Re: [chimerax-users] [Chimera-users] ChimeraX won't start on Ubuntu 16.04
(This is really a question for the chimerax-users mailing list, not the chimera-users one.)
If you can wait a week or so, I'll have a ChimeraX .deb package for Ubuntu 16.04 (and another for 18.04).
But to answer your question, you do not need a system-wide replacement of Qt5. libQt5core.so.5 is in CHIMERAX/lib/python3.6/site-packages/PyQt5/Qt/lib/libQt5Core.so.5, where CHIMERAX is where ChimeraX was installed. So add that directory to the LD_LIBRARY_PATH environment variable and rerun ldd on libqxcb.so. And please let me know what you find out so I can make sure the .deb package avoids that problem.
Regards,
Greg
On 06/21/2018 10:34 AM, Petr Leiman wrote:
Dear ChimeraX users and Developers,
ChimeraX v. 0.5 or 0.6 would not start on our stock Ubuntu 16.04 machines. The error message is as follows:
This application failed to start because it could not find or load the Qt platform plugin "xcb" in "".
Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, xcb.
Reinstalling the application may fix this problem. Fatal Python error: Aborted
Current thread 0x000014f406ce7740 (most recent call first): File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/chimerax/ui/gui.py", line 93 in __init__ File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", line 485 in init File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", line 788 in <module> File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line 85 in _run_code File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line 193 in _run_module_as_main Aborted (core dumped)
A few more errors while checking for missing libraries (ldd) of ChimeraX-supplied libqxcb.so, libqxcb-glx-integration.so or libqxcb-egl-integration.so /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5.9' not found /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5' not found /usr/lib/x86_64-linux-gnu/libQt5XcbQpa.so.5: version `Qt_5_PRIVATE_API' not found /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5: version `Qt_5' not found /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5
Do I need to do a system-wide replacement of Qt5 for a different flavor (OpenGLES)?
Thanks,
Petr
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Greg,
Will the Ubuntu 18.04 be CUDA capable ?
Regards Paul
On Jun 21, 2018, at 2:04 PM, Greg Couch gregc@cgl.ucsf.edu wrote:
(This is really a question for the chimerax-users mailing list, not the chimera-users one.)
If you can wait a week or so, I'll have a ChimeraX .deb package for Ubuntu 16.04 (and another for 18.04).
But to answer your question, you do not need a system-wide replacement of Qt5. libQt5core.so.5 is in CHIMERAX/lib/python3.6/site-packages/PyQt5/Qt/lib/libQt5Core.so.5, where CHIMERAX is where ChimeraX was installed. So add that directory to the LD_LIBRARY_PATH environment variable and rerun ldd on libqxcb.so. And please let me know what you find out so I can make sure the .deb package avoids that problem. Regards,
GregOn 06/21/2018 10:34 AM, Petr Leiman wrote:
Dear ChimeraX users and Developers,
ChimeraX v. 0.5 or 0.6 would not start on our stock Ubuntu 16.04 machines. The error message is as follows:
This application failed to start because it could not find or load the Qt platform plugin "xcb" in "".
Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, xcb.
Reinstalling the application may fix this problem. Fatal Python error: Aborted
Current thread 0x000014f406ce7740 (most recent call first): File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/chimerax/ui/gui.py", line 93 in __init__ File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", line 485 in init File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", line 788 in <module> File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line 85 in _run_code File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line 193 in _run_module_as_main Aborted (core dumped)
A few more errors while checking for missing libraries (ldd) of ChimeraX-supplied libqxcb.so, libqxcb-glx-integration.so or libqxcb-egl-integration.so /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5.9' not found /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5' not found /usr/lib/x86_64-linux-gnu/libQt5XcbQpa.so.5: version `Qt_5_PRIVATE_API' not found /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5: version `Qt_5' not found /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5
Do I need to do a system-wide replacement of Qt5 for a different flavor (OpenGLES)?
Thanks,
Petr
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ChimeraX does not come with CUDA, it has to already be installed on your system. And ChimeraX doesn't directly use CUDA or OpenCL yet. But extensions, like Tristan Croll's ISOLDE, which in turn uses OpenMM which uses CUDA or OpenCL, would benefit.
Does that answer your question?
Greg
June 22, 2018 8:02 AM, "Paul Buscemi" <busce004@umn.edu (mailto:busce004@umn.edu?to=%22Paul%20Buscemi%22%20busce004@umn.edu)> wrote: Greg, Will the Ubuntu 18.04 be CUDA capable ? Regards Paul On Jun 21, 2018, at 2:04 PM, Greg Couch <gregc@cgl.ucsf.edu (mailto:gregc@cgl.ucsf.edu)> wrote: (This is really a question for the chimerax-users mailing list, not the chimera-users one.)
If you can wait a week or so, I'll have a ChimeraX .deb package for Ubuntu 16.04 (and another for 18.04).
But to answer your question, you do not need a system-wide replacement of Qt5. libQt5core.so.5 is in CHIMERAX/lib/python3.6/site-packages/PyQt5/Qt/lib/libQt5Core.so.5, where CHIMERAX is where ChimeraX was installed. So add that directory to the LD_LIBRARY_PATH environment variable and rerun ldd on libqxcb.so. And please let me know what you find out so I can make sure the .deb package avoids that problem.
Regards,
Greg On 06/21/2018 10:34 AM, Petr Leiman wrote: Dear ChimeraX users and Developers, ChimeraX v. 0.5 or 0.6 would not start on our stock Ubuntu 16.04 machines. The error message is as follows: This application failed to start because it could not find or load the Qt platform plugin "xcb" in "". Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, xcb. Reinstalling the application may fix this problem. Fatal Python error: Aborted Current thread 0x000014f406ce7740 (most recent call first): File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/chimerax/ui/gui.py", line 93 in __init__ File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", line 485 in init File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", line 788 in <module> File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line 85 in _run_code File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line 193 in _run_module_as_main Aborted (core dumped) A few more errors while checking for missing libraries (ldd) of ChimeraX-supplied libqxcb.so, libqxcb-glx-integration.so or libqxcb-egl-integration.so /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5.9' not found /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5' not found /usr/lib/x86_64-linux-gnu/libQt5XcbQpa.so.5: version `Qt_5_PRIVATE_API' not found /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5: version `Qt_5' not found /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5 Do I need to do a system-wide replacement of Qt5 for a different flavor (OpenGLES)? Thanks, Petr
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Greg,
Thank you very much for the response. Yes it does.. I was hoping…. Chimera is a fine program and I hope you see your way into incorporating it or as a GUI/ file preparation system
I will look ino ISOLDE/OpenMM
Regards, Paul
On Jun 22, 2018, at 2:22 PM, gregc@cgl.ucsf.edu wrote:
ChimeraX does not come with CUDA, it has to already be installed on your system. And ChimeraX doesn't directly use CUDA or OpenCL yet. But extensions, like Tristan Croll's ISOLDE, which in turn uses OpenMM which uses CUDA or OpenCL, would benefit.
Does that answer your question?
Greg
June 22, 2018 8:02 AM, "Paul Buscemi" <busce004@umn.edu mailto:busce004@umn.edu?to=%22Paul%20Buscemi%22%20%3Cbusce004@umn.edu%3E> wrote: Greg, Will the Ubuntu 18.04 (package ) be CUDA capable ? Regards Paul
On Jun 21, 2018, at 2:04 PM, Greg Couch <gregc@cgl.ucsf.edu mailto:gregc@cgl.ucsf.edu> wrote: (This is really a question for the chimerax-users mailing list, not the chimera-users one.)
If you can wait a week or so, I'll have a ChimeraX .deb package for Ubuntu 16.04 (and another for 18.04).
But to answer your question, you do not need a system-wide replacement of Qt5. libQt5core.so.5 is in CHIMERAX/lib/python3.6/site-packages/PyQt5/Qt/lib/libQt5Core.so.5, where CHIMERAX is where ChimeraX was installed. So add that directory to the LD_LIBRARY_PATH environment variable and rerun ldd on libqxcb.so. And please let me know what you find out so I can make sure the .deb package avoids that problem.
Regards,
Greg
On 06/21/2018 10:34 AM, Petr Leiman wrote:
Dear ChimeraX users and Developers, ChimeraX v. 0.5 or 0.6 would not start on our stock Ubuntu 16.04 machines. The error message is as follows: This application failed to start because it could not find or load the Qt platform plugin "xcb" in "". Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, xcb. Reinstalling the application may fix this problem. Fatal Python error: Aborted Current thread 0x000014f406ce7740 (most recent call first): File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/chimerax/ui/gui.py", line 93 in __init__ File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", line 485 in init File "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", line 788 in <module> File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line 85 in _run_code File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line 193 in _run_module_as_main Aborted (core dumped) A few more errors while checking for missing libraries (ldd) of ChimeraX-supplied libqxcb.so, libqxcb-glx-integration.so or libqxcb-egl-integration.so /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5.9' not found /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5' not found /usr/lib/x86_64-linux-gnu/libQt5XcbQpa.so.5: version `Qt_5_PRIVATE_API' not found /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5: version `Qt_5' not found /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5 Do I need to do a system-wide replacement of Qt5 for a different flavor (OpenGLES)? Thanks, Petr
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participants (3)
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Greg Couch -
gregc＠cgl.ucsf.edu
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Paul Buscemi