2.0 vs 1.4 performance differences

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2.0 vs 1.4 performance differences

mglotzer
I am running MM on two machines. One is Win10 the other Win7pro. Both 2.0 and
1.4 have been running similarly on the Win10 machine. The machines are
fairly comparable Dell Precision 5810 (win 7)/5820 (win10)

On the Win7 machine, 1.4 runs well, but 2.0 is slow and exhibit odd
behaviors even when using the identical configuration file.

- Changing properties in the Groups and preferences is slow.
- The choice of the light interface doesn't stick
- Windows show persistent tearing
- When running the calibration routine in the projector plugin, the moving
spot does not update in the imaging window.
These behaviors persist through restarts. Are their any major changes that
can account for the distinct behavior between MM1.4 and 2.0?
Thanks
best,
Michael




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Re: 2.0 vs 1.4 performance differences

Stuurman, Nico
Hi Michael,

> I am running MM on two machines. One is Win10 the other Win7pro. Both 2.0 and
> 1.4 have been running similarly on the Win10 machine. The machines are
> fairly comparable Dell Precision 5810 (win 7)/5820 (win10)
>
> On the Win7 machine, 1.4 runs well, but 2.0 is slow and exhibit odd
> behaviors even when using the identical configuration file.
>
> - Changing properties in the Groups and preferences is slow.
> - The choice of the light interface doesn't stick
> - Windows show persistent tearing
> - When running the calibration routine in the projector plugin, the moving
> spot does not update in the imaging window.
> These behaviors persist through restarts. Are their any major changes that
> can account for the distinct behavior between MM1.4 and 2.0?

Which Java version are you using on these machines?

1.4 uses Java 6, 2.0-gamma needs Java 8.  I forgot whether or not MM
packages its own version of Java (I think that it does not). Earlier
versions of Java 8 were quite bad, but for the last couple of years, it
has been pretty good.  You can check the Java version by clicking on the
ImageJ window (in the "empty area" at the bottom).  Anything later than
~1.8.0_160 should be fine, but when in doubt, install the latest.

This all needs some looking into, especially since the terms for
re-distribution from Oracle are changing.  If you need a new JRE, you
can try the "unencumbered" version from:
https://adoptopenjdk.net/upstream.html.  Note, I have not tried this
myself yet, so sharing your experience will be appreciated.

Best,

Nico





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Re: 2.0 vs 1.4 performance differences

mglotzer
So I had a look into the Java version situation. I am sure you are aware of
all the following and I hope this is correct.

Micro-manager 1.4 Java 6.0_31
Micro-manager 2.0 Java 8.0_152
Latest Fiji Java 8.0_112
Latest Java from adoptopenjdk 8.0_212

In order to have m-m use a newer version of Java (more recent than 8.0_160,
I followed the instructions   FAQ
<https://imagej.net/Frequently_Asked_Questions#How_do_I_launch_ImageJ_with_a_different_version_of_Java.3F>  

“Install Java 8, and delete or rename the ImageJ.app\java and/or
ImageJ.app\jre folders, if they exist. If this does not result in ImageJ
using the expected Java version, check the Environment Variables ( Control
Panel  ▶ System and Security  ▶ System  ▶ Advanced Settings  ▶ Advanced  ▶
Environment Variables) for the variable "JAVA_HOME". Update or create this
variable as needed; its value should be the desired JDK or JRE that you
would like to use for ImageJ (for instance: "C:\Program
Files\Java\jdk1.8.0_172"). See also Java environment variable setup.”

This did allow me to use a newer version of Java, but it had the unfortunate
effect of preventing Metamorph from communicating with the Zeiss MTB even
after quitting Micro-manager. I am not convinced that this was the cause of
the slowdown. I think it may have to do with slow communication with one of
the devices. I will recreate a new hardware cfg and try to track this down.

For troubleshooting such issues, is there a simple way to temporarily
inactivate a specific device without removing it from the cfg file.

Thanks
best,
Michael





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Re: 2.0 vs 1.4 performance differences

Stuurman, Nico
On 6/5/19 9:23 AM, mglotzer wrote:

> So I had a look into the Java version situation. I am sure you are aware of
> all the following and I hope this is correct.
>
> Micro-manager 1.4 Java 6.0_31
> Micro-manager 2.0 Java 8.0_152
> Latest Fiji Java 8.0_112
> Latest Java from adoptopenjdk 8.0_212
>
> In order to have m-m use a newer version of Java (more recent than 8.0_160,
> I followed the instructions   FAQ
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__imagej.net_Frequently-5FAsked-5FQuestions-23How-5Fdo-5FI-5Flaunch-5FImageJ-5Fwith-5Fa-5Fdifferent-5Fversion-5Fof-5FJava.3F&d=DwIGaQ&c=iORugZls2LlYyCAZRB3XLg&r=UwP8SWqih8VHO1LwZpgcx83I4o21yLj6V6QD-25Dt4I&m=bmraaHJY4Mw-QZoGYGa-RFSRx2XjtZ2vHwxgTrZKImk&s=DDWDFCMcGE39pjXO_5G16JOC7lpWL7pYcHt-unw87mg&e= >
>
> “Install Java 8, and delete or rename the ImageJ.app\java and/or
> ImageJ.app\jre folders, if they exist. If this does not result in ImageJ
> using the expected Java version, check the Environment Variables ( Control
> Panel  ▶ System and Security  ▶ System  ▶ Advanced Settings  ▶ Advanced  ▶
> Environment Variables) for the variable "JAVA_HOME". Update or create this
> variable as needed; its value should be the desired JDK or JRE that you
> would like to use for ImageJ (for instance: "C:\Program
> Files\Java\jdk1.8.0_172"). See also Java environment variable setup.”
>
> This did allow me to use a newer version of Java, but it had the unfortunate
> effect of preventing Metamorph from communicating with the Zeiss MTB even
> after quitting Micro-manager.

Yikes.  I suspect that the MTB has its own environment variable that you
may have accidentally changed (as I doubt very much that the MTB or
Metamorph uses Java).  Re-installing the MTB should restore the correct
path.

> I am not convinced that this was the cause of the slowdown. I think it may have to do with slow communication with one of
> the devices. I will recreate a new hardware cfg and try to track this down.

However, since 1.4 and 2.0-gamma use the same code for hardware
interfacing, it would be strange if one of the device is slow for
2.0-gamma and fast for 1.4.

> For troubleshooting such issues, is there a simple way to temporarily inactivate a specific device without removing it from the cfg file.

Not really.  Best to start from scratch and add devices one by one.


Best,

Nico




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Re: 2.0 vs 1.4 performance differences

mglotzer
<
> This did allow me to use a newer version of Java, but it had the
> unfortunate
> effect of preventing Metamorph from communicating with the Zeiss MTB even
> after quitting Micro-manager.

Yikes.  I suspect that the MTB has its own environment variable that you
may have accidentally changed (as I doubt very much that the MTB or
Metamorph uses Java).  Re-installing the MTB should restore the correct
path.

_______

Amazingly, it really was the system JAVA_HOME variable. As soon as I deleted
it meta was able to see the MTB!

I think JAVA may have been holding on to the COM1 port.
best,
Michael




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Re: 2.0 vs 1.4 performance differences

mglotzer
Thanks to help from Nico, I sorted out the basis of the problem and an easy
fix. The major symptom were sluggish updating of the camera (Photometrics
Prime 95B) and some parts of the UI.

The problem was traced to a problem in the user profile (though the exact
nature of the problem was not identified).

Creating a new user profile completely solved the problem.

best,
Michael




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