Posted by
Benoit Lombardot on
URL: http://imagej.273.s1.nabble.com/System-specific-issues-with-FIJI-tp5011752.html
Dear IJ users,
I am bumping in little issues with FIJI. I have some issue occuring on
one system but not on another with the same FIJI installation. That
would be great if anyone had advise to get me started with that
debugging. I have read through the fiji debug page but am not sure what
to do, let say, after starting FIJI in debug mode. For now, I am a bit
stuck, but willing to learn.
Below is a description of the 2 (independent) issues I have met. It is a
quite general description but just let me know what additional
information could be needed here.
1 - One plugin I wrote works on a mac with mac os 10.9.3 (it also works
with win7, ubuntu and centos systems) but crashes on a mac os 10.10.1
throwing an out of memory error (despite a small dataset, proper
physical memory and adequate memory settings in FIJI). It is not clear
to me where the error is happening as it does not refer explicitly to
the function of the plugin. I added the error message below.
2 - I have another issue with saving overlay in tiff image with Fiji. It
works fine on my laptop (a mac with osx 10.9.3) but does not save the
overlay on my user laptop ( a mac with osx 10.9.5) and does not output
errors. I copied his Fiji installation on my laptop and the the overlay
is saved properly on my machine. Any idea of what could be the issue?
For the 2 cases I used FIJI (IJ 2.0.0-rc-24 / IJ 1.49m)
Thanks for your help,
Best,
Benoit
Error message of case 1:
Exception in thread "SciJava-111bda67-Thread-2203"
java.lang.OutOfMemoryError: unable to create new native thread
at java.lang.Thread.start0(Native Method)
at java.lang.Thread.start(Thread.java:673)
at
java.util.concurrent.ThreadPoolExecutor.addThread(ThreadPoolExecutor.java:681)
at
java.util.concurrent.ThreadPoolExecutor.addIfUnderMaximumPoolSize(ThreadPoolExecutor.java:727)
at
java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:655)
at
java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:78)
at org.scijava.thread.DefaultThreadService.run(DefaultThreadService.java:80)
at org.scijava.event.DefaultEventBus.publishLater(DefaultEventBus.java:217)
at org.scijava.event.DefaultEventBus.publishLater(DefaultEventBus.java:105)
at
org.scijava.event.DefaultEventService.publishLater(DefaultEventService.java:111)
at
org.scijava.app.DefaultStatusService.publish(DefaultStatusService.java:112)
at
org.scijava.app.DefaultStatusService.showStatus(DefaultStatusService.java:73)
at
net.imagej.minmax.DefaultMinMaxMethod.report(DefaultMinMaxMethod.java:301)
at
net.imagej.minmax.DefaultMinMaxMethod.compute(DefaultMinMaxMethod.java:234)
at net.imagej.minmax.DefaultMinMaxMethod$1.run(DefaultMinMaxMethod.java:180)
at java.lang.Thread.run(Thread.java:695)
Exception in thread "SciJava-111bda67-Thread-2199"
java.lang.OutOfMemoryError: unable to create new native thread
at java.lang.Thread.start0(Native Method)
at java.lang.Thread.start(Thread.java:673)
at
java.util.concurrent.ThreadPoolExecutor.addThread(ThreadPoolExecutor.java:681)
at
java.util.concurrent.ThreadPoolExecutor.addIfUnderMaximumPoolSize(ThreadPoolExecutor.java:727)
at
java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:655)
at
java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:78)
at org.scijava.thread.DefaultThreadService.run(DefaultThreadService.java:80)
at org.scijava.event.DefaultEventBus.publishLater(DefaultEventBus.java:217)
at org.scijava.event.DefaultEventBus.publishLater(DefaultEventBus.java:105)
at
org.scijava.event.DefaultEventService.publishLater(DefaultEventService.java:111)
at
org.scijava.app.DefaultStatusService.publish(DefaultStatusService.java:112)
at
org.scijava.app.DefaultStatusService.showStatus(DefaultStatusService.java:73)
at
net.imagej.minmax.DefaultMinMaxMethod.report(DefaultMinMaxMethod.java:301)
at
net.imagej.minmax.DefaultMinMaxMethod.compute(DefaultMinMaxMethod.java:234)
at net.imagej.minmax.DefaultMinMaxMethod$1.run(DefaultMinMaxMethod.java:180)
at java.lang.Thread.run(Thread.java:695)
Exception in thread "SciJava-111bda67-Thread-2201"
java.lang.OutOfMemoryError: unable to create new native thread
at java.lang.Thread.start0(Native Method)
at java.lang.Thread.start(Thread.java:673)
at
java.util.concurrent.ThreadPoolExecutor.addThread(ThreadPoolExecutor.java:681)
at
java.util.concurrent.ThreadPoolExecutor.addIfUnderMaximumPoolSize(ThreadPoolExecutor.java:727)
at
java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:655)
at
java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:78)
at org.scijava.thread.DefaultThreadService.run(DefaultThreadService.java:80)
at org.scijava.event.DefaultEventBus.publishLater(DefaultEventBus.java:217)
at org.scijava.event.DefaultEventBus.publishLater(DefaultEventBus.java:105)
at
org.scijava.event.DefaultEventService.publishLater(DefaultEventService.java:111)
at
org.scijava.app.DefaultStatusService.publish(DefaultStatusService.java:112)
at
org.scijava.app.DefaultStatusService.showStatus(DefaultStatusService.java:73)
at
net.imagej.minmax.DefaultMinMaxMethod.report(DefaultMinMaxMethod.java:301)
at
net.imagej.minmax.DefaultMinMaxMethod.compute(DefaultMinMaxMethod.java:234)
at net.imagej.minmax.DefaultMinMaxMethod$1.run(DefaultMinMaxMethod.java:180)
at java.lang.Thread.run(Thread.java:695)
Exception in thread "SciJava-111bda67-Thread-2202"
java.lang.OutOfMemoryError: unable to create new native thread
at java.lang.Thread.start0(Native Method)
at java.lang.Thread.start(Thread.java:673)
at
java.util.concurrent.ThreadPoolExecutor.addThread(ThreadPoolExecutor.java:681)
at
java.util.concurrent.ThreadPoolExecutor.addIfUnderMaximumPoolSize(ThreadPoolExecutor.java:727)
at
java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:655)
at
java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:78)
at org.scijava.thread.DefaultThreadService.run(DefaultThreadService.java:80)
at org.scijava.event.DefaultEventBus.publishLater(DefaultEventBus.java:217)
at org.scijava.event.DefaultEventBus.publishLater(DefaultEventBus.java:105)
at
org.scijava.event.DefaultEventService.publishLater(DefaultEventService.java:111)
at
org.scijava.app.DefaultStatusService.publish(DefaultStatusService.java:112)
at
org.scijava.app.DefaultStatusService.showStatus(DefaultStatusService.java:73)
at
net.imagej.minmax.DefaultMinMaxMethod.report(DefaultMinMaxMethod.java:301)
at
net.imagej.minmax.DefaultMinMaxMethod.compute(DefaultMinMaxMethod.java:234)
at net.imagej.minmax.DefaultMinMaxMethod$1.run(DefaultMinMaxMethod.java:180)
at java.lang.Thread.run(Thread.java:695)
Exception in thread "SciJava-111bda67-Thread-2200"
java.lang.OutOfMemoryError: unable to create new native thread
at java.lang.Thread.start0(Native Method)
at java.lang.Thread.start(Thread.java:673)
at
java.util.concurrent.ThreadPoolExecutor.addThread(ThreadPoolExecutor.java:681)
at
java.util.concurrent.ThreadPoolExecutor.addIfUnderMaximumPoolSize(ThreadPoolExecutor.java:727)
at
java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:655)
at
java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:78)
at org.scijava.thread.DefaultThreadService.run(DefaultThreadService.java:80)
at org.scijava.event.DefaultEventBus.publishLater(DefaultEventBus.java:217)
at org.scijava.event.DefaultEventBus.publishLater(DefaultEventBus.java:105)
at
org.scijava.event.DefaultEventService.publishLater(DefaultEventService.java:111)
at
org.scijava.app.DefaultStatusService.publish(DefaultStatusService.java:112)
at
org.scijava.app.DefaultStatusService.showStatus(DefaultStatusService.java:73)
at
net.imagej.minmax.DefaultMinMaxMethod.report(DefaultMinMaxMethod.java:301)
at
net.imagej.minmax.DefaultMinMaxMethod.compute(DefaultMinMaxMethod.java:234)
at net.imagej.minmax.DefaultMinMaxMethod$1.run(DefaultMinMaxMethod.java:180)
at java.lang.Thread.run(Thread.java:695)
--
Benoit Lombardot
Bio-Image informatics, Scientific Computing Facility
Max Planck Institute CBG
Pfotenhauer Str. 108, 01307 Dresden
--
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