[GraphBolt][CUDA] Incremental GPU graph caching. #7470

mfbalin · 2024-06-20T20:38:29Z

Description

Follow up PR will add the dataloader logic so that the cache can be utilized for faster GPU sampling.

Checklist

Please feel free to remove inapplicable items for your PR.

The PR title starts with [$CATEGORY] (such as [NN], [Model], [Doc], [Feature]])
I've leverage the tools to beautify the python and c++ code.
The PR is complete and small, read the Google eng practice (CL equals to PR) to understand more about small PR. In DGL, we consider PRs with less than 200 lines of core code change are small (example, test and documentation could be exempted).
All changes have test coverage
Code is well-documented
To the best of my knowledge, examples are either not affected by this change, or have been fixed to be compatible with this change
Related issue is referred in this PR
If the PR is for a new model/paper, I've updated the example index here.

Changes

dgl-bot · 2024-06-20T20:38:56Z

To trigger regression tests:

@dgl-bot run [instance-type] [which tests] [compare-with-branch];
For example: @dgl-bot run g4dn.4xlarge all dmlc/master or @dgl-bot run c5.9xlarge kernel,api dmlc/master

dgl-bot · 2024-06-20T20:45:18Z

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dgl-bot · 2024-06-20T21:28:10Z

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dgl-bot · 2024-06-20T21:38:32Z

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mfbalin · 2024-06-20T23:59:08Z

@frozenbugs let's land this PR and the followup PR before we release DGL 2.3. That way, we can say the new release has this major feature.

dgl-bot · 2024-06-20T23:59:34Z

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mfbalin · 2024-06-21T02:50:39Z

@dgl-bot

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graphbolt/src/cuda/extension/gpu_graph_cache.h

graphbolt/src/cuda/extension/gpu_graph_cache.cu

python/dgl/graphbolt/impl/gpu_graph_cache.py

graphbolt/src/cuda/extension/gpu_graph_cache.cu

dgl-bot · 2024-06-26T03:06:50Z

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dgl-bot · 2024-06-26T03:44:00Z

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graphbolt/src/cuda/extension/gpu_graph_cache.h

dgl-bot · 2024-06-26T04:09:36Z

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dgl-bot · 2024-06-26T04:39:15Z

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mfbalin · 2024-06-26T04:40:07Z

@Rhett-Ying CI failure output:

tests/distributed/test_mp_dataloader.py::test_edge_dataloader_homograph[False-self-False-0] Fatal Python error: Segmentation fault

Thread 0x00007fb4b8fdf700 (most recent call first):
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/threading.py", line 324 in wait
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/threading.py", line 607 in wait
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/tqdm/_monitor.py", line 60 in run
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/threading.py", line 1016 in _bootstrap_inner
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/threading.py", line 973 in _bootstrap

Current thread 0x00007fb4e5ce6800 (most recent call first):
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/codecs.py", line 322 in decode
  File "/home/ubuntu/jenkins/workspace/dgl_PR-7470@2/python/dgl/partition.py", line 271 in get_peak_mem
  File "/home/ubuntu/jenkins/workspace/dgl_PR-7470@2/python/dgl/distributed/partition.py", line 921 in partition_graph
  File "/home/ubuntu/jenkins/workspace/dgl_PR-7470@2/tests/distributed/test_mp_dataloader.py", line 770 in check_dataloader
  File "/home/ubuntu/jenkins/workspace/dgl_PR-7470@2/tests/distributed/test_mp_dataloader.py", line 914 in test_edge_dataloader_homograph
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/_pytest/python.py", line 162 in pytest_pyfunc_call
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/_pytest/python.py", line 1627 in runtest
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/_pytest/runner.py", line 173 in pytest_runtest_call
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/_pytest/runner.py", line 241 in &lt;lambda&gt;
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/_pytest/runner.py", line 341 in from_call
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/_pytest/runner.py", line 240 in call_and_report
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/_pytest/runner.py", line 135 in runtestprotocol
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/_pytest/runner.py", line 116 in pytest_runtest_protocol
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/_pytest/main.py", line 364 in pytest_runtestloop
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/_pytest/main.py", line 339 in _main
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/_pytest/main.py", line 285 in wrap_session
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/_pytest/main.py", line 332 in pytest_cmdline_main
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/_pytest/config/__init__.py", line 178 in main
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/_pytest/config/__init__.py", line 206 in console_main
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/site-packages/pytest/__main__.py", line 7 in &lt;module&gt;
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/runpy.py", line 86 in _run_code
  File "/opt/conda/envs/pytorch-ci/lib/python3.10/runpy.py", line 196 in _run_module_as_main

Extension modules: numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, torch._C, torch._C._fft, torch._C._linalg, torch._C._nested, torch._C._nn, torch._C._sparse, torch._C._special, dgl._ffi._cy3.core, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, psutil._psutil_linux, psutil._psutil_posix, pyarrow.lib, pyarrow._parquet, pyarrow._fs, pyarrow._azurefs, pyarrow._hdfs, pyarrow._gcsfs, pyarrow._s3fs, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pyarrow._compute, pandas._libs.ops, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, scipy.io.matlab._mio_utils, scipy.io.matlab._streams, scipy.io.matlab._mio5_utils, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, yaml._yaml (total: 115)
tests/scripts/task_distributed_test.sh: line 37:   638 Segmentation fault      (core dumped) python3 -m pytest -v --capture=tee-sys --junitxml=pytest_distributed.xml --durations=100 tests/distributed/*.py
FAIL: distributed

Rhett-Ying · 2024-06-26T05:12:43Z

@mfbalin pls skip it. It's known issue

mfbalin · 2024-06-26T05:14:05Z

@mfbalin pls skip it. It's known issue

I can not skip it. I don't have the permissions to merge into master when the CI does not clear.

dgl-bot · 2024-06-26T05:17:30Z

Commit ID: 5ed6d0c

Build ID: 32

Status: ❌ CI test failed in Stage [Torch CPU Example test].

Report path: link

Full logs path: link

mfbalin · 2024-06-26T05:18:15Z

another test failure:

+ bash tests/scripts/task_example_test.sh cpu
============================= test session starts ==============================
platform linux -- Python 3.10.14, pytest-8.2.0, pluggy-1.5.0 -- /opt/conda/envs/pytorch-ci/bin/python3
cachedir: .pytest_cache
rootdir: /home/ubuntu/jenkins/workspace/dgl_PR-7470
configfile: pyproject.toml
collecting ... collected 12 items

tests/examples/test_sampling_examples.py::test_node_classification PASSED [  8%]
tests/examples/test_sampling_examples.py::test_link_prediction PASSED    [ 16%]
tests/examples/test_sparse_examples.py::test_gcn PASSED                  [ 25%]
tests/examples/test_sparse_examples.py::test_gcnii PASSED                [ 33%]
tests/examples/test_sparse_examples.py::test_appnp PASSED                [ 41%]
tests/examples/test_sparse_examples.py::test_c_and_s PASSED              [ 50%]
tests/examples/test_sparse_examples.py::test_gat PASSED                  [ 58%]
tests/examples/test_sparse_examples.py::test_hgnn PASSED                 [ 66%]
tests/examples/test_sparse_examples.py::test_hypergraphatt PASSED        [ 75%]
tests/examples/test_sparse_examples.py::test_sgc PASSED                  [ 83%]
tests/examples/test_sparse_examples.py::test_sign FAILED                 [ 91%]
tests/examples/test_sparse_examples.py::test_twirls PASSED               [100%]

=================================== FAILURES ===================================
__________________________________ test_sign ___________________________________

    def test_sign():
        script = os.path.join(EXAMPLE_ROOT, "sign.py")
        out = subprocess.run(["python", str(script)], capture_output=True)
        assert (
            out.returncode == 0
        ), f"stdout: {out.stdout.decode('utf-8')}\nstderr: {out.stderr.decode('utf-8')}"
        stdout = out.stdout.decode("utf-8")
&gt;       assert float(stdout[-5:]) &gt; 0.7
E       AssertionError: assert 0.697 &gt; 0.7
E        +  where 0.697 = float('.697\n')

tests/examples/test_sparse_examples.py:101: AssertionError
- generated xml file: /home/ubuntu/jenkins/workspace/dgl_PR-7470/pytest_backend.xml -
============================ slowest 100 durations =============================
34.74s call     tests/examples/test_sparse_examples.py::test_twirls
21.53s call     tests/examples/test_sparse_examples.py::test_gcnii
9.20s call     tests/examples/test_sparse_examples.py::test_hypergraphatt
8.06s call     tests/examples/test_sampling_examples.py::test_node_classification
7.80s call     tests/examples/test_sampling_examples.py::test_link_prediction
6.16s call     tests/examples/test_sparse_examples.py::test_hgnn
3.27s call     tests/examples/test_sparse_examples.py::test_appnp
3.22s call     tests/examples/test_sparse_examples.py::test_gat
3.18s call     tests/examples/test_sparse_examples.py::test_gcn
2.82s call     tests/examples/test_sparse_examples.py::test_sign
2.61s call     tests/examples/test_sparse_examples.py::test_sgc
2.55s call     tests/examples/test_sparse_examples.py::test_c_and_s

(24 durations &lt; 0.005s hidden.  Use -vv to show these durations.)
=========================== short test summary info ============================
FAILED tests/examples/test_sparse_examples.py::test_sign - AssertionError: assert 0.697 &gt; 0.7
 +  where 0.697 = float('.697\n')
=================== 1 failed, 11 passed in 105.21s (0:01:45) ===================
FAIL: sparse examples on cpu

Rhett-Ying · 2024-06-26T05:18:49Z

I've just made a change on CI and rebased this PR. let's see if it works well now. If not, I will merge it if other CI tests pass.

mfbalin · 2024-06-26T05:20:10Z

I've just made a change on CI and rebased this PR. let's see if it works well now. If not, I will merge it if other CI tests pass.

The CI already passed: #7470 (comment)
The only change I made is to improve a comment in the code. I would appreciate it if you merged it now.

[GraphBolt][CUDA] Incremental GPU graph caching.

0c0f115

mfbalin requested a review from frozenbugs June 20, 2024 20:38

mfbalin marked this pull request as draft June 20, 2024 20:38

fix the replace fnction

2a74efc

make progress on python side

8f170b9

add test file, rename to gpu_graph_cache.py

66c9336

Implementation working now.

bba8975

mfbalin marked this pull request as ready for review June 20, 2024 23:57

linting

58302d4

mfbalin force-pushed the gb_cuda_gpu_graph_cache branch from daa9d36 to 3366909 Compare June 21, 2024 01:49

make num_nodes argument unnecessary.

58bfe3c

mfbalin force-pushed the gb_cuda_gpu_graph_cache branch from 3366909 to 58bfe3c Compare June 21, 2024 01:50

early stop if there is not enough space

bade092

mfbalin added 2 commits June 21, 2024 19:27

add shortcut for when there is no miss.

d8fa4f0

map capacity resize improvement.

d251473

add doc

be19dd6

address more reviews by adding more doc.

08cc956

frozenbugs reviewed Jun 26, 2024

View reviewed changes

address reviews

9ed6e9c

mfbalin requested a review from frozenbugs June 26, 2024 03:05

Merge branch 'master' into gb_cuda_gpu_graph_cache

b2e10fc

frozenbugs approved these changes Jun 26, 2024

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frozenbugs reviewed Jun 26, 2024

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graphbolt/src/cuda/extension/gpu_graph_cache.h Outdated Show resolved Hide resolved

mfbalin added 2 commits June 26, 2024 04:08

address minor review comment.

968b1a8

Merge branch 'master' into gb_cuda_gpu_graph_cache

bb18427

mfbalin added the Release Candidate Candidate PRs for the upcoming release label Jun 26, 2024

Merge branch 'master' into gb_cuda_gpu_graph_cache

5ed6d0c

mfbalin mentioned this pull request Jun 26, 2024

[CI] Spurious test failures #7481

Open

Merge branch 'master' into gb_cuda_gpu_graph_cache

494d7f9

Rhett-Ying merged commit c822bc1 into master Jun 26, 2024
1 of 2 checks passed

Rhett-Ying deleted the gb_cuda_gpu_graph_cache branch June 26, 2024 05:26

This pull request was closed.

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[GraphBolt][CUDA] Incremental GPU graph caching. #7470

[GraphBolt][CUDA] Incremental GPU graph caching. #7470

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[GraphBolt][CUDA] Incremental GPU graph caching. #7470

[GraphBolt][CUDA] Incremental GPU graph caching. #7470

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