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Author SHA1 Message Date
Jiaming Yuan c1a62b5fa2 Expect gpu external memory to fail. (#6381) 2020-11-12 19:24:48 +08:00
Jiaming Yuan c90f968d92 Update Python documents. (#6376) 2020-11-12 17:51:32 +08:00
Jiaming Yuan d711d648cb Fix label errors in graph visualization (#6369) 2020-11-11 17:44:59 -08:00
Jiaming Yuan debeae2509 [R] Fix warnings from R check --as-cran (#6374) 
* Remove exit and printf.

* Fix warnings.
 2020-11-11 18:39:37 +08:00
Jiaming Yuan 6e12c2a6f8 [dask] Supoort running on GKE. (#6343) 
* Avoid accessing `scheduler_info()['workers']`.
* Avoid calling `client.gather` inside task.
* Avoid using `client.scheduler_address`.
 2020-11-11 18:04:34 +08:00
Jiaming Yuan 8a17610666 Implement GPU predict leaf. (#6187) 2020-11-11 17:33:47 +08:00
Jiaming YuanandPhilip Hyunsu Cho a5cfa7841e Run R check as cran on action. [skip ci] (#6371) 
Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
 2020-11-11 12:02:53 +08:00
Jiaming Yuan 43efadea2e Deterministic data partitioning for external memory (#6317) 
* Make external memory data partitioning deterministic.

* Change the meaning of `page_size` from bytes to number of rows.

* Design a data pool.

* Note for external memory.

* Enable unity build on Windows CI.

* Force garbage collect on test.
 2020-11-11 06:11:06 +08:00
Jiaming Yuan e65e3cf36e Support shared library in system path. (#6362) 2020-11-10 16:04:25 +08:00
Jiaming Yuan 184e2eac7d Add period to evaluation monitor. (#6348) 2020-11-10 07:47:48 +08:00
Jiaming Yuan 519cee115a Avoid resetting seed for every configuration. (#6349) 2020-11-06 10:28:35 +08:00
Jiaming YuanandPhilip Hyunsu Cho 2cc9662005 Support slicing tree model (#6302) 
This PR is meant the end the confusion around best_ntree_limit and unify model slicing. We have multi-class and random forests, asking users to understand how to set ntree_limit is difficult and error prone.

* Implement the save_best option in early stopping.

Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
 2020-11-02 23:27:39 -08:00
Jiaming Yuan 7756192906 [dask] Fix prediction on DaskDMatrix with multiple meta data. (#6333) 
* Unify the meta handling methods.
 2020-11-02 19:18:44 -05:00
Jiaming Yuan 5a7b3592ed Optional find_package for sanitizers. (#6329) 2020-11-02 19:17:17 -05:00
Jiaming Yuan 048acf81cd Enable shap sparse test. (#6332) 2020-11-01 20:59:27 +08:00
Jiaming Yuan 6ff331b705 Fix Python callback. (#6320) 2020-10-30 05:03:44 +08:00
Jiaming Yuan c80657b542 Fix flaky data initialization test. (#6318) 2020-10-30 03:11:22 +08:00
Jiaming Yuan 74ea82209b Lazy import dask libraries. (#6309) 
* Lazy import dask libraries.

* Lint && fix.

* Use short name.
 2020-10-28 15:50:11 -07:00
Jiaming Yuan dfac5f89e9 Group CLI demo into subdirectory. (#6258) 
CLI is not most developed interface. Putting them into correct directory can help new users to avoid it as most of the use cases are from a language binding.
 2020-10-28 14:40:44 -07:00
Jiaming Yuan e8884c4637 Document tree method for feature weights. (#6312) 2020-10-28 13:42:13 -07:00
Jiaming Yuan c4da967b5c Support unity build. (#6295) 
* Support unity build.

* Setup on Windows Jenkins.

* Revert "Setup on Windows Jenkins."

This reverts commit 8345cb8d2b009eec8ae9fa6f16412a7c9b6ec12c.
 2020-10-28 11:49:28 -07:00
Jiaming Yuan 3310e208fd Fix inplace prediction interval. (#6259) 
* Add back the interval in call.
* Make the interval non-optional.
 2020-10-28 13:13:59 +08:00
Jiaming Yuan cc76724762 Reduce warning. (#6273) 2020-10-27 12:24:19 -07:00
Jiaming Yuan b180223d18 Cleanup RABIT. (#6290) 
* Remove recovery and MPI speed tests.
* Remove readme.
* Remove Python binding.
* Add checks in C API.
 2020-10-27 08:48:22 +08:00
Jiaming Yuan bcfab4d726 Revert "Disable JSON full serialization for now. (#6248)" (#6266) 
This reverts commit 6d293020fb.
 2020-10-27 03:30:47 +08:00
Jiaming Yuan d61b628bf5 Remove RABIT CMake targets. (#6275) 
* Now it's built as part of libxgboost.
* Set correct C API error in RABIT initialization and finalization.
* Remove redundant message.
* Guard the tracker print C API.
 2020-10-27 01:30:20 +08:00
Jiaming YuanandHyunsu Cho 2686d32a36 Skip dask tests on ARM. (#6267) 
Co-authored-by: Hyunsu Cho <chohyu01@cs.washington.edu>
 2020-10-26 15:09:05 +08:00
Jiaming Yuan b5c2a47b20 Drop single point model recovery (#6262) 
* Pass rabit params in JVM package.
* Implement timeout using poll timeout parameter.
* Remove OOB data check.
 2020-10-21 15:27:03 +08:00
Jiaming Yuan 81c37c28d5 Time the CPU tests on Jenkins. (#6257) 
* Time the CPU tests on Jenkins.
* Reduce thread contention.
* Add doc.
* Skip heavy tests on ARM.
 2020-10-20 17:19:07 -07:00
Jiaming Yuan ddf37cca30 Unify thread configuration. (#6186) 2020-10-19 16:05:42 +08:00
Jiaming Yuan 5037abeb86 Fix linear gpu input (#6255) 2020-10-19 12:02:36 +08:00
Jiaming Yuan 6d293020fb Disable JSON full serialization for now. (#6248) 
* Disable JSON serialization for now.

* Multi-class classification is checkpointing for each iteration.
This brings significant overhead.

Revert: 90355b4f00

* Set R tests to use binary.
 2020-10-16 17:59:54 +08:00
Jiaming Yuan 52452bebb9 Fix cls typo. (#6247) 2020-10-16 16:40:44 +08:00
Jiaming Yuan 3da5a69dc9 Fix typo in dask interface. (#6240) 2020-10-15 15:26:29 +08:00
Jiaming Yuan bed7ae4083 Loop over thrust::reduce. (#6229) 
* Check input chunk size of dqdm.
* Add doc for current limitation.
 2020-10-14 10:40:56 +13:00
Jiaming Yuan b05073bda5 [dask] Test for data initializaton. (#6226) 2020-10-13 11:08:35 +08:00
Jiaming Yuan 2443275891 Cleanup Python code. (#6223) 
* Remove pathlike as XGBoost 1.2 requires Python 3.6.
* Move conditional import of dask/distributed into dask module.
 2020-10-12 15:44:41 +08:00
Jiaming Yuan 70c2039748 Catch all standard exceptions in C API. (#6220) 
* `std::bad_alloc` is not guaranteed to be caught.
 2020-10-12 14:01:46 +08:00
Jiaming Yuan 2241563f23 Handle duplicated values in sketching. (#6178) 
* Accumulate weights in duplicated values.
* Fix device id in iterative dmatrix.
 2020-10-10 19:32:44 +08:00
Jiaming Yuan ab5b35134f Rework Python callback functions. (#6199) 
* Define a new callback interface for Python.
* Deprecate the old callbacks.
* Enable early stopping on dask.
 2020-10-10 17:52:36 +08:00
Jiaming Yuan b5b24354b8 More categorical tests and disable shap sparse test. (#6219) 
* Fix tree load with 32 category.
 2020-10-10 16:12:37 +08:00
Jiaming Yuan 70ce5216b5 Add high level tests for categorical data. (#6179) 
* Fix unique.
 2020-10-09 09:27:23 +08:00
Jiaming Yuan 4cfdcaaf7b Move non-OpenMP gtest to GitHub Actions (#6210) 2020-10-08 00:58:21 -07:00
Jiaming Yuan ddc4f20e54 Add JSON schema for categorical splits. (#6194) 2020-10-07 17:33:31 +08:00
Jiaming Yuan fd58005edf Ignore cachedir by joblib. [skip ci] (#6193) 2020-10-04 14:54:32 +08:00
Jiaming Yuan f0c63902ff Use default allocator in sketching. (#6182) 2020-09-30 14:55:59 +08:00
Jiaming Yuan 444131a2e6 Add categorical data support to GPU Hist. (#6164) 2020-09-29 11:27:25 +08:00
Jiaming Yuan 798af22ff4 Add categorical data support to GPU predictor. (#6165) 2020-09-29 11:25:34 +08:00
Jiaming Yuan 7622b8cdb8 Enable categorical data support on Python DMatrix. (#6166) 
* Only pandas is recognized.
 2020-09-29 11:22:56 +08:00
Jiaming Yuan 52c0b3f100 Fix error message. (#6176) 2020-09-29 11:18:25 +08:00
Jiaming Yuan 434a3f35a3 Add TAGS to gitignore. [skip ci] (#6175) 2020-09-27 21:27:40 +08:00
Jiaming Yuan 07355599c2 Option for generating device debug info. (#6168) 
* Supply `-G;-src-in-ptx` when `USE_DEVICE_DEBUG` is set and debug mode is selected.
* Refactor CMake script to gather all CUDA configuration.
* Use CMAKE_CUDA_ARCHITECTURES.  Close #6029.
* Add compute 80.  Close #5999
 2020-09-27 03:26:56 +08:00
Jiaming Yuan 14afdb4d92 Support categorical data in ellpack. (#6140) 2020-09-24 19:28:57 +08:00
Jiaming Yuan 78d72ef936 Add DaskDeviceQuantileDMatrix demo. (#6156) 2020-09-24 14:08:28 +08:00
Jiaming Yuan e033caa3ba Remove linking RMM library. (#6146) 
* Remove linking RMM library.

* RMM is now header only.

* Remove remaining reference.
 2020-09-22 16:59:33 -07:00
Jiaming Yuan 452ac8ea62 Time GPU tests on CI. (#6141) 2020-09-22 14:25:10 +08:00
Jiaming Yuan 33d80ffad0 [dask] Support more meta data on functional interface. (#6132) 
* Add base_margin, label_(lower|upper)_bound.
* Test survival training with dask.
 2020-09-21 16:56:37 +08:00
Jiaming Yuan 7065779afa Improve JSON format for categorical features. (#6128) 
* Gather categories for all nodes.
 2020-09-21 15:35:05 +08:00
Jiaming Yuan 210c131ce7 Support categorical data in GPU sketching. (#6137) 2020-09-21 13:53:06 +08:00
Jiaming Yuan a069a21e03 Implement intrusive ptr (#6129) 
* Use intrusive ptr for JSON.
 2020-09-20 20:07:16 +08:00
Jiaming Yuan e319b63f9e Merge extract cuts into QuantileContainer. (#6125) 
* Use pruning for initial summary construction.
 2020-09-18 16:36:39 +08:00
Jiaming Yuan cc82ca167a [dask] Refactor meta data handling. (#6130) 2020-09-18 13:26:40 +08:00
Jiaming Yuan 5384ed85c8 Use caching allocator from RMM, when RMM is enabled (#6131) 2020-09-17 21:51:49 -07:00
Jiaming Yuan b5f52f0b1b Validate weights are positive values. (#6115) 2020-09-15 09:03:55 +08:00
Jiaming YuanandRory Mitchell c6f2b8c841 Upgrade gputreeshap. (#6099) 
* Upgrade gputreeshap.

Co-authored-by: Rory Mitchell <r.a.mitchell.nz@gmail.com>
 2020-09-15 12:57:22 +12:00
Jiaming Yuan 07945290a2 Remove unused RABIT targets. (#6110) 
* Remove rabit mock.
* Remove rabit base.
 2020-09-11 14:09:44 +08:00
Jiaming Yuan c92d751ad1 Enable building rabit on Windows (#6105) 2020-09-11 11:54:46 +08:00
Jiaming Yuan 08bdb2efc8 Fix dask doc. [skip ci] (#6108) 2020-09-11 10:56:12 +08:00
Jiaming Yuan 3dcd85fab5 Refactor rabit tests (#6096) 
* Merge rabit tests into XGBoost.
* Run them On CI.
* Simplification for CMake scripts.
 2020-09-09 12:30:29 +08:00
Jiaming Yuan 318bffaa10 Fix custom obj link. [skip ci] (#6100) 2020-09-09 10:55:38 +08:00
Jiaming Yuan b0001a6e29 Correct style warnings from clang-tidy for rabit. (#6095) 2020-09-08 12:13:58 +08:00
Jiaming Yuan 93e9af43bb Unify set index data. (#6062) 2020-09-08 11:38:41 +08:00
Jiaming Yuan e5d40b39cd [Breaking] Don't save leaf child count in JSON. (#6094) 
The field is deprecated and not used anywhere in XGBoost.
 2020-09-08 11:11:13 +08:00
Jiaming Yuan 5994f3b14c Don't link imported target. (#6093) 2020-09-07 02:51:09 -07:00
Jiaming Yuan 2fcc4f2886 Unify evaluation functions. (#6037) 2020-08-26 14:23:27 +08:00
Jiaming Yuan 80c8547147 Make binary bin search reusable. (#6058) 
* Move binary search row to hist util.
* Remove dead code.
 2020-08-26 05:05:11 +08:00
Jiaming Yuan 81d8dd79ca Bump header version. (#6056) 2020-08-26 00:29:00 +08:00
Jiaming YuanandPhilip Hyunsu Cho 20c95be625 Expand categorical node. (#6028) 
Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
 2020-08-25 18:53:57 +08:00
Jiaming Yuan a144daf034 Limit tree depth for GPU hist. (#6045) 2020-08-22 19:34:52 +08:00
Jiaming Yuan b9ebbffc57 Fix plotting test. (#6040) 
Previously the test loads a model generated by `test_basic.py`, now we generate
the model explicitly.

* Cleanup saved files for basic tests.
 2020-08-22 13:18:48 +08:00
Jiaming Yuan 7a46515d3d Remove win2016 jvm github action test. (#6042) 2020-08-20 19:39:46 -07:00
Jiaming Yuan 7be2e04bd4 Fix scikit learn cls doc. (#6041) 2020-08-20 19:23:06 -07:00
Jiaming Yuan 29b7fea572 Optimize cpu sketch allreduce for sparse data. (#6009) 
* Bypass RABIT serialization reducer and use custom allgather based merging.
 2020-08-19 10:03:45 +08:00
Jiaming Yuan 90355b4f00 Make JSON the default full serialization format. (#6027) 2020-08-19 09:57:43 +08:00
Jiaming Yuan 4d99c58a5f Feature weights (#5962) 2020-08-18 19:55:41 +08:00
Jiaming Yuan a418278064 Merge pull request #6023 from trivialfis/merge-rabit 
Merge rabit
 2020-08-18 09:01:56 +08:00
fis 111968ca58 Merge rabit 2020-08-18 03:52:33 +08:00
fis 1c5904df3f Remove rabit. 2020-08-18 03:48:36 +08:00
Jiaming Yuan d240463b38 Revert "Remove warning about memset. (#6003)" (#6020) 
This reverts commit 12e3fb6a6c.
 2020-08-17 20:10:15 +08:00
Jiaming Yuan 674c409e9d Remove rabit dependency on public headers. (#6005) 2020-08-13 08:26:20 +08:00
Jiaming Yuan 12e3fb6a6c Remove warning about memset. (#6003) 2020-08-13 08:25:46 +08:00
Jiaming Yuan c3ea3b7e37 Fix nightly build doc. [skip ci] (#6004) 
* Fix nightly build doc. [skip ci]

* Fix title too short. [skip ci]
 2020-08-12 15:00:40 +08:00
Jiaming Yuan ee70a2380b Unify CPU hist sketching (#5880) 2020-08-12 01:33:06 +08:00
Jiaming Yuan 6f7112a848 Move warning about empty dataset. (#5998) 2020-08-11 14:10:51 +08:00
Jiaming Yuan f93f1c03fc Rabit update. (#5978) 
* Remove parameter on JVM Packages.
 2020-08-11 09:17:32 +08:00
Jiaming Yuan 0b2a26fa74 Remove skmaker. (#5971) 2020-08-09 15:23:31 +08:00
Jiaming Yuan 801e6b6800 Fix dask predict shape infer. (#5989) 2020-08-08 14:29:22 +08:00
Jiaming Yuan 4acdd7c6f6 Remove stop process. (#143) 2020-08-05 10:12:00 -07:00
Jiaming Yuan 9c6e791e64 Enforce tree order in JSON. (#5974) 
* Make JSON model IO more future proof by using tree id in model loading.
 2020-08-05 16:44:52 +08:00
Jiaming Yuan dde9c5aaff Fix missing data warning. (#5969) 
* Fix data warning.

* Add numpy/scipy test.
 2020-08-05 16:19:12 +08:00