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Frequently Asked and Troubleshooting Questions

If your question is not addressed here, please send email to vcell_support@uchc.edu.

Include the version of Virtual Cell used, operating system, your User Name. For questions about your model, also set the permissions of your model to allow the user, VCellSupport, access.

Why doesn't the software download?

If your download stalls

The Virtual Cell Client is downloaded via java webstart. If the webstart link does not work, try the following:

Why can't I log in?

If you see the error message
  • cannot contact server: Connection refused to host: ms4.vcell.uchc.edu; nested exception is: java.net.ConnectException?: Connection refused: connect
Your institution may be blocking the connection of Virtual Cell to your computer. Contact your IT department and ask them to allow connections: of ms3.vcell.uchc.edu:80 for VCell release and ms4.vcell.uchc.edu:40105 for VCell beta. If difficulties persist with VCell release, use VCell beta.

Why can't I connect?

If you see the error message
  • Server connection failed: Error unmarshaling return header; nested exception is: java.net.SocketException?: Connection reset

Your java cache is outdated. First try clicking the web link (Run VCell 4.#) from VCell Software page on vcell.org. If that fails, open a Command window (Run, Cmd) and at the Command Prompt, type "javaws -viewer". This should open the "Java Cache Viewer". Delete all instances of the "unable to launch" VCell application. Then retry the web link on the VCell Software page.

Virtual Cell Release. A new version of the Virtual Cell is released, on average, every six months. During the update of the software, it is not possible to connect to the server. To receive notifications of upcoming Virtual Cell releases, be sure to set your User Registration Info (accessed under Server menu in the application) to receive email notifications. Try again in 30 minutes, by running the application from http://vcell.org/vcell_software/login.html. This will refresh your cache.

Unable to launch application?

If you see the error message

  • Unable to launch application

Your java cache is outdated.

First try clicking the web link (Run VCell 4.#) from VCell Software page on vcell.org. If that fails on PC, open a Command window and at the Command Prompt, type "javaws -viewer". This should open the "Java Cache Viewer". Delete all instances of the "unable to launch" VCell application. Then retry the web link on the VCell Software page.

Why does "{ }" show up in my application?

Your java cache is outdated.

First try clicking the web link (Run VCell 4.#) from VCell Software page on vcell.org. If that fails, open a Command window and at the Command Prompt, type "javaws -viewer". This should open the "Java Cache Viewer". Delete all instances of the VCell application that is not showing the proper icons. This will delete your local cache/ Then retry the web link on the VCell Software page to recreate the cache with the up to date files.

Why am I getting the "Invalid geometry subvolumns..." error?

The error message "Invalid geometry subvolumns '1 and 2' are not resolved in geometry domain". When I enter data for each subvolumn in the editor, it doesn't like the values I entered and and tells me to enter new data.

The order of your subvolumn/subdomain values matter

Assuming you are trying to create a 2-D analytic geometry and started the process from menu action "File->New->Geometry->Analytic->2-D". A geometry editor window will appear with 1 red colored subdomain named subDomain0, a size of (10,10) and origon of (0,0). Click "Add Subdomain..." and enter a new analytic expression expression, for example "x<5" and click "Add New Subdomain". Now there will be 2 subdomains. Subdomains are resolved starting from the bottom of the "name,value" table list. Each domain higher in the table overlays all other subdomains and only the visible parts of the lower subdomains will be resolved. Your problem is probably that a subdomain definition in the "name,value" table list has completely covered a lower subdomain and the lower subdomain is therefore not resolved.

See Section 6.2 of the User Guide, pages 26-29

How do I get VCell to run on my Linux machine?

You have to have javaws in order to run VCell. This can be in different places depending on your machine.

Why does my SBML import fail on my Linux machine?

We use libSBML native library. To support import of an SBML document by users on different platforms, we compiled the library on our windows, mac and linux machines. Our linux machine may be different from yours. Or your linux may be missing some required libraries.

If you are unable to make use of a windows machine, contact us to help you obtain the appropriate libraries.

Why am I getting solver errors with my simulations?

Simulation 'Simulation' failed [IDA ERROR] IDACalcIC The linesearch algorithm failed with too small a step. IDAStandalone failed : IDA_LINESEARCH_FAIL: The linesearch algorithm failed to find a solution with a step larger than steptol in weighted RMS norm. (/share/apps/vcell/deployed/rel/numerics64/IdaStandalone/IDAStandalone /share/apps/vcell/users/susana/SimID_37718358_0_.idaInput /share/apps/vcell/users/susana/SimID_37718358_0_.ida)

The Virtual Cell solvers have been improved. If your model contains fast reactions, your solver options are IDA and Forward Euler. You may need to modify your simulation parameters, i.e. max step size, to avoid errors.

-- RaquellHolmes - 30 Jun 2009

Topic revision: r13 - 2011-03-03 - 03:58:39 - IonMoraru
 
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