[Chimera-users] Trying to get Chimera 1.13.1 working on RHEL 7.6
Greg Couch
gregc at cgl.ucsf.edu
Mon Apr 22 15:30:08 PDT 2019
You really need to consult the documentation for AWS Workspace. For
example, see
https://aws.amazon.com/blogs/compute/deploying-4k-gpu-backed-linux-desktop-instance-on-aws/.
That information might be incomplete or out of date. I don't know, but
it should help you get your AWS Workspace properly configured.
HTH,
Greg
On 4/19/19 10:51 AM, Darin Lory wrote:
> Greg,
>
> Thank you very much for getting back to me.
>
> RHEL 7.6 server is an AWS EC2 p3xxxx/Tesla V100 GPUs with NVidia
> Toolkit 10.0 and NVIDIA Driver Version: 410.48.
>
> Also has the MesaGL stuff installed. Do you think it needs to be removed?
>
>
> REHL 7.6:
> $ glxinfo
> name of display: localhost:10.0
> X Error of failed request: BadValue (integer parameter out of range
> for operation)
> Major opcode of failed request: 149 (GLX)
> Minor opcode of failed request: 24 (X_GLXCreateNewContext)
> Value in failed request: 0x0
> Serial number of failed request: 19
> Current serial number in output stream: 20
>
> $ export LD_LIBRARY_PATH=/usr/local/cuda/lib64:${LD_LIBRARY_PATH}
> #added /usr/local/cuda/lib64 to LD_LIBRARY_PATH to see if that would
> make a difference. It didn't.
>
> $ glxinfo
> name of display: localhost:10.0
> X Error of failed request: BadValue (integer parameter out of range
> for operation)
> Major opcode of failed request: 149 (GLX)
> Minor opcode of failed request: 24 (X_GLXCreateNewContext)
> Value in failed request: 0x0
> Serial number of failed request: 19
> Current serial number in output stream: 20
>
> -Darin
>
>
> ++++++++++++++++++++
> ++++++++++++++++++++
>
> Amazon Workspace:
>
> # glxinfo | grep "OpenGL version"
> OpenGL version string: 2.1 Mesa 17.2.3
>
> glxinfo list is long...
>
> # glxinfo |wc -l
> 716
>
>
> # ls -l *GL*
> lrwxrwxrwx 1 root root 20 Sep 28 2018 libEGL_mesa.so.0 ->
> libEGL_mesa.so.0.0.0
> -rwxr-xr-x 1 root root 240200 Aug 2 2018 libEGL_mesa.so.0.0.0
> lrwxrwxrwx 1 root root 15 Sep 28 2018 libEGL.so.1 -> libEGL.so.1.0.0
> -rwxr-xr-x 1 root root 83952 Jul 30 2018 libEGL.so.1.0.0
> lrwxrwxrwx 1 root root 22 Sep 28 2018 libGLdispatch.so.0 ->
> libGLdispatch.so.0.0.0
> -rwxr-xr-x 1 root root 641176 Jul 30 2018 libGLdispatch.so.0.0.0
> lrwxrwxrwx 1 root root 21 Sep 28 2018 libGLESv1_CM.so.1 ->
> libGLESv1_CM.so.1.0.0
> -rwxr-xr-x 1 root root 45680 Jul 30 2018 libGLESv1_CM.so.1.0.0
> lrwxrwxrwx 1 root root 18 Sep 28 2018 libGLESv2.so.2 ->
> libGLESv2.so.2.0.0
> -rwxr-xr-x 1 root root 75136 Jul 30 2018 libGLESv2.so.2.0.0
> lrwxrwxrwx 1 root root 17 Sep 28 2018 libGLEW.so.1.10 ->
> libGLEW.so.1.10.0
> -rwxr-xr-x 1 root root 495032 Aug 2 2018 libGLEW.so.1.10.0
> lrwxrwxrwx 1 root root 14 Sep 28 2018 libGL.so.1 -> libGL.so.1.0.0
> -rwxr-xr-x 1 root root 582136 Jul 30 2018 libGL.so.1.0.0
> lrwxrwxrwx 1 root root 15 Sep 28 2018 libGLU.so.1 -> libGLU.so.1.3.1
> -rwxr-xr-x 1 root root 516208 Aug 18 2018 libGLU.so.1.3.1
> lrwxrwxrwx 1 root root 27 Sep 28 2018 libGLX_indirect.so.0 ->
> /usr/lib64/libGLX_mesa.so.0
> lrwxrwxrwx 1 root root 20 Sep 28 2018 libGLX_mesa.so.0 ->
> libGLX_mesa.so.0.0.0
> -rwxr-xr-x 1 root root 485096 Aug 2 2018 libGLX_mesa.so.0.0.0
> lrwxrwxrwx 1 root root 15 Sep 28 2018 libGLX.so.0 -> libGLX.so.0.0.0
> -rwxr-xr-x 1 root root 70776 Jul 30 2018 libGLX.so.0.0.0
> lrwxrwxrwx 1 root root 20 Sep 28 2018 libQtOpenGL.so.4 ->
> libQtOpenGL.so.4.8.5
> lrwxrwxrwx 1 root root 20 Sep 28 2018 libQtOpenGL.so.4.8 ->
> libQtOpenGL.so.4.8.5
> -rwxr-xr-x 1 root root 1060432 Aug 18 2018 libQtOpenGL.so.4.8.5
>
>
>
> On Thu, Apr 18, 2019 at 6:17 PM Greg Couch <gregc at cgl.ucsf.edu
> <mailto:gregc at cgl.ucsf.edu>> wrote:
>
> Chimera works best when it is running directly on your local
> computer. So you would ideally copy the data you want to
> visualize from the AWS Workspace (i.e, cloud) to your local disk
> to visualize it. Or, perhaps, you could use a program like sshfs
> to remotely mount your data. And on your local computer, if you
> have NVIDIA graphics, you should install the proprietary NVIDIA
> graphics driver; if you have AMD graphics, both the open source
> and the proprietary drivers should work; and if you have Intel
> graphics, your only choice is the open source driver.
>
> However, remotely displaying, like you are trying to do, should
> work if your local computer is running Linux. Since the AWS
> Workspace has open source drivers installed, you might need to
> switch your local graphics to the open source version. Or copy
> the libGL.so from your local computer, to the AWS Workspace. That
> is, the two drivers need to be compatible.
>
> In the AWS workspace, run the glxinfo problem to see what its
> OpenGL setup is like. glxinfo is in the glx-utils package.
>
> Good luck,
>
> Greg
>
> On 4/18/19 1:23 PM, Darin Lory wrote:
>> Dear ChimeraGurus,
>>
>> I'm trying to get Chimera 1.13.1 working on RHEL 7.6. I have it
>> working on Amazon Linux 2 in AWS Workspace.
>>
>> Does anybody know what the yum package dependencies are for REHL
>> or CentOS 7?
>>
>> Chimera is crashing after "initializing graphics" as per the
>> --debug command line option.
>>
>> I know that I had to do this to fix a few errors:
>>
>> yum install tkinter
>> yum install tk-devel
>> yum install libXScrnSaver
>> yum install mesa-libGL mesa-libGL-devel
>> yum install firefox
>>
>> Kindly advise.
>>
>> Best regards,
>>
>> -Darin
>>
>> on RHEL 7.6:
>> $ which chimera
>> /usr/local/bin/chimera
>> [s.darin.lory at ip-10-246-148-209 ~]$ chimera --debug
>> initializing general preferences
>> loading Tix
>> initializing graphics
>> X Error of failed request: BadValue (integer parameter out of
>> range for operation)
>> Major opcode of failed request: 149 (GLX)
>> Minor opcode of failed request: 3 (X_GLXCreateContext)
>> Value in failed request: 0x0
>> Serial number of failed request: 1439
>> Current serial number in output stream: 1440
>>
>> RHEL 7.6:
>>
>> $ cat /etc/redhat-release
>> Red Hat Enterprise Linux Server release 7.6 (Maipo)
>>
>> $ rpm -qa |grep mesa
>> mesa-libGLw-8.0.0-4.el7.x86_64
>> mesa-libGLw-devel-8.0.0-4.el7.x86_64
>> mesa-libGL-devel-18.0.5-4.el7_6.x86_64
>> mesa-libGLES-18.0.5-4.el7_6.x86_64
>> mesa-libGL-18.0.5-4.el7_6.x86_64
>> mesa-libGLU-9.0.0-4.el7.x86_64
>> mesa-libxatracker-18.0.5-3.el7.x86_64
>> mesa-dri-drivers-18.0.5-3.el7.x86_64
>> mesa-libEGL-18.0.5-4.el7_6.x86_64
>> mesa-libglapi-18.0.5-4.el7_6.x86_64
>> mesa-filesystem-18.0.5-3.el7.x86_64
>> mesa-libGLU-devel-9.0.0-4.el7.x86_64
>> mesa-libgbm-18.0.5-4.el7_6.x86_64
>> +++++++++++++++++++++++
>> $ rpm -qa |grep GL
>> mesa-libGLw-8.0.0-4.el7.x86_64
>> mesa-libGLw-devel-8.0.0-4.el7.x86_64
>> mesa-libGL-devel-18.0.5-4.el7_6.x86_64
>> ghc-GLUT-2.4.0.0-40.el7.x86_64
>> mesa-libGLES-18.0.5-4.el7_6.x86_64
>> ghc-OpenGL-devel-2.8.0.0-40.el7.x86_64
>> mesa-libGL-18.0.5-4.el7_6.x86_64
>> mesa-libGLU-9.0.0-4.el7.x86_64
>> mesa-libEGL-18.0.5-4.el7_6.x86_64
>> ghc-OpenGLRaw-1.3.0.0-40.el7.x86_64
>> ghc-GLURaw-devel-1.3.0.0-40.el7.x86_64
>> ghc-GLURaw-1.3.0.0-40.el7.x86_64
>> ghc-OpenGL-2.8.0.0-40.el7.x86_64
>> ghc-OpenGLRaw-devel-1.3.0.0-40.el7.x86_64
>> ghc-GLUT-devel-2.4.0.0-40.el7.x86_64
>> mesa-libGLU-devel-9.0.0-4.el7.x86_64
>> +++++++++++++++++++++++
>> $ rpm -qa |grep tk
>> gtk-update-icon-cache-3.22.30-3.el7.x86_64
>> libreport-gtk-2.1.11-42.el7.x86_64
>> webkitgtk4-2.20.5-1.el7.x86_64
>> atk-2.28.1-1.el7.x86_64
>> gtk2-2.24.31-1.el7.x86_64
>> gtk3-3.22.30-3.el7.x86_64
>> webkitgtk4-jsc-2.20.5-1.el7.x86_64
>> tk-8.5.13-6.el7.x86_64
>> libpeas-gtk-1.22.0-1.el7.x86_64
>> webkitgtk3-2.4.11-2.el7.x86_64
>> webkitgtk4-plugin-process-gtk2-2.20.5-1.el7.x86_64
>> tk-devel-8.5.13-6.el7.x86_64
>> gtksourceview3-3.24.8-1.el7.x86_64
>> adwaita-gtk2-theme-3.28-2.el7.x86_64
>> at-spi2-atk-2.26.2-1.el7.x86_64
>> tkinter-2.7.5-77.el7_6.x86_64
>>
>>
>> Amazon Linux 2:
>>
>> on Amazon Linux 2:
>>
>> $ chimera --debug
>> initializing general preferences
>> loading Tix
>> initializing graphics
>> create application
>> loading Pmw
>> creating main window
>> creating menus
>> creating toolbar
>> creating viewer
>> initializing OpenGL
>> initializing preferences
>> initializing dialogs
>> initializing COM
>> initializing extensions
>>
>> $cat /etc/os-release
>> NAME="Amazon Linux"
>> VERSION="2"
>> ID="amzn"
>> ID_LIKE="centos rhel fedora"
>> VERSION_ID="2"
>> PRETTY_NAME="Amazon Linux 2"
>> ANSI_COLOR="0;33"
>> CPE_NAME="cpe:2.3:o:amazon:amazon_linux:2"
>> HOME_URL="https://amazonlinux.com/"
>>
>> $ uname -a
>> Linux xxxxxxx 4.14.106-97.85.amzn2.x86_64 #1 SMP Fri Mar 15
>> 17:07:54 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>>
>> $ rpm -qa |grep mesa
>> mesa-libEGL-17.2.3-8.20171019.amzn2.0.4.x86_64
>> mesa-libGL-17.2.3-8.20171019.amzn2.0.4.x86_64
>> mesa-private-llvm-3.9.1-3.amzn2.0.2.x86_64
>> mesa-libglapi-17.2.3-8.20171019.amzn2.0.4.x86_64
>> mesa-dri-drivers-17.2.3-8.20171019.amzn2.0.4.x86_64
>> mesa-libgbm-17.2.3-8.20171019.amzn2.0.4.x86_64
>> mesa-libwayland-egl-17.2.3-8.20171019.amzn2.0.4.x86_64
>> mesa-libGLU-9.0.0-4.amzn2.0.2.x86_64
>> mesa-filesystem-17.2.3-8.20171019.amzn2.0.4.x86_64
>> +++++++++++++++++++++++
>> $ rpm -qa |grep GL
>> mesa-libEGL-17.2.3-8.20171019.amzn2.0.4.x86_64
>> mesa-libGL-17.2.3-8.20171019.amzn2.0.4.x86_64
>> libGLEW-1.10.0-5.amzn2.0.2.x86_64
>> mesa-libGLU-9.0.0-4.amzn2.0.2.x86_64
>> +++++++++++++++++++++++
>> $ rpm -qa |grep tk
>> gtk2-2.24.31-1.amzn2.0.2.x86_64
>> pinentry-gtk-0.8.1-17.amzn2.0.2.x86_64
>> webkitgtk4-jsc-2.14.7-3.amzn2.0.1.x86_64
>> ibus-gtk3-1.5.17-2.amzn2.x86_64
>> libappindicator-gtk3-12.10.0-13.amzn2.0.1.x86_64
>> xdg-user-dirs-gtk-0.10-4.amzn2.0.1.x86_64
>> fltk-1.3.4-1.amzn2.0.2.x86_64
>> gtkspell3-3.0.3-4.amzn2.0.2.x86_64
>> gtk-murrine-engine-0.98.2-13.amzn2.x86_64
>> libdbusmenu-gtk2-16.04.0-4.amzn2.0.1.x86_64
>> gtk3-3.22.26-4.amzn2.x86_64
>> rtkit-0.11-10.amzn2.0.1.x86_64
>> gtk-update-icon-cache-3.22.26-4.amzn2.x86_64
>> libreoffice-gtk3-5.3.6.1-19.amzn2.0.1.x86_64
>> adwaita-gtk2-theme-3.22.2-2.amzn2.x86_64
>> tk-8.5.13-6.amzn2.0.2.x86_64
>> libcanberra-gtk3-0.30-5.amzn2.0.2.x86_64
>> libdbusmenu-gtk3-16.04.0-4.amzn2.0.1.x86_64
>> libpeas-gtk-1.20.0-1.amzn2.0.2.x86_64
>> tk-devel-8.5.13-6.amzn2.0.2.x86_64
>> gtk2-engines-2.20.2-14.amzn2.x86_64
>> gtksourceview2-2.11.2-24.amzn2.x86_64
>> libreoffice-gtk2-5.3.6.1-19.amzn2.0.1.x86_64
>> gtkspell-2.0.16-8.amzn2.0.2.x86_64
>> webkitgtk4-plugin-process-gtk2-2.14.7-3.amzn2.0.1.x86_64
>> ibus-gtk2-1.5.17-2.amzn2.x86_64
>> pygtk2-2.24.0-9.amzn2.0.2.x86_64
>> atk-2.22.0-3.amzn2.0.2.x86_64
>> at-spi2-atk-2.22.0-2.amzn2.0.2.x86_64
>> gstreamer1-plugins-bad-free-gtk-1.10.4-3.amzn2.x86_64
>> gtksourceview3-3.22.2-1.amzn2.0.2.x86_64
>> pygtksourceview-2.10.1-16.amzn2.x86_64
>> atkmm-2.24.2-1.amzn2.0.2.x86_64
>> webkitgtk4-2.14.7-3.amzn2.0.1.x86_64
>> libindicator-gtk3-12.10.1-6.amzn2.0.1.x86_64
>> gtkmm30-3.22.2-1.amzn2.x86_64
>>
>> -Darin
>>
>> "The most exciting phrase to hear in science, the one that
>> heralds new discoveries, is not 'Eureka!' (I found it!) but
>> 'That's funny ...'" -Issac Asimov
>>
>>
>> _______________________________________________
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>
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