It turned out that with the default settings Cassandra's cqlsh (command line client) behaves differently. All of a sudden, my script (a sequence of DDL queries run in the beginning of an integration test to prepare database) has failed. The first error was OperationTimedOut, but the following ones were caused by the fact that the first query did not yet finish. For example, in my case the first query was DROP KEYSPACE, while the second was CREATE KEYSPACE with the same name. Of course, if failed, and the following CREATE TABLE queries failed as well.
Why does this happen? Because cqlsh has a limit (by default it is 10 seconds, according to documentation). If your query runs more than this limit, the client just fails with OperationTimedOut error message, but the query is still running on the server.
OK, how do we disable this limit, or at least configure it to be long enough?
Good news: cqlsh in Cassandra 2.1.16 has --request-timeout command line parameter and you can specify the limit there (in seconds). --request-timeout 3600 would be a good start.
Bad news: cqlsh in Cassandra 2.1.12 does NOT have that parameter yet, so this parameter is not that universal.
By the way, version reported by cqlsh (with the usual --version) is strange. I tried it with cqlsh included into Cassandra distribution for Cassandra 2.1.8, 2.1.12, 2.1.16, and in all these cases the version was reported as 5.0.1, even though 2.1.16 reports support for --request-timeout (and really supports it) and the other two versions don't.
But let's return to out limit.
Good news: ~/.cassandra/cqlshrc file allows to define this timeout in [connection] section.
Bad news: the documentation is not accurate. Although it says that the option was added in version 2.1.1 and is called request_timeout, and this is true for 2.1.16, it is NOT true for 2.1.12. In it, you have to call the option client_timeout. Moreover: in 2.1.12, according to this article, you could completely disable the timeout by assigning None. Alas, in 2.1.16 (with request_timeout) this does not work.
It is not possible to (reliably) completely disable the timeout. If you set request_timeout to 0, this will mean that any request will timeout. Negative values cause errors. So the only option is to set it to some large value (like the abovementioned 3600 seconds).
So, a kinda universal way to make sure your integration tests don't stumble upon this, is to put the following in your ~/.cassandra/cqlshrc:
[connection]
request_timeout = 3600
client_timeout = 3600
BTW, how come that DROP KEYSPACE for a keyspace with a few tables with no data in them where the cluster contains just one node could not fit into the default timeout (presumably 10 seconds) on a machine with a decent HDD which was not overloaded? It's a different story...