memory issue when loading demo config with micromanager 2.0

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memory issue when loading demo config with micromanager 2.0

Karl Bellve-3

When I load the attached config file in the starting dialog, µManager just starts sucking up memory until my computer comes to a standstill. 

If I instead load the same config file after loading µManager (Config->Load Hardware Configuration), it behaves normally. 



Log (until I killed it)

[kdb@oxygen micro-manager]$ micromanager  
class path = /usr/local/share/micro-manager/jars/bigdataviewer-core-2.1.0.jar:/usr/local/share/micro-manager/jars/Big.jar:/usr/local/share/micro-manager/jars/
bsh-2.0b4.jar:/usr/local/share/micro-manager/jars/bsh-2.0b6.jar:/usr/local/share/micro-manager/jars/clojure-1.3.0.jar:/usr/local/share/micro-manager/jars/cloo
j-0.2.7.jar:/usr/local/share/micro-manager/jars/commons-math-2.2.jar:/usr/local/share/micro-manager/jars/commons-math3-3.4.1.jar:/usr/local/share/micro-manage
r/jars/core.cache-0.6.2.jar:/usr/local/share/micro-manager/jars/core.memoize-0.5.2.jar:/usr/local/share/micro-manager/jars/data.json-0.1.1.jar:/usr/local/shar
e/micro-manager/jars/eventbus-1.4.jar:/usr/local/share/micro-manager/jars/formats-api-5.1.1.jar:/usr/local/share/micro-manager/jars/formats-common-5.1.1.jar:/
usr/local/share/micro-manager/jars/gentyref-1.1.0.jar:/usr/local/share/micro-manager/jars/gson-2.2.4.jar:/usr/local/share/micro-manager/jars/guava-17.0.jar:/u
sr/local/share/micro-manager/jars/iconloader-GIT.jar:/usr/local/share/micro-manager/jars/ij-1.48v.jar:/usr/local/share/micro-manager/jars/ij-1.49h.jar:/usr/lo
cal/share/micro-manager/jars/imagej-common-0.17.0.jar:/usr/local/share/micro-manager/jars/imglib2-2.4.0.jar:/usr/local/share/micro-manager/jars/imglib2-algori
thm-0.3.1.jar:/usr/local/share/micro-manager/jars/imglib2-realtransform-2.0.0-beta-29.jar:/usr/local/share/micro-manager/jars/imglib2-roi-0.3.2.jar:/usr/local
/share/micro-manager/jars/imglib2-ui-2.0.0-beta-29.jar:/usr/local/share/micro-manager/jars/jama-1.0.3.jar:/usr/local/share/micro-manager/jars/jcommon-1.0.23.j
ar:/usr/local/share/micro-manager/jars/jdom-2.0.2.jar:/usr/local/share/micro-manager/jars/jdom2-2.0.5.jar:/usr/local/share/micro-manager/jars/jfreechart-1.0.1
9.jar:/usr/local/share/micro-manager/jars/jhdf5-14.12.0.jar:/usr/local/share/micro-manager/jars/joda-time-2.2.jar:/usr/local/share/micro-manager/jars/kryo-2.2
4.0.jar:/usr/local/share/micro-manager/jars/logback-classic-1.1.1.jar:/usr/local/share/micro-manager/jars/logback-core-1.1.1.jar:/usr/local/share/micro-manage
r/jars/miglayout-core-4.2.jar:/usr/local/share/micro-manager/jars/miglayout-swing-4.2.jar:/usr/local/share/micro-manager/jars/minlog-1.2.jar:/usr/local/share/
micro-manager/jars/MMAcqEngine.jar:/usr/local/share/micro-manager/jars/MMCoreJ.jar:/usr/local/share/micro-manager/jars/MMJ_.jar:/usr/local/share/micro-manager
/jars/objenesis-2.1.jar:/usr/local/share/micro-manager/jars/ome-xml-5.1.1.jar:/usr/local/share/micro-manager/jars/Projector.jar:/usr/local/share/micro-manager
/jars/protobuf-java-2.5.0.jar:/usr/local/share/micro-manager/jars/rsyntaxtextarea-2.5.2.jar:/usr/local/share/micro-manager/jars/scijava-common-2.46.0.jar:/usr
/local/share/micro-manager/jars/serializer-2.7.1.jar:/usr/local/share/micro-manager/jars/slf4j-api-1.7.6.jar:/usr/local/share/micro-manager/jars/spim_data-2.0
.1.jar:/usr/local/share/micro-manager/jars/swingx-0.9.5.jar:/usr/local/share/micro-manager/jars/trove4j-3.0.3.jar:/usr/local/share/micro-manager/jars/TSFProto
-SVN.jar:/usr/local/share/micro-manager/jars/udunits-4.3.18.jar:/usr/local/share/micro-manager/jars/xalan-2.7.1.jar:/usr/local/share/micro-manager/jars/xml-ap
is-1.3.04.jar
Load MMCoreJ_wrap: Start loading...
Load MMCoreJ_wrap: Try path given by mmcorej.library.path
Load MMCoreJ_wrap: Try loading: /usr/local/lib/micro-manager/libMMCoreJ_wrap.so
Load MMCoreJ_wrap: Successfully loaded: /usr/local/lib/micro-manager/libMMCoreJ_wrap.so
2017-07-26T15:02:56.532315 tid139788598261504 [IFO,LogManager] Enabled logging to stderr
Asked to load file at path /mnt/alcor/VolGroup03-LogVol00/kdb/projects/workspace/micro-manager/GlobalUserProfile.txt which doesn't exist; instead providing a
default empty PropertyMap.
2017-07-26T15:02:56.729602 tid139788598261504 [IFO,LogManager] Enabled primary log file /tmp/CoreLog20170726T150256_pid8319.txt
2017-07-26T15:02:56.729722 tid139788598261504 [IFO,App] User: kdb
2017-07-26T15:02:56.729775 tid139788598261504 [IFO,App] Host: oxygen.umassmed.edu
2017-07-26T15:02:56.729789 tid139788598261504 [IFO,App] MM Studio version: 2.0.x dev
2017-07-26T15:02:56.729827 tid139788598261504 [IFO,App] MMCore version 8.5.0
2017-07-26T15:02:56.729865 tid139788598261504 [IFO,App] Device API version 67, Module API version 10
2017-07-26T15:02:56.729882 tid139788598261504 [IFO,App] Operating System: Linux (amd64) 4.11.11-200.fc25.x86_64
2017-07-26T15:02:56.729898 tid139788598261504 [IFO,App] JVM: OpenJDK 64-Bit Server VM, version 1.8.0_131, 64-bit
2017-07-26T15:02:56.739780 tid139788598261504 [IFO,App] EDTHangLogger: Started monitoring of EDT hangs
                                             [       ] [heartbeat timeout = 4500 ms, hang check interval = 1000 ms]
2017-07-26T15:02:56.871863 tid139787905943296 [IFO,App] Searching for plugins in /usr/local/share/micro-manager/mmplugins
2017-07-26T15:02:57.169687 tid139787905943296 [IFO,App] Found plugin com.asiimaging.CRISPv2.ASI_CRISP_V2@77a3d418
2017-07-26T15:02:57.172506 tid139787905943296 [IFO,App] Found plugin org.micromanager.zprojector.ZProjectorPlugin@669093d3
2017-07-26T15:02:57.172756 tid139787905943296 [IFO,App] Found plugin org.micromanager.intelligentacquisition.IntelligentAcquisition@10f44a39
2017-07-26T15:02:57.173053 tid139787905943296 [IFO,App] Found plugin PMQI.AutoWB@4c5794b0
2017-07-26T15:02:57.173290 tid139787905943296 [IFO,App] Found plugin org.micromanager.CRISP.CRISP@59c62943
2017-07-26T15:02:57.173496 tid139787905943296 [IFO,App] Found plugin org.micromanager.acquiremultipleregions.AcquireMultipleRegions@3b2a37a3
2017-07-26T15:02:57.173728 tid139787905943296 [IFO,App] Found plugin org.micromanager.multicamera.MultiCamera@9bd177d
2017-07-26T15:02:57.174483 tid139787905943296 [IFO,App] Found plugin org.micromanager.multichannelshading.MultiChannelShading@1cffb5cc
2017-07-26T15:02:57.175002 tid139787905943296 [IFO,App] Found plugin org.micromanager.pixelcalibrator.PixelCalibratorPlugin@577ae2f2
2017-07-26T15:02:57.175798 tid139787905943296 [IFO,App] Found plugin org.micromanager.recall.RecallPlugin@68c4e870
2017-07-26T15:02:57.176039 tid139787905943296 [IFO,App] Found plugin org.micromanager.duplicator.DuplicatorPlugin@6829eae8
2017-07-26T15:02:57.176522 tid139787905943296 [IFO,App] Found plugin org.micromanager.patternoverlay.PatternOverlayPlugin@12aa78e6
2017-07-26T15:02:57.176719 tid139787905943296 [IFO,App] Found plugin org.micromanager.slideexplorer.SlideExplorerPlugin@35f3aef1
2017-07-26T15:02:57.176960 tid139787905943296 [IFO,App] Found plugin GaussianTrack_@70292e7c
2017-07-26T15:02:57.178817 tid139787905943296 [IFO,App] Found plugin org.micromanager.splitview.SplitView@499ba0e2
2017-07-26T15:02:57.179033 tid139787905943296 [IFO,App] Found plugin org.micromanager.hcs.HCSPlugin@1c313d41
2017-07-26T15:02:57.179861 tid139787905943296 [IFO,App] Found plugin org.micromanager.pipelinesaver.SaverPlugin@483cfe55
2017-07-26T15:02:57.180104 tid139787905943296 [IFO,App] Found plugin org.micromanager.imageflipper.FlipperPlugin@5c34db00
2017-07-26T15:02:57.180334 tid139787905943296 [IFO,App] Found plugin org.micromanager.plugins.sequencebuffermonitor.SequenceBufferMonitor@497a2ef2
2017-07-26T15:02:57.180601 tid139787905943296 [IFO,App] Found plugin org.micromanager.projector.ProjectorPlugin@67e8f130
2017-07-26T15:02:57.180824 tid139787905943296 [IFO,App] Found plugin com.imaging100x.tracker.TrackerPlugin@488965ce
2017-07-26T15:02:57.182849 tid139787905943296 [IFO,App] Found plugin org.micromanager.asidispim.ASIdiSPIM@41e075cb
2017-07-26T15:02:57.183558 tid139787905943296 [IFO,App] Found plugin org.micromanager.plugins.framecombiner.FrameCombinerPlugin@692106fe
2017-07-26T15:02:57.184897 tid139787905943296 [IFO,App] Found plugin edu.umassmed.pgfocus.pgFocus@5d1d574f
2017-07-26T15:02:57.185234 tid139787905943296 [IFO,App] Found plugin org.micromanager.plugins.snaponmove.SnapOnMovePlugin@3ceabce4
2017-07-26T15:02:57.185440 tid139787905943296 [IFO,App] Found plugin ch.epfl.leb.autolase.AutoLasePlugin@6fc67c92
2017-07-26T15:02:57.185671 tid139787905943296 [IFO,App] Found plugin edu.umassmed.big.mmremote.mmKNIME@1dc20700
2017-07-26T15:02:57.185813 tid139787905943296 [IFO,App] Searching for plugins in /usr/local/share/micro-manager/mmautofocus
2017-07-26T15:02:57.223101 tid139787905943296 [IFO,App] Found plugin org.micromanager.autofocus.AutofocusTB@10327b3a
2017-07-26T15:02:57.226678 tid139787905943296 [IFO,App] Found plugin org.micromanager.autofocus.HardwareFocusExtender@132f1285
2017-07-26T15:02:57.227753 tid139787905943296 [IFO,App] Found plugin org.micromanager.autofocus.AutofocusDuo@4b9da7a
2017-07-26T15:02:57.229344 tid139787905943296 [IFO,App] Found plugin org.micromanager.autofocus.Autofocus@27afc079
2017-07-26T15:02:57.238066 tid139787905943296 [IFO,App] Found plugin org.micromanager.autofocus.OughtaFocus@2792b8b3
2017-07-26T15:02:57.239231 tid139787905943296 [IFO,App] Searching for plugins in class loader
2017-07-26T15:02:57.399565 tid139787905943296 [IFO,App] Found plugin org.micromanager.acquisition.internal.DefaultMDAPlugin@51ba502f
2017-07-26T15:02:57.399865 tid139787905943296 [IFO,App] Found plugin org.micromanager.display.internal.gearmenu.ExportImagesItem@627abca2
2017-07-26T15:02:57.400031 tid139787905943296 [IFO,App] Found plugin org.micromanager.display.internal.gearmenu.LineProfileItem@101ae7f
2017-07-26T15:02:57.401078 tid139787905943296 [IFO,App] Found plugin org.micromanager.display.internal.inspector.OverlaysPlugin@51a53fa5
2017-07-26T15:02:57.401254 tid139787905943296 [IFO,App] Found plugin org.micromanager.display.internal.overlays.ScaleBarPlugin@765df5db
2017-07-26T15:02:57.401411 tid139787905943296 [IFO,App] Found plugin org.micromanager.display.internal.overlays.TimestampPlugin@27eda72a
2017-07-26T15:02:57.402300 tid139787905943296 [IFO,App] Found plugin org.micromanager.quickaccess.internal.controls.AutofocusButtons@1a38d484
2017-07-26T15:02:57.402491 tid139787905943296 [IFO,App] Found plugin org.micromanager.quickaccess.internal.controls.CloseAllButton@5a3ed583
2017-07-26T15:02:57.403016 tid139787905943296 [IFO,App] Found plugin org.micromanager.quickaccess.internal.controls.ExposureTime@3d2f94f8
2017-07-26T15:02:57.403662 tid139787905943296 [IFO,App] Found plugin org.micromanager.quickaccess.internal.controls.LiveButton@17f43630
2017-07-26T15:02:57.404586 tid139787905943296 [IFO,App] Found plugin org.micromanager.quickaccess.internal.controls.MDAButtons@4f45eb0a
2017-07-26T15:02:57.405330 tid139787905943296 [IFO,App] Found plugin org.micromanager.quickaccess.internal.controls.PresetButton@35fcc47b
2017-07-26T15:02:57.405520 tid139787905943296 [IFO,App] Found plugin org.micromanager.quickaccess.internal.controls.RefreshButton@55016475
2017-07-26T15:02:57.406043 tid139787905943296 [IFO,App] Found plugin org.micromanager.quickaccess.internal.controls.SavedMDAButton@11053d87
2017-07-26T15:02:57.406501 tid139787905943296 [IFO,App] Found plugin org.micromanager.quickaccess.internal.controls.ScriptButton@202eacc9
2017-07-26T15:02:57.406808 tid139787905943296 [IFO,App] Found plugin org.micromanager.quickaccess.internal.controls.ShutterControl@18ff444e
2017-07-26T15:02:57.407393 tid139787905943296 [IFO,App] Found plugin org.micromanager.quickaccess.internal.controls.SnapButton@1a02b467
2017-07-26T15:02:57.407588 tid139787905943296 [IFO,App] Found plugin org.micromanager.quickaccess.internal.controls.TextLabel@783d5e5d
2017-07-26T15:02:57.407782 tid139787905943296 [IFO,App] Plugin loading took 536ms
2017-07-26T15:02:57.407937 tid139788598261504 [IFO,App] Finished waiting for plugins to load
2017-07-26T15:03:03.277117 tid139788598261504 [IFO,Core] Did unload all devices
2017-07-26T15:03:03.280267 tid139788598261504 [IFO,Core] Did load device DHub from DemoCamera; label = DHub
2017-07-26T15:03:03.280369 tid139788598261504 [IFO,Core] Did load device DCam from DemoCamera; label = DCam
2017-07-26T15:03:03.280413 tid139788598261504 [IFO,Core] Did load device DWheel from DemoCamera; label = DWheel
2017-07-26T15:03:03.280450 tid139788598261504 [IFO,Core] Did load device DStage from DemoCamera; label = DStage
2017-07-26T15:03:03.280491 tid139788598261504 [IFO,Core] Did load device DXYStage from DemoCamera; label = DXYStage
2017-07-26T15:03:03.280525 tid139788598261504 [IFO,Core] Did load device DShutter from DemoCamera; label = DShutter
2017-07-26T15:03:03.280600 tid139788598261504 [IFO,Core] Will initialize 6 devices
2017-07-26T15:03:03.280604 tid139788598261504 [IFO,Core] Will initialize device DHub
2017-07-26T15:03:03.280609 tid139788598261504 [IFO,Core] Did initialize device DHub
2017-07-26T15:03:03.280614 tid139788598261504 [IFO,Core] Will initialize device DCam
2017-07-26T15:03:03.280903 tid139788598261504 [IFO,Core] Did initialize device DCam
2017-07-26T15:03:03.280910 tid139788598261504 [IFO,Core] Default camera set to DCam
2017-07-26T15:03:03.280914 tid139788598261504 [IFO,Core] Will initialize device DWheel
2017-07-26T15:03:03.280964 tid139788598261504 [IFO,Core] Did initialize device DWheel
2017-07-26T15:03:03.280967 tid139788598261504 [IFO,Core] Will initialize device DStage
2017-07-26T15:03:03.280992 tid139788598261504 [IFO,Core] Did initialize device DStage
2017-07-26T15:03:03.280995 tid139788598261504 [IFO,Core] Will initialize device DXYStage
2017-07-26T15:03:03.281003 tid139788598261504 [IFO,Core] Did initialize device DXYStage
2017-07-26T15:03:03.281014 tid139788598261504 [IFO,Core] Default xy stage set to DXYStage
2017-07-26T15:03:03.281017 tid139788598261504 [IFO,Core] Will initialize device DShutter
2017-07-26T15:03:03.281027 tid139788598261504 [IFO,Core] Did initialize device DShutter
2017-07-26T15:03:03.281030 tid139788598261504 [IFO,Core] Default shutter set to DShutter
2017-07-26T15:03:03.281032 tid139788598261504 [IFO,Core] Finished initializing 6 devices
2017-07-26T15:03:03.281245 tid139788598261504 [IFO,Core] Default camera set to DCam
2017-07-26T15:03:03.281474 tid139788598261504 [IFO,Core] Default stage set to DStage
2017-07-26T15:03:03.282225 tid139788598261504 [IFO,Core] Did update system state cache
2017-07-26T15:03:26.580558 tid139787911546624 [IFO,App] EDTHangLogger: Missed heartbeat; waiting to see if we are stuck on a single event
2017-07-26T15:03:26.580766 tid139787910493952 [IFO,App] EDTHangLogger: First heartbeat after miss (11839 ms since timebase)


Cheers Karl

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MicroManager2-Test.cfg (1K) Download Attachment
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