Installation: Difference between revisions

Installation (view source)

Revision as of 13:22, 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).
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 === 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
-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/
   echo "[wsl2]" > .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 ==
 [[Cluster Installation]]