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* [SPARK-4384] [PySpark] improve sort spillingDavies Liu2014-11-191-1/+10
| | | | | | | | | | | | If there some big broadcasts (or other object) in Python worker, the free memory could be used for sorting will be too small, then it will keep spilling small files into disks, finally failed with too many open files. This PR try to delay the spilling until the used memory goes over limit and start to increase since last spilling, it will increase the size of spilling files, improve the stability and performance in this cases. (We also do this in ExternalAggregator). Author: Davies Liu <davies@databricks.com> Closes #3252 from davies/sort and squashes the following commits: 711fb6c [Davies Liu] improve sort spilling
* [SPARK-3886] [PySpark] simplify serializer, use AutoBatchedSerializer by ↵Davies Liu2014-11-031-4/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | default. This PR simplify serializer, always use batched serializer (AutoBatchedSerializer as default), even batch size is 1. Author: Davies Liu <davies@databricks.com> This patch had conflicts when merged, resolved by Committer: Josh Rosen <joshrosen@databricks.com> Closes #2920 from davies/fix_autobatch and squashes the following commits: e544ef9 [Davies Liu] revert unrelated change 6880b14 [Davies Liu] Merge branch 'master' of github.com:apache/spark into fix_autobatch 1d557fc [Davies Liu] fix tests 8180907 [Davies Liu] Merge branch 'master' of github.com:apache/spark into fix_autobatch 76abdce [Davies Liu] clean up 53fa60b [Davies Liu] Merge branch 'master' of github.com:apache/spark into fix_autobatch d7ac751 [Davies Liu] Merge branch 'master' of github.com:apache/spark into fix_autobatch 2cc2497 [Davies Liu] Merge branch 'master' of github.com:apache/spark into fix_autobatch b4292ce [Davies Liu] fix bug in master d79744c [Davies Liu] recover hive tests be37ece [Davies Liu] refactor eb3938d [Davies Liu] refactor serializer in scala 8d77ef2 [Davies Liu] simplify serializer, use AutoBatchedSerializer by default.
* [SPARK-3786] [PySpark] speedup testsDavies Liu2014-10-061-3/+2
| | | | | | | | | | | | | | | | | | | | | | | | | This patch try to speed up tests of PySpark, re-use the SparkContext in tests.py and mllib/tests.py to reduce the overhead of create SparkContext, remove some test cases, which did not make sense. It also improve the performance of some cases, such as MergerTests and SortTests. before this patch: real 21m27.320s user 4m42.967s sys 0m17.343s after this patch: real 9m47.541s user 2m12.947s sys 0m14.543s It almost cut the time by half. Author: Davies Liu <davies.liu@gmail.com> Closes #2646 from davies/tests and squashes the following commits: c54de60 [Davies Liu] revert change about memory limit 6a2a4b0 [Davies Liu] refactor of tests, speedup 100%
* [SPARK-3463] [PySpark] aggregate and show spilled bytes in PythonDavies Liu2014-09-131-3/+16
| | | | | | | | | | | | | | | | | | Aggregate the number of bytes spilled into disks during aggregation or sorting, show them in Web UI. ![spilled](https://cloud.githubusercontent.com/assets/40902/4209758/4b995562-386d-11e4-97c1-8e838ee1d4e3.png) This patch is blocked by SPARK-3465. (It includes a fix for that). Author: Davies Liu <davies.liu@gmail.com> Closes #2336 from davies/metrics and squashes the following commits: e37df38 [Davies Liu] remove outdated comments 1245eb7 [Davies Liu] remove the temporary fix ebd2f43 [Davies Liu] Merge branch 'master' into metrics 7e4ad04 [Davies Liu] Merge branch 'master' into metrics fbe9029 [Davies Liu] show spilled bytes in Python in web ui
* [SPARK-3073] [PySpark] use external sort in sortBy() and sortByKey()Davies Liu2014-08-261-8/+83
| | | | | | | | | | | | | | | | | Using external sort to support sort large datasets in reduce stage. Author: Davies Liu <davies.liu@gmail.com> Closes #1978 from davies/sort and squashes the following commits: bbcd9ba [Davies Liu] check spilled bytes in tests b125d2f [Davies Liu] add test for external sort in rdd eae0176 [Davies Liu] choose different disks from different processes and instances 1f075ed [Davies Liu] Merge branch 'master' into sort eb53ca6 [Davies Liu] Merge branch 'master' into sort 644abaf [Davies Liu] add license in LICENSE 19f7873 [Davies Liu] improve tests 55602ee [Davies Liu] use external sort in sortBy() and sortByKey()
* [SPARK-2974] [SPARK-2975] Fix two bugs related to spark.local.dirsJosh Rosen2014-08-191-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | This PR fixes two bugs related to `spark.local.dirs` and `SPARK_LOCAL_DIRS`, one where `Utils.getLocalDir()` might return an invalid directory (SPARK-2974) and another where the `SPARK_LOCAL_DIRS` override didn't affect the driver, which could cause problems when running tasks in local mode (SPARK-2975). This patch fixes both issues: the new `Utils.getOrCreateLocalRootDirs(conf: SparkConf)` utility method manages the creation of local directories and handles the precedence among the different configuration options, so we should see the same behavior whether we're running in local mode or on a worker. It's kind of a pain to mock out environment variables in tests (no easy way to mock System.getenv), so I added a `private[spark]` method to SparkConf for accessing environment variables (by default, it just delegates to System.getenv). By subclassing SparkConf and overriding this method, we can mock out SPARK_LOCAL_DIRS in tests. I also fixed a typo in PySpark where we used `SPARK_LOCAL_DIR` instead of `SPARK_LOCAL_DIRS` (I think this was technically innocuous, but it seemed worth fixing). Author: Josh Rosen <joshrosen@apache.org> Closes #2002 from JoshRosen/local-dirs and squashes the following commits: efad8c6 [Josh Rosen] Address review comments: 1dec709 [Josh Rosen] Minor updates to Javadocs. 7f36999 [Josh Rosen] Use env vars to detect if running in YARN container. 399ac25 [Josh Rosen] Update getLocalDir() documentation. bb3ad89 [Josh Rosen] Remove duplicated YARN getLocalDirs() code. 3e92d44 [Josh Rosen] Move local dirs override logic into Utils; fix bugs: b2c4736 [Josh Rosen] Add failing tests for SPARK-2974 and SPARK-2975. 007298b [Josh Rosen] Allow environment variables to be mocked in tests. 6d9259b [Josh Rosen] Fix typo in PySpark: SPARK_LOCAL_DIR should be SPARK_LOCAL_DIRS
* [SPARK-2627] [PySpark] have the build enforce PEP 8 automaticallyNicholas Chammas2014-08-061-10/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | As described in [SPARK-2627](https://issues.apache.org/jira/browse/SPARK-2627), we'd like Python code to automatically be checked for PEP 8 compliance by Jenkins. This pull request aims to do that. Notes: * We may need to install [`pep8`](https://pypi.python.org/pypi/pep8) on the build server. * I'm expecting tests to fail now that PEP 8 compliance is being checked as part of the build. I'm fine with cleaning up any remaining PEP 8 violations as part of this pull request. * I did not understand why the RAT and scalastyle reports are saved to text files. I did the same for the PEP 8 check, but only so that the console output style can match those for the RAT and scalastyle checks. The PEP 8 report is removed right after the check is complete. * Updates to the ["Contributing to Spark"](https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark) guide will be submitted elsewhere, as I don't believe that text is part of the Spark repo. Author: Nicholas Chammas <nicholas.chammas@gmail.com> Author: nchammas <nicholas.chammas@gmail.com> Closes #1744 from nchammas/master and squashes the following commits: 274b238 [Nicholas Chammas] [SPARK-2627] [PySpark] minor indentation changes 983d963 [nchammas] Merge pull request #5 from apache/master 1db5314 [nchammas] Merge pull request #4 from apache/master 0e0245f [Nicholas Chammas] [SPARK-2627] undo erroneous whitespace fixes bf30942 [Nicholas Chammas] [SPARK-2627] PEP8: comment spacing 6db9a44 [nchammas] Merge pull request #3 from apache/master 7b4750e [Nicholas Chammas] merge upstream changes 91b7584 [Nicholas Chammas] [SPARK-2627] undo unnecessary line breaks 44e3e56 [Nicholas Chammas] [SPARK-2627] use tox.ini to exclude files b09fae2 [Nicholas Chammas] don't wrap comments unnecessarily bfb9f9f [Nicholas Chammas] [SPARK-2627] keep up with the PEP 8 fixes 9da347f [nchammas] Merge pull request #2 from apache/master aa5b4b5 [Nicholas Chammas] [SPARK-2627] follow Spark bash style for if blocks d0a83b9 [Nicholas Chammas] [SPARK-2627] check that pep8 downloaded fine dffb5dd [Nicholas Chammas] [SPARK-2627] download pep8 at runtime a1ce7ae [Nicholas Chammas] [SPARK-2627] space out test report sections 21da538 [Nicholas Chammas] [SPARK-2627] it's PEP 8, not PEP8 6f4900b [Nicholas Chammas] [SPARK-2627] more misc PEP 8 fixes fe57ed0 [Nicholas Chammas] removing merge conflict backups 9c01d4c [nchammas] Merge pull request #1 from apache/master 9a66cb0 [Nicholas Chammas] resolving merge conflicts a31ccc4 [Nicholas Chammas] [SPARK-2627] miscellaneous PEP 8 fixes beaa9ac [Nicholas Chammas] [SPARK-2627] fail check on non-zero status 723ed39 [Nicholas Chammas] always delete the report file 0541ebb [Nicholas Chammas] [SPARK-2627] call Python linter from run-tests 12440fa [Nicholas Chammas] [SPARK-2627] add Scala linter 61c07b9 [Nicholas Chammas] [SPARK-2627] add Python linter 75ad552 [Nicholas Chammas] make check output style consistent
* [SPARK-2538] [PySpark] Hash based disk spilling aggregationDavies Liu2014-07-241-0/+439
During aggregation in Python worker, if the memory usage is above spark.executor.memory, it will do disk spilling aggregation. It will split the aggregation into multiple stage, in each stage, it will partition the aggregated data by hash and dump them into disks. After all the data are aggregated, it will merge all the stages together (partition by partition). Author: Davies Liu <davies.liu@gmail.com> Closes #1460 from davies/spill and squashes the following commits: cad91bf [Davies Liu] call gc.collect() after data.clear() to release memory as much as possible. 37d71f7 [Davies Liu] balance the partitions 902f036 [Davies Liu] add shuffle.py into run-tests dcf03a9 [Davies Liu] fix memory_info() of psutil 67e6eba [Davies Liu] comment for MAX_TOTAL_PARTITIONS f6bd5d6 [Davies Liu] rollback next_limit() again, the performance difference is huge: e74b785 [Davies Liu] fix code style and change next_limit to memory_limit 400be01 [Davies Liu] address all the comments 6178844 [Davies Liu] refactor and improve docs fdd0a49 [Davies Liu] add long doc string for ExternalMerger 1a97ce4 [Davies Liu] limit used memory and size of objects in partitionBy() e6cc7f9 [Davies Liu] Merge branch 'master' into spill 3652583 [Davies Liu] address comments e78a0a0 [Davies Liu] fix style 24cec6a [Davies Liu] get local directory by SPARK_LOCAL_DIR 57ee7ef [Davies Liu] update docs 286aaff [Davies Liu] let spilled aggregation in Python configurable e9a40f6 [Davies Liu] recursive merger 6edbd1f [Davies Liu] Hash based disk spilling aggregation
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