PathLike wrapper/cache for ExternalStorage #186

dwhswenson · 2023-04-26T18:35:14Z

This is a start to solving #120. We've identified the following goals:

We want to be able to use an arbitrary external backend to shared (as well as permanent), which we already have via ExternalStorage, instead of it needing to be a directory on the same host.
We want the user experience to mirror conveniences of pathlib.Path, which will (we hope) minimize frustration with the transition for users.

So far, this PR doesn't integrate that into any of the execution process. That can be either part of this PR or a future one.

The basic approach here involves 2 classes:

SharedRoot: represents the root directory for a given unit. By default, this will exist at $SCRATCH/.holding/$UNIT_LABEL. This is where most of the actual logic is. It contains references to all the paths that have been registered with it. On deletion (or on demand) this transfers all paths registered with it to the ExternalStorage.
SharedPath: represents any path within SharedRoot. Contains information on the actual file path on the system, as well as the label used as the key for the external key-value store. Creation is typically from root / "some_path" or some_path / "subpath". A SharedPath can be used like any other PathLike in open, and can be converted via pathlib.Path(shared_path) to get all the functionality of pathlib.

As I'm opening this, code is still in progress. But at least the tests should give a picture of usage; please take a look!

Update for some final to-do items.

Remove prefix; I believe it is no longer used
Reconsider when dag_label needs to be given
Switch delete_empty_dirs to keep_empty_dirs (consistent with other keep_*)
Check special cases where a directory gets registered as a StagedPath (due to __fspath__ getting called)
StagingDirectory => StagingRegistry
Re-read docs and comments for accuracy
Make StagingRegistry objects non-FileLike (potential footgun on os.path.join(context.shared, "filename.txt")).

codecov · 2023-04-26T18:40:34Z

Codecov Report

Attention: 3 lines in your changes are missing coverage. Please review.

Comparison is base (a426dce) 99.21% compared to head (8489c24) 99.15%.

Files	Patch %	Lines
gufe/storage/stagingregistry.py	97.81%	3 Missing ⚠️

Additional details and impacted files

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dwhswenson · 2023-04-26T18:45:07Z

gufe/storage/pseudodirectory.py

+ read_only : bool
+ write to prevent NEW files from being written within this shared
+ directory. NOTE: This will not prevent overwrite of existing files,
+ in scratch space, but it will prevent changed files from uploading
+ to the external storage.


This read_only is mainly to prevent the following mistake:

shared = root.get_other_shared(other_unit_prefix) with open(shared / "oldfile.txt") as f: ... # good so far! with open(shared / "newfile.txt", mode='wb') as f: ... # uh-oh -- now we're writing into the wrong unit's space!

However, it won't stop open(shared / "oldfile.txt", mode='wb'). You can still overwrite that data. If that data is in a separate permanent storage, it will be fine -- only overwrite locally. (If you set shared up such that the directory it uses is identical to the internal holding cache here, of course, it would overwrite that.)

…o shared-object-v2

richardjgowers · 2023-04-26T20:41:00Z

gufe/storage/pseudodirectory.py

+ def __del__(self):
+ # take everything in self.shared_dir and write to it shared; keeping
+ # our prefix
+ self.transfer_holding_to_external()
+ if self.delete_holding:
+ shutil.rmtree(self.shared_dir)


iirc __del__ isn't called on del obj but instead when garbage collection happens. Maybe instead make transfer_holding_to_external always explicit and don't rely on garbage collection related things

works for me ... it's an executor-level thing anyway, and I don't mind asking the executor writer to think about how files get moved around (don't want to ask the protocol writer to think about that)

or maybe if you want this behaviour, use a context manager, so instead of __del__ use __exit__

This started out as a context manager. I switched it away because it makes actual usage kind of weird -- the entirety of the execution block where this is used gets indented by one level, which I don't particularly like. It gets worse if you have one of these for shared and one for permanent -- there's a syntax for setting multiple context managers at once, but I've also always found that kind of weird.

But I can switch it back to a context manager if you want 🤷‍♂️

gufe/storage/pseudodirectory.py

…ect-v2

dwhswenson · 2023-05-31T19:33:58Z

Still in progress, but here's a quick update to what is included in this PR now. Before I dive any further into writing unit tests, take a quick look, @richardjgowers (at least at the contents of this comment).

Main idea: We have "staging" directories that are local. From a protocol author's perspective, shared, permanent, and scratch are PathLikes. However, the paths pointed to by shared and permanent are in the local scratch space, and the files there are transferred to external storage as part of the executor.

I've expanded this PR to include some tools for handling the entirety of the scratch / shared / permanent storage lifecycle. There are two context managers: one for the unit level that provides the PathLikes that are used by the protocol author, and which handles the cleanup at the end of that level, and one for the dag level that provides the thing that creates the unit-level context manager, and which cleans up at the dag level.

Here's an example from a protocol author's viewpoint (kind of faking our real units, but this gives the rough picture):

gufe/gufe/tests/storage/test_storagemanager.py

Lines 27 to 53 in ed5e83c

 class Unit1: 

 key = "unit1" 

 def run(self, scratch, shared, permanent): 

 (scratch / "foo.txt").touch() 

 with open(shared / "bar.txt", mode='w') as f: 

 f.write("bar was written") 

 with open(permanent / "baz.txt", mode='w') as f: 

 f.write("baz was written") 

 return "done 1" 

 class Unit2: 

 key = "unit2" 

 def run(self, scratch, shared, permanent): 

 (scratch / "foo2.txt").touch() 

 with shared.other_shared("unit1") as prev_shared: 

 with open(prev_shared / "bar.txt", mode='r') as f: 

 bar = f.read() 

 # note that you can open a file from permanent as if it was 

 # from shared -- everything in permanent is in shared 

 with open(prev_shared / "baz.txt", mode='r') as f: 

 baz = f.read() 

 return {"bar": bar, "baz": baz}

For the executor, the basic picture is something like this:

manager = StorageManager(scratch, shared_external, permanent_external)
with manager.running_dag(dag_label) as dag_ctx:
    for unit in ordered_dag_units:
        with dag_ctx.running_unit(unit.key) as (scratch, shared, permanent):
            unit_result = unit.run(scratch, shared, permanent)  # or however we run the unit
        # when this context ends, scratch will be deleted, shared external storage will be
        # updated, and shared holding will be deleted
# when this context ends, permanent external storage will be updated, and permanent holding 
# will be deleted

For much more detail, see this lifecycle test:

gufe/gufe/tests/storage/test_storagemanager.py

Lines 59 to 131 in ed5e83c

 def test_lifecycle(request, manager, dag_units): 

 # heavy integration test to ensure that the whole process works 

 # this is the primary test of _DAGStorageManager 

 storage_manager = request.getfixturevalue(f"storage_manager_{manager}") 

 permanent_root = storage_manager.permanent_root 

 shared_root = storage_manager.shared_root 

 results = [] 

 unit1_dir = Path(storage_manager.get_shared("dag_label", "unit1")) 

 scratch1 = Path(storage_manager.get_scratch("dag_label", "unit1")) 

 scratch2 = Path(storage_manager.get_scratch("dag_label", "unit2")) 

 barfile = unit1_dir / "bar.txt" 

 bazfile = unit1_dir / "baz.txt" 

 foofile = scratch1 / "foo.txt" 

 foo2file = scratch2 / "foo2.txt" 

 all_files = {barfile, bazfile, foofile, foo2file} 

 with storage_manager.running_dag("dag_label") as dag_ctx: 

 for unit in dag_units: 

 with dag_ctx.running_unit(unit.key) as (scratch, shared, permanent): 

 results.append(unit.run(scratch, shared, permanent)) 

 # check that the expected files are found in staging 

 exists = { 

 "unit1": {barfile, bazfile, foofile}, 

 "unit2": {foo2file, bazfile} 

 }[unit.key] 

 for file in exists: 

 assert file.exists() 

 for file in all_files - exists: 

 assert not file.exists() 

 # check that shared store is as expected 

 expected_in_shared = { 

 "unit1": set(), 

 "unit2": {"unit1/bar.txt", "unit1/baz.txt"} 

 }[unit.key] 

 assert set(shared_root.iter_contents()) == expected_in_shared 

 # check that permanent store is empty 

 assert list(permanent_root.iter_contents()) == [] 

 # AFTER THE RUNNING_UNIT CONTEXT 

 # Same for both units because unit2 doesn't add anything to 

 # shared/permanent 

 # Files staged for shared should be transferred to shared and 

 # removed from the staging directories; files staged for 

 # permanent should remain 

 for_permanent = {bazfile} 

 for file in for_permanent: 

 assert file.exists() 

 for file in all_files - for_permanent: 

 assert not file.exists() 

 # check that we have things in shared 

 expected_in_shared = {"unit1/bar.txt", "unit1/baz.txt"} 

 assert set(shared_root.iter_contents()) == expected_in_shared 

 # ensure that we haven't written to permanent yet 

 assert list(permanent_root.iter_contents()) == [] 

 # AFTER THE RUNNING_DAG CONTEXT 

 # all staged files should be deleted 

 for file in all_files: 

 assert not file.exists() 

 # shared still contains everything it had; but this isn't something we 

 # guarantee, so we don't actually test for it 

 # assert set(shared_root.iter_contents()) == {"unit1/bar.txt", 

 # "unit1/baz.txt"} 

 assert list(permanent_root.iter_contents()) == ["unit1/baz.txt"] 

 # check the results 

 assert results == [ 

 "done 1", 

 {"bar": "bar was written", "baz": "baz was written"} 

 ]

Next tests will be to check the special cases that shared or permanent represent the same directories as the staging directory, or each other.

dotsdl · 2023-06-02T17:08:11Z

From power hour:

         with shared.other_shared("unit1") as prev_shared: 
             with open(prev_shared / "bar.txt", mode='r') as f: 
                 bar = f.read()

Instead of having shared.other_shared("unit1"), which would allow a e.g. unitX to access unitA's shared space even if unitA wasn't an explicit dependency of unitX.

Instead, making unitX access unitA's shared via its ProtocolDAGResult object passed into run would avoid this issue.

Makes much more sense as _safe_to_delete_holding

dotsdl · 2023-09-09T01:33:04Z

docs/guide/storage.rst

+protocol authors. In detail, this provides protocol authors with
+``PathLike`` objects for ``scratch``, ``shared``, and ``permanent``. All
+three of these objects actually point to special subdirectories of the
+scratch space for a specific unit, but are managed by context manangers at


Suggested change

scratch space for a specific unit, but are managed by context manangers at

local execution space for a specific unit, but are managed by context managers at

…o shared-object-v2

dotsdl · 2023-09-09T02:07:11Z

docs/guide/storage.rst

+:class:`.DAGContextManager` to create a context to run a unit. That context
+creates a :class:`.SharedStaging` and a :class:`.PermanentStaging`
+associated with the specific unit. Those staging directories, with the
+scratch directory, are provided to the :class:`.ProtocolDAGUnit`, so that


Suggested change

scratch directory, are provided to the :class:`.ProtocolDAGUnit`, so that

scratch directory, are provided to the :class:`.ProtocolUnit`, so that

pep8speaks · 2023-09-19T03:59:40Z

Hello @dwhswenson! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2024-01-22 17:35:13 UTC

…ect-v2

…o shared-object-v2

also, some docs cleanup/updates

richardjgowers

this is partial, I'm still going to go through the tests and try breaking this locally myself

richardjgowers · 2023-12-06T13:23:15Z

docs/guide/storage.rst

+ network-scale analysis. Anything stored here will be usable after the
+ calculation has completed.


"after the calculation" could equally apply to a Unit. Maybe instead "Anything stored here will be retrievable after the Protocol estimation has completed"

richardjgowers · 2023-12-06T13:24:40Z

docs/guide/storage.rst

+In an abstract sense, as used by protocol developers, these three levels
+correspond to three lifetimes of data:
+


Another last chance to rename things, what if we instead just named the storage lifetimes against the thing they're scoped to. So scratch -> unit_storage, shared -> dag_storage and permanent -> campaign_storage. The idea being it's easier to remember their scope.

richardjgowers · 2023-12-06T13:25:54Z

docs/guide/storage.rst

+ the end of the :class:`.ProtocolDAG`, but is not guaranteed to exist after
+ the :class:`.ProtocolDAG` terminates.
+* ``permanent``: This is the data that will be needed beyond the scope of a
+ single rough estimate of the calculation. This could include anything that


not sure I like "single rough estimate" here, a single estimate might be perfectly fine. Maybe instead, "this is the data that will be available for post-simulation analysis beyond the scope of a single DAG"

richardjgowers · 2023-12-06T13:26:32Z

docs/guide/storage.rst

+
+The ``scratch`` area is always a local directory. However, ``shared`` and
+``permanent`` can be external (remote) resources, using the
+:class:`.ExternalResource` API.


maybe mention that whilst these might not be a local directory, they will still act like one?

richardjgowers · 2023-12-06T13:27:55Z

docs/guide/storage.rst

+As a practical matter, the GUFE storage system can be handled with a
+:class:`.StorageManager`. This automates some aspects of the transfer
+between stages of the GUFE storage system, and simplifies the API for
+protocol authors. In detail, this provides protocol authors with


can we use "developers" instead of "protocol authors"? I'm thinking developer is more common, someone might get confused thinking "protocol author" is the agent which is submitting protocols or something daft

richardjgowers · 2023-12-06T13:36:06Z

gufe/storage/stagingregistry.py

+ """Transfer a given file from staging into external storage
+ """


if I've followed this, it returns the held_file back if it was transferred, but otherwise None? Can store_path ever (knowingly) fail?

if I've followed this, it returns the held_file back if it was transferred, but otherwise None?

Yes. The real point here is that transfer_staging_to_external, which tries to transfer everything, returns the list of files that have been transferred. That was needed because it turned out that the successfully transferred files are needed by the StorageManager if keep_shared is False. I might be able to move that responsibility into a delete_transferred method on StagingRegistry, though.

Can store_path ever (knowingly) fail?

I'm not sure what you mean here by "knowingly." If store_path does not successfully store the path, it should raise an exception. The only way it can communicate failure is via exception, and if it fails silently, that's a bug.

richardjgowers · 2023-12-06T14:03:02Z

gufe/storage/stagingregistry.py

+ """
+ other = self._get_other_shared(prefix, delete_staging)
+ yield other
+ other.cleanup()


Could we instead put a __enter__/__exit__ etc on SharedStaging? This feels strange to have some of the class' intended behaviour defined in this method?

So other_shared here would just return be return SharedStaging(...)

richardjgowers · 2023-12-06T14:08:38Z

gufe/storage/storagemanager.py

+ self.shared_staging = SharedStaging(
+ scratch=self.scratch_root,
+ external=self.shared_root,
+ staging=self.staging,
+ delete_empty_dirs=delete_empty_dirs,
+ prefix="" # TODO: remove prefix
+ )


why is shared scoped to the lifetime of the StorageManager? Could you not create this inside the scope of the running_dag method?

richardjgowers · 2023-12-06T14:09:09Z

gufe/storage/storagemanager.py

+from .stagingregistry import StagingPath # typing
+
+
+class StorageManager:


doccing this with some usage examples would be handy

This required a pretty significant rewrite of the code.

Mainly matters for the StorageManager

…o shared-object-v2

Make a function that returns a pathlib.Path be the main thing, instead of the property that returns a string. Almost all usage of `.fspath` was to then wrap it in a pathlib.Path. This is more convenient for users.

This is to avoid likely footguns related to using os.path.join. Includes test of error on os.path.join.

richardjgowers · 2024-01-01T15:57:02Z

docs/guide/storage.rst

+ network, are not recommended for ``shared``.
+
+
+Details: Manangement of the Storage Lifetime


typo: management

dwhswenson and others added 2 commits April 26, 2023 13:05

PathLike wrapper/cache for ExternalStorage

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Merge branch 'main' into shared-object-v2

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…o shared-object-v2

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docstrings

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Merge branch 'main' of github.com:OpenFreeEnergy/gufe into shared-obj…

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…ect-v2

Add StorageManager code

472151e

rename to Stagine

b692c2f

Add tests for _delete_empty_dirs

7432ff4

Storage docs

319d0d0

outline of storage manager tests

5650609

minor improvements on staging directory

ddbbd19

first storage lifecycle test works

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Merge branch 'main' of github.com:OpenFreeEnergy/gufe into shared-obj…

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…ect-v2

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lots of updates; switched to harness for tests

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Big reorg for shared overlapping staging

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remove _storage_path_conflict

1e4ca2c

Makes much more sense as _safe_to_delete_holding

docs & types

a6d26f3

docs, types, logging

aabbc33

finish TestHoldingOverlapsPermanentStorageManager

b4d73b3

mypy

7af006e

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58a58bc

renaming around DAGContextManager

8e429f5

Merge branch 'main' into shared-object-v2

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…o shared-object-v2

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This was referenced Sep 19, 2023

Refactor Task system to retain ProtocolDAG, upload ProtocolUnitResults and ResultFiles as they complete OpenFreeEnergy/alchemiscale#180

Open

[WIP] Result path conversion and upload to object store OpenFreeEnergy/alchemiscale#104

Open

dwhswenson and others added 5 commits November 3, 2023 15:37

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Merge branch 'main' of github.com:OpenFreeEnergy/gufe into shared-obj…

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…ect-v2

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dwhswenson mentioned this pull request Dec 1, 2023

[WIP] Use StorageManager in execute_DAG #258

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remove prefix; remove get_other_shared

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This required a pretty significant rewrite of the code.

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Mainly matters for the StorageManager

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Make a function that returns a pathlib.Path be the main thing, instead of the property that returns a string. Almost all usage of `.fspath` was to then wrap it in a pathlib.Path. This is more convenient for users.

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PathLike wrapper/cache for ExternalStorage #186

PathLike wrapper/cache for ExternalStorage #186

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	scratch space for a specific unit, but are managed by context manangers at
	local execution space for a specific unit, but are managed by context managers at

	scratch directory, are provided to the :class:`.ProtocolDAGUnit`, so that
	scratch directory, are provided to the :class:`.ProtocolUnit`, so that

		network-scale analysis. Anything stored here will be usable after the
		calculation has completed.

		In an abstract sense, as used by protocol developers, these three levels
		correspond to three lifetimes of data:

		"""Transfer a given file from staging into external storage
		"""

		from .stagingregistry import StagingPath # typing


		class StorageManager:

		network, are not recommended for ``shared``.


		Details: Manangement of the Storage Lifetime

PathLike wrapper/cache for ExternalStorage #186

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PathLike wrapper/cache for ExternalStorage #186

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