= 2011-05-04 =

== Bioinformatics ==

 * [wiki:biocluster/Velvet Velvet 安裝紀錄(2009-11-11)]
 * 測試 Velvet 1.1.03 (支援 OpenMP）
 * 系統：Debian Squeeze
{{{
~$ sudo apt-get update; sudo apt-get upgrade; sudo apt-get dist-upgrade
~$ sudo apt-get install build-essential 
~$ wget http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.1.03.tgz
~$ tar zxvf velvet_1.1.03.tgz
~$ cd velvet_1.1.03
~/velvet_1.1.03$ make
~/velvet_1.1.03$ ./velveth output 17 -fasta -short data/test_long.fa
~/velvet_1.1.03$ ./velvetg output/ -exp_cov 3 -min_contig_lgth 100
}}}
 * 使用 [http://packages.debian.org/valgrind valgrind] 來進行記憶體分析 - (1) Memory Leak 分析
{{{
~/velvet_1.1.03$ sudo apt-get install valgrind
~/velvet_1.1.03$ valgrind -v --leak-check=full --show-reachable=yes --read-var-info=yes ./velveth output 17 -fasta -short data/test_long.fa 2> velveth.log
~/velvet_1.1.03$ valgrind -v --leak-check=full --show-reachable=yes --read-var-info=yes ./velvetg output/ -exp_cov 3 -min_contig_lgth 100 2> velvetg.log
}}}
 * 使用 [http://packages.debian.org/valgrind valgrind] 的 [http://valgrind.org/docs/manual/ms-manual.html Massif] 工具來進行記憶體分析 - (2) Memory Usage 分析
 * Valgrind's skin Massif ('valgrind --tool=massif application') traces memory usage of the application.[http://ktown.kde.org/~seli/memory/analysis.html 參考#1]
{{{
~/velvet_1.1.03$ valgrind --tool=massif ./velveth output 17 -fasta -short data/test_long.fa
~/velvet_1.1.03$ ms_print massif.out.10571
~/velvet_1.1.03$ valgrind --tool=massif ./velvetg output/ -exp_cov 3 -min_contig_lgth 100
~/velvet_1.1.03$ ms_print massif.out.10561
}}}
{{{
--------------------------------------------------------------------------------
Command:            ./velveth output 17 -fasta -short data/test_long.fa
Massif arguments:   (none)
ms_print arguments: massif.out.10571
--------------------------------------------------------------------------------


    MB
66.60^                                                             @@@@@@@@@@#
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   0 +----------------------------------------------------------------------->Mi
     0                                                                   120.8

Number of snapshots: 71
 Detailed snapshots: [2, 4, 57, 67, 68 (peak)]

--------------------------------------------------------------------------------
  n        time(i)         total(B)   useful-heap(B) extra-heap(B)    stacks(B)
--------------------------------------------------------------------------------
  0              0                0                0             0            0
  1        201,656           34,224           34,099           125            0
  2     14,964,257           33,864           33,747           117            0
}}}
 * 使用 gprof 進行 profile 分析
{{{
~/velvet_1.1.03$ cat Makefile | sed "s#^CFLAG.*#CFLAGS = -Wall -pg#" > 
~/velvet_1.1.03$ mv Makefile.new Makefile
~/velvet_1.1.03$ make
~/velvet_1.1.03$ ./velveth output 17 -fasta -short data/test_long.fa
~/velvet_1.1.03$ du -sh gmon.out 
56K	gmon.out
~/velvet_1.1.03$ ./velvetg output/ -exp_cov 3 -min_contig_lgth 100
~/velvet_1.1.03$ du -sh gmon.out 
152K	gmon.out
}}}
 * 使用 [http://code.google.com/p/jrfonseca/wiki/Gprof2Dot gprof2dot] 把 gprof log 轉成 graphviz 的 dot 格式，就可以畫出圖形了。
{{{
~/velvet_1.1.03$ sudo apt-get install graphviz python
~/velvet_1.1.03$ wget http://gprof2dot.jrfonseca.googlecode.com/hg/gprof2dot.py
~/velvet_1.1.03$ chmod a+x gprof2dot.py
~/velvet_1.1.03$ gprof velveth | ./gprof2dot.py | dot -Tpng -o velveth.png
~/velvet_1.1.03$ gprof velvetg | ./gprof2dot.py | dot -Tpng -o velvetg.png
}}}
 * [[Image(jazz/11-05-04:velveth.png)]]
 * [[Image(jazz/11-05-04:velvetg.png)]]