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Installing JSim on Mac OS X

NOTE: JSim's Macintosh version 2.05 requires Snow Leopard or better and Java 1.6 to be installed (See below for further Java install details). JSim's Macintosh version 2.03 and above run only on Intel-based Macs. Version 2.02 and below run on both Intel-based and PowerPC-based Macs under OS X.

  1. Download the appropriate JSim zip archive. Providing the following information will help us demonstrate JSim's continued utility to the funding agencies upon which we rely. Filling out this form will not result in your addition to any mailing lists other than a JSim usage survey that is sent once a year. Your response to that survey will help us to retain our funding. If you wish to receive news about JSim on a more frequent basis, please contact us.


    JSim is free for non-commercial use. View complete license terms

  2. After unzipping the JSim file, you should now find a folder called JSim_macos_2_xx (where 'xx' is the minor version number) on your Desktop (or in your Downloads directory).
  3. To run JSim, open the JSim_macos_2_xx folder and double-click on the JSim application icon to launch JSim. If double-click launch does not work, see paragraphs below, Java install notes, or contact us.

    Apple Mac OS 10.8.5 (Mountain Lion) and higher (10.9.5 Mavericks, 10.10 Yosemite, 10.11 El Capitan, 10.12 Sierra): With the release of OS X Mavericks 10.9.5, the way that OS X recognizes signed apps has changed. Signatures created with OS X Mountain Lion 10.8.5 or earlier (v1 signatures) will be obsoleted and Gatekeeper will no longer recognize them. For previous versions of JSim, version 2.14 and earlier, you will, upon running JSim for the first time, see the follow message: ' "JSim" can't be opened because the identity of the developer cannot be confirmed'. You must change your 'Security and Privacy' settings to allow 'Applications downloaded from anywhere' to be run on the computer. See below for further details. JSim version 2.15 is signed correctly and should not give a signature error.

    Apple Mac OS 10.7 (Lion): By default Lion does not have Java installed. When starting JSim for the first time, a popup window will appear stating Java is not installed, and would you like to install it. If you click 'yes' Java will then be installed on your Lion machine. After the Java install you will have to restart JSim.

    If you do not find the JSim_macos_2_xx folder on your desktop, check the configuration of your browser. If you use Safari , you can find where downloaded files are saved by choosing Preferences from the Safari menu and clicking General. The Open "safe" files after downloading box has to be checked. If it is not, you should find a file named; double-click on its icon to create the JSim_macos file.

  4. JSim 2.07 and above requests 1500MB of heap memory by default. If your system has less than 2GB of memory, you will probably need to reconfigure JSim to use less memory before JSim can launch properly.
  5. Most Macintosh users do not require running JSim from the command-line, which requires some additional setup. If you do, do as follows (familiarity with Unix is assumed). Inside your installation directory, the sub-directory macos/bin contains the various programs in the JSim suite:

    • jsim : the JSim GUI application;
    • jsbatch : the JSim text-based batch application;
    • jsfim : command-line based functional imaging application;
    • jsserver : the JSim remote server computational engine.

    You should either add this sub-directory to your PATH or copy the program suite to a path-searchable directory on your system. You must also set the environment variable JSIMHOME to the absolute path (to the absolute path of JSim_macos for version 1.6.93 and lower) before starting one of these program. Consult a Unix tutorial (for example, here) to learn how to set environment variables.

  6. Optional advanced administration:
Getting JSim installed on Apple OS 10.8 (Mountain Lion) and above (10.9, 10.10, 10.11, 10.12)
  1. After unzipping JSim, double click the JSim app.
    If you do not have Java 1.6 installed then you will see this message:

    Apple OS 10.12 Sierra:
    To open "" you need to install the legacy JAVA SE6 runtime.
    Go to the Apple website to download java. You may not see this pop-up message (On newer machines you may only see a flash). Currently (Nov, 2016), the Apple link is here (Download Java for OS X 2015-001). You will need to restart JSim after the Java install.

    Apple OS 10.10 Yosemite:
    To open "" you need to install the legacy JAVA SE6 runtime.
    Pick 'More info' button which will take you to the Apple website to download java. You will need to restart JSim.

    Apple OS 10.8:
    To open "JSim," you need a Java SE 6 runtime. Would you like to install one now?
    Pick 'Install' and go through the Java installation.You will need to restart JSim.

  2. If you have not changed the default behavior of Gatekeeper, then you may see this message after clicking the JSim icon:
    "JSim" is damaged and can't be opened. You should move it to the Trash.
    Pick 'cancel', do not move to trash.

    This message is apparently caused by JSim's distribution of JavaApplicationStub be improperly signed. Normally, unsigned applications get a nicer message like: "This app is from an unknown developer, go change your preferences to allow unsigned apps to be run".

  3. On your computer, Open up 'System preferences' -> 'Security & Privacy'
  4. Under 'General' in the section titled 'Application downloaded from:' Check 'Anywhere'
  5. Now go back and double click the JSim app icon. You should see the message:
    "JSim" is an application downloaded from the Internet. Are you sure you want to open it?
    Select 'Open' and JSim will start up.
  6. After opening up and using JSim for the first time you can change the Gatekeeper security settings back to "Mac App Store and identified developers" and still be able to use the installed version of JSim.
Comments or Questions?

[This page was last modified 18Nov16, 9:42 am.]

Model development and archiving support at provided by the following grants: NIH/NIBIB BE08407 Software Integration, JSim and SBW 6/1/09-5/31/13; NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.