Changes

From XDSwiki
Jump to navigationJump to search
709 bytes added ,  10:25, 20 April 2021
m
→‎WSL2: coot error msg
Line 155: Line 155:  
I got CCP4 7.1 including coot-0.9.3 to work on Ubuntu 20.04 LTS with Xming but not with VcXsrc. Getting the Xserver to work properly requires addition of 3 lines in ~/.bashrc :
 
I got CCP4 7.1 including coot-0.9.3 to work on Ubuntu 20.04 LTS with Xming but not with VcXsrc. Getting the Xserver to work properly requires addition of 3 lines in ~/.bashrc :
 
  export DISPLAY=$(grep -m 1 nameserver /etc/resolv.conf | awk '{print $2}'):0.0                                           
 
  export DISPLAY=$(grep -m 1 nameserver /etc/resolv.conf | awk '{print $2}'):0.0                                           
# (David Waterman) if the above does not work, use: export DISPLAY=$(ip route|awk '/^default/{print $3}'):0.0                                           
+
# (David Waterman) if the above does not work, use: export DISPLAY=$(ip route|awk '/^default/{print $3}'):0.0                                           
 
  export LIBGL_ALWAYS_INDIRECT=1                                                                                           
 
  export LIBGL_ALWAYS_INDIRECT=1                                                                                           
 
  source /opt/xtal/ccp4-7.1/bin/ccp4.setup-sh  
 
  source /opt/xtal/ccp4-7.1/bin/ccp4.setup-sh  
Line 162: Line 162:  
  echo "[wsl2]" > .wslconfig
 
  echo "[wsl2]" > .wslconfig
 
  echo "kernelCommandLine = vsyscall=emulate" >> .wslconfig
 
  echo "kernelCommandLine = vsyscall=emulate" >> .wslconfig
to make the shelx* programs happy (see https://github.com/microsoft/WSL/issues/4694 ), and "vsyscall=emulate" appear in /proc/cmdline. After creating the file, WSL must be restarted (or the machine booted).
+
to make the shelx* programs happy (see https://github.com/microsoft/WSL/issues/4694 ), and "vsyscall=emulate" appear in /proc/cmdline. After creating the file, WSL must be restarted with "wsl.exe --shutdown" (or the machine booted).
    
A few libraries also needed installation (tcsh is needed by CCP4, the others are graphics libraries):
 
A few libraries also needed installation (tcsh is needed by CCP4, the others are graphics libraries):
Line 172: Line 172:  
Performance of coot is good enough for me (100 frames/sec for "Spin view" of a thaumatin molecule, on a Dell XPS13 7390 2-in-1 notebook). XDSGUI and multi-threaded XDS work as expected. For reading .h5 files, the NEGGIA plugin works correctly, but the DURIN plugin currently crashes (a [https://github.com/DiamondLightSource/durin/issues/22 bug] has been reported).
 
Performance of coot is good enough for me (100 frames/sec for "Spin view" of a thaumatin molecule, on a Dell XPS13 7390 2-in-1 notebook). XDSGUI and multi-threaded XDS work as expected. For reading .h5 files, the NEGGIA plugin works correctly, but the DURIN plugin currently crashes (a [https://github.com/DiamondLightSource/durin/issues/22 bug] has been reported).
   −
Update concerning coot 0.9.5: it crashes for me. Other applications, like ccp4i, still work.
+
Update concerning coot 0.9.5: it crashes for me. Other applications, like ccp4i, still work. The error message is:
 +
(set-display-intro-string "Good afternoon ,,,. Welcome to Coot 0.9.5")
 +
(set-display-lists-for-maps 1)
 +
coot-bin: Fatal IO error 11 (Resource temporarily unavailable) on X server 172.17.112.1:0.0.
 +
coot-bin: Fatal IO error 11 (Resource temporarily unavailable) on X server 172.17.112.1:0.0.
 +
. ------ Coot crashed - trying to diagnose -----
 +
ldd -r on guile gives:
 +
        linux-vdso.so.1 (0x00007fffd4f93000)
 +
        libguile.so.17 => /opt/xtal/ccp4-7.1/libexec/../lib/libguile.so.17 (0x00007f7c5df33000)
 +
        libgmp.so.10 => /opt/xtal/ccp4-7.1/libexec/../lib/libgmp.so.10 (0x00007f7c5dcb2000)
 +
and more lines with library names that exist on the disk.
    
== See also ==
 
== See also ==
    
[[Cluster Installation]]
 
[[Cluster Installation]]
2,522

edits

Cookies help us deliver our services. By using our services, you agree to our use of cookies.

Navigation menu