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Executing a code with in R connecting to Impala via JDBC ( RJDBC) results in: Error in .jcall(rp, "I", "fetch", stride) : java.lang.OutOfMemoryError: Java heap space RJDBC(dbGetQuery) - GC overhead limit exceeded

Troubleshooting


Problem

Executing a code with in R connecting to Impala via JDBC ( RJDBC) results in: Error in .jcall(rp, "I", "fetch", stride) : java.lang.OutOfMemoryError: Java heap space
RJDBC(dbGetQuery) - GC overhead limit exceeded

Symptom

Executing a code with in R connecting to Impala via JDBC ( RJDBC) results in: Error in .jcall(rp, "I", "fetch", stride) : java.lang.OutOfMemoryError: Java heap space
RJDBC(dbGetQuery) - GC overhead limit exceeded

Cause

java.lang.OutOfMemoryError: Java heap space

Environment

Linux

DSXL 1.2.0.3

Resolving The Problem

The java.lang.OutOfMemoryError on fetch means that the result set is bigger than the default heap size for rJava: 512MB.
To increase the java heap size use the following in your code:
options(java.parameters = "-Xmx4g") where 4g is the size you want to set.   It might be different depending on specific needs and availability.
Note:  that this step must be performed prior to loading any packages and it will be the first line in the code snippet.

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Document Information

More support for:
IBM Data Science Experience Local

Software version:
1.2.0.3

Operating system(s):
Linux

Document number:
737231

Modified date:
24 October 2018

UID

ibm10737231

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