Installing JSim on Mac OS X


  • MacOS 11.6 ( latest update for BigSur): You can no longer download, install, and execute JSim on a Mac running MacOS 11.6. There is no longer an override option for Gatekeeper on a case by case basis, to execute an application, not signed with an Apple developer certificate. One way to remove the quarantine attribute from JSim is through the use of the xattr command within a terminal window.
    • Open a terminal window. find the path of JSim. Typically it is /Applications/JSim_macos2.21/ .
    • Now type 'sudo chmod -R 755 /Applications/JSim_macos2.21/' 
      • This gives read/write/execute privileges.
    • Next type: 'sudo xattr -dr /Applications/JSim_macos2.21/'
      • This uses xattr to recursively remove the quarantine flag from the directory.
    • That should allow you to execute JSim.
  • Another work around that has worked is to download the zip file on another computer and then copy it over to your Mac. Then unzip and install as normal. Apple quarantines apps that are downloaded from the internet but not copied from another computer on your network.
  • JSim version 2.21 and above no longer requires separate Java Installation. JSim now comes with Java JRE 1.8 ( Java 8 ).


  1. Download the current public release of the JSim zip archive. If you wish to receive news about JSim, please contact us.

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


  1. 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). Folder may possibly be labeled macos_2_xx. Drag and drop the folder into the /Applications directory of your Mac computer.
  2. 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 and higher (from 10.9.5 through 11.1, Big Sur): 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 various versions of JSim, you may, 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.

    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.

  3. 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.
  4. 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 /Application/JSim_macos if your JSim install is in the /Applications directory. Before starting one of these program. Consult a Unix tutorial (for example, here) to learn how to set environment variables. As these programs are scripts you can easily view them to see what they are doing.

  5. Optional advanced administration:

Getting JSim installed on Apple OS 10.8 (Mountain Lion) and above (10.9, 10.10, 10.11, 10.12, 11.1)

  1. (JSim version 2.17 to 2.20) After unzipping JSim, double click the JSim app.
    If you do not have Java 1.8 installed then you may see an error message. Regardless, JSim will not open without Java 1.8 installed,
    • Apple OS 10.10-10.12 (Yosemite through Sierra, earlier Mac OSes are not supported):
      You may or may not see an error message if Java 1.8 is not installed.
      Go to the Oracle website to download Java 1.8 Runtime Environment (jre) . The Oracle link is here (Java SE Runtime Environment 8 Downloads). You will need to restart JSim after the Java install 
  2. As JSim is not signed with an Apple developer certificate, 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.

NOTE: JSim's Macintosh version 2.05 and up, 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.

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Model development and archiving support at provided by the following grants: NIH U01HL122199 Analyzing the Cardiac Power Grid, 09/15/2015 - 05/31/2020, 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.