GLX, (xserver-)xorg(-dev), and nvidia-driver under jessie(-backports)
I have installed jessie. Among other packages installed, I have
apt-get -y install gnome
apt-get -y install xorg
apt-get -y install xserver-xorg-dev
apt-get -y install afni
apt-get -y -t jessie-backports install nvidia-driver
apt-get -y -t jessie-backports install nvidia-cuda-toolkit
I installed skype with:
# https://wiki.debian.org/skype#Debian_7_.22Wheezy.22
# wget -O /tmp/usb/skype-install.deb http://www.skype.com/go/getskype-linux-deb
dpkg --add-architecture i386
apt-get update
dpkg -i /tmp/usb/skype-install.deb
apt-get -y -f install
apt-get clean
There appear to be two (possibly related) problems with GLX. One is that I run
xvfb-run \
--auto-servernum \
--server-num=20 \
-s "-screen 0 1024x768x24 -ac +extension GLX +render -noreset" \
align_epi_anat.py ...
This used to work under wheezy. Now I get.
3dSkullStrip -orig_vol -input ./__tt_subject01-anat+orig -prefix ./__tt_subject01-anat_ns
Xlib: extension "GLX" missing on display ":20".
freeglut (3dSkullStrip): OpenGL GLX extension not supported by display ':20'
** ERROR: Could not strip skull
** ERROR - script failed
The second is that I run
qobi@tlamachilistli>ldd `which skype`|fgrep not
libGL.so.1 => not found
libGL.so.1 => not found
qobi@tlamachilistli>
Despite the fact that the problems manifest when running 3dSkullStrip (afni)
and skype, I believe that the problems do not lie in those packages. They lie
in the way that nvidia-driver changes the alternatives for xorg and
xserver-xorg-dev.
Note that I did not manually select alternatives. All I did was the above
apt-get and dpkg commands.
Any suggestions for how to properly fix would be appreciated.
Jeff (http://engineering.purdue.edu/~qobi)
--------------------------------------------------------------------------------
qobi@tlamachilistli>ls -l /usr/lib/x86_64-linux-gnu/libGL.so
lrwxrwxrwx 1 root root 48 Jun 16 16:16 /usr/lib/x86_64-linux-gnu/libGL.so -> /etc/alternatives/glx--libGL.so-x86_64-linux-gnu
qobi@tlamachilistli>ls -l /etc/alternatives/glx--libGL.so-x86_64-linux-gnu
lrwxrwxrwx 1 root root 48 Jun 16 16:16 /etc/alternatives/glx--libGL.so-x86_64-linux-gnu -> /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so
qobi@tlamachilistli>ls -l /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so
lrwxrwxrwx 1 root root 10 Jun 16 16:16 /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so -> libGL.so.1
qobi@tlamachilistli>ls -l /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so.1
lrwxrwxrwx 1 root root 14 Aug 19 2015 /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so.1 -> libGL.so.1.2.0
qobi@tlamachilistli>ls -l /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so.1.2.0
-rw-r--r-- 1 root root 627320 Aug 19 2015 /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so.1.2.0
qobi@tlamachilistli>ls -l /usr/lib/mesa-diverted/i386-linux-gnu/libGL.so.1
lrwxrwxrwx 1 root root 14 Aug 19 2015 /usr/lib/mesa-diverted/i386-linux-gnu/libGL.so.1 -> libGL.so.1.2.0
qobi@tlamachilistli>ls -l /usr/lib/mesa-diverted/i386-linux-gnu/libGL.so.1.2.0
-rw-r--r-- 1 root root 695836 Aug 19 2015 /usr/lib/mesa-diverted/i386-linux-gnu/libGL.so.1.2.0
qobi@tlamachilistli>ls -l /usr/lib/mesa-diverted/libGL.so-master
lrwxrwxrwx 1 root root 33 Jun 16 16:16 /usr/lib/mesa-diverted/libGL.so-master -> /etc/alternatives/libGL.so-master/
qobi@tlamachilistli>ls -l /etc/alternatives/libGL.so-master/
total 12
drwxr-xr-x 2 root root 4096 Apr 19 17:54 arm-linux-gnueabihf/
drwxr-xr-x 2 root root 4096 Jun 16 16:23 i386-linux-gnu/
lrwxrwxrwx 1 root root 33 Jun 16 16:16 libGL.so-master -> /etc/alternatives/libGL.so-master/
drwxr-xr-x 2 root root 4096 Jun 16 16:16 x86_64-linux-gnu/
qobi@tlamachilistli>ls -l /usr/lib/x86_64-linux-gnu/libGL.so
lrwxrwxrwx 1 root root 48 Jun 16 16:16 /usr/lib/x86_64-linux-gnu/libGL.so -> /etc/alternatives/glx--libGL.so-x86_64-linux-gnu
qobi@tlamachilistli>ls -l /etc/alternatives/glx--libGL.so-x86_64-linux-gnu
lrwxrwxrwx 1 root root 48 Jun 16 16:16 /etc/alternatives/glx--libGL.so-x86_64-linux-gnu -> /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so
qobi@tlamachilistli>ls -l /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so
lrwxrwxrwx 1 root root 10 Jun 16 16:16 /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so -> libGL.so.1
qobi@tlamachilistli>ls -l /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so.1
lrwxrwxrwx 1 root root 14 Aug 19 2015 /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so.1 -> libGL.so.1.2.0
qobi@tlamachilistli>ls -l /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so.1.2.0
-rw-r--r-- 1 root root 627320 Aug 19 2015 /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so.1.2.0
qobi@tlamachilistli>ls -l /usr/lib/x86_64-linux-gnu/nvidia/libGL.so.1
lrwxrwxrwx 1 root root 53 Jun 16 16:16 /usr/lib/x86_64-linux-gnu/nvidia/libGL.so.1 -> /etc/alternatives/nvidia--libGL.so.1-x86_64-linux-gnu
qobi@tlamachilistli>ls -l /etc/alternatives/nvidia--libGL.so.1-x86_64-linux-gnu
lrwxrwxrwx 1 root root 51 Jun 16 16:19 /etc/alternatives/nvidia--libGL.so.1-x86_64-linux-gnu -> /usr/lib/x86_64-linux-gnu/nvidia/current/libGL.so.1
qobi@tlamachilistli>ls -l /usr/lib/x86_64-linux-gnu/nvidia/current/libGL.so.1
lrwxrwxrwx 1 root root 15 Feb 2 08:53 /usr/lib/x86_64-linux-gnu/nvidia/current/libGL.so.1 -> libGL.so.352.79
qobi@tlamachilistli>ls -l /usr/lib/x86_64-linux-gnu/nvidia/current/libGL.so.352.79
-rw-r--r-- 1 root root 1218248 Jan 13 2016 /usr/lib/x86_64-linux-gnu/nvidia/current/libGL.so.352.79
qobi@tlamachilistli>ls -l /usr/lib/x86_64-linux-gnu/libGL.so.1
lrwxrwxrwx 1 root root 50 Jun 16 16:16 /usr/lib/x86_64-linux-gnu/libGL.so.1 -> /etc/alternatives/glx--libGL.so.1-x86_64-linux-gnu
qobi@tlamachilistli>ls -l /etc/alternatives/glx--libGL.so.1-x86_64-linux-gnu
lrwxrwxrwx 1 root root 43 Jun 16 16:17 /etc/alternatives/glx--libGL.so.1-x86_64-linux-gnu -> /usr/lib/x86_64-linux-gnu/nvidia/libGL.so.1
qobi@tlamachilistli>ls -l /usr/lib/x86_64-linux-gnu/nvidia/libGL.so.1
lrwxrwxrwx 1 root root 53 Jun 16 16:16 /usr/lib/x86_64-linux-gnu/nvidia/libGL.so.1 -> /etc/alternatives/nvidia--libGL.so.1-x86_64-linux-gnu
qobi@tlamachilistli>ls -l /etc/alternatives/nvidia--libGL.so.1-x86_64-linux-gnu
lrwxrwxrwx 1 root root 51 Jun 16 16:19 /etc/alternatives/nvidia--libGL.so.1-x86_64-linux-gnu -> /usr/lib/x86_64-linux-gnu/nvidia/current/libGL.so.1
qobi@tlamachilistli>ls -l /usr/lib/x86_64-linux-gnu/nvidia/current/libGL.so.1
lrwxrwxrwx 1 root root 15 Feb 2 08:53 /usr/lib/x86_64-linux-gnu/nvidia/current/libGL.so.1 -> libGL.so.352.79
qobi@tlamachilistli>ls -l /usr/lib/x86_64-linux-gnu/nvidia/current/libGL.so.352.79
-rw-r--r-- 1 root root 1218248 Jan 13 2016 /usr/lib/x86_64-linux-gnu/nvidia/current/libGL.so.352.79
qobi@tlamachilistli>dpkg --get-selections '*' | fgrep xauth
xauth install
qobi@tlamachilistli>dpkg --get-selections '*' | fgrep libgl1-mesa-dri
libgl1-mesa-dri:amd64 install
libgl1-mesa-dri:i386 install
qobi@tlamachilistli>dpkg --get-selections '*' | fgrep mesa-utils
mesa-utils install
qobi@tlamachilistli>dpkg --get-selections '*' | fgrep libjpeg
libjpeg-dev install
libjpeg-turbo-progs install
libjpeg62-turbo:amd64 install
libjpeg62-turbo:i386 install
libjpeg62-turbo-dev:amd64 install
qobi@tlamachilistli>dpkg --get-selections '*'|fgrep glx
glx-alternative-mesa install
glx-alternative-nvidia install
glx-diversions install
libgl1-mesa-glx:amd64 install
libgl1-mesa-glx:i386 install
libgl1-nvidia-glx:amd64 install
libxcb-glx0:amd64 install
libxcb-glx0:i386 install
libxcb-glx0-dev:amd64 install
update-glx install
qobi@tlamachilistli>update-alternatives --list glx
/usr/lib/mesa-diverted
/usr/lib/nvidia
/usr/lib/nvidia/bumblebee
qobi@tlamachilistli>update-alternatives --query glx
Name: glx
Link: /usr/lib/glx
Slaves:
glx--libEGL.so.1-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/libEGL.so.1
glx--libGL.so.1-i386-linux-gnu /usr/lib/i386-linux-gnu/libGL.so.1
glx--libGL.so.1-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/libGL.so.1
glx--libGLESv1_CM.so.1-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/libGLESv1_CM.so.1
glx--libGLESv2.so.2-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/libGLESv2.so.2
glx--libnvidia-cfg.so.1-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/libnvidia-cfg.so.1
glx--linux-libglx.so /usr/lib/xorg/modules/linux/libglx.so
glx--nvidia-blacklists-nouveau.conf /etc/modprobe.d/nvidia-blacklists-nouveau.conf
glx--nvidia-bug-report.sh /usr/bin/nvidia-bug-report.sh
glx--nvidia-drm-outputclass.conf /usr/share/X11/xorg.conf.d/nvidia-drm-outputclass.conf
glx--nvidia-load.conf /etc/modules-load.d/nvidia.conf
glx--nvidia-modprobe.conf /etc/modprobe.d/nvidia.conf
glx--nvidia_drv.so /usr/lib/xorg/modules/drivers/nvidia_drv.so
Status: auto
Best: /usr/lib/nvidia
Value: /usr/lib/nvidia
Alternative: /usr/lib/mesa-diverted
Priority: 5
Slaves:
glx--libEGL.so.1-x86_64-linux-gnu /usr/lib/mesa-diverted/x86_64-linux-gnu/libEGL.so.1
glx--libGL.so.1-i386-linux-gnu /usr/lib/mesa-diverted/i386-linux-gnu/libGL.so.1
glx--libGL.so.1-x86_64-linux-gnu /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so.1
glx--libGLESv1_CM.so.1-x86_64-linux-gnu /usr/lib/mesa-diverted/x86_64-linux-gnu/libGLESv1_CM.so.1
glx--libGLESv2.so.2-x86_64-linux-gnu /usr/lib/mesa-diverted/x86_64-linux-gnu/libGLESv2.so.2
Alternative: /usr/lib/nvidia
Priority: 100
Slaves:
glx--libEGL.so.1-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/nvidia/libEGL.so.1
glx--libGL.so.1-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/nvidia/libGL.so.1
glx--libGLESv1_CM.so.1-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/nvidia/libGLESv1_CM.so.1
glx--libGLESv2.so.2-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/nvidia/libGLESv2.so.2
glx--libnvidia-cfg.so.1-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/nvidia/libnvidia-cfg.so.1
glx--linux-libglx.so /usr/lib/nvidia/libglx.so
glx--nvidia-blacklists-nouveau.conf /etc/nvidia/nvidia-blacklists-nouveau.conf
glx--nvidia-bug-report.sh /usr/lib/nvidia/nvidia-bug-report.sh
glx--nvidia-drm-outputclass.conf /etc/nvidia/nvidia-drm-outputclass.conf
glx--nvidia-load.conf /etc/nvidia/nvidia-load.conf
glx--nvidia-modprobe.conf /etc/nvidia/nvidia-modprobe.conf
glx--nvidia_drv.so /usr/lib/nvidia/nvidia_drv.so
Alternative: /usr/lib/nvidia/bumblebee
Priority: 95
Slaves:
glx--libEGL.so.1-x86_64-linux-gnu /usr/lib/mesa-diverted/x86_64-linux-gnu/libEGL.so.1
glx--libGL.so.1-x86_64-linux-gnu /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so.1
glx--libGLESv1_CM.so.1-x86_64-linux-gnu /usr/lib/mesa-diverted/x86_64-linux-gnu/libGLESv1_CM.so.1
glx--libGLESv2.so.2-x86_64-linux-gnu /usr/lib/mesa-diverted/x86_64-linux-gnu/libGLESv2.so.2
glx--nvidia-blacklists-nouveau.conf /etc/nvidia/nvidia-blacklists-nouveau.conf
glx--nvidia-bug-report.sh /usr/lib/nvidia/nvidia-bug-report.sh
glx--nvidia-modprobe.conf /etc/nvidia/nvidia-modprobe.conf
qobi@tlamachilistli>update-alternatives --display glx
glx - auto mode
link currently points to /usr/lib/nvidia
/usr/lib/mesa-diverted - priority 5
slave glx--libEGL.so.1-x86_64-linux-gnu: /usr/lib/mesa-diverted/x86_64-linux-gnu/libEGL.so.1
slave glx--libGL.so.1-i386-linux-gnu: /usr/lib/mesa-diverted/i386-linux-gnu/libGL.so.1
slave glx--libGL.so.1-x86_64-linux-gnu: /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so.1
slave glx--libGLESv1_CM.so.1-x86_64-linux-gnu: /usr/lib/mesa-diverted/x86_64-linux-gnu/libGLESv1_CM.so.1
slave glx--libGLESv2.so.2-x86_64-linux-gnu: /usr/lib/mesa-diverted/x86_64-linux-gnu/libGLESv2.so.2
/usr/lib/nvidia - priority 100
slave glx--libEGL.so.1-x86_64-linux-gnu: /usr/lib/x86_64-linux-gnu/nvidia/libEGL.so.1
slave glx--libGL.so.1-x86_64-linux-gnu: /usr/lib/x86_64-linux-gnu/nvidia/libGL.so.1
slave glx--libGLESv1_CM.so.1-x86_64-linux-gnu: /usr/lib/x86_64-linux-gnu/nvidia/libGLESv1_CM.so.1
slave glx--libGLESv2.so.2-x86_64-linux-gnu: /usr/lib/x86_64-linux-gnu/nvidia/libGLESv2.so.2
slave glx--libnvidia-cfg.so.1-x86_64-linux-gnu: /usr/lib/x86_64-linux-gnu/nvidia/libnvidia-cfg.so.1
slave glx--linux-libglx.so: /usr/lib/nvidia/libglx.so
slave glx--nvidia-blacklists-nouveau.conf: /etc/nvidia/nvidia-blacklists-nouveau.conf
slave glx--nvidia-bug-report.sh: /usr/lib/nvidia/nvidia-bug-report.sh
slave glx--nvidia-drm-outputclass.conf: /etc/nvidia/nvidia-drm-outputclass.conf
slave glx--nvidia-load.conf: /etc/nvidia/nvidia-load.conf
slave glx--nvidia-modprobe.conf: /etc/nvidia/nvidia-modprobe.conf
slave glx--nvidia_drv.so: /usr/lib/nvidia/nvidia_drv.so
/usr/lib/nvidia/bumblebee - priority 95
slave glx--libEGL.so.1-x86_64-linux-gnu: /usr/lib/mesa-diverted/x86_64-linux-gnu/libEGL.so.1
slave glx--libGL.so.1-x86_64-linux-gnu: /usr/lib/mesa-diverted/x86_64-linux-gnu/libGL.so.1
slave glx--libGLESv1_CM.so.1-x86_64-linux-gnu: /usr/lib/mesa-diverted/x86_64-linux-gnu/libGLESv1_CM.so.1
slave glx--libGLESv2.so.2-x86_64-linux-gnu: /usr/lib/mesa-diverted/x86_64-linux-gnu/libGLESv2.so.2
slave glx--nvidia-blacklists-nouveau.conf: /etc/nvidia/nvidia-blacklists-nouveau.conf
slave glx--nvidia-bug-report.sh: /usr/lib/nvidia/nvidia-bug-report.sh
slave glx--nvidia-modprobe.conf: /etc/nvidia/nvidia-modprobe.conf
Current 'best' version is '/usr/lib/nvidia'.
qobi@tlamachilistli>
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