Cytoscape 3.7 Problem when clicking on Prefuse Force Directed OpenCL Layout, Cytoscape shuts down

[dawn ap]

Hello,

When I tried to apply the Prefuse Force Directed OpenCL Layout, Cytoscape immediately shut down.

I was lucky and didn't have anything unsaved, but it could be an issue for someone else so I thought it was worth mentioning.

I tried it on selected nodes and all nodes, also using the network I was working with as well as a small new network made through Cytoscape.

Every time, Cytoscape closes instantly as I click for that Layout.

I experimented with all other layout options, no such problem.

My pc is running Windows 7 32 bit, if that's relevant.

Other than this glitch, everything has been running smoothly with 3.7 and I find the changes made to be very useful.

Congratulations and thank you to the Cytoscape team!

Best regards,

Dawn

[Brett Settle]

Hi Dawn,

Sorry to hear that the OpenCL layout is not working for you. We reduced our testing environments and are deprecating support for 32 bit Windows systems. 

The OpenCL Layout runs on your GPU, and most tests for old platforms are run on simple VMs, in which the OpenCL layout is not even shown in the Layout menu. It sounds as though you have tested this thoroughly, could you also post your log file (located in ~/CytoscapeConfiguration/3/framework-cytoscape.log) so that we can further debug the issue. I assume your machine has a GPU?

Thank you for the positive feedback! 

Brett

[dawn ap]

Hi Brett

Yes, it has Intel® HD Graphics 2000.

I have attached the file you requested.

It's understandable that you stop supporting old systems like this.

Thanks

[Brett Settle]

Interesting, there is nothing in the log file about the OpenCL layout failing. Only that the previous session closed unsuccessfully. It could be that the error is not getting sent to the log. Another way to debug is to open a command prompt, cd to the directory of cytoscape and run it there to see what is printed to the console.

1. Click Start and type "cmd" into the search bar

2. Run the "cmd.exe" result that pops up

3. type cd /"Program Files"/Cytoscape_v3.7.0 and press Enter

    a. It looks like you are using RC2, which may be a different folder in your Program Files directory

4. type cytoscape.bat and press Enter to run Cytoscape

5. Open your network and run the OpenCL layout

6. Take a screenshot of (or copy and paste) the contents of the command prompt window and post it here

Hopefully this will give us more information :)

[dawn ap]

Ok, I did as you said.

I am attaching a print screen and the error report file it mentions, in case it helps.