dvc.data: save and try loading raw dir objects #7597

dtrifiro · 2022-04-19T11:41:11Z

When staging a directory, always save a "raw dir object" to the odb. If the corresponding ".dir" object has not been added to the odb, stage() calls can load the tree from the raw dir object instead of rebuilding it by walking the directory.
This can lead to significant speed improvements when calling dvc status for modified directories.

Fixes #7390

dvc/data/stage.py

efiop · 2022-04-30T22:03:30Z

@dtrifiro Thanks for the benches! 🙏

Btw, could you take a look at what is still taking that long in relation to this PR? I suppose it is mostly the overhead of those ref obj recreations? Just wondering if there are any low hangers that we could pick until a proper solution with persistent refobjects arrives.

dvc/data/stage.py

efiop · 2022-05-02T09:34:26Z

@dtrifiro Thanks for the traces 🙏 Any particular points you were able to identify? Any particular ideas?

dvc/hash_info.py

dvc/data/stage.py

dtrifiro · 2022-05-11T10:23:53Z

Updated benchmarks can be found here:
https://github.com/dtrifiro/dvc-bench/runs/6368942357?check_suite_focus=true#step:8:13

A summary for test_status:

----------------------------------------------------------------------------------- benchmark 'test_status-status': 3 tests ------------------------------------------------------------------------------------
Name (time in s)                                      Min                Max               Mean            StdDev             Median               IQR            Outliers     OPS            Rounds  Iterations
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_status-status (test_status/0001_fix-739)     25.2779 (1.0)      25.2779 (1.0)      25.2779 (1.0)      0.0000 (1.0)      25.2779 (1.0)      0.0000 (1.0)           0;0  0.0396 (1.0)           1           1
test_status-status (test_status/0002_main)        36.9391 (1.46)     36.9391 (1.46)     36.9391 (1.46)     0.0000 (1.0)      36.9391 (1.46)     0.0000 (1.0)           0;0  0.0271 (0.68)          1           1
test_status-status (test_status/0003_2.10.0)      36.9755 (1.46)     36.9755 (1.46)     36.9755 (1.46)     0.0000 (1.0)      36.9755 (1.46)     0.0000 (1.0)           0;0  0.0270 (0.68)          1           1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

----------------------------------------------------------------------------------- benchmark 'test_status-status-changed': 3 tests ------------------------------------------------------------------------------------
Name (time in s)                                              Min                Max               Mean            StdDev             Median               IQR            Outliers     OPS            Rounds  Iterations
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_status-status-changed (test_status/0001_fix-739)     14.9064 (1.0)      14.9064 (1.0)      14.9064 (1.0)      0.0000 (1.0)      14.9064 (1.0)      0.0000 (1.0)           0;0  0.0671 (1.0)           1           1
test_status-status-changed (test_status/0002_main)        26.9573 (1.81)     26.9573 (1.81)     26.9573 (1.81)     0.0000 (1.0)      26.9573 (1.81)     0.0000 (1.0)           0;0  0.0371 (0.55)          1           1
test_status-status-changed (test_status/0003_2.10.0)      27.1236 (1.82)     27.1236 (1.82)     27.1236 (1.82)     0.0000 (1.0)      27.1236 (1.82)     0.0000 (1.0)           0;0  0.0369 (0.55)          1           1
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

------------------------------------------------------------------------------------ benchmark 'test_status-status-changed-noop': 3 tests -----------------------------------------------------------------------------------
Name (time in s)                                                   Min                Max               Mean            StdDev             Median               IQR            Outliers     OPS            Rounds  Iterations
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_status-status-changed-noop (test_status/0001_fix-739)      3.9865 (1.0)       3.9865 (1.0)       3.9865 (1.0)      0.0000 (1.0)       3.9865 (1.0)      0.0000 (1.0)           0;0  0.2508 (1.0)           1           1
test_status-status-changed-noop (test_status/0002_main)        26.6765 (6.69)     26.6765 (6.69)     26.6765 (6.69)     0.0000 (1.0)      26.6765 (6.69)     0.0000 (1.0)           0;0  0.0375 (0.15)          1           1
test_status-status-changed-noop (test_status/0003_2.10.0)      27.0214 (6.78)     27.0214 (6.78)     27.0214 (6.78)     0.0000 (1.0)      27.0214 (6.78)     0.0000 (1.0)           0;0  0.0370 (0.15)          1           1
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

efiop · 2022-05-11T11:14:35Z

dvc/data/stage.py

+        tree = Tree.load(odb, hash_info.as_raw())
+        tree.check(odb)
+    except ObjectFormatError:
+        raise FileNotFoundError


Suggested change

raise FileNotFoundError

raise FileNotFoundError from exc

While we are here:

Suggested change

raise FileNotFoundError

raise FileNotFoundError(errno.ENOENT, "No such object", odb.hash_to_path(hash_info.value))

Or, just use hash_info.value for simplicity.

dtrifiro · 2022-05-11T15:45:46Z

@dtrifiro Thanks for the traces 🙏 Any particular points you were able to identify? Any particular ideas?

We could push performance a little bit more by avoiding calling stat when creating the ReferenceHashFile in staging.add (calling fs.checksum).

Hacking around, I was able to get a working prototype and ran some benchmarks with dvc-bench's test_status. For the large dataset it's around a 4% speedup, although this comes at the price overriding of ReferenceObjectDB.add and duplicating some code, so it might not be worth it.

When staging a directory, always save a "raw dir object" to the odb. If the corresponding ".dir" object has not been added to the odb, `stage()` calls can load the tree from the raw dir object instead of rebuilding it by walking the directory. This can lead to significant speed improvements when calling `dvc status` for modified directories. Fixes iterative#7390

skshetry · 2022-05-11T16:06:16Z

@dtrifiro, are those improvements on test_status-status and test_status-status-changed expected?

dtrifiro · 2022-05-12T10:46:39Z

@dtrifiro, are those improvements on test_status-status and test_status-status-changed expected?

I forgot to update the main branch for fork after rebasing, meaning the comparison was against a slightly outdated revision. Here's a comparison for this PR against its base (main@3faf4132):

https://github.com/dtrifiro/dvc-bench/runs/6404025103?check_suite_focus=true#step:8:258

-------------------------------- benchmark 'test_status-status': 5 tests --------------------------------
Name (time in s)                                   Median            StdDev            Rounds  Iterations
---------------------------------------------------------------------------------------------------------
test_status-status (test_status/0001_fix-739)     22.8981 (1.10)     0.0000 (1.0)           1           1
test_status-status (test_status/0002_main)        21.4079 (1.03)     0.0000 (1.0)           1           1
test_status-status (test_status/0003_2.10.2)      20.7695 (1.0)      0.0000 (1.0)           1           1
test_status-status (test_status/0004_2.9.5)       32.8662 (1.58)     0.0000 (1.0)           1           1
test_status-status (test_status/0005_2.6.3)       36.3975 (1.75)     0.0000 (1.0)           1           1
---------------------------------------------------------------------------------------------------------

-------------------------------- benchmark 'test_status-status-changed': 5 tests --------------------------------
Name (time in s)                                           Median            StdDev            Rounds  Iterations
-----------------------------------------------------------------------------------------------------------------
test_status-status-changed (test_status/0001_fix-739)     12.6867 (1.0)      0.0000 (1.0)           1           1
test_status-status-changed (test_status/0002_main)        12.7397 (1.00)     0.0000 (1.0)           1           1
test_status-status-changed (test_status/0003_2.10.2)      12.8673 (1.01)     0.0000 (1.0)           1           1
test_status-status-changed (test_status/0004_2.9.5)       25.0225 (1.97)     0.0000 (1.0)           1           1
test_status-status-changed (test_status/0005_2.6.3)       25.2563 (1.99)     0.0000 (1.0)           1           1
-----------------------------------------------------------------------------------------------------------------

-------------------------------- benchmark 'test_status-status-changed-noop': 5 tests --------------------------------
Name (time in s)                                                Median            StdDev            Rounds  Iterations
----------------------------------------------------------------------------------------------------------------------
test_status-status-changed-noop (test_status/0001_fix-739)      3.7390 (1.0)      0.0000 (1.0)           1           1
test_status-status-changed-noop (test_status/0002_main)        12.7007 (3.40)     0.0000 (1.0)           1           1
test_status-status-changed-noop (test_status/0003_2.10.2)      11.8403 (3.17)     0.0000 (1.0)           1           1
test_status-status-changed-noop (test_status/0004_2.9.5)       24.2830 (6.49)     0.0000 (1.0)           1           1
test_status-status-changed-noop (test_status/0005_2.6.3)       25.2839 (6.76)     0.0000 (1.0)           1           1
----------------------------------------------------------------------------------------------------------------------

efiop

Ok, it looks like we could clean this up a bit more, but let's run with it for now and get back to it when we safe ref objects.

efiop · 2022-05-29T21:15:30Z

dvc/data/stage.py

+            obj = load(odb, hash_info)
+            check(odb, obj, check_hash=False)


Btw, this PR introduced a typo: it should be _odb here 🙁

Introduced in iterative/dvc#7597

dtrifiro changed the title ~~speed up status calls with modified dirs~~ WIP: speed up status calls with modified dirs Apr 19, 2022

efiop self-requested a review April 19, 2022 13:32

dtrifiro force-pushed the fix/7390-status-recalculating-hashes branch 2 times, most recently from 86c491e to d6152f7 Compare April 20, 2022 12:58

daavoo mentioned this pull request Apr 20, 2022

DVC very slow for datasets with many files #7607

Closed

dtrifiro force-pushed the fix/7390-status-recalculating-hashes branch 7 times, most recently from 8d4fc81 to 73e1716 Compare April 27, 2022 17:13

skshetry mentioned this pull request Apr 29, 2022

introduce data:status command #7663

Closed

dtrifiro force-pushed the fix/7390-status-recalculating-hashes branch from 73e1716 to a207fcf Compare April 29, 2022 16:15

This comment was marked as outdated.

Sign in to view

dtrifiro changed the title ~~WIP: speed up status calls with modified dirs~~ speed up status calls for modified dirs Apr 30, 2022

dtrifiro force-pushed the fix/7390-status-recalculating-hashes branch from a207fcf to 22fe50b Compare April 30, 2022 16:04

dtrifiro added the A: status Related to the dvc diff/list/status label Apr 30, 2022

dtrifiro marked this pull request as ready for review April 30, 2022 16:04

dtrifiro requested a review from a team as a code owner April 30, 2022 16:04

efiop reviewed Apr 30, 2022

View reviewed changes

dvc/data/stage.py Outdated Show resolved Hide resolved

efiop reviewed Apr 30, 2022

View reviewed changes

dvc/data/stage.py Outdated Show resolved Hide resolved

This comment was marked as outdated.

Sign in to view

dtrifiro force-pushed the fix/7390-status-recalculating-hashes branch from 22fe50b to 6124165 Compare May 2, 2022 09:02

efiop reviewed May 2, 2022

View reviewed changes

dvc/data/stage.py Outdated Show resolved Hide resolved

efiop reviewed May 2, 2022

View reviewed changes

dvc/hash_info.py Outdated Show resolved Hide resolved

efiop changed the title ~~speed up status calls for modified dirs~~ status: speed up for modified dirs May 2, 2022

efiop added the optimize Optimizes DVC label May 2, 2022

pmrowla reviewed May 9, 2022

View reviewed changes

dvc/data/stage.py Outdated Show resolved Hide resolved

dtrifiro commented May 9, 2022

View reviewed changes

dvc/data/stage.py Outdated Show resolved Hide resolved

dtrifiro changed the title ~~status: speed up for modified dirs~~ dvc.stage: save and try loading raw dir hashes May 9, 2022

dtrifiro marked this pull request as draft May 9, 2022 11:03

dtrifiro changed the title ~~dvc.stage: save and try loading raw dir hashes~~ dvc.stage: save and try loading raw dir objects May 9, 2022

skshetry mentioned this pull request May 9, 2022

TqdmCallback: make it lazy #7715

Merged

dtrifiro force-pushed the fix/7390-status-recalculating-hashes branch 3 times, most recently from 352517c to 27b7927 Compare May 10, 2022 08:14

dtrifiro marked this pull request as ready for review May 10, 2022 08:14

skshetry reviewed May 10, 2022

View reviewed changes

dvc/data/stage.py Outdated Show resolved Hide resolved

dtrifiro force-pushed the fix/7390-status-recalculating-hashes branch from 27b7927 to 3f24f91 Compare May 10, 2022 09:11

dtrifiro changed the title ~~dvc.stage: save and try loading raw dir objects~~ dvc.data: save and try loading raw dir objects May 11, 2022

dtrifiro force-pushed the fix/7390-status-recalculating-hashes branch from 3f24f91 to b8362bc Compare May 11, 2022 07:39

efiop reviewed May 11, 2022

View reviewed changes

dtrifiro force-pushed the fix/7390-status-recalculating-hashes branch from b8362bc to 3c7d08e Compare May 11, 2022 14:06

dtrifiro force-pushed the fix/7390-status-recalculating-hashes branch from 3c7d08e to 42f87aa Compare May 11, 2022 15:47

dtrifiro force-pushed the fix/7390-status-recalculating-hashes branch from 42f87aa to 1f92c4b Compare May 11, 2022 15:57

efiop approved these changes May 12, 2022

View reviewed changes

efiop merged commit 7a795f7 into iterative:main May 12, 2022

dtrifiro deleted the fix/7390-status-recalculating-hashes branch May 12, 2022 16:48

efiop reviewed May 29, 2022

View reviewed changes

efiop added a commit to iterative/dvc-data that referenced this pull request May 29, 2022

stage: use odb_ instead of odb

d3c74ec

Introduced in iterative/dvc#7597

efiop mentioned this pull request May 29, 2022

stage: use odb_ instead of odb iterative/dvc-data#34

Merged

efiop added a commit to iterative/dvc-data that referenced this pull request May 29, 2022

stage: use odb_ instead of odb

4b4c034

Introduced in iterative/dvc#7597

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

dvc.data: save and try loading raw dir objects #7597

dvc.data: save and try loading raw dir objects #7597

dtrifiro commented Apr 19, 2022 •

edited

Loading

This comment was marked as outdated.

efiop commented Apr 30, 2022

This comment was marked as outdated.

efiop commented May 2, 2022 •

edited

Loading

dtrifiro commented May 11, 2022

efiop May 11, 2022

skshetry May 11, 2022 •

edited

Loading

dtrifiro commented May 11, 2022

skshetry commented May 11, 2022

dtrifiro commented May 12, 2022

efiop left a comment

efiop May 29, 2022

	raise FileNotFoundError
	raise FileNotFoundError(errno.ENOENT, "No such object", odb.hash_to_path(hash_info.value))

dvc.data: save and try loading raw dir objects #7597

dvc.data: save and try loading raw dir objects #7597

Conversation

dtrifiro commented Apr 19, 2022 • edited Loading

This comment was marked as outdated.

efiop commented Apr 30, 2022

This comment was marked as outdated.

efiop commented May 2, 2022 • edited Loading

dtrifiro commented May 11, 2022

efiop May 11, 2022

Choose a reason for hiding this comment

skshetry May 11, 2022 • edited Loading

Choose a reason for hiding this comment

dtrifiro commented May 11, 2022

skshetry commented May 11, 2022

dtrifiro commented May 12, 2022

efiop left a comment

Choose a reason for hiding this comment

efiop May 29, 2022

Choose a reason for hiding this comment

dtrifiro commented Apr 19, 2022 •

edited

Loading

efiop commented May 2, 2022 •

edited

Loading

skshetry May 11, 2022 •

edited

Loading