Vlog files use lots of disk space: Add option to set LSMOnly option when opening p dir

diggy · July 20, 2020, 6:47pm

Moved from GitHub dgraph/3511

Posted by shamil:

Hi,

We have about 10MB of actual data in Dgraph, but the wal directory with vlog files taking about 56GB, I understand that there should be some kind of GC running each 10 minutes or per each GB, but I don’t see the space was ever reclaimed.

Can you explain how this works, and what I’m missing…

Here is information from the badger info --dir /data/dgraph/w command:

[     2019-06-02T13:37:33Z] MANIFEST       16 B MA
[           5 days earlier] 000000.vlog  1.1 GB VL
[           5 days earlier] 000001.vlog  1.1 GB VL
[           5 days earlier] 000002.vlog  1.1 GB VL
[           5 days earlier] 000003.vlog  1.1 GB VL
[           5 days earlier] 000004.vlog  1.1 GB VL
[           5 days earlier] 000005.vlog  1.1 GB VL
[           5 days earlier] 000006.vlog  1.1 GB VL
[           5 days earlier] 000007.vlog  1.1 GB VL
[           5 days earlier] 000008.vlog  1.1 GB VL
[           5 days earlier] 000009.vlog  1.1 GB VL
[           5 days earlier] 000010.vlog  1.1 GB VL
[           4 days earlier] 000011.vlog  1.1 GB VL
[           4 days earlier] 000012.vlog  1.1 GB VL
[           4 days earlier] 000013.vlog  1.1 GB VL
[           4 days earlier] 000014.vlog  1.1 GB VL
[           4 days earlier] 000015.vlog  1.1 GB VL
[           4 days earlier] 000016.vlog  1.1 GB VL
[           4 days earlier] 000017.vlog  1.1 GB VL
[           4 days earlier] 000018.vlog  1.1 GB VL
[           4 days earlier] 000019.vlog  1.1 GB VL
[           4 days earlier] 000020.vlog  1.1 GB VL
[           4 days earlier] 000021.vlog  1.1 GB VL
[           4 days earlier] 000022.vlog  1.1 GB VL
[           4 days earlier] 000023.vlog  1.1 GB VL
[           4 days earlier] 000024.vlog  1.1 GB VL
[           4 days earlier] 000025.vlog  1.1 GB VL
[           4 days earlier] 000026.vlog  1.1 GB VL
[           4 days earlier] 000027.vlog  1.1 GB VL
[           4 days earlier] 000028.vlog  1.1 GB VL
[           4 days earlier] 000029.vlog  1.1 GB VL
[           4 days earlier] 000030.vlog  1.1 GB VL
[           4 days earlier] 000031.vlog  1.1 GB VL
[           4 days earlier] 000032.vlog  1.1 GB VL
[           4 days earlier] 000033.vlog  1.1 GB VL
[           4 days earlier] 000034.vlog  1.1 GB VL
[           4 days earlier] 000035.vlog  1.1 GB VL
[           4 days earlier] 000036.vlog  1.1 GB VL
[           4 days earlier] 000037.vlog  1.1 GB VL
[           4 days earlier] 000038.vlog  1.1 GB VL
[           4 days earlier] 000039.vlog  1.1 GB VL
[           3 days earlier] 000040.vlog  1.1 GB VL
[           3 days earlier] 000041.vlog  1.1 GB VL
[           3 days earlier] 000042.vlog  1.1 GB VL
[           3 days earlier] 000043.vlog  1.1 GB VL
[           3 days earlier] 000044.vlog  1.1 GB VL
[           3 days earlier] 000045.vlog  1.1 GB VL
[           2 days earlier] 000046.vlog  1.1 GB VL
[       25 minutes earlier] 000047.vlog  1.1 GB VL
[        9 minutes earlier] 000048.vlog  1.1 GB VL
[           21 hours later] 000049.vlog  1.1 GB VL
[              1 day later] 000050.vlog  1.1 GB VL
[             2 days later] 000051.vlog   19 MB VL

[EXTRA]
[2019-06-02T13:37:33Z] LOCK            5 B

[Summary]
Total index size:      0 B
Value log size:      56 GB

Abnormalities:
1 extra file.
0 missing files.
0 empty files.
0 truncated manifests.

diggy · July 20, 2020, 6:47pm

manishrjain commented :

Not enough keys in your system. Instead of DefaultOption, you can use LSMOnlyOption to build this DB, so it would try it’s best to colocate keys and values, which would work better in your case.

diggy · July 20, 2020, 6:47pm

shamil commented :

Hi @manishrjain

I’m using dgraph 1.0.15, I don’t see there badger.options argument, so how do I set it to lsmonly?

diggy · July 20, 2020, 6:47pm

manishrjain commented :

Ahh… yeah. We don’t expose that option. Maybe we can add a flag to expose it.

FWIW, I don’t see even a single SST file in your badger info output. So, looks like you’re just writing data to the same keys repeatedly. This would be eventually GCed as SSTs do compactions, not before.

diggy · July 20, 2020, 6:47pm

shamil commented :

yes we write data to the same keys (mostly), in that case we will never have SST file? Is this means our disk will be filled up?

How you suggest to tackle such case?

diggy · July 20, 2020, 6:47pm

shamil commented :

@manishrjain by the way, the above command was invoked for wal dir
here is same command for postings dir

badger info --dir /data/dgraph/p


[     2019-06-04T00:00:27Z] MANIFEST     1.5 kB MA
[          9 hours earlier] 000079.sst    37 MB L0 
[                      now] 000080.sst    42 MB L0 
[              1 day later] 000002.vlog   69 MB VL

[EXTRA]
[2019-06-02T13:44:16Z] LOCK            5 B

[Summary]
Level 0 size:        79 MB
Level 1 size:          0 B
Total index size:    79 MB
Value log size:      69 MB

Abnormalities:
1 extra file.
0 missing files.
0 empty files.
0 truncated manifests.

so we have sst files there
the question is what I do with wal dir how do I clean it?

diggy · July 20, 2020, 6:47pm

Grool commented :

I have the same problem. How did you solve it?

diggy · July 20, 2020, 6:47pm

anurags92 commented :

@jarifibrahim @MichelDiz Have you seen this issue before? Trying to understand if this still needs a fix.

diggy · July 20, 2020, 6:47pm

jarifibrahim commented :

Hey @anurags92, @shamil and @Grool , the value file size issue is because GC is unable to reclaim space. Let me explain how badger vlog GC works.

The data being written to badger is stored in memory
The in-memory data will be flushed to disk when there’s enough data. The flushed data is written on the disk in the form of SSTs.
Badger GC will not delete any data from the value log (vlog) file unless the data is stored in the value log file is also flushed to the disk in the form of SST. (which translates to badger will not delete data from value log file unless it’s sure this data can be discarded).
The GC also performs some sampling to ensure that there is enough data to for the vlog file to be GCed.

The reason value log GC is not working for @shamil is because the data is actively being updated. If the data is being updated (no new data is added) then the in-memory data in badger will never be flushed to the disk. This is because the flush happens after we have enough data to be written on the disk.

Badger has a 64 mb in-memory skiplist. Unless this skiplist is filled up, we cannot flush it and convet it into SSTs and unless there are on disk SSTs, we cannot GC the value log.

@anurags92 I see two things that we can do here.

Expose an option so that users can run alpha in LSM Only mode. With LSM only mode, the keys and values will be stored together which means the in-memory data structure will fill up quickly and it will be flushed sooner. So, the GC will have some SSTs to work with.
Expose an option to enable/disable badger.KeepL0InMemory option. This option enabled by default and it means badger stores the level 0 in memory. This means, there are two structures in memory (skiplist and level 0 tables) and GC will work only after both the structures are flushed to the disk.

Ideally, we should have some kind of small-data mode which sets both these options internally. A user might not know the implications of setting these options and dgraph should take care of it.

vnium · December 5, 2020, 11:11pm

I have the same problem as the OP. I have around 25 GB of actual data, but the disk space consumed by dgraph grew after a few days to 200GB. Similar to the OP I rarely add data and rather do frequent updates on existing data.

Are any of the options mentioned in the previous post implemented? How can I deal with this problem?

I’m running Dgraph v20.07

mrjn · December 6, 2020, 11:57pm

The upcoming release fixes this behavior.

vnium · January 18, 2021, 11:22am

I have upgraded to the newest release (v20.11) a few weeks ago. Sadly the problem still exist. A lot of .sst and .vlog files are getting generated.
After the upgrade to v20.11 I started at ~25-30 GB, now I am at 690 GB. As mentioned above I mainly do updates on existing data (connecting existing nodes to other existing nodes) and only rarely add data.

Do I have to set some flag to enable the new behavior?

Database directory space distribution:

691G    ./p
1.3M    ./zw
4.0K    ./t
83M     ./w
691G    .

Command used for starting alpha:

dgraph alpha --my=alpha:7080 --lru_mb=87040 --zero=zero:5080 --query_edge_limit 10000000 --enable_sentry=false

llooper-dev · March 2, 2021, 6:06am

Are you using set LSMOnly option to solve the problem of Vlog taking up a lot of space? thk!

mrjn · March 2, 2021, 6:28am

Master has a fix for this. We set the value log threshold to 1MB in Badger by default.

llooper-dev · March 2, 2021, 7:18am

@mrjn Does v20.11.2 include a fix for this issue or when will the latest tag be used to solve this problem?

MichelDiz · March 2, 2021, 1:45pm

Probably not, usually when we say it is in master It is because it hasn’t been released yet.

llooper-dev · March 4, 2021, 7:06am

@mrjn @MichelDiz Can you let me know when the Released Tag containing this change will be published？

MichelDiz · March 4, 2021, 1:55pm

Not sure, I don’t know what commit is the fix. But if not this release, next will be.

vvbalaji · April 14, 2021, 5:25am

compaction improvements that minimize the additional disk space usage are in Release Notes v21.03.0 - Resilient Rocket

Naman · April 14, 2021, 7:26am

In addition, this fix is also a part of v20.11.3 patch release. Use Badger's value log threshold of 1MB (#7415) by danielmai · Pull Request #7474 · dgraph-io/dgraph · GitHub