
log { source(src); filter(name_for_filter); destination(name_for_dest); };

nfs usage

show NFS server export list
$ showmount -e nfshost

show all clients and mounted directories
$ showmount -a nfshos

iptables and NFS - a solution for NFS server under firewall
$ NFSTCP=`rpcinfo -p | grep -v program| awk '{ print $3 " " $4 }' | sort | uniq |\
grep tcp | awk '{print $2}' | xargs| sed 's/ /,/g'`
$ NFSUDP=`rpcinfo -p | grep -v program| awk '{ print $3 " " $4 }' | sort | uniq |\
grep udp | awk '{print $2}' | xargs| sed 's/ /,/g'`
$ iptables -N NFS
$ iptables -N PESC
$ iptables -A INPUT -p tcp -m multiport --dport $NFSTCP -j NFS
$ iptables -A INPUT -p udp -m multiport --dport $NFSUDP -j NFS
$ iptables -A NFS -j PESC
$ iptables -A NFS -j DROP
$ iptables -A PESC -s 10.0.0.0/24 -j ACCEPT
$ iptables -A PESC -s 10.2.0.0/24 -j ACCEPT


rsync usage

sync via rsync daemon (need to start rsynd service)
$ rsync -av host:/src /dest
$ rsync -av host::module/src /dest
$ rsync -av authuser@host::module_for_authuser/src /dest

sync through ssh tunnel
$ rsync -av -e "ssh -l sshuser" host:/src /dest
$ rsync -av -e "ssh -l sshuser" authuser@host::module_for_authuser/src /dest


mrtg usage
 
create the index page
$ indexmaker --output=path_to_your_index path_to_config




optimize Q-CHEM by INTEL
2006-12-20T02:11:00.000+08:00
Q-CHEM 的 makefile 相當混亂,
特別是 for intel 的, linker option 居然設在 optimization,
還有一些從 PGI 時期留下來的選項, 早該移除了, 避免混亂.

目前有幾個計畫:
一是提升 optimization 的 level (machine specific) 還有搞清楚 non-optimization 需不需要設定.
二是 static link to ALL library. 因為 glibc 跟 gcc 變化太快了, 還是編死好了.
三是 平行版本的最佳化.

update

make FFTW 這個 -assume nounderscore 別忘了


poster to TCD conference
2006-12-10T11:57:00.001+08:00



Fast Inverted Square - 1/sqrt(x)
2006-12-04T16:38:00.000+08:00
How fast is it ?float InvSqrt (float x) {
  float xhalf = 0.5f*x;
  int i = *(int*)&x;
  i = 0x5f3759df - (i>>1);
  x = *(float*)&i;
  x = x*(1.5f - xhalf*x*x);
  return x;
}



chemical formula of different type of chlorophyll
2006-12-01T16:33:00.001+08:00

Chlorophyll a : C₅₅H₇₂MgN₄O₅ (137)
Bacteriochlorophyll a : C₅₅H₇₄MgN₄O₆ (140), T₁ - 8240 cm^-1 (triethylamine), - 8190 cm^-1 (pyridine/2-methylTHF), - 7580 cm^-1 (Rsp. molischianum LH2)
Bchl a without phytol chain : C₃₅H₃₆MgN₄O₆ (82)
Spheroidene (10) : C₄₁H₆₀O, T₁ - 7050 cm^-1 (14100 cm^-1/2), - 6920 cm^-1 (Rb. sphaeroides 2.4.1 LH2)
Carotene (11) : C₄₀H₅₆,  T₁ - 7400 cm^-1 (C₆D₆)
Lycopene (11) : C₄₀H₅₆, T₁ - 6870 cm^-1 (Rsp. molischianum LH2)
Phytol : C₂₀H₄₀O



mpich with icc 8.1
2006-11-19T05:58:00.000+08:00
from beowulf.org: http://www.beowulf.org/archive/2004-December/011486.html

Oops - sorry, I just showed my complete ignorance of the profiling
interface.

The configure option --disable-weak-symbols will give you separate
libpmpich.a and libmpich.a libraries, containing respectively the
"PMPI_xxx" and "MPI_xxx" versions of the code.  The "PMPI_xxx" versions
are the "real" versions.  The "MPI_xxx" versions allow implementation of
routines which intercept a given call, say to do profiling, and which
also call the "PMPI_xxx"  versions.

If I'm interpreting the documentation correctly, with
"--disable-weak-symbols" if you want to profile some calls and not other
calls, you'd have to use a link command something like:
     cc ... -lprof -lpmpi -lmpi
where libprof.a contains profiling versions of selected routines, eg,
MPI_Send, which in turn call the base version, PMPI_Send, resolved in
libpmpi.a.  Other routines not defined in libprof.a would be resolved in
libmpi.   With weak symbols, on the other hand, it is sufficient to use
     cc ... -lprof -lmpi
and then an "MPI_xxx" symbol not defined in libprof.a will be resolved
by "PMPI_xxx" in libmpi.a

See, for example,
  http://www.netlib.org/utk/papers/mpi-book/node190.html

I just checked on two versions of mvapich on one of my machines, one
built with the Intel 7.1 compiler and the other with the 8.1 compiler.
The latter required "--disable-weak-symbols".  I verified that mpif77,
for example, explicitly linked with "-lpmpich -lmpich" on the 8.1
version, but only with "-lmpich" on the 7.1 version.

Don Holmgren
Fermilab



The rank function does not work in RPA ?
2006-11-14T13:36:00.000+08:00
The rankings I used in StS module is wrong. The cause is that the CisRnk writes the rankings back to disk only for SET_TYPE = 0. Hence, when reading the rankings from FILE_SET_RANK, I get TDA results. Q-Chem developers do not think this is a bug. The reason I guess is the rankings for TDA will be used in latter case.


Löwdin Population Analysis in StS module
2006-11-09T17:52:00.000+08:00
Reform the density matrix which is made by a non-orthogonal basis set to a new density matrix in terms of a symmetrically orthogonalized basis set. The diagonal elements of the new density matrix are commonly used for a Löwdin population analysis.

What I do is to extract the coefficient matrix in terms of an orthogonal basis set obtained by canonical orthogonalization from the canonical molecular orbitals. The SCF procedure in Q-Chem keeps the lastest Fock matrices (which is formed by a non-orthogonal basis set) in scratch, named as FILE_TEMP_FOCK. I gonna going to hack or learn from liblas/fock2mo.F which makes a coefficients matrix in terms of a non-orthogonal basis set.

Damn it !! It's not so complicated as I think. Don't worry about the linear dependence problem due to multiplying with the root-squared eigenvalue of the overlap matrix, not dividing it.

The one-particle density matrix in discrete basis can be presented as sum of


Abstract to 11/30 Seminar
2006-11-03T00:58:00.000+08:00
Non-photochemical quenching - is the molecular mechanism illuminated by the high resolution crystal structures of light-harvesting complex II ?


The photosynthetic systems in higher plant efficiently utilizes low intensity of sunlight in shade and avoids oxidative damage to the photosynthetic apparatus under excess light condition. The latter is known as non-photochemical quenching (NPQ) which can be measured in vivo as a reduction in the yield of chlorophyll fluorescence. This quenching is a complex process over a range of different time scales. One fast component (qE) of NPQ has been associated with the lowering of the pH in the thylakoid lumen side, induction of the xanthophyll cycle, the presence of the PsbS protein and conformation change of light-harvesting complex II (LHCII) [1-5]. However, the molecular mechanism for NPQ is still not clear. Recent high-resolution crystals of LHCII [6-7] have been found in the quenched state and might provide molecule-based solution for NPQ. In my presentation, I am going to report the work by Pascal et al. (see the attachment). Their spectra data showed the evidence of conformation change in quenched LHCII and two possible quenching sites are addressed. Furthermore, my different point view to this paper and the demand of theoretical study will be given in this presentation.


Horton, P. et al. (1996) Regulation of light-harvesting in green plants. Annu. Rev. Plant Physiol. 47, 665-684
Horton, P. et al. (2000) Allosteric regulation of the light-harvesting system of photosysmte II. Phil. Trans. R. Soc. Lond. B 355, 1361-1370
Niyogi K. K. et al. (2001) Non-photochemical quenching. A response to excess light energy. Plant Physiology 125, 1558-1566
Li, X. P. et al. (2000) A pigment-binding protein essential for regulation of photosynthetic light-harvesting. Nature 403, 391-395
Demmig-Adams, B. (1990) Carotenoids and photoprotection: a role for the xanthophyll zeaxanthin. Biochim. Biophys. Acta 1020, 1-24
Liu, Z. et al. (2004) Crystal structure of spinach major light-harvesting complex at 2.72A resolution. Nature 428, 287-292
Standfuss, J. et al. (2005) Mechanisms of photoprotection and nonphotochemical quenching in pea light-harvesting complex at 2.5A resolution. EMBO J. 24, 919-928






 The overall time cost for releasing oxygen and protons is around 20ms.
 PQ pool release 2 protons around 5ms.

 fluorescence lifetime in LHCII, PSII, and vivo
LHCII-trimer: 4ns
LHCII-oligomer: 0.2-1.5ns (Moya, I, BIOCHEM40; Mullineaux, CW, BBA1141)
LHCII-oligomer: 0.65ns (by FLIM)
LHCII-crystal (plane?): 0.89ns (by FLIM)

 the way to induce conformation changes of light-harvesting complexes (LHCII), which result in wanted highly energy dissipating state.
literal aggregation in the membrane plane
perpendicularly stacking to the membrane plane
other non-LHCII proteins presented
lipid-environment presented


outline
photochemistry in photosynthetic apparatus
harvesting sunlight safely (materials from Nature paper by Demmig-Adams, Babara)
chlorophyll fluorescence
non-photochemical quenching (introduction to three kinds of NPQ and focus on qE which is dependent on the gradient of pH and the xanthophyll  cycle)
slow component of qE
fast component of qE
structure related to fast one (chlorophyll self-quenching ?)



Abstract to TCD conference
2006-10-30T12:55:00.000+08:00
Triplet-triplet energy transfer in light-harvesting complex II of purple bacteria: ab-initio calculation for the energy transfer matrix element by fragment spin difference method


Photoprotective function prevents the photosynthetic apparatus from damages by highly reactive singlet oxygen. Little is known on the theoretical basis of the photoprotection processes involving triplet states of the chromophores in photosynthesis. Theoretical estimate of the triplet-triplet energy transfer matrix element provides an important clue to the understanding of photoprotective function. Recently, we have developed the fragment spin difference (FSD) method which allow us to estimate the electronic coupling for many systems. In this presentation, we first compare the FSD results with our previous data [1] derived from other methods. We then apply the FSD method to the calculation of the electronic coupling between pigments in light-harvesting complex II of purple bacteria. The ab-initio coupling values are larger than previous semi-empirical values by one order magnitude. We will discuss the implication of these new coupling values in their possible role of avoiding singlet oxygen formation.