User:Lindenb/Notebook/UMR915/20110615: Difference between revisions

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bin/hadoop fs -tail /user/lindenb/myfolder/Axiom_GW_Hu_SNP.r2.na31.annot.csv
bin/hadoop fs -tail /user/lindenb/myfolder/Axiom_GW_Hu_SNP.r2.na31.annot.csv
s.135270 // CRMP1 // 1400 // collapsin response mediator protein 1 /// NM_001099433 // downstream // 100570 // Hs.479066 // JAKMIP1 // 152789 // janus kinase and microtubule interacting protein 1","10.7510808767857 // D4S2925 // D4S2366 // --- // --- /// 11.4380209151363 // D4S2285 // D4S431 // UT5936 // AFM262VG9 /// 10.964419629995 // --- // D4S2366 // 58988 // ---","D4S1059 // upstream // 121041 /// D4S2509E // downstream // 104845","0.108333333 // 0.891666667 // Caucasian /// 0.055555556 // 0.944444444 // Han Chinese /// 0.011111111 // 0.988888889 // Japanese /// 0.041666667 // 0.958333333 // Yoruban","0.183333333 // Caucasian /// 0.066666667 // Han Chinese /// 0.022222222 // Japanese /// 0.083333333 // Yoruban","60.0 // Caucasian /// 45.0 // Han Chinese /// 45.0 // Japanese /// 60.0 // Yoruban","YES","same","1","0","T // Caucasian /// T // Han Chinese /// T // Japanese /// T // Yoruban","0.108333333 // Caucasian /// 0.055555556 // Han Chinese /// 0.011111111 // Japanese /// 0.041666667 // Yoruban","---"
s.135270 // CRMP1 // 1400 // collapsin response mediator protein 1 /// NM_001099433 // downstream // 100570 // Hs.479066 // JAKMIP1 // 152789 // janus kinase and microtubule interacting protein 1","10.7510808767857 // D4S2925 // D4S2366 // --- // --- /// 11.4380209151363 // D4S2285 // D4S431 // UT5936 // AFM262VG9 /// 10.964419629995 // --- // D4S2366 // 58988 // ---","D4S1059 // upstream // 121041 /// D4S2509E // downstream // 104845","0.108333333 // 0.891666667 // Caucasian /// 0.055555556 // 0.944444444 // Han Chinese /// 0.011111111 // 0.988888889 // Japanese /// 0.041666667 // 0.958333333 // Yoruban","0.183333333 // Caucasian /// 0.066666667 // Han Chinese /// 0.022222222 // Japanese /// 0.083333333 // Yoruban","60.0 // Caucasian /// 45.0 // Han Chinese /// 45.0 // Japanese /// 60.0 // Yoruban","YES","same","1","0","T // Caucasian /// T // Han Chinese /// T // Japanese /// T // Yoruban","0.108333333 // Caucasian /// 0.055555556 // Han Chinese /// 0.011111111 // Japanese /// 0.041666667 // Yoruban","---"
</pre>
<pre>#serveur1: scp  /CGH/data/users/cdina/DATAS/CEDRIC/Axiom2/resultat/AxiomGT1.calls.txt lindenb@serveur4:</pre>
<pre>bin/hadoop fs -copyFromLocal ~/AxiomGT1.calls.txt myfolder/
$ ls -lah ~/Axiom*
-rw-r--r-- 1 lindenb lindenb 111M jun 15 09:03 /home/lindenb/AxiomGT1.calls.txt
-rw-r--r-- 1 lindenb lindenb 766M jun 10 12:35 /home/lindenb/Axiom_GW_Hu_SNP.r2.na31.annot.csv
du -h ~/tmp/HADOOP | tail -1
884M /home/lindenb/tmp/HADOOP
</pre>
</pre>

Revision as of 00:06, 15 June 2011

20110614        Top        20110615       


hadoop

(started on User:Lindenb/Notebook/UMR915/20110610 }

trying to change /etc/hosts: https://twitter.com/#!/fredebibs/status/79170165312454656

then 

sudo /etc/rc.d/init.d/network restart

success ! 

[lindenb@srv-clc-04 hadoop-0.20.203.0]$  bin/hadoop namenode -format
11/06/15 08:32:13 INFO namenode.NameNode: STARTUP_MSG: 
/************************************************************
STARTUP_MSG: Starting NameNode
STARTUP_MSG:   host = srv-clc-04.u915.irt.univ-nantes.prive3/127.0.0.1
STARTUP_MSG:   args = [-format]
STARTUP_MSG:   version = 0.20.203.0
STARTUP_MSG:   build = http://svn.apache.org/repos/asf/hadoop/common/branches/branch-0.20-security-203 -r 1099333; compiled by 'oom' on Wed May  4 07:57:50 PDT 2011
************************************************************/
11/06/15 08:32:13 INFO util.GSet: VM type       = 64-bit
11/06/15 08:32:13 INFO util.GSet: 2% max memory = 19.1675 MB
11/06/15 08:32:13 INFO util.GSet: capacity      = 2^21 = 2097152 entries
11/06/15 08:32:13 INFO util.GSet: recommended=2097152, actual=2097152
11/06/15 08:32:13 INFO namenode.FSNamesystem: fsOwner=lindenb
11/06/15 08:32:13 INFO namenode.FSNamesystem: supergroup=supergroup
11/06/15 08:32:13 INFO namenode.FSNamesystem: isPermissionEnabled=true
11/06/15 08:32:13 INFO namenode.FSNamesystem: dfs.block.invalidate.limit=100
11/06/15 08:32:13 INFO namenode.FSNamesystem: isAccessTokenEnabled=false accessKeyUpdateInterval=0 min(s), accessTokenLifetime=0 min(s)
11/06/15 08:32:13 INFO namenode.NameNode: Caching file names occuring more than 10 times 
11/06/15 08:32:13 INFO common.Storage: Image file of size 113 saved in 0 seconds.
11/06/15 08:32:14 INFO common.Storage: Storage directory /home/lindenb/tmp/HADOOP/dfs/name has been successfully formatted.
11/06/15 08:32:14 INFO namenode.NameNode: SHUTDOWN_MSG: 
/************************************************************
SHUTDOWN_MSG: Shutting down NameNode at srv-clc-04.u915.irt.univ-nantes.prive3/127.0.0.1

start the server

[lindenb@srv-clc-04 hadoop-0.20.203.0]$ ./bin/start-all.sh 
namenode running as process 1151. Stop it first.
localhost: starting datanode, logging to /home/lindenb/package/hadoop-0.20.203.0/bin/../logs/hadoop-lindenb-datanode-srv-clc-04.u915.irt.univ-nantes.prive3.out
localhost: secondarynamenode running as process 1490. Stop it first.
jobtracker running as process 1588. Stop it first.
localhost: starting tasktracker, logging to /home/lindenb/package/hadoop-0.20.203.0/bin/../logs/hadoop-lindenb-tasktracker-srv-clc-04.u915.irt.univ-nantes.prive3.out

copy cDINA data

bin/hadoop fs  -mkdir myfolder
fs -copyFromLocal ~/Axiom_GW_Hu_SNP.r2.na31.annot.csv myfolder/


bin/hadoop fs -tail /user/lindenb/myfolder/Axiom_GW_Hu_SNP.r2.na31.annot.csv
s.135270 // CRMP1 // 1400 // collapsin response mediator protein 1 /// NM_001099433 // downstream // 100570 // Hs.479066 // JAKMIP1 // 152789 // janus kinase and microtubule interacting protein 1","10.7510808767857 // D4S2925 // D4S2366 // --- // --- /// 11.4380209151363 // D4S2285 // D4S431 // UT5936 // AFM262VG9 /// 10.964419629995 // --- // D4S2366 // 58988 // ---","D4S1059 // upstream // 121041 /// D4S2509E // downstream // 104845","0.108333333 // 0.891666667 // Caucasian /// 0.055555556 // 0.944444444 // Han Chinese /// 0.011111111 // 0.988888889 // Japanese /// 0.041666667 // 0.958333333 // Yoruban","0.183333333 // Caucasian /// 0.066666667 // Han Chinese /// 0.022222222 // Japanese /// 0.083333333 // Yoruban","60.0 // Caucasian /// 45.0 // Han Chinese /// 45.0 // Japanese /// 60.0 // Yoruban","YES","same","1","0","T // Caucasian /// T // Han Chinese /// T // Japanese /// T // Yoruban","0.108333333 // Caucasian /// 0.055555556 // Han Chinese /// 0.011111111 // Japanese /// 0.041666667 // Yoruban","---"



#serveur1: scp  /CGH/data/users/cdina/DATAS/CEDRIC/Axiom2/resultat/AxiomGT1.calls.txt lindenb@serveur4:
bin/hadoop fs -copyFromLocal ~/AxiomGT1.calls.txt myfolder/


$ ls -lah ~/Axiom*
-rw-r--r-- 1 lindenb lindenb 111M jun 15 09:03 /home/lindenb/AxiomGT1.calls.txt
-rw-r--r-- 1 lindenb lindenb 766M jun 10 12:35 /home/lindenb/Axiom_GW_Hu_SNP.r2.na31.annot.csv

du -h ~/tmp/HADOOP | tail -1
884M	/home/lindenb/tmp/HADOOP
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