id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2593 Various graphics/install/toolshed problems jmholton@… Greg Couch "{{{ Hello, I've been trying to install ISOLDE on a CentOS 7 system.  I want all users to be able to execute it.  Having trouble with the chimerax install that I thought you might want to know about. I'm running as root because I want to install for all users. **[root@graphics1 install]#** inxi -CGM Machine:   Type: Server System: Supermicro product: Super Server v: 0123456789 serial: 0123456789            Mobo: Supermicro model: X11SRA-F v: 1.01 serial: UM17AS000306 UEFI [Legacy]: American Megatrends v: 1.0            date: 10/11/2017 CPU:       Topology: 10-Core model: Intel Xeon W-2155 bits: 64 type: MT MCP L2 cache: 13.8 MiB            Speed: 1297 MHz min/max: 1200/4500 MHz Core speeds (MHz): 1: 1297 2: 1259 3: 1200 4: 1238 5: 1200 6: 1200 7: 1235            8: 1200 9: 1222 10: 4491 11: 1206 12: 1204 13: 1200 14: 1200 15: 1200 16: 1200 17: 1293 18: 4377 19: 1200 20: 1200 Graphics:  Device-1: NVIDIA TU104 [GeForce RTX 2080] driver: nvidia v: 418.87.01            Display: server: X.Org 1.12.2 driver: nvidia unloaded: fbdev,modesetting,nouveau,vesa resolution: 1920x1137~60Hz            OpenGL: renderer: Rasterizer v: 1.4 (2.1 Mesa 10.0.1) * [root@graphics1 install]#* yum install /programs/install/chimerax-daily.rpm ... Installed:   ucsf-chimerax-daily.x86_64 0:2019.11.20-1.el7 Complete! *[root@graphics1 install]#* ls -l /usr/bin/chimerax-daily lrwxrwxrwx 1 root root 42 Nov 20 08:48 /usr/bin/chimerax-daily -> ../../opt/UCSF/ChimeraX-daily/bin/ChimeraX [root@graphics1 install]# chimerax-daily NOTE: available bundle cache has not been initialized yet NOTE: Traceback (most recent call last):   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py"", line 193, in _run_module_as_main     ""__main__"", mod_spec)   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py"", line 85, in _run_code     exec(code, run_globals)   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/ChimeraX_main.py"", line 871, in     exit_code = init(sys.argv)   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/ChimeraX_main.py"", line 580, in init     check_available=opts.get_available_bundles)   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 1682, in init     _toolshed = Toolshed(*args, **kw)   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py"", line 380, in __init__     settings.toolshed_last_check = now.isoformat()   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/settings.py"", line 190, in __setattr__     ConfigFile.__setattr__(self, name, value)   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 365, in __setattr__     ConfigFile.save(self)   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/configfile.py"", line 314, in save     with SaveTextFile(self._filename) as f:   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/safesave.py"", line 162, in __init__     SaveFile.__init__(self, filename, open=open_text, critical=critical)   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/safesave.py"", line 69, in __init__     raise OSError(errno.ENOTDIR, os.strerror(errno.ENOTDIR), save_dir) NotADirectoryError: [Errno 20] Not a directory: '/non/existent/directory/.config/ChimeraX' BUG: NotADirectoryError: [Errno 20] Not a directory: '/non/existent/directory/.config/ChimeraX' File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/safesave.py"", line 69, in __init__ raise OSError(errno.ENOTDIR, os.strerror(errno.ENOTDIR), save_dir)  _See log for complete Python traceback._ *[root@graphics1 install]#* mkdir -p /non/existent/directory/.config/ChimeraX *[root@graphics1 install]#* chimerax-daily NOTE: available bundle cache has not been initialized yet [14105:14105:1120/123101.581741:ERROR:zygote_host_impl_linux.cc(89)] Running as root without --no-sandbox is not supported. See https://crbug.com/638180. *[root@graphics1 install]#* chimerax-daily --no-sandbox /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/ChimeraX_main.py: option --no-sandbox not recognized *[root@graphics1 install]#* su - jamesh *jamesh@graphics1:/home/jamesh 103%* setenv DISPLAY gateway2:1002.0 *jamesh@graphics1:/home/jamesh 104%* xterm *jamesh@graphics1:/home/jamesh 105%* chimerax-daily QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-jamesh' NOTE: available bundle cache has not been initialized yet ERROR: ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.4 Try updating your graphics driver. WARNING: No statusbar messages will be shown due to inadequate OpenGL WARNING: QOpenGLShader::compile(Vertex): failed WARNING: QOpenGLShader::compile(Fragment): failed WARNING: Could not link shader program:  """" Fatal Python error: Segmentation fault Current thread 0x00007fec1e598740 (most recent call first):   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 743 in rapid_access_shown   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 203 in build   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/ChimeraX_main.py"", line 623 in init   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/ChimeraX_main.py"", line 871 in   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py"", line 85 in _run_code   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py"", line 193 in _run_module_as_main Segmentation fault (core dumped) # #  this was running remotely over an X11 connection to our gateway machine, which does not have an nvidia graphics card #  trying a different machine: *[root@bl831 ~]#* inxi -CGM Machine:   Type: Server System: Supermicro product: Super Server v: 0123456789 serial: 0123456789            Mobo: Supermicro model: X11SPi-TF v: 1.02 serial: OM17AS033975 UEFI [Legacy]: American Megatrends v: 2.0b            date: 02/26/2018 CPU:       Topology: 12-Core model: Intel Xeon Silver 4116 bits: 64 type: MT MCP L2 cache: 16.5 MiB            Speed: 899 MHz min/max: 800/3000 MHz Core speeds (MHz): 1: 988 2: 999 3: 2100 4: 2100 5: 2100 6: 1503 7: 1554            8: 896 9: 890 10: 2668 11: 2676 12: 1743 13: 999 14: 2100 15: 868 16: 2100 17: 2100 18: 800 19: 926 20: 2487            21: 1797 22: 800 23: 2100 24: 1300 Graphics:  Device-1: ASPEED Graphics Family driver: ast v: kernel            Device-2: NVIDIA GV100 [TITAN V] driver: nvidia v: 418.87.01            Display: server: X.Org 1.12.2 driver: modesetting resolution: 1920x1200~60Hz            OpenGL: renderer: Rasterizer v: 1.4 (2.1 Mesa 13.0.2) *[root@bl831 ~]#* su - jamesh *jamesh@bl831%* chimerax-daily ERROR: ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 2.1 Try updating your graphics driver. WARNING: No statusbar messages will be shown due to inadequate OpenGL Fatal Python error: Segmentation fault Thread 0x00007f1560ceb740 (most recent call first):   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/ui/gui.py"", line 268 in event_loop   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/ChimeraX_main.py"", line 747 in init   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/ChimeraX_main.py"", line 871 in   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py"", line 85 in _run_code   File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py"", line 193 in _run_module_as_main [237414:237414:0100/000000.772113:ERROR:command_buffer_proxy_impl.cc(130)] ContextResult::kTransientFailure: Failed to send GpuChannelMsg_CreateCommandBuffer. [237323:237323:0100/000000.772256:ERROR:command_buffer_proxy_impl.cc(130)] ContextResult::kTransientFailure: Failed to send GpuChannelMsg_CreateCommandBuffer. Segmentation fault (core dumped) We then tried moving to the display directly connected to the ""graphics1"" machine above. On this console we can get the ChimeraX gui to open and stay open. However, all attempts to install ISOLDE for all users have failed. we get the ""Permission Denied"" error trying to install for ""All users"". the |opts.get_available_bundles = False| trick has no effect. Any advice? -James Holton }}} " defect assigned normal Tool Shed Tristan Croll Conrad Huang Tom Goddard all ChimeraX