Protege 5.5.0 hangs during file operation on Mac OS X

[Daniel B.]

Hello there!

I was wondering if you could maybe help me out with a problem I’m struggling with.

I can’t seem to open or save files with Protege 5.5.0 on my Mac.

Here’s my log in case you want to take a look at it.

https://pastebin.com/A6g4abx2

Thanks so much!

Daniel B.

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[samsontu]

On Nov 7, 2019, at 10:16 PM, [hidden email] wrote:

Hello there!

I was wondering if you could maybe help me out with a problem I’m struggling
with.

I can’t seem to open or save files with Protege 5.5.0 on my Mac.

Here’s my log in case you want to take a look at it.

https://pastebin.com/A6g4abx2

You have Java out-of-memory exceptions. Open the “Content” of Protege-app in your Protege 5.5.0 installation. Edit the info.plist file and add a line like

<string>-Xmx5G</string> in the JVMOptions key value. Instead of 5G, you can use a reasonable fraction of the physical memory you Mac has.

With best regards,

Samson

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[Daniel B.]

Thanks for the reply!

I have an 8 GB 2133 MHz LPDDR3 of RAM and a 3.1 GHz Intel Core i5 processor.

How much Xmx would you recommend I use?

Thanks again!!



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[samsontu]

How much memory to allocate also depends on the size and complexity of the ontologies that you are dealing with. Experiment with 3 GB or so and see whether that’s sufficient.

On Nov 9, 2019, at 9:51 AM, Daniel B. <[hidden email]> wrote:

Thanks for the reply!

I have an 8 GB 2133 MHz LPDDR3 of RAM and a 3.1 GHz Intel Core i5 processor.

How much Xmx would you recommend I use?

With best regards,

Samson

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[Daniel B.]

I tried with up to 5G and it hangs just the same. These are my "best"
settings and still the same.

<string>-Xss16M</string>
<string>-Xms500M</string>
<string>-Xmx5G</string>

I tried creating and saving an ontology just with 1 instance of the class
owl:Thing with no success. I also tried opening a 2KB ontology I manually
wrote.

I will attach that ontology in case you want to check it.

Thanks for the help! I hope you can help me fix this :(

Meta.ttl



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[samsontu]

I have no problem opening and saving your ontology.

Check the log to see if you are still getting out-of-memory exceptions.

Try to re-install Protege.

With best regards,

Samson

On Nov 9, 2019, at 10:53 AM, Daniel B. <[hidden email]> wrote:

I tried with up to 5G and it hangs just the same. These are my "best"
settings and still the same.

<string>-Xss16M</string>
<string>-Xms500M</string>
<string>-Xmx5G</string>

I tried creating and saving an ontology just with 1 instance of the class
owl:Thing with no success. I also tried opening a 2KB ontology I manually
wrote.

I will attach that ontology in case you want to check it.

Thanks for the help! I hope you can help me fix this :(

Meta.ttl <http://protege-project.136.n4.nabble.com/file/t377156/Meta.ttl>  



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[Daniel B.]

Hi there!

I don't get the memory exceptions anymore, but Protégé still hangs anytime I
try to save or load a file Protegé freezes.

I have also tried opening from a URL and then saving that file and I had
absolutely no problem with that.

The problem arises when handling local files.

I have tried reinstalling around 5 times with the latest and previous
versions without success.

**UPDATE**
I also get this message if I have an open file on my Visual Studio Code editor while Protégé is hanging. Maybe this can provide some context:

The git repository at '/Users/danielbakas' has too many active changes, only a subset of Git features will be enabled.

Cheers

Daniel B.



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samsontu wrote

I have no problem opening and saving your ontology.

Check the log to see if you are still getting out-of-memory exceptions.

Try to re-install Protege.

With best regards,
Samson


> On Nov 9, 2019, at 10:53 AM, Daniel B. <[hidden email]> wrote:
>
> I tried with up to 5G and it hangs just the same. These are my "best"
> settings and still the same.
>
> <string>-Xss16M</string>
> <string>-Xms500M</string>
> <string>-Xmx5G</string>
>
> I tried creating and saving an ontology just with 1 instance of the class
> owl:Thing with no success. I also tried opening a 2KB ontology I manually
> wrote.
>
> I will attach that ontology in case you want to check it.
>
> Thanks for the help! I hope you can help me fix this :(
>
> Meta.ttl <http://protege-project.136.n4.nabble.com/file/t377156/Meta.ttl> 
>
>
>
> -----
> Daniel B.
> --
> Sent from: http://protege-project.136.n4.nabble.com/Protege-User-f4659818.html
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> [hidden email]
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smime.p7s (1K) <http://protege-project.136.n4.nabble.com/attachment/4672837/0/smime.p7s>

[samsontu]

You need to examine the log file to see what’s going on.

With best regards,

Samson

On Nov 9, 2019, at 11:49 AM, Daniel B. <[hidden email]> wrote:

Hi there!

I don't get the memory exceptions anymore, but Protégé still hangs anytime I
try to save or load a file Protegé freezes.

I have also tried opening from a URL and then saving that file and I had
absolutely no problem with that.

The problem arises when handling local files.

I have tried reinstalling around 5 times with the latest and previous
versions without success.

Cheers

Daniel B.



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[Daniel B.]

Hi there!

I made a test now. The time is 15:43 GMT-6.

These were the steps I followed:
1. Open Protégé.
2. Change the ontology name to "http://archive.semantyk.com/meta/".
3. Created a node on the "Classes" tab under "owl:Thing" called "Test".
4. Opened Log window.
5. Saved the Protegé file to my Desktop folder as "Test.ttl".
6. Tried to interact with program without success.
7. Waited 30 minutes.
8. Saved the log file.
9. Wrote this message.

And here is the log file:
Log.log <http://protege-project.136.n4.nabble.com/file/t377156/Log.log> 

As you can see, the log does not present any errors, but still, the program
is frozen.

I hope this shares more context of the situation.

Cheers!

Daniel B.



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[samsontu]

You are saving the ontology file in your home directory (which presumably has a lot of subdirectories).

Try to create an empty folder and save the ontology in it.

With best regards,

Samson

On Nov 9, 2019, at 2:16 PM, Daniel B. <[hidden email]> wrote:

Hi there!

I made a test now. The time is 15:43 GMT-6.

These were the steps I followed:
1. Open Protégé.
2. Change the ontology name to "http://archive.semantyk.com/meta/".
3. Created a node on the "Classes" tab under "owl:Thing" called "Test".
4. Opened Log window.
5. Saved the file to my Desktop folder as "Test.ttl".
6. Tried to interact with program without success.
7. Waited 30 minutes.
8. Saved the log as a file.
9. Wrote this message.

And here is the log file:
Log.log <http://protege-project.136.n4.nabble.com/file/t377156/Log.log>  

As you can see, the log does not present any errors, but still, the program
is frozen.

I hope this shares more context of the situation.

Cheers!

Daniel B.



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[Daniel B.]

I saved it in the Desktop folder, not on the home directory

Nonetheless I tried what you suggested without success.

Here's the log file of the attempt:
Log.log

What else would you suggest?

Thanks

Daniel B.



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[Daniel B.]

Bump



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[Matthew Horridge-2]

Hi Daniel,

I’m sorry that you’re having these problems.  

I’ve tried to reproduce the behavior, using your test steps, but I cannot.  

Looking at your log file it appears that the ontology is saved, but something else is happening after that.

I see that you have some plugins installed (note that these may be in the .Protege directory inside your home directory).  I’d like to rule out that a plugin is the culprit.  Please could you remove all plugins and perform the test again?

Thanks,

Matthew

> On Nov 10, 2019, at 21:20, Daniel B. <[hidden email]> wrote:
>
> Bump
>
>
>
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[Daniel B.]

Hi there!

Thanks for the suggestion.

I deleted all the plugins from the .Protegé and tried to save an ontology to
a subdirectory of my home directory.

Like you say, the files have always been successfully saved. The problem
arises either, right after the save is completed, or in any attempt to load
a local file. I have no problem with loading from a URL though.

After the last attempt (after I erased the files on the .Protegé folder) the
results were the following:
1. Upon opening Protegé I was greeted with an "Update Plugins" window which
I dismissed to attempt the file save.
2. The program saved the file succesfully.
3. Like all the previous attempts, the program froze.
4. I forced quit the program.

Here is the log in case you want to review it:
Log.log <http://protege-project.136.n4.nabble.com/file/t377156/Log.log>  

Thanks again for your response.

Daniel B.



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[Matthew Horridge-2]

Hi Daniel,

Thanks for extra info and for trying without plugins.

Are menu items, on the Mac menubar at the top of the screen grayed out after the save operation?

Cheers,

Matthew

> On Nov 11, 2019, at 09:47, Daniel B. <[hidden email]> wrote:
>
> Hi there!
>
> Thanks for the suggestion.
>
> I deleted all the plugins from the .Protegé and tried to save an ontology to
> a subdirectory of my home directory.
>
> Like you say, the files have always been successfully saved. The problem
> arises either, right after the save is completed, or in any attempt to load
> a local file. I have no problem with loading from a URL though.
>
> After the last attempt (after I erased the files on the .Protegé folder) the
> results were the following:
> 1. Upon opening Protegé I was greeted with an "Update Plugins" window which
> I dismissed to attempt the file save.
> 2. The program saved the file succesfully.
> 3. Like all the previous attempts, the program froze.
> 4. I forced quit the program.
>
> Here is the log in case you want to review it:
> Log.log <http://protege-project.136.n4.nabble.com/file/t377156/Log.log>  
>
> Thanks again for your response.
>
> Daniel B.
>
>
>
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[Daniel B.]

Hi again!

Nope. They're unselected and unmodified.

<http://protege-project.136.n4.nabble.com/file/t377156/Captura_de_Pantalla_2019-11-11_a_la%28s%29_12.png>

Daniel B.



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[Matthew Horridge-2]

Hi Daniel,

After Protege freezes, if you click on the Metrics view to select one of the rows in it, does a row get selected, and if so, what is the highlight color of the row?

Cheers,

Matthew

> On Nov 11, 2019, at 10:55, Daniel B. <[hidden email]> wrote:
>
> Hi again!
>
> Nope. They're unselected and unmodified.
>
> <http://protege-project.136.n4.nabble.com/file/t377156/Captura_de_Pantalla_2019-11-11_a_la%28s%29_12.png>
>
> Daniel B.
>
>
>
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[Daniel B.]

Hi again!

I could not select any rows after the freeze, but the rows were coloured
gray.

Daniel B.



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[Matthew Horridge-2]

Hi Daniel,

Thanks for the info, it’s helpful.

What version of macOS are you running?

Cheers,

Matthew

> On Nov 11, 2019, at 12:57, Daniel B. <[hidden email]> wrote:
>
> Hi again!
>
> I could not select any rows after the freeze, but the rows were coloured
> gray.
>
> Daniel B.
>
>
>
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[Daniel B.]

Hi.

Hope this helps:
Captura_de_Pantalla_2019-11-11_a_la(s)_3.png
<http://protege-project.136.n4.nabble.com/file/t377156/Captura_de_Pantalla_2019-11-11_a_la%28s%29_3.png>  

Daniel B.




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