No suitable graphics backend found

[nmtimme]

Hello

I'm attempting to run phy2 on a virtual desktop and I'm encountering an error. I've previously run phy2 on this same virtual desktop, so I know it is possible. However, I had to reinstall phy2 and some new update since the previous version must have produced problems. Specifically, I ran:

conda create -n phy2 -y cython dask h5py joblib matplotlib numpy pillow pip pyopengl pyqt pyqtwebengine pytest python=3.11 qtconsole requests responses scikit-learn scipy traitlets

conda activate phy2

pip install git+https://github.com/cortex-lab/phy.git

Note, I had to use python=3.11 to avoid the missing imp module in python 3.12 (see issue #1224 ).

Then, when I run phy template-gui params.py --debug, I get:

12:00:52.894 [D] __init__:68          Start capturing exceptions.
12:00:52.897 [W] model:1408           File /N/project/lapishLabWorkspace/SpikeInterfaceSpikeSorting/NeuropixelProbeSpikeSortingResults/2023-11-15_12-27-09/temp/sorter_output/temp_wh.dat does not exist.
12:00:52.919 [W] model:603            Unreferenced clusters found in templates (generally not a problem)
12:00:52.928 [D] model:619            Loading spike clusters.
12:00:52.938 [W] model:625            Unreferenced clusters found in spike_clusters (generally not a problem)
12:00:52.953 [D] model:569            No channel shank file found.
12:00:52.955 [D] model:692            Loading templates.
12:00:52.982 [D] model:724            Templates are dense.
12:00:52.983 [W] model:667            Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
12:00:52.983 [D] model:730            Loading the whitening matrix.
12:00:52.984 [D] model:737            Loading the inverse of the whitening matrix.
12:00:52.987 [W] traces:462           File /N/project/lapishLabWorkspace/SpikeInterfaceSpikeSorting/NeuropixelProbeSpikeSortingResults/2023-11-15_12-27-09/temp/sorter_output/temp_wh.dat does not exist.
12:00:52.987 [W] traces:462           File /N/project/lapishLabWorkspace/SpikeInterfaceSpikeSorting/NeuropixelProbeSpikeSortingResults/2023-11-15_12-27-09/temp/sorter_output/temp_wh.dat does not exist.
12:00:52.987 [D] model:766            Loading features.
12:00:52.987 [D] model:803            Loading template features.
12:00:52.990 [D] model:504            Load `cluster_ContamPct.tsv`.
12:00:52.992 [D] model:504            Load `cluster_KSLabel.tsv`.
12:00:52.994 [D] model:504            Load `cluster_Amplitude.tsv`.
12:00:52.996 [D] model:504            Load `cluster_group.tsv`.
12:00:54.355 [D] context:100          Initialize joblib cache dir at `/N/project/lapishLabWorkspace/SpikeInterfaceSpikeSorting/NeuropixelProbeSpikeSortingResults/2023-11-15_12-27-09/sorter_output/.phy`.
12:00:54.356 [D] context:101          Reducing the size of the cache if needed.
12:00:54.440 [D] base:102             Add filter `high_pass`.
12:00:54.445 [D] config:31            Load config file `/N/u/nmtimme/BigRed200/.phy/phy_config.py`.
12:00:54.446 [D] plugin:145           Loading 0 plugins.
12:00:54.446 [D] context:126          Load memcache for `phy.apps.base._get_mean_waveforms`.
12:00:54.447 [D] context:126          Load memcache for `phy.apps.base._get_mean_waveforms`.
12:00:54.448 [D] context:126          Load memcache for `phy.apps.base._get_template_waveforms`.
12:00:54.450 [D] context:126          Load memcache for `phy.apps.base.get_mean_spike_template_amplitudes`.
12:00:54.451 [D] context:126          Load memcache for `phy.apps.base.get_template_counts`.
12:00:54.451 [D] context:126          Load memcache for `phy.apps.base.get_template_for_cluster`.
12:00:54.452 [D] context:126          Load memcache for `phy.apps.template.gui.get_template_amplitude`.
12:00:54.453 [D] context:126          Load memcache for `phy.apps.base.get_cluster_amplitude`.
12:00:54.454 [D] context:126          Load memcache for `phy.apps.base.get_mean_firing_rate`.
12:00:54.455 [D] context:126          Load memcache for `phy.apps.base.get_best_channel`.
12:00:54.456 [D] context:126          Load memcache for `phy.apps.template.gui.get_best_channels`.
12:00:54.457 [D] context:126          Load memcache for `phy.apps.base.get_channel_shank`.
12:00:54.458 [D] context:126          Load memcache for `phy.apps.base.get_probe_depth`.
12:00:54.459 [D] context:126          Load memcache for `phy.apps.base.peak_channel_similarity`.
12:00:54.461 [D] context:209          The file `/N/project/lapishLabWorkspace/SpikeInterfaceSpikeSorting/NeuropixelProbeSpikeSortingResults/2023-11-15_12-27-09/sorter_output/.phy/new_cluster_id.pkl` doesn't exist.
12:00:54.469 [D] context:185          Save data to `/N/project/lapishLabWorkspace/SpikeInterfaceSpikeSorting/NeuropixelProbeSpikeSortingResults/2023-11-15_12-27-09/sorter_output/.phy/spikes_per_cluster.pkl`.
12:00:54.486 [D] gui:463              Creating GUI.
12:00:54.640 [D] state:46             Load /N/u/nmtimme/BigRed200/.phy/TemplateGUI/state.json for GUIState.
12:00:54.641 [D] state:46             Load /N/project/lapishLabWorkspace/SpikeInterfaceSpikeSorting/NeuropixelProbeSpikeSortingResults/2023-11-15_12-27-09/sorter_output/.phy/state.json for GUIState.
No suitable graphics backend found

Aborted (core dumped)

I'd appreciate any advice you can provide. Thank you!

~Nick

[zm711]

@nmtimme,

Howdy Nick. Yeah there were a couple updates. Could you try to install with the conda yaml instead. It is listed as enviroment.yml on the main page. As you noted you need to limit python to 3.11 (my PR to fix this is awaiting review #1229) in the yml so once you download it just edit python in the dependencies.

Could I also get some info about what the virtual machine and actual machine are (OS-wise)?

[nmtimme]

Hi @zm711,

The environment.yml file worked! I guess there was some other dependency that was missing using the command line environment creation method. Thank you!

~Nick

[zm711]

I wish all issues were this easy :). Happy to help! Zach