Technical FAQ

What is different about version 10?

Version 10 is a 64-bit application with the following advantages:

  • It is about 2-5 times faster than version 9 depending on the mathematical model.
  • Memory limitations imposed by running in 32-bit mode on version 9 are alleviated allowing for models with essentially unlimited memory usage on modern hardware.
  • Graphs and fonts are higher resolution.
  • We have revamped our Monte Carlo dialog for stochastic simulations, added a histogram plotting feature, and added new built-in functions.
  • Code redesign will also facilitate porting to Linux, which we expect to do in late 2023.
  • Two version 8 features have yet to be implemented: oscilloscope mode and check dt.

How do I cite version 9 and 10?

Please acknowledge Berkeley Madonna versions 9 and 10 in your published work by citing the following manuscript:

Marcoline et al. (2022) CPT Pharmacometrics Syst Pharmacol.11:290–301.

This manuscript outlines new features in 9 and 10, and it provides a simple tutorial on building and analyzing a classic PBPK model from the literature. The paper is free to download here.

Installing Berkeley Madonna version 10.

Version 10 comes bundled with all required dependences on Windows. On macOS, Apple's Xcode command line tools must be subsequently downloaded, and this download will start automatically once you run Berkeley Madonna for the first time. Please contact MadonnaExec@gmail.com if you are having trouble with your installation.

For Windows 7 users, please navigate to the installation directory and run BerkeleyMadonna.bat instead of BerkeleyMadonna.exe.

Do you provide a User Guide?

Yes, please download a pdf copy of version 10 here, version 9 here, or version 8 here. 

I get an error message saying "Can't install the software because it is not currently available from the Software Update server."

Please see the section below on compiler error messages.

I get an error message saying "Berkeley Madonna could not run Apple's xcode command line tools."

Please see the next section on compiler error messages.

I get a compiler error message in Berkeley Madonna 10 on macOS and cannot run models.

On macOS, Berkeley Madonna requires Apple's Xcode utilities. These tools come from Apple in two forms: the smaller xcode command line tools, and the much larger Xcode app. Either one will suffice for Berkeley Madonna. If you do not have the tools installed, Berkeley Madonna will attempt to start the installation for you. If that fails, you may have to install them manually.

  • Method 1:  Install Xcode from the App Store. If you already have the Xcode app installed, you may need to run it once to accept an updated license agreement from Apple, particularly if you updated macOS sometime after installing Berkeley Madonna. If you do not have enough disk space to install Xcode, or would prefer a smaller, faster download, use Method 2.
  • Method 2:  Cut and paste the following commands into the Terminal app and hit Return:
    xcode-select --install

    I can't read old models into Berkeley Madonna 9 or 10 on Mac.

    We use a new file format to store models, and the converter is not incorporated into the macOS versions. You have two options:
    1. If you have access to Windows, download version 9 or 10 and open your old file. It will automatically be converted to the new format and saved in the same directory. You can then open this file on your Mac.
    2. Send your model to MadonnaExec@gmail.com with the subject "Please Convert", and we will do it for you. This may take 2-5 days.

    I can't read old models into Berkeley Madonna 9 or 10 on Windows.

    You may see errors when loading version old models in Berkeley Madonna 9 or 10 on Windows. To make the file converter work, change the compatibility mode of the executable to Windows 7 or earlier, and set it to run as administrator. The executables can be found here for version 9 (C:\Program Files (x86)\Berkeley Madonna\BerkeleyMadonna.app\Content\Resources\cmadonnawin\madonnaconvert.exe) and here for version 10 (C:\Program Files\Berkeley Madonna\BerkeleyMadonna.app\Content\Resources\cmadonnawin\madonnaconvert.exe)

    If this does not work for you, please send your model to MadonnaExec@gmail.com with the subject "Please Convert", and we will do it for you. This may take 2-5 days.

        Running Berkeley Madonna version 9 or 10 on Windows 7. 

        After installing version 9 or 10, each time you run the program you must double click on the file BerkeleyMadonna.BAT to launch.

        Installing Berkeley Madonna version 9. 

        After installing version 9, you may have to install legacy Java 6 or Java 8 for macOS or Windows, respectively. Follow these instructions:

        macOS. Berkeley Madonna 9 currently requires Java 6 for macOS. Berkeley Madonna will take you to the appropriate download page at Apple, or you can download it now from here.

        Windows. Please visit the Oracle Java 8 download page here, and download a 32-bit Java installer with a file name ending in windows-i586.exe, for example: jre-8u171-windows-i586.exe. Berkeley Madonna will not work with the 64-bit versions (*-windows-x64.exe) at this time. 

        Please note that Berkeley Madonna version 9 will not run on macOS Catalina (macOS 10.15) or later - you will have to use version 10. 

        Please email MadonnaExec@gmail.com if you have any questions.

        I have the latest Java - why doesn't Berkeley Madonna 9 work?

        Berkeley Madonna 9 requires older versions of Java. Please see the installation instructions for version 9 above.

        I get the Java VM out of memory error.

        There are many ways to reduce the memory used by your model including switching to a stiff solver, increasing the time step (if your model still converges), changing DTOUT, etc. If these all fail, you can attempt to increase the memory allocated to Berkeley Madonna as follows.

        Getting this error on version 10:

        macOS. Assuming Berkeley Madonna is installed in the standard location (/Applications), edit the file /Applications/Berkeley Madonna.app/Contents/Resources/Java/BerkeleyMadonna.txt. This file describes how to change the maximum amount of accessible memory from the default value (1/2 of your total RAM) to your desired value.

        Windows. Assuming Berkeley Madonna is installed in the standard location (C:\Program Files), edit the file C:\Program Files\Berkeley Madonna\BerkeleyMadonna.app\Contents\Resources\Java\BerkeleyMadonna.txt. This file describes how to change the maximum amount of accessible memory from the default value (1/4 of your total RAM) to your desired value.

        Getting this error on version 9:

        macOS. Using a text editor, open the file /Applications/BerkeleyMadonna.app/Contents/Info.plist. Find the line that says: <string>-d32 -Xmx1024m</string> and change 1024m to suit your needs. To see your current maximum available memory, select "About Berkeley Madonna" in the main menu, select "Memory", and then hit the "Information" button. 

        Windows. Open BerkeleyMadonna.ini in Notepad, and add the following text to the end of the file on a new line: vmarg.1=-Xmx1024m This tells Java to use at most 1024 MB of memory. You may experiment with this number to suit your needs. 2048 MB may be the maximum available at this time. To see the effect of this argument on your maximum available memory, select "About..." in the Help menu, select "Memory", and hit the "Information" button.

        The Chemical Reactions Module gives an error at start up on Windows.

        For versions 9 and 10 follow the instructions above for reading old models in Berkeley Madonna versions 9 and 10 on Windows. If you are getting this error on Berkeley Madonna version 8, please right-click C:\Program Files\Macey & Oster\Berkeley Madonna\madonna.exe, select the Compatibility tab, and set the Compatibility mode to Windows XP (Service Pack 3). If this does not eliminate the errors at startup, you may also need to go back to the Compatibility tab and set this program to run as an administrator. 

        Please note that these errors, while annoying, can safely be ignored for any models which do not use the Chemical Reactions Module. If your model does use the chemical reactions module, and the above steps do not work for you, please send us your model and we will convert the portion created using the Chemical Reactions Module into normal equations or flowchart elements.

        I get a compiler error saying "Code execution cannot proceed because vcruntime140.dll was not found" on Windows.

        If you get this compiler error on Windows, please install vc_redist.x64.exe from Microsoft, which can be found here.

        The fonts on my Windows computer are too small.

        Sometimes the font scaling on Windows computers fails to produce readable text. In our testing, we found that the following procedure worked to fix the font scaling, though some times we had to repeat the procedure:

        1) Exit Berkeley Madonna.
        2) In Windows, click the gear icon on the Windows/Start menu to get to Settings. Then navigate to System -> Display. There should be a section labeled "Scale and layout" with a dropdown box labeled "Change the size of text, apps, and other items".
        3) Change the scale to 100%.
        4) Run Berkeley Madonna.
        5) Adjust the scale to your preferred display scale and check the font sizes in Berkeley Madonna.
        6) Exit and restart Berkeley Madonna to see if the scaling in Berkeley Madonna is the same as in step 5.