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From Andre Kelpe <ake...@concurrentinc.com>
Subject Re: Running Contrail on hadoop
Date Tue, 03 Sep 2013 15:36:22 GMT
I don't know anything about contrail, I believe it is a better idea,
to ask on their mailing list for help:
http://sourceforge.net/p/contrail-bio/mailman/?source=navbar

- André

On Tue, Sep 3, 2013 at 5:27 PM, Felipe Gutierrez
<felipe.o.gutierrez@gmail.com> wrote:
> I configure the languages but the error persists
>
> I wrote:
> $ export LANG=en_EN.UTF-8
> $ export LANGUAGE=en_US:en
> $ locale
> locale: Cannot set LC_CTYPE to default locale: No such file or directory
> locale: Cannot set LC_MESSAGES to default locale: No such file or directory
> locale: Cannot set LC_ALL to default locale: No such file or directory
> LANG=en_EN.UTF-8
> LANGUAGE=en_US:en
> LC_CTYPE="en_EN.UTF-8"
> LC_NUMERIC="en_EN.UTF-8"
> LC_TIME="en_EN.UTF-8"
> LC_COLLATE="en_EN.UTF-8"
> LC_MONETARY="en_EN.UTF-8"
> LC_MESSAGES="en_EN.UTF-8"
> LC_PAPER="en_EN.UTF-8"
> LC_NAME="en_EN.UTF-8"
> LC_ADDRESS="en_EN.UTF-8"
> LC_TELEPHONE="en_EN.UTF-8"
> LC_MEASUREMENT="en_EN.UTF-8"
> LC_IDENTIFICATION="en_EN.UTF-8"
> LC_ALL=
>
> $ bin/hadoop jar contrail-1.0-SNAPSHOT.jar contrail.Contrail -asm assembly
> -k 25 -reads reads
> == Starting time 2013-09-03 12:12:56
> Preprocess reads:       job_201309030936_0016 9 s  250 converted
> Build Initial:  job_201309030936_0017 363 s  2814 nodes [250 (100.00%) good
> reads, 9000 bp]
>   Quick Merge:  java.lang.NumberFormatException: For input string: "1,00"
>         at
> sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1242)
>         at java.lang.Float.parseFloat(Float.java:439)
>         at contrail.Node.cov(Node.java:1098)
>         at contrail.Node.toNodeMsg(Node.java:664)
>         at contrail.QuickMerge$QuickMergeMapper.map(QuickMerge.java:69)
>         at contrail.QuickMerge$QuickMergeMapper.map(QuickMerge.java:47)
>         at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:50)
>         at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:436)
>         at org.apache.hadoop.mapred.MapTask.run(MapTask.java:372)
>         at org.apache.hadoop.mapred.Child$4.run(Child.java:255)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at javax.security.auth.Subject.doAs(Subject.java:416)
>         at
> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1149)
>         at org.apache.hadoop.mapred.Child.main(Child.java:249)
>
>
>
>
> On Tue, Sep 3, 2013 at 11:00 AM, Andre Kelpe <akelpe@concurrentinc.com>
> wrote:
>>
>> This is usually a String.format() problem, when the developer was
>> using an English locale and was not aware of the fact, that
>> String.format is locale dependent.
>>
>> Try this:
>>
>> export LANG=en_EN.UTF-8
>> <your hadoop command>
>>
>> - André
>>
>> On Tue, Sep 3, 2013 at 3:20 PM, Felipe Gutierrez
>> <felipe.o.gutierrez@gmail.com> wrote:
>> > Hi,
>> >
>> > I am trying to run Contrail on Hadoop and it starts ok, but after some
>> > time
>> > throws an error. Some java class can't convert a string to float because
>> > there is a comma.
>> >
>> > I think the problem is not at contrail code. Maybe the location of my
>> > timezone? Does anyone already passed through this?
>> >
>> > $ bin/hadoop jar contrail-1.0-SNAPSHOT.jar contrail.Contrail -asm
>> > assembly
>> > -k 25 -reads reads
>> > == Starting time 2013-09-03 10:08:59
>> > Preprocess reads:       2
>> > job_201309030936_0005 9 s  250 converted
>> > Build Initial:  4
>> >
>> > job_201309030936_0006 358 s  2814 nodes [250 (100,00%) good reads, 9000
>> > bp]
>> >   Quick Merge:  java.lang.NumberFormatException: For input string:
>> > "1,00"
>> >         at
>> > sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1242)
>> >         at java.lang.Float.parseFloat(Float.java:439)
>> >         at contrail.Node.cov(Node.java:1096)
>> >         at contrail.Node.toNodeMsg(Node.java:664)
>> >         at contrail.QuickMerge$QuickMergeMapper.map(QuickMerge.java:69)
>> >         at contrail.QuickMerge$QuickMergeMapper.map(QuickMerge.java:47)
>> >         at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:50)
>> >         at
>> > org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:436)
>> >         at org.apache.hadoop.mapred.MapTask.run(MapTask.java:372)
>> >         at org.apache.hadoop.mapred.Child$4.run(Child.java:255)
>> >         at java.security.AccessController.doPrivileged(Native Method)
>> >         at javax.security.auth.Subject.doAs(Subject.java:416)
>> >         at
>> >
>> > org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1149)
>> >         at org.apache.hadoop.mapred.Child.main(Child.java:249)
>> >
>> >
>> >
>> > --
>> > --
>> > -- Felipe Oliveira Gutierrez
>> > -- Felipe.o.Gutierrez@gmail.com
>> > -- https://sites.google.com/site/lipe82/Home/diaadia
>>
>>
>>
>> --
>> André Kelpe
>> andre@concurrentinc.com
>> http://concurrentinc.com
>
>
>
>
> --
> --
> -- Felipe Oliveira Gutierrez
> -- Felipe.o.Gutierrez@gmail.com
> -- https://sites.google.com/site/lipe82/Home/diaadia



-- 
André Kelpe
andre@concurrentinc.com
http://concurrentinc.com

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