Looking into  JMeter Bug 61279
<https://bz.apache.org/bugzilla/show_bug.cgi?id=61279>   it isn't something
connected with JMeter, I can think of the following reasons for the
behaviour:1. You have more than 1  JVM
<https://en.wikipedia.org/wiki/Java_virtual_machine>  running on the EC2
machine and these JVMs are suffering from a form of a  race condition
<https://en.wikipedia.org/wiki/Race_condition>   when trying to obtain the
lock on the same file to store the preferences2. There is a problem with
Linux file permissions and JVM, i.e. you're running out of  free handles
<https://www.cyberciti.biz/tips/linux-procfs-file-descriptors.html>  The
solution for point 1 would be explicitly specifying the store for 
systemRoot
<https://docs.oracle.com/javase/7/docs/api/java/util/prefs/PreferencesFactory.html#systemRoot()>
 
and  userRoot
<https://docs.oracle.com/javase/7/docs/api/java/util/prefs/PreferencesFactory.html#userRoot()>
 
for the JVM which hosts JMeter so it would use the separate preferences
storage not shared with other JVMs. The properties can be defined either via 
-D command-line argument
<https://jmeter.apache.org/usermanual/get-started.html#override>   like:
> ./jmeter -Djava.util.prefs.systemRoot=/some/folder/.jmeter
> -Djava.util.prefs.userRoot=/some/folder/.jmeter/.userPrefs

In order to make the changes persistent you can add the same lines to
/system.properties/ file (lives in "bin" folder of your JMeter installation)
> java.util.prefs.systemRoot=/some/folder/.jmeterjava.util.prefs.userRoot=/some/folder/.jmeter/.userPrefs

More information:  Apache JMeter Properties Customization Guide
<https://www.blazemeter.com/blog/apache-jmeter-properties-customization/> 
In case of point 2 I would recommend checking / raising  Linux process
limits <https://gerardnico.com/os/linux/limits.conf>   



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