The instructions for installing Gephi can be found at:
They seem simple enough. But I found out that on a 64 bit server, it’s really important that you have a full 64/64/64 bit combination. That represents the operating system, Java, and Gephi. Here are some hints to get it right.
Be sure to download the right java file.
I’m more of a database guy. But even though I’ve done a java course, it still gets really confusing just how many java selections there are for download: se, jdk, sdk, jre, jvm, ee, etc.
If that’s not enough, there is also the confusion of 32 versus 64 bit.
And then there are the bizarre naming conventions. Is it version 1.7, or 7? You would figure after all these years, that they would have sorted this out, but I’m still seeing 1.7 meaning 7.
BTW, the term Java SE (Standard Edition) is now being used interchangeably with JDK (Java Development Kit). And the JDK includes the JavaFX SDK.
How are those terms for unique identifiers? I guess you are just supposed to know these things, and run algorithms in your head.
The key point is that you should download and install the 64 bit java JDK, for your 64 bit machine. Don’t get creative.
In July 2013, go to this link and click the JDK icon.
Windows And Java:
On Windows 7, I had installed a recent 32 bit java version to sync up with the java course I was doing.
When I went to install Gephi, it didn’t occur to me to check the version of java, and I had some issues. Finally, I downloaded and installed: jdk-7u25-windows-x64.exe (note the x64 in the name).
Linux And Java:
Gephi says that they don’t support OpenJDK.
“OpenJDK is not supported, be sure to run the official Java 6 version from Oracle’s website. Gephi may be able to start with OpenJDK but the graph window will fail to load in most cases.”
Interestingly, I have OpenJDK on my 64 bit Redhat 6.4 server. And a whole lot of other java RPMs.
My system runs Gephi with the JRE (Java Runtime Environment) instead.
rpm -qa | grep -i “jre”
find / -type f -iname “java” 2> /dev/null | grep -i “7″
Use the file command to see if they are 32 or 64 bit.
/usr/java/jre1.7.0_21/bin/java: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped
You need to configure the correct environment variables with the correct paths!
You can also configure the file: gephi.conf.
Windows Environment Variables:
C:\>set | grep -i “java”
- no bin
- with bin
- no bin
Note that the 64 bit path is NOT found under:
C:\Program Files (x86)
(x86) represents Window’s 32 bit subdirectory on 64 bit Windows. If your java paths are under an (x86) directory, you are not using 64 bit java.
Linux Environment Variables:
env | grep -i “java”
Use The Correct Executable:
On Linux, Gephi is launched with a POSIX shell script text executable file.
The shell script runs java commands that open many .jar files:
ps -ef | grep -i “gephi”
oracle 4005 3933 1 21:23 pts/2 00:00:00 /bin/bash ./../platform/lib/nbexec –jdkhome –clusters ./../gephi:./../platform: –userdir /home/oracle/.gephi/0.8.2/dev –branding gephi -J-Xms64m -J-Xmx512m -J-Xverify:none -J-Dsun.java2d.noddraw=true -J-Dsun.awt.noerasebackground=true -J-Dnetbeans.indexing.noFileRefresh=true -J-Dplugin.manager.check.interval=EVERY_DAY
oracle 4380 4005 56 21:23 pts/2 00:00:11 /usr/lib/jvm/java-1.7.0-openjdk.x86_64/bin/java -Djdk.home=/usr/lib/jvm/java-1.7.0-openjdk.x86_64 -classpath /gephi/gephi/platform/lib/boot.jar:/gephi/gephi/platform/lib/org-openide-modules.jar:/gephi/gephi/platform/lib/org-openide-util.jar:/gephi/gephi/platform/lib/org-openide-util-lookup.jar:/gephi/gephi/platform/lib/locale/boot_ar_SA.jar:/gephi/gephi/platform/l
On my Windows install, the commands to start gephi are found at:
01/04/2013 04:38 PM 2,346 gephi
01/04/2013 04:38 PM 477,184 gephi.exe
01/04/2013 04:38 PM 1,448,960 gephi64.exe
Note that the executable files for Windows 32 bit, Linux, and Windows 64 bit are all included in the same directory. Using cygwin, the file types are:
gephi: Bourne shell script text executable
gephi.exe: MS-DOS executable PE for MS Windows (GUI) Intel 80386 32-bit
gephi64.exe: MS-DOS executable PE for MS Windows (GUI) Mono/.Net assembly
When I did the Windows install, the Gephi icon defaulted to the 32 bit executable. I’ve since changed it to the 64 bit version.
When I first installed Gephi on Windows 7 64 bit, I was running 32 bit java and 32 bit Gephi.exe. And, the NEO4J import did not work.
However, after I changed to the 64/64/64 combination, this issue disappeared. Good!
So, I hope that helps out any other poor soul fighting with installs. See also what I wrote about Gephi and the video drivers on Redhat Linux.
BTW, I have no experience so far installing on Apple, only Windows and Redhat Linux. But I’m sure the principles still apply.
How To Install JDK 7
What is the path for JDK on Windows 7 64-bit?