wiki:jazz/11-05-04

Version 14 (modified by jazz, 14 years ago) (diff)

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2011-05-04

Bioinformatics

  • 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
    
  • <參考 1> 讓程序飛 之 性能工具: gprof & gprof2dot
  • <參考 2> 讓程序飛 之 內存工具: valgrind –tool=memcheck
  • <參考 3> 讓程序飛 之 內存工具: valgrind –tool=massif & massif-visualizer
  • <參考 4> 讓程序飛 之 性能工具: valgrind –tool=callgrind & kcachegrind
  • 使用 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 valgrindMassif 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.參考來源
    ~/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
    
    --------------------------------------------------------------------------------
    Command:            ./velvetg output/ -exp_cov 3 -min_contig_lgth 100
    Massif arguments:   (none)
    ms_print arguments: massif.out.10561
    --------------------------------------------------------------------------------
    
    
        MB
    2.277^                       #                                                
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         |            :::@  :::::#:::::::@:::::::::@:::@::::::::::::::::::::::::::
       0 +----------------------------------------------------------------------->Mi
         0                                                                   125.5
    
    Number of snapshots: 73
     Detailed snapshots: [2, 5, 6, 14, 16, 22, 30 (peak), 42, 58, 68]
    
    --------------------------------------------------------------------------------
      n        time(i)         total(B)   useful-heap(B) extra-heap(B)    stacks(B)
    --------------------------------------------------------------------------------
      0              0                0                0             0            0
      1        896,153            8,888            8,478           410            0
      2      1,973,156           11,872           11,099           773            0
    
  • <註> 目前有兩個工具可以把 ms_print 的 ASCII 圖變成更好看,一個是 KDE 的 massif-visualizer,另一個是 GNOME 的 MassifG(有 Ubuntu 套件在 PPA)
  • 使用 valgrindcallgrind 工具來進行動態連結分析
    ~/velvet_1.1.03$ valgrind --tool=callgrind ./velveth output 17 -fasta -short data/test_long.fa
    ~/velvet_1.1.03$ valgrind --tool=callgrind ./velvetg output/ -exp_cov 3 -min_contig_lgth 100
    ~/velvet_1.1.03$ callgrind_annotate callgrind.out.12046 > velveth_callgrind.log
    ~/velvet_1.1.03$ callgrind_annotate callgrind.out.12074 > velvetg_callgrind.log
    
  • 使用 gprof 進行 profile 分析
    ~/velvet_1.1.03$ cat Makefile | sed "s#^CFLAG.*#CFLAGS = -Wall -pg#" > Makefile.new
    ~/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
    ~/velvet_1.1.03$ gprof velveth > velveth.log
    ~/velvet_1.1.03$ gprof velvetg > velvetg.log
    
  • 使用 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
    

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