how to increase Heap on Mac

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how to increase Heap on Mac

John Graybeal
When I go to info.plist per the instructions at https://protegewiki.stanford.edu/wiki/Setting_Heap_Size#Start_Protege_by_double-clicking_on_the_Protege_icon_.28Mac.29, it seems the instructions are out of date compared to my 5.5 protege info.plist.

The only likely option is Xss16M, but that seemed so ridiculously low that I couldn't believe it. These days wouldn't 256MB be a reasonable number? Or is there a hidden cost to that?

 <key>JVMOptions</key>
        <array>
            <string>-Dapple.laf.useScreenMenuBar=true</string>
            <string>-Xss16M</string>
            <string>-Xdock:name=Protégé</string>
            <string>-DentityExpansionLimit=100000000</string>
            <string>-Dlogback.configurationFile=conf/logback.xml</string>
            <string>-Dfile.encoding=UTF-8</string>
            <string>-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot</string>
        </array>
========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632



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Re: how to increase Heap on Mac

Matthew Horridge-2
Administrator
Hi John,

You’ll want to add a line to the array XML element

<string>-Xmx5000M</string>

(for however many megs you want to give it).  Protege will use the default max memory on a Mac, which I seem to recall is a percentage of free memory (or possibly system memory – I can’t quite remember now).

Cheers,

Matthew

On May 24, 2019, at 16:27, John Graybeal <[hidden email]> wrote:

When I go to info.plist per the instructions at https://protegewiki.stanford.edu/wiki/Setting_Heap_Size#Start_Protege_by_double-clicking_on_the_Protege_icon_.28Mac.29, it seems the instructions are out of date compared to my 5.5 protege info.plist.

The only likely option is Xss16M, but that seemed so ridiculously low that I couldn't believe it. These days wouldn't 256MB be a reasonable number? Or is there a hidden cost to that?

 <key>JVMOptions</key>
        <array>
            <string>-Dapple.laf.useScreenMenuBar=true</string>
            <string>-Xss16M</string>
            <string>-Xdock:name=Protégé</string>
            <string>-DentityExpansionLimit=100000000</string>
            <string>-Dlogback.configurationFile=conf/logback.xml</string>
            <string>-Dfile.encoding=UTF-8</string>
            <string>-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot</string>
        </array>
========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


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protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: how to increase Heap on Mac

John Graybeal
Thanks Tania, thanks Matthew. (I'll copy those answers to the list so other people who might look at the mailing list for answers can see them, yes?)

So I tried opening a 600MB file with the setting at 3000M, and it just hangs. I've confirmed that my process of merging files works with smaller files, Protege can open them. Possibly there is a bad file in there (see following).

First, is there a process I can use to troubleshoot what is going on, rather than continually adding more triples until I break it, then seeing if the particular file has an issue?  

And in a related question, if I open a file that should have lots of statements in it (file is enclosed), but the only window where I can find any statements looks like the below screenshot and takes forever to respond to clicks (other tabs and other ontologies of the same size are snappy), do you have any thoughts about what might be going on?

Feel free to point me to documentation, I admit I haven't been hunting it up just yet.

I may or may not return to this before the holiday ends, don't feel obligated to respond immediately! (Or at all, in Tania's case. :->)

John




On May 24, 2019, at 4:31 PM, Matthew Horridge <[hidden email]> wrote:

Hi John,

You’ll want to add a line to the array XML element

<string>-Xmx5000M</string>

(for however many megs you want to give it).  Protege will use the default max memory on a Mac, which I seem to recall is a percentage of free memory (or possibly system memory – I can’t quite remember now).

Cheers,

Matthew

On May 24, 2019, at 16:27, John Graybeal <[hidden email]> wrote:

When I go to info.plist per the instructions at https://protegewiki.stanford.edu/wiki/Setting_Heap_Size#Start_Protege_by_double-clicking_on_the_Protege_icon_.28Mac.29, it seems the instructions are out of date compared to my 5.5 protege info.plist.

The only likely option is Xss16M, but that seemed so ridiculously low that I couldn't believe it. These days wouldn't 256MB be a reasonable number? Or is there a hidden cost to that?

 <key>JVMOptions</key>
        <array>
            <string>-Dapple.laf.useScreenMenuBar=true</string>
            <string>-Xss16M</string>
            <string>-Xdock:name=Protégé</string>
            <string>-DentityExpansionLimit=100000000</string>
            <string>-Dlogback.configurationFile=conf/logback.xml</string>
            <string>-Dfile.encoding=UTF-8</string>
            <string>-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot</string>
        </array>
========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632



_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

AATOut_WikidataCoref.rdf (2M) Download Attachment
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Re: how to increase Heap on Mac

Lorenz Buehmann
1.
That file is not a proper RDF file in N-Triples format. The dot at the end of each line is missing.


2.
The attached file contains just skos:exactMatch triples. Those are not OWL axioms but used for SKOS taxonomies. Protege resp. its underlying OWL API is used to handle proper OWL. Anything beyond can only be handled as annotations. In your case, the SKOS devs also provide an OWL DL ontology [2] for their vocabulary, but you have to import it such that Protege knows the SKOS schema. Just add the following lines at the beginning of the file (note, the RDF format will become Turtle here)



You can read more about SKOS vs OWL vs RDF here [2]


Thanks Tania, thanks Matthew. (I'll copy those answers to the list so other people who might look at the mailing list for answers can see them, yes?)

So I tried opening a 600MB file with the setting at 3000M, and it just hangs. I've confirmed that my process of merging files works with smaller files, Protege can open them. Possibly there is a bad file in there (see following).

First, is there a process I can use to troubleshoot what is going on, rather than continually adding more triples until I break it, then seeing if the particular file has an issue?  

And in a related question, if I open a file that should have lots of statements in it (file is enclosed), but the only window where I can find any statements looks like the below screenshot and takes forever to respond to clicks (other tabs and other ontologies of the same size are snappy), do you have any thoughts about what might be going on?

Feel free to point me to documentation, I admit I haven't been hunting it up just yet.

I may or may not return to this before the holiday ends, don't feel obligated to respond immediately! (Or at all, in Tania's case. :->)

John




On May 24, 2019, at 4:31 PM, Matthew Horridge <[hidden email]> wrote:

Hi John,

You’ll want to add a line to the array XML element

<string>-Xmx5000M</string>

(for however many megs you want to give it).  Protege will use the default max memory on a Mac, which I seem to recall is a percentage of free memory (or possibly system memory – I can’t quite remember now).

Cheers,

Matthew

On May 24, 2019, at 16:27, John Graybeal <[hidden email]> wrote:

When I go to info.plist per the instructions at https://protegewiki.stanford.edu/wiki/Setting_Heap_Size#Start_Protege_by_double-clicking_on_the_Protege_icon_.28Mac.29, it seems the instructions are out of date compared to my 5.5 protege info.plist.

The only likely option is Xss16M, but that seemed so ridiculously low that I couldn't believe it. These days wouldn't 256MB be a reasonable number? Or is there a hidden cost to that?

 <key>JVMOptions</key>
        <array>
            <string>-Dapple.laf.useScreenMenuBar=true</string>
            <string>-Xss16M</string>
            <string>-Xdock:name=Protégé</string>
            <string>-DentityExpansionLimit=100000000</string>
            <string>-Dlogback.configurationFile=conf/logback.xml</string>
            <string>-Dfile.encoding=UTF-8</string>
            <string>-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot</string>
        </array>
========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632



_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
-- 
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center

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