Protege Wiki - User contributions [en]

Setting Heap Size

2010-08-30T14:38:20Z

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<span style="font-weight:bold;font-size:18px;">Setting the Heap Size</span>

<span style="font-weight:bold;font-size:16px;">Recommendations for setting the heap size (read first!)</span>

The maximum amount of memory that a Java VM can use is 1.6 GB on Windows XP and 2 GB on most Unix machines.

You must be careful about setting the heap size parameter. If you set it too low then you will get "out of memory" errors. If you set it too high then your system will hang or you will suffer poor performance because parts of the jvm will be swapped in and out of memory. A rule of thumb is that you should not set this parameter larger than about 80% of your free physical memory. On Windows XP machines you can determine your free physical memory from the Performance tab of the Task Manager application. On Mac machines, click the apple (upper left hand corner and "about this mac"). On Linux machines, you can use the wonderful proc filesystem and look at the meminfo "file".

Boosting the heap size parameter will allow you to read in larger file-based projects. It will also improve the performance of the database back-end since more memory is available for caching.

The most common source of very slow performance on older systems (or laptops) is having the heap size set too large. If your system does not have 100MB of free memory then even the Protege default value is too big and you should make it smaller (or buy more memory).

There are several ways of setting the heap size depending on how you run Protege.

__TOC__

==== Start Protege by Protege.exe/Protege or by double-cliking on the Protege icon (Windows/Linux) ====

If you start Protege on a Windows/Linux machine by double clicking on the Protege.exe/Protege or the Protege icon, you need to update the Protege.lax file.

By default the Protege.lax file specifies a heap of 100MB for Protege 3.x and 200MB for Protege 4.

For '''Protege 3.x''' you can do this in the Protege UI.
* Go to '''File -> Preferences menu -> Protege.lax'''
* Update the second column of the row containing <code>lax.nl.java.option.java.heap.size.max</code>
* Click on OK

Please note that the changes take effect the next time you start Protege.

Below is a screenshot of the Protege.lax panel.

[[Image:Preferences-protege.lax.png]]

For '''Protege 4''', you must edit directly the Protege.lax file in a text editor.

Edit the following line in the Protege.lax file in the Protege installation directory:

lax.nl.java.option.java.heap.size.max=100000000

==== Start Protege by double-clicking on the Protege icon (Mac) ====

If you run Protege on a Mac by double clicking an icon, you need to edit the Info.plist file that is hidden within that icon. Right click the icon (or ^-click for one button mouses) and click "show package contents". A new finder window will come up. Double click "Contents" and then "Info.plist". Traverse down the tree as follows: "Root" --> "Java" --> "VMOptions". In VMOptions edit the -Xmx line to indicate the correct memory usage.

==== Start Protege by double-clicking on the applescript file (Mac) ====

If you run Protege on a Mac by double clicking the applescript file then you need to modify the -Xmx line in the script.

==== Start Protege from the command line ====

If you run Protege from the java command line then you need to pass in the heap size with the -Xmx command line switch. Example, if you want to run Protege with 500 MB of heap size, you would specify:

<code>-Xmx500M</code>

[http://www.mac-how.net/ Backup your Hard Drive with Time Machine]

[[Category:Protege documentation]]

OWLViz

2010-08-18T11:29:55Z

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{{Plugin
|Description=Enables class hierarchies in an OWL ontology to be viewed and incrementally navigated, allowing comparison of the asserted class hierarchy and the inferred class hierarchy.
|PluginType=Tab Widget
|ForApplication1=Protege-OWL
|Screenshot=OwlViz.jpg
|HomepageURL=http://www.co-ode.org/downloads/plugins-3.x.php
|DeveloperID1=Matthew Horridge
|LastUpdated=March 4, 2010
|Topic1=Visualization
|License=LGPL
|Affiliation1=The University Of Manchester
|Affiliation2=The CO-ODE Project
}}
<div style="float:left;">
== More Details ==

=== Description ===
OWLViz is designed to be used with the [http://protege.stanford.edu/overview/protege-owl.html Protege-OWL editor]. It enables class hierarchies in an OWL Ontology to be viewed and incrementally navigated, allowing comparison of the asserted class hierarchy and the inferred class hierarchy. OWLViz integrates with the Protege-OWL editor, using the same color scheme so that primitive and defined classes can be distinguished, computed changes to the class hierarchy may be clearly seen, and inconsistent concepts are highlighted in red. OWLViz has the facility to save both the asserted and inferred views of the class hierarchy to various concrete graphics formats including PNG, JPEG, and SVG.

=== Installation ===
OWLViz is bundled with the [http://protege.stanford.edu/download/download.html "full" installation of Protege]. After you have installed Protege, there are two additional steps you need to perform for this plugin to work properly:

* [http://www.graphviz.org Download and install] a recent version of Graphviz, which is a free, open source graph visualization software from AT&T Research. <span style="color: red">Mac users please see Troubleshooting below.</span>

* Protege will make an educated guess about where to find graphviz depending on your operating system, but if it does not get it right you will need to configure this yourself:

** '''Protege3.x''' and '''Protege4.0 (pre build 105)''' on the OWLViz tab, click the Options button to bring up the Options dialog. On the Layout Options panel, specify the path to the location of the DOT executable (dot.exe). The Options dialog will look something like the following, after performing this step:

** '''Protege4.x (build 105 onwards)''' these settings have moved into the OWLViz preferences panel. Again, specify the path to the dot executable in the appropriate place.

[[Image:OwlViz-configure-path-to-dot.jpg|frame|none|OWLViz Options dialog]]

=== Documentation ===
All of the OWLViz documentation is located on the [http://www.co-ode.org/ CO-ODE Website]. The [http://www.co-ode.org/downloads/owlviz/OWLVizGuide.pdf OWLVizGuide] is somewhat outdated, but still very helpful. Also, you may refer to the home pages for the OWLViz plugin for additional information:

Home page for build 17 (Protege3.x): http://www.co-ode.org/downloads/owlviz/.<br />
Home page for build 18 (Protege4.x): http://code.google.com/p/co-ode-owl-plugins/wiki/OWLViz.

=== Level of Support ===
OWLViz build 17, which is distributed with [[Protege-OWL 3.3.1]] is no longer under active development. If you need help with this version of OWLViz, please try posting your questions on the [http://mailman.stanford.edu/mailman/listinfo/protege-owl protege-owl mailing list], and someone from the Protege user community may be able to help you.

OWLViz build 18, which is bundled with [[Protege-OWL 4.0]] is under active development and all comments, suggestions, and/or feature requests are appreciated! Please post questions and requests on the [http://mailman.stanford.edu/mailman/listinfo/p4-feedback p4-feedback mailing list].

=== Troubleshooting ===

==== Resolving the "An error related to DOT..." message ====

Many people report the following error the first time they try to use the OWLViz plugin:

[[Image:OwlViz-dot-error.jpg]]

This error message indicates that

a) you need to install Graphviz and/or

b) you need to tell OWLViz where you installed Graphviz.

Instructions for doing both of these things is located above in the [[OWLViz#Installation|Installation]] section.

==== Mac users - finding the right version of Graphviz ====

The current status of Graphviz for the Mac OS is very unclear.

The latest binaries they point to directly (the pixelglow implementation) no longer contain the dot application required by OWLViz. According to their [http://www.graphviz.org/Download..php download page] this distribution is out of date and not maintained.

Install version 2.14 from [http://www.ryandesign.com/graphviz/ one of their alternatives] and point to that instead (it gets installed in '''/usr/local/graphviz-2.14/'''). This contains the necessary binaries in the bin/ folder.

In Preferences, the string you want is: /usr/local/bin/dot
<br /><br />
</div>

OWLViz

2010-08-18T11:24:24Z

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Apple's missing Java 6

2010-08-12T12:00:51Z

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=The Problem and Our Current Options =

It looks as though Apple has stopped development on the powerpc and the 32 bit intel macs. Apple has always had a very hard time keeping up with Java development but they are now working on being four years behind on these two platforms. Even for Apple this is excessive. Though there does not appear to be any information coming from Cupertino, my suspicion is that there will never be an apple or sun supported java 6 on the powerpc. This creates a problem for the Protege group who are now considering the possibility that java 6 will never arrive. Here is my analysis of the options that I see. All the choices are bad.

We could stick with Java 5 as the final Protege development platform. I am having a great deal of trouble stomaching this option.

We have also considered dropping the problematic platforms. All of us in the protege group are uncomfortable with this option. In particular we know people who are using protege (including me!) on the laptops and desktops in question. This option has not entirely been ruled out but we are favoring rejecting it. Over time this may become more palatable.

I have looked into building java 6 on the problematic platforms using openjdk. This is cool but I think there are several problems that make me think that this is not workable. First we would then be supporting our own java distribution - a game that I really don't want to get involved in. Also my experiments indicate that openjdk will have several dependencies. So we would have to install several packages multiplying the problems that will arise. Alternatively there is this macports technology (very cool!!) that will automatically build java 6 openjdk. It doesn't work now on the powerpc but probably will soon. But this is time consuming (several hours to build java 6) and I suspect that there will be build issues. I have pretty much decided to reject this option.

The final two options - which is where I am beginning to go - both involve maintaining code bases for java 5 and the latest java. To support this we would do nightly builds and junit runs in both java 5 and java 6. We would only have to take further measures if, for some reason, the nightly java 5 builds and junits started to fail. It may very well be that there will not be too many cases where the code bases are different. There will be many issues that we have not yet figured out like whether a java 5 client can safely connect to a java 6 server.

So there are two different remaining proposals. First we could create a java 5 branch for the projects that need some additional work. We would create nightly scripts that would merge changes from the trunk into the java 5 branch. If the compile, junits or merge failed then the merge would not be committed. We would have to be somewhat careful with the script but we would probably get it right after a few tries. An advantage of this approach is that regular java 6 developers would not have to be aware of the java 5 issue.

Alternatively, we would not create a branch. Instead we would create multiple source trees. Regular developers would use src and src.java6. Developers maintaining the java 5 platforms would use src and src.java5. The advantage of this would be that there would be no branches and all the additional sources of error associated with this would be removed. It would also be very easy to switch between java 6 and java 5 builds. But I think that this is a bit awkward because classes could move between the src and src.java6. The packages would remain the same but there would be movement of classes from src to src.java6 when issues are discovered.

Actually I guess we could also do this in a single source tree and distinguish the java 6 vs java 5 specific code with a package name. This is easy to manage in the build files but might be more awkward in ides such as eclipse.

We haven't taken the plunge yet but I think that we are getting closer to doing this.

== Building Java 6 on the PowerPC ==

There is a [http://wikis.sun.com/display/OpenJDK/BSDPort new wiki] starting up about this. The mac ports didn't work on the g4 when I tried it because the bootstrap openjdk did not include a g4 version.

If I can succeed, the Protege team will consider the policy of not waiting for Apple once a java release reaches its end of life. The disadvantage of such a policy is that apple users will probably be unhappy about needing to install and run on X11.

This will probably get more detailed when I do it the next time. I am trying the build from icedtea which I got with the following mercurial command.
<pre>
hg clone http://icedtea.classpath.org/hg/icedtea6
</pre>
I needed to get/install
* mercurial
* md5sum
* gawk
* eclipse-ecj.jar ([http://archive.eclipse.org/eclipse/downloads/drops/R-3.3.1.1-200710231652/index.php eclipse.org])
* xalan.jar ([http://xml.apache.org/xalan-j/downloads.html xml.apache.org])
* giflib-devel ([http://sourceforge.net/projects/giflib/ sourceforge.net])
Thus far my configure line looks like this:
<pre>
./configure --enable-zero=yes \
--with-project=bsd --with-gcj-home=/usr/local/lib/gcj-4.2.2 \
--with-ecj-jar=${jars}/eclipse-ecj.jar \
--with-xalan2-jar=${jars}/xalan.jar \
--with-xalan2-serializer-jar=${jars}/serializer.jar \
--with-xerces2-jar=${jars}/xercesImpl.jar \
--with-rhino=${jars}/js.jar
</pre>
My current error is
<pre>
./configure: line : syntax error near unexpected token `XPROTO,'
./configure: line 11028: `PKG_CHECK_MODULES(XPROTO, xproto,XPROTO_FOUND=yes,XPROTO_FOUND=no)'
</pre>

From this [http://lists.freebsd.org/pipermail/freebsd-questions/2008-April/172377.html] I found that pkg.m4 needs to be in autoconf's library path. I'm using fink and found that pkg.m4 was already in /sw/share/aclocal. I stuck a command line parameter (-B) into autogen.sh, but next time I'd just symlink /usr/local/share/aclocal.

== Dealing with Java5 Compiler issues ==

Sometimes there are problems getting correct files to compile in java 5. Here is a page I made about how to troubleshoot these problems.
[[DealingWithJava5CompilerIssues|dealing with Java 5 compiler issues]]

= External Links =
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