upgradesstables strips active data from sstables

From the discussion here: http://mail-archives.apache.org/mod_mbox/cassandra-user/201207.mbox/%3CCAOac0GCtyDqS6ocuHOuQqre4re5wKj3o-ZpUZGkGsjCHzDVbTA%40mail.gmail.com%3E

We are trying to migrate a 0.8.8 cluster to 1.1.2 by migrating the sstables from the 0.8.8 ring to a parallel 1.1.2 ring. However, every time we run the `nodetool upgradesstables` step we find it removes active data from our CFs – leading to lost data in our application.

The steps we took were:

1. Bring up a 1.1.2 ring in the same AZ/data center configuration with
tokens matching the corresponding nodes in the 0.8.8 ring.
2. Create the same keyspace on 1.1.2.
3. Create each CF in the keyspace on 1.1.2.
4. Flush each node of the 0.8.8 ring.
5. Rsync each non-compacted sstable from 0.8.8 to the corresponding node in
1.1.2.
6. Move each 0.8.8 sstable into the 1.1.2 directory structure by renaming the file to the /cassandra/data/<keyspace>/<cf>/<keyspace>-<cf>... format. For example, for the keyspace "Metrics" and CF "epochs_60" we get:
"cassandra/data/Metrics/epochs_60/Metrics-epochs_60-g-941-Data.db".
7. On each 1.1.2 node run `nodetool -h localhost refresh Metrics <CF>` for each CF in the keyspace. We notice that storage load jumps accordingly.
8. On each 1.1.2 node run `nodetool -h localhost upgradesstables`.

Afterwards we would test the validity of the data by comparing it with data from the original 0.8.8 ring. After an upgradesstables command the data was always incorrect.

With further testing we found that we could successfully use scrub to convert our sstables without data loss. However, any invocation of upgradesstables causes active data to be culled from the sstables:

INFO [CompactionExecutor:4] 2012-07-24 04:27:36,837 CompactionTask.java (line 109) Compacting [SSTableReader(path='/raid0/cassandra/data/Metrics/metrics_900/Metrics-metrics_900-hd-51-Data.db')]
INFO [CompactionExecutor:4] 2012-07-24 04:27:51,090 CompactionTask.java (line 221) Compacted to [/raid0/cassandra/data/Metrics/metrics_900/Metrics-metrics_900-hd-58-Data.db,]. 60,449,155 to 2,578,102 (~4% of original) bytes for 4,002 keys at 0.172562MB/s. Time: 14,248ms.

These are the steps we've tried:

WORKS refresh -> scrub
WORKS refresh -> scrub -> major compaction
WORKS refresh -> scrub -> cleanup
WORKS refresh -> scrub -> repair

FAILS refresh -> upgradesstables
FAILS refresh -> scrub -> upgradesstables
FAILS refresh -> scrub -> repair -> upgradesstables
FAILS refresh -> scrub -> major compaction -> upgradesstables

We have fewer than 143 million row keys in the CFs we're testing and none
of the *-Filter.db files are > 10MB, so I don't believe this is our
problem: https://issues.apache.org/jira/browse/CASSANDRA-3820

The keyspace is defined as:

Keyspace: Metrics:
Replication Strategy: org.apache.cassandra.locator.NetworkTopologyStrategy
Durable Writes: true
Options: [us-east:3]

And the column family that we tested with is defined as:

ColumnFamily: metrics_900
Key Validation Class: org.apache.cassandra.db.marshal.UTF8Type
Default column value validator: org.apache.cassandra.db.marshal.BytesType
Columns sorted by: org.apache.cassandra.db.marshal.CompositeType(org.apache.cassandra.db.marshal.LongType,org.apache.cassandra.db.marshal.UTF8Type,org.apache.cassandra.db.marshal.UTF8Type)
GC grace seconds: 0
Compaction min/max thresholds: 4/32
Read repair chance: 0.1
DC Local Read repair chance: 0.0
Replicate on write: true
Caching: KEYS_ONLY
Bloom Filter FP chance: default
Built indexes: []
Compaction Strategy: org.apache.cassandra.db.compaction.SizeTieredCompactionStrategy
Compression Options:
sstable_compression: org.apache.cassandra.io.compress.SnappyCompressor

All rows have a TTL of 30 days and a gc_grace=0 so it's possible that a small number of older columns would be removed during a compaction/scrub/upgradesstables step. However, the majority should still be kept as their TTL's have not expired yet.