How to solve "can not import name 'Brain' from 'Surfer'

CliffordTHU · February 9, 2022, 2:20pm

Somehow I can not run python programme from MNE successfully due to this error, I have already installed pysurfer.
running on linux, python 3.7 installed on linux.

mmagnuski · February 9, 2022, 2:59pm

What installation steps did you follow? Currently, we recommend installing mne to a separate conda environment. If you need to use 3d plotting, we have a separate section for that in the installtion instructions.

CliffordTHU · February 10, 2022, 4:34am

Hello, it seems I have already installed all packages which needed, however when I tried to install mne-python, it came with:

(py37) [root@i]# conda create --name=mne --channel=conda-forge mne
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: /

then stucked ：(

CliffordTHU · February 10, 2022, 6:16am

when I run my python on linux, it comes with:
File “/www/wwwroot/p.dongyangthu.com/codes/SplcV3.py”, line 10, in
from surfer import Brain #用于可视化大脑皮层表面的三维网格上绘制数据
ImportError: cannot import name ‘Brain’ from ‘surfer’ (/opt/miniconda3/envs/py37/lib/python3.7/site-packages/surfer/init.py)

and packages I installed:
^C(py37) [root@xxx]# conda create --name=mne channel=conda-forge mne
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done

when python -c “import mne; mne.sys_info()”

ERROR:root:1:
2022-02-10 14:14:33.162 ( 6.105s) [ 71FD41C0] vtkShaderProgram.cxx:453 ERR| vtkShaderProgram (0x558b1926c800): 0:31(22): error: syntax error, unexpected NEW_IDENTIFIER, expecting ‘{’

ERROR:root:error: syntax error, unexpected NEW_IDENTIFIER, expecting ‘{’
2022-02-10 14:14:33.162 ( 6.105s) [ 71FD41C0]vtkOpenGLVertexArrayObj:265 ERR| vtkOpenGLVertexArrayObject (0x558b1931d680): attempt to add attribute without a program for attribute ndCoordIn
ERROR:root:attempt to add attribute without a program for attribute ndCoordIn
2022-02-10 14:14:33.163 ( 6.105s) [ 71FD41C0]vtkOpenGLQuadHelper.cxx:62 WARN| Error binding ndCoords to VAO.
2022-02-10 14:14:33.163 ( 6.105s) [ 71FD41C0]vtkOpenGLRenderWindow.c:1102 ERR| vtkXOpenGLRenderWindow (0x558b186bed80): Couldn’t build the shader program for resolving msaa.
ERROR:root:Couldn’t build the shader program for resolving msaa.
Platform: Linux-5.10.60-9.al8.x86_64-x86_64-with-centos-3-Soaring_Falcon
Python: 3.7.11 (default, Jul 27 2021, 14:32:16) [GCC 7.5.0]
Executable: /opt/miniconda3/envs/py37/bin/python
CPU: x86_64: 2 cores
Memory: 3.6 GB

mne: 0.24.1
numpy: 1.21.5 {blas=openblas, lapack=openblas}
scipy: 1.7.3
matplotlib: 2.2.2 {backend=TkAgg}

sklearn: 1.0.2
numba: 0.55.1
nibabel: 3.2.1
nilearn: 0.9.0
dipy: 1.4.1
cupy: Not found
pandas: 1.3.5
mayavi: 4.7.4
pyvista: 0.33.2 {OpenGL 3.1 Mesa 20.3.3 via llvmpipe (LLVM 11.0.0, 256 bits)}
pyvistaqt: 0.7.0
ipyvtklink: 0.2.2
vtk: 9.1.0
PyQt5: 5.15.4
ipympl: 0.8.7
mne_qt_browser: 0.1.7
pooch: v1.6.0
QLibraryPrivate::unload succeeded on “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforminputcontexts/libcomposeplatforminputcontextplugin.so”
QLibraryPrivate::unload succeeded on “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so”
QLibraryPrivate::unload succeeded on “Xcursor” (faked)

dont know how to solve :(((((

mmagnuski · February 10, 2022, 12:17pm

Pinging @richard as he may know what is wrong.
@CliffordTHU, so you manage to create the mne env in the end, right? Do you activate this environment (conda activate mne) before you try the mne.sys_info() command?

mmagnuski · February 10, 2022, 12:18pm

Judging from the output it seems you did not activate the mne environment as the executable is /opt/miniconda3/envs/py37/bin/python.

CliffordTHU · February 10, 2022, 12:19pm

yes,which shows:
[root@xxx ~]# conda activate mne
Could not find conda environment: mne
You can list all discoverable environments with conda info --envs.

CliffordTHU · February 10, 2022, 12:20pm

[root@xxx ~]# conda info --envs

conda environments:

base * /opt/miniconda3
py37 /opt/miniconda3/envs/py37

mmagnuski · February 10, 2022, 12:21pm

@CliffordTHU Ok, so you couldn’t install the mne environment, right? Did it take too long (you previously said that conda was stuck on solving environment) or did you get some conflict errors?

CliffordTHU · February 10, 2022, 12:24pm

sorry I iddnt understand, I need to install mne environment first then run my python programme, is it right?
Then how can I install mne environment? Is it installed in linux system but not python?

CliffordTHU · February 10, 2022, 12:26pm

“(py37) [root@i]# conda create --name=mne --channel=conda-forge mne”
It truly takes a long time but succeed at last.

CliffordTHU · February 10, 2022, 12:36pm

(py37) [root@xxx ~]# conda create --name=mne --channel=conda-forge mne
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done

mmagnuski · February 10, 2022, 12:50pm

ok, make sure you accept the installation (user input like y (from “yes”) may be required). Then activate mne:

conda activate mne

and only then see if things work.

CliffordTHU · February 10, 2022, 2:21pm

Still

(py37) [root@xxx~]# conda create --name=mne --channel=conda-forge mne
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: - (py37) [root@xxx ~]# conda activate mne
Could not find conda environment: mne
You can list all discoverable environments with conda info --envs.

mmagnuski · February 10, 2022, 2:30pm

You’d have to write exactly what happens setp by step - currently it is difficult to know what is wrong, as it seems you copy only parts of the console messages. Did you get any warnings or errors when trying to install?

CliffordTHU · February 10, 2022, 2:38pm

steps:
1、I installed python3.7 and pip those packages, and the list:
Platform: Linux-5.10.60-9.al8.x86_64-x86_64-with-centos-3-Soaring_Falcon
Python: 3.7.11 (default, Jul 27 2021, 14:32:16) [GCC 7.5.0]
Executable: /opt/miniconda3/envs/py37/bin/python
CPU: x86_64: 2 cores
Memory: 3.6 GB

mne: 0.24.1
numpy: 1.21.5 {blas=openblas, lapack=openblas}
scipy: 1.7.3
matplotlib: 2.2.2 {backend=TkAgg}

sklearn: 1.0.2
numba: 0.55.1
nibabel: 3.2.1
nilearn: 0.9.0
dipy: 1.4.1
cupy: Not found
pandas: 1.3.5
mayavi: 4.7.4
pyvista: 0.33.2 {OpenGL 3.1 Mesa 20.3.3 via llvmpipe (LLVM 11.0.0, 256 bits)}
pyvistaqt: 0.7.0
ipyvtklink: 0.2.2
vtk: 9.1.0
PyQt5: 5.15.4
ipympl: 0.8.7
mne_qt_browser: 0.1.7
pooch: v1.6.0
QLibraryPrivate::unload succeeded on “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforminputcontexts/libcomposeplatforminputcontextplugin.so”
QLibraryPrivate::unload succeeded on “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so”
QLibraryPrivate::unload succeeded on “Xcursor” (faked)

when I run 'python -c “import mne; mne.sys_info()”, it will comes with some errors, and I will put it on next comment

2、I installed mne-python by ‘(py37) [root@xxx~]# conda create --name=mne --channel=conda-forge mne’, and it shows ‘Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done’
3、I run my programme and shows cannot import brain from surfer

mmagnuski · February 10, 2022, 7:22pm

You don’t have to complete the step 1 you describe, you only need anaconda or miniconda, to be able to perfrom step 2. However, your description of step 2 is incomplete. The installation didn’t even begin in your description of step 2. There should be another “Solving environment” (hopefully successful) information and then a list of packages that will be installed that you would have to accept by pressing “y”. Then there would be progress bars as the packages are downloaded and finally everything would be installed.
Maybe you close the console / command prompt too soon and don’t allow the installation to progress?

CliffordTHU · February 11, 2022, 1:36am

Sorry, this account is a new account which means I can only comment 13 messages per day,

actually this is all I got:
(There do have some errors at last)

(py37) [root@xxx ~]# conda create --name=mne --channel=conda-forge mne
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: - (py37) [root@xxx~]# conda activate mne
Could not find conda environment: mne
You can list all discoverable environments with conda info --envs.

(py37) [root@ixxx~]# conda info --envs

conda environments:

base /opt/miniconda3
py37 * /opt/miniconda3/envs/py37

(py37) [root@ixxx~]# python -c “import mne; mne.sys_info()”
QFactoryLoader::QFactoryLoader() checking directory path “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms” …
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqeglfs.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqeglfs.so, metadata=
{
“IID”: “org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3”,
“MetaData”: {
“Keys”: [
“eglfs”
]
},
“archreq”: 0,
“className”: “QEglFSIntegrationPlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“eglfs”)
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqlinuxfb.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqlinuxfb.so, metadata=
{
“IID”: “org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3”,
“MetaData”: {
“Keys”: [
“linuxfb”
]
},
“archreq”: 0,
“className”: “QLinuxFbIntegrationPlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“linuxfb”)
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqminimal.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqminimal.so, metadata=
{
“IID”: “org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3”,
“MetaData”: {
“Keys”: [
“minimal”
]
},
“archreq”: 0,
“className”: “QMinimalIntegrationPlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“minimal”)
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqminimalegl.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqminimalegl.so, metadata=
{
“IID”: “org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3”,
“MetaData”: {
“Keys”: [
“minimalegl”
]
},
“archreq”: 0,
“className”: “QMinimalEglIntegrationPlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“minimalegl”)
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqoffscreen.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqoffscreen.so, metadata=
{
“IID”: “org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3”,
“MetaData”: {
“Keys”: [
“offscreen”
]
},
“archreq”: 0,
“className”: “QOffscreenIntegrationPlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“offscreen”)
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqvnc.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqvnc.so, metadata=
{
“IID”: “org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3”,
“MetaData”: {
“Keys”: [
“vnc”
]
},
“archreq”: 0,
“className”: “QVncIntegrationPlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“vnc”)
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-egl.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-egl.so, metadata=
{
“IID”: “org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3”,
“MetaData”: {
“Keys”: [
“wayland-egl”
]
},
“archreq”: 0,
“className”: “QWaylandEglPlatformIntegrationPlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“wayland-egl”)
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-generic.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-generic.so, metadata=
{
“IID”: “org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3”,
“MetaData”: {
“Keys”: [
“wayland”
]
},
“archreq”: 0,
“className”: “QWaylandIntegrationPlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“wayland”)
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-egl.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-egl.so, metadata=
{
“IID”: “org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3”,
“MetaData”: {
“Keys”: [
“wayland-xcomposite-egl”
]
},
“archreq”: 0,
“className”: “QWaylandXCompositeEglPlatformIntegrationPlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“wayland-xcomposite-egl”)
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-glx.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqwayland-xcomposite-glx.so, metadata=
{
“IID”: “org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3”,
“MetaData”: {
“Keys”: [
“wayland-xcomposite-glx”
]
},
“archreq”: 0,
“className”: “QWaylandXCompositeGlxPlatformIntegrationPlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“wayland-xcomposite-glx”)
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqwebgl.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqwebgl.so, metadata=
{
“IID”: “org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3”,
“MetaData”: {
“Keys”: [
“webgl”
]
},
“archreq”: 0,
“className”: “QWebGLIntegrationPlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“webgl”)
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so, metadata=
{
“IID”: “org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3”,
“MetaData”: {
“Keys”: [
“xcb”
]
},
“archreq”: 0,
“className”: “QXcbIntegrationPlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“xcb”)
QFactoryLoader::QFactoryLoader() checking directory path “/opt/miniconda3/envs/py37/bin/platforms” …
loaded library “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so”
loaded library “Xcursor”
QFactoryLoader::QFactoryLoader() checking directory path “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platformthemes” …
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platformthemes/libqgtk3.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platformthemes/libqgtk3.so, metadata=
{
“IID”: “org.qt-project.Qt.QPA.QPlatformThemeFactoryInterface.5.1”,
“MetaData”: {
“Keys”: [
“gtk3”
]
},
“archreq”: 0,
“className”: “QGtk3ThemePlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“gtk3”)
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platformthemes/libqxdgdesktopportal.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platformthemes/libqxdgdesktopportal.so, metadata=
{
“IID”: “org.qt-project.Qt.QPA.QPlatformThemeFactoryInterface.5.1”,
“MetaData”: {
“Keys”: [
“xdgdesktopportal”,
“flatpak”,
“snap”
]
},
“archreq”: 0,
“className”: “QXdgDesktopPortalThemePlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“xdgdesktopportal”, “flatpak”, “snap”)
QFactoryLoader::QFactoryLoader() checking directory path “/opt/miniconda3/envs/py37/bin/platformthemes” …
QFactoryLoader::QFactoryLoader() checking directory path “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforminputcontexts” …
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforminputcontexts/libcomposeplatforminputcontextplugin.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforminputcontexts/libcomposeplatforminputcontextplugin.so, metadata=
{
“IID”: “org.qt-project.Qt.QPlatformInputContextFactoryInterface.5.1”,
“MetaData”: {
“Keys”: [
“compose”,
“xim”
]
},
“archreq”: 0,
“className”: “QComposePlatformInputContextPlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“compose”, “xim”)
QFactoryLoader::QFactoryLoader() looking at “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforminputcontexts/libibusplatforminputcontextplugin.so”
Found metadata in lib /opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforminputcontexts/libibusplatforminputcontextplugin.so, metadata=
{
“IID”: “org.qt-project.Qt.QPlatformInputContextFactoryInterface.5.1”,
“MetaData”: {
“Keys”: [
“ibus”
]
},
“archreq”: 0,
“className”: “QIbusPlatformInputContextPlugin”,
“debug”: false,
“version”: 331520
}

Got keys from plugin meta data (“ibus”)
QFactoryLoader::QFactoryLoader() checking directory path “/opt/miniconda3/envs/py37/bin/platforminputcontexts” …
loaded library “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforminputcontexts/libcomposeplatforminputcontextplugin.so”
QFactoryLoader::QFactoryLoader() checking directory path “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/styles” …
QFactoryLoader::QFactoryLoader() checking directory path “/opt/miniconda3/envs/py37/bin/styles” …
/opt/miniconda3/envs/py37/lib/python3.7/site-packages/traits/etsconfig/etsconfig.py:412: UserWarning: Environment variable “HOME” not set, setting home directory to /tmp
% (environment_variable, parent_directory)
2022-02-10 22:36:46.627 ( 9.244s) [ 427A31C0] vtkShaderProgram.cxx:452 ERR| vtkShaderProgram (0x55f4c762be90): 1:
2: #version 140
3: #ifdef GL_ES
4: #ifdef GL_FRAGMENT_PRECISION_HIGH
5: precision highp float;
6: precision highp sampler2D;
7: precision highp sampler3D;
8: #else
9: precision mediump float;
10: precision mediump sampler2D;
11: precision mediump sampler3D;
12: #endif
13: #define texelFetchBuffer texelFetch
14: #define texture1D texture
15: #define texture2D texture
16: #define texture3D texture
17: #else // GL_ES
18: #define highp
19: #define mediump
20: #define lowp
21: #if VERSION == 150
22: #define texelFetchBuffer texelFetch
23: #define texture1D texture
24: #define texture2D texture
25: #define texture3D texture
26: #endif
27: #endif // GL_ES
28: #define varying in
29:
30: in vec2 texCoord;
31: uniform sampler2DMS tex;
32: uniform int samplecount;
33: out vec4 fragOutput0;
34:
35:
36: void main()
37: {
38: float gamma = 2.2;
39:
40: // for each sample in the multi sample buffer…
41: ivec2 itexcoords = ivec2(floor(textureSize(tex) * texCoord));
42: vec3 accumulate = vec3(0.0,0.0,0.0);
43: float alpha = 0.0;
44:
45: for (int i = 0; i < samplecount; i++)
46: {
47: vec4 sample = texelFetch(tex, itexcoords, i);
48: // apply gamma correction and sum
49: accumulate += pow(sample.rgb, vec3(gamma));
50: alpha += sample.a;
51: }
52:
53: // divide and reverse gamma correction
54: accumulate /= float(samplecount);
55: fragOutput0 = vec4(pow(accumulate, vec3(1.0/gamma)), alpha/float(samplecount));
56: }
57:

ERROR:root:1:
2022-02-10 22:36:46.628 ( 9.245s) [ 427A31C0] vtkShaderProgram.cxx:453 ERR| vtkShaderProgram (0x55f4c762be90): 0:31(22): error: syntax error, unexpected NEW_IDENTIFIER, expecting ‘{’

ERROR:root:error: syntax error, unexpected NEW_IDENTIFIER, expecting ‘{’
2022-02-10 22:36:46.629 ( 9.245s) [ 427A31C0]vtkOpenGLVertexArrayObj:265 ERR| vtkOpenGLVertexArrayObject (0x55f4c76f6b70): attempt to add attribute without a program for attribute ndCoordIn
ERROR:root:attempt to add attribute without a program for attribute ndCoordIn
2022-02-10 22:36:46.629 ( 9.246s) [ 427A31C0]vtkOpenGLQuadHelper.cxx:62 WARN| Error binding ndCoords to VAO.
2022-02-10 22:36:46.629 ( 9.246s) [ 427A31C0]vtkOpenGLRenderWindow.c:1102 ERR| vtkXOpenGLRenderWindow (0x55f4c6a7efe0): Couldn’t build the shader program for resolving msaa.
ERROR:root:Couldn’t build the shader program for resolving msaa.
Platform: Linux-5.10.60-9.al8.x86_64-x86_64-with-centos-3-Soaring_Falcon
Python: 3.7.11 (default, Jul 27 2021, 14:32:16) [GCC 7.5.0]
Executable: /opt/miniconda3/envs/py37/bin/python
CPU: x86_64: 2 cores
Memory: 3.6 GB

mne: 0.24.1
numpy: 1.21.5 {blas=openblas, lapack=openblas}
scipy: 1.7.3
matplotlib: 2.2.2 {backend=TkAgg}

sklearn: 1.0.2
numba: 0.55.1
nibabel: 3.2.1
nilearn: 0.9.0
dipy: 1.4.1
cupy: Not found
pandas: 1.3.5
mayavi: 4.7.4
pyvista: 0.33.2 {OpenGL 3.1 Mesa 20.3.3 via llvmpipe (LLVM 11.0.0, 256 bits)}
pyvistaqt: 0.7.0
ipyvtklink: 0.2.2
vtk: 9.1.0
PyQt5: 5.15.4
ipympl: 0.8.7
mne_qt_browser: 0.1.7
pooch: v1.6.0
QLibraryPrivate::unload succeeded on “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforminputcontexts/libcomposeplatforminputcontextplugin.so”
QLibraryPrivate::unload succeeded on “/opt/miniconda3/envs/py37/lib/python3.7/site-packages/PyQt5/Qt5/plugins/platforms/libqxcb.so”
QLibraryPrivate::unload succeeded on “Xcursor” (faked)

mmagnuski · February 11, 2022, 11:45pm

To clarify, in case my previous instructions were confusing:

the python command (trying to show mne.sys_info()) you are using is evaluated in your py27 environment where you seem to have some dependency conflict. You could try fixing that conflict (maybe updating pysurfer would be enough), but my suggestion was to make sure that you are able to install a new mne environment along the installation instructions in the docs
installing that environment does not seem to work, as new mne conda env is not created and the conda install progress that you paste seems to stop at some point. Because this point is recommended in the docs it would be good to know why it fails for you

To make it clearer how installation should work, a copy from just a part of installation progress for a new mne env I created today (last one got tangled in dependency conflicts). This is not exactly the same command as the one you should be running but the output should be similar:

(base) C:\src>conda env create --file environment.yml --name mnedev
Collecting package metadata (repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.10.3
  latest version: 4.11.0

Please update conda by running

    $ conda update -n base -c defaults conda



Downloading and Extracting Packages
charls-2.2.0         | 93 KB     | ############################################################################ | 100%
jbig-2.1             | 45 KB     | ############################################################################ | 100%
libtiff-4.3.0        | 1.1 MB    | ############################################################################ | 100%
numba-0.53.1         | 3.7 MB    | ############################################################################ | 100%
pyvistaqt-0.7.0      | 166 KB    | ############################################################################ | 100%
nomkl-1.0            | 4 KB      | ############################################################################ | 100%
libopenblas-0.3.18   | 5.5 MB    | ############################################################################ | 100%
utfcpp-3.2.1         | 11 KB     | ############################################################################ | 100%
libwebp-base-1.2.2   | 393 KB    | ############################################################################ | 100%
pydicom-2.2.2        | 1.4 MB    | ############################################################################ | 100%
tifffile-2022.2.9    | 140 KB    | ############################################################################ | 100%
h5py-3.3.0           | 1.1 MB    | ############################################################################ | 100%
deprecated-1.2.13    | 12 KB     | ############################################################################ | 100%
importlib_metadata-4 | 4 KB      | ############################################################################ | 100%
nibabel-3.2.2        | 2.7 MB    | ############################################################################ | 100%
xorg-libxau-1.0.9    | 57 KB     | ############################################################################ | 100%
mffpy-0.7.0          | 87 KB     | ############################################################################ | 100%
win32_setctime-1.1.0 | 7 KB      | ############################################################################ | 100%
zstd-1.5.2           | 1010 KB   | ############################################################################ | 100%
threadpoolctl-3.1.0  | 18 KB     | ############################################################################ | 100%
tbb-devel-2020.2     | 2.3 MB    | ############################################################################ | 100%
pthread-stubs-0.4    | 6 KB      | ############################################################################ | 100%
pyreadline-2.1       | 147 KB    | ############################################################################ | 100%
gl2ps-1.4.2          | 74 KB     | ############################################################################ | 100%

and so it goes - multiple packages are installed into the new environement.
That’s why I wanted to investigate what exactly happens in your case:

whether conda install command hangs and you have to close it (close the console or kill the process by ctrl+c for example)
or maybe the command print exactly what you paste and then silently returns you controle of the console without installing the mne evironment (that would be surprising)
or maybe something else happens, an error is displayed for example (but I’m not referring to any errors later on - you get an error later because the mne env is not present, it cannot be activated and the python code is not evaluated in a new mne env)?

CliffordTHU · February 12, 2022, 3:02am

I tried to install 2d mne-python and it succeed, somehow 3d can not install:

(py37) [root@xxx ~]# conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): done
Solving environment: done

# All requested packages already installed.

(py37) [root@xxx ~]# conda info --envs
# conda environments:
#
base                     /opt/miniconda3
new_environment_name     /opt/miniconda3/envs/new_environment_name
py37                  *  /opt/miniconda3/envs/py37

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