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Running Fiji by SSH command line

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Griffa, Michele

Running Fiji by SSH command line

Dear ImageJ users/developers,

I'm facing the following issue.
I connect via SSH to a Linux workstation running on Cent OS 6.4 from a MS Windows laptop, via Putty.
I have the Cygwin X-server installed and running on the Windows laptop.
On the Linux workstation, Fiji ver. 2.0.0-rc-15/1.49j10 with Java 1.6.0_24 [64 bit] is installed and runs properly.

If I call Fiji from the command line, it does not run and the following error message is returned:

[grm@lin3a308 ~]$ log4j:WARN No appenders could be found for logger (org.bushe.swing.event.EventService).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Error while executing the main() method of class 'net.imagej.Main':
sun.awt.X11.XException: Cannot write XdndAware property
at sun.awt.X11.XDnDDropTargetProtocol.registerDropTarget(XDnDDropTargetProtocol.java:79)
at sun.awt.X11.XDropTargetRegistry.registerDropSite(XDropTargetRegistry.java:554)
at sun.awt.X11.XWindowPeer.addDropTarget(XWindowPeer.java:1633)
at sun.awt.X11.XComponentPeer.addDropTarget(XComponentPeer.java:1509)
at java.awt.dnd.DropTarget.addNotify(DropTarget.java:493)
at java.awt.Component.addNotify(Component.java:6688)
at java.awt.Container.addNotify(Container.java:2567)
at java.awt.Window.addNotify(Window.java:663)
at java.awt.Frame.addNotify(Frame.java:470)
at java.awt.Window.pack(Window.java:704)
at net.imagej.legacy.IJ1Helper.setVisible(IJ1Helper.java:260)
at net.imagej.legacy.ui.LegacyUI.show(LegacyUI.java:133)
at org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:180)
at org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:165)
at net.imagej.Main.launch(Main.java:67)
at net.imagej.Main.main(Main.java:73)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)

Notice: the command I ran is /opt/Fiji.app/ImageJ-linux64 --allow-multiple

With the previous versions of Fiji I could run it and export to the remote Windows desktop the GUI without any problem.
Does anybody have any suggestion where should I look for the problem?

Thanks a lot in advance.

Best regards,

Michele Griffa, PhD
Senior Research Scientist
Topic Leader „3D Image Analysis and Simulation“

Concrete and Construction Chemistry Laboratory
and
Center for X-Ray Analytics

Empa
Swiss Federal Laboratories for Materials Science and Technology
ETH Domain

Überlandstrasse 129
8600 Dübendorf
Switzerland

Tel +41 58 765 4360
Fax +41 58 765 4035
[hidden email]
www.empa.ch
www.empa.ch/x-ray

Upcoming Workshops at Empa in Dübendorf:

- CCMX Advanced Course “Advanced X-Ray Diffraction Methods for Coatings”: 26.-28. Nov. 2014

Diese Mitteilung ist ausschliesslich für die als Empfänger aufgeführte Person(en) oder Firma bestimmt. Sie kann persönliche und/oder vertrauliche Informationen enthalten. Sollten Sie diese Mitteilung irrtümlicherweise erhalten haben, bitten wir Sie, uns umgehend per E-Mail zu informieren, sämtliche Ausdrucke zu vernichten und die E-Mail-Dateien zu löschen.

This message is intended for the exclusive use of the individual(s) or entity to whom it is addressed. It may contain information that is privileged and/or confidential. Should you have received this message erroneously, please notify us immediately by e-mail, destroy any printouts and delete all electronic files contained in this message.
-----------------------------------------------------------------------------------------------

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Mark Hiner

Re: Running Fiji by SSH command line

Hi Michele,

After googling around a bit it sounds like this may be a problem with Java
<http://bugs.java.com/bugdatabase/view_bug.do?bug_id=7100524>. There is
some discussion of workarounds
<https://groups.google.com/forum/#!topic/openjump-users/fO5hpxth1o0> by
switching to Java 1.6.0_22 or OpenJDK, for example. So I would recommend
trying to run Fiji with a different version of Java
<http://imagej.net/FAQ#How_do_I_launch_ImageJ_with_a_different_version_of_Java.3F>
.

Hope that helps!

Best,
Mark

On Mon, Nov 17, 2014 at 8:08 AM, Michele Griffa <[hidden email]>
wrote:

> Dear ImageJ users/developers,
>
> I'm facing the following issue.
> I connect via SSH to a Linux workstation running on Cent OS 6.4 from a MS
> Windows laptop, via Putty.
> I have the Cygwin X-server installed and running on the Windows laptop.
> On the Linux workstation, Fiji ver. 2.0.0-rc-15/1.49j10 with Java 1.6.0_24
> [64 bit] is installed and runs properly.
>
> If I call Fiji from the command line, it does not run and the following
> error message is returned:
>
> [grm@lin3a308 ~]$ log4j:WARN No appenders could be found for logger
> (org.bushe.swing.event.EventService).
> log4j:WARN Please initialize the log4j system properly.
> log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
> more info.
> Error while executing the main() method of class 'net.imagej.Main':
> sun.awt.X11.XException: Cannot write XdndAware property
> at
> sun.awt.X11.XDnDDropTargetProtocol.registerDropTarget(XDnDDropTargetProtocol.java:79)
> at
> sun.awt.X11.XDropTargetRegistry.registerDropSite(XDropTargetRegistry.java:554)
> at sun.awt.X11.XWindowPeer.addDropTarget(XWindowPeer.java:1633)
> at
> sun.awt.X11.XComponentPeer.addDropTarget(XComponentPeer.java:1509)
> at java.awt.dnd.DropTarget.addNotify(DropTarget.java:493)
> at java.awt.Component.addNotify(Component.java:6688)
> at java.awt.Container.addNotify(Container.java:2567)
> at java.awt.Window.addNotify(Window.java:663)
> at java.awt.Frame.addNotify(Frame.java:470)
> at java.awt.Window.pack(Window.java:704)
> at net.imagej.legacy.IJ1Helper.setVisible(IJ1Helper.java:260)
> at net.imagej.legacy.ui.LegacyUI.show(LegacyUI.java:133)
> at
> org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:180)
> at
> org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:165)
> at net.imagej.Main.launch(Main.java:67)
> at net.imagej.Main.main(Main.java:73)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
> at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
> at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
>
> Notice: the command I ran is /opt/Fiji.app/ImageJ-linux64 --allow-multiple
>
> With the previous versions of Fiji I could run it and export to the remote
> Windows desktop the GUI without any problem.
> Does anybody have any suggestion where should I look for the problem?
>
> Thanks a lot in advance.
>
> Best regards,
>
> Michele Griffa, PhD
> Senior Research Scientist
> Topic Leader „3D Image Analysis and Simulation“
>
> Concrete and Construction Chemistry Laboratory
> and
> Center for X-Ray Analytics
>
> Empa
> Swiss Federal Laboratories for Materials Science and Technology
> ETH Domain
>
> Überlandstrasse 129
> 8600 Dübendorf
> Switzerland
>
> Tel +41 58 765 4360
> Fax +41 58 765 4035
> [hidden email]
> www.empa.ch
> www.empa.ch/x-ray
>
> Upcoming Workshops at Empa in Dübendorf:
>
> - CCMX Advanced Course “Advanced X-Ray Diffraction Methods for Coatings”:
> 26.-28. Nov. 2014
>
> Diese Mitteilung ist ausschliesslich für die als Empfänger aufgeführte
> Person(en) oder Firma bestimmt. Sie kann persönliche und/oder vertrauliche
> Informationen enthalten. Sollten Sie diese Mitteilung irrtümlicherweise
> erhalten haben, bitten wir Sie, uns umgehend per E-Mail zu informieren,
> sämtliche Ausdrucke zu vernichten und die E-Mail-Dateien zu löschen.
>
> This message is intended for the exclusive use of the individual(s) or
> entity to whom it is addressed. It may contain information that is
> privileged and/or confidential. Should you have received this message
> erroneously, please notify us immediately by e-mail, destroy any printouts
> and delete all electronic files contained in this message.
>
> -----------------------------------------------------------------------------------------------
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Paul van Schayck

Re: Running Fiji by SSH command line

Hi Michele,

I've also seen this error now and then when running a tunelled SSH session
with X forwarding (-X). But I could often resolve it by just trying to
start a few times, or restarting the session.

Let me know if you find a real workarround.

Paul

On Mon, Nov 17, 2014 at 3:36 PM, Mark Hiner <[hidden email]> wrote:

> Hi Michele,
>
> After googling around a bit it sounds like this may be a problem with Java
> <http://bugs.java.com/bugdatabase/view_bug.do?bug_id=7100524>. There is
> some discussion of workarounds
> <https://groups.google.com/forum/#!topic/openjump-users/fO5hpxth1o0> by
> switching to Java 1.6.0_22 or OpenJDK, for example. So I would recommend
> trying to run Fiji with a different version of Java
> <
> http://imagej.net/FAQ#How_do_I_launch_ImageJ_with_a_different_version_of_Java.3F
> >
> .
>
> Hope that helps!
>
> Best,
> Mark
>
> On Mon, Nov 17, 2014 at 8:08 AM, Michele Griffa <[hidden email]>
> wrote:
>
> > Dear ImageJ users/developers,
> >
> > I'm facing the following issue.
> > I connect via SSH to a Linux workstation running on Cent OS 6.4 from a MS
> > Windows laptop, via Putty.
> > I have the Cygwin X-server installed and running on the Windows laptop.
> > On the Linux workstation, Fiji ver. 2.0.0-rc-15/1.49j10 with Java
> 1.6.0_24
> > [64 bit] is installed and runs properly.
> >
> > If I call Fiji from the command line, it does not run and the following
> > error message is returned:
> >
> > [grm@lin3a308 ~]$ log4j:WARN No appenders could be found for logger
> > (org.bushe.swing.event.EventService).
> > log4j:WARN Please initialize the log4j system properly.
> > log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
> > more info.
> > Error while executing the main() method of class 'net.imagej.Main':
> > sun.awt.X11.XException: Cannot write XdndAware property
> > at
> >
> sun.awt.X11.XDnDDropTargetProtocol.registerDropTarget(XDnDDropTargetProtocol.java:79)
> > at
> >
> sun.awt.X11.XDropTargetRegistry.registerDropSite(XDropTargetRegistry.java:554)
> > at sun.awt.X11.XWindowPeer.addDropTarget(XWindowPeer.java:1633)
> > at
> > sun.awt.X11.XComponentPeer.addDropTarget(XComponentPeer.java:1509)
> > at java.awt.dnd.DropTarget.addNotify(DropTarget.java:493)
> > at java.awt.Component.addNotify(Component.java:6688)
> > at java.awt.Container.addNotify(Container.java:2567)
> > at java.awt.Window.addNotify(Window.java:663)
> > at java.awt.Frame.addNotify(Frame.java:470)
> > at java.awt.Window.pack(Window.java:704)
> > at net.imagej.legacy.IJ1Helper.setVisible(IJ1Helper.java:260)
> > at net.imagej.legacy.ui.LegacyUI.show(LegacyUI.java:133)
> > at
> > org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:180)
> > at
> > org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:165)
> > at net.imagej.Main.launch(Main.java:67)
> > at net.imagej.Main.main(Main.java:73)
> > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> > at
> >
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> > at
> >
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > at java.lang.reflect.Method.invoke(Method.java:597)
> > at
> net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
> > at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
> > at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
> >
> > Notice: the command I ran is /opt/Fiji.app/ImageJ-linux64
> --allow-multiple
> >
> > With the previous versions of Fiji I could run it and export to the
> remote
> > Windows desktop the GUI without any problem.
> > Does anybody have any suggestion where should I look for the problem?
> >
> > Thanks a lot in advance.
> >
> > Best regards,
> >
> > Michele Griffa, PhD
> > Senior Research Scientist
> > Topic Leader „3D Image Analysis and Simulation“
> >
> > Concrete and Construction Chemistry Laboratory
> > and
> > Center for X-Ray Analytics
> >
> > Empa
> > Swiss Federal Laboratories for Materials Science and Technology
> > ETH Domain
> >
> > Überlandstrasse 129
> > 8600 Dübendorf
> > Switzerland
> >
> > Tel +41 58 765 4360
> > Fax +41 58 765 4035
> > [hidden email]
> > www.empa.ch
> > www.empa.ch/x-ray
> >
> > Upcoming Workshops at Empa in Dübendorf:
> >
> > - CCMX Advanced Course “Advanced X-Ray Diffraction Methods for Coatings”:
> > 26.-28. Nov. 2014
> >
> > Diese Mitteilung ist ausschliesslich für die als Empfänger aufgeführte
> > Person(en) oder Firma bestimmt. Sie kann persönliche und/oder
> vertrauliche
> > Informationen enthalten. Sollten Sie diese Mitteilung irrtümlicherweise
> > erhalten haben, bitten wir Sie, uns umgehend per E-Mail zu informieren,
> > sämtliche Ausdrucke zu vernichten und die E-Mail-Dateien zu löschen.
> >
> > This message is intended for the exclusive use of the individual(s) or
> > entity to whom it is addressed. It may contain information that is
> > privileged and/or confidential. Should you have received this message
> > erroneously, please notify us immediately by e-mail, destroy any
> printouts
> > and delete all electronic files contained in this message.
> >
> >
> -----------------------------------------------------------------------------------------------
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Alex Krolick

Re: Running Fiji by SSH command line

Paul & Michelle,
Does the error appear when you use the -Y flag as well? X is unauthenticated X11 forwarding, Y authenticates.

Alex Krolick
Sent from my Windows Phone
907 229 9406

-----Original Message-----
From: "Paul van Schayck" <[hidden email]>
Sent: ‎11/‎17/‎2014 9:44 AM
To: "[hidden email]" <[hidden email]>
Subject: Re: Running Fiji by SSH command line

Hi Michele,

I've also seen this error now and then when running a tunelled SSH session
with X forwarding (-X). But I could often resolve it by just trying to
start a few times, or restarting the session.

Let me know if you find a real workarround.

Paul

On Mon, Nov 17, 2014 at 3:36 PM, Mark Hiner <[hidden email]> wrote:

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

David Gene Morgan

Re: Running Fiji by SSH command line

In reply to this post by Mark Hiner

Hi,

This is probably a silly question, but can you send _any_ X-based
graphics through the ssh tunnel? By default, some systems disable
X-forwarding, and if it were turned off, you might possibly see strange
java messages. This probably isn't the issue, but it's a thought...

On 11/17/2014 09:36 AM, Mark Hiner wrote:

> Hi Michele,
>
> After googling around a bit it sounds like this may be a problem with Java
> <http://bugs.java.com/bugdatabase/view_bug.do?bug_id=7100524>. There is
> some discussion of workarounds
> <https://groups.google.com/forum/#!topic/openjump-users/fO5hpxth1o0> by
> switching to Java 1.6.0_22 or OpenJDK, for example. So I would recommend
> trying to run Fiji with a different version of Java
> <http://imagej.net/FAQ#How_do_I_launch_ImageJ_with_a_different_version_of_Java.3F>
> .
>
> Hope that helps!
>
> Best,
> Mark
>
> On Mon, Nov 17, 2014 at 8:08 AM, Michele Griffa <[hidden email]>
> wrote:
>
>> Dear ImageJ users/developers,
>>
>> I'm facing the following issue.
>> I connect via SSH to a Linux workstation running on Cent OS 6.4 from a MS
>> Windows laptop, via Putty.
>> I have the Cygwin X-server installed and running on the Windows laptop.
>> On the Linux workstation, Fiji ver. 2.0.0-rc-15/1.49j10 with Java 1.6.0_24
>> [64 bit] is installed and runs properly.
>>
>> If I call Fiji from the command line, it does not run and the following
>> error message is returned:
>>
>> [grm@lin3a308 ~]$ log4j:WARN No appenders could be found for logger
>> (org.bushe.swing.event.EventService).
>> log4j:WARN Please initialize the log4j system properly.
>> log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
>> more info.
>> Error while executing the main() method of class 'net.imagej.Main':
>> sun.awt.X11.XException: Cannot write XdndAware property
>> at
>> sun.awt.X11.XDnDDropTargetProtocol.registerDropTarget(XDnDDropTargetProtocol.java:79)
>> at
>> sun.awt.X11.XDropTargetRegistry.registerDropSite(XDropTargetRegistry.java:554)
>> at sun.awt.X11.XWindowPeer.addDropTarget(XWindowPeer.java:1633)
>> at
>> sun.awt.X11.XComponentPeer.addDropTarget(XComponentPeer.java:1509)
>> at java.awt.dnd.DropTarget.addNotify(DropTarget.java:493)
>> at java.awt.Component.addNotify(Component.java:6688)
>> at java.awt.Container.addNotify(Container.java:2567)
>> at java.awt.Window.addNotify(Window.java:663)
>> at java.awt.Frame.addNotify(Frame.java:470)
>> at java.awt.Window.pack(Window.java:704)
>> at net.imagej.legacy.IJ1Helper.setVisible(IJ1Helper.java:260)
>> at net.imagej.legacy.ui.LegacyUI.show(LegacyUI.java:133)
>> at
>> org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:180)
>> at
>> org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:165)
>> at net.imagej.Main.launch(Main.java:67)
>> at net.imagej.Main.main(Main.java:73)
>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>> at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>> at java.lang.reflect.Method.invoke(Method.java:597)
>> at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
>> at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
>> at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
>>
>> Notice: the command I ran is /opt/Fiji.app/ImageJ-linux64 --allow-multiple
>>
>> With the previous versions of Fiji I could run it and export to the remote
>> Windows desktop the GUI without any problem.
>> Does anybody have any suggestion where should I look for the problem?
>>
>> Thanks a lot in advance.
>>
>> Best regards,
>>
>> Michele Griffa, PhD
>> Senior Research Scientist
>> Topic Leader „3D Image Analysis and Simulation“
>>
>> Concrete and Construction Chemistry Laboratory
>> and
>> Center for X-Ray Analytics
>>
>> Empa
>> Swiss Federal Laboratories for Materials Science and Technology
>> ETH Domain
>>
>> Überlandstrasse 129
>> 8600 Dübendorf
>> Switzerland
>>
>> Tel +41 58 765 4360
>> Fax +41 58 765 4035
>> [hidden email]
>> www.empa.ch
>> www.empa.ch/x-ray
>>
>> Upcoming Workshops at Empa in Dübendorf:
>>
>> - CCMX Advanced Course “Advanced X-Ray Diffraction Methods for Coatings”:
>> 26.-28. Nov. 2014
>>
>> Diese Mitteilung ist ausschliesslich für die als Empfänger aufgeführte
>> Person(en) oder Firma bestimmt. Sie kann persönliche und/oder vertrauliche
>> Informationen enthalten. Sollten Sie diese Mitteilung irrtümlicherweise
>> erhalten haben, bitten wir Sie, uns umgehend per E-Mail zu informieren,
>> sämtliche Ausdrucke zu vernichten und die E-Mail-Dateien zu löschen.
>>
>> This message is intended for the exclusive use of the individual(s) or
>> entity to whom it is addressed. It may contain information that is
>> privileged and/or confidential. Should you have received this message
>> erroneously, please notify us immediately by e-mail, destroy any printouts
>> and delete all electronic files contained in this message.
>>
>> -----------------------------------------------------------------------------------------------
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
David Gene Morgan
Electron Microscopy Center
047D Simon Hall
IU Bloomington
812 856 1457 (office)
812 856 3221 (3200)
http://bio.indiana.edu/~cryo

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