Hadoop configurations seem not to be read - permissions

Question

Every time when I try to start my mapreduce application (in standalone Hadoop), it tries to put stuff in the tmp directory, which it can't:
Exception in thread "main" java.io.IOException: Failed to set permissions of path: \tmp\hadoop-username\mapred\staging\username-1524148556\.staging to 0700
It ties to use an invalid path (slashes should be the other way around for cygwin).
I set hadoop.tmp.dir in core-site.xml (in the conf folder of Hadoop), but it seems that the config file is never read (if I put syntax errors in the file, it makes no difference). I added:
--config /home/username/hadoop-1.0.1/conf
To the command, but no difference. I also tried:
export HADOOP_CONF_DIR=/home/username/hadoop-1.0.1/conf
but also that does not seem to have an effect....
Any pointers on why the configs would not be read, or what else I am failing to see here?
Thanks!

Answer 1

It's not that the slashes are inverted, it's that /tmp is a cygwin path which actually maps to /cygwin/tmp or c:\cygwin\tmp. since hadoop is java and doesn't know about cygwin mappings, it takes /tmp to mean c:\tmp.
there's an awful lot of stuff to patch if you want to get 1.0.1 running on cygwin.
see: http://en.wikisource.org/wiki/User:Fkorning/Code/Hadoop-on-Cygwin

Answer 2

I found the following link useful, it seems that the problem stands with newer version of Hadoop. I'm using version 1.0.4 and I'm still facing this problem.
http://comments.gmane.org/gmane.comp.jakarta.lucene.hadoop.user/25837
UPDATED: in Mahout 0.7 and for the ones who use the "Mahoot in Action" book example, you shoud change the example code as follows:
File outFile = new File("output");
if (!outFile.exists()) {
outFile.mkdir();
}
Path output = new Path("output");
HadoopUtil.delete(conf, output);
KMeansDriver.run(conf, new Path("testdata/points"), new Path("testdata/clusters"),
output, new EuclideanDistanceMeasure(), 0.001, 10,
true, 0.1, true);