[Chimera-users] Trying to get Chimera 1.13.1 working on RHEL 7.6

Tue Apr 23 09:37:38 PDT 2019

Greg,

Looks like we have to copy the data or sshfs to the Amazon Workspace X11 is
the only X11 client that displays Chimera from a Linux server or get the
scientist a Linux workstation.

Macintosh XQuartz was what was crashing Chimera from my RHEL 7.6 EC2.

Chimera crashed MobaXterm on Windows when displaying from the RHEL 7.6 EC2
as well.

Thank you very much for all your help.

-Darin

On Thu, Apr 18, 2019 at 6:17 PM Greg Couch <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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