Installing the software
Windows
- Make sure you have a recent Java JRE installed on your system. Gephi is compatible with Java 7 and 8 versions. Download Free Java here.
- After the download completes, run the installer and follow the steps.
Mac OS X
- After the download completes, click on the downloaded .dmg file.
- Drag the gephi application in your Application folder.
Linux
A Java Native Interface (JNI) library suitable for communicating with a range of USB interface chips from FTDI via the D2XX driver. It currently supports OS X 10.10+ and Windows 7/8 x64. On OS X, the 64 bit JVM is supported. On Windows, support is limited to the 64 bit JVM (Java 1.8 is now 64 bit).
Here you can download the Java JDK 1.8. After installing it, it should appear as an option inside IntelliJ. UPDATE: Find File - Project structure menu and go to Project Settings - Project tab. If on Project SDK the Java version 1.8 SDK is not selected, change it and click OK. Java Development Kit for Mac includes a wide variety of tools for streamlined developing, debugging, testing, and monitoring of Java applications. The package contains more than 30 individual tools and services which can be used to control every aspect of Java application development, from concept to final phase and deployment to end users.
- Update your distribution with the last official JRE 7 ir 8 packages.
- After the download completes, unzip and untar the file in a directory.
- Run it by executing ./bin/gephi script file.
Troubleshooting
Java 7 standard edition or newer required
Check you have Java properly installed on your system. If you're on Linux, you may provide the path to the jdk with ./bin/gephi --jdkhome $JAVA_HOME
JVM Creation failed
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This error message is due to memory settings, see following section.
Memory
Memory available to Gephi is determined by Java. Less or more memory can be allocated by configuring Gephi’s startup settings. If too less memory is allocated, Gephi will stop running when it reached the limit and you will loose your current work. If more memory than what the system is equipped with is set, Java will not be able to start and return “JVM Creation failed” message. By default, maximum memory is set to 512mo.
To modify memory settings, you need to edit gephi settings file. Modify the value after the -Xmx option to change the maximum heap space. For example, to use a heap size between 256 and 1024 MB, change the options to -Xms256m and -Xmx1024m. If you have Gephi open, you must close and reopen Gephi before new options take effect. On computers with 2GB of memory, you can set -Xmx1400 to get maximum performance.
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How to edit gephi.conf:
- On Windows, go to the Gephi folder in Start menu and click on Startup Settings. Edit this file with Notepad or WordPad. Alternatively, go in C:Program Files (x86)Gephi 0.9etcgephi.conf and edit file manually.
- On Mac OS X, right-click on Gephi application icon and select Show Package Contents to open a new Finder window displaying a Contents folder. Open the Contents folder, and then open the Resources/gephi/etc folder, in which the gephi.conf file resides. Use TextEdit to edit the file.
- On Linux, go into your application directory and then into the etc folder. Edit the file with a text editor.
When multiple JRE or JDK are installed on the same machine, you can specifty to Gephi to use a particular path. Edit gephi.conf as described in the upper section, uncomment the jdkhome line and set the JRE or JDK path.
User files
Locate and delete gephi user directory to clean your installation.
- On Windows 2K/XP, user diretory is located in
C:Documents and SettingsusernameApplication Data.gephi
- On Windows Vista/Seven/8/10, user directory is located in
C:UsersusernameAppDataRoaming.gephi
- On Mac OS X, user directory is located in
/Users/username/Library/Application Support/gephi
- On Linux, user diretory is located in
/home/username/.gephi
This page describes how to install and uninstall JDK 8 for OS X computers.
Download Jre 1.8
This page has these topics:
See 'JDK 8 and JRE 8 Installation Start Here' for general information about installing JDK 8 and JRE 8.
See 'OS X Platform Install FAQ' for general information about installing JDK 8 on OS X.
System Requirements
Observe the following requirements:
- Any Intel-based computer running OS X 10.8 (Mountain Lion) or later.
- Administrator privileges.
Note that installing the JDK on OS X is performed on a system wide basis, for all users, and administrator privileges are required. You cannot install Java for a single user.
Installing the JDK also installs the JRE. The one exception is that the system will not replace the current JRE with a lower version. To install a lower version of the JRE, first uninstall the current version as described in 'Uninstalling the JRE'.
JDK Installation Instructions
When you install the Java Development Kit (JDK), the associated Java Runtime Environment (JRE) is installed at the same time. The JavaFX SDK and Runtime are also installed and integrated into the standard JDK directory structure.
Depending on your processor, the downloaded file has one of the following names:
jdk-8u
version
-macosx-amd64.dmg
jdk-8u
version
-macosx-x64.dmg
Where
version
is 6 or later.- Download the file.Before the file can be downloaded, you must accept the license agreement.
- From either the Downloads window of the browser, or from the file browser, double click the
.dmg
file to launch it.A Finder window appears containing an icon of an open box and the name of the.pkg
file. - Double click the package icon to launch the Install app.The Install app displays the Introduction window.Note:In some cases, a Destination Select window appears. This is a bug, as there is only one option available. If you see this window, select Install for all users of this computer to enable the Continue button.
- Click Continue.The Installation Type window appears.
- Click Install.A window appears that says 'Installer is trying to install new software. Type your password to allow this.'
- Enter the Administrator login and password and click Install Software.The software is installed and a confirmation window appears.
- Refer to
http://www.oracle.com/technetwork/java/javase/downloads/jdk-for-mac-readme-1564562.html
for more information about the installation. - After the software is installed, delete the
.dmg
file if you want to save disk space.
Determining the Default Version of the JDK
If you have not yet installed Apple's Java OS X 2012-006 update, then you are still using a version of Apple Java 6 that includes the plug-in and the Java Preferences app. See 'Note for Users of OS X that Include Apple Java 6 Plug-in'.
There can be multiple JDKs installed on a system, as many as you wish.
When launching a Java application through the command line, the system uses the default JDK. It is possible for the version of the JRE to be different than the version of the JDK.
You can determine which version of the JDK is the default by typing
java -version
in a Terminal window. If the installed version is 8u6, you will see a string that includes the text 1.8.0_06. For example:To run a different version of Java, either specify the full path, or use the
java_home
tool:For more information, see the java_home(1) man page.
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Uninstalling the JDK
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To uninstall the JDK, you must have Administrator privileges and execute the remove command either as root or by using the sudo(8) tool.
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For example, to uninstall 8u6:
Do not attempt to uninstall Java by removing the Java tools from
/usr/bin
. This directory is part of the system software and any changes will be reset by Apple the next time you perform an update of the OS.