Fixing mmap performance for RocksDB

RocksDB inherited support for mmap from LevelDB. Performance was worse than expected because filesystem readahead fetched more data than needed as I explained in a previous post. I am not a fan of the standard workaround which is to tune kernel settings to reduce readahead because that has an impact for everything running on that server. The DBMS knows more about the IO patterns and can use madvise to provide hints to the OS, just as RocksDB uses fadvise for POSIX IO.

Good news, issue 9931 has been fixed and the results are impressive. 

Benchmark

I used db_bench with an IO-bound workload - the same as was used for my previous post. Two binaries were tested:

• old - this binary was compiled at git hash ce419c0f and does not have the fix for issue 9931
• fix - this binary was compiled at git hash 69a32ee and has the fix for issue 9931.

Note that git hash ce419c0f and 69a32ee are adjacent in the commit log.

The verify_checksums option was false for all tests. The CPU overhead would be much larger were it true because checksum verification would be done on each block access. Tests were repeated with cache_index_and_filter_blocks set to true and false. That didn't have a big impact on results.

Results

The graphs have results for these binary+config pairs:

• cache0.old - cache_index_and_filter_blocks=false, does not have fix for issue 9931
• cache0.fix - cache_index_and_filter_blocks=false, has fix for issue 9931
• cache1.old - cache_index_and_filter_blocks=true, does not have fix for issue 9931
• cache1.fix - cache_index_and_filter_blocks=true, has fix for issue 9931

The improvements from the fix are impressive for benchmark steps that do reads for user queries -- see the green and red bars. The average value for the average read request size (rareq-sz in iostat) is:

• for readwhilewriting: 115kb without the fix, 4kb with the fix
• for fwdrangewhilewriting: 79kb without the fix, 4kb with the fix

Tell me how you really feel about mmap + DBMS

It hasn't been great for me. Long ago I did some perf work with an mmap DBMS and Linux 2.6 kernels suffered from severe mutex contention in VM code. Performance was lousy back then. But I didn't write this to condemn mmap and IO-bound workloads where the read working set is much larger than memory might not be the best choice for mmap.

For the results above if you compare the improved mmap numbers with the POSIX/buffered IO numbers in my previous post -- peak QPS for the IO-bound tests (everything but fillseq and overwrite) is ~100k/second with mmap vs ~250k/second with buffered IO.

From the vmstat results collected during the benchmark I see:

• more mutex contention with mmap based on the cs column
• more CPU overhead with mmap based on the us and sy columns

Legend:

* qps - throughput from the benchmark

* cs - context switches from the cs column in vmstat

* us - user CPU from the us column in vmstat

* sy - system CPU from the sy column in vmstat

Average values

IO      qps     cs      us      sy

mmap     91757  475279  15.0    7.0

bufio   248543  572470  13.8    7.0

Values per query (column divided by QPS, for us and sy result is multiplied by 1000)

IO      qps     cs      us      sy

mmap    1       5.2     163     76

bufio   1       2.3      55     28

Insert Benchmark for Postgres 12, 13, 14 and 15: part 2

This has graphs of throughput vs time for three of the Insert Benchmark steps. The goal is to determine whether there is too much variance. A common source of variance is checkpoint stalls when using a B-Tree. This is a follow up to my blog post on the Insert Benchmark for Postgres versions 12.11, 13.7, 14.3 and 15b1. 

The benchmark steps for which graphs are provided are:

• l.i0 - load in PK order without secondary indexes
• l.i1 - load in PK order with 3 secondary indexes

The benchmark is repeated for two workloads -- cached and IO-bound. 

Cached

The database fits in memory for the cached workload.

There isn't much variance for the l.i0 workload.

The graph for the l.i1 workload is more exciting which is expected. For the l.i0 workload the inserts are in PK order and there are no secondary indexes. So each insert makes R/P pages dirty where R is the row size, P is the page size and R/P is much less than 1. But for l.i1 each insert is likely to make (3 + R/P) pages dirty so there is much more stress on page writeback and storage. The "3" in the estimate is from doing secondary index maintenance for each of the 3 secondary indexes. The drops in the graph are usually stalls when writeback falls behind.

IO-bound

The database is much larger than memory for the IO-bound workload.

The graph for l.i0 shows occasional drops that I assume are from writeback falling behind. However they can also be from the SSD that I use.

The graph for l.i1 is more interesting which is expected because it does more IO to storage per insert. The pattern is very regular and the insert rate gradually rises from ~2000/s to ~2800/s and this repeats every ~300 seconds. Were I to bet, this is caused by Postgres rather than my SSD. Perhaps one day I will do experiments to determine whether tuning the Postgres config can reduce the variance.

Insert Benchmark for Postgres 12, 13, 14 and 15

I ran the Insert Benchmark for Postgres versions 12.11, 13.7, 14.3 and 15b1. Reports are provided for cached and IO-bound workloads. The benchmark is run on Intel NUC servers at low concurrency. The goal is to determine how performance changes over time. A description of the Insert Benchmark is here.

tl;dr

• I am not a Postgres expert
• regressions are small in most cases
• the l.i0 benchmark step has regressions that are worth investigating in versions 14 and 15b1
• these regressions might have been fixed, see the perf report for the patch (15b1p1)

Updates:

• added links to the configuration files
• part 2 with throughput vs time graphs is here
• provided data on the percentage of time in parse, analyze, optimize, execute
• added command lines 
• added the index + relation sizes after each test step
• added links to performance reports when prepared statements were used for queries
• added links to performance reports with a patch to improve version 15b1
• added a second set of results for 15b1p1 (15b1 with the patch) for cached and IO-bound. Results are similar to the first set.
• livestreaming my debugging efforts, see Debugging the regression below

The regression

After I shared this blog post a possible cause for the regression was discussed here and the community quickly provided a patch for me to test. The results are excellent as 15b1p1 (15b1 with the patch) almost matches the results for version 13.7 on the cached workload. For the IO-bound workload the patch fixes the regression for all but one of the benchmark steps (l.i1).

The improvement is obvious in the cached workload Summary. The improvement is also there for the IO-bound workload, but less obvious. In the IO-bound workload Summary the throughput for l.i0 (load without secondary indexes) and q100.1 are better than results for version 14.3 and almost match version 13.7. While the throughput for l.i1 (inserts with secondary index maintenance) did not improve. From the IO-bound metrics for l.i1 I see that CPU (cpupq == CPU per statement) has been reducing with each major release, but with the patch (15b1p1) the value increased to match the value for version 13.7. I don't see this effect in the l.i1 metrics with the cached workload.

Summer has arrived and thermal throttling might be an issue for my SSDs which would be an unfortunate source of variance. The next step is to repeat the IO-bound workload at night when it is cooler and then look at CPU profiles for l.i1.

A guide to the performance reports is here. For explaining performance the most interesting metric is cpupq (CPU/query or CPU/insert depending on the benchmark step). From the guide, cpupq includes CPU by the client, DBMS and anything else running on the server. The benchmark client, written in Python, uses a lot of CPU. That can make it harder to see how CPU changes from the DBMS. With MySQL, I can also measure the CPU time used by mysqld. With Postgres I am still figuring out how to provide a DBMS-only measurement of the CPU overheads.

Test setup

Tests are run on Intel NUC servers I have at home. The OS is Ubuntu 20.04, hyperthreading and turbo-boost are disabled. All binaries are compiled using the same gcc/glibc toolchain and all tests used the same server.

The benchmark is repeated for a cached and IO-bound workload. The database fits in memory for the cached workload and is larger than memory for the IO-bound workload. The Postgres configuration files are here for 12.11, 13.7, 14.3 and 15b1.

The Insert Benchmark description has more details. In summary the benchmark has several steps and I focus on the ones where performance changes:

• l.i0 - load in PK order, the table that has no secondary indexes
• l.x - create three secondary indexes
• l.i1 - insert in PK order, the table that has 3 secondary indexes
• q100.1 - measure range query QPS from one client while another does 100 inserts/s
• q500.1 - measure range query QPS from one client while another does 500 inserts/s
• q1000.1 - measure range query QPS from one client while another does 1000 inserts/s

The l.i0 step inserts 20m (500m) rows for the cached (IO-bound) workload. The l.i1 step inserts 20m (10m) rows for the cached (IO-bound) workload. The q100.1, q500.1 and q1000.1 steps each run for 2 hours.

Command lines to try out the insert benchmark:

# old school, no prepared statements

python3 iibench.py --db_user=foo --db_host=127.0.0.1 \

  --db_password=bar --dbms=postgres --db_name=ib --setup \

  --query_threads=1 --max_rows=1000000 --secs_per_report=1

# try out the new support for prepared statements

python3 iibench.py --db_user=foo --db_host=127.0.0.1 \

  --db_password=bar --dbms=postgres --db_name=ib --setup \

  --query_threads=1 --max_rows=1000000 --secs_per_report=1 \

  --use_prepared_insert --use_prepared_query

Cached workload

The reports are here for ibench without and with prepared statements used for queries. Next is a report for prepared statements and a patch for 15b1 (I call it 15b1p1) that fixes a CPU regression. Postgres query throughput improves by ~1.5X when prepared statements are used for queries. Prepared statements are not yet used for inserts because I need to debug CPU perf issues on the ibench client.

I use relative throughput to document performance changes. It is: my_throughput / base_throughput where base_throughput is the result from Postgres 13.7. The interesting changes are below. The results aren't surprising. In most cases the regressions are small because Postgres is good at avoiding them. The regressions for 15b1 are larger because it is a beta and a newer release.

Throughput relative to 13.7

version l.i0    l.i1    q100.1
14.3    0.934   0.971   0.971
15b1    0.856   0.946   0.953

The percentage of samples from pg_plan_queries, pg_parse_query, pg_analyze_and_rewrite and query execution from v14.3. Prepared statements were not used.

step    plan    parse   analyze execute
l.i0    20      11      25      44
l.i1    8       5       10      77
q100.1  33      6       10      51

Cached - l.i0

The largest regressions are from the l.i0 step. While this test doesn't run for a long time, the results are similar for the IO-bound workload. Flamegraphs are here for 12.11, 13.7, 14.3 and 15b1. Differential flamegraphs are here for 13.7 vs 14.3 and 14.3 vs 15b1. For 15b1 I renamed ExecInitExprInternal to ExecInitExpr to match the names used in older versions.

I also have a benchmark report here for Postgres versions 14.0, 14.1, 14.2 and 14.3. There is little change across them so any regressions from 13.7 to 14.3 are likely in 13.7 to 14.0.

Before looking at the differential flamegraphs I compared the output by hand. For functions called by PostgresMain not much changes between versions in pg_plan_queries and pg_parse_queries. There is a small improvement for pg_analyze_and_rewrite and a small regression for PortalRun. The rest of the drill down is here with a focus on functions called under PortalRun. There are regressions in a few functions when ExecScan is on the call stack.

Percentage of samples for children of PostgresMain

12.11   13.7    14.3    15b1    function
-----   -----   -----   -----   --------
21.50   20.27   20.44   19.84   pg_plan_queries
11.56   12.19   11.34   10.34   pg_parse_queries
25.76   25.70   24.92   22.64   pg_analyze_and_rewrite
33.02   33.06   34.94   37.31   PortalRun

Cached - l.i1

Flamegraphs are here for 12.11, 13.7, 14.3 and 15b1. Differential flamegraphs are here for 13.7 vs 14.3 and 14.3 vs 15b1. I didn't do the summary by hand because the differences are small.

Cached - q100.1

Flamegraphs are here for 12.11, 13.7, 14.3 and 15b1. Differential flamegraphs are here for 13.7 vs 14.3 and 14.3 vs 15b1. I didn't do the summary by hand because the differences are small. ReadyForQuery is much less prominent in 15b1 relative to earlier versions. It isn't clear that the differential graph for 14.3 vs 15b1 is useful. Perhaps too much code has changed.

Table and index sizes

These are the sizes from pg_index_sizes, pg_relation_size and pg_total_relation_size. I suspect that the improvements (size reduction) in recent Postgres versions don't reproduce here because the workload is insert only.

Legend
* all sizes are in MB unless indicated with G (for GB)
* index is value from pg_index_sizes
* rel is value from pg_relation_size
* total is value from pg_total_relation_size

l.i0 - after load in PK order without secondary indexes
version index   rel     total
12.11   428     1531    1959
13.7    428     1531    1959
14.3    428     1531    1959
15b1    428     1531    1959

l.x - after create 3 secondary indexes
version index   rel     total
12.11   2243    1538    3782
13.7    2243    1538    3782
14.3    2243    1538    3782
15b1    2243    1538    3782

l.i1 - after load more data with 3 secondary indexes to maintain
version index   rel     total
12.11   5299    3069    8368
13.7    5308    3069    8378
14.3    5308    3069    8378
15b1    5308    3069    8378

q3.1000 - at the end of the read+write steps
version index   rel     total
12.11   8338    3951    12G
13.7    8333    3950    12G
14.3    8333    3950    12G
15b1    8333    3950    12G

IO-bound workload

The reports are here for ibench without and with prepared statements used for queries. Next is a report for prepared statements and a patch for 15b1 (I call it 15b1p1) that fixes a CPU regression.

Postgres query throughput improves by ~1.5X when prepared statements are used for queries. Prepared statements are not yet used for inserts because I need to debug CPU perf issues on the ibench client. I still need to figure out why more IO isn't done per query for this workload given that it is IO bound and index indexes are much larger than memory.

I don't think the IO-bound report needs additional analysis as the regression for l.i0 is analyzed above. I also have a benchmark report here for Postgres versions 14.0, 14.1, 14.2 and 14.3. There is little change across them so any regressions from 13.7 to 14.3 are likely in 13.7 to 14.0.

Table and index sizes

These are the sizes from pg_index_sizes, pg_relation_size and pg_total_relation_size. I suspect that the improvements (size reduction) in recent Postgres versions don't reproduce here because the workload is insert only.

Legend
* all sizes are in GB
* index is value from pg_index_sizes
* rel is value from pg_relation_size
* total is value from pg_total_relation_size

l.i0 - after load in PK order without secondary indexes
version index   rel     total
12.11   10      37      48
13.7    10      37      48
14.3    10      37      48
15b1    10      37      48

l.x - after create 3 secondary indexes
version index   rel     total
12.11   55      37      92
13.7    55      37      92
14.3    55      37      92
15b1    55      37      92

l.i1 - after load more data with 3 secondary indexes to maintain
version index   rel     total
12.11   55      38      94
13.7    55      38      94
14.3    55      38      94
15b1    55      38      94

q3.1000 - at the end of the read+write steps
version index   rel     total
12.11   57      39      96
13.7    57      39      96
14.3    57      39      96
15b1    57      39      96

Debugging the regression

This section has details from trying to debug the regression while I collaborate with a few experts from the Postgres community. For the regression in the l.i1 benchmark step (load in PK order with 3 secondary indexes) on the IO-bound workload there is:

• ~7% increase in KB written per insert(wkbpi)
• ~7% increase in KB read per insert (rkbpq)
• ~12% increase in CPU per insert (cpupq), but note that CPU here includes everything on the host, including the benchmark client

From pg_stat_bgwriter there are differences between 15b1 and 15b1p1 ...

select * from pg_stat_bgwriter is here for pg15b1p1:

checkpoints_timed     | 32

checkpoints_req       | 6

checkpoint_write_time | 7734090

checkpoint_sync_time  | 6471

buffers_checkpoint    | 12444695

buffers_clean         | 13580345

maxwritten_clean      | 0

buffers_backend       | 7593943

buffers_backend_fsync | 0

buffers_alloc         | 19970817

stats_reset           | 2022-06-23 21:45:38.834884-07

And then for pg15b1:

checkpoints_timed     | 37

checkpoints_req       | 2

checkpoint_write_time | 8283432

checkpoint_sync_time  | 6109

buffers_checkpoint    | 12753126

buffers_clean         | 13702867

maxwritten_clean      | 0

buffers_backend       | 6500038

buffers_backend_fsync | 0

buffers_alloc         | 20002787

stats_reset           | 2022-06-20 16:55:15.35976-07

And finally the graph of throughput vs time for l.i1 shows some kind of stall for 15b1p1 that doesn't occur for 15b1, and this stall is repeatable. It occurs in both runs of the benchmark I did for 15b1p1.

First is the graph for 15b1 which don't have the stall. The x-axis is time, the y-axis is inserts/s and the results are reported by the benchmark client at 1-second intervals.

Next is the graph for 15b1p1 which has a stall.