Thank You Ewan for pointing us to patch. Will make use of it and troubleshoot the error. Appreciate the help. Naga
-----Original Message----- From: Ewan Mellor [mailto:ctakes-...@ewanmellor.org.uk] Sent: Tuesday, May 01, 2018 5:24 PM To: dev@ctakes.apache.org Subject: Re: cTakes on Apache Spark - Error 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://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D501&d=DwIBAg&c=A-GX6P9ovB1qTBp7iQve2Q&r=XKrHrIXqmdSXbdk4FWNCxNg6U89BilpFu7mhvHYmxp0&m=2ESez2jFD_fXg1r29anNuVEtg8IaC9VcV-X2JVazdwY&s=-VeCagWj7ufaFlaKzprWxsdGEnbsrxbznX5cSflfF1k&e=, which includes some additional logging in this area. HTH, Ewan. 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 option > > 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:1 > 512) at > org.apache.ctakes.lvg.ae.LvgAnnotator.copyLvgFiles(LvgAnnotator.java:6 > 20) at > org.apache.ctakes.lvg.ae.LvgAnnotator.createAnnotatorDescription(LvgAn > notator.java:649) at > org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.getTokenPro > cessingPipeline(ClinicalPipelineFactory.java:110) > at > org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.getDefaultP > ipeline(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. > > > CONFIDENTIALITY NOTICE: This e-mail message, including any > attachments, is for the sole use of the intended recipient(s) and may > contain confidential and privileged information or may otherwise be > protected by law. Any unauthorized review, use, disclosure or > distribution is prohibited. If you are not the intended recipient, > please contact the sender by reply e-mail and destroy all copies of the > original message and any attachment thereto. CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information or may otherwise be protected by law. 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