Sun,
I am using spark in yarn client mode in a 2-node cluster with hadoop-2.7.2. My
R version is 3.3.1.
I have the following in my spark-defaults.conf:spark.executor.extraJavaOptions
=-XX:+PrintGCDetails
-XX:+HeapDumpOnOutOfMemoryErrorspark.r.command=c:/R/R-3.3.1/bin/x64/Rscriptspark.ui.killEnabled=truespark.executor.instances
= 3
spark.serializer =
org.apache.spark.serializer.KryoSerializerspark.shuffle.file.buffer =
1mspark.driver.maxResultSize=0spark.executor.memory=8gspark.executor.cores = 6
I also ran into some other R errors that I was able to bypass by modifying the
worker.R file (attached). In a nutshell I was getting the "argument is length
of zero" error sporadically so I put in extra checks for it.
Thanks,
Shane
On Monday, August 8, 2016 11:53 PM, Sun Rui <sunrise_...@163.com> wrote:
I can’t reproduce your issue with len=10000 in local mode.Could you give more
environment information?
On Aug 9, 2016, at 11:35, Shane Lee <shane_y_...@yahoo.com.INVALID> wrote:
Hi All,
I am trying out SparkR 2.0 and have run into an issue with repartition.
Here is the R code (essentially a port of the pi-calculating scala example in
the spark package) that can reproduce the behavior:
schema <- structType(structField("input", "integer"), structField("output",
"integer"))
library(magrittr)
len = 3000data.frame(n = 1:len) %>% as.DataFrame %>%
SparkR:::repartition(10L) %>% dapply(., function (df) { library(plyr) ddply(df,
.(n), function (y)
{ data.frame(z = { x1 = runif(1) * 2 - 1 y1 = runif(1) * 2 - 1 z = x1 * x1 +
y1 * y1 if (z < 1) { 1L } else { 0L } }) }) } , schema ) %>%
SparkR:::summarize(total = sum(.$output)) %>% collect * 4 / len
For me it runs fine as long as len is less than 5000, otherwise it errors out
with the following message:
Error in invokeJava(isStatic = TRUE, className, methodName, ...) :
org.apache.spark.SparkException: Job aborted due to stage failure: Task 6 in
stage 56.0 failed 4 times, most recent failure: Lost task 6.3 in stage 56.0
(TID 899, LARBGDV-VM02): org.apache.spark.SparkException: R computation failed
with Error in readBin(con, raw(), stringLen, endian = "big") : invalid 'n'
argumentCalls: <Anonymous> -> readBinExecution halted at
org.apache.spark.api.r.RRunner.compute(RRunner.scala:108) at
org.apache.spark.sql.execution.r.MapPartitionsRWrapper.apply(MapPartitionsRWrapper.scala:59)
at
org.apache.spark.sql.execution.r.MapPartitionsRWrapper.apply(MapPartitionsRWrapper.scala:29)
at
org.apache.spark.sql.execution.MapPartitionsExec$$anonfun$6.apply(objects.scala:178)
at
org.apache.spark.sql.execution.MapPartitionsExec$$anonfun$6.apply(objects.scala:175)
at
org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$24.apply(RDD.scala:784)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$
If the repartition call is removed, it runs fine again, even with very large
len.
After looking through the documentations and searching the web, I can't seem to
find any clues how to fix this. Anybody has seen similary problem?
Thanks in advance for your help.
Shane
worker.R
Description: Binary data
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