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>
