uManager + MATLAB sporadically crashing on Windows 7

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uManager + MATLAB sporadically crashing on Windows 7

Kyle Karhohs
Hi,
I'm running uManager from MATLAB and often when I try to interact with the Windows file system MATLAB crashes. This tends to happen after I create the core object and then open an m-file to edit, or use the uigetfile() command. The error I get is an "access violation" and it references some Windows dlls and a Nikon dll. Has anyone experienced this? Has anyone found a solution?
Thanks,
Kyle

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Re: uManager + MATLAB sporadically crashing on Windows 7

Mark Tsuchida-2
Hi Kyle,

On Wed, Jul 30, 2014 at 02:30:58PM -0400, Kyle Karhohs wrote:
> I'm running uManager from MATLAB and often when I try to interact with the
> Windows file system MATLAB crashes. This tends to happen after I create the
> core object and then open an m-file to edit, or use the uigetfile()
> command. The error I get is an "access violation" and it references some
> Windows dlls and a Nikon dll. Has anyone experienced this? Has anyone found
> a solution?

Very strange.... Is there any more information in the error? I can't
tell if it resembles one of the crashes I've seen in the past with the
Nikon Ti without seeing the actual error message.

Best,
Mark

--
Mark Tsuchida
Micro-Manager Team (UCSF Vale Lab)

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Re: uManager + MATLAB sporadically crashing on Windows 7

Kyle Karhohs-2
Hi Mark,
These two files keep appearing in the error report...

C:\Windows\system32\OLEAUT32.dll+00013490 SysAllocString+00000050
C:\Program Files\Nikon\Shared\Bin\NikonTi.dll+00629315 DllUnregisterServer+00192571

Does this mean anything?

Thanks,
Kyle


On Thu, Jul 31, 2014 at 9:16 PM, Mark Tsuchida <[hidden email]> wrote:
Hi Kyle,

On Wed, Jul 30, 2014 at 02:30:58PM -0400, Kyle Karhohs wrote:
> I'm running uManager from MATLAB and often when I try to interact with the
> Windows file system MATLAB crashes. This tends to happen after I create the
> core object and then open an m-file to edit, or use the uigetfile()
> command. The error I get is an "access violation" and it references some
> Windows dlls and a Nikon dll. Has anyone experienced this? Has anyone found
> a solution?

Very strange.... Is there any more information in the error? I can't
tell if it resembles one of the crashes I've seen in the past with the
Nikon Ti without seeing the actual error message.

Best,
Mark

--
Mark Tsuchida
Micro-Manager Team (UCSF Vale Lab)

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Re: uManager + MATLAB sporadically crashing on Windows 7

Mark Tsuchida-2
Hi Kyle,

> On Thu, Jul 31, 2014 at 9:16 PM, Mark Tsuchida <[hidden email]>
> wrote:
> > On Wed, Jul 30, 2014 at 02:30:58PM -0400, Kyle Karhohs wrote:
> > > I'm running uManager from MATLAB and often when I try to interact with the
> > > Windows file system MATLAB crashes. This tends to happen after I create the
> > > core object and then open an m-file to edit, or use the uigetfile()
> > > command. The error I get is an "access violation" and it references some
> > > Windows dlls and a Nikon dll. Has anyone experienced this? Has anyone found
> > > a solution?
> >
> > Very strange.... Is there any more information in the error? I can't
> > tell if it resembles one of the crashes I've seen in the past with the
> > Nikon Ti without seeing the actual error message.

On Fri, Aug 01, 2014 at 01:46:57AM -0400, Kyle Karhohs wrote:
> These two files keep appearing in the error report...
>
> C:\Windows\system32\OLEAUT32.dll+00013490 SysAllocString+00000050
> C:\Program Files\Nikon\Shared\Bin\NikonTi.dll+00629315
> DllUnregisterServer+00192571

Indeed, I have seen this exact pattern before. The case I've seen for
which I have received the most detail was also in the context of running
from MATLAB, although I vaguely remember seeing this or a similar crash
(very rarely) with just Micro-Manager and the Ti.

On the other hand, one person has reported that they tried eliminating
Micro-Manager and programming directly to the Nikon Ti SDK from MATLAB
and still got sporadic crashes of the same nature, suggesting that the
problem may be in the Ti driver or DLLs (this was with Ti SDK 4.4.1.714
64-bit, MATLAB R2013a, Ti firmware 5.10, Windows 7, and the crash
happened once every few days during continuous running). It is also
possible that the crash is triggered by some complex interaction between
the Ti SDK and other pieces of software.

However, the fact uigetfile() may induce the crash is a new discovery.
How easy is it for you to induce the crashes? If it happens frequently
enough to deliberately reproduce, it _might_ be possible to narrow down
the conditions enough to come up with an actionable bug report, though
my sense is that it will not be straightforward.

Best,
Mark


P.S. Please avoid top-posting. For details see:
http://micro-manager.3463995.n2.nabble.com/Please-avoid-top-posting-td7582368.html
--
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Micro-Manager Team (UCSF Vale Lab)

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Re: uManager + MATLAB sporadically crashing on Windows 7

Kyle Karhohs-2
Hi Mark,

On Mon, Aug 4, 2014 at 1:19 PM, Mark Tsuchida <[hidden email]> wrote:
Hi Kyle,

> On Thu, Jul 31, 2014 at 9:16 PM, Mark Tsuchida <[hidden email]>
> wrote:
> > On Wed, Jul 30, 2014 at 02:30:58PM -0400, Kyle Karhohs wrote:
> > > I'm running uManager from MATLAB and often when I try to interact with the
> > > Windows file system MATLAB crashes. This tends to happen after I create the
> > > core object and then open an m-file to edit, or use the uigetfile()
> > > command. The error I get is an "access violation" and it references some
> > > Windows dlls and a Nikon dll. Has anyone experienced this? Has anyone found
> > > a solution?
> >
> > Very strange.... Is there any more information in the error? I can't
> > tell if it resembles one of the crashes I've seen in the past with the
> > Nikon Ti without seeing the actual error message.

On Fri, Aug 01, 2014 at 01:46:57AM -0400, Kyle Karhohs wrote:
> These two files keep appearing in the error report...
>
> C:\Windows\system32\OLEAUT32.dll+00013490 SysAllocString+00000050
> C:\Program Files\Nikon\Shared\Bin\NikonTi.dll+00629315
> DllUnregisterServer+00192571

Indeed, I have seen this exact pattern before. The case I've seen for
which I have received the most detail was also in the context of running
from MATLAB, although I vaguely remember seeing this or a similar crash
(very rarely) with just Micro-Manager and the Ti.

On the other hand, one person has reported that they tried eliminating
Micro-Manager and programming directly to the Nikon Ti SDK from MATLAB
and still got sporadic crashes of the same nature, suggesting that the
problem may be in the Ti driver or DLLs (this was with Ti SDK 4.4.1.714
64-bit, MATLAB R2013a, Ti firmware 5.10, Windows 7, and the crash
happened once every few days during continuous running). It is also
possible that the crash is triggered by some complex interaction between
the Ti SDK and other pieces of software.

However, the fact uigetfile() may induce the crash is a new discovery.
How easy is it for you to induce the crashes? If it happens frequently
enough to deliberately reproduce, it _might_ be possible to narrow down
the conditions enough to come up with an actionable bug report, though
my sense is that it will not be straightforward.

Best,
Mark



The uigetfile() crashes frequently, enough so I'd call it reproducible. If I ran uManager from a different operating system do you think I could get rid of the crashes? We just upgraded to Windows 7 and it has a complex administrative rights system. I feel like the administrative rights might have something to do with this issue, because of the file access aspect of the crash.

Thanks,
Kyle

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Re: uManager + MATLAB sporadically crashing on Windows 7

Mark Tsuchida-2
Hi Kyle,

On Mon, Aug 04, 2014 at 01:32:00PM -0400, Kyle Karhohs wrote:

> On Mon, Aug 4, 2014 at 1:19 PM, Mark Tsuchida <[hidden email]>
> wrote:
> > > On Thu, Jul 31, 2014 at 9:16 PM, Mark Tsuchida <[hidden email]>
> > > wrote:
> > > > On Wed, Jul 30, 2014 at 02:30:58PM -0400, Kyle Karhohs wrote:
> > > > > I'm running uManager from MATLAB and often when I try to interact
> > with the
> > > > > Windows file system MATLAB crashes. This tends to happen after I
> > create the
> > > > > core object and then open an m-file to edit, or use the uigetfile()
> > > > > command. The error I get is an "access violation" and it references
> > some
> > > > > Windows dlls and a Nikon dll. Has anyone experienced this? Has
> > anyone found
> > > > > a solution?
> > > >
> > > > Very strange.... Is there any more information in the error? I can't
> > > > tell if it resembles one of the crashes I've seen in the past with the
> > > > Nikon Ti without seeing the actual error message.
> >
> > On Fri, Aug 01, 2014 at 01:46:57AM -0400, Kyle Karhohs wrote:
> > > These two files keep appearing in the error report...
> > >
> > > C:\Windows\system32\OLEAUT32.dll+00013490 SysAllocString+00000050
> > > C:\Program Files\Nikon\Shared\Bin\NikonTi.dll+00629315
> > > DllUnregisterServer+00192571
> >
> > Indeed, I have seen this exact pattern before. The case I've seen for
> > which I have received the most detail was also in the context of running
> > from MATLAB, although I vaguely remember seeing this or a similar crash
> > (very rarely) with just Micro-Manager and the Ti.
> >
> > On the other hand, one person has reported that they tried eliminating
> > Micro-Manager and programming directly to the Nikon Ti SDK from MATLAB
> > and still got sporadic crashes of the same nature, suggesting that the
> > problem may be in the Ti driver or DLLs (this was with Ti SDK 4.4.1.714
> > 64-bit, MATLAB R2013a, Ti firmware 5.10, Windows 7, and the crash
> > happened once every few days during continuous running). It is also
> > possible that the crash is triggered by some complex interaction between
> > the Ti SDK and other pieces of software.
> >
> > However, the fact uigetfile() may induce the crash is a new discovery.
> > How easy is it for you to induce the crashes? If it happens frequently
> > enough to deliberately reproduce, it _might_ be possible to narrow down
> > the conditions enough to come up with an actionable bug report, though
> > my sense is that it will not be straightforward.
> >
> The uigetfile() crashes frequently, enough so I'd call it reproducible. If
> I ran uManager from a different operating system do you think I could get
> rid of the crashes? We just upgraded to Windows 7 and it has a complex
> administrative rights system. I feel like the administrative rights might
> have something to do with this issue, because of the file access aspect of
> the crash.

Could you be a little more specific, such as "about a third of the
time"? I'm trying to see if it is practical to try to reproduce it here
and debug.

Also, what are the versions of Windows 7, MATLAB, Nikon Ti drivers (see
Micro-Manager Device Property Browser read-only properties for TIScope),
and Micro-Manager, including 32-bit vs 64-bit? Also, which of the
devices on the Ti are you controlling? Are there specific steps I could
follow in order to trigger the crash (is loading the Ti devices and just
calling uigetfile() sufficient)?

As for the OS version, I can't really predict anything, except that I
would note that Nikon seems to officially only support Windows 7 SP 1
with their most recent drivers.

Best,
Mark

--
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Micro-Manager Team (UCSF Vale Lab)

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Re: uManager + MATLAB sporadically crashing on Windows 7

Kyle Karhohs-2
Hi Mark,
 
> > > On Thu, Jul 31,
> > > C:\Windows\system32\OLEAUT32.dll+00013490 SysAllocString+00000050
> > > C:\Program Files\Nikon\Shared\Bin\NikonTi.dll+00629315
> > > DllUnregisterServer+00192571
> >
> > Indeed, I have seen this exact pattern before. The case I've seen for
> > which I have received the most detail was also in the context of running
> > from MATLAB, although I vaguely remember seeing this or a similar crash
> > (very rarely) with just Micro-Manager and the Ti.
> >
> > On the other hand, one person has reported that they tried eliminating
> > Micro-Manager and programming directly to the Nikon Ti SDK from MATLAB
> > and still got sporadic crashes of the same nature, suggesting that the
> > problem may be in the Ti driver or DLLs (this was with Ti SDK 4.4.1.714
> > 64-bit, MATLAB R2013a, Ti firmware 5.10, Windows 7, and the crash
> > happened once every few days during continuous running). It is also
> > possible that the crash is triggered by some complex interaction between
> > the Ti SDK and other pieces of software.
> >
> > However, the fact uigetfile() may induce the crash is a new discovery.
> > How easy is it for you to induce the crashes? If it happens frequently
> > enough to deliberately reproduce, it _might_ be possible to narrow down
> > the conditions enough to come up with an actionable bug report, though
> > my sense is that it will not be straightforward.
> >
> The uigetfile() crashes frequently, enough so I'd call it reproducible. If
> I ran uManager from a different operating system do you think I could get
> rid of the crashes? We just upgraded to Windows 7 and it has a complex
> administrative rights system. I feel like the administrative rights might
> have something to do with this issue, because of the file access aspect of
> the crash.

Could you be a little more specific, such as "about a third of the
time"? I'm trying to see if it is practical to try to reproduce it here
and debug.

Also, what are the versions of Windows 7, MATLAB, Nikon Ti drivers (see
Micro-Manager Device Property Browser read-only properties for TIScope),
and Micro-Manager, including 32-bit vs 64-bit? Also, which of the
devices on the Ti are you controlling? Are there specific steps I could
follow in order to trigger the crash (is loading the Ti devices and just
calling uigetfile() sufficient)?

As for the OS version, I can't really predict anything, except that I
would note that Nikon seems to officially only support Windows 7 SP 1
with their most recent drivers.

Best,
Mark


Thanks for your diligence and help. I can recreate the crash by running this script and then calling uigetfile until MATLAB crashes. It should only take a few uigetfile calls before the system goes down. The basics of the script are:

import org.micromanager.MMStudioMainFrame;
obj.gui = MMStudioMainFrame(false);
obj.gui.show;
obj.core = obj.gui.getMMCore;
obj.mda = obj.gui.getAcquisitionEngine();

I am controlling a shutter, Prior stage, two shutters, and a camera. The most common command to the scope is to change filters and open the brightfield lamp shutter.

Luckily, I have access to two machines and one of them works with my MATLAB configuration. I've listed the specs for the two machines below:

"good" machine:

OS: Windows 7 Professional 32-bit, Service Pack 1
MATLAB ver: R2014a 32-bit
uManager ver: 1.4.17 20140317, 32-bit
TIScope-DriverVersion: timicusb.sys 2.0.2.0
TIScope-FirmwareVersion: Ti-E V4.01
TIScope-SoftwareVersion: 4.3.3.628

"bad" machine:

OS: Windows 7 Professional 64-bit, Service Pack 1
MATLAB ver: R2014a 64-bit
uManager ver: 1.4.17, 64-bit
TIScope-DriverVersion: micusb.sys 2.0.5.1
TIScope-Firmware Version: Ti-E V 1.21
TIScope-SoftwareVersion: 4.4.1.174

Do you see anything in the hardware configuration? Could there be a conflict between 64-bit Windows and the TI driver? Or 64-bit MATLAB and the TI driver?

Thanks,
Kyle


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Re: uManager + MATLAB sporadically crashing on Windows 7

Mark Tsuchida-2
Hi Kyle,

On Mon, Aug 11, 2014 at 04:06:23PM -0400, Kyle Karhohs wrote:

> > > > > On Thu, Jul 31,
> > > > > C:\Windows\system32\OLEAUT32.dll+00013490 SysAllocString+00000050
> > > > > C:\Program Files\Nikon\Shared\Bin\NikonTi.dll+00629315
> > > > > DllUnregisterServer+00192571
> > > >
> > > > Indeed, I have seen this exact pattern before. The case I've seen for
> > > > which I have received the most detail was also in the context of running
> > > > from MATLAB, although I vaguely remember seeing this or a similar crash
> > > > (very rarely) with just Micro-Manager and the Ti.
> > > >
> > > > On the other hand, one person has reported that they tried eliminating
> > > > Micro-Manager and programming directly to the Nikon Ti SDK from MATLAB
> > > > and still got sporadic crashes of the same nature, suggesting that the
> > > > problem may be in the Ti driver or DLLs (this was with Ti SDK 4.4.1.714
> > > > 64-bit, MATLAB R2013a, Ti firmware 5.10, Windows 7, and the crash
> > > > happened once every few days during continuous running). It is also
> > > > possible that the crash is triggered by some complex interaction between
> > > > the Ti SDK and other pieces of software.
> > > >
> > > > However, the fact uigetfile() may induce the crash is a new discovery.
> > > > How easy is it for you to induce the crashes? If it happens frequently
> > > > enough to deliberately reproduce, it _might_ be possible to narrow down
> > > > the conditions enough to come up with an actionable bug report, though
> > > > my sense is that it will not be straightforward.
[...]

> Thanks for your diligence and help. I can recreate the crash by running this
> script
> <https://github.com/balvahal/MMClosetScope/blob/master/Core/Core_MicroManagerHandle.m>
> and
> then calling uigetfile until MATLAB crashes. It should only take a few
> uigetfile calls before the system goes down. The basics of the script are:
>
> import org.micromanager.MMStudioMainFrame;
> obj.gui = MMStudioMainFrame(false);
> obj.gui.show;
> obj.core = obj.gui.getMMCore;
> obj.mda = obj.gui.getAcquisitionEngine();
>
> I am controlling a shutter, Prior stage, two shutters, and a camera. The
> most common command to the scope is to change filters and open the
> brightfield lamp shutter.

Great, I'll see if I can reproduce this when I get a chance.

> Luckily, I have access to two machines and one of them works with my MATLAB
> configuration. I've listed the specs for the two machines below:
>
> "good" machine:
>
> OS: Windows 7 Professional 32-bit, Service Pack 1
> MATLAB ver: R2014a 32-bit
> uManager ver: 1.4.17 20140317, 32-bit
> TIScope-DriverVersion: timicusb.sys 2.0.2.0
> TIScope-FirmwareVersion: Ti-E V4.01
> TIScope-SoftwareVersion: 4.3.3.628
>
> "bad" machine:
>
> OS: Windows 7 Professional 64-bit, Service Pack 1
> MATLAB ver: R2014a 64-bit
> uManager ver: 1.4.17, 64-bit
> TIScope-DriverVersion: micusb.sys 2.0.5.1
> TIScope-Firmware Version: Ti-E V 1.21
> TIScope-SoftwareVersion: 4.4.1.174
>
> Do you see anything in the hardware configuration? Could there be a
> conflict between 64-bit Windows and the TI driver? Or 64-bit MATLAB and the
> TI driver?

It could be, or it could be a 64-bit-specific issue in the Ti software
(not necessarily driver), or it could be due to any of the version
differences you listed (or something else). Unless your Nikon rep has
any information about the versions (I am more or less in the dark when
it comes to that), the only way to tell is to try swapping the
microscopes between the computers (to eliminate firmware version as the
cause) and to try installing the different Ti software (including
driver) versions (but you may not want to hazard this unless you have
the installers for the old version that is working for you; also, making
sure that the intended driver version is used takes some care when
downgrading).

Best,
Mark

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Micro-Manager Team (UCSF Vale Lab)

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Re: uManager + MATLAB sporadically crashing on Windows 7

Kyle Karhohs-2



It could be, or it could be a 64-bit-specific issue in the Ti software
(not necessarily driver), or it could be due to any of the version
differences you listed (or something else). Unless your Nikon rep has
any information about the versions (I am more or less in the dark when
it comes to that), the only way to tell is to try swapping the
microscopes between the computers (to eliminate firmware version as the
cause) and to try installing the different Ti software (including
driver) versions (but you may not want to hazard this unless you have
the installers for the old version that is working for you; also, making
sure that the intended driver version is used takes some care when
downgrading).

Best,
Mark


Hi Mark,

I installed on the 64-bit Windows 7 machine a 32-bit version of MATLAB, a 32-bit version of uManager, and the 32-bit TIscope redistribution found on micro-manager.org. I ran my code with this configuration and the crashing stopped altogether. I'm happy, but what does it all mean?

Best,
Kyle 

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Re: uManager + MATLAB sporadically crashing on Windows 7

Ippei Kotera
In reply to this post by Kyle Karhohs-2
Hi Kyle and Mark,

I had the same exact problem for long time: MATLAB crashed randomly
(rarely even BSOD) when using uManager API and the error message
contained OLEAUT32.dll and NikonTi.dll.

I just realized that there is a new version of Nikon Ti SDK (4.4.1.728 64bit).

http://www.nisdk.net/nisdk

Installing this version eliminated the problem completely for our
system (MATLAB R2014a 64bit, Windows 7). Considering the severity of
the problem, I think we should stop recommending the older versions on
the web site and place a link to the new version.

Hope this helps.

Ippei

On Fri, Aug 1, 2014 at 1:46 AM, Kyle Karhohs
<[hidden email]> wrote:

> Hi Mark,
> These two files keep appearing in the error report...
>
> C:\Windows\system32\OLEAUT32.dll+00013490 SysAllocString+00000050
> C:\Program Files\Nikon\Shared\Bin\NikonTi.dll+00629315
> DllUnregisterServer+00192571
>
> Does this mean anything?
>
> Thanks,
> Kyle
>
>
> On Thu, Jul 31, 2014 at 9:16 PM, Mark Tsuchida <[hidden email]>
> wrote:
>>
>> Hi Kyle,
>>
>> On Wed, Jul 30, 2014 at 02:30:58PM -0400, Kyle Karhohs wrote:
>> > I'm running uManager from MATLAB and often when I try to interact with
>> > the
>> > Windows file system MATLAB crashes. This tends to happen after I create
>> > the
>> > core object and then open an m-file to edit, or use the uigetfile()
>> > command. The error I get is an "access violation" and it references some
>> > Windows dlls and a Nikon dll. Has anyone experienced this? Has anyone
>> > found
>> > a solution?
>>
>> Very strange.... Is there any more information in the error? I can't
>> tell if it resembles one of the crashes I've seen in the past with the
>> Nikon Ti without seeing the actual error message.
>>
>> Best,
>> Mark
>>
>> --
>> Mark Tsuchida
>> Micro-Manager Team (UCSF Vale Lab)
>>
>>
>> ------------------------------------------------------------------------------
>> Want fast and easy access to all the code in your enterprise? Index and
>> search up to 200,000 lines of code with a free copy of Black Duck
>> Code Sight - the same software that powers the world's largest code
>> search on Ohloh, the Black Duck Open Hub! Try it now.
>> http://p.sf.net/sfu/bds
>> _______________________________________________
>> micro-manager-general mailing list
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>
>
>
> ------------------------------------------------------------------------------
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Ippei Kotera, PhD

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Re: uManager + MATLAB sporadically crashing on Windows 7

nodice
Hi All,

I was experiencing similar issues on a Windows 7 64-bit system. I tried installing 32-bit SDK/MATLAB/Micro-manager, but the problem persisted.

The good news is that updating to the latest (64-bit) SDK as suggested by Ippei appears to have completely solved the problem.

Best,
Adam
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Re: uManager + MATLAB sporadically crashing on Windows 7

Roy Wollman-3
In reply to this post by Ippei Kotera
Hi All, 

After upgrading Matlab version the system became unstable. Searching the mailing list pointed me to this thread that suggests that upgrading Nikon SDK would solve the problem. Alas, my account with Nikon SDK was with an email address I can't access anymore and I am waiting for a new application for over a month. 

If anyone has access to the new Nikon SDK 64-bit I would be very thankful if you could either update the wiki with a new version (https://micro-manager.org/wiki/NikonTI) or just email me off-list ([hidden email]) to share the files.  

Thanks!
Roy 

On Mon, Mar 14, 2016 at 7:01 AM, nodice <[hidden email]> wrote:
Hi All,

I was experiencing similar issues on a Windows 7 64-bit system. I tried
installing 32-bit SDK/MATLAB/Micro-manager, but the problem persisted.

The good news is that updating to the latest (64-bit) SDK as suggested by
Ippei appears to have completely solved the problem.

Best,
Adam



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View this message in context: http://micro-manager.3463995.n2.nabble.com/uManager-MATLAB-sporadically-crashing-on-Windows-7-tp7583465p7586767.html
Sent from the Micro-Manager mailing list archive at Nabble.com.

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Roy Wollman, PhD

Associate Professor

University of California - Los Angeles
Department of Integrative Biology and Physiology
Department Chemistry and Biochemistry 
Institute of Quantitative and Computational biology


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