Unix and Linux 64 Instructions

First extract everything from the Maud.tar.gz you downloaded using
tar -zxvf Maud.tar.gz
You should get a Maud directory with the following structure:

  • Maud.sh (to start Maud))
  • Maud.jar
  • Readme.txt
  • lib (directory)
  • licenses (directory)
  • plugins (directory)

Extract/Move the maud directory with all the content in the place you are more comfortable with. Be sure you have the rights to write in that directory.
Open a terminal window, navigate to the Maud directory and from inside it, type
to start Maud. If everything is ok, Maud should start, otherwise you may get some errors in the terminal, insect case see the troubleshooting.
The first time Maud run, it will show the license agreement window and after you press the OK button it will show a dialog asking for a directory where to extract some files. These are files needed by Maud (databases, preferences etc. plus some examples) and to avoid to pollute your Maud directory it is advised to create another directory (it can be located inside the Maud one, we will call it the examples directory in the following). Be sure to enter inside the newly created example directory before pressing the Extract here button.
To check everything is ok, from the File menu, choose Open analysis… and choose the alzrc.par file inside the example directory. After loading it, press the calculator button in the toolbar to calculate the pattern. You should see a nice fit of the data with the residuals. You are set and ready to use Maud. If not check the troubleshooting section.

Tips (before or after installation)

  • How to check if you have a 32bit or 64bit java VM installed:
    Open a terminal window and type:
    java -version
    and check on the line starting with Java Hotspot if it written 32 or 64bit. If java is unrecognized as a command, you have the same problem as described in troubleshooting Case 1. Use the full path to specify the command.
  • If you have some troubles starting or running Maud and nothing you do can solve it, check first you have a startingLog file in the Maud directory. If there is not this file you don’t have a working java VM installed or the Maud.sh cannot find it, check the troubleshooting section. Otherwise you can send it to the Maud author for help along with the content of the Maud console if you can reach the Maud main window.
  • How to activate the Maud console and get more output, info and errors reported: when the Maud main window opens, select console visible from the Interface menu.
  • How to use the same Maud installation for multiple users: install Maud in a directory accessible by all users and where all users have the rights to write in. Then each user has to start Maud using the Maud.sh (you can make a link or a copy editing the content to make sure Maud starts in the correct directory to find the class path and lib, plugins directories) and on the first run extract all databases and examples in his own home directory (create a suitable directory somewhere and extract everything there). How it works: when Maud starts, it checks in the same directory where the Maud.jar is located for a file named .maudpath_username where username is the User name. If the file does not exist, it will prompt for the license agreement and then ask for a directory where to extract the databases and example files. This directory is also used to store the preferences of Maud. The path to such directory is saved in the .maudpath_username file. This way each user will have his own directory with preferences etc. The unix environment should take care of running multiple instances of the program and each user keep separated files, analyses, preferences etc.

If something does not work, be sure your java virtual machine is properly installed and working and that you didn’t have a corrupted download of Maud. Re-downloading it sometimes solves the corrupted download problem. But be aware of proxy caching the downloads, it means that if the corrupted download is in the cache of the proxy server, you will download again the same corrupted archive. Changing network for the download or forcing a refresh and download 1-2 days after may solve the caching problem.
The java VM coming by default with Linux is not always working properly with Maud (actually the one in Linux Mint it works but the one in Ubuntu as of the time of writing not, it stops during files extraction on the first run or on opening the main window). You have to download the one from Oracle (wwww.java.com) to have one working for Maud. If you have to do it, the best is to check on internet for instructions on how to do it, as everything is changing nearly with every new version. In general you can use the following (be aware that the # is for the java version and the name oracle-java may have a different naming scheme):

  • In the synaptic package manager enable software restricted by copyright or legal issues (multiverse) for ubuntu software and Canonical Partners under other software
  • In the packages install the oracle-java#-xxx, in principle you just need the oracle-java7-jre
  • IMPORTANT: you need to specify that the sun-java# is the default java, otherwise the openjdk of ubuntu will still be used for java. To do it, you can either remove the openjdk-#-jre and related packages (some people do this), or you can specify to use the oracle-java by typing in the terminal:
    sudo update-alternatives --config java
    then type your administrator password and the choose java-#-oracle as the default java VM.

List of troubleshooting:

  • Maud does not start using the Maud.sh.
    Open a terminal window and type:
    java -version
    if java is a recognised command and it is not the openjdk version but the one from Oracle then proceed with I have Java; if Maud does not start, install java from the official website, or using the synaptic package manager as explained in the previous section and then try again with the Maud.sh
  • I have java but Maud does not start.
    There are two possible problems and for both you have to edit the Maud.sh using a text editor in the terminal or in the GUI. The Maud.sh has few lines but the important one is the last containing the following:
    java -mx4096M -Duser.dir=$MAUD_PATH -cp Maud.jar;lib/ij.jar it.unitn.ing.rista.Maud
    The first word, java, invokes the java virtual machine, -Duser.dir=$MAUD_PATH specify the directory where to start Maud that should be the same as the one containing the Maud.jar, then -mx4096M specify the maximum memory java can use for Maud (4Gb in this case), the -cp specify the classpath for Maud (the jar libraries to use) and finally it.unitn.ing.rista.Maud the starting class (that is contained in the Maud.jar). So the possible two problems are:

    • Case 1: java is not a recognised command. You need to add the full path to Maud.sh. So first locate in your computer where the java command is installed. Use the command in terminal:
      sudo update-alternatives --config java
      and check where java is and which one you have selected. If you have multiple java installations select the one properly installed or if no one is working re-install a new one.
      If Maud still does not start using the Maud.sh check Case 2
    • Case 2: the maximum memory specified is more than what your java virtual machine can support. You may have a java 32 bit VM installed, so the maximum memory usable by java is lower than 2 Gb depending on System configuration and loading. Edit the Maud.sh file and change the -mx option to -mx1024M to check if the memory is the problem. If it works you have installed a 32bit java VM. You may want to uninstall it and install or select a 64bit one if you need more than 2 Gb of memory for Maud (working with complex analyses, many datafiles and/or huge number of reflections).
  • Maud start, but you are not able to arrive to the Maud main window.
    You may have either a Java VM not working properly or a corrupted Maud installation, in either case try to re-download one or the others or both and re-install them. Otherwise, check the startingLog file created inside the Maud directory when Maud starts and in case send it to Maud author. Check the Tips section for more.

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