ChimeraX 1.4 frozen on RHEL 8.6 and 9.0
Dear ChimeraX developers, I installed ChimeraX 1.4 (both stable release and daily built) on RHEL 8.6 and 9.0. I installed all the ChimeraX 1.4 dependencies using "yum install" from RHEL installation USB. After the installation, I was able to start the GUI, but unable to click any button on the GUI, therefore, I was unable to report the bug from the GUI either. I also tried ChimeraX 1.3 stable release on RHEL 8.6, and everything was normal. Steven -- Steven Chou
When I logined to RHEL8.6 from RHEL 7.9 using ssh, everything worked fine. Which subversion of RHEL 8 was used to compile ChimeraX 1.4? I may try the same version. Steven On Sat, Jul 16, 2022 at 9:01 PM Steven Chou <stevezchou@gmail.com> wrote:
Dear ChimeraX developers,
I installed ChimeraX 1.4 (both stable release and daily built) on RHEL 8.6 and 9.0.
I installed all the ChimeraX 1.4 dependencies using "yum install" from RHEL installation USB.
After the installation, I was able to start the GUI, but unable to click any button on the GUI, therefore, I was unable to report the bug from the GUI either.
I also tried ChimeraX 1.3 stable release on RHEL 8.6, and everything was normal.
Steven
-- Steven Chou
-- Steven Chou
ChimeraX was compiled on "CentOS Linux release 8.5.2111", but that is extremely unlikely to matter. The main GUI change between ChimeraX 1.4 and 1.3 is that ChimeraX 1.3 uses Qt 5 and ChimeraX 1.4 uses Qt 6. So, from your original description, the most likely bug is that we missed a dependency that is needed for Qt 6 to work. So you should try installing Qt 6 separately from https://www.qt.io/download (eg., get the open source version's Qt Online Installer), and see if that fixes the problem. But you also mention trying to run ChimeraX by logging into a remote system running RHEL 8.6 from RHEL 7.9. Running ChimeraX remotely frequently fails to work. Officially, that is not supported. There are too many possible points of failure. It does work sometimes, and especially when the local and remote system are running the exact same version of Linux and have the exact same graphics driver installed. The graphics driver is the usual culprit, and that can be mitigated by running ChimeraX under VirtualGL on the remote system. For completeness, if you are stuck with a RHEL 7 desktop, and your data is on your local system, you could run ChimeraX in a virtual machine. So instead of logging in via ssh, you startup the virtual machine, and login to it directly. Some virtual machines are better than others. I've been happy running different flavors of Linux on VMware Workstation Player on a Windows desktop with a Nvidia GeForce GTX 970 (remember to enable 3D graphics support). There is also a Linux version of VMware Workstation Player. HTH, Greg On 7/16/2022 6:04 PM, Steven Chou via ChimeraX-users wrote:
When I logined to RHEL8.6 from RHEL 7.9 using ssh, everything worked fine. Which subversion of RHEL 8 was used to compile ChimeraX 1.4? I may try the same version. Steven
On Sat, Jul 16, 2022 at 9:01 PM Steven Chou <stevezchou@gmail.com> wrote:
Dear ChimeraX developers,
I installed ChimeraX 1.4 (both stable release and daily built) on RHEL 8.6 and 9.0.
I installed all the ChimeraX 1.4 dependencies using "yum install" from RHEL installation USB.
After the installation, I was able to start the GUI, but unable to click any button on the GUI, therefore, I was unable to report the bug from the GUI either.
I also tried ChimeraX 1.3 stable release on RHEL 8.6, and everything was normal.
Steven
-- Steven Chou
-- Steven Chou
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Greg, Thank you so much for your detailed explanation! I tried ChimeraX 1.4 (both the latest stable release and daily build) on RHEL 8.1, 8.6, and 9.0, because it can only be installed on RHEL 8 or 9. They all had the same problem (frozen after launching the GUI). I also had an old daily build (04/12/2022) of version 1.4, which allowed me to install it on RHEL7.9, but not RHEL 8 or 9. I'm running v1.4 (04/12/2022) on RHEL7.9 now because the helix cylinder functionality is only available in v1.4. All the best, Steven On Sun, Jul 17, 2022 at 2:44 AM Greg Couch <gregc@cgl.ucsf.edu> wrote:
ChimeraX was compiled on "CentOS Linux release 8.5.2111", but that is extremely unlikely to matter.
The main GUI change between ChimeraX 1.4 and 1.3 is that ChimeraX 1.3 uses Qt 5 and ChimeraX 1.4 uses Qt 6. So, from your original description, the most likely bug is that we missed a dependency that is needed for Qt 6 to work. So you should try installing Qt 6 separately from https://www.qt.io/download (eg., get the open source version's Qt Online Installer), and see if that fixes the problem.
But you also mention trying to run ChimeraX by logging into a remote system running RHEL 8.6 from RHEL 7.9. Running ChimeraX remotely frequently fails to work. Officially, that is not supported. There are too many possible points of failure. It does work sometimes, and especially when the local and remote system are running the exact same version of Linux and have the exact same graphics driver installed. The graphics driver is the usual culprit, and that can be mitigated by running ChimeraX under VirtualGL on the remote system.
For completeness, if you are stuck with a RHEL 7 desktop, and your data is on your local system, you could run ChimeraX in a virtual machine. So instead of logging in via ssh, you startup the virtual machine, and login to it directly. Some virtual machines are better than others. I've been happy running different flavors of Linux on VMware Workstation Player on a Windows desktop with a Nvidia GeForce GTX 970 (remember to enable 3D graphics support). There is also a Linux version of VMware Workstation Player.
HTH,
Greg On 7/16/2022 6:04 PM, Steven Chou via ChimeraX-users wrote:
When I logined to RHEL8.6 from RHEL 7.9 using ssh, everything worked fine. Which subversion of RHEL 8 was used to compile ChimeraX 1.4? I may try the same version. Steven
On Sat, Jul 16, 2022 at 9:01 PM Steven Chou <stevezchou@gmail.com> wrote:
Dear ChimeraX developers,
I installed ChimeraX 1.4 (both stable release and daily built) on RHEL 8.6 and 9.0.
I installed all the ChimeraX 1.4 dependencies using "yum install" from RHEL installation USB.
After the installation, I was able to start the GUI, but unable to click any button on the GUI, therefore, I was unable to report the bug from the GUI either.
I also tried ChimeraX 1.3 stable release on RHEL 8.6, and everything was normal.
Steven
-- Steven Chou
-- Steven Chou
_______________________________________________ ChimeraX-users mailing listChimeraX-users@cgl.ucsf.edu Manage subscription:https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Steven Chou
I was able to ssh -XY into a Rocky 9 (RHEL 9) system, run chimerax, have it display on my local system and the GUI works. So it can work. So there is something incompatible between your two systems that you need to figure out. I'd recommend eliminating the graphics driver being incompatible issue by using VirtualGL. And if that doesn't fix it, use your daily build on RHEL 7, to file a bug. And describe the problem in the Description section. You should also include information about the remote system, specifically to the OS and version, and which graphics card it has and the driver version. -- Greg On 7/17/2022 5:24 AM, Steve Chou wrote:
Hi Greg,
Thank you so much for your detailed explanation!
I tried ChimeraX 1.4 (both the latest stable release and daily build) on RHEL 8.1, 8.6, and 9.0, because it can only be installed on RHEL 8 or 9. They all had the same problem (frozen after launching the GUI).
I also had an old daily build (04/12/2022) of version 1.4, which allowed me to install it on RHEL7.9, but not RHEL 8 or 9. I'm running v1.4 (04/12/2022) on RHEL7.9 now because the helix cylinder functionality is only available in v1.4.
All the best, Steven
On Sun, Jul 17, 2022 at 2:44 AM Greg Couch <gregc@cgl.ucsf.edu> wrote:
ChimeraX was compiled on "CentOS Linux release 8.5.2111", but that is extremely unlikely to matter.
The main GUI change between ChimeraX 1.4 and 1.3 is that ChimeraX 1.3 uses Qt 5 and ChimeraX 1.4 uses Qt 6. So, from your original description, the most likely bug is that we missed a dependency that is needed for Qt 6 to work. So you should try installing Qt 6 separately from https://www.qt.io/download (eg., get the open source version's Qt Online Installer), and see if that fixes the problem.
But you also mention trying to run ChimeraX by logging into a remote system running RHEL 8.6 from RHEL 7.9. Running ChimeraX remotely frequently fails to work. Officially, that is not supported. There are too many possible points of failure. It does work sometimes, and especially when the local and remote system are running the exact same version of Linux and have the exact same graphics driver installed. The graphics driver is the usual culprit, and that can be mitigated by running ChimeraX under VirtualGL on the remote system.
For completeness, if you are stuck with a RHEL 7 desktop, and your data is on your local system, you could run ChimeraX in a virtual machine. So instead of logging in via ssh, you startup the virtual machine, and login to it directly. Some virtual machines are better than others. I've been happy running different flavors of Linux on VMware Workstation Player on a Windows desktop with a Nvidia GeForce GTX 970 (remember to enable 3D graphics support). There is also a Linux version of VMware Workstation Player.
HTH,
Greg
On 7/16/2022 6:04 PM, Steven Chou via ChimeraX-users wrote:
When I logined to RHEL8.6 from RHEL 7.9 using ssh, everything worked fine. Which subversion of RHEL 8 was used to compile ChimeraX 1.4? I may try the same version. Steven
On Sat, Jul 16, 2022 at 9:01 PM Steven Chou <stevezchou@gmail.com> wrote:
Dear ChimeraX developers,
I installed ChimeraX 1.4 (both stable release and daily built) on RHEL 8.6 and 9.0.
I installed all the ChimeraX 1.4 dependencies using "yum install" from RHEL installation USB.
After the installation, I was able to start the GUI, but unable to click any button on the GUI, therefore, I was unable to report the bug from the GUI either.
I also tried ChimeraX 1.3 stable release on RHEL 8.6, and everything was normal.
Steven
-- Steven Chou
-- Steven Chou
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Steven Chou
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Greg Couch -
Steve Chou -
Steven Chou