Installation: Difference between revisions

Installation (view source)

Revision as of 19:21, 20 May 2022

1,130 bytes added , 20 May 2022

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→‎considerations for a macOS machine with Apple M1 processor

Kay

Bureaucrats

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 Furthermore, you want the [https://www.dectris.com/company/news/newsroom/news-details/process-eiger-data-with-xds-fast Neggia] library (does not work for HDF5 data from DLS) or the [https://github.com/DiamondLightSource/durin Durin plugin]. These may be installed through the <code>get_folder.sh</code> script, in <code>/usr/local/lib64</code>.
-== Mac OSX ==
+== macOS ==
 === [[XDS]] package ===
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   xattr -dr XDS-OSX_64/*
 if you get a security error popup (google "xattr com.apple.quarantine catalina").
+Then make sure that the binaries are in the search path for executables, as explained in https://xds.mr.mpg.de/html_doc/downloading.html .
+==== considerations for a macOS machine with Apple M1 processor ====
+Change the above <code>curl</code> and <code>ln</code> commands to
+ curl -L -o - https://xds.mr.mpg.de/XDS-Apple_M1.tar.gz | tar xzvf -
+ ln -sf XDS-Apple_M1/* .
+If you want to process .h5 files written by Dectris' Eiger detectors, use the [https://strucbio.biologie.uni-konstanz.de/pub/mac_bin/dectris-neggia-Apple-arm64.so Neggia plugin for Apple ARM64 processors] in the LIB= line of [[XDS.INP]]. However, for data from Diamond Light Source use the [https://strucbio.biologie.uni-konstanz.de/pub/mac_bin/durin-plugin-Apple-arm64.so Durin plugin for Apple ARM64 processors] ([https://github.com/DiamondLightSource/durin source code]).
+A message like "Note: The following floating-point exceptions are signalling: IEEE_DIVIDE_BY_ZERO IEEE_UNDERFLOW_FLAG" may be printed after running XDS or XSCALE. This is harmless.
 === Prerequisites (Xcode, CCP4) for [[generate_XDS.INP]], [[XDSGUI]] and other programs ===
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 -rw-r--r--  1 kay   staff  107  7 Mär 09:41 .zprofile
 kay@Kays-MacBook-Air-2018 ~ % cat .zprofile
-source /Users/kay/.profile
+source $HOME/.profile
 # Added by CCP4 package manager:
 . '/Applications/ccp4-7.1/bin/ccp4.setup-sh'
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 In order to enable [[Eiger]] data processing, the <code>get_folder.sh</code> script
-# copies Dectris' Neggia library and DLS's Durin library into <code>/usr/local/lib64</code>
+# copies Dectris' Neggia library and DLS's Durin library into <code>/usr/local/lib64</code> (see above for Neggia and Durin on M1 Macs; the script does not yet handle this automatically)
 # copies [https://www.globalphasing.com GlobalPhasing's] <code>hdf2mini-cbf</code> into <code>/usr/local/bin</code>, but under the name <code>H5ToXds</code> (consider getting a [https://www.globalphasing.com/autoproc/ autoPROC] license!)
 # copies <code>h5dump</code> [https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/bin/unix/hdf5-1.12.1-Std-macos11_64-clang.tar.gz] into <code>/usr/local/bin</code>
-A [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.13.dmg 10.13] Qt5 version of XDS-viewer (compiled by T. Hauß) works on macOS Catalina, and is installed by <code>get_folder.sh</code>. Older Macs need [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-0.6 this version]; newer macOS should install [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.15.dmg 10.15]. For XDSGUI, the [https://{{SERVERNAME}}/pub/mac_bin/xdsgui_qt4.dmg Qt4 version] is still the default, but a [https://{{SERVERNAME}}/pub/mac_bin/xdsgui_qt5.dmg Qt5 version] is available (but needs Qt5 libraries!).
+A [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.13.dmg 10.13] Qt5 version of XDS-viewer (compiled by T. Hauß) works on macOS Catalina, and is installed by <code>get_folder.sh</code>. Older Macs need [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-0.6.dmg this version]; newer macOS should install [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.15.dmg 10.15]. For XDSGUI, the [https://{{SERVERNAME}}/pub/mac_bin/xdsgui_qt4.dmg Qt4 version] is still the default, but a [https://{{SERVERNAME}}/pub/mac_bin/xdsgui_qt5.dmg Qt5 version] is available (but needs Qt5 libraries!).
 Lastly, it is useful (for e.g. XDSGUI) to install <code>xxdiff</code> from http://furius.ca/downloads/xxdiff/releases/macosx/ . I had to go to System Preferences > Security & Privacy > Privacy and add <code>xxdiff</code> to the programs with full disk access.
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 A lot of technical detail is at [https://docs.microsoft.com/en-us/windows/wsl/compare-versions] .
-CCP4 supports WSL-1 ; see info at http://www.ccp4.ac.uk/download/#os=wsl .
+CCP4 documents use of WSL-1 ; see info at http://www.ccp4.ac.uk/download/#os=wsl .
 Graphical Linux programs require installation of a X server like [https://sourceforge.net/projects/xming/files/latest/download Xming] or [https://sourceforge.net/projects/vcxsrv VcXsvr] or [https://mobaxterm.mobatek.net/ Mobaxterm] on the Windows host. There are helpful writeups (e.g. [https://wiki.ubuntu.com/WSL#Running_Graphical_Applications] and [http://wsl-guide.org/en/latest/]). VcXsrc seems to have a problem with coot for some people (see [https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=COOT;6ef4a967.2011 WSL2 installation] and responses). To use the X server with WSL, one has to say in the shell window