Download Tableau for Macos 10.8.5
For my research I'yard recently doing a lot of graph and network analysis. So far the tools in ESRI ArcGIS have been sufficient for what I was trying to achieve. I used their Network Annotator Extension and also the Urban Network Analysis toolbox by the Urban center Form Lab at the MIT/SUTD for a more scientific application: the calculation of centrality measures. While these warrant some more than in-depth articles in themselves, here I'd like to put a more than technical focus on a really annoying problem when using Gephi on a more contempo MacOS Ten system.
Gephi is an open source graph visualization and analysis software. They themselves depict it equally follows:
Gephi is a tool for people that have to explore and understand graphs. Like Photoshop but for data, the user interacts with the representation, dispense the structures, shapes and colors to reveal subconscious properties. The goal is to help data analysts to make hypothesis, intuitively find patterns, isolate construction singularities or faults during data sourcing. It is a complementary tool to traditional statistics, as visual thinking with interactive interfaces is now recognized to facilitate reasoning. This is a software for Exploratory Data Analysis, a paradigm appeared in the Visual Analytics field of research.
It'due south a Java-based application and hence bachelor for a number of platforms, including Windows, MacOS and Linux. At present, this should brand MacOS X users already listen up, since the story of Java on MacOS X has not been an like shooting fish in a barrel one over the past few months twelvemonth or and then. Basically Apple deemed the official (i.e. Oracle) releases of Java six insecure and therefore started to publish their own. With the release of Java vii Oracle stopped publishing Java 6 for the MacOS Ten platform completely. This sounds like a good thing, and it definitely is in terms of security. Nowadays MacOS 10 has complete control over the Java installed and running on more than recent MacOS X systems. I think this is true for everything from 10.vi Snow Leopard, but may be wrong hither, but definitely from x.7 Lion and upwards (ten.8 Mount King of beasts and besides x.ix Mavericks).
The bug kickoff when yous try to run a Java-based application that requires Coffee 6 on one of these machines. Basically using such software doesn't sound like a good idea, but in the case of Gephi there'southward no way effectually information technology: it'due south developed by a non-profit organization (the Gephi Consortium) and therefore doesn't really have the means (in monetary terms) or the manpower to keep up with this kind of fast-moving developments. I don't arraign them! The interesting thing is that this poses quite a problem, since Gephi in its latest release 0.eight.2 is not able to run on those MacOS 10 systems with Java vii installed. (Interesting side note: when I tried to install the very same Gephi 0.8.2-beta release on my Windows 7 virtual machine it ran perfectly fine with the Coffee 7 installed there…) Since I'm working with quite extensive network graphs in my research I really wanted to take Gephi run natively (well, kind of, since it'southward however Java…) on my Mac for memory reasons. So I scoured the web and numerous spider web forums for a solution to this problem. Two things quickly became obviuos: 1) I'm not the only one with this problem, and 2) the solution is actually quite simple but I only establish information technology subconscious deeply in a thread on the Gephi GitHub page. So to make things easier for fellow sufferers I decided to chop-chop put together a write-up of my experience. Spoiler alert: I solved the issue in the end!
I started unprejudiced with downloading said gephi-0.eight.2-beta release for MacOS X from the official Gephi website: https://gephi.org/users/download/
Information technology's a 42 MB .dmg file that contains the Gephi awarding. The installation is therefore simple: only drag the .app file into the Applications folder on your Mac and y'all're done. Or then I idea.
When I first fired upward Gephi everything seemed to exist fine. Later on a splash screen the chief plan window opened:
Gephi 0.8.ii-beta first commencement-up on MacOS X 10.8.v
I selected the Les Miserables.gexf file to open, and confirmed the Import Report, after setting the graph type to "directed" (I found this data in the Gephi Quick Start Tutorial):
Gephi 0.eight.2 Import Written report
This was the event:
Gephi 0.8.2-beta empty Graph window on MacOS Ten x.eight.5
The graph window in the center of the awarding stayed empty. In addition, what you tin't see from the screenshot, I also got the bluish beachball when my mouse crossed the (empty) graph window and the application was more often than not unresponsive. It even refused to shutdown when quit by ⌘Q. This final fact and some early search results directed me into the right management: we're dealing with a Coffee-related result.
Basically, what virtually forum posts recommended was to install an old Java 6 JDK and exist done. Yet, that's easier said than done. Every bit I mentioned above, Oracle stopped providing Java vi for MacOS on their download page. Nigh commenters therefore pointed at the old Apple Software Updates for Java 6. Information technology took me quite a while to find one that solved my problem by really installing a Java six JDK onto my system. As recommended on some sites I tried the Java for OS 10 2012-005 update, but to no avail. Later on an afternoon of cursing and digging deeper into the topic I finally institute what I was looking for on the Apple Developer Platform: the Java for Bone X 2012-006 Developer Bundle:
Java half-dozen Download from Apple
Please note that in order to access the Apple Programmer Platform you need to login using just a valid Apple ID – no programmer account necessary!
This will download a 158.1 MB image file chosen javadeveloper_for_os_x_2012006__11m3909.dmg onto your system which in turn contains a software package chosen JavaDeveloper.pkg. Later installing this, I finally found a Java half dozen JDK on my system!
You can check the installed Coffee Virtual Machines past looking into the binder /Library/Java/JavaVirtualMachines. Before this installation all that was in there was the near recent Coffee 7 JDK in a binder jdk1.7.0_45.jdk. (Yes, information technology's a folder, even though it's ending in what seems like a file extension .jdk) At present I was happy to meet a new 1.half-dozen.0_37-b06-434.jdk in there, besides!
$ ls -la total 0 drwxr-xr-x five root wheel 170 12 6 17:34 . drwxrwxr-x v root admin 170 12 6 17:34 .. drwxr-xr-10 three root wheel 102 x 5 2012 one.six.0_37-b06-434.jdk drwxr-xr-x 3 root cycle 102 12 half-dozen 17:08 jdk1.seven.0_45.jdk
Stay with me, nosotros're almost there!
All that's left to do now is to tell Gephi to really apply this Coffee half-dozen JDK. While in a terminal window you lot can (and should!) make sure that your arrangement still regards Java 7 every bit the currently active JDK by running the following command:
$ java -version java version "1.7.0_45" Java(TM) SE Runtime Environment (build one.vii.0_45-b18) Java HotSpot(TM) 64-Fleck Server VM (build 24.45-b08, mixed fashion)
So here everything is alright, MacOS X ignores the newly installed Java 6 JDK and continues to go to Java 7 (1.seven.0_45) for all its Java needs. Instead, Gephi needs a pointer as to where it can discover Coffee 6. This tin can be done by editing the file gephi.conf. Information technology's living inside the Gephi awarding package and can exist accessed in one of ii ways:
MacOS X Finder: Open Bundle Contents
Afterward right-clicking the Gephi application in your Applications folder in a Finder window, select the option "Testify Package Contents". So navigate to the subfolder Contents > Resources > gephi > etc. Alternatively you lot tin can use the Finder tool "Go To Binder…" from the "Get" bill of fare (or press ⌘⇧G) and enter /Applications/Gephi.app/Contents/Resources/gephi/etc. In there you detect the file we're looking for, which tin be opened in any text editor. Information technology should look like this:
# ${HOME} will be replaced past user abode directory according to platform default_userdir="${HOME}/.${APPNAME}/0.eight.ii/dev" default_mac_userdir="${HOME}/Library/Application Support/${APPNAME}/0.8.2/dev" # options used by the launcher by default, tin can be overridden by explicit # command line switches default_options="--branding gephi -J-Xms64m -J-Xmx512m -J-Xverify:none -J-Dsun.java2d.noddraw=truthful -J-Dsun.awt.noerasebackground=true -J-Dnetbeans.indexing.noFileRefresh=true -J-Dplugin.manager.cheque.interval=EVERY_DAY" # for development purposes you lot may wish to suspend: -J-Dnetbeans.logger.console=true -J-ea # default location of JDK/JRE, can exist overridden past using --jdkhome switch #jdkhome="/path/to/jdk" # clusters' paths separated by path.separator (semicolon on Windows, colon on Unices) #extra_clusters= The relevant part is the second-to-last section (lines x-11) most the JDK/JRE locations. Here you need to uncomment (i.e. remove the leading # from) the second line and modify the contents of the variable jdkhome to match the actual location of the newly installed Java half dozen JDK on your arrangement. In my case information technology looks like this:
# default location of JDK/JRE, tin be overridden by using --jdkhome switch jdkhome="/Library/Java/JavaVirtualMachines/1.6.0_37-b06-434.jdk/Contents/Dwelling/"
Notice that it is non sufficient to enter the path to the same ...jdk folder, merely instead you accept to actually reference the subfolder Contents/Home/! Should yous neglect to do and then you will notice that Gephi won't showtime upward anymore without any annotate or fault message. I have to acknowledge that it took me a while to figure this out. The forum mail service that pointed me into this direction can exist constitute hither.
Gephi 0.8.2-beta running on MacOS X 10.8.5
And at present nosotros're done! Later installing a Java 6 JDK onto MacOS Ten 10.8.5 Mountain Lion and pointing Gephi 0.viii.ii-beta to it, we can actually fire up Gephi and outset using it! I hope this quick walkthrough can assistance at least a few lost souls – just permit me know in the comments if y'all ran into any additional bug.
Download Tableau for Macos 10.8.5
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