TLDR; set workers' memory to 4G.
I reduced the test to the build-in Pi calculation:
./bin/run-example SparkPi 10
And got the same result; apparently 1G memory is insufficient even for simplest experiments. Increasing both master and workers memory to 4G and the problematic behaviour was not reproducible. However before the systems start computation the message still could appear but just once, seems it is printed in a waiting loop.