Help viewer is blank after upgrading to Fedora 35
Hello,
I am just getting started with ChimeraX. I installed the latest production release (Centos 8 version, ucsf-chimerax-1.3-1.el8.x86_64) on my Fedora 33 workstation. It worked great. I installed Isolde and Clipper through the help viewer winder and everything was great. Yesterday I upgraded the operating system to Fedora 35, and now the help viewer no longer works. It is just blank. I can't get it to show other web sites, files from my hard drive - nothing. I installed ChimeraX on 3 other workstations, and all have the same problem. This is very curious and there is no error output that I can find to help point me to the problem. Has anyone else experienced this?
Thanks for your help, Nick Silvaggi
P.S. I also tried uninstalling the production release and installing the Centos 8 version of the latest nightly build - same problem persists.
Nicholas R Silvaggi, Ph.D. University of Wisconsin, Milwaukee Department of Chemistry and Biochemistry 3210 North Cramer St Milwaukee, WI 53211
Office: Chemistry 372D Phone: 414-229-2647 silvaggi@uwm.edu
Yes, the problem is that your operating system is too new :-). You will need to wait for a newer version of ChimeraX that uses Qt 6 instead of Qt 5. Fortunately, we are working on that right now, and there should be a version available within a week. It is a major change, so it will be in a "technology preview" build before it shows up in the daily builds. Unfortunately, ISOLDE doesn't work with daily builds. So you are effectively stuck until there is a ChimeraX 1.4 release and ISOLDE is updated for 1.4.
In the interim, you might be able to run ChimeraX in a singularity or docker container that is based on Fedora 33. Or it might work in a virtual machine. I think a singular container version would be best (most efficient and performant), especially if the graphics driver is the same version as the one in the host OS. But I've been pleasantly surprised with how well ChimeraX graphics works on a Linux VM running in VmWare Workstation on my Windows desktop.
Best,
Greg
On 1/26/2022 12:17 PM, Nicholas R Silvaggi via ChimeraX-users wrote:
Hello,
I am just getting started with ChimeraX. I installed the latest production release (Centos 8 version, ucsf-chimerax-1.3-1.el8.x86_64) on my Fedora 33 workstation. It worked great. I installed Isolde and Clipper through the help viewer winder and everything was great. Yesterday I upgraded the operating system to Fedora 35, and now the help viewer no longer works. It is just blank. I can't get it to show other web sites, files from my hard drive - nothing. I installed ChimeraX on 3 other workstations, and all have the same problem. This is very curious and there is no error output that I can find to help point me to the problem. Has anyone else experienced this?
Thanks for your help, Nick Silvaggi
P.S. I also tried uninstalling the production release and installing the Centos 8 version of the latest nightly build - same problem persists.
Nicholas R Silvaggi, Ph.D. University of Wisconsin, Milwaukee Department of Chemistry and Biochemistry 3210 North Cramer St Milwaukee, WI 53211
Office: Chemistry 372D Phone: 414-229-2647 silvaggi@uwm.edu
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Greg,
This is just the Qt window toolkit html panels such as the Log failing. Qt renders each of those panels from a separate process and it seems likely that separate process simply fails because of a missing system shared library. Have you looked to see which needed shared library is missing, since it could perhaps just be installed on the newer Fedora to make ChimeraX work?
Tom
On Jan 26, 2022, at 1:16 PM, Greg Couch via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Yes, the problem is that your operating system is too new :-). You will need to wait for a newer version of ChimeraX that uses Qt 6 instead of Qt 5. Fortunately, we are working on that right now, and there should be a version available within a week. It is a major change, so it will be in a "technology preview" build before it shows up in the daily builds. Unfortunately, ISOLDE doesn't work with daily builds. So you are effectively stuck until there is a ChimeraX 1.4 release and ISOLDE is updated for 1.4.
In the interim, you might be able to run ChimeraX in a singularity or docker container that is based on Fedora 33. Or it might work in a virtual machine. I think a singular container version would be best (most efficient and performant), especially if the graphics driver is the same version as the one in the host OS. But I've been pleasantly surprised with how well ChimeraX graphics works on a Linux VM running in VmWare Workstation on my Windows desktop.
Best, GregOn 1/26/2022 12:17 PM, Nicholas R Silvaggi via ChimeraX-users wrote:
Hello,
I am just getting started with ChimeraX. I installed the latest production release (Centos 8 version, ucsf-chimerax-1.3-1.el8.x86_64) on my Fedora 33 workstation. It worked great. I installed Isolde and Clipper through the help viewer winder and everything was great. Yesterday I upgraded the operating system to Fedora 35, and now the help viewer no longer works. It is just blank. I can't get it to show other web sites, files from my hard drive - nothing. I installed ChimeraX on 3 other workstations, and all have the same problem. This is very curious and there is no error output that I can find to help point me to the problem. Has anyone else experienced this?
Thanks for your help, Nick Silvaggi
P.S. I also tried uninstalling the production release and installing the Centos 8 version of the latest nightly build - same problem persists.
Nicholas R Silvaggi, Ph.D. University of Wisconsin, Milwaukee Department of Chemistry and Biochemistry 3210 North Cramer St Milwaukee, WI 53211
Office: Chemistry 372D Phone: 414-229-2647 silvaggi@uwm.edu mailto:silvaggi@uwm.edu
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 https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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 https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
The problem isn't a missing shared library. Using ldd on the shared libraries doesn't find anything missing. And if you don't blink on a slow computer, you can see the contents being drawn and then written over so it's blank. And if you install PyQt6 and PyQt6-WebEngine into a current daily build, then it works.
sudo /usr/libexec/UCSF-ChimeraX-daily/bin/python3.9 -m pip install PyQt6 PyQt6-WebEngine
Well, the file history and log widgets are correctly drawn. I still have an OpenGL issue running Fedora 35 in a VM:
QWaylandGLContext::makeCurrent: eglError: 3009, this: 0x37918d0
and that is fixed by turning off wayland in /etc/gdm/custom.conf and rebooting.
-- Greg
On 1/26/2022 4:22 PM, Tom Goddard wrote:
Hi Greg,
This is just the Qt window toolkit html panels such as the Log failing. Qt renders each of those panels from a separate process and it seems likely that separate process simply fails because of a missing system shared library. Have you looked to see which needed shared library is missing, since it could perhaps just be installed on the newer Fedora to make ChimeraX work?
Tom
On Jan 26, 2022, at 1:16 PM, Greg Couch via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Yes, the problem is that your operating system is too new :-). You will need to wait for a newer version of ChimeraX that uses Qt 6 instead of Qt 5. Fortunately, we are working on that right now, and there should be a version available within a week. It is a major change, so it will be in a "technology preview" build before it shows up in the daily builds. Unfortunately, ISOLDE doesn't work with daily builds. So you are effectively stuck until there is a ChimeraX 1.4 release and ISOLDE is updated for 1.4.
In the interim, you might be able to run ChimeraX in a singularity or docker container that is based on Fedora 33. Or it might work in a virtual machine. I think a singular container version would be best (most efficient and performant), especially if the graphics driver is the same version as the one in the host OS. But I've been pleasantly surprised with how well ChimeraX graphics works on a Linux VM running in VmWare Workstation on my Windows desktop.
Best,
Greg
On 1/26/2022 12:17 PM, Nicholas R Silvaggi via ChimeraX-users wrote:
Hello,
I am just getting started with ChimeraX. I installed the latest production release (Centos 8 version, ucsf-chimerax-1.3-1.el8.x86_64) on my Fedora 33 workstation. It worked great. I installed Isolde and Clipper through the help viewer winder and everything was great. Yesterday I upgraded the operating system to Fedora 35, and now the help viewer no longer works. It is just blank. I can't get it to show other web sites, files from my hard drive - nothing. I installed ChimeraX on 3 other workstations, and all have the same problem. This is very curious and there is no error output that I can find to help point me to the problem. Has anyone else experienced this?
Thanks for your help, Nick Silvaggi
P.S. I also tried uninstalling the production release and installing the Centos 8 version of the latest nightly build - same problem persists.
Nicholas R Silvaggi, Ph.D. University of Wisconsin, Milwaukee Department of Chemistry and Biochemistry 3210 North Cramer St Milwaukee, WI 53211
Office: Chemistry 372D Phone: 414-229-2647 silvaggi@uwm.edu
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Greg Couch -
Nicholas R Silvaggi -
Tom Goddard