Changes between Initial Version and Version 1 of III121201/Lab10

Timestamp:

Dec 1, 2012, 11:16:28 AM (11 years ago)

Author:

jazz

Comment:

--

III121201/Lab10

@@ +1 @@
+[[PageOutline]]
+
+◢ <[wiki:III121201/Lab9 實作九]> | <[wiki:III121201 回課程大綱]> ▲ | <[wiki:III121201/Lab11 實作十一]> ◣
+
+= 實作十 Lab10 =
+
+{{{
+#!html
+<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>
+}}}
+
+== 準備輸入資料集 Input Dataset ==
+
+ * 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）
+{{{
+~$ cp /usr/share/doc/velvet-example/examples/data/test_long.fa.gz .
+~$ gunzip test_long.fa.gz
+~$ for ((i=1;i<100;i++)); do hadoop fs -put test_long.fa sample-$i.fa; done
+~$ for ((i=1;i<20;i++)); do echo /user/$(whoami)/sample-$i.fa; done > sample-01.txt
+~$ for ((i=20;i<40;i++)); do echo /user/$(whoami)/sample-$i.fa; done > sample-02.txt
+~$ for ((i=40;i<60;i++)); do echo /user/$(whoami)/sample-$i.fa; done > sample-03.txt
+~$ for ((i=60;i<80;i++)); do echo /user/$(whoami)/sample-$i.fa; done > sample-04.txt
+~$ for ((i=80;i<100;i++)); do echo /user/$(whoami)/sample-$i.fa; done > sample-05.txt
+~$ hadoop fs -mkdir lab10_input
+~$ hadoop fs -put sample-0* lab10_input
+}}}
+ * 檢查輸入檔案
+{{{
+~$ hadoop fs -ls
+~$ hadoop fs -ls lab10_input
+}}}
+
+== 觀察 Hadoop Streaming 執行身份與工作目錄 ==
+
+ * 撰寫 testmapper.sh
+{{{
+#!sh
+#!/bin/bash
+
+id="h998"
+mkdir -p /tmp/$id
+host=`hostname`
+pwd=`pwd`
+uid=`whoami`
+
+while read line; do 
+  input=$line
+  filename=`basename $input`
+  echo "$uid@$host:$pwd> hadoop fs -get $input /tmp/$id/$filename"
+  echo "$uid@$host:$pwd> velveth output-$filename 17 -fasta -short /tmp/$id/$filename"
+  echo "$uid@$host:$pwd> hadoop fs -put output-$filename ."
+done
+rm -rf /tmp/$id
+}}}
+ * 接著，讓我們在本地端先驗證一下 testmapper.sh 的運作
+{{{
+~$ head -n 2 sample-01.txt > sample-00.txt
+~$ cat > testmapper.sh << EOF
+#!/bin/bash
+
+id="`whoami`"
+mkdir -p /tmp/\$id
+host=\`hostname\`
+pwd=\`pwd\`
+uid=\`whoami\`
+
+while read line; do 
+  input=\$line
+  filename=\`basename \$input\`
+  echo "\$uid@\$host:\$pwd> hadoop fs -get \$input /tmp/\$id/\$filename"
+  echo "\$uid@\$host:\$pwd> velveth output-\$filename 17 -fasta -short /tmp/\$id/\$filename"
+  echo "\$uid@\$host:\$pwd> hadoop fs -put output-\$filename ."
+done
+rm -rf /tmp/\$id
+EOF
+~$ chmod a+x testmapper.sh
+~$ cat sample-00.txt | ./testmapper.sh 
+h998@hadoop:/home/h998> hadoop fs -get /user/h998/sample-1.fa /tmp/h998/sample-1.fa
+h998@hadoop:/home/h998> velveth output-sample-1.fa 17 -fasta -short /tmp/h998/sample-1.fa
+h998@hadoop:/home/h998> hadoop fs -put output-sample-1.fa .
+h998@hadoop:/home/h998> hadoop fs -get /user/h998/sample-2.fa /tmp/h998/sample-2.fa
+}}}
+ * 讓我們用 Hadoop Streaming 的方式來執行 testmapper.sh
+{{{
+~$ hadoop jar hadoop-streaming.jar -input lab10_input -output lab10_out1 -mapper testmapper.sh -file testmapper.sh 
+}}}
+ * 觀察 lab10_out1 的結果，看與本機執行有何不同呢？
+{{{
+~$ hadoop fs -cat /user/$(whoami)/lab10_out1/part-00000 | head
+hadoop@hadoop104:/var/lib/hadoop/cache/hadoop/mapred/local/taskTracker/jobcache/job_201106041247_1820/attempt_201106041247_1820_m_000002_0/work> hadoop fs -get /user/h998/sample-60.fa /tmp/h998/sample-60.fa  
+hadoop@hadoop104:/var/lib/hadoop/cache/hadoop/mapred/local/taskTracker/jobcache/job_201106041247_1820/attempt_201106041247_1820_m_000002_0/work> hadoop fs -get /user/h998/sample-61.fa /tmp/h998/sample-61.fa  
+hadoop@hadoop104:/var/lib/hadoop/cache/hadoop/mapred/local/taskTracker/jobcache/job_201106041247_1820/attempt_201106041247_1820_m_000002_0/work> hadoop fs -get /user/h998/sample-62.fa /tmp/h998/sample-62.fa  
+}}}
+
+== 實作透過 Hadoop Streaming 執行 99 組 velvet 運算 ==
+
+ * 撰寫 mapper.sh
+{{{
+#!sh
+#!/bin/bash
+
+id="h998"
+mkdir -p /tmp/$id
+host=`hostname`
+pwd=`pwd`
+uid=`whoami`
+
+while read line; do 
+  input=$line
+  filename=`basename $input`
+  echo "$uid@$host> hadoop fs -get $input /tmp/$id/$filename"
+  hadoop fs -get $input /tmp/$id/$filename
+  echo "$uid@$host> velveth output-$filename 17 -fasta -short /tmp/$id/$filename"
+  velveth output-$filename 17 -fasta -short /tmp/$id/$filename
+  echo "$uid@$host> hadoop fs -put output-$filename /user/$id/."
+  hadoop fs -put output-$filename /user/$id/.
+  hadoop fs -chown $id /user/$id/output-$filename
+done
+rm -rf /tmp/$id
+}}}
+ * 於本機測試 mapper.sh
+{{{
+~$ cat > mapper.sh << EOF
+#!/bin/bash
+
+id="`whoami`"
+mkdir -p /tmp/\$id
+host=\`hostname\`
+pwd=\`pwd\`
+uid=\`whoami\`
+
+while read line; do 
+  input=\$line
+  filename=\`basename \$input\`
+  echo "\$uid@\$host> hadoop fs -get \$input /tmp/\$id/\$filename"
+  hadoop fs -get \$input /tmp/\$id/\$filename
+  echo "\$uid@\$host> velveth output-\$filename 17 -fasta -short /tmp/\$id/\$filename"
+  velveth output-\$filename 17 -fasta -short /tmp/\$id/\$filename
+  echo "\$uid@\$host> hadoop fs -put output-\$filename /user/\$id/."
+  hadoop fs -put output-\$filename /user/\$id/.
+  hadoop fs -chown \$id /user/\$id/output-\$filename
+done
+rm -rf /tmp/\$id
+EOF
+~$ chmod a+x mapper.sh
+~$ cat sample-00.txt | ./mapper.sh 
+~$ hadoop fs -rmr output-*
+~$ rm -rf output-sample-*
+}}}
+ * 接著用 hadoop streaming 來執行
+{{{
+~$ hadoop jar hadoop-streaming.jar -input lab10_input -output lab10_out2 -mapper mapper.sh -file mapper.sh
+}}}