I have Cassandra 1.1.9 with large column family 1.5Tb of size per node. This one has a LeveledCompaction configured.
What is the most appropriate value of sstable_size_in_mb should I choose? Currently we use value of 100Mb and as a result ~20,000 files per node. What issues should I keep in mind while choosing it?
Larger is probably better. For an optimum size, some work was recently done on finding a better size than the small 5M default. The new default size is 160M. You can read about it in CASSANDRA-5727.
If you are using LCS you should consider upgrading to 1.2.x sometime for a lot of improvements there.
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