Re: Very poor read performance, query independent

All,

Here is a list of what I did based of the suggestions made after my initial
post:
*Reduce max_parallel_workers to 4: Values higher makes the workers wait for
data as the RAID0 array can't deliver high enough IOPS.
*Reduce random_page_cost to 1: Forcing the use of index makes queries
faster despite low random throughput.
*Increase shared_buffer to 66GB and effective_cache_size to 53GB: With the
new server having 144GB of RAM, increasing shared_buffer allows Postgresql
to keep a lot of data in memory reducing the need to go to disk.
*Reduce min_parallel_relation_size to 512kB to have more workers when doing
sequential parallel scan
*Increased the /sys/block/sd[ac]/queue/read_ahead_kb to 16384 for my arrays
using HDD
*Reused old SSDs (that are compatible with my RAID controller, to my
surprise) to put my most used index and tables.

Thanks to everybody who made suggestions. I now know more about Postgresql
tuning.

Charles

On Mon, Jul 10, 2017 at 4:03 PM, Charles Nadeau <charles(dot)nadeau(at)gmail(dot)com>
wrote:

> I’m running PostgreSQL 9.6.3 on Ubuntu 16.10 (kernel 4.4.0-85-generic).
> Hardware is:
>
> *2x Intel Xeon E5550
>
> *72GB RAM
>
> *Hardware RAID10 (4 x 146GB SAS 10k) P410i controller with 1GB FBWC (80%
> read/20% write) for Postgresql data only:
>
> Logical Drive: 3
>
> Size: 273.4 GB
>
> Fault Tolerance: 1+0
>
> Heads: 255
>
> Sectors Per Track: 32
>
> Cylinders: 65535
>
> Strip Size: 128 KB
>
> Full Stripe Size: 256 KB
>
> Status: OK
>
> Caching: Enabled
>
> Unique Identifier: 600508B1001037383941424344450A00
>
> Disk Name: /dev/sdc
>
> Mount Points: /mnt/data 273.4 GB
>
> OS Status: LOCKED
>
> Logical Drive Label: A00A194750123456789ABCDE516F
>
> Mirror Group 0:
>
> physicaldrive 2I:1:5 (port 2I:box 1:bay 5, SAS, 146 GB, OK)
>
> physicaldrive 2I:1:6 (port 2I:box 1:bay 6, SAS, 146 GB, OK)
>
> Mirror Group 1:
>
> physicaldrive 2I:1:7 (port 2I:box 1:bay 7, SAS, 146 GB, OK)
>
> physicaldrive 2I:1:8 (port 2I:box 1:bay 8, SAS, 146 GB, OK)
>
> Drive Type: Data
>
> Formatted with ext4 with: sudo mkfs.ext4 -E stride=32,stripe_width=64 -v
> /dev/sdc1.
>
> Mounted in /etc/fstab with this line: "UUID=99fef4ae-51dc-4365-9210-0b153b1cbbd0
> /mnt/data ext4 rw,nodiratime,user_xattr,noatime,nobarrier,errors=remount-ro
> 0 1"
>
> Postgresql is the only application running on this server.
>
>
> Postgresql is used as a mini data warehouse to generate reports and do
> statistical analysis. It is used by at most 2 users and fresh data is added
> every 10 days. The database has 16 tables: one is 224GB big and the rest
> are between 16kB and 470MB big.
>
>
> My configuration is:
>
>
> name | current_setting | source
>
> ---------------------------------+--------------------------
> ----------------------+----------------------
>
> application_name | psql | client
>
> autovacuum_vacuum_scale_factor | 0 | configuration file
>
> autovacuum_vacuum_threshold | 2000 | configuration file
>
> checkpoint_completion_target | 0.9 | configuration file
>
> checkpoint_timeout | 30min | configuration file
>
> client_encoding | UTF8 | client
>
> client_min_messages | log | configuration file
>
> cluster_name | 9.6/main | configuration file
>
> cpu_index_tuple_cost | 0.001 | configuration file
>
> cpu_operator_cost | 0.0005 | configuration file
>
> cpu_tuple_cost | 0.003 | configuration file
>
> DateStyle | ISO, YMD | configuration file
>
> default_statistics_target | 100 | configuration file
>
> default_text_search_config | pg_catalog.english | configuration file
>
> dynamic_shared_memory_type | posix | configuration file
>
> effective_cache_size | 22GB | configuration file
>
> effective_io_concurrency | 4 | configuration file
>
> external_pid_file | /var/run/postgresql/9.6-main.pid | configuration file
>
> lc_messages | C | configuration file
>
> lc_monetary | en_CA.UTF-8 | configuration file
>
> lc_numeric | en_CA.UTF-8 | configuration file
>
> lc_time | en_CA.UTF-8 | configuration file
>
> listen_addresses | * | configuration file
>
> lock_timeout | 100s | configuration file
>
> log_autovacuum_min_duration | 0 | configuration file
>
> log_checkpoints | on | configuration file
>
> log_connections | on | configuration file
>
> log_destination | csvlog | configuration file
>
> log_directory | /mnt/bigzilla/data/toburn/hp/postgresql/pg_log |
> configuration file
>
> log_disconnections | on | configuration file
>
> log_error_verbosity | default | configuration file
>
> log_file_mode | 0600 | configuration file
>
> log_filename | postgresql-%Y-%m-%d_%H%M%S.log | configuration file
>
> log_line_prefix | user=%u,db=%d,app=%aclient=%h | configuration file
>
> log_lock_waits | on | configuration file
>
> log_min_duration_statement | 0 | configuration file
>
> log_min_error_statement | debug1 | configuration file
>
> log_min_messages | debug1 | configuration file
>
> log_rotation_size | 1GB | configuration file
>
> log_temp_files | 0 | configuration file
>
> log_timezone | localtime | configuration file
>
> logging_collector | on | configuration file
>
> maintenance_work_mem | 3GB | configuration file
>
> max_connections | 10 | configuration file
>
> max_locks_per_transaction | 256 | configuration file
>
> max_parallel_workers_per_gather | 14 | configuration file
>
> max_stack_depth | 2MB | environment variable
>
> max_wal_size | 4GB | configuration file
>
> max_worker_processes | 14 | configuration file
>
> min_wal_size | 2GB | configuration file
>
> parallel_setup_cost | 1000 | configuration file
>
> parallel_tuple_cost | 0.012 | configuration file
>
> port | 5432 | configuration file
>
> random_page_cost | 22 | configuration file
>
> seq_page_cost | 1 | configuration file
>
> shared_buffers | 34GB | configuration file
>
> shared_preload_libraries | pg_stat_statements | configuration file
>
> ssl | on | configuration file
>
> ssl_cert_file | /etc/ssl/certs/ssl-cert-snakeoil.pem | configuration file
>
> ssl_key_file | /etc/ssl/private/ssl-cert-snakeoil.key | configuration file
>
> statement_timeout | 1000000s | configuration file
>
> stats_temp_directory | /var/run/postgresql/9.6-main.pg_stat_tmp |
> configuration file
>
> superuser_reserved_connections | 1 | configuration file
>
> syslog_facility | local1 | configuration file
>
> syslog_ident | postgres | configuration file
>
> syslog_sequence_numbers | on | configuration file
>
> temp_file_limit | 80GB | configuration file
>
> TimeZone | localtime | configuration file
>
> track_activities | on | configuration file
>
> track_counts | on | configuration file
>
> track_functions | all | configuration file
>
> unix_socket_directories | /var/run/postgresql | configuration file
>
> vacuum_cost_delay | 1ms | configuration file
>
> vacuum_cost_limit | 5000 | configuration file
>
> vacuum_cost_page_dirty | 200 | configuration file
>
> vacuum_cost_page_hit | 10 | configuration file
>
> vacuum_cost_page_miss | 100 | configuration file
>
> wal_buffers | 16MB | configuration file
>
> wal_compression | on | configuration file
>
> wal_sync_method | fdatasync | configuration file
>
> work_mem | 1468006kB | configuration file
>
>
> The part of /etc/sysctl.conf I modified is:
>
> vm.swappiness = 1
>
> vm.dirty_background_bytes = 134217728
>
> vm.dirty_bytes = 1073741824
>
> vm.overcommit_ratio = 100
>
> vm.zone_reclaim_mode = 0
>
> kernel.numa_balancing = 0
>
> kernel.sched_autogroup_enabled = 0
>
> kernel.sched_migration_cost_ns = 5000000
>
>
> The problem I have is very poor read. When I benchmark my array with fio I
> get random reads of about 200MB/s and 1100IOPS and sequential reads of
> about 286MB/s and 21000IPS. But when I watch my queries using pg_activity,
> I get at best 4MB/s. Also using dstat I can see that iowait time is at
> about 25%. This problem is not query-dependent.
>
> I backed up the database, I reformated the array making sure it is well
> aligned then restored the database and got the same result.
>
> Where should I target my troubleshooting at this stage? I reformatted my
> drive, I tuned my postgresql.conf and OS as much as I could. The hardware
> doesn’t seem to have any issues, I am really puzzled.
>
> Thanks!
>
>
> Charles
>
> --
> Charles Nadeau Ph.D.
>

--
Charles Nadeau Ph.D.
http://charlesnadeau.blogspot.com/