Open UedaHH opened 6 months ago
Can you list the packages in your environment with conda list -n env_name
?
And does PyMOL version 2.5 work?
I would appreciate your reply.
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alsa-lib 1.2.11 hd590300_1 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
blosc 1.21.5 hc2324a3_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.28.1 hd590300_0 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
expat 2.6.2 h59595ed_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
gettext 0.22.5 h59595ed_2 conda-forge
gettext-tools 0.22.5 h59595ed_2 conda-forge
glew 2.1.0 h9c3ff4c_2 conda-forge
glib 2.80.0 hf2295e7_4 conda-forge
glib-tools 2.80.0 hde27a5a_4 conda-forge
glm 0.9.9.8 h00ab1b0_0 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
gst-plugins-base 1.24.1 hfa15dee_1 conda-forge
gstreamer 1.24.1 h98fc4e7_1 conda-forge
harfbuzz 8.3.0 h3d44ed6_0 conda-forge
hdf4 4.2.15 h2a13503_7 conda-forge
hdf5 1.14.3 nompi_h4f84152_100 conda-forge
icu 73.2 h59595ed_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libasprintf 0.22.5 h661eb56_2 conda-forge
libasprintf-devel 0.22.5 h661eb56_2 conda-forge
libblas 3.9.0 22_linux64_openblas conda-forge
libcap 2.69 h0f662aa_0 conda-forge
libcblas 3.9.0 22_linux64_openblas conda-forge
libclang-cpp15 15.0.7 default_h127d8a8_5 conda-forge
libclang13 18.1.3 default_h5d6823c_0 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.7.1 hca28451_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.6.2 h59595ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc-ng 13.2.0 h807b86a_5 conda-forge
libgcrypt 1.10.3 hd590300_0 conda-forge
libgettextpo 0.22.5 h59595ed_2 conda-forge
libgettextpo-devel 0.22.5 h59595ed_2 conda-forge
libgfortran-ng 13.2.0 h69a702a_5 conda-forge
libgfortran5 13.2.0 ha4646dd_5 conda-forge
libglib 2.80.0 hf2295e7_4 conda-forge
libglu 9.0.0 hac7e632_1003 conda-forge
libgomp 13.2.0 h807b86a_5 conda-forge
libgpg-error 1.48 h71f35ed_0 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 22_linux64_openblas conda-forge
libllvm15 15.0.7 hb3ce162_4 conda-forge
libllvm18 18.1.3 h2448989_0 conda-forge
libnetcdf 4.9.2 nompi_h9612171_113 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libpq 16.2 h33b98f1_1 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsqlite 3.45.2 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge
libsystemd0 255 h3516f8a_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.7.0 h662e7e4_0 conda-forge
libxml2 2.12.6 h232c23b_1 conda-forge
libzip 1.10.1 h2629f0a_3 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
mpg123 1.32.6 h59595ed_0 conda-forge
mysql-common 8.3.0 hf1915f5_4 conda-forge
mysql-libs 8.3.0 hca2cd23_4 conda-forge
ncurses 6.4.20240210 h59595ed_0 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.98 h1d7d5a4_0 conda-forge
numpy 1.26.4 py312heda63a1_0 conda-forge
openssl 3.2.1 hd590300_1 conda-forge
packaging 24.0 pyhd8ed1ab_0 conda-forge
pcre2 10.43 hcad00b1_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
ply 3.11 pyhd8ed1ab_2 conda-forge
pmw 2.0.1 py312h7900ff3_1008 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pulseaudio-client 17.0 hb77b528_0 conda-forge
pymol-open-source 3.0.0 py312h270e5e6_7 conda-forge
pyqt 5.15.9 py312h949fe66_5 conda-forge
pyqt5-sip 12.12.2 py312h30efb56_5 conda-forge
python 3.12.2 hab00c5b_0_cpython conda-forge
python_abi 3.12 4_cp312 conda-forge
qt-main 5.15.8 hc9dc06e_21 conda-forge
readline 8.2 h8228510_1 conda-forge
setuptools 69.5.1 pyhd8ed1ab_0 conda-forge
sip 6.7.12 py312h30efb56_0 conda-forge
snappy 1.2.0 hdb0a2a9_1 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
xcb-util 0.4.0 hd590300_1 conda-forge
xcb-util-image 0.4.0 h8ee46fc_1 conda-forge
xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge
xcb-util-renderutil 0.3.9 hd590300_1 conda-forge
xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge
xkeyboard-config 2.41 hd590300_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.9 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
ImportError: libvtkm_cont-1.5.so.1: cannot open shared object file: No such file or directory
I was able to start PyMOL 3.0.0 with Python 3.12 on Ubuntu 22.04, but I was using WSL on Windows to run it. Are you running Linux natively? And are you trying to run PyMOL locally or over X or a remote desktop? The error about not being able to connect to a display is concerning. Can you start another graphical application? Something like xeyes
?
Thank you very much.
I tried to run pymol locally using WSL1 on Windows. And in this condition, xeyes
also failed to work.
Then, I modified the following topic.
To update WSL1 to WSL2, I commanded wsl --set-version Ubuntu 2
on Windows Command Prompt. After this update, xeyes
successfully worked, and the browser of pymol 3.0.0 opened, but the following error messages appeared.
QStandardPaths: wrong permissions on runtime directory /run/user/1000/, 0755 instead of 0700
PyMOL(TM) Molecular Graphics System, Version 3.0.0.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
PyMOL is user-supported open-source software. Although some versions
are freely available, PyMOL is not in the public domain.
If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.
More information can be found at "http://www.pymol.org".
Enter "help" for a list of commands.
Enter "help <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 4.1. Shaders available.
ShaderPrg-Error: vertex shader compilation failed.; name='bezier'
ShaderPrg-Error-InfoLog:
0:1(10): error: GLSL 4.50 is not supported. Supported versions are: 1.10, 1.20, 1.30, 1.40, 1.50, 3.30, 4.00, 4.10, 1.00 ES, and 3.00 ES
Detected GLSL version 4.10.
OpenGL graphics engine:
GL_VENDOR: Microsoft Corporation
GL_RENDERER: D3D12 (Intel(R) UHD Graphics 630)
GL_VERSION: 4.1 (Compatibility Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
ShaderPrg-Error: vertex shader compilation failed.; name='bezier'
ShaderPrg-Error-InfoLog:
0:1(10): error: GLSL 4.50 is not supported. Supported versions are: 1.10, 1.20, 1.30, 1.40, 1.50, 3.30, 4.00, 4.10, 1.00 ES, and 3.00 ES
Detected 6 CPU cores. Enabled multithreaded rendering.
To address the first error message (i.e., QStandardPaths: wrong permissions on runtime directory /run/user/1000/, 0755 instead of 0700
), I commanded chmod 0700 /run/user/1000/
, resulting the message disappeared.
However, the other messages (i.e., ShaderPrg-Error: vertex shader compilation failed.; name='bezier'
and ShaderPrg-Error-InfoLog: 0:1(10): error: GLSL 4.50 is not supported. Supported versions are: 1.10, 1.20, 1.30, 1.40, 1.50, 3.30, 4.00, 4.10, 1.00 ES, and 3.00 ES
) remain.
pymol 2.5 still didn't start, and the error message was the same.
ImportError: libvtkm_cont-1.5.so.1: cannot open shared object file: No such file or directory
I want to solve topic 3 especially. I'd be pleased if there is any idea.
Can you try the solution described here? (https://github.com/microsoft/WSL/issues/9753#issuecomment-1459626307)
Basically,
mesa
Ubuntu package with sudo apt-get upgrade
. This updates everything on your Ubuntu installation. You can also try upgrading specific packages.glxinfo -B
. If you see Device: D3D12
in the output, then run export LIBGL_ALWAYS_SOFTWARE=true
to force software rendering before running glxinfo -B
again. You should see Device: llvmpipe
in the output.LIBGL_ALWAYS_SOFTWARE=true
if you needed it in step 2)If you still get an error, please paste the output from glxinfo -B
.
Thank you very much. In conclusion, thanks to your advice, pymol 3.0.0 successfully started without any error message. The process is described below.
I updated Ubuntu packages with sudo apt-get upgrade
and ran glxinfo -B
, resulting
Command 'glxinfo' not found, but can be installed with:
sudo apt install mesa-utils
Then I executed sudo apt install mesa-utils
and updated again.
I ran glxinfo -B
, and the output was
name of display: :0
display: :0 screen: 0
direct rendering: Yes
Extended renderer info (GLX_MESA_query_renderer):
Vendor: Microsoft Corporation (0xffffffff)
Device: D3D12 (Intel(R) UHD Graphics 630) (0xffffffff)
Version: 23.2.1
Accelerated: yes
Video memory: 4157MB
Unified memory: yes
Preferred profile: core (0x1)
Max core profile version: 4.1
Max compat profile version: 4.1
Max GLES1 profile version: 1.1
Max GLES[23] profile version: 3.0
OpenGL vendor string: Microsoft Corporation
OpenGL renderer string: D3D12 (Intel(R) UHD Graphics 630)
OpenGL core profile version string: 4.1 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL core profile shading language version string: 4.10
OpenGL core profile context flags: (none)
OpenGL core profile profile mask: core profile
OpenGL version string: 4.1 (Compatibility Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2 OpenGL shading language version string: 4.10 OpenGL context flags: (none) OpenGL profile mask: compatibility profile
OpenGL ES profile version string: OpenGL ES 3.0 Mesa 23.2.1-1ubuntu3.1~22.04.2 OpenGL ES profile shading language version string: OpenGL ES GLSL ES 3.00
Since `Device: D3D12` was shown, I ran `export LIBGL_ALWAYS_SOFTWARE=true`. Then the output of `glxinfo -B` was
name of display: :0 display: :0 screen: 0 direct rendering: Yes Extended renderer info (GLX_MESA_query_renderer): Vendor: Mesa (0xffffffff) Device: llvmpipe (LLVM 15.0.7, 256 bits) (0xffffffff) Version: 23.2.1 Accelerated: no Video memory: 3852MB Unified memory: yes Preferred profile: core (0x1) Max core profile version: 4.5 Max compat profile version: 4.5 Max GLES1 profile version: 1.1 Max GLES[23] profile version: 3.2 Memory info (GL_ATI_meminfo): VBO free memory - total: 31 MB, largest block: 31 MB VBO free aux. memory - total: 3074 MB, largest block: 3074 MB Texture free memory - total: 31 MB, largest block: 31 MB Texture free aux. memory - total: 3074 MB, largest block: 3074 MB Renderbuffer free memory - total: 31 MB, largest block: 31 MB Renderbuffer free aux. memory - total: 3074 MB, largest block: 3074 MB Memory info (GL_NVX_gpu_memory_info): Dedicated video memory: 4294837284 MB Total available memory: 4294841136 MB Currently available dedicated video memory: 31 MB OpenGL vendor string: Mesa OpenGL renderer string: llvmpipe (LLVM 15.0.7, 256 bits) OpenGL core profile version string: 4.5 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2 OpenGL core profile shading language version string: 4.50 OpenGL core profile context flags: (none) OpenGL core profile profile mask: core profile
OpenGL version string: 4.5 (Compatibility Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2 OpenGL shading language version string: 4.50 OpenGL context flags: (none) OpenGL profile mask: compatibility profile
OpenGL ES profile version string: OpenGL ES 3.2 Mesa 23.2.1-1ubuntu3.1~22.04.2 OpenGL ES profile shading language version string: OpenGL ES GLSL ES 3.20
I saw `Device: llvmpipe`, according to you.
3. Finally, I ran `pymol` and opened the browser without error. The output is
PyMOL(TM) Molecular Graphics System, Version 3.0.0. Copyright (c) Schrodinger, LLC. All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
PyMOL is user-supported open-source software. Although some versions
are freely available, PyMOL is not in the public domain.
If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.
More information can be found at "http://www.pymol.org".
Enter "help" for a list of commands.
Enter "help <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 4.5. Shaders available. Detected GLSL version 4.50. OpenGL graphics engine: GL_VENDOR: Mesa GL_RENDERER: llvmpipe (LLVM 15.0.7, 256 bits) GL_VERSION: 4.5 (Compatibility Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2 Detected 6 CPU cores. Enabled multithreaded rendering.
I would appreciate sincerely your responses to a beginner like me. And I hope that this chat will be helpful for people having the same problem.
Comment:
Hi, I'm trying to install pymol-open-source-3.0.0 in a virtual env of miniconda3 under Ubuntu 22.04.4 LTS. After installed, I commanded
pymol
, but pymol didn't start and the following message appeared.To address the problem, I tried two commands.
export DISPLAY=:0
export QT_QPA_PLATFORM_PLUGIN_PATH=/home/usr_name/miniconda3/envs/env_name/plugins/platforms/
However, pymol remains to start, and the error message is
I would like to thank you if you tell me any solution.