Hi Ogden,
You didn't mention any details about your postgresql.conf settings. Why
don't you set them optimally for your loads and try again and see if
there is any difference. Make sure you do a DB restart since some of
these parameters require it.
======================================
parameter before after
---------------- ------ -------
shared_buffers Reduce this value to about 25% of total memory
temp_buffers Decrease this value to 8MB since we are not using
temporary tables or doing intermediate sorts
work_mem Reduce significantly (1MB) since we are not doing
memory sorts or hashes per SQL
maintenance_work_mem Increase signficantly for DDL bulk loading, restore
operations
fsync off (so that time is not being spent waiting for stuff
to be written to disk). Note: you may not be able to recover your database
after a crash when set to off.
checkpoint_segments Increase this significantly for DML bulk loading,
restore operations
max_wal_size Increase significantly like you would to
checkpoint_segments
min_wal_size Increase significantly like you would to
checkpoint_segments
checkpoint_timeout Increase to at least 30min
archive_mode off
autovacuum off
synchronous_commit off
wal_level minimal
max_wal_senders 0
full_page_writes off during DML bulk loading, restore operations
wal_buffers 16MB during DML bulk loading, restore operations
Regards,
Michael Vitale
Ogden Brash wrote on 10/3/2019 4:30 PM:
I recently performed a pg_dump (data-only) of a relatively large
database where we store intermediate results of calculations. It is
approximately 3 TB on disk and has about 20 billion rows.
We do the dump/restore about once a month and as the dataset has
grown, the restores have gotten very slow. So, this time I decided to
do it a different way and have some observations that puzzle me.
Background:
The data is extremely simple. The rows consist only of numbers and are
all fixed length. There are no foreign keys, constraints, null values,
or default values. There are no strings or arrays. There are 66 tables
and the number of rows in each table forms a gaussian distribution; so
there are 3 tables which have about 3 billion rows each and the rest
of the tables have significantly fewer rows.
I used the directory format when doing the pg_dump. The compressed
data of the dump is 550 GB.
I am using: (PostgreSQL) 11.5 (Ubuntu 11.5-1.pgdg18.04+1)
The machine that I attempted to do a pg_restore to is a dedicated
server just for one instance of posgresql. It has 32 GB of memory and
is running Ubuntu 18.04 (headless). It physical hardware, not
virtualized. Nothing else runs on the machine and the postgresql.conf
settings have been tuned (to the best of my postgresql abilities which
are suspect). While the operating system is installed on an SSD, there
is one extra large, fast HDD that is dedicated to the posgresql
server. It has been in use for this particular purpose for a while and
has not had performance issues. (Just with pg_restore)
Autovacuum is off and all indexes have been deleted before the restore
is started. There is nothing in the db except for the empty data tables.
Restoring over the net:
In the past we have always restored in a way where the dumped data is
read over a gigabit connection while being restored to the local
drive. But, the last time we did it it took 2 days and I was looking
for something faster. So, I decided to copy the dumped directory to
the local drive and restore from the dump locally. I knew that because
the machine only had one drive that would fit the data, there would be
some I/O contention, but I hoped that it might not be as bad as
reading over the network.
The pg_restore went unbearably slowly... after many hours it had
written less than 20GB to the database, so I started tracking it with
iostat to see what was going on. The following is iostat output every
60 seconds. I tracked it for several hours and this is representative
of what was happening consistently.
avg-cpu: %user %nice %system %iowait %steal %idle
0.39 0.00 0.40 43.10 0.00 56.11
Device tps kB_read/s kB_wrtn/s kB_read kB_wrtn
loop0 0.00 0.00 0.00 0 0
loop1 0.00 0.00 0.00 0 0
loop2 0.00 0.00 0.00 0 0
sda 263.33 132.87 2990.93 7972 179456
sdb 0.17 0.00 0.73 0 44
avg-cpu: %user %nice %system %iowait %steal %idle
0.34 0.00 0.41 44.43 0.00 54.82
Device tps kB_read/s kB_wrtn/s kB_read kB_wrtn
loop0 0.00 0.00 0.00 0 0
loop1 0.00 0.00 0.00 0 0
loop2 0.00 0.00 0.00 0 0
sda 262.95 140.47 2983.00 8428 178980
sdb 0.08 0.00 0.40 0 24
While I was tracking this I started experimenting with the IO
scheduler to see if it had a noticable impact. I had been using cfq
(ubuntu 18.04 default). Changing to deadline did not have a noticable
difference. Changing to noop made things much slower. I went back to
cfq. I also experimented with turning fsync off; that did speed things
up a bit but not enough for me to leave it off.
What puzzled me is that the OS was spending such a large percentage of
time in iowait, yet there was so little IO going on.
So, I decided to go back to restoring over the net. While the slow
pg_restore was still going on, and while I was still tracking iostat,
I copied the 550 GB dumps to an nfs drive. The copy happened pretty
much at full speed (limit being the gigabit ethernet) and
interestingly, it did not slow down kb_wrtn and kb_wrtn/s numbers in
iostat (which was the postgresql server continuing with the restore).
To me that seemed to indicate that it was not really a disk I/O
limitation.
Restoring over the net:
After copying the dump files to an NFS drive, I stopped the restore,
truncated the tables and started exactly the same command, but this
time taking its input from the nfs drive. I did not reboot the machine
or restart the postgresql server. I tracked iostate every 60 seconds
and this is what it looks like:
avg-cpu: %user %nice %system %iowait %steal %idle
8.87 0.00 1.62 39.89 0.00 49.61
Device tps kB_read/s kB_wrtn/s kB_read kB_wrtn
loop0 0.00 0.00 0.00 0 0
loop1 0.00 0.00 0.00 0 0
loop2 0.00 0.00 0.00 0 0
sda 252.77 527.87 37837.47 31672 2270248
sdb 0.22 0.00 1.00 0 60
avg-cpu: %user %nice %system %iowait %steal %idle
8.57 0.00 2.21 35.26 0.00 53.97
Device tps kB_read/s kB_wrtn/s kB_read kB_wrtn
loop0 0.00 0.00 0.00 0 0
loop1 0.00 0.00 0.00 0 0
loop2 0.00 0.00 0.00 0 0
sda 236.10 465.27 54312.00 27916 3258720
sdb 0.08 0.00 0.40 0 24
Notice that the database is writing approximately 15 times as fast
(and I have verified that by tracking the size of the posgresql data
directory over time) while the number of i/o transactions per second
has actually dropped a little bit. It has now been running about 24
hours and has maintained that speed.
My interpretation
At first sight this seems to me as being symptomatic of the pg_restore
process doing a huge number of very small input operations when
reading from the dump. If the proportion of input to output operations
is the same now as it was when trying to restore from the local drive,
that implies that the vast majority of i/o operations were inputs and
not outputs.
However, I am not sure that even that would cause such a slowdown
because the compressed data files in the directory format dump
correspond to the tables and so there are 3 very large files that it
starts with. So all of these stats were gathered in the first 24 hours
of the restore when it was just restoring the first 3 tables (I have
verbose on, so I know). Because those files are gzipped, we know that
they are being read sequentially and because the machine has lots of
memory we know that the OS has allocated a lot of space to disk
buffers and so even if postgresql was doing lots of small reads,
bouncing around between the 3 files, it would not hit the disk that often.
Now that restore is happening 15 times faster when reading from an nfs
drive, I looked at the nfsiostat output for a while and it does not
show any indication of any untoward behavior:
192.168.17.146:/volume1/Backups mounted on /nas/Backups:
ops/s rpc bklog
27.000 0.000
read: ops/s kB/s kB/op retrans
avg RTT (ms) avg exe (ms)
27.000 3464.332 128.309 0 (0.0%)
13.500 13.511
write: ops/s kB/s kB/op
retrans avg RTT (ms) avg exe (ms)
0.000 0.000 0.000 0 (0.0%)
0.000 0.000
192.168.17.146:/volume1/Backups mounted on /nas/Backups:
ops/s rpc bklog
24.000 0.000
read: ops/s kB/s kB/op retrans
avg RTT (ms) avg exe (ms)
24.000 3079.406 128.309 0 (0.0%)
28.492 28.504
write: ops/s kB/s kB/op
retrans avg RTT (ms) avg exe (ms)
0.000 0.000 0.000 0 (0.0%)
0.000 0.000
The nubmer of operations per second (if those correspond to reads from
postgresql, which I do not know for a fact) does not seem high at all.
I actually do not have a great theory for what is going on but it
might be more obvious to someone who knows the postgresql
implementation well. I would love to hear any thoughts that would be
helpful on how to get my restores even faster.
