PyCharm 2019.2 Crashes While Running Long Running Script

Have been using Pycharm 2019.1 on Ubuntu 18.10 to automate running some experiments in another program. Consequently a big part of the program is a long running subprocess call (that calls the simulation program with a script of the simulation to run) that can take up to an hour to complete (as the simulation environment has to generate a lot of data). With 2019.1 this was never a problem and the program just kept running but now (after upgrading to 2019.2) after a short amount of time PyCharm simply crashes. Looking in the idea.log the only thing of note is this:

2019-08-02 09:32:27,762 [ 287014] WARN - n.process.BaseOSProcessHandler - Process hasn't generated any output for a long time.
If it's a long-running mostly idle daemon process, consider overriding OSProcessHandler#readerOptions with 'BaseOutputReader.Options.forMostlySilentProcess()' to reduce CPU usage.
Command line: /home/jonathanrainer/Documents/PhD/Ichijou/venv/bin/python /home/jonathanrainer/Documents/PhD/Ichijou/ichijou/main.py /home/jonathanrainer/Documents/PhD/Ichijou/benchmarks /home/jonathanrainer/Documents/PhD/Ichijou/experiments /home/jonathanrainer/Documents/PhD/Ichijou/data/results.xlsx 
java.lang.Throwable: Process creation:
at com.intellij.execution.process.BaseOSProcessHandler.<init>(BaseOSProcessHandler.java:33)
at com.intellij.execution.process.OSProcessHandler.<init>(OSProcessHandler.java:151)
at com.intellij.execution.process.OSProcessHandler.<init>(OSProcessHandler.java:38)
at com.intellij.execution.process.KillableProcessHandler.<init>(KillableProcessHandler.java:35)
at com.intellij.execution.process.ColoredProcessHandler.<init>(ColoredProcessHandler.java:24)
at com.intellij.execution.process.KillableColoredProcessHandler.<init>(KillableColoredProcessHandler.java:38)
at com.jetbrains.python.run.PythonProcessHandler.<init>(PythonProcessHandler.java:37)
at com.jetbrains.python.run.PythonProcessRunner.createProcess(PythonProcessRunner.java:37)
at com.jetbrains.python.run.PythonProcessRunner.createProcess(PythonProcessRunner.java:42)
at com.jetbrains.python.run.PythonCommandLineState.doCreateProcess(PythonCommandLineState.java:289)
at com.jetbrains.python.run.PythonScriptCommandLineState.doCreateProcess(PythonScriptCommandLineState.java:202)
at com.jetbrains.python.run.PythonCommandLineState.a(PythonCommandLineState.java:239)
at com.jetbrains.python.run.PythonCommandLineState.startProcess(PythonCommandLineState.java:219)
at com.jetbrains.python.run.PythonCommandLineState.execute(PythonCommandLineState.java:145)
at com.jetbrains.python.run.PythonScriptCommandLineState.execute(PythonScriptCommandLineState.java:109)
at com.jetbrains.python.run.PythonCommandLineState.execute(PythonCommandLineState.java:139)
at com.jetbrains.python.run.PythonRunner.doExecute(PythonRunner.java:52)
at com.intellij.execution.runners.GenericProgramRunner$execute$$inlined$runProfileStarter$1.executeAsync(GenericProgramRunner.kt:56)
at com.intellij.execution.runners.GenericProgramRunnerKt$startRunProfile$$inlined$runProfileStarter$1.executeAsync(GenericProgramRunner.kt:56)
at com.intellij.execution.impl.ExecutionManagerKtImpl$startRunProfile$startRunnable$1.run(ExecutionManagerKtImpl.kt:63)
at com.intellij.openapi.application.TransactionGuardImpl.runSyncTransaction(TransactionGuardImpl.java:82)
at com.intellij.openapi.application.TransactionGuardImpl.lambda$submitTransaction$1(TransactionGuardImpl.java:106)
at com.intellij.openapi.application.TransactionGuardImpl.submitTransaction(TransactionGuardImpl.java:115)
at com.intellij.openapi.application.TransactionGuard.submitTransaction(TransactionGuard.java:121)
at com.intellij.execution.impl.ExecutionManagerKtImpl$startRunProfile$2.run(ExecutionManagerKtImpl.kt:116)
at com.intellij.execution.impl.ExecutionManagerImpl.compileAndRun(ExecutionManagerImpl.java:278)
at com.intellij.execution.impl.ExecutionManagerKtImpl.startRunProfile(ExecutionManagerKtImpl.kt:116)
at com.intellij.execution.runners.GenericProgramRunnerKt.startRunProfile(GenericProgramRunner.kt:50)
at com.intellij.execution.runners.GenericProgramRunner.execute(GenericProgramRunner.kt:17)
at com.intellij.execution.runners.BaseProgramRunner.execute(BaseProgramRunner.java:46)
at com.intellij.execution.runners.BaseProgramRunner.execute(BaseProgramRunner.java:35)
at com.intellij.execution.ProgramRunnerUtil.executeConfigurationAsync(ProgramRunnerUtil.java:92)
at com.intellij.execution.ProgramRunnerUtil.executeConfiguration(ProgramRunnerUtil.java:40)
at com.intellij.execution.impl.ExecutionManagerImpl.restart(ExecutionManagerImpl.java:94)
at com.intellij.execution.impl.ExecutionManagerImpl.access$300(ExecutionManagerImpl.java:45)
at com.intellij.execution.impl.ExecutionManagerImpl$3.run(ExecutionManagerImpl.java:470)
at com.intellij.util.concurrency.QueueProcessor.runSafely(QueueProcessor.java:231)
at com.intellij.util.Alarm$Request.runSafely(Alarm.java:368)
at com.intellij.util.Alarm$Request.run(Alarm.java:355)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at com.intellij.util.concurrency.SchedulingWrapper$MyScheduledFutureTask.run(SchedulingWrapper.java:224)
at com.intellij.openapi.application.TransactionGuardImpl$2.run(TransactionGuardImpl.java:312)
at com.intellij.openapi.application.impl.LaterInvocator$FlushQueue.doRun(LaterInvocator.java:433)
at com.intellij.openapi.application.impl.LaterInvocator$FlushQueue.runNextEvent(LaterInvocator.java:416)
at com.intellij.openapi.application.impl.LaterInvocator$FlushQueue.run(LaterInvocator.java:399)
at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:776)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:727)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:746)
at com.intellij.ide.IdeEventQueue.defaultDispatchEvent(IdeEventQueue.java:873)
at com.intellij.ide.IdeEventQueue._dispatchEvent(IdeEventQueue.java:822)
at com.intellij.ide.IdeEventQueue.lambda$dispatchEvent$8(IdeEventQueue.java:461)
at com.intellij.openapi.progress.impl.CoreProgressManager.computePrioritized(CoreProgressManager.java:704)
at com.intellij.ide.IdeEventQueue.dispatchEvent(IdeEventQueue.java:460)
at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

I've looked around online but the only errors I can find related to this don't match my situation at all. Has a configuration been changed somewhere that I need to change back, or have I done something wrong?

Thanks