Running into an issue with DSE 4.7.
The tombstones are not being deleted even after compactions, cleanup, rebuild_index and repair. records have a 15 day ttl.
sstablemetadata output suggests that there are 90% tombstones
Any ideas?
sstablemetadata output
SSTable: ./abcd-abcd-ka-478675
Partitioner: org.apache.cassandra.dht.Murmur3Partitioner
Bloom Filter FP chance: 0.010000
Minimum timestamp: 1527521280829593
Maximum timestamp: 1527596173976435
SSTable max local deletion time: 1528892173
Compression ratio: 0.36967428395684393
Estimated droppable tombstones: 0.9073013816277629
SSTable Level: 0
Repaired at: 0
ReplayPosition(segmentId=1520529283052, position=4626679)
Estimated tombstone drop times:%n
1528817679: 18318196
1528818619: 20753822
1528819513: 24176310
.
.
.
Count Row Size Cell Count
1 0 0
2 0 1752560
3 0 0
4 0 6355421
5 0 0
6 0 687302
7 0 0
8 0 529613
10 0 444801
12 0 410107
14 0 456011
17 0 1347893
20 0 184960
24 0 152814
.
.
.
770 1347893 137
924 184960 109
1109 220403 68
1331 121620 86
1597 2044030 102
1916 185601 195
2299 184816 158273
2759 868754 0
3311 62795 0
3973 1668 0
4768 2143 0
5722 1812541 0
6866 828 0
.
.
.
Ancestors: [476190, 474027, 475201, 478160]
Estimated cardinality: 20059264
Cassandra marks TTL data with a tombstone after the requested amount of time has expired. A tombstone exists for gc_grace_seconds. After data is marked with a tombstone, the data is automatically removed during the normal compaction process.
you can try to run major compaction to evict tombstone out.
Tombstones gets deleted after normal compaction. But, still sometime you find stale data (even in prod)in tombstone.The reason could be out of all the nodes in that cluster one is down and the data from tombstone did not got deleted because of that node. Also sometimes null values are inserted in primary key causing tombstone data.
Related
I am seeing high CPU and memory usage of cassandra on the seed node. Is it advisable to stop compaction(nodetool stop) and enable in offpeak hours. Should I do manual compaction or enable autocompaction. I see lot of Native-Transport-Requests. I have three seed nodes. This is the first seed node.
Pool Name Active Pending Completed Blocked All time blocked
ReadStage 0 0 54255 0 0
MiscStage 0 0 0 0 0
CompactionExecutor 2 2566 352765 0 0
MutationStage 0 0 2659921760 0 0
MemtableReclaimMemory 0 0 180958 0 0
PendingRangeCalculator 0 0 21 0 0
GossipStage 0 0 338375 0 0
SecondaryIndexManagement 0 0 0 0 0
HintsDispatcher 0 0 63 0 0
RequestResponseStage 0 1 1684328696 0 0
Native-Transport-Requests 4 0 1538523706 0 47006391
ReadRepairStage 0 0 2197 0 0
CounterMutationStage 0 0 0 0 0
MigrationStage 0 0 0 0 0
MemtablePostFlush 1 1 216220 0 0
PerDiskMemtableFlushWriter_0 1 1 180958 0 0
ValidationExecutor 0 0 33250 0 0
Sampler 0 0 0 0 0
MemtableFlushWriter 1 1 180958 0 0
InternalResponseStage 0 0 141677 0 0
ViewMutationStage 0 0 0 0 0
AntiEntropyStage 0 0 166254 0 0
CacheCleanupExecutor 0 0 0 0 0
Repair#9 0 0 5719 0 0
I do see high compactions. Is it advisable to disable compactions using nodetool stop
$ nodetool info
ID : ebeda774-cea8-40bb-9322-69c6fcded5a9
Gossip active : true
Thrift active : true
Native Transport active: true
Load : 535.37 GiB
Generation No : 1636316595
Uptime (seconds) : 73152
Heap Memory (MB) : 19542.18 / 32168.00
Off Heap Memory (MB) : 1337.98
Data Center : us-west2
Rack : a
Exceptions : 15
Key Cache : entries 152283, size 23.07 MiB, capacity 100 MiB, 23835 hits, 280738 requests, 0.085 recent hit rate, 14400 save period in seconds
Row Cache : entries 0, size 0 bytes, capacity 0 bytes, 0 hits, 0 requests, NaN recent hit rate, 0 save period in seconds
Counter Cache : entries 0, size 0 bytes, capacity 50 MiB, 0 hits, 0 requests, NaN recent hit rate, 7200 save period in seconds
Chunk Cache : entries 6782, size 423.88 MiB, capacity 480 MiB, 23947952 misses, 24381819 requests, 0.018 recent hit rate, 250.977 microseconds miss latency
Percent Repaired : 0.49796724500672584%
Token : (invoke with -T/--tokens to see all 256 tokens)
$ free -h
total used free shared buff/cache available
Mem: 62G 53G 658M 1.0M 8.5G 8.5G
Swap: 0B 0B 0B
~$ nodetool compactionstats
pending tasks: 197
....
id compaction type keyspace table completed total unit progress
5e555610-40b2-11ec-9b5a-27bc920e6e55 Compaction mykeyspace table1 27299674 89930474 bytes 30.36%
5e55f251-40b2-11ec-9b5a-27bc920e6e55 Compaction mykeyspace table2 13922048 74426264 bytes 18.71%
Active compaction remaining time : 0h00m02s
I would definitely not run compaction manually. Much of the compaction thresholds are file-size based, which means that forcing it creates files sized outside of the normal progression. The result, is that the chances of compaction running on that table again are extremely slim. Basically, once you start down that path, you'll be running manual compactions forever.
I would also say that compaction is a good thing. You want it to happen, as compacted files are necessary to keep reads performing well. Of course, that's not much of a consolation when the compaction process is affecting operational activity.
tl;dr;
One I have done in the past, is to lower compaction throughput during the day. Not sure what throughput you're running with currently, but you can find this out by running nodetool getcompactionthroughput:
% bin/nodetool getcompactionthroughput
Current compaction throughput: 64 MB/s
So at the times when customer/operational traffic is high, you can reduce that significantly:
% bin/nodetool setcompactionthroughput 1
% bin/nodetool getcompactionthroughput
Current compaction throughput: 1 MB/s
1 MB / second is the lowest that compaction throughput can be set. If you set it to zero, it's "un-throttled," which means it'll consume all the resources that it can get at. Setting it to 1 brings its resource use (and speed) down to a trickle.
Once the busy daily traffic subsides, that setting can be turned back up:
% bin/nodetool setcompactionthroughput 256
Current compaction throughput: 256 MB/s
This can be accomplished with a scheduled job for each command.
When I query secondary index with pagination, query becomes slower when data grows.
I thought with pagination, no matter how large your data grow, it takes same time to query one page. Is that true? Why my query get slower?
My simplified table is
CREATE TABLE closed_executions (
domain_id uuid,
workflow_id text,
start_time timestamp,
workflow_type_name text,
PRIMARY KEY ((domain_id), start_time)
) WITH CLUSTERING ORDER BY (start_time DESC)
AND COMPACTION = {
'class': 'org.apache.cassandra.db.compaction.LeveledCompactionStrategy'
}
AND GC_GRACE_SECONDS = 172800;
And I create a secondary index as
CREATE INDEX closed_by_type ON closed_executions (workflow_type_name);
I query with following CQL
SELECT workflow_id, start_time, workflow_type_name
FROM closed_executions
WHERE domain_id = ?
AND start_time >= ?
AND start_time <= ?
AND workflow_type_name = ?
and code
query := v.session.Query(templateGetClosedWorkflowExecutionsByType,
request.DomainUUID,
common.UnixNanoToCQLTimestamp(request.EarliestStartTime),
common.UnixNanoToCQLTimestamp(request.LatestStartTime),
request.WorkflowTypeName).Consistency(gocql.One)
iter := query.PageSize(request.PageSize).PageState(request.NextPageToken).Iter()
// PageSize is 10, but could be thousand
Environement:
MacBook Pro
Cassandra: 3.11.0
GoCql: github.com/gocql/gocql master
Observation:
10K rows, within second
100K rows, ~3 second
1M rows, ~17 second
Debug log:
INFO [ScheduledTasks:1] 2018-09-11 16:29:48,349 NoSpamLogger.java:91 - Some operations were slow, details available at debug level (debug.log)
DEBUG [ScheduledTasks:1] 2018-09-11 16:29:48,357 MonitoringTask.java:173 - 1 operations were slow in the last 5005 msecs:
<SELECT * FROM cadence_visibility.closed_executions WHERE workflow_type_name = code.uber.internal/devexp/cadence-bench/load/basic.stressWorkflowExecute AND token(domain_id, domain_partition) >= token(d3138e78-abe7-48a0-adb9-8c466a9bb3fa, 0) AND token(domain_id, domain_partition) <= token(d3138e78-abe7-48a0-adb9-8c466a9bb3fa, 0) AND start_time >= 2018-09-11 16:29-0700 AND start_time <= 1969-12-31 16:00-0800 LIMIT 10>, time 2747 msec - slow timeout 500 msec
DEBUG [COMMIT-LOG-ALLOCATOR] 2018-09-11 16:31:47,774 AbstractCommitLogSegmentManager.java:107 - No segments in reserve; creating a fresh one
DEBUG [ScheduledTasks:1] 2018-09-11 16:40:22,922 ColumnFamilyStore.java:899 - Enqueuing flush of size_estimates: 23.997MiB (2%) on-heap, 0.000KiB (0%) off-heap
Related ref (no answer for my questions):
https://lists.apache.org/thread.html/%3CCAAiKoBidknHVOz8oQQmncZFZHdFiDfW6HTs63vxXCOhisQYZgg#mail.gmail.com%3E
https://www.datastax.com/dev/blog/cassandra-native-secondary-index-deep-dive
https://docs.datastax.com/en/developer/java-driver/3.2/manual/paging/
-- Edit
tablestats returns
Total number of tables: 105
----------------
Keyspace : cadence_visibility
Read Count: 19
Read Latency: 0.5125263157894736 ms.
Write Count: 3220964
Write Latency: 0.04900822269357869 ms.
Pending Flushes: 0
Table: closed_executions
SSTable count: 1
SSTables in each level: [1, 0, 0, 0, 0, 0, 0, 0, 0]
Space used (live): 20.3 MiB
Space used (total): 20.3 MiB
Space used by snapshots (total): 0 bytes
Off heap memory used (total): 6.35 KiB
SSTable Compression Ratio: 0.40192660515179696
Number of keys (estimate): 3
Memtable cell count: 28667
Memtable data size: 7.35 MiB
Memtable off heap memory used: 0 bytes
Memtable switch count: 9
Local read count: 9
Local read latency: NaN ms
Local write count: 327024
Local write latency: NaN ms
Pending flushes: 0
Percent repaired: 0.0
Bloom filter false positives: 0
Bloom filter false ratio: 0.00000
Bloom filter space used: 16 bytes
Bloom filter off heap memory used: 8 bytes
Index summary off heap memory used: 38 bytes
Compression metadata off heap memory used: 6.3 KiB
Compacted partition minimum bytes: 150
Compacted partition maximum bytes: 62479625
Compacted partition mean bytes: 31239902
Average live cells per slice (last five minutes): NaN
Maximum live cells per slice (last five minutes): 0
Average tombstones per slice (last five minutes): NaN
Maximum tombstones per slice (last five minutes): 0
Dropped Mutations: 0 bytes
----------------
Why pagination doesn't scale as the main table?
Your data in your secondary index is disperse
pagination will only apply logic
until it hits the page number
since your data is not clustered by time
you still have to sift through lots and lots of rows
before you can find your first 10 for example .
Query Tracing do show pagination plays at the very late phase.
Why secondary index is slow?
First Cassandra reads the index table to retrieve the primary key of all matching rows and for each of them, it will read the original table to fetch out the data. It is known anti-patterns with low cardinality index. (reference https://www.datastax.com/dev/blog/cassandra-native-secondary-index-deep-dive)
I have create a keyspace and table within it for documents store.
The code I used is
CREATE KEYSPACE space WITH replication = {'class':'SimpleStrategy', 'replication_factor' : 3};
USE space;
CREATE TABLE documents (
doc_id text,
path text,
content text,
metadata_id text,
PRIMARY KEY (doc_id)
)
WITH compression = { 'sstable_compression' : 'LZ4Compressor' };
Then I've pushed some data into it and with using a command nodetool cfstats orpd.documents I wanted to check compression ratio.
$ nodetool cfstats space.documents
Keyspace: space
Read Count: 0
Read Latency: NaN ms.
Write Count: 2005
Write Latency: 0.050547132169576056 ms.
Pending Flushes: 0
Table: documents
SSTable count: 0
Space used (live): 0
Space used (total): 0
Space used by snapshots (total): 0
Off heap memory used (total): 0
SSTable Compression Ratio: 0.0
Number of keys (estimate): 978
Memtable cell count: 8020
Memtable data size: 92999622
Memtable off heap memory used: 0
Memtable switch count: 0
Local read count: 0
Local read latency: NaN ms
Local write count: 2005
Local write latency: 0.051 ms
Pending flushes: 0
Bloom filter false positives: 0
Bloom filter false ratio: 0.00000
Bloom filter space used: 0
Bloom filter off heap memory used: 0
Index summary off heap memory used: 0
Compression metadata off heap memory used: 0
Compacted partition minimum bytes: 0
Compacted partition maximum bytes: 0
Compacted partition mean bytes: 0
Average live cells per slice (last five minutes): 0.0
Maximum live cells per slice (last five minutes): 0.0
Average tombstones per slice (last five minutes): 0.0
Maximum tombstones per slice (last five minutes): 0.0
----------------
However, I got confused because the ratio is 0.0, even though I use a compressor.
I am curious whether more data needs to be put into DB in order to get the measure or I am doing somethig wrong.
Your all data is in memtable
Run the below command to flush your memtable data to sstable
nodetool flush
We have a cluster with 7 nodes and we use the datastax java driver to connect to the cluster. The problem is that I am getting constant NoHostAvailableException like this:
Caused by:
com.datastax.driver.core.exceptions.NoHostAvailableException: All
host(s) tried for query failed (tried: /172.31.7.243:9042
(com.datastax.driver.core.exceptions.DriverException: Timeout while
trying to acquire available connection (you may want to increase the
driver number of per-host connections)), /172.31.7.245:9042
(com.datastax.driver.core.exceptions.DriverException: Timeout while
trying to acquire available connection (you may want to increase the
driver number of per-host connections)), /172.31.7.246:9042
(com.datastax.driver.core.exceptions.DriverException: Timeout while
trying to acquire available connection (you may want to increase the
driver number of per-host connections)), /172.31.7.247:9042,
/172.31.7.232:9042, /172.31.7.233:9042, /172.31.7.244:9042 [only
showing errors of first 3 hosts, use getErrors() for more details])
All the nodes are up:
UN 172.31.7.244 152.21 GB 256 14.5% 58abea69-e7ba-4e57-9609-24f3673a7e58 RAC1
UN 172.31.7.245 168.4 GB 256 14.5% bc11b4f0-cf96-4ca5-9a3e-33cc2b92a752 RAC1
UN 172.31.7.246 177.71 GB 256 13.7% 8dc7bb3d-38f7-49b9-b8db-a622cc80346c RAC1
UN 172.31.7.247 158.57 GB 256 14.1% 94022081-a563-4042-81ab-75ffe4d13194 RAC1
UN 172.31.7.243 176.83 GB 256 14.6% 0dda3410-db58-42f2-9351-068bdf68f530 RAC1
UN 172.31.7.233 159 GB 256 13.6% 01e013fb-2f57-44fb-b3c5-fd89d705bfdd RAC1
UN 172.31.7.232 166.05 GB 256 15.0% 4d009603-faa9-4add-b3a2-fe24ec16a7c1 RAC1
but two of them have high cpu load, especially the 232 because I am running a lot of deletes using cqlsh in that node.
I know that deletes generate tombstones, but with 7 nodes in the cluster I do not think is normal that all the host are not accesible.
Our configuration for the java connection is:
com.datastax.driver.core.Cluster cluster = null;
//Get contact points
String[] contactPoints=this.environment.getRequiredProperty(CASSANDRA_CLUSTER_URL).split(",");
cluster = com.datastax.driver.core.Cluster.builder()
.addContactPoints(contactPoints))
.withCredentials(this.environment.getRequiredProperty(CASSANDRA_CLUSTER_USERNAME),
this.environment.getRequiredProperty(CASSANDRA_CLUSTER_PASSWORD))
.withQueryOptions(new QueryOptions()
.setConsistencyLevel(ConsistencyLevel.QUORUM))
.withLoadBalancingPolicy(new TokenAwarePolicy(new RoundRobinPolicy()))
.withRetryPolicy(new LoggingRetryPolicy(DowngradingConsistencyRetryPolicy.INSTANCE))
.withPort(Integer.parseInt(this.environment.getRequiredProperty(CASSANDRA_CLUSTER_PORT)))
.build();
Metadata metadata = cluster.getMetadata();
for ( Host host : metadata.getAllHosts() ) {
LOG.info("Datacenter: "+host.getDatacenter()+"; Host: "+host.getAddress()+"; DC: "+host.getDatacenter()+"\n");
}
and the contact points are:
172.31.7.244,172.31.7.243,172.31.7.245,172.31.7.246,172.31.7.247
Anyone knows how I can solve this problem? Or at least have anyone some hint about how to deal with this situation?
Update: If I get the error messages withe.getErrors() I obtain:
/172.31.7.243:9042=com.datastax.driver.core.OperationTimedOutException: [/172.31.7.243:9042] Operation timed out,
/172.31.7.244:9042=com.datastax.driver.core.OperationTimedOutException: [/172.31.7.244:9042] Operation timed out,
/172.31.7.245:9042=com.datastax.driver.core.OperationTimedOutException: [/172.31.7.245:9042] Operation timed out,
/172.31.7.246:9042=com.datastax.driver.core.OperationTimedOutException: [/172.31.7.246:9042] Operation timed out,
/172.31.7.247:9042=com.datastax.driver.core.OperationTimedOutException: [/172.31.7.247:9042] Operation timed out}
UPDATE:
The replication factor of the keyspace is 3.
For the deletes Im running them using different files with the cql queries:
cqlsh ip_node_1 -f script-1.duplicates
cqlsh ip_node_1 -f script-2.duplicates
cqlsh ip_node_1 -f script-3.duplicates
...
I am not specifying any consistency level, so is using the default one which is ONE.
Each of the previous files contain deletes like this:
DELETE FROM keyspace_name.search WHERE idline1 = 837 and idline2 = 841 and partid = 8558 and id = 18c04c20-8a3a-11e5-9e20-0025905a2ab2;
And the column family is:
CREATE TABLE search (
idline1 bigint,
idline2 bigint,
partid int,
id uuid,
field3 int,
field4 int,
field5 int,
field6 int,
field7 int,
field8 int,
field9 double,
field10 bigint,
field11 bigint,
field12 bigint,
field13 boolean,
field14 boolean,
field15 int,
field16 bigint,
field17 int,
field18 int,
field19 int,
field20 int,
field21 uuid,
field22 boolean,
PRIMARY KEY ((idline1, idline2, partid), id)
) WITH
bloom_filter_fp_chance=0.010000 AND
caching='KEYS_ONLY' AND
comment='Table with the snp between lines' AND
dclocal_read_repair_chance=0.000000 AND
gc_grace_seconds=0 AND
index_interval=128 AND
read_repair_chance=0.100000 AND
replicate_on_write='true' AND
populate_io_cache_on_flush='false' AND
default_time_to_live=0 AND
speculative_retry='99.0PERCENTILE' AND
memtable_flush_period_in_ms=0 AND
compaction={'class': 'SizeTieredCompactionStrategy'} AND
compression={'sstable_compression': 'LZ4Compressor'};
CREATE INDEX search_partid ON search (partid);
CREATE INDEX search_field8 ON search (field8);
UPDATE (18-03-2016):
After the deletes start to be executed I found the cpu of some of the nodes increases a lot:
I check the processes on that nodes and only cassandra is running but consuming a lot of cpu. The rest of the nodes are not using almost cpu.
UPDATE (04-04-2016): I do not know if it is related. I check the nodes which a lot of CPU (near 96%) and th gc activity remains on 1.6% (using only 3 GB from the 10 which have assigned).
Checing the thread pool stats:
nodetool tpstats
Pool Name Active Pending Completed Blocked All time blocked
ReadStage 0 0 20042001 0 0
RequestResponseStage 0 0 149365845 0 0
MutationStage 32 117720 181498576 0 0
ReadRepairStage 0 0 799373 0 0
ReplicateOnWriteStage 0 0 13624173 0 0
GossipStage 0 0 5580503 0 0
CacheCleanupExecutor 0 0 0 0 0
AntiEntropyStage 0 0 32173 0 0
MigrationStage 0 0 9 0 0
MemtablePostFlusher 0 0 45044 0 0
MemoryMeter 0 0 9553 0 0
FlushWriter 0 0 9425 0 18
ValidationExecutor 0 0 15980 0 0
MiscStage 0 0 0 0 0
PendingRangeCalculator 0 0 7 0 0
CompactionExecutor 0 0 1293147 0 0
commitlog_archiver 0 0 0 0 0
InternalResponseStage 0 0 0 0 0
HintedHandoff 0 0 273 0 0
Message type Dropped
RANGE_SLICE 0
READ_REPAIR 0
PAGED_RANGE 0
BINARY 0
READ 0
MUTATION 0
_TRACE 0
REQUEST_RESPONSE 0
COUNTER_MUTATION 0
I realize that the pending mutation stages are growing but the active value remain the same, could be this the problem?
I see two problems with your datamodel.
You use two secondary indexes. One is on a field on the partition key. I don't know how cassandra behaves in this case. Worst case is, that even if you use the complete partition key (like you do in your example delete) cassandra does a lookup in the secondary index. In that case this would mean a full cluster scan, because secondary indexes are only stored per partition. Since only a part of the partition key is indexed cassandra does not know on which partition the index informations lies. This behavior at least would explain the timeouts.
You said, you delete a lot of rows in a specific partition. That is also a problem. For each deletion cassandra creates a tombstone. The more tombstones there are, the slower the read will become. This will sooner or later lead to timeouts or exceptions (I believe cassandra will write warnings when 1000 tombstones are reached and throw exceptions when 10.000 tombstones are reached). Btw. these tombstones are also created in the secondary index. By default cassandra will remove tombstones after gc_grace_seconds (by default 10 days) when a compaction is performed. You could change this property per table. More information on these table properties can be found here: Table Properties
I believe the first point could be the reason for the timeouts.
I have CF with 1280 rows.
Each row has 6 columns. Im trying to $cf->get_range('pq_questions','','',1200) and it gets all rows but too slow(about 4-6 sec)
Column Family: pq_questions
SSTable count: 1
Space used (live): 668363
Space used (total): 668363
Number of Keys (estimate): 1280
Memtable Columns Count: 0
Memtable Data Size: 0
Memtable Switch Count: 0
Read Count: 0
Read Latency: NaN ms.
Write Count: 0
Write Latency: NaN ms.
Pending Tasks: 0
Key cache capacity: 200000
Key cache size: 1000
Key cache hit rate: 0.10998439937597504
Row cache capacity: 1000
Row cache size: 1000
Row cache hit rate: 0.0
Compacted row minimum size: 373
Compacted row maximum size: 1331
Compacted row mean size: 574
It is strange but read latency in cfstats is NaN ms
When i calling htop on debian i see that the most load causes phpcassa
I has only one node and use consistency level ONE.
What can cause so slow quering?
I'm guessing you don't have the C extension installed. Without it, a similar query takes 1-2 seconds for me. With it installed, the same query takes about 0.2 seconds.
Regarding the NaN read latency, latencies aren't captured for get_range_slices (get_range in phpcassa).