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Posted to reviews@spark.apache.org by buckhx <gi...@git.apache.org> on 2016/04/14 16:53:49 UTC

[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

GitHub user buckhx opened a pull request:

    https://github.com/apache/spark/pull/12398

    [SPARK-5929][PYSPARK] Context addPyPackage and addRequirementsFile

    ## What changes were proposed in this pull request?
    
    Context.addPyPackage()
    Context.addRequirementsFile()
    
    Both of these methods take a package on the master and ship it to the workers when called instead of having to manually install packages on all workers.
    
    ## How was this patch tested?
    
    Unit tests are written, but I do not believe they accurately reflect a distributed environment. The test_add_py_package is not using addPyPackage and still works. The addRequirementsFile method requires internet access to hit the global pypi server and won't work on the current Jenkins build system.
    
    We have had this patch running at Palantir for about a year in production.
    


You can merge this pull request into a Git repository by running:

    $ git pull https://github.com/buckhx/spark master

Alternatively you can review and apply these changes as the patch at:

    https://github.com/apache/spark/pull/12398.patch

To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:

    This closes #12398
    
----
commit 0ed060df2ec5a1a0427df6c160bd51c7014b29da
Author: buck heroux <bh...@palantir.com>
Date:   2015-02-18T17:50:27Z

    added requirements file to pyspark

commit 6b8bcde60378b58998f5c14d81d72de81f44d718
Author: buck heroux <bh...@palantir.com>
Date:   2015-02-18T23:30:28Z

    tarfile has no contextmanager in python2.

commit 2773483ea6cc244cb7de02c7dc184391a94d29e6
Author: buck heroux <bh...@palantir.com>
Date:   2015-02-19T01:52:06Z

    reqs fix

commit 0371ad9b13f96dcc534d897789ccd32f907d5ed9
Author: buck heroux <bh...@palantir.com>
Date:   2015-02-19T02:06:48Z

    temp tar file

commit f2a46e5d6e309a5ba29259cc1f77e594d932b0f5
Author: buck heroux <bh...@palantir.com>
Date:   2015-03-05T00:51:46Z

    bubbled up try finally

commit fca4be61c6542b807a0d5370f761ef031fc7eb86
Author: buck heroux <bh...@palantir.com>
Date:   2015-03-05T00:53:17Z

    forgot to remove

commit d28752297ec5b10f6afce49713f4efe20f8d533f
Author: buck heroux <bh...@palantir.com>
Date:   2015-04-03T20:35:44Z

    added requirementsFile tests and switch to __import__

commit 76ff63733b9d293c43218aa743a74bcce36a20c9
Author: buck heroux <bh...@palantir.com>
Date:   2015-04-03T20:41:30Z

    merged tests

commit 565bf7fc0889390178f8f96d0ed9a917b287e164
Author: buck heroux <bh...@palantir.com>
Date:   2015-07-14T17:54:12Z

    pep8 styling

commit 23771fde4674c73d5fb0bbb478385d9cf55c648b
Author: buck heroux <bh...@palantir.com>
Date:   2015-10-05T22:07:48Z

    support namespace packages and extract addModule logic

commit cd21c5c06d6a611f4e738199f20582aeb6087fd7
Author: buck heroux <bh...@palantir.com>
Date:   2015-10-05T22:10:17Z

    tmp_dir to mod

commit 39f26d93b7030f2d7bfe7782414dc5b016cdd852
Author: buck heroux <bh...@palantir.com>
Date:   2015-10-21T20:22:06Z

    remove reqs from context constructor

commit 49a4ed0931b20dd2982c16e1ca3533cef65303af
Author: buck heroux <bh...@palantir.com>
Date:   2015-10-21T20:39:24Z

    upstream merge

commit 1501d0f4744d4645a239f3c3fb931469c2038fa8
Author: buckhx <bu...@gmail.com>
Date:   2016-03-31T17:30:58Z

    upstream merge

commit 3af35bb5f54518f2d07db7665c78d18c5fe2bdf2
Author: buck heroux <bh...@palantir.com>
Date:   2016-04-13T19:08:06Z

    Merge remote-tracking branch 'upstream/master'

commit 88a1d6ceffaddfc5f3aa5afc07d65a1d9ddb54e9
Author: buck heroux <bh...@palantir.com>
Date:   2016-04-13T22:57:23Z

    add_py_package test

commit 93b9e9fdd464744f90eb3a7eb325f853e2f113d4
Author: buck heroux <bh...@palantir.com>
Date:   2016-04-14T14:39:17Z

    uncommented pip_requirements test

commit 82476a632c5da724c3ca45ed8b888a946d934104
Author: buck heroux <bh...@palantir.com>
Date:   2016-04-14T14:42:05Z

    removed todo

commit ce9966e875a6d00bbe6325dc5fc9519ce5292c04
Author: buck heroux <bh...@palantir.com>
Date:   2016-04-14T14:47:36Z

    spacing

----


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by holdenk <gi...@git.apache.org>.
Github user holdenk commented on a diff in the pull request:

    https://github.com/apache/spark/pull/12398#discussion_r59800417
  
    --- Diff: python/pyspark/context.py ---
    @@ -814,6 +817,40 @@ def addPyFile(self, path):
                 import importlib
                 importlib.invalidate_caches()
     
    +    def addPyPackage(self, pkg):
    +        """
    +        Add a package to the spark context, the package must have already been
    +        imported by the driver via __import__ semantics. Supports namespace
    +        packages by simulating the loading __path__ as a set of modules from
    +        the __path__ list in a single package.
    +        """
    +        tmp_dir = tempfile.mkdtemp()
    +        try:
    +            tar_path = os.path.join(tmp_dir, pkg.__name__+'.tar.gz')
    +            tar = tarfile.open(tar_path, "w:gz")
    +            for mod in pkg.__path__[::-1]:
    +                # adds in reverse to simulate namespace loading path
    +                tar.add(mod, arcname=os.path.basename(mod))
    +            tar.close()
    +            self.addPyFile(tar_path)
    +        finally:
    +            shutil.rmtree(tmp_dir)
    +
    +    def addRequirementsFile(self, path):
    +        """
    +        Add a pip requirements file to distribute dependencies for all tasks
    +        on thie SparkContext in the future. An ImportError will be thrown if
    +        a module in the file can't be downloaded.
    +        See https://pip.pypa.io/en/latest/user_guide.html#requirements-files
    +        Raises ImportError if the requirement can't be found
    +        """
    +        import pip
    +        for req in pip.req.parse_requirements(path, session=uuid.uuid1()):
    +            if not req.check_if_exists():
    +                pip.main(['install', req.req.__str__()])
    --- End diff --
    
    So it seems that this can sometimesrequire elevated privileges based on the issues with the previous jenkins run. What about if at startup we created a fixed temp directory per context adding it to our path with `sys.path.insert(0, self.pipBase)` and at install did something along the lines of:
    `pip.main(['install', req.req.__str__(), '--target', self.pipBase])` so that we don't have to have write permissions to the default pip target?



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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by buckhx <gi...@git.apache.org>.
Github user buckhx commented on the pull request:

    https://github.com/apache/spark/pull/12398#issuecomment-217902925
  
    Added an addPyPackage example to the docstring and that test formatting. We're looking into adding the spark-submit arg for --py-requirements.
    
    The pip API takes a file path via pip.req.parse_requirements https://github.com/pypa/pip/blob/develop/pip/req/req_file.py#L64 but it looks like it might be possible to take a string and break it out line by with a mock file name via pip.req.process_line & pip.req.preprocess https://github.com/pypa/pip/blob/develop/pip/req/req_file.py#L110


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[GitHub] spark issue #12398: [SPARK-5929][PYSPARK] Context addPyPackage and addPyRequ...

Posted by buckhx <gi...@git.apache.org>.
Github user buckhx commented on the issue:

    https://github.com/apache/spark/pull/12398
  
    @davies how's this looking?


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[GitHub] spark issue #12398: [SPARK-5929][PYSPARK] Context addPyPackage and addPyRequ...

Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:

    https://github.com/apache/spark/pull/12398
  
    **[Test build #3068 has started](https://amplab.cs.berkeley.edu/jenkins/job/NewSparkPullRequestBuilder/3068/consoleFull)** for PR 12398 at commit [`9c37e06`](https://github.com/apache/spark/commit/9c37e0649a75d22d5712b08dcd6c3acee412f719).


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[GitHub] spark issue #12398: [SPARK-5929][PYSPARK] Context addPyPackage and addPyRequ...

Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:

    https://github.com/apache/spark/pull/12398
  
    **[Test build #3068 has finished](https://amplab.cs.berkeley.edu/jenkins/job/NewSparkPullRequestBuilder/3068/consoleFull)** for PR 12398 at commit [`9c37e06`](https://github.com/apache/spark/commit/9c37e0649a75d22d5712b08dcd6c3acee412f719).
     * This patch **fails Spark unit tests**.
     * This patch merges cleanly.
     * This patch adds no public classes.


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[GitHub] spark issue #12398: [SPARK-5929][PYSPARK] Context addPyPackage and addPyRequ...

Posted by holdenk <gi...@git.apache.org>.
Github user holdenk commented on the issue:

    https://github.com/apache/spark/pull/12398
  
    @buckhx any interest in updating this against master?


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by davies <gi...@git.apache.org>.
Github user davies commented on a diff in the pull request:

    https://github.com/apache/spark/pull/12398#discussion_r61992299
  
    --- Diff: python/pyspark/context.py ---
    @@ -814,6 +817,40 @@ def addPyFile(self, path):
                 import importlib
                 importlib.invalidate_caches()
     
    +    def addPyPackage(self, pkg):
    +        """
    +        Add a package to the spark context, the package must have already been
    +        imported by the driver via __import__ semantics. Supports namespace
    +        packages by simulating the loading __path__ as a set of modules from
    +        the __path__ list in a single package.
    +        """
    +        tmp_dir = tempfile.mkdtemp()
    +        try:
    +            tar_path = os.path.join(tmp_dir, pkg.__name__+'.tar.gz')
    +            tar = tarfile.open(tar_path, "w:gz")
    +            for mod in pkg.__path__[::-1]:
    +                # adds in reverse to simulate namespace loading path
    +                tar.add(mod, arcname=os.path.basename(mod))
    +            tar.close()
    +            self.addPyFile(tar_path)
    +        finally:
    +            shutil.rmtree(tmp_dir)
    +
    +    def addRequirementsFile(self, path):
    --- End diff --
    
    Will it be better to pass the requirements as string?


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by davies <gi...@git.apache.org>.
Github user davies commented on a diff in the pull request:

    https://github.com/apache/spark/pull/12398#discussion_r61992444
  
    --- Diff: python/pyspark/context.py ---
    @@ -814,6 +817,40 @@ def addPyFile(self, path):
                 import importlib
                 importlib.invalidate_caches()
     
    +    def addPyPackage(self, pkg):
    +        """
    +        Add a package to the spark context, the package must have already been
    +        imported by the driver via __import__ semantics. Supports namespace
    +        packages by simulating the loading __path__ as a set of modules from
    +        the __path__ list in a single package.
    +        """
    --- End diff --
    
    Could you add an example here?


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by holdenk <gi...@git.apache.org>.
Github user holdenk commented on the pull request:

    https://github.com/apache/spark/pull/12398#issuecomment-210179401
  
    Since @andrewor14 got Jenkins to run the earlier iteration of this PR maybe you could do the same here?


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by buckhx <gi...@git.apache.org>.
Github user buckhx commented on the pull request:

    https://github.com/apache/spark/pull/12398#issuecomment-211420495
  
    I could see the pipBase approach working.
    
    The other testing blocker I have is that it seems like that context that's getting created in the test is able to use local packages. The test package that's created is able to be imported on the workers without distributing it via addPyPackage. https://github.com/apache/spark/pull/12398/files#diff-388a156f4ce454fe98d7a99a0f7f0012R1950
    
    Is there a way to get the mocked workers to not use the master python path?
    
    The pip part is nice, but I think the meat of this PR is in the addPyPackage.
    
    I looked into adding a flag to the CLI, but kind of went down a rabbit hole trying to figure it out. I'd advocate adding it to the CLI, but think someone working in the spark core space could get that integrated much more efficiently than myself.


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by holdenk <gi...@git.apache.org>.
Github user holdenk commented on the pull request:

    https://github.com/apache/spark/pull/12398#issuecomment-210171984
  
    So looking back on the predecessor PR it seemed like @davies suggested adding support for specifying these at runtime with `spark-submit` & it seems like the pip install permissions issue might still be present for testing.


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[GitHub] spark pull request #12398: [SPARK-5929][PYSPARK] Context addPyPackage and ad...

Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:

    https://github.com/apache/spark/pull/12398


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by davies <gi...@git.apache.org>.
Github user davies commented on a diff in the pull request:

    https://github.com/apache/spark/pull/12398#discussion_r61992184
  
    --- Diff: python/pyspark/tests.py ---
    @@ -1947,6 +1947,33 @@ def test_with_stop(self):
                 sc.stop()
             self.assertEqual(SparkContext._active_spark_context, None)
     
    +    def test_add_py_package(self):
    +        name = "test_tmp"
    +        try:
    +            os.mkdir(name)
    +            with open(os.path.join(name, "__init__.py"), 'w+') as temp:
    +                temp.write("triple = lambda x: 3*x")
    +            pkg = __import__(name)
    +            with SparkContext() as sc:
    +                #trips = sc.parallelize([0, 1, 2, 3]).map(test_tmp.triple)
    +                #sc.addPyPackage(pkg)
    +                trips = sc.parallelize([0, 1, 2, 3]).map(lambda x: pkg.triple(x))
    +                self.assertSequenceEqual([0, 3, 6, 9], trips.collect())
    +        finally:
    +            shutil.rmtree(name)
    +        
    --- End diff --
    
    remove the extra empty line


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by holdenk <gi...@git.apache.org>.
Github user holdenk commented on the pull request:

    https://github.com/apache/spark/pull/12398#issuecomment-210172335
  
    I think having this supported could be very useful :)


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:

    https://github.com/apache/spark/pull/12398#issuecomment-216749580
  
    **[Test build #2967 has finished](https://amplab.cs.berkeley.edu/jenkins/job/NewSparkPullRequestBuilder/2967/consoleFull)** for PR 12398 at commit [`ce9966e`](https://github.com/apache/spark/commit/ce9966e875a6d00bbe6325dc5fc9519ce5292c04).
     * This patch **fails Python style tests**.
     * This patch merges cleanly.
     * This patch adds no public classes.


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by davies <gi...@git.apache.org>.
Github user davies commented on the pull request:

    https://github.com/apache/spark/pull/12398#issuecomment-216751245
  
    @buckhx  These API seems useful, could you also add an argument for bin/spark-submit (only for requirement file) ?


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[GitHub] spark issue #12398: [SPARK-5929][PYSPARK] Context addPyPackage and addPyRequ...

Posted by holdenk <gi...@git.apache.org>.
Github user holdenk commented on the issue:

    https://github.com/apache/spark/pull/12398
  
    @buckhx Just following up to see if this is something you are still interested in working on?


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[GitHub] spark issue #12398: [SPARK-5929][PYSPARK] Context addPyPackage and addPyRequ...

Posted by HyukjinKwon <gi...@git.apache.org>.
Github user HyukjinKwon commented on the issue:

    https://github.com/apache/spark/pull/12398
  
    ping @buckhx


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by buckhx <gi...@git.apache.org>.
Github user buckhx commented on the pull request:

    https://github.com/apache/spark/pull/12398#issuecomment-218478989
  
    @robert3005 added the --py-requirements to spark-submit. I'm looking at passing the requirements as a list or a line delimited string currently.


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the pull request:

    https://github.com/apache/spark/pull/12398#issuecomment-209986241
  
    Can one of the admins verify this patch?


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the pull request:

    https://github.com/apache/spark/pull/12398#issuecomment-216749512
  
    **[Test build #2967 has started](https://amplab.cs.berkeley.edu/jenkins/job/NewSparkPullRequestBuilder/2967/consoleFull)** for PR 12398 at commit [`ce9966e`](https://github.com/apache/spark/commit/ce9966e875a6d00bbe6325dc5fc9519ce5292c04).


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by andrewor14 <gi...@git.apache.org>.
Github user andrewor14 commented on the pull request:

    https://github.com/apache/spark/pull/12398#issuecomment-216711127
  
    ok to test
    
    @dvaies


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by buckhx <gi...@git.apache.org>.
Github user buckhx commented on the pull request:

    https://github.com/apache/spark/pull/12398#issuecomment-219136325
  
    changed addRequirementsFile to addPyRequirements which takes a list of requirement strings


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[GitHub] spark pull request: [SPARK-5929][PYSPARK] Context addPyPackage and...

Posted by davies <gi...@git.apache.org>.
Github user davies commented on the pull request:

    https://github.com/apache/spark/pull/12398#issuecomment-217919681
  
    @buckhx Even the pip API only takes a file path, we could write the as temporary file, I think.


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