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Installation (view source)

Revision as of 14:22, 21 April 2021

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This article has some little script snippets that should ease the installation of XDS and related programs like ([[XDS-viewer]], [[xdsstat]], [[XDSGUI|xdsgui]]). It is assumed that binaries (or links to binaries) should go to /usr/local/bin . This means that you should do this as the administrator (root), or have sudo rights (Mac, and some Linux distros).
This article has some little script snippets that should ease the installation of XDS and related programs like ([[XDS-viewer]], [[xdsstat]], [[XDSGUI|xdsgui]]). It is assumed that binaries (or links to binaries) should go to /usr/local/bin . This means that you should do this as the administrator (root), or have sudo rights (Mac, and some Linux distros).
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=== WSL2 ===
=== WSL2 ===


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-0.9.5 to work on Ubuntu 20.04 LTS running under WSL2, with https://mobaxterm.mobatek.net/ MobaXterm as the Xserver (but not with Xming or VcXsrc). My ~/.bashrc has the line (which the CCP4 installation created):
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                                         
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  
and creating a file (replace MYUSERNAME with your Windows username)
and I created a file (replace MYUSERNAME with your Windows username) in the Windows filesystem:
  cd /mnt/c/Users/MYUSERNAME/
  cd /mnt/c/Users/MYUSERNAME/
  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 with "wsl.exe --shutdown" (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, WSL2 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):
sudo apt install tcsh libqt5opengl5 libqt5printsupport5 libqt5gui5 libxcb-render0 libxcb-shm0 libglu1-mesa
In addition, the Xming Xlaunch needed a box checked that prevents access control; and the Windows firewall needed a rule for port 6000 as shown in https://stackoverflow.com/questions/61110603/how-to-set-up-working-x11-forwarding-on-wsl2 .
 
It seems that XLaunch has to be started before the Ubuntu terminal in which I start the graphical application.
 
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 when using XMing. 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.


'''I tried MobaXterm (private edition) and this works better - coot runs!'''
A few libraries also needed installation (tcsh is needed by CCP4, the others are mostly graphics libraries):
sudo apt install tcsh libqt5opengl5 libqt5printsupport5 libqt5gui5 libxcb-render0 libxcb-shm0 libglu1-mesa libgomp1
Performance of coot is good enough for occasional work. 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).


== See also ==
== See also ==


[[Cluster Installation]]
[[Cluster Installation]]
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