Running Java 8 ImageJ headless

[Avital Steinberg]

Hi,
I have a problem running ImageJ 1.51i java 1.8.0_112 (64 bit) in the
headless mode on LinuxMint 17 Qiana. I posted this question also in the
ImageJ developers forum, but I still haven't been able to solve this issue.
When I run the following command:

[path_to_ImageJ]/ij.jar helloImageJ.py -b &

It works. (helloImageJ.py just prints hello to the console)

On the other hand, when I write the following command:

[path_to_ImageJ]/ImageJ helloImageJ.py -b &

I get the following error message:

Java HotSpot(TM) 64-Bit Server VM warning: ignoring option
PermSize=128m; support was removed in 8.0
Unrecognized option: -b
Warning: falling back to System JVM
Unrecognized option: -b
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

Any idea how to fix this problem? I need to work in batch mode, because the
goal is to obviously run my image analysis script in headless mode. (rather
than the hello world program)

Thanks,
Avital

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

[ctrueden]

Hi Avital,

When asking questions in multiple places, it is always good to cross-link,
so people can follow the whole discussion.

The forum thread is here:
http://forum.imagej.net/t/a-problem-running-imagej-in-headless-mode/3909

And as I said there, I will be releasing a new version of ImageJ2 later
this week which fixes the issue you are having with the "--ij2 --headless
--run" syntax.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Sun, Jan 29, 2017 at 8:07 AM, Avital Steinberg <[hidden email]
> wrote:

> Hi,
> I have a problem running ImageJ 1.51i java 1.8.0_112 (64 bit) in the
> headless mode on LinuxMint 17 Qiana. I posted this question also in the
> ImageJ developers forum, but I still haven't been able to solve this issue.
> When I run the following command:
>
> [path_to_ImageJ]/ij.jar helloImageJ.py -b &
>
> It works. (helloImageJ.py just prints hello to the console)
>
> On the other hand, when I write the following command:
>
> [path_to_ImageJ]/ImageJ helloImageJ.py -b &
>
> I get the following error message:
>
> Java HotSpot(TM) 64-Bit Server VM warning: ignoring option
> PermSize=128m; support was removed in 8.0
> Unrecognized option: -b
> Warning: falling back to System JVM
> Unrecognized option: -b
> Error: Could not create the Java Virtual Machine.
> Error: A fatal exception has occurred. Program will exit.
>
> Any idea how to fix this problem? I need to work in batch mode, because the
> goal is to obviously run my image analysis script in headless mode. (rather
> than the hello world program)
>
> Thanks,
> Avital
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Avital Steinberg]

Thanks, Curtis - sorry for forgetting to cross-link, multiple people were
making various requests from me simultaneously.

I'm looking forward to using the new release of ImageJ2.

See you in Portugal,
Avital



On Sun, Jan 29, 2017 at 8:48 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Avital,
>
> When asking questions in multiple places, it is always good to cross-link,
> so people can follow the whole discussion.
>
> The forum thread is here:
> http://forum.imagej.net/t/a-problem-running-imagej-in-headless-mode/3909
>
> And as I said there, I will be releasing a new version of ImageJ2 later
> this week which fixes the issue you are having with the "--ij2 --headless
> --run" syntax.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Sun, Jan 29, 2017 at 8:07 AM, Avital Steinberg <
> [hidden email]
> > wrote:
>
> > Hi,
> > I have a problem running ImageJ 1.51i java 1.8.0_112 (64 bit) in the
> > headless mode on LinuxMint 17 Qiana. I posted this question also in the
> > ImageJ developers forum, but I still haven't been able to solve this
> issue.
> > When I run the following command:
> >
> > [path_to_ImageJ]/ij.jar helloImageJ.py -b &
> >
> > It works. (helloImageJ.py just prints hello to the console)
> >
> > On the other hand, when I write the following command:
> >
> > [path_to_ImageJ]/ImageJ helloImageJ.py -b &
> >
> > I get the following error message:
> >
> > Java HotSpot(TM) 64-Bit Server VM warning: ignoring option
> > PermSize=128m; support was removed in 8.0
> > Unrecognized option: -b
> > Warning: falling back to System JVM
> > Unrecognized option: -b
> > Error: Could not create the Java Virtual Machine.
> > Error: A fatal exception has occurred. Program will exit.
> >
> > Any idea how to fix this problem? I need to work in batch mode, because
> the
> > goal is to obviously run my image analysis script in headless mode.
> (rather
> > than the hello world program)
> >
> > Thanks,
> > Avital
> >
> > --
> > 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