Installing Gephi On 64 bit Machines


The instructions for installing Gephi can be found at:

https://gephi.org/users/install/

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.


Java
:

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”

jre-1.7.0_21-fcs.x86_64

find / -type f -iname “java” 2> /dev/null  | grep -i “7”

/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.25.x86_64/bin/java
/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.25.x86_64/jre/bin/java
/usr/java/jre1.7.0_21/bin/java

Use the file command to see if they are 32 or 64 bit.

file /usr/java/jre1.7.0_21/bin/java
/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


Environment Variables
:

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”

JAVA_HOME=C:\Program Files\Java\jdk1.7.0_25\

– no bin

JAVA_PATH=C:\Program Files\Java\jdk1.7.0_25\bin

– with bin

JRE_HOME=C:\Program Files\Java\jdk1.7.0_25

– 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”

JAVA_PATH=/usr/java/jre1.7.0_21/bin
JAVA_HOME=/usr/java/jre1.7.0_21


Use The Correct Executable
:


Linux
:

On Linux, Gephi is launched with a POSIX shell script text executable file.

cd /gephi/gephi/bin
./gephi &

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


Windows EXE
:

On my Windows install, the commands to start gephi are found at:

dir  C:\gephi\Gephi-0.8.2\bin

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:

file *

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.


Issues Corrected
:

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.


Useful Links
:

How To Install JDK 7

http://www3.ntu.edu.sg/home/ehchua/programming/howto/JDK_Howto.html

What is the path for JDK on Windows 7 64-bit?

http://superuser.com/questions/193873/what-is-the-path-for-jdk-on-windows-7-64-bit

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4 Responses to Installing Gephi On 64 bit Machines

  1. Luz Congosto says:

    Thanks for sharing this information was very useful for me

  2. Thank you very much for this comprehensive description!
    I didn’t succeed assigning more than around 800MB of RAM to Gephi in the config file until I read your description, installed the right 64bit JDK and set the correct Java Home Path in gephi.conf via >>jdkhome=”C:\Program Files\Java\jdk1.7.0_40″<<

    Now it runs like a charm with 4096MB (-J-Xms64m -J-Xmx4096m) assigned!

    THANK YOU!

  3. […] Installing Gephi On 64 bit Machines | Rodger’s Notes – Jul 08, 2013 · The instructions for installing Gephi can be found at: https://gephi.org/users/install/ They seem simple enough. But I found out that on a 64 …… […]

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