Dear Chimera team, I'm from the ConSurf webservere https://consurf.tau.ac.il/consurf_index.php We have been working with chimera for many years and we want to update to chimerax. We have trouble installing chimerax on our unix system. We did manage to install it on our local computers in windows but when installing on unix we get an error: missing library PyQT6 Can you help us? Barak
Hi Barak, The ChimeraX Linux daily build was broken yesterday, missing Qt, but is fixed today. You might want to use ChimeraX 1.5 instead. We released it just a few weeks ago and that is the version most ChimeraX users will have. Tom
On Dec 9, 2022, at 10:45 AM, Barak Yariv via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera team,
I'm from the ConSurf webservere https://consurf.tau.ac.il/consurf_index.php
We have been working with chimera for many years and we want to update to chimerax. We have trouble installing chimerax on our unix system. We did manage to install it on our local computers in windows but when installing on unix we get an error: missing library PyQT6
Can you help us?
Barak _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thank you Tom, I was trying to install chimeraX 1.5 on linux. We have centos 7, and I downloaded ChimeraX-1.5.tar.gz from https://www.cgl.ucsf.edu/chimerax/download.html However, apparently it contains binaries and not source code. The binaries did not work in our centos 7.9 (glibc) So I tried to use singularity - I installed ubuntu 22.04, and tried there the deb file: ucsf-chimerax_1.5ubuntu22.04_amd64.deb However, got the pyqt6 error I tried to download to the singularity image the binaries from ChimeraX-1.5.tar.gz, and got the same error The singularity file I have built is attached I activated it within command * singularity build --sandbox /powerapps/singularity/images/chimara/ChimeraX1.5.img chimerax.build While putting the binaries in a directory I transferred to the image * singularity shell --writable /powerapps/singularity/images/chimara/ChimeraX1.5.img And then within singularity: Singularity> echo $PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin Singularity> export PATH=/chimerax-1.5/bin:$PATH Singularity> echo $LD_LIBRARY_PATH /chimerax-1.5/lib:/.singularity.d/libs Singularity> ls /chimerax-1.5/lib/libQt6Core.so.6 /chimerax-1.5/lib/libQt6Core.so.6 Singularity> Singularity> ChimeraX NOTE: Traceback (most recent call last): File "/chimerax-1.5/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/chimerax-1.5/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035, in <module> exit_code = init(sys.argv) File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py", line 579, in init from chimerax.ui import initialize_qt File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/__init__.py", line 21, in <module> from .gui import MainToolWindow, initialize_qt, menu_capitalize File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/gui.py", line 29, in <module> from Qt.QtWidgets import QApplication File "/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py", line 64, in <module> from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory BUG: ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory File "/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py", line 64, in from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION _See log for complete Python traceback._ Singularity> Singularity> python Python 3.9.11 (main, Nov 28 2022, 23:56:15) [GCC 8.3.0] on linux Type "help", "copyright", "credits" or "license" for more information.
import PyQt6 import PyQt6.QtCore Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory
From: Tom Goddard <goddard@sonic.net> Sent: Saturday, December 10, 2022 12:39 AM To: Barak Yariv <barakyariv@gmail.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>; Nir Ben-Tal <bental@tauex.tau.ac.il>; Dvora Shait <dvory@tauex.tau.ac.il>; Danny Shaked <danny@shaked.tau.ac.il> Subject: Re: [chimerax-users] using chimerx on unix Hi Barak, The ChimeraX Linux daily build was broken yesterday, missing Qt, but is fixed today. You might want to use ChimeraX 1.5 instead. We released it just a few weeks ago and that is the version most ChimeraX users will have. Tom On Dec 9, 2022, at 10:45 AM, Barak Yariv via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear Chimera team, I'm from the ConSurf webservere https://consurf.tau.ac.il/consurf_index.php We have been working with chimera for many years and we want to update to chimerax. We have trouble installing chimerax on our unix system. We did manage to install it on our local computers in windows but when installing on unix we get an error: missing library PyQT6 Can you help us? Barak _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
As you noticed on the ChimeraX download page, there is no CentOS 7 version of ChimeraX 1.5. CentOS 7 is not supported by Qt 6, so we only have CentOS/RHEL/Rocky/AlmaLinux 8 and 9 rpms. Running a newer version of Linux via singularity on CentOS 7 does not work because singularity uses the base OS kernel, and CentOS 7's 3.10 kernel is too old for Qt 6. See the discussion at https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-June/003870.html. I think you might like the singularity script in that discussion better. If you follow the discussion, there are a couple of workarounds: (1) update the CentOS 7 kernel via the elrepo-kernel repo, or (2) remove the .note.ABI-tag section from ChimeraX's copy of libQt6Core.so.6. (1) should always work, (2) appears to work in practice. Both are considered unsupported. And don't forget to install the appropriate graphics driver in the singularity kernel (potentially non-trivial). The best solution is to update your system from CentOS 7 to a current version of Linux. -- Greg On 12/10/2022 11:39 PM, Dvora Shait via ChimeraX-users wrote:
Thank you Tom,
I was trying to install chimeraX 1.5 on linux.
We have centos 7, and I downloaded ChimeraX-1.5.tar.gz from https://www.cgl.ucsf.edu/chimerax/download.html
However, apparently it contains binaries and not source code.
The binaries did not work in our centos 7.9 (glibc)
So I tried to use singularity – I installed ubuntu 22.04, and tried there the deb file: ucsf-chimerax_1.5ubuntu22.04_amd64.deb
However, got the pyqt6 error
I tried to download to the singularity image the binaries from ChimeraX-1.5.tar.gz, and got the same error
The singularity file I have built is attached
I activated it within command
* singularity build --sandbox /powerapps/singularity/images/chimara/ChimeraX1.5.img chimerax.build
While putting the binaries in a directory I transferred to the image
* singularity shell --writable /powerapps/singularity/images/chimara/ChimeraX1.5.img
And then within singularity:
*Singularity>*echo $PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
*Singularity>*export PATH=/chimerax-1.5/bin:$PATH
*Singularity>*echo $LD_LIBRARY_PATH
/chimerax-1.5/lib:/.singularity.d/libs
*Singularity>*ls /chimerax-1.5/lib/libQt6Core.so.6
/chimerax-1.5/lib/libQt6Core.so.6
*Singularity>*
*Singularity>*ChimeraX
NOTE: Traceback (most recent call last):
File "/chimerax-1.5/lib/python3.9/runpy.py", line 197, in
_run_module_as_main
return _run_code(code, main_globals, None,
File "/chimerax-1.5/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py",
line 1035, in <module>
exit_code = init(sys.argv)
File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py",
line 579, in init
from chimerax.ui import initialize_qt
File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/__init__.py",
line 21, in <module>
from .gui import MainToolWindow, initialize_qt, menu_capitalize
File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/gui.py", line
29, in <module>
from Qt.QtWidgets import QApplication
File "/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py", line 64, in
<module>
from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION
ImportError: libQt6Core.so.6: cannot open shared object file: No such file or
directory
BUG: ImportError: libQt6Core.so.6: cannot open shared object file: No such file or
directory
File "/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py", line 64, in
from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION
_See log for complete Python traceback._
*Singularity>*
*Singularity> *python
Python 3.9.11 (main, Nov 28 2022, 23:56:15)
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
import PyQt6
import PyQt6.QtCore
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory
Thank you so much Greg Barak, Nir, we are now in a process of building slurm scheduler on Almalinux 8, Danny suggested to install chimeraX there as soon as it is ready BR Dvory From: Greg Couch <gregc@cgl.ucsf.edu> Sent: Sunday, December 11, 2022 9:20 PM To: Dvora Shait <dvory@tauex.tau.ac.il>; Barak Yariv <barakyariv@gmail.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>; Danny Shaked <danny@shaked.tau.ac.il>; Nir Ben-Tal <bental@tauex.tau.ac.il> Subject: Re: [chimerax-users] using chimerx on unix As you noticed on the ChimeraX download page, there is no CentOS 7 version of ChimeraX 1.5. CentOS 7 is not supported by Qt 6, so we only have CentOS/RHEL/Rocky/AlmaLinux 8 and 9 rpms. Running a newer version of Linux via singularity on CentOS 7 does not work because singularity uses the base OS kernel, and CentOS 7's 3.10 kernel is too old for Qt 6. See the discussion at https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-June/003870.html. I think you might like the singularity script in that discussion better. If you follow the discussion, there are a couple of workarounds: (1) update the CentOS 7 kernel via the elrepo-kernel repo, or (2) remove the .note.ABI-tag section from ChimeraX's copy of libQt6Core.so.6. (1) should always work, (2) appears to work in practice. Both are considered unsupported. And don't forget to install the appropriate graphics driver in the singularity kernel (potentially non-trivial). The best solution is to update your system from CentOS 7 to a current version of Linux. -- Greg On 12/10/2022 11:39 PM, Dvora Shait via ChimeraX-users wrote: Thank you Tom, I was trying to install chimeraX 1.5 on linux. We have centos 7, and I downloaded ChimeraX-1.5.tar.gz from https://www.cgl.ucsf.edu/chimerax/download.html However, apparently it contains binaries and not source code. The binaries did not work in our centos 7.9 (glibc) So I tried to use singularity – I installed ubuntu 22.04, and tried there the deb file: ucsf-chimerax_1.5ubuntu22.04_amd64.deb However, got the pyqt6 error I tried to download to the singularity image the binaries from ChimeraX-1.5.tar.gz, and got the same error The singularity file I have built is attached I activated it within command 1. singularity build --sandbox /powerapps/singularity/images/chimara/ChimeraX1.5.img chimerax.build While putting the binaries in a directory I transferred to the image 1. singularity shell --writable /powerapps/singularity/images/chimara/ChimeraX1.5.img And then within singularity: Singularity> echo $PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin Singularity> export PATH=/chimerax-1.5/bin:$PATH Singularity> echo $LD_LIBRARY_PATH /chimerax-1.5/lib:/.singularity.d/libs Singularity> ls /chimerax-1.5/lib/libQt6Core.so.6 /chimerax-1.5/lib/libQt6Core.so.6 Singularity> Singularity> ChimeraX NOTE: Traceback (most recent call last): File "/chimerax-1.5/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/chimerax-1.5/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035, in <module> exit_code = init(sys.argv) File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py", line 579, in init from chimerax.ui import initialize_qt File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/__init__.py", line 21, in <module> from .gui import MainToolWindow, initialize_qt, menu_capitalize File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/gui.py", line 29, in <module> from Qt.QtWidgets import QApplication File "/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py", line 64, in <module> from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory BUG: ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory File "/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py", line 64, in from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION _See log for complete Python traceback._ Singularity> Singularity> python Python 3.9.11 (main, Nov 28 2022, 23:56:15) [GCC 8.3.0] on linux Type "help", "copyright", "credits" or "license" for more information.
import PyQt6 import PyQt6.QtCore Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory
Hi Dvori/Danny, When will you finish this and start ChimeraX’s installation? Best, Nir From: Dvora Shait Sent: Monday, December 12, 2022 7:22 AM To: Greg Couch <gregc@cgl.ucsf.edu>; Barak Yariv <barakyariv@gmail.com> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>; Danny Shaked <danny@shaked.tau.ac.il>; Nir Ben-Tal <bental@tauex.tau.ac.il> Subject: RE: [chimerax-users] using chimerx on unix Thank you so much Greg Barak, Nir, we are now in a process of building slurm scheduler on Almalinux 8, Danny suggested to install chimeraX there as soon as it is ready BR Dvory From: Greg Couch <gregc@cgl.ucsf.edu<mailto:gregc@cgl.ucsf.edu>> Sent: Sunday, December 11, 2022 9:20 PM To: Dvora Shait <dvory@tauex.tau.ac.il<mailto:dvory@tauex.tau.ac.il>>; Barak Yariv <barakyariv@gmail.com<mailto:barakyariv@gmail.com>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>>; Danny Shaked <danny@shaked.tau.ac.il<mailto:danny@shaked.tau.ac.il>>; Nir Ben-Tal <bental@tauex.tau.ac.il<mailto:bental@tauex.tau.ac.il>> Subject: Re: [chimerax-users] using chimerx on unix As you noticed on the ChimeraX download page, there is no CentOS 7 version of ChimeraX 1.5. CentOS 7 is not supported by Qt 6, so we only have CentOS/RHEL/Rocky/AlmaLinux 8 and 9 rpms. Running a newer version of Linux via singularity on CentOS 7 does not work because singularity uses the base OS kernel, and CentOS 7's 3.10 kernel is too old for Qt 6. See the discussion at https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-June/003870.html. I think you might like the singularity script in that discussion better. If you follow the discussion, there are a couple of workarounds: (1) update the CentOS 7 kernel via the elrepo-kernel repo, or (2) remove the .note.ABI-tag section from ChimeraX's copy of libQt6Core.so.6. (1) should always work, (2) appears to work in practice. Both are considered unsupported. And don't forget to install the appropriate graphics driver in the singularity kernel (potentially non-trivial). The best solution is to update your system from CentOS 7 to a current version of Linux. -- Greg On 12/10/2022 11:39 PM, Dvora Shait via ChimeraX-users wrote: Thank you Tom, I was trying to install chimeraX 1.5 on linux. We have centos 7, and I downloaded ChimeraX-1.5.tar.gz from https://www.cgl.ucsf.edu/chimerax/download.html However, apparently it contains binaries and not source code. The binaries did not work in our centos 7.9 (glibc) So I tried to use singularity – I installed ubuntu 22.04, and tried there the deb file: ucsf-chimerax_1.5ubuntu22.04_amd64.deb However, got the pyqt6 error I tried to download to the singularity image the binaries from ChimeraX-1.5.tar.gz, and got the same error The singularity file I have built is attached I activated it within command 1. singularity build --sandbox /powerapps/singularity/images/chimara/ChimeraX1.5.img chimerax.build While putting the binaries in a directory I transferred to the image 1. singularity shell --writable /powerapps/singularity/images/chimara/ChimeraX1.5.img And then within singularity: Singularity> echo $PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin Singularity> export PATH=/chimerax-1.5/bin:$PATH Singularity> echo $LD_LIBRARY_PATH /chimerax-1.5/lib:/.singularity.d/libs Singularity> ls /chimerax-1.5/lib/libQt6Core.so.6 /chimerax-1.5/lib/libQt6Core.so.6 Singularity> Singularity> ChimeraX NOTE: Traceback (most recent call last): File "/chimerax-1.5/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/chimerax-1.5/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035, in <module> exit_code = init(sys.argv) File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/core/__main__.py", line 579, in init from chimerax.ui import initialize_qt File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/__init__.py", line 21, in <module> from .gui import MainToolWindow, initialize_qt, menu_capitalize File "/chimerax-1.5/lib/python3.9/site-packages/chimerax/ui/gui.py", line 29, in <module> from Qt.QtWidgets import QApplication File "/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py", line 64, in <module> from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory BUG: ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory File "/chimerax-1.5/lib/python3.9/site-packages/Qt/__init__.py", line 64, in from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION _See log for complete Python traceback._ Singularity> Singularity> python Python 3.9.11 (main, Nov 28 2022, 23:56:15) [GCC 8.3.0] on linux Type "help", "copyright", "credits" or "license" for more information.
import PyQt6 import PyQt6.QtCore Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory
participants (5)
-
Barak Yariv -
Dvora Shait -
Greg Couch -
Nir Ben-Tal -
Tom Goddard