Tutorial

How to install Gephi 0.9.2 on Ubuntu 18.04

Terminal with commands to install Gephi
The three commands to download, extract and start Gephi on Ubuntu.

Installing Gephi on Ubuntu or and Debian based system is fast and easy, once you know how it works.

1. Download the latest Gephi release

You could navigate to the download section on the Gephi website and save the latest release, but that takes multiple clicks. It’s faster to use to terminal and either wget or curl to download the file. We need to know the URL of the file though. For the 0.9.2 release (the current one as of 2020-02-26) you can use the URL below. For other ones, you will have to look them up. I will put the files in my home directory, if you want them somewhere else, you would need to navigate there first (cd…).

wget -q --show-progress https://github.com/gephi/gephi/releases/download/v0.9.2/gephi-0.9.2-linux.tar.gz

-q tells wget to be quiet (no output), --show-progress tells it that we still want to see how fast it downloads the file.

2. Extract Gephi

Currently the files are still in an archive. To use them you have to extract them. Again, this is possible through the graphical interface (right click, extract here), but using the terminal is more convenient as we already used it to download the file. If you have a different release, you could use the ls command to find out its name. If you downloaded 0.9.2, just use this:

tar xzf gephi-0.9.2-linux.tar.gz

3. Try to start Gephi

Now we can start Gephi with the following command:

./gephi-0.9.2/bin/gephi

This will fail if you don’t have Java installed on your system. If it fails, it will say: Cannot find java. Please use the --jdkhome switch. To fix this, you need to install java.

4. Install Java

Update: On Ubuntu 20.04, you don’t need to add the repository anymore. See comments at the bottom.

Gephi needs Java to run. You can install it by executing these commands in your terminal:

sudo add-apt-repository ppa:openjdk-r/ppa
sudo apt update
sudo apt install openjdk-8-jdk openjdk-8-jre
Installing Java

The first command adds the repository, which is maintained by Matthias Klose. The second retrieves which software is currently available in all added repositories. The last command installs the jdk and jre.

(If you ever want to uninstall it: sudo apt purge openjdk-*)

To see if and which Java version you have installed, you can use java -v and javac -v.

5. Start Gephi

Now that Java is installed, you will be able to actually start Gephi:

./gephi-0.9.2/bin/gephi

Optional: Increase RAM available to Gephi

Per default Gephi only get 512MB of RAM. Depending on you computer, you should give it more. You can either do this by navigating with Files to gephi-0.9.2/etc/gephi.conf, open it with any text editor and change it. Or you use the Terminal and nano or vim. Once you changed the value, save and exit (ctrl+o, ctrl+x in nano).

nano gephi-0.9.2/etc/gephi.conf

The relevant part is -J-Xmx512m. I changed it to -J-Xmx60g, which allows Gephi to use up to 60GB of RAM. In the past I tested values that are bigger than my actual RAM and it worked fine. Only try this if you have a SATA or better NVMe SSD and be aware that Gephi will use the SSD as RAM once the RAM is full. This will reduce the lifespan of your SSD.

Let me know in the comments if this helped you or if you have any questions.

11 Comments Add New Comment

  1. This is great, but for some reason netbeans doesn’t really work well with openjdk, and wants Oracles’s proprietary version of java 8.

    Installing that is a whole other mess.

  2. I get the following error and gephi doesn’t start:

    OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
    WARNING: An illegal reflective access operation has occurred
    WARNING: Illegal reflective access by org.netbeans.ProxyURLStreamHandlerFactory (file:/home/nidish/Software/gephi-0.9.2/platform/lib/boot.jar) to field java.net.URL.handler
    WARNING: Please consider reporting this to the maintainers of org.netbeans.ProxyURLStreamHandlerFactory
    WARNING: Use –illegal-access=warn to enable warnings of further illegal reflective access operations
    WARNING: All illegal access operations will be denied in a future release
    Inconsistency detected by ld.so: dl-lookup.c: 111: check_match: Assertion `version->filename == NULL || ! _dl_name_match_p (version->filename, map)’ failed!

    1. The following version is currently working for me:
      Java: 1.8.0_152-release; OpenJDK 64-Bit Server VM 25.152-b12
      Runtime: OpenJDK Runtime Environment 1.8.0_152-release-1056-b12

      I have “-J-Xverify:none” in my gephi.conf, but haven’t found -noverify. Removing “-J-Xverify:none” from the conf did not break my install. According to the oracle documentation (https://docs.oracle.com/cd/E19685-01/819-2807/chap_usingcommandline.html), it speeds up startup by removing some bytecode checks. You could try removing it, to see if it solves the problem.

      Some people solved it by uninstalling and reinstalling OpenJDK (https://stackoverflow.com/questions/55847497/how-do-i-troubleshoot-inconsistency-detected-dl-lookup-c-111-java-result-12).

      1. Hi,
        I have the following version fo Java:
        Java: openjdk version “1.8.0_282”; OpenJDK 64-Bit Server VM (build 25.282-b08, mixed mode)
        Runtime environment: build 1.8.0_282-8u282-b08-0ubuntu1~20.04-b08

        I get this error while starting gephi:

        WARNING: An illegal reflective access operation has occurred
        WARNING: Illegal reflective access by org.netbeans.ProxyURLStreamHandlerFactory (file:/home/damessina/gephi-0.9.2/platform/lib/boot.jar) to field java.net.URL.handler
        WARNING: Please consider reporting this to the maintainers of org.netbeans.ProxyURLStreamHandlerFactory
        WARNING: Use –illegal-access=warn to enable warnings of further illegal reflective access operations
        WARNING: All illegal access operations will be denied in a future release
        Inconsistency detected by ld.so: dl-lookup.c: 111: check_match: Assertion `version->filename == NULL || ! _dl_name_match_p (version->filename, map)’ failed!

        I checked my current my java setting with sudo update-alternatives –config java command, and my current setting is on /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java (so, it should be fine). I eventually removed the OpenJDK packages which could point to Java 11 and reinstalled the right Java 8 packages, but still get the error. Finally I removed -J-Xverify:none from gephi.conf file, but nothing changed. I tried everything I found online about this issue, but still gephi doesn’t open… Advice?

  3. Thank Luca!
    ————————
    JFYI – this works “out-of-the-box” on Ubuntu 20.04
    – Pull down 0.9.2 linux as shown above & untar/uncompress
    – openjdk8-jdk via apt-get install openjdk-8-jdk
    – bin/gephi as shown above

    At present janusgraph only runs on java 8, so this isn’t a problem for a ‘local dev’ setup.

  4. Help!!!

    WARNING: All illegal access operations will be denied in a future release
    Inconsistency detected by ld.so: dl-lookup.c: 111: check_match: Assertion `version->filename == NULL || ! _dl_name_match_p (version->filename, map)’ failed!

    1. I had the same problem.

      Assuming:
      $ readlink -f $(which java)
      > /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java

      $ export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/
      $ ./bin/gephi –jdkhome $JAVA_HOME

      Works for me

  5. Hello, to solve the error select from:

    Inconsistency detected by ld.so: dl-lookup.c: 111: check_match: Assertion `version->filename == NULL || ! _dl_name_match_p (version->filename, map)’ failed!

    $ sudo update-alternatives –config java
    or
    $ sudo update-alternatives –config javac

    and select java8

Leave a Reply

Your email address will not be published. Required fields are marked *