Hi Michael
https://github.com/apache/spark/archive/v1.6.0.tar.gz
Both 1.6.0 and 1.5.2 my unit test work when I call reparation(1) before
saving output. Coalesce still fails.
Coalesce(1) spark-1.5.2
Caused by:
java.io.IOException: Unable to acquire 33554432 bytes of memory
Coalesce(1) spark-1.6.0
Caused by:
java.lang.OutOfMemoryError: Unable to acquire 28 bytes of memory,
got 0
Hope this helps
Andy
From: Michael Armbrust <mich...@databricks.com>
Date: Monday, December 28, 2015 at 2:41 PM
To: Andrew Davidson <a...@santacruzintegration.com>
Cc: "user @spark" <user@spark.apache.org>
Subject: Re: trouble understanding data frame memory usage
³java.io.IOException: Unable to acquire memory²
> Unfortunately in 1.5 we didn't force operators to spill when ran out of memory
> so there is not a lot you can do. It would be awesome if you could test with
> 1.6 and see if things are any better?
>
> On Mon, Dec 28, 2015 at 2:25 PM, Andy Davidson <a...@santacruzintegration.com>
> wrote:
>> I am using spark 1.5.1. I am running into some memory problems with a java
>> unit test. Yes I could fix it by setting Xmx (its set to 1024M) how ever I
>> want to better understand what is going on so I can write better code in the
>> future. The test runs on a Mac, master="Local[2]"
>>
>> I have a java unit test that starts by reading a 672K ascii file. I my output
>> data file is 152K. Its seems strange that such a small amount of data would
>> cause an out of memory exception. I am running a pretty standard machine
>> learning process
>>
>> 1. Load data
>> 2. create a ML pipeline
>> 3. transform the data
>> 4. Train a model
>> 5. Make predictions
>> 6. Join the predictions back to my original data set
>> 7. Coalesce(1), I only have a small amount of data and want to save it in a
>> single file
>> 8. Save final results back to disk
>>
>> Step 7: I am unable to call Coalesce() “java.io.IOException: Unable to
>> acquire memory”
>>
>> To try and figure out what is going I put log messages in to count the number
>> of partitions
>>
>> Turns out I have 20 input files, each one winds up in a separate partition.
>> Okay so after loading I call coalesce(1) and check to make sure I only have a
>> single partition.
>>
>> The total number of observations is 1998.
>>
>> After calling step 7 I count the number of partitions and discovered I have
>> 224 partitions!. Surprising given I called Coalesce(1) before I did anything
>> with the data. My data set should easily fit in memory. When I save them to
>> disk I get 202 files created with 162 of them being empty!
>>
>> In general I am not explicitly using cache.
>>
>> Some of the data frames get registered as tables. I find it easier to use
>> sql.
>>
>> Some of the data frames get converted back to RDDs. I find it easier to
>> create RDD<LabeledPoint> this way
>>
>> I put calls to unpersist(true). In several places
>>
>> private void memoryCheck(String name) {
>>
>> Runtime rt = Runtime.getRuntime();
>>
>> logger.warn("name: {} \t\ttotalMemory: {} \tfreeMemory: {} df.size:
>> {}",
>>
>> name,
>>
>> String.format("%,d", rt.totalMemory()),
>>
>> String.format("%,d", rt.freeMemory()));
>>
>> }
>>
>>
>> Any idea how I can get a better understanding of what is going on? My goal is
>> to learn to write better spark code.
>>
>> Kind regards
>>
>> Andy
>>
>> Memory usages at various points in my unit test
>> name: rawInput totalMemory: 447,741,952 freeMemory: 233,203,184
>>
>> name: naiveBayesModel totalMemory: 509,083,648 freeMemory: 403,504,128
>>
>> name: lpRDD totalMemory: 509,083,648 freeMemory: 402,288,104
>>
>> name: results totalMemory: 509,083,648 freeMemory: 368,011,008
>>
>>
>>
>> DataFrame exploreDF = results.select(results.col("id"),
>>
>> results.col("label"),
>>
>> results.col("binomialLabel"),
>>
>> results.col("labelIndex"),
>>
>> results.col("prediction"),
>>
>> results.col("words"));
>>
>> exploreDF.show(10);
>>
>>
>>
>> Yes I realize its strange to switch styles how ever this should not cause
>> memory problems
>>
>>
>>
>> final String exploreTable = "exploreTable";
>>
>> exploreDF.registerTempTable(exploreTable);
>>
>> String fmt = "SELECT * FROM %s where binomialLabel = ’signal'";
>>
>> String stmt = String.format(fmt, exploreTable);
>>
>>
>>
>> DataFrame subsetToSave = sqlContext.sql(stmt);// .show(100);
>>
>>
>>
>> name: subsetToSave totalMemory: 1,747,451,904 freeMemory: 1,049,447,144
>>
>>
>>
>> exploreDF.unpersist(true); does not resolve memory issue
>>
>>
>>
>
