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From Abdeali Kothari <abdealikoth...@gmail.com>
Subject Re: OversizedAllocationException for pandas_udf in pyspark
Date Sat, 02 Mar 2019 06:20:52 GMT
Hi Li Jin, thanks for the note.

I get this error only for larger data - when I reduce the number of records
or the number or columns in my data it all works fine - so if it is binary
incompatibility it should be something related to large data.
I am using Spark 2.3.1 on Amazon EMR for this testing.
https://github.com/apache/spark/blob/v2.3.1/pom.xml#L192 seems to indicate
arrow version is 0.8 for this.

I installed pyarrow-0.8.0 in the python environment on my cluster with pip
and I am still getting this error.
The stacktrace is very similar, just some lines moved in the pxi files:

Caused by: org.apache.spark.api.python.PythonException: Traceback (most
recent call last):
  File
"/mnt/yarn/usercache/hadoop/appcache/application_1551469777576_0018/container_1551469777576_0018_01_000002/pyspark.zip/pyspark/worker.py",
line 230, in main
    process()
  File
"/mnt/yarn/usercache/hadoop/appcache/application_1551469777576_0018/container_1551469777576_0018_01_000002/pyspark.zip/pyspark/worker.py",
line 225, in process
    serializer.dump_stream(func(split_index, iterator), outfile)
  File
"/mnt/yarn/usercache/hadoop/appcache/application_1551469777576_0018/container_1551469777576_0018_01_000002/pyspark.zip/pyspark/serializers.py",
line 260, in dump_stream
    for series in iterator:
  File
"/mnt/yarn/usercache/hadoop/appcache/application_1551469777576_0018/container_1551469777576_0018_01_000002/pyspark.zip/pyspark/serializers.py",
line 279, in load_stream
    for batch in reader:
  File "pyarrow/ipc.pxi", line 268, in __iter__
(/arrow/python/build/temp.linux-x86_64-3.6/lib.cxx:70278)
  File "pyarrow/ipc.pxi", line 284, in
pyarrow.lib._RecordBatchReader.read_next_batch
(/arrow/python/build/temp.linux-x86_64-3.6/lib.cxx:70534)
  File "pyarrow/error.pxi", line 79, in pyarrow.lib.check_status
(/arrow/python/build/temp.linux-x86_64-3.6/lib.cxx:8345)
pyarrow.lib.ArrowIOError: read length must be positive or -1

Other notes:
 - My data is just integers, strings, and doubles. No complex types like
arrays/maps/etc.
 - I don't have any NULL/None values in my data
 - Increasing executor-memory for spark does not seem to help here

As always: Any thoughts or notes would be great so I can get some pointers
in which direction to debug



On Sat, Mar 2, 2019 at 2:24 AM Li Jin <ice.xelloss@gmail.com> wrote:

> The 2G limit that Uwe mentioned definitely exists, Spark serialize each
> group as a single RecordBatch currently.
>
> The "pyarrow.lib.ArrowIOError: read length must be positive or -1" is
> strange, I think Spark is on an older version of the Java side (0.10 for
> Spark 2.4 and 0.8 for Spark 2.3). I forgot whether there is binary
> incompatibility between these versions and pyarrow 0.12.
>
> On Fri, Mar 1, 2019 at 3:32 PM Abdeali Kothari <abdealikothari@gmail.com>
> wrote:
>
> > Forgot to mention: The above testing is with 0.11.1
> > I tried 0.12.1 as you suggested - and am getting the
> > OversizedAllocationException with the 80char column. And getting read
> > length must be positive or -1 without that. So, both the issues are
> > reproducible with pyarrow 0.12.1
> >
> > On Sat, Mar 2, 2019 at 1:57 AM Abdeali Kothari <abdealikothari@gmail.com
> >
> > wrote:
> >
> > > That was spot on!
> > > I had 3 columns with 80characters => 80*21*10^6 = 1.56 bytes
> > > I removed these columns and replaced each with 10 doubleType columns
> (so
> > > it would still be 80 bytes of data) - and this error didn't come up
> > anymore.
> > > I also removed all the other columns and just kept 1 column with
> > > 80characters - I got the error again.
> > >
> > > I'll make a simpler example and report it to spark - as I guess these
> > > columns would need some special handling.
> > >
> > > Now, when I run - I get a different error:
> > > 19/03/01 20:16:49 WARN TaskSetManager: Lost task 108.0 in stage 8.0
> (TID
> > > 12, ip-172-31-10-249.us-west-2.compute.internal, executor 1):
> > > org.apache.spark.api.python.PythonException: Traceback (most recent
> call
> > > last):
> > >   File
> > >
> >
> "/mnt/yarn/usercache/hadoop/appcache/application_1551469777576_0010/container_1551469777576_0010_01_000002/pyspark.zip/pyspark/worker.py",
> > > line 230, in main
> > >     process()
> > >   File
> > >
> >
> "/mnt/yarn/usercache/hadoop/appcache/application_1551469777576_0010/container_1551469777576_0010_01_000002/pyspark.zip/pyspark/worker.py",
> > > line 225, in process
> > >     serializer.dump_stream(func(split_index, iterator), outfile)
> > >   File
> > >
> >
> "/mnt/yarn/usercache/hadoop/appcache/application_1551469777576_0010/container_1551469777576_0010_01_000002/pyspark.zip/pyspark/serializers.py",
> > > line 260, in dump_stream
> > >     for series in iterator:
> > >   File
> > >
> >
> "/mnt/yarn/usercache/hadoop/appcache/application_1551469777576_0010/container_1551469777576_0010_01_000002/pyspark.zip/pyspark/serializers.py",
> > > line 279, in load_stream
> > >     for batch in reader:
> > >   File "pyarrow/ipc.pxi", line 265, in __iter__
> > >   File "pyarrow/ipc.pxi", line 281, in
> > > pyarrow.lib._RecordBatchReader.read_next_batch
> > >   File "pyarrow/error.pxi", line 83, in pyarrow.lib.check_status
> > > pyarrow.lib.ArrowIOError: read length must be positive or -1
> > >
> > > Again, any pointers on what this means and what it indicates would be
> > > really useful for me.
> > >
> > > Thanks for the replies!
> > >
> > >
> > > On Fri, Mar 1, 2019 at 11:26 PM Uwe L. Korn <uwelk@xhochy.com> wrote:
> > >
> > >> There is currently the limitation that a column in a single
> RecordBatch
> > >> can only hold 2G on the Java side. We work around this by splitting
> the
> > >> DataFrame under the hood into multiple RecordBatches. I'm not familiar
> > with
> > >> the Spark<->Arrow code but I guess that in this case, the Spark code
> can
> > >> only handle a single RecordBatch.
> > >>
> > >> Probably it is best to construct a
> https://stackoverflow.com/help/mcve
> > >> and create an issue with the Spark project. Most likely this is not a
> > bug
> > >> in Arrow but just requires a bit more complicated implementation
> around
> > the
> > >> Arrow libs.
> > >>
> > >> Still, please have a look at the exact size of your columns. We
> support
> > >> 2G per column, if it is only 1.5G, then there is probably a rounding
> > error
> > >> in the Arrow. Alternatively, you might also be in luck that the
> > following
> > >> patch
> > >>
> >
> https://github.com/apache/arrow/commit/bfe6865ba8087a46bd7665679e48af3a77987cef
> > >> which is part of Apache Arrow 0.12 already fixes your problem.
> > >>
> > >> Uwe
> > >>
> > >> On Fri, Mar 1, 2019, at 6:48 PM, Abdeali Kothari wrote:
> > >> > Is there a limitation that a single column cannot be more than 1-2G
> ?
> > >> > One of my columns definitely would be around 1.5GB of memory.
> > >> >
> > >> > I cannot split my DF into more partitions as I have only 1 ID and
> I'm
> > >> > grouping by that ID.
> > >> > So, the UDAF would only run on a single pandasDF
> > >> > I do have a requirement to make a very large DF for this UDAF (8GB
> as
> > i
> > >> > mentioned above) - trying to figure out what I need to do here to
> make
> > >> this
> > >> > work.
> > >> > Increasing RAM, etc. is no issue (i understand I'd need huge
> executors
> > >> as I
> > >> > have a huge data requirement). But trying to figure out how much to
> > >> > actually get - cause 20GB of RAM for the executor is also erroring
> out
> > >> > where I thought ~10GB would have been enough
> > >> >
> > >> >
> > >> >
> > >> > On Fri, Mar 1, 2019 at 10:25 PM Uwe L. Korn <uwelk@xhochy.com>
> wrote:
> > >> >
> > >> > > Hello Abdeali,
> > >> > >
> > >> > > a problem could here be that a single column of your dataframe
is
> > >> using
> > >> > > more than 2GB of RAM (possibly also just 1G). Try splitting your
> > >> DataFrame
> > >> > > into more partitions before applying the UDAF.
> > >> > >
> > >> > > Cheers
> > >> > > Uwe
> > >> > >
> > >> > > On Fri, Mar 1, 2019, at 9:09 AM, Abdeali Kothari wrote:
> > >> > > > I was using arrow with spark+python and when I'm trying
some
> > >> pandas-UDAF
> > >> > > > functions I am getting this error:
> > >> > > >
> > >> > > > org.apache.arrow.vector.util.OversizedAllocationException:
> Unable
> > to
> > >> > > > expand
> > >> > > > the buffer
> > >> > > > at
> > >> > > >
> > >> > >
> > >>
> >
> org.apache.arrow.vector.BaseVariableWidthVector.reallocDataBuffer(BaseVariableWidthVector.java:457)
> > >> > > > at
> > >> > > >
> > >> > >
> > >>
> >
> org.apache.arrow.vector.BaseVariableWidthVector.handleSafe(BaseVariableWidthVector.java:1188)
> > >> > > > at
> > >> > > >
> > >> > >
> > >>
> >
> org.apache.arrow.vector.BaseVariableWidthVector.setSafe(BaseVariableWidthVector.java:1026)
> > >> > > > at
> > >> > > >
> > >> > >
> > >>
> >
> org.apache.spark.sql.execution.arrow.StringWriter.setValue(ArrowWriter.scala:256)
> > >> > > > at
> > >> > > >
> > >> > >
> > >>
> >
> org.apache.spark.sql.execution.arrow.ArrowFieldWriter.write(ArrowWriter.scala:122)
> > >> > > > at
> > >> > > >
> > >> > >
> > >>
> >
> org.apache.spark.sql.execution.arrow.ArrowWriter.write(ArrowWriter.scala:87)
> > >> > > > at
> > >> > > >
> > >> > >
> > >>
> >
> org.apache.spark.sql.execution.python.ArrowPythonRunner$$anon$2$$anonfun$writeIteratorToStream$1.apply$mcV$sp(ArrowPythonRunner.scala:84)
> > >> > > > at
> > >> > > >
> > >> > >
> > >>
> >
> org.apache.spark.sql.execution.python.ArrowPythonRunner$$anon$2$$anonfun$writeIteratorToStream$1.apply(ArrowPythonRunner.scala:75)
> > >> > > > at
> > >> > > >
> > >> > >
> > >>
> >
> org.apache.spark.sql.execution.python.ArrowPythonRunner$$anon$2$$anonfun$writeIteratorToStream$1.apply(ArrowPythonRunner.scala:75)
> > >> > > > at
> > org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1380)
> > >> > > > at
> > >> > > >
> > >> > >
> > >>
> >
> org.apache.spark.sql.execution.python.ArrowPythonRunner$$anon$2.writeIteratorToStream(ArrowPythonRunner.scala:95)
> > >> > > > at
> > >> > > >
> > >> > >
> > >>
> >
> org.apache.spark.api.python.BasePythonRunner$WriterThread$$anonfun$run$1.apply(PythonRunner.scala:215)
> > >> > > > at
> > >> org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1991)
> > >> > > > at
> > >> > > >
> > >> > >
> > >>
> >
> org.apache.spark.api.python.BasePythonRunner$WriterThread.run(PythonRunner.scala:170)
> > >> > > >
> > >> > > > I was initially getting a RAM is insufficient error - and
> > >> theoretically
> > >> > > > (with no compression) realized that the pandas DataFrame
it
> would
> > >> try to
> > >> > > > create would be ~8GB (21million records with each record
having
> > ~400
> > >> > > > bytes). I have increased my executor memory to be 20GB per
> > >> executor, but
> > >> > > am
> > >> > > > now getting this error from Arrow.
> > >> > > > Looking for some pointers so I can understand this issue
better.
> > >> > > >
> > >> > > > Here's what I am trying. I have 2 tables with string columns
> where
> > >> the
> > >> > > > strings always have a fixed length:
> > >> > > > *Table 1*:
> > >> > > >     id: integer
> > >> > > >    char_column1: string (length = 30)
> > >> > > >    char_column2: string (length = 40)
> > >> > > >    char_column3: string (length = 10)
> > >> > > >    ...
> > >> > > > In total, in table1, the char-columns have ~250 characters
> > >> > > >
> > >> > > > *Table 2*:
> > >> > > >     id: integer
> > >> > > >    char_column1: string (length = 50)
> > >> > > >    char_column2: string (length = 3)
> > >> > > >    char_column3: string (length = 4)
> > >> > > >    ...
> > >> > > > In total, in table2, the char-columns have ~150 characters
> > >> > > >
> > >> > > > I am joining these tables by ID. In my current dataset,
I have
> > >> filtered
> > >> > > my
> > >> > > > data so only id=1 exists.
> > >> > > > Table1 has ~400 records for id=1 and table2 has 50k records
for
> > >> id=1.
> > >> > > > Hence, total number of records (after joining) for table1_join2
> =
> > >> 400 *
> > >> > > 50k
> > >> > > > = 20*10^6 records
> > >> > > > Each row has ~400bytes (150+250) => overall memory =
8*10^9
> bytes
> > >> => ~8GB
> > >> > > >
> > >> > > > Now, when I try an executor with 20GB RAM, it does not work.
> > >> > > > Is there some data duplicity happening internally ? What
should
> be
> > >> the
> > >> > > > estimated RAM I need to give for this to work ?
> > >> > > >
> > >> > > > Thanks for reading,
> > >> > > >
> > >> > >
> > >> >
> > >>
> > >
> >
>

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