Install ChimeraX on Linux without sudo
Dear ChimeraX Team, The install notes for all the current distributions for the Linx system require sudo. I wonder is it possible without sudo? On Rocky Linux VERSION 9.4 (Blue Onyx), I tried the following. $ flatpak --user install ChimeraX-1.8.flatpak error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires the runtime org.freedesktop.Platform/x86_64/23.08 which was not found $ rpm -ivh ucsf-chimerax-1.8-1.el9.x86_64.rpm error: Failed dependencies: fftw-libs-single is needed by ucsf-chimerax-1.8-1.el9.x86_64 mesa-libOSMesa is needed by ucsf-chimerax-1.8-1.el9.x86_64 sqlite is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-cursor is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-image is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-keysyms is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-renderutil is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-wm is needed by ucsf-chimerax-1.8-1.el9.x86_64 Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
As noted in the flatpak instructions, you need to configure the per-user flathub repository first. That way the correct runtime will be installed when installing ChimeraX. So do:
flatpak remote-add --user --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo then do:
flatpak install --user ChimeraX.flatpak I'll rework the instructions to make that more obvious.
HTH, Greg On 7/8/24 03:49, Roden Deng Luo via ChimeraX-users wrote:
Dear ChimeraX Team,
The install notes for all the current distributions for the Linx system require sudo. I wonder is it possible without sudo?
On Rocky Linux VERSION 9.4 (Blue Onyx), I tried the following.
$ flatpak --user install ChimeraX-1.8.flatpak error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires the runtime org.freedesktop.Platform/x86_64/23.08 which was not found
$ rpm -ivh ucsf-chimerax-1.8-1.el9.x86_64.rpm error: Failed dependencies: fftw-libs-single is needed by ucsf-chimerax-1.8-1.el9.x86_64 mesa-libOSMesa is needed by ucsf-chimerax-1.8-1.el9.x86_64 sqlite is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-cursor is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-image is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-keysyms is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-renderutil is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-wm is needed by ucsf-chimerax-1.8-1.el9.x86_64
Thanks, Roden
Hi Greg, Thanks very much! Following the instructions, I did get ChimeraX installed. (This might be a global setting for flatpak that I am not aware of. I am a first-time user of Flatpak.) On the website, there is the following command for running. flatpak run edu.ucsf.rbvi.Chimerax The last character should be capitalized in my case. And I need to add "--user" for non-sudo. ======= The part below might go beyond your support. But if you do have some hints, please kindly let me know. After I corrected the naming, I still got errors, and the graphics did not look correct (attached). I was running the command in a NICE EnginFrame Views ( https://www.ni-sp.com/products/enginframe-views/) environment. (base) [luod@rsws06 ~]$ flatpak run edu.ucsf.rbvi.Chimerax error: While opening repository /var/lib/flatpak/repo: opening repo: opendir(/var/lib/flatpak/repo): No such file or directory (base) [luod@rsws06 ~]$ flatpak run edu.ucsf.rbvi.ChimeraX error: While opening repository /var/lib/flatpak/repo: opening repo: opendir(/var/lib/flatpak/repo): No such file or directory (base) [luod@rsws06 ~]$ flatpak run --user edu.ucsf.rbvi.Chimerax error: app/edu.ucsf.rbvi.Chimerax/x86_64/master not installed (base) [luod@rsws06 ~]$ flatpak run --user edu.ucsf.rbvi.ChimeraX F: Can't get document portal: GDBus.Error:org.freedesktop.DBus.Error.NoReply: Message recipient disconnected from message bus without replying NOTE: available bundle cache has not been initialized yet WARNING: WebEngineContext is used before QtWebEngineQuick::initialize() or OpenGL context creation failed. WARNING: QGLXContext: Failed to create dummy context WARNING: QRhiGles2: Failed to create temporary context WARNING: QRhiGles2: Failed to create context WARNING: Failed to create QRhi for QBackingStoreRhiSupport ERROR: Could not create OpenGL context WARNING: QRhiGles2: Failed to create temporary context WARNING: QRhiGles2: Failed to create context WARNING: Failed to create QRhi for QBackingStoreRhiSupport WARNING: QQuickWidget: Failed to get a QRhi from the top-level widget's window WARNING: QQuickWidget::resizeEvent() no QRhi WARNING: QRhiGles2: Failed to create temporary context WARNING: QRhiGles2: Failed to create context WARNING: Failed to create QRhi for QBackingStoreRhiSupport WARNING: QQuickWidget: Failed to get a QRhi from the top-level widget's window Thanks, Roden On Tue, Jul 9, 2024 at 2:44 AM Greg Couch <gregc@cgl.ucsf.edu> wrote:
As noted in the flatpak instructions, you need to configure the per-user flathub repository first. That way the correct runtime will be installed when installing ChimeraX. So do:
flatpak remote-add --user --if-not-exists flathub
https://urldefense.com/v3/__https://dl.flathub.org/repo/flathub.flatpakrepo_... then do:
flatpak install --user ChimeraX.flatpak I'll rework the instructions to make that more obvious.
HTH,
Greg
On 7/8/24 03:49, Roden Deng Luo via ChimeraX-users wrote:
Dear ChimeraX Team,
The install notes for all the current distributions for the Linx system require sudo. I wonder is it possible without sudo?
On Rocky Linux VERSION 9.4 (Blue Onyx), I tried the following.
$ flatpak --user install ChimeraX-1.8.flatpak error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires the runtime org.freedesktop.Platform/x86_64/23.08 which was not found
$ rpm -ivh ucsf-chimerax-1.8-1.el9.x86_64.rpm error: Failed dependencies: fftw-libs-single is needed by ucsf-chimerax-1.8-1.el9.x86_64 mesa-libOSMesa is needed by ucsf-chimerax-1.8-1.el9.x86_64 sqlite is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-cursor is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-image is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-keysyms is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-renderutil is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-wm is needed by ucsf-chimerax-1.8-1.el9.x86_64
Thanks, Roden
-- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
Which web page has the typo in it? I'm only finding 'flatpak run ChimeraX'. Also, for 'flatpak run' you shouldn't need the --user option. In Flatpak 1.10, it is documented to look in the per-user and system locations, so it should find the user version first. Which version of flatpak are you using and on which version of Linux? And for the record, we do not support NICE EnginFrame Views Views. We expect ChimeraX to run directly on the computer with the graphics card. But Georg Kempf reported a workaround for NICE DCV in https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/.... Perhaps a similar fix will work for you? -- Greg On 7/9/2024 10:20 AM, Roden Deng Luo wrote:
Hi Greg,
Thanks very much! Following the instructions, I did get ChimeraX installed. (This might be a global setting for flatpak that I am not aware of. I am a first-time user of Flatpak.)
On the website, there is the following command for running.
flatpak run edu.ucsf.rbvi.Chimerax
The last character should be capitalized in my case. And I need to add "--user" for non-sudo.
======= The part below might go beyond your support. But if you do have some hints, please kindly let me know. After I corrected the naming, I still got errors, and the graphics did not look correct (attached). I was running the command in a NICE EnginFrame Views (https://www.ni-sp.com/products/enginframe-views/) environment.
(base) [luod@rsws06 ~]$ flatpak run edu.ucsf.rbvi.Chimerax error: While opening repository /var/lib/flatpak/repo: opening repo: opendir(/var/lib/flatpak/repo): No such file or directory (base) [luod@rsws06 ~]$ flatpak run edu.ucsf.rbvi.ChimeraX error: While opening repository /var/lib/flatpak/repo: opening repo: opendir(/var/lib/flatpak/repo): No such file or directory (base) [luod@rsws06 ~]$ flatpak run --user edu.ucsf.rbvi.Chimerax error: app/edu.ucsf.rbvi.Chimerax/x86_64/master not installed (base) [luod@rsws06 ~]$ flatpak run --user edu.ucsf.rbvi.ChimeraX F: Can't get document portal: GDBus.Error:org.freedesktop.DBus.Error.NoReply: Message recipient disconnected from message bus without replying NOTE: available bundle cache has not been initialized yet WARNING: WebEngineContext is used before QtWebEngineQuick::initialize() or OpenGL context creation failed. WARNING: QGLXContext: Failed to create dummy context WARNING: QRhiGles2: Failed to create temporary context WARNING: QRhiGles2: Failed to create context WARNING: Failed to create QRhi for QBackingStoreRhiSupport ERROR: Could not create OpenGL context WARNING: QRhiGles2: Failed to create temporary context WARNING: QRhiGles2: Failed to create context WARNING: Failed to create QRhi for QBackingStoreRhiSupport WARNING: QQuickWidget: Failed to get a QRhi from the top-level widget's window WARNING: QQuickWidget::resizeEvent() no QRhi WARNING: QRhiGles2: Failed to create temporary context WARNING: QRhiGles2: Failed to create context WARNING: Failed to create QRhi for QBackingStoreRhiSupport WARNING: QQuickWidget: Failed to get a QRhi from the top-level widget's window
Thanks, Roden
On Tue, Jul 9, 2024 at 2:44 AM Greg Couch <gregc@cgl.ucsf.edu> wrote:
As noted in the flatpak instructions, you need to configure the per-user flathub repository first. That way the correct runtime will be installed when installing ChimeraX. So do:
> flatpak remote-add --user --if-not-exists flathub > https://urldefense.com/v3/__https://dl.flathub.org/repo/flathub.flatpakrepo_...
then do:
> flatpak install --user ChimeraX.flatpak I'll rework the instructions to make that more obvious.
HTH,
Greg
On 7/8/24 03:49, Roden Deng Luo via ChimeraX-users wrote: > Dear ChimeraX Team, > > The install notes for all the current distributions for the Linx > system require sudo. I wonder is it possible without sudo? > > On Rocky Linux VERSION 9.4 (Blue Onyx), I tried the following. > > $ flatpak --user install ChimeraX-1.8.flatpak > error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires > the runtime org.freedesktop.Platform/x86_64/23.08 which was not found > > $ rpm -ivh ucsf-chimerax-1.8-1.el9.x86_64.rpm > error: Failed dependencies: > fftw-libs-single is needed by ucsf-chimerax-1.8-1.el9.x86_64 > mesa-libOSMesa is needed by ucsf-chimerax-1.8-1.el9.x86_64 > sqlite is needed by ucsf-chimerax-1.8-1.el9.x86_64 > xcb-util-cursor is needed by ucsf-chimerax-1.8-1.el9.x86_64 > xcb-util-image is needed by ucsf-chimerax-1.8-1.el9.x86_64 > xcb-util-keysyms is needed by ucsf-chimerax-1.8-1.el9.x86_64 > xcb-util-renderutil is needed by ucsf-chimerax-1.8-1.el9.x86_64 > xcb-util-wm is needed by ucsf-chimerax-1.8-1.el9.x86_64 > > Thanks, > Roden >
------------------------------------------------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
It is this page: https://www.cgl.ucsf.edu/chimerax/download.html (screenshot attached). I am using Flatpak 1.12.9 on Rocky Linux VERSION 9.4 (Blue Onyx). Thanks for the hints for NICE DCV. I have no write access to "/etc/dcv/dcv-gl.conf". I will try to find more local users for this environment and then try to escalate the installation or this issue to the admin people. Best, Roden On Wed, Jul 10, 2024 at 9:11 AM Greg Couch <gregc@cgl.ucsf.edu> wrote:
Which web page has the typo in it? I'm only finding 'flatpak run ChimeraX'. Also, for 'flatpak run' you shouldn't need the --user option. In Flatpak 1.10, it is documented to look in the per-user and system locations, so it should find the user version first. Which version of flatpak are you using and on which version of Linux?
And for the record, we do not support NICE EnginFrame Views Views. We expect ChimeraX to run directly on the computer with the graphics card. But Georg Kempf reported a workaround for NICE DCV in https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/... <https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/...>. Perhaps a similar fix will work for you?
-- Greg On 7/9/2024 10:20 AM, Roden Deng Luo wrote:
Hi Greg,
Thanks very much! Following the instructions, I did get ChimeraX installed. (This might be a global setting for flatpak that I am not aware of. I am a first-time user of Flatpak.)
On the website, there is the following command for running.
flatpak run edu.ucsf.rbvi.Chimerax
The last character should be capitalized in my case. And I need to add "--user" for non-sudo.
======= The part below might go beyond your support. But if you do have some hints, please kindly let me know. After I corrected the naming, I still got errors, and the graphics did not look correct (attached). I was running the command in a NICE EnginFrame Views ( https://www.ni-sp.com/products/enginframe-views/ <https://urldefense.com/v3/__https://www.ni-sp.com/products/enginframe-views/...>) environment.
(base) [luod@rsws06 ~]$ flatpak run edu.ucsf.rbvi.Chimerax error: While opening repository /var/lib/flatpak/repo: opening repo: opendir(/var/lib/flatpak/repo): No such file or directory (base) [luod@rsws06 ~]$ flatpak run edu.ucsf.rbvi.ChimeraX error: While opening repository /var/lib/flatpak/repo: opening repo: opendir(/var/lib/flatpak/repo): No such file or directory (base) [luod@rsws06 ~]$ flatpak run --user edu.ucsf.rbvi.Chimerax error: app/edu.ucsf.rbvi.Chimerax/x86_64/master not installed (base) [luod@rsws06 ~]$ flatpak run --user edu.ucsf.rbvi.ChimeraX F: Can't get document portal: GDBus.Error:org.freedesktop.DBus.Error.NoReply: Message recipient disconnected from message bus without replying NOTE: available bundle cache has not been initialized yet WARNING: WebEngineContext is used before QtWebEngineQuick::initialize() or OpenGL context creation failed. WARNING: QGLXContext: Failed to create dummy context WARNING: QRhiGles2: Failed to create temporary context WARNING: QRhiGles2: Failed to create context WARNING: Failed to create QRhi for QBackingStoreRhiSupport ERROR: Could not create OpenGL context WARNING: QRhiGles2: Failed to create temporary context WARNING: QRhiGles2: Failed to create context WARNING: Failed to create QRhi for QBackingStoreRhiSupport WARNING: QQuickWidget: Failed to get a QRhi from the top-level widget's window WARNING: QQuickWidget::resizeEvent() no QRhi WARNING: QRhiGles2: Failed to create temporary context WARNING: QRhiGles2: Failed to create context WARNING: Failed to create QRhi for QBackingStoreRhiSupport WARNING: QQuickWidget: Failed to get a QRhi from the top-level widget's window
Thanks, Roden
On Tue, Jul 9, 2024 at 2:44 AM Greg Couch <gregc@cgl.ucsf.edu> wrote:
As noted in the flatpak instructions, you need to configure the per-user flathub repository first. That way the correct runtime will be installed when installing ChimeraX. So do:
flatpak remote-add --user --if-not-exists flathub
https://urldefense.com/v3/__https://dl.flathub.org/repo/flathub.flatpakrepo_... then do:
flatpak install --user ChimeraX.flatpak I'll rework the instructions to make that more obvious.
HTH,
Greg
On 7/8/24 03:49, Roden Deng Luo via ChimeraX-users wrote:
Dear ChimeraX Team,
The install notes for all the current distributions for the Linx system require sudo. I wonder is it possible without sudo?
On Rocky Linux VERSION 9.4 (Blue Onyx), I tried the following.
$ flatpak --user install ChimeraX-1.8.flatpak error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires the runtime org.freedesktop.Platform/x86_64/23.08 which was not found
$ rpm -ivh ucsf-chimerax-1.8-1.el9.x86_64.rpm error: Failed dependencies: fftw-libs-single is needed by ucsf-chimerax-1.8-1.el9.x86_64 mesa-libOSMesa is needed by ucsf-chimerax-1.8-1.el9.x86_64 sqlite is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-cursor is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-image is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-keysyms is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-renderutil is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-wm is needed by ucsf-chimerax-1.8-1.el9.x86_64
Thanks, Roden
------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
-- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
Found the Chimerax. It wasn't directly in the download page, but in the per-release JSON data. If you have a NICE support contract, I'd recommend reporting the bug to them. With enough complaints, they might fix the underlying bug. -- Greg On 7/10/2024 1:35 AM, Roden Deng Luo wrote:
It is this page: https://www.cgl.ucsf.edu/chimerax/download.html (screenshot attached). I am using Flatpak 1.12.9 on Rocky Linux VERSION 9.4 (Blue Onyx).
Thanks for the hints for NICE DCV. I have no write access to "/etc/dcv/dcv-gl.conf". I will try to find more local users for this environment and then try to escalate the installation or this issue to the admin people.
Best, Roden
On Wed, Jul 10, 2024 at 9:11 AM Greg Couch <gregc@cgl.ucsf.edu> wrote:
Which web page has the typo in it? I'm only finding 'flatpak run ChimeraX'. Also, for 'flatpak run' you shouldn't need the --user option. In Flatpak 1.10, it is documented to look in the per-user and system locations, so it should find the user version first. Which version of flatpak are you using and on which version of Linux?
And for the record, we do not support NICE EnginFrame Views Views. We expect ChimeraX to run directly on the computer with the graphics card. But Georg Kempf reported a workaround for NICE DCV in https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/... <https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/...>. Perhaps a similar fix will work for you?
-- Greg
On 7/9/2024 10:20 AM, Roden Deng Luo wrote:
Hi Greg,
Thanks very much! Following the instructions, I did get ChimeraX installed. (This might be a global setting for flatpak that I am not aware of. I am a first-time user of Flatpak.)
On the website, there is the following command for running.
flatpak run edu.ucsf.rbvi.Chimerax
The last character should be capitalized in my case. And I need to add "--user" for non-sudo.
======= The part below might go beyond your support. But if you do have some hints, please kindly let me know. After I corrected the naming, I still got errors, and the graphics did not look correct (attached). I was running the command in a NICE EnginFrame Views (https://www.ni-sp.com/products/enginframe-views/ <https://urldefense.com/v3/__https://www.ni-sp.com/products/enginframe-views/...>) environment.
(base) [luod@rsws06 ~]$ flatpak run edu.ucsf.rbvi.Chimerax error: While opening repository /var/lib/flatpak/repo: opening repo: opendir(/var/lib/flatpak/repo): No such file or directory (base) [luod@rsws06 ~]$ flatpak run edu.ucsf.rbvi.ChimeraX error: While opening repository /var/lib/flatpak/repo: opening repo: opendir(/var/lib/flatpak/repo): No such file or directory (base) [luod@rsws06 ~]$ flatpak run --user edu.ucsf.rbvi.Chimerax error: app/edu.ucsf.rbvi.Chimerax/x86_64/master not installed (base) [luod@rsws06 ~]$ flatpak run --user edu.ucsf.rbvi.ChimeraX F: Can't get document portal: GDBus.Error:org.freedesktop.DBus.Error.NoReply: Message recipient disconnected from message bus without replying NOTE: available bundle cache has not been initialized yet WARNING: WebEngineContext is used before QtWebEngineQuick::initialize() or OpenGL context creation failed. WARNING: QGLXContext: Failed to create dummy context WARNING: QRhiGles2: Failed to create temporary context WARNING: QRhiGles2: Failed to create context WARNING: Failed to create QRhi for QBackingStoreRhiSupport ERROR: Could not create OpenGL context WARNING: QRhiGles2: Failed to create temporary context WARNING: QRhiGles2: Failed to create context WARNING: Failed to create QRhi for QBackingStoreRhiSupport WARNING: QQuickWidget: Failed to get a QRhi from the top-level widget's window WARNING: QQuickWidget::resizeEvent() no QRhi WARNING: QRhiGles2: Failed to create temporary context WARNING: QRhiGles2: Failed to create context WARNING: Failed to create QRhi for QBackingStoreRhiSupport WARNING: QQuickWidget: Failed to get a QRhi from the top-level widget's window
Thanks, Roden
On Tue, Jul 9, 2024 at 2:44 AM Greg Couch <gregc@cgl.ucsf.edu> wrote:
As noted in the flatpak instructions, you need to configure the per-user flathub repository first. That way the correct runtime will be installed when installing ChimeraX. So do:
> flatpak remote-add --user --if-not-exists flathub > https://urldefense.com/v3/__https://dl.flathub.org/repo/flathub.flatpakrepo_...
then do:
> flatpak install --user ChimeraX.flatpak I'll rework the instructions to make that more obvious.
HTH,
Greg
On 7/8/24 03:49, Roden Deng Luo via ChimeraX-users wrote: > Dear ChimeraX Team, > > The install notes for all the current distributions for the Linx > system require sudo. I wonder is it possible without sudo? > > On Rocky Linux VERSION 9.4 (Blue Onyx), I tried the following. > > $ flatpak --user install ChimeraX-1.8.flatpak > error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires > the runtime org.freedesktop.Platform/x86_64/23.08 which was not found > > $ rpm -ivh ucsf-chimerax-1.8-1.el9.x86_64.rpm > error: Failed dependencies: > fftw-libs-single is needed by ucsf-chimerax-1.8-1.el9.x86_64 > mesa-libOSMesa is needed by ucsf-chimerax-1.8-1.el9.x86_64 > sqlite is needed by ucsf-chimerax-1.8-1.el9.x86_64 > xcb-util-cursor is needed by ucsf-chimerax-1.8-1.el9.x86_64 > xcb-util-image is needed by ucsf-chimerax-1.8-1.el9.x86_64 > xcb-util-keysyms is needed by ucsf-chimerax-1.8-1.el9.x86_64 > xcb-util-renderutil is needed by ucsf-chimerax-1.8-1.el9.x86_64 > xcb-util-wm is needed by ucsf-chimerax-1.8-1.el9.x86_64 > > Thanks, > Roden >
------------------------------------------------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
------------------------------------------------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
Sure. Will post here if I get any updates. Thanks, Roden On Wed, Jul 10, 2024 at 7:15 PM Greg Couch <gregc@cgl.ucsf.edu> wrote:
Found the Chimerax. It wasn't directly in the download page, but in the per-release JSON data.
If you have a NICE support contract, I'd recommend reporting the bug to them. With enough complaints, they might fix the underlying bug.
-- Greg On 7/10/2024 1:35 AM, Roden Deng Luo wrote:
It is this page: https://www.cgl.ucsf.edu/chimerax/download.html <https://urldefense.com/v3/__https://www.cgl.ucsf.edu/chimerax/download.html_...> (screenshot attached). I am using Flatpak 1.12.9 on Rocky Linux VERSION 9.4 (Blue Onyx).
Thanks for the hints for NICE DCV. I have no write access to "/etc/dcv/dcv-gl.conf". I will try to find more local users for this environment and then try to escalate the installation or this issue to the admin people.
Best, Roden
On Wed, Jul 10, 2024 at 9:11 AM Greg Couch <gregc@cgl.ucsf.edu> wrote:
Which web page has the typo in it? I'm only finding 'flatpak run ChimeraX'. Also, for 'flatpak run' you shouldn't need the --user option. In Flatpak 1.10, it is documented to look in the per-user and system locations, so it should find the user version first. Which version of flatpak are you using and on which version of Linux?
And for the record, we do not support NICE EnginFrame Views Views. We expect ChimeraX to run directly on the computer with the graphics card. But Georg Kempf reported a workaround for NICE DCV in https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/... <https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/...>. Perhaps a similar fix will work for you?
-- Greg On 7/9/2024 10:20 AM, Roden Deng Luo wrote:
Hi Greg,
Thanks very much! Following the instructions, I did get ChimeraX installed. (This might be a global setting for flatpak that I am not aware of. I am a first-time user of Flatpak.)
On the website, there is the following command for running.
flatpak run edu.ucsf.rbvi.Chimerax
The last character should be capitalized in my case. And I need to add "--user" for non-sudo.
======= The part below might go beyond your support. But if you do have some hints, please kindly let me know. After I corrected the naming, I still got errors, and the graphics did not look correct (attached). I was running the command in a NICE EnginFrame Views ( https://www.ni-sp.com/products/enginframe-views/ <https://urldefense.com/v3/__https://www.ni-sp.com/products/enginframe-views/...>) environment.
(base) [luod@rsws06 ~]$ flatpak run edu.ucsf.rbvi.Chimerax error: While opening repository /var/lib/flatpak/repo: opening repo: opendir(/var/lib/flatpak/repo): No such file or directory (base) [luod@rsws06 ~]$ flatpak run edu.ucsf.rbvi.ChimeraX error: While opening repository /var/lib/flatpak/repo: opening repo: opendir(/var/lib/flatpak/repo): No such file or directory (base) [luod@rsws06 ~]$ flatpak run --user edu.ucsf.rbvi.Chimerax error: app/edu.ucsf.rbvi.Chimerax/x86_64/master not installed (base) [luod@rsws06 ~]$ flatpak run --user edu.ucsf.rbvi.ChimeraX F: Can't get document portal: GDBus.Error:org.freedesktop.DBus.Error.NoReply: Message recipient disconnected from message bus without replying NOTE: available bundle cache has not been initialized yet WARNING: WebEngineContext is used before QtWebEngineQuick::initialize() or OpenGL context creation failed. WARNING: QGLXContext: Failed to create dummy context WARNING: QRhiGles2: Failed to create temporary context WARNING: QRhiGles2: Failed to create context WARNING: Failed to create QRhi for QBackingStoreRhiSupport ERROR: Could not create OpenGL context WARNING: QRhiGles2: Failed to create temporary context WARNING: QRhiGles2: Failed to create context WARNING: Failed to create QRhi for QBackingStoreRhiSupport WARNING: QQuickWidget: Failed to get a QRhi from the top-level widget's window WARNING: QQuickWidget::resizeEvent() no QRhi WARNING: QRhiGles2: Failed to create temporary context WARNING: QRhiGles2: Failed to create context WARNING: Failed to create QRhi for QBackingStoreRhiSupport WARNING: QQuickWidget: Failed to get a QRhi from the top-level widget's window
Thanks, Roden
On Tue, Jul 9, 2024 at 2:44 AM Greg Couch <gregc@cgl.ucsf.edu> wrote:
As noted in the flatpak instructions, you need to configure the per-user flathub repository first. That way the correct runtime will be installed when installing ChimeraX. So do:
flatpak remote-add --user --if-not-exists flathub
https://urldefense.com/v3/__https://dl.flathub.org/repo/flathub.flatpakrepo_... then do:
flatpak install --user ChimeraX.flatpak I'll rework the instructions to make that more obvious.
HTH,
Greg
On 7/8/24 03:49, Roden Deng Luo via ChimeraX-users wrote:
Dear ChimeraX Team,
The install notes for all the current distributions for the Linx system require sudo. I wonder is it possible without sudo?
On Rocky Linux VERSION 9.4 (Blue Onyx), I tried the following.
$ flatpak --user install ChimeraX-1.8.flatpak error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires the runtime org.freedesktop.Platform/x86_64/23.08 which was not found
$ rpm -ivh ucsf-chimerax-1.8-1.el9.x86_64.rpm error: Failed dependencies: fftw-libs-single is needed by ucsf-chimerax-1.8-1.el9.x86_64 mesa-libOSMesa is needed by ucsf-chimerax-1.8-1.el9.x86_64 sqlite is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-cursor is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-image is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-keysyms is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-renderutil is needed by ucsf-chimerax-1.8-1.el9.x86_64 xcb-util-wm is needed by ucsf-chimerax-1.8-1.el9.x86_64
Thanks, Roden
------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
-- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
participants (2)
-
Greg Couch -
Roden Deng Luo