1 Topic by admin

(0 replies, posted in Latest Version)

The latest version of the Virtual Ecology Workbench is 3.4.775 updated on 7th July 2016

3.4.775 COMPILER: Fix compiler code for ERA40 calculated heat fluxes - but still problems with this method.
3.4.774 COMPILER: Fix numerical overflow for PM rules in 1958.
3.4.773 COMPILER: Fix logging of ambient particulate chemicals
3.4.772 PLANKTONICA: Replace ln=log (base e).  log10 = log base 10.
3.4.771 COMPILER: Another related fix with tutorial models...
3.4.770 COMPILER: Fix some faulty compiled LiveSim code
3.4.769 COMPILER: Include chemical pools in agents even if not explicitly used.
3.4.768 PLANKTONICA: Fix problem setting cell division parameter
3.4.768 COMPILER: Regression of 3.3.763 - fix problems with no chemicals present
3.4.767 VEW: Fix Java 7 compile problem. Fix faulty variety-based booleans in GUI.
3.4.766 VEW: Fix an error handling runtime arguments.
3.4.765 LIVESIM: Fix an array error when displaying multi-species same-fg data.
3.4.764 COMPILER: New Kernel. Faster, sleaker, smaller memory footprint. (Still single-core)
3.4.764 SNAPSHOT: Note that snapshot version is new - old ones must be discarded.

-------------------------

3.3.763 COMPILER: Fix livesim compilation problems for models with no chemicals.
3.3.762 COMPILER: Fix a potential issue of missing ScenarioData files.
3.3.762 COMPILER: Fix a bug compiling models with no chemicals.
3.3.761 SNAPSHOT: Update version numbers for latest VEW.
3.3.760 QUICK-FIX: Faulty Update.zip.
3.3.759 COMPILER: Further improvements for ERA40
3.3.758 COMPILER: Improve file performance for ERA40 decompression
3.3.757 COMPILER: Correct faulty logging start-time for non-restarted simulations.
3.3.756 COMPILER: Correct faulty logging - audit-trail of ambient particulate chemical.
3.3.755 COMPILER: Correct two faults that prevented BLayer compiling on Java 1.4.2 (Mac OS 10.3.9)
3.3.755 COMPILER: Mac can't handle spaces/quotes on an exec line - fix 754 undone. No spaces in names for now.
3.3.754 COMPILER: Fix for models containing spaces.
3.3.753 LOGGING: Fault in layer-based demographic stage-based ingestion logging.
3.3.751 LIVESIM: Fix faulty display of stages in multi-species simulations. (Thanks Matteo)
3.3.750 VEW-CONTROLLER: Fix a potential way of leaving VC without saving changes.
3.3.749 JOB-LAUNCHER: Fix problems with spaces in model names/directories.
3.3.745 JOB-LAUNCHER: Fix case-insensitive directory error (Thanks Melissa)
3.3.744 ANALYSER: Fix problem with concatenating field data
3.3.742 AUDIT-TRAIL: Fix a bug reported with multi-species audit trail output.
3.3.741 PHYSICS: Only use pool (not incoming) for biofeedback - fixes a transitional ingestion issue.
3.3.740 JOB-LAUNCHER: Fix: VEW was detecting Javac compiler warnings as errors.
3.3.740 JOB-LAUNCHER: Clear button wasn't removing jobs that reported as having errors.
3.3.739 COMPILER: Fix a snapshot bug with the new efficient pool variables.
3.3.738 COMPILER: Fix problems with species names that contain "."
3.3.737 First release of VEW 3.3. Download, and click Update.

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2 Topic by admin

(0 replies, posted in Installation)

Here are the step-by-step installation notes for Windows users. They are also available, (with pictures!) in the VEW Handbook, available from http://www.virtualecology.org in the support section.

(A) Installing a Java Development Kit (JDK)
(see note below about 64-bit)

1. Download and run the latest JDK installer from http://java.sun.com/javase/downloads/index.jsp - Choose the simplest "JDK Update"
2. It comes with a public JRE, which you should also let it install. (I set the install directory to jre1.8.0_91)
3. By default, the installation will be to a directory similar to C:\Program Files\Java\jdk1.8.0_91
4. Go into Settings, Control Panel, System, Advanced, Environment Variables.
5. Ensure that "C:\Program Files\Java\jdk1.8.0_91\bin" is in the PATH variable.
6. Also remove any references to any older versions of the JDK you may find on the PATH.

(B) Upgrading the JDK

The most reliable way of ensuring you are running the latest version is to uninstall any other versions from Control Panel, Add/Remove programs, so that the latest version is the only version you have installed. Then go through the steps in (A). I know it's a bit tedious, but it does keep everything clean and tidy. Ideally, you should copy the new version of tools.jar into VEW's directory and recompile, but in general unless you are jumping from Java 8 to Java 9, it won't be strictly necessary.

(C) Installing the VEW

IMPORTANT NOTE FOR WINDOWS VISTA or later:

To compile/update/even run the VEW, you need to be able to create files - ie, you must be an administrator. Windows Vista by default makes it extremely tedious to run the VEW as administrator; it wouldn't let us tick the "always run as admin" box, so we had to explicitly choose Run As Admin every time. The only way I found to make this sane was to turn off UAC - go to Control Panel, User Accounts, and for the desired account, click on "Turn User Account Control on or off", then choose to turn it off. I know this probably isn't the most secure thing, (although we seemed to be ok in older OSes without all these tiring confirmation windows every time you click anything), but I tried all other possible options involving keeping UAC on, and none of them allowed me to get past step 4, without it complaining about writing files, and eventually failing. Thanks Vista...

1. Obtain the windows installer by contacting us.
2. Run the installer.
3. Copy C:\Program Files\Java\Jdk1.8.0_91\lib\tools.jar into C:\Program Files\VEW\VEW - assuming the installer used the default installation directory. When pasting, you should be in the same directory as "vew.bat".
4. Choose Start, Programs, VEW, Compile VEW from the Windows start menu. You will only need to do this once.
5. Choose Start, Programs, VEW, Run VEW.
6. If a red "Update" button is visible, click it, to download and patch the VEW to the latest version.
7. ALSO, you may like to populate the C:\Program Files\VEW\ScenarioData directory with the input climate data. If the VEW cannot find the data, it will ask you to locate it when it needs it.

REGARDING 32-BIT OR 64-BIT:

VEW runs fine in 32-bit or 64-bit modes. It will use whatever Java installation you have - essentially, whatever version of Java runs when you type "java" at a command line, will be used to run the VEW, and it doesn't mind which. If you run models that require more than 4Gb of RAM though, then 64-bit is the way.

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3 Topic by admin

(0 replies, posted in Installation)

Installation for Linux is easy, although we don't have many Linux machines to test on, so please send your experiences and any improvements. Thanks Melissa for the feedback so far.

1. Contact us for an install package.
2. Run the installer
3. You'll need to copy tools.jar into the root of the VEW directory - same place as the other JAR libraries. The tools.jar file is in the lib directory of your Java installation - which seems to vary by default between some Linux installations. On Mandriva 2008, we found it in /usr/lib/jvm/java-1.6.0-sun-1.6.0.05/lib
4. Also on some breeds of Linux, you may need to chmod 755 *.sh to make the scripts runable.
5. Shortcuts should have been created for compiling, and running the VEW - compile it first, then run it!

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4 Topic by admin

(0 replies, posted in Installation)

Installing on MAC is now quite straightforward, except with just a couple of niggles.

1. Contact us for an install package.
2. Run the install package!
3. The installer create two scripts, one for compiling the VEW, one for running it.
4. You need to convince the MAC to run these using Terminal, rather than opening them in the text editor.
5. Control+Click on the compile script first. Choose "Open With".
6. Select "All Applications" (not just recommended ones).
7. Choose Utilities/Terminal in the window.
8. Tick "Always open with this" - for all the good it does.
9. Then click on the script.
10. You'll probably have to do this again for the Run script, but after that, you should be up and running.

If anyone knows how to iron out this last problem, please tell me!

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