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OS X pre-release - schema-34

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@tph-thuering tph-thuering released this 03 Jun 18:22
schema-34-pre-OSX
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This is a OS X only pre-release version and has not been tested. The state of the schema can and probably will change before the final release. Please report any issues back to us here.

Please consult the section about Troubleshooting below, if you get stuck.

  1. Install dependencies
  2. Installation
  3. Test Installation
  4. Run
  5. Troubleshooting
  6. Feedback

Install dependencies

Note: Instruction for OS X only, tested with Yosemite (OS X 10.10.2)

Open a terminal and paste the following in:

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew update
brew install cmake gcc xerces-c cxxtest boost gsl xsd

Installation

Copy the following files from the Download section below.

  • openMalaria
  • scenario_34.xsd

Put those files into your desired folder called "ExperimentFolder" and do the following:

  1. Open a terminal

  2. run the following command to change to your directory (Please adjust "ExperimentFolder" to your desired folder)

  3. Give yourself permission to run the file (Downloaded files usually cannot be executed, without any modification)

cd "ExperimentFolder"

chmod +x ./openMalaria

Test Installation

run the downloaded "openMalaria" file to test if it works:

After Installation put the first line in the terminal and hit Enter. (the rest is the expected output)

./openMalaria --version

You should see the following output:

OpenMalaria simulator of malaria epidemiology and control, schema version 34
(oldest compatible: 32). For more information, see
https://github.com/SwissTPH/openmalaria/wiki

This is a prerelease version
OpenMalaria is copyright © 2005-2015 Swiss Tropical Institute and Liverpool
School Of Tropical Medicine.
OpenMalaria comes with ABSOLUTELY NO WARRANTY. This is free software, and you
are welcome to redistribute it under certain conditions. See the file COPYING
or http://www.gnu.org/licenses/gpl-2.0.html for details of warranty or terms of
redistribution.

Printed help; exiting...

Run openMalaria

You need the following files for this release in the same folder:

  • openMalaria (in version 34)
  • scenario_34.xsd (for scenario.xml validation)
  • a scenario.xml (Version in the XML header must match version 34 and the filename of "scenario_34.xsd")

If you see something like this below, openMalaria works, but obviously scenario.xml is not at the right place.

./openMalaria 
BoincWrapper: not using BOINC
Error: Error: unable to open scenario.xml
In: scenario.xml
OpenMalaria: No such file or directory

Read the page about Scenario Design on how to assemble a valid scenario.xml file.

Troubleshooting

File permissions

You might need to give the file permission to run as an executable like so:

chmod +x openMalaria

after this you should be able to run openMalaria

Scenario.xml validation / XSD error

If you see something like this:

./openMalaria 
BoincWrapper: not using BOINC
XSD error: instance document parsing failed

Then something is wrong with your scenario description (scenario.xml).

Feedback

if you experience any other errors then please open a new issue here https://github.com/SwissTPH/openmalaria/issues/new
and tell us what is happening (or not)

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