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Task #9214 (closed)

Last modified 11 months ago

Bug: Hammamatsu VMS causes out of memory error

Reported by:	rleigh	Owned by:
Priority:	major	Milestone:	OMERO-4.4
Component:	Import	Keywords:	n.a.
Cc:	ux@…, mlinkert, jburel, cxallan	Remaining Time:	n.a.
Sprint:	n.a.	Resources:	n.a.
References:	n.a.	Referenced By:	n.a.

Description

Importing instantly causes an out of memory error, even after raising the limit to -mx 6GB.

References

Change History

comment:1 Changed 11 months ago by jburel

Cc ux@…, mlinkert-x, jburel, cxallan added

comment:2 Changed 11 months ago by mlinkert

Status changed from new to closed
Resolution set to fixed

Should be fixed with: https://github.com/melissalinkert/bioformats/commit/dc713d1f5a63f4494089af0405f32ec30625e5a6 and https://github.com/aleksandra-tarkowska/openmicroscopy/commit/cdffc2cf73fd37ecb50aa1110b02a047243d1f9b

comment:3 Changed 11 months ago by rleigh

Still causing OOM errors on import:

java.lang.OutOfMemoryError: Java heap space
	at loci.formats.codec.JPEGTileDecoder.initialize(JPEGTileDecoder.java:137)
	at loci.formats.in.TileJPEGReader.initFile(TileJPEGReader.java:118)
	at loci.formats.FormatReader.setId(FormatReader.java:1105)
	at loci.formats.in.HamamatsuVMSReader.initFile(HamamatsuVMSReader.java:205)
	at loci.formats.FormatReader.setId(FormatReader.java:1105)
	at loci.formats.ImageReader.setId(ImageReader.java:695)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:310)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:486)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6286)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1248)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:111)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6335)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1248)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:111)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.OutOfMemoryError: Java heap space
	at loci.formats.codec.JPEGTileDecoder.initialize(JPEGTileDecoder.java:137)
	at loci.formats.in.TileJPEGReader.initFile(TileJPEGReader.java:118)
	at loci.formats.FormatReader.setId(FormatReader.java:1105)
	at loci.formats.in.HamamatsuVMSReader.initFile(HamamatsuVMSReader.java:205)
	at loci.formats.FormatReader.setId(FormatReader.java:1105)
	at loci.formats.ImageReader.setId(ImageReader.java:695)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:310)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:486)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6286)
	... 11 more

comment:4 Changed 11 months ago by rleigh

Status changed from closed to reopened
Resolution fixed deleted

comment:5 Changed 11 months ago by mlinkert

Status changed from reopened to closed
Resolution set to fixed

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