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Old 03-13-2019, 04:09 AM
adidob adidob is offline
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Default out of memory reading from mongodb

I have a simple javascript that reads from MongoDB and constructs HL7 messages.
It works great but after about 1 hour mirth runs out of memory. The administrator dumpt several error messages, here is the first one:

(com.mirth.connect.connectors.js.JavaScriptReceive r:135): Error executing JavaScript Reader script 1b68468d-52c5-4388-926d-c81b4b350fcd.
com.mirth.connect.server.util.javascript.JavaScrip tExecutorException: java.lang.OutOfMemoryError: unable to create native thread: possibly out of memory or process/resource limits reached
at com.mirth.connect.server.util.javascript.JavaScrip tUtil.execute(JavaScriptUtil.java:75)
at com.mirth.connect.connectors.js.JavaScriptReceiver .poll(JavaScriptReceiver.java:101)
at com.mirth.connect.donkey.server.channel.PollConnec torJob.execute(PollConnectorJob.java:49)
at org.quartz.core.JobRunShell.run(JobRunShell.java:2 13)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run (SimpleThreadPool.java:557)Caused by: java.lang.OutOfMemoryError: unable to create native thread: possibly out of memory or process/resource limits reached
at java.base/java.lang.Thread.start0(Native Method)
at java.base/java.lang.Thread.start(Thread.java:813)
at com.mongodb.internal.connection.DefaultServerMonit or.start(DefaultServerMonitor.java:83)
at com.mongodb.internal.connection.DefaultServer.<ini t>(DefaultServer.java:78)
at com.mongodb.internal.connection.DefaultClusterable ServerFactory.create(DefaultClusterableServerFacto ry.java:80)
at com.mongodb.internal.connection.BaseCluster.create Server(BaseCluster.java:376)
at com.mongodb.internal.connection.SingleServerCluste r.<init>(SingleServerCluster.java:58)
at com.mongodb.connection.DefaultClusterFactory.creat eCluster(DefaultClusterFactory.java:187)
at com.mongodb.Mongo.createCluster(Mongo.java:749)
at com.mongodb.Mongo.createCluster(Mongo.java:743)
at com.mongodb.Mongo.<init>(Mongo.java:295)
at com.mongodb.Mongo.<init>(Mongo.java:290)
at com.mongodb.Mongo.<init>(Mongo.java:286)
at com.mongodb.MongoClient.<init>(MongoClient.java:18 0)
at com.mongodb.MongoClient.<init>(MongoClient.java:15 5)
at com.mongodb.MongoClient.<init>(MongoClient.java:14 5)
at jdk.internal.reflect.GeneratedConstructorAccessor1 10.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessor Impl.newInstance(DelegatingConstructorAccessorImpl .java:45)
at java.base/java.lang.reflect.Constructor.newInstance(Construc tor.java:488)
at org.mozilla.javascript.MemberBox.newInstance(Membe rBox.java:159)
at org.mozilla.javascript.NativeJavaClass.constructIn ternal(NativeJavaClass.java:266)
at org.mozilla.javascript.NativeJavaClass.constructSp ecific(NativeJavaClass.java:205)
at org.mozilla.javascript.NativeJavaClass.construct(N ativeJavaClass.java:166)
at org.mozilla.javascript.Interpreter.interpretLoop(I nterpreter.java:1525)
at org.mozilla.javascript.Interpreter.interpret(Inter preter.java:815)
at org.mozilla.javascript.InterpretedFunction.call(In terpretedFunction.java:109)
at org.mozilla.javascript.ContextFactory.doTopCall(Co ntextFactory.java:405)
at org.mozilla.javascript.ScriptRuntime.doTopCall(Scr iptRuntime.java:3508)
at org.mozilla.javascript.InterpretedFunction.exec(In terpretedFunction.java:120)
at com.mirth.connect.server.util.javascript.JavaScrip tTask.executeScript(JavaScriptTask.java:150)
at com.mirth.connect.server.util.javascript.JavaScrip tUtil.executeScript(JavaScriptUtil.java:542)
at com.mirth.connect.connectors.js.JavaScriptReceiver $JavaScriptReceiverTask.doCall(JavaScriptReceiver. java:159)
at com.mirth.connect.server.util.javascript.JavaScrip tTask.call(JavaScriptTask.java:113)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.jav a:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker( ThreadPoolExecutor.java:1135)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run (ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:844)

Also here you have my javascript:

var mongoClient = new Packages.com.mongodb.MongoClient("localhost", 27017);
var database = mongoClient.getDatabase("db");
var collection = database.getCollection("foo");

var qdoc = Packages.org.bson.Document.parse(JSON.stringify({" status": { $ne: true }}));
var myDoc = collection.find(qdoc).first();

if (!myDoc) {
return null;

var jdoc = myDoc.toJson();
var oJ = JSON.parse(jdoc);

var curdate = DateUtil.getCurrentDate('yyyyMMddhhmmss');

var uQ = Packages.org.bson.Document.parse(JSON.stringify({" uid": oJ.uid}));
var uU = Packages.org.bson.Document.parse(JSON.stringify({$ set : {"status": true}}));
collection.updateOne(uQ, uU);


var msg = <HL7Message/>;

createSegment('MSH', msg);
msg.MSH['MSH.1'] = '|';
msg.MSH['MSH.2'] = '^~\\&';
msg.MSH['MSH.3']['MSH.3.1'] = 'foo';
msg.MSH['MSH.4']['MSH.4.1'] = 'foo';
msg.MSH['MSH.6']['MSH.6.1'] = 'foo';
msg.MSH['MSH.7']['MSH.7.1'] = 'foo';
msg.MSH['MSH.9']['MSH.9.1'] = 'ORU^R01';
msg.MSH['MSH.10']['MSH.10.1'] = 'foo???';
msg.MSH['MSH.11']['MSH.11.1'] = 'P';
msg.MSH['MSH.12']['MSH.12.1'] = '1.0';
msg.MSH['MSH.16']['MSH.16.1'] = '';

var message = SerializerFactory.getSerializer('HL7V2').fromXML(m sg);

return message;
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Old 03-13-2019, 03:32 PM
agermano agermano is offline
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Join Date: Apr 2017
Location: Indiana, USA
Posts: 1,175
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Is the server actually out of memory? How much memory is mirth using? How much have you allocated to the JVM? The error description says, "unable to create native thread: possibly out of memory or process/resource limits reached." When mirth runs out of memory, it's much more common to see heap errors than errors creating native threads.

I've never used Mongodb before. Do you need to also close the database and collection? Maybe something isn't getting cleaned up? Typically you would want to have your code in a try block and the close statements in a finally block in case an exception is thrown so you aren't left with lingering connections.
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Old 04-17-2019, 05:51 AM
adidob adidob is offline
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Join Date: Mar 2019
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it looks like it is the message returned by JavaScript reader is leaking memory.

Here you have the last few lines from reader:

var message = SerializerFactory.getSerializer('HL7V2').fromXML(m sg);

return message;

If I do not return this message then there is no problem with memory, but then what do I have to do to have mirth free this message.
Where my source connector type is "javascript reader" and destination is 'tcp'
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connector, javascript, mongodb, out of memory error

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