It appeared that during the deployment Ambari python code was compiled and somehow those two files, version.py and format_jvm_option.py, were kept out so that the deployment failed. I could not identify the place that caused the problem. But I copied the ambari-agent directory from a good node to the corrupted node, under /usr/lib/ and deployment was completed successfully. I believe that’s a bug in Ambari but I don’t have a good way to reproduce it. Just keep it in mind if you have a similar issue like this.
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