[Chimera-users] Trying to get Chimera 1.13.1 working on RHEL 7.6
Darin Lory
darin.lory at gmail.com
Fri Apr 19 10:51:38 PDT 2019
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> 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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