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jonescompneurolab / hnn

The Human Neocortical Neurosolver (HNN) is a software tool that gives researchers/clinicians the ability to develop/test hypotheses on circuit mechanisms underlying EEG/MEG data.
http://hnn.brown.edu
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Running GUI with Oscar Issue #258

Closed lzimbalist closed 4 years ago

lzimbalist commented 4 years ago

I've been having some trouble getting the GUI up and running while trying to run HNN through Oscar. It seems that everything is working properly, but the GUI never appears. Is there any way to troubleshoot this?

rythorpe commented 4 years ago

Can you share the commands you entered to initialize the singularity container?

lzimbalist commented 4 years ago

After logging onto Oscar I ran:

interact -n 16
singularity pull docker://jonescompneurolab/hnn
singularity run hnn_latest.sif

I know the setup instructions say that the run command should be running hnn.simg but when I try that it gives me a "FATAL" message that it couldn't open the image. My directory has hnn_lastest.sif in it which is why I tried running that

rythorpe commented 4 years ago

Ahh yes, we need to update the instructions because there was a change in how Oscar implements singularity runscripts (@blakecaldwell was this due to an update on Singularity's end, a problem with our runscript, or an issue with Oscar?). @lzimbalist now that you have hnn_latest.sif in your home directory, try

singularity shell hnn_latest.sif
source /home/hnn_user/hnn_envs
cd /home/hnn_user/hnn_source_code
python3 hnn.py
lzimbalist commented 4 years ago

I get 

qt.qpa.xcb: could not connect to display 172.20.200.74:24.0
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.

Aborted (core dumped)

when running that

lzimbalist commented 4 years ago

Does this mean there's a problem with my XQuartz?

rythorpe commented 4 years ago

Does this mean there's a problem with my XQuartz?

I'm assuming you initialized your ssh connection with x-forwarding enabled (i.e., ssh -X usrname@ssh.ccv.brown.edu for linux or ssh -Y usrname@ssh.ccv.brown.edu for Mac)?

lzimbalist commented 4 years ago

Oops! I was running with -X instead of -Y. Just confirming that in the future I need to run the shell to get the GUI working

rythorpe commented 4 years ago

Oops! I was running with -X instead of -Y. Just confirming that in the future I need to run the shell to get the GUI working

Great! Yes, you will need to use a singularity shell to initialize HNN at least for the time being.

lzimbalist commented 4 years ago

Sorry one last question! If I want to transfer files between the two, is there anything special I need to do? I have tried just using scp but it doesn't seem to recognize a lot of the HNN folders and I think it's because of the need to open up a shell in order to get to HNN?

rythorpe commented 4 years ago

HNN always writes simulation param and data files to hnn_out in your home directory. You should be able to transfer files via scp by referencing files contained in ~/hnn_out/data or ~/hnn_out/param.

lzimbalist commented 4 years ago

Hi! I've been using HNN without trouble for the last couple of weeks (since you helped me get it set up – thanks!). It was working fine this morning, but when I tried to open it up just now I got this error message: 

qt.qpa.xcb: could not connect to display 172.20.4.217:19.0
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.

Aborted

When I tried reinstalling (rerunning the singularity docker pull message, I got a "FATAL" error) Have you seen this before? Any ideas on what could fix this?

rythorpe commented 4 years ago

Hi! I've been using HNN without trouble for the last couple of weeks (since you helped me get it set up – thanks!). It was working fine this morning, but when I tried to open it up just now I got this error message:

qt.qpa.xcb: could not connect to display 172.20.4.217:19.0
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.

Aborted

When I tried reinstalling (rerunning the singularity docker pull message, I got a "FATAL" error) Have you seen this before? Any ideas on what could fix this?

This looks like the same error you got earlier when x-forwarding wasn't enabled properly. Did anything change with your local x-client or how you initiated x-forwarding in your ssh session?

lzimbalist commented 4 years ago

I'm not sure what was happening but this morning it seemed to be working again, thanks!

rythorpe commented 4 years ago

Great! I'm going to go ahead and close this issue. Feel free to open again if the issue arises again @lzimbalist.