1. Welcome to the NSR Physiome Project!
  2. Physiome JSim
  3. The JSim Documentation Set
  4. Building JSim From Source

Building JSim From Source

Introduction

This page describes how JSim source code is structured, and how to build a JSim binary distribution from that source code. JSim source code may currently be obtained in two ways:

There are minor differences in the build procedure depending upon which method of source code access you use, which are noted in this document. Use of JSim source code must be in accordance with the file license.html found in the distribution root directory.

 

  • Source distribution contents
  • Building JSim on Linux
  • Building JSim on MacIntosh
  • Building JSim on Windows
  • Creating a JSim binary distribution
  • The JSim Verification Suite
  • Comments or Questions?
    Give feedback

Source distribution contents

  • README - read this first
  • license.html - JSim licensing agreement, read before use
  • JSim/ - JSim's java and non-java source code
  • home/ - $JSIMHOME for source builds
  • build/ - build, test and distribution scripts
  • linux/ - linux OS specific directory
  • macos/ - Macintosh OS X specific directory
  • win64/ - Windows OS specific directory
  • unix/ - Common material for Unix-based OS'es (Linux & MacOS)
  • third/ - misc 3rd party contributions to JSim
  • fpack/ - JSim Fortran package of XSIM-compatible models
  • verify/ - verification suite

Building JSim from Source

Please use instructions found on the JSim GitHub repository for building JSim from source on Linux, MacOS, and Windows platforms.

Link: https://github.com/NSR-Physiome/JSim/wiki/Building-JSim-from-source

 

Creating JSim binary distribution

Binary distribution may be created for all 3 supported platforms (Windows, MacIntosh, Linux) from either a Linux or MacIntosh workstation.

  1. Build JSim from source on your Linux or MacIntosh workstation.
  2. If you wish to build binary distributions for other platforms as well, build on those platforms and copy the architecture-specific files to $JSIMSRC/native.
  3. Run jsdist.bin ARCH, where ARCH is one of linux, macos, or win32. The resulting .zip archive will be created in $JSIMSRC/dist.
  4. Install your newly created .zip archive using the standard installation instructions for the target machine.

Running the JSim verify suite

$JSIMSRC/verify contains various regression tests of JSim computational functionality. These regressions tests are fairly exact for Linux builds, and somewhat less exact for other architectures. The fpack, xsim and xfunc tests are not currently supported under Windows. Run the suite as follows:

  1. Perform the following in a Bash shell.
  2. run ". jsverify.env DIST" where DIST is either "src" for the JSim source build or a home directory for a JSim binary distribution.
  3. cd $JSIMSRC/verify
  4. Execture "runall [SWITCHES] [DIRS]" where DIRS is a list of subdirectories to verify. If DIRS is empty, all subdirectories are verified. If DIRS is the special value "win64" (which is not a subdirectory), all subdirectories except fpack, xfunc and xsim are verified.
  5. The results of runall are saved in "log" and echoed to the screen. Examine the runall script for further details.

Comments or Questions?

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Model development and archiving support at https://www.imagwiki.nibib.nih.gov/physiome 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.