Spyder on Yggrasil

HPC Support HPC issues
1

Dear admins and users,

I have huge trouble using MNE-Python on Yggdrasil. In baobab, a simple code allows me to use spyder after MNE-Python pip installation of a MNE environnement and Spyder installed using anaconda-navigator

module load Anaconda3
conda activate mne
spyder

In Yggdrasil I run into errors, you cannot install spyder in this environnement or Failed to initialize GLX. The node attribution have the flag X11

Is there somthing I am doing wrong?

Best

Damien

2

Update : l’output terminal aprés une clean install de Spyder sur un environnement dédié

X server does not support XInput 2
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-benis'
qglx_findConfig: Failed to finding matching FBConfig for QSurfaceFormat(version 2.0, options QFlags<QSurfaceFormat::FormatOption>(), depthBufferSize -1, redBufferSize 1, greenBufferSize 1, blueBufferSize 1, alphaBufferSize -1, stencilBufferSize -1, samples -1, swapBehavior QSurfaceFormat::SingleBuffer, swapInterval 1, colorSpace QSurfaceFormat::DefaultColorSpace, profile  QSurfaceFormat::NoProfile)
qglx_findConfig: Failed to finding matching FBConfig for QSurfaceFormat(version 2.0, options QFlags<QSurfaceFormat::FormatOption>(), depthBufferSize -1, redBufferSize 1, greenBufferSize 1, blueBufferSize 1, alphaBufferSize -1, stencilBufferSize -1, samples -1, swapBehavior QSurfaceFormat::SingleBuffer, swapInterval 1, colorSpace QSurfaceFormat::DefaultColorSpace, profile  QSurfaceFormat::NoProfile)
Could not initialize GLX

admin edit: code syntax

3

I tried

(spyder) (yggdrasil)-[benis@login1 ~]$ module load GCC/9.3.0  OpenMPI/4.0.3
(spyder) (yggdrasil)-[benis@login1 ~]$ module load Spyder/4.1.5
(spyder) (yggdrasil)-[benis@login1 ~]$ spyder

Results :

Traceback (most recent call last):
  File "/home/benis/.conda/envs/spyder/bin/spyder", line 7, in <module>
    from spyder.app.start import main
  File "/opt/ebsofts/Spyder/4.1.5-foss-2020a-Python-3.8.2/lib/python3.8/site-packages/spyder/app/start.py", line 21, in <module>
    import zmq
  File "/opt/ebsofts/IPython/7.15.0-foss-2020a-Python-3.8.2/lib/python3.8/site-packages/zmq/__init__.py", line 47, in <module>
    from zmq import backend
  File "/opt/ebsofts/IPython/7.15.0-foss-2020a-Python-3.8.2/lib/python3.8/site-packages/zmq/backend/__init__.py", line 40, in <module>
    reraise(*exc_info)
  File "/opt/ebsofts/IPython/7.15.0-foss-2020a-Python-3.8.2/lib/python3.8/site-packages/zmq/utils/sixcerpt.py", line 34, in reraise
    raise value
  File "/opt/ebsofts/IPython/7.15.0-foss-2020a-Python-3.8.2/lib/python3.8/site-packages/zmq/backend/__init__.py", line 27, in <module>
    _ns = select_backend(first)
          ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/ebsofts/IPython/7.15.0-foss-2020a-Python-3.8.2/lib/python3.8/site-packages/zmq/backend/select.py", line 28, in select_backend
    mod = __import__(name, fromlist=public_api)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/ebsofts/IPython/7.15.0-foss-2020a-Python-3.8.2/lib/python3.8/site-packages/zmq/backend/cython/__init__.py", line 6, in <module>
    from . import (constants, error, message, context,
ImportError: cannot import name 'constants' from partially initialized module 'zmq.backend.cython' (most likely due to a circular import) (/opt/ebsofts/IPython/7.15.0-foss-2020a-Python-3.8.2/lib/python3.8/site-packages/zmq/backend/cython/__init__.py)
(spyder) (yggdrasil)-[benis@login1 ~]$
4

Dear Damien,

Did you solve the issue, I have done some research but this is not trivial. Let me know if you need more help.

Best regards,

5

Update: I solved the problem. I really dont get it. It should not change anything but it does :slight_smile:

ssh -Y cpu100
module load Anaconda3
module load GCC/9.3.0 OpenMPI/4.0.3
module load Spyder/4.1.5-Python-3.8.2
module unload Spyder/4.1.5-Python-3.8.2
conda activate mne
spyder

In case someone runs into the same problem.

Best
Damien

6

Update no, it loads a spyder from the base, no access to MNE. A potential explanation : The installed conda version should be 23.10.0 or newer… Perhaps a conda update --all by the administrator could solve the problem?

https://mne.tools/stable/install/manual_install.html

7

As an alternative, I tried Jupyter Lab, but the tab keep crashing, and I do not know why.

8

Here it is:

9

I loaded the module, now the same error appears on Baobab, i cannot use Spyder in Baobab either

X server does not support XInput 2
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to ‘/scratch/runtime-benis’
qglx_findConfig: Failed to finding matching FBConfig for QSurfaceFormat(version 2.0, options QFlagsQSurfaceFormat::FormatOption(), depthBufferSize -1, redBufferSize 1, greenBufferSize 1, blueBufferSize 1, alphaBufferSize -1, stencilBufferSize -1, samples -1, swapBehavior QSurfaceFormat::SingleBuffer, swapInterval 1, colorSpace QSurfaceFormat::DefaultColorSpace, profile QSurfaceFormat::NoProfile)
qglx_findConfig: Failed to finding matching FBConfig for QSurfaceFormat(version 2.0, options QFlagsQSurfaceFormat::FormatOption(), depthBufferSize -1, redBufferSize 1, greenBufferSize 1, blueBufferSize 1, alphaBufferSize -1, stencilBufferSize -1, samples -1, swapBehavior QSurfaceFormat::SingleBuffer, swapInterval 1, colorSpace QSurfaceFormat::DefaultColorSpace, profile QSurfaceFormat::NoProfile)
Could not initialize GLX
Aborted (core dumped)

10

This is what I tried:

  1. connect to openondemand, launch a desktop session on a compute node
  2. open a terminal and type module load Anaconda3
  3. launch spyder on the terminal spyder

It opens the graphical windows without issue.

Best

11

Ok, I never used openondemand, I will try, thank you for the reply.

12

Hello,

I found a solution,

conda deactivate
conda activate mne

I needed to use the command deactivate before activating my environnment. Using only activate created conflict.

Best