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From Ewan Mellor <ctakes-...@ewanmellor.org.uk>
Subject Re: cTakes on Apache Spark - Error
Date Tue, 01 May 2018 21:23:36 GMT
There is a point in LvgCmdApiResourceImpl where it changes the working
directory so that LVG can find the config file.  I have no idea how this
would be supposed to work on Spark, but I guess that using relative paths
in your config is going to be a problem.

There is also a point in LvgCmdApiResourceImpl where it is converting a URI
to a File instance.  You should check whether that's ending up with an
hdfs URL, and if so whether it is doing the right thing.

I would make sure that you have all the logging coming out from
LvgCmdApiResourceImpl and check that the paths are correct.  You could
also look at my patch on https://issues.apache.org/jira/browse/CTAKES-501,
which includes some additional logging in this area.



On Tue, May 01, 2018 at 04:40:16PM +0000, Eskala, Nagakalyana wrote:

> More update on the issue:
> We have extracted the lvg related files in the exact folder structure, and are copying
all the folders recursively in the spark executor working directory using addFiles option.
But the LvgAnnotator is not able to find the lvg.properties file in the classpath of the spark
executor even though we have set up using the configuration spark.executor.extraClassPath
> Code snippet:
> sc.addFile("hdfs:///ctakes_4.0.0/resources", true);
> sparkConf.set("spark.executor.extraClassPath", "./resources/");
> sparkConf.set("spark.driver.extraClassPath", "./resources/");
> From: Eskala, Nagakalyana
> Sent: Monday, April 30, 2018 8:50 PM
> To: 'dev@ctakes.apache.org' <dev@ctakes.apache.org>
> Subject: cTakes on Apache Spark - Error
> Background:
> We are trying to run the Apache ctakes Default clinical pipeline in a spark streaming
application. We intend to parse all input text sent to a socket on spark streaming by executing
a default clinical pipeline in individual executors of a spark application.
> Challenges:
> The ctakes pipeline requires external resources to be available in the classpath. We
have used JavaSparkContext.addFiles to provide all the resources (dictionaries) recursively
from HDFS to each individual executor working directory. Once the addFiles copies the resources
to each executor, we try to include it in the classpath of each executor using the configuration.
> sc.addFile("hdfs:///ctakes_4.0.0/resources", true);
> sparkConf.set("spark.executor.extraClassPath", "./resources/");
> sparkConf.set("spark.driver.extraClassPath", "./resources/");
> Error:
> The error occurs in LvgAnnotator class which tries to access the lvg.properties file
through the lookup. It is not able to locate the file and hence there is an error.
> 18/04/30 15:55:50 INFO scheduler.TaskSetManager: Starting task 0.0 in stage 1.0 (TID
1, localhost, executor driver, partition 0, ANY, 4744 bytes)
> 18/04/30 15:55:50 INFO executor.Executor: Running task 0.0 in stage 1.0 (TID 1)
> 18/04/30 15:55:51 INFO ae.LvgAnnotator: URL==null
> 18/04/30 15:55:51 INFO ae.LvgAnnotator: Unable to find org/apache/ctakes/lvg/data/config/lvg.properties.
> 18/04/30 15:55:51 INFO ae.LvgAnnotator: Copying files and directories to under /tmp/
> 18/04/30 15:55:51 INFO ae.LvgAnnotator: Copying lvg-related file to /tmp/data/config/lvg.properties
> 18/04/30 15:55:51 ERROR executor.Executor: Exception in task 0.0 in stage 1.0 (TID 1)
> java.lang.NullPointerException
> at org.apache.commons.io.IOUtils.copyLarge(IOUtils.java:1792)
> at org.apache.commons.io.IOUtils.copyLarge(IOUtils.java:1769)
> at org.apache.commons.io.IOUtils.copy(IOUtils.java:1744)
> at org.apache.commons.io.FileUtils.copyInputStreamToFile(FileUtils.java:1512)
> at org.apache.ctakes.lvg.ae.LvgAnnotator.copyLvgFiles(LvgAnnotator.java:620)
> at org.apache.ctakes.lvg.ae.LvgAnnotator.createAnnotatorDescription(LvgAnnotator.java:649)
> at org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.getTokenProcessingPipeline(ClinicalPipelineFactory.java:110)
> at org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.getDefaultPipeline(ClinicalPipelineFactory.java:68)
> Question:
> Ideally, since the resources folder has been recursively added to each executor node
and the classpath has been set, the internal executor should be able to locate the properties
and other resource files. However, that is not the case. Is there something we should be differently
doing (configuration, classpath, etc) so that the ctakes pipeline can be run in a spark executor
with all the resources and classpath set appropriately.
> Thanks for the help.
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