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Installation: Difference between revisions
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(→WSL2: thanks David Waterman for providing an alternative way to set DISPLAY ; coot 0.9.5 crash) |
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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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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 | ||
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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): | ||
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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 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!''' | |||
== See also == | == See also == | ||
[[Cluster Installation]] | [[Cluster Installation]] | ||