Changes between Initial Version and Version 1 of FDC110829/Lab6


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Timestamp:
Aug 29, 2011, 11:12:49 PM (13 years ago)
Author:
jazz
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  • FDC110829/Lab6

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     1[[PageOutline]]
     2
     3◢ <[wiki:FDC110829/Lab5 實作五]> | <[wiki:FDC110829 回課程大綱]> ▲ | ◣
     4
     5= 實作六 Lab6 =
     6
     7{{{
     8#!html
     9<div style="text-align: center;"><big style="font-weight: bold;"><big>HDFS、MapReduce 與 Hadoop Streaming 觀念驗證<br/>Running Hadoop Streaming with HDFS and MapReduce</big></big></div>
     10}}}
     11
     12== 準備輸入資料集 Input Dataset ==
     13
     14 * 首先準備輸入,包含兩部份:(1) 供 Velvet 計算的 *.fa 檔案,這裡為了方便示範起見,採用 test_long.fa 當範本,並複製 99 份不同檔名,當輸入 (2) 供 Mapper 運算的輸入檔案(內含 HDFS 的檔名路徑)
     15{{{
     16~$ cp /usr/share/doc/velvet-example/examples/data/test_long.fa.gz .
     17~$ gunzip test_long.fa.gz
     18~$ for ((i=1;i<100;i++)); do hadoop fs -put test_long.fa sample-$i.fa; done
     19~$ for ((i=1;i<20;i++)); do echo /user/$(whoami)/sample-$i.fa; done > sample-01.txt
     20~$ for ((i=20;i<40;i++)); do echo /user/$(whoami)/sample-$i.fa; done > sample-02.txt
     21~$ for ((i=40;i<60;i++)); do echo /user/$(whoami)/sample-$i.fa; done > sample-03.txt
     22~$ for ((i=60;i<80;i++)); do echo /user/$(whoami)/sample-$i.fa; done > sample-04.txt
     23~$ for ((i=80;i<100;i++)); do echo /user/$(whoami)/sample-$i.fa; done > sample-05.txt
     24~$ hadoop fs -mkdir lab9_input
     25~$ hadoop fs -put sample-0* lab9_input
     26}}}
     27 * 檢查輸入檔案
     28{{{
     29~$ hadoop fs -ls
     30~$ hadoop fs -ls lab9_input
     31}}}
     32
     33== 觀察 Hadoop Streaming 執行身份與工作目錄 ==
     34
     35 * 撰寫 testmapper.sh
     36{{{
     37#!sh
     38#!/bin/bash
     39
     40id="h998"
     41mkdir -p /tmp/$id
     42host=`hostname`
     43pwd=`pwd`
     44uid=`whoami`
     45
     46while read line; do
     47  input=$line
     48  filename=`basename $input`
     49  echo "$uid@$host:$pwd> hadoop fs -get $input /tmp/$id/$filename"
     50  echo "$uid@$host:$pwd> velveth output-$filename 17 -fasta -short /tmp/$id/$filename"
     51  echo "$uid@$host:$pwd> hadoop fs -put output-$filename ."
     52done
     53rm -rf /tmp/$id
     54}}}
     55 * 接著,讓我們在本地端先驗證一下 testmapper.sh 的運作
     56{{{
     57~$ head -n 2 sample-01.txt > sample-00.txt
     58~$ cat > testmapper.sh << EOF
     59#!/bin/bash
     60
     61id="`whoami`"
     62mkdir -p /tmp/\$id
     63host=\`hostname\`
     64pwd=\`pwd\`
     65uid=\`whoami\`
     66
     67while read line; do
     68  input=\$line
     69  filename=\`basename \$input\`
     70  echo "\$uid@\$host:\$pwd> hadoop fs -get \$input /tmp/\$id/\$filename"
     71  echo "\$uid@\$host:\$pwd> velveth output-\$filename 17 -fasta -short /tmp/\$id/\$filename"
     72  echo "\$uid@\$host:\$pwd> hadoop fs -put output-\$filename ."
     73done
     74rm -rf /tmp/\$id
     75EOF
     76~$ chmod a+x testmapper.sh
     77~$ cat sample-00.txt | ./testmapper.sh
     78h998@hadoop:/home/h998> hadoop fs -get /user/h998/sample-1.fa /tmp/h998/sample-1.fa
     79h998@hadoop:/home/h998> velveth output-sample-1.fa 17 -fasta -short /tmp/h998/sample-1.fa
     80h998@hadoop:/home/h998> hadoop fs -put output-sample-1.fa .
     81h998@hadoop:/home/h998> hadoop fs -get /user/h998/sample-2.fa /tmp/h998/sample-2.fa
     82}}}
     83 * 讓我們用 Hadoop Streaming 的方式來執行 testmapper.sh
     84{{{
     85~$ hadoop jar hadoop-streaming.jar -input lab9_input -output lab9_out1 -mapper testmapper.sh -file testmapper.sh
     86}}}
     87 * 觀察 lab9_out1 的結果,看與本機執行有何不同呢?
     88{{{
     89~$ hadoop fs -cat /user/$(whoami)/lab9_out1/part-00000 | head
     90hadoop@hadoop104:/var/lib/hadoop/cache/hadoop/mapred/local/taskTracker/jobcache/job_201106041247_1820/attempt_201106041247_1820_m_000002_0/work> hadoop fs -get /user/h998/sample-60.fa /tmp/h998/sample-60.fa 
     91hadoop@hadoop104:/var/lib/hadoop/cache/hadoop/mapred/local/taskTracker/jobcache/job_201106041247_1820/attempt_201106041247_1820_m_000002_0/work> hadoop fs -get /user/h998/sample-61.fa /tmp/h998/sample-61.fa 
     92hadoop@hadoop104:/var/lib/hadoop/cache/hadoop/mapred/local/taskTracker/jobcache/job_201106041247_1820/attempt_201106041247_1820_m_000002_0/work> hadoop fs -get /user/h998/sample-62.fa /tmp/h998/sample-62.fa 
     93}}}
     94
     95== 實作透過 Hadoop Streaming 執行 99 組 velvet 運算 ==
     96
     97 * 撰寫 mapper.sh
     98{{{
     99#!sh
     100#!/bin/bash
     101
     102id="h998"
     103mkdir -p /tmp/$id
     104host=`hostname`
     105pwd=`pwd`
     106uid=`whoami`
     107
     108while read line; do
     109  input=$line
     110  filename=`basename $input`
     111  echo "$uid@$host> hadoop fs -get $input /tmp/$id/$filename"
     112  hadoop fs -get $input /tmp/$id/$filename
     113  echo "$uid@$host> velveth output-$filename 17 -fasta -short /tmp/$id/$filename"
     114  velveth output-$filename 17 -fasta -short /tmp/$id/$filename
     115  echo "$uid@$host> hadoop fs -put output-$filename /user/$id/."
     116  hadoop fs -put output-$filename /user/$id/.
     117  hadoop fs -chown $id /user/$id/output-$filename
     118done
     119rm -rf /tmp/$id
     120}}}
     121 * 於本機測試 mapper.sh
     122{{{
     123~$ cat > mapper.sh << EOF
     124#!/bin/bash
     125
     126id="`whoami`"
     127mkdir -p /tmp/\$id
     128host=\`hostname\`
     129pwd=\`pwd\`
     130uid=\`whoami\`
     131
     132while read line; do
     133  input=\$line
     134  filename=\`basename \$input\`
     135  echo "\$uid@\$host> hadoop fs -get \$input /tmp/\$id/\$filename"
     136  hadoop fs -get \$input /tmp/\$id/\$filename
     137  echo "\$uid@\$host> velveth output-\$filename 17 -fasta -short /tmp/\$id/\$filename"
     138  velveth output-\$filename 17 -fasta -short /tmp/\$id/\$filename
     139  echo "\$uid@\$host> hadoop fs -put output-\$filename /user/\$id/."
     140  hadoop fs -put output-\$filename /user/\$id/.
     141  hadoop fs -chown \$id /user/\$id/output-\$filename
     142done
     143rm -rf /tmp/\$id
     144EOF
     145~$ chmod a+x mapper.sh
     146~$ cat sample-00.txt | ./mapper.sh
     147~$ hadoop fs -rmr output-*
     148~$ rm -rf output-sample-*
     149}}}
     150 * 接著用 hadoop streaming 來執行
     151{{{
     152~$ hadoop jar hadoop-streaming.jar -input lab9_input -output lab9_out2 -mapper mapper.sh -file mapper.sh
     153}}}
     154