In a RHEL 8 cluster I’m trying to use Singularity container that has mrview 3.0.4. I know about the Remote Display Issues, particularly with a Mac and XQuartz. I am using mesa r23.05.1 an mesa sdk 23.7.3 and loading as an environment module to attempt to work around the below errors. What environment variables are needed by mrview from mesa? So far I have:
set root /path/to/mesa/mesa-r23.05.1
prepend-path PATH $root/binary
setenv MESASDK_ROOT /path/to/mesa/sdk23.7.3/mesasdk
setenv OMP_NUM_THREADS 2
setenv MESA_DIR /path/to/mesa/mesa-r23.05.1
prepend-path PATH /path/to/mesa/sdk23.7.3/mesasdk/bin/
prepend-path MANPATH /path/to/mesa/sdk23.7.3/mesasdk/share/man/
setenv PGPLOT_DIR /path/to/mesa/sdk23.7.3/mesasdk/lib/pgplot
if { [ module-info mode load ] } {
system "source /path/to/mesa/sdk23.7.3/mesasdk/bin/mesasdk_init.sh"
}
Still getting the below ending with a seg fault:
singularity -v run --cleanenv --env DISPLAY=$DISPLAY,XDG_RUNTIME_DIR=$XDG_RUNTIME_DIR -B /run MRtrix3.sif mrview --debug
VERBOSE: Forwarding SINGULARITYENV_DISPLAY as DISPLAY environment variable
VERBOSE: Not forwarding SINGULARITY_TMPDIR environment variable
VERBOSE: Forwarding SINGULARITYENV_XDG_RUNTIME_DIR as XDG_RUNTIME_DIR environment variable
VERBOSE: Not forwarding SINGULARITY_BINDPATH environment variable
VERBOSE: Skipping XDG_RUNTIME_DIR environment variable, overridden by SINGULARITYENV_XDG_RUNTIME_DIR
VERBOSE: Setting HOME=/burg/home/rk3199
VERBOSE: Setting PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
VERBOSE: Set messagelevel to: 4
VERBOSE: Starter initialization
VERBOSE: Check if we are running as setuid
VERBOSE: Drop root privileges
VERBOSE: Drop root privileges permanently
VERBOSE: Spawn stage 1
VERBOSE: Execute stage 1
VERBOSE: stage 1 exited with status 0
VERBOSE: Get root privileges
VERBOSE: Change filesystem uid to xxx
VERBOSE: Spawn master process
VERBOSE: Create mount namespace
VERBOSE: Entering in mount namespace
VERBOSE: Create mount namespace
VERBOSE: Spawn RPC server
VERBOSE: Execute master process
VERBOSE: Serve RPC requests
VERBOSE: Default mount: /proc:/proc
VERBOSE: Default mount: /sys:/sys
VERBOSE: Default mount: /dev:/dev
VERBOSE: Found 'bind path' = /etc/localtime, /etc/localtime
VERBOSE: Found 'bind path' = /etc/hosts, /etc/hosts
VERBOSE: Default mount: /tmp:/tmp
VERBOSE: Default mount: /var/tmp:/var/tmp
VERBOSE: Default mount: /etc/resolv.conf:/etc/resolv.conf
VERBOSE: Checking for template passwd file: /path/o/singularity-3.7/var/singularity/mnt/session/rootfs/etc/passwd
VERBOSE: Creating passwd content
VERBOSE: Creating template passwd file and appending user data: /path/to/singularity-3.7/var/singularity/mnt/session/rootfs/etc/passwd
VERBOSE: Default mount: /etc/passwd:/etc/passwd
VERBOSE: Checking for template group file: /path.to/singularity-3.7/var/singularity/mnt/session/rootfs/etc/group
VERBOSE: Creating group content
VERBOSE: Default mount: /etc/group:/etc/group
VERBOSE: /path/to/me found within container
VERBOSE: rpc server exited with status 0
VERBOSE: Execute stage 2
mrview: [DEBUG] No config file found at "/etc/mrtrix.conf"
mrview: [DEBUG] No config file found at "/path/to/me/.mrtrix.conf"
libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast
QOpenGLWidget: Failed to make context current
QOpenGLShaderProgram: could not create shader program
QOpenGLShader: could not create shader
Could not link shader program:
""
mrview: [SYSTEM FATAL CODE: SIGSEGV (11)] Segmentation fault: Invalid memory access