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→XDS package for Intel Macs
(→tools and helper programs for generate_XDS.INP and XDSGUI, and libraries: remove Qt4 stuff) Tags: Mobile edit Mobile web edit Advanced mobile edit |
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This article has | This article has information 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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Since XDSGUI depends on graphics packages that may need to be installed, you can check the xdsgui binary with | Since XDSGUI depends on graphics packages that may need to be installed, you can check the xdsgui binary with | ||
ldd `which xdsgui` | grep found | ldd `which xdsgui` | grep found | ||
and that should show you the libraries | and that should show you the libraries it didn't find. Your friendly system administrator knows the specific commands to install those libraries. | ||
N.B. this may list libpng15.so for the latest XDSGUI (compiled May 2023), but you can ignore that! | |||
For RedHat-type distributions, that would typically be e.g. | For RedHat-type distributions, that would typically be e.g. | ||
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sudo apt-file update | sudo apt-file update | ||
Ubuntu 20.04: If the Qt5 libraries are missing, use <code>sudo apt install libqt5gui5 libqt5printsupport5 libqt5opengl5</code>. | Versions of XDSGUI compiled before 2021: Ubuntu 20.04: If the Qt5 libraries are missing, use <code>sudo apt install libqt5gui5 libqt5printsupport5 libqt5opengl5</code>. On CentOS7, this would be <code>yum -y install qt5-qtbase-gui qt5-qtbase</code> . | ||
On | On Ubuntu, latest XDSGUI may require <code>sudo apt install libxcb-xinerama0</code> | ||
<code>xxdiff</code> is likely available for your distribution - google for it, or try e.g. | <code>xxdiff</code> is likely available for your distribution - google for it, or try e.g. | ||
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As an alternative that does not require root for installation, one may create a directory $HOME/bin and use that for the programs and links. Also, this requires modification of the $PATH, by a one-time | As an alternative that does not require root for installation, one may create a directory $HOME/bin and use that for the programs and links. Also, this requires modification of the $PATH, by a one-time | ||
mkdir $HOME/bin | mkdir $HOME/bin | ||
echo 'export PATH=$PATH:$HOME/bin' >> ~/.zprofile | echo 'export PATH=$PATH:$HOME/bin' >> ~/.zprofile | ||
=== [[XDS]] package for Intel Macs === | === [[XDS]] package for Intel Macs === | ||
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(If you don't have root privileges and run in $HOME/bin, only the curl and ln commands have to be run) | (If you don't have root privileges and run in $HOME/bin, only the curl and ln commands have to be run) | ||
Starting with macOS Catalina, you may also need | Starting with macOS Catalina, you may also need | ||
sudo xattr -dr XDS-OSX_64 | sudo xattr -dr com.apple.quarantine XDS-OSX_64 | ||
if you get a security error popup (google "xattr com.apple.quarantine catalina"). | if you get a security error popup (google "xattr com.apple.quarantine catalina"). | ||
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==== XDS package for Macs with Apple M processors ==== | ==== XDS package for Macs with Apple M processors ==== | ||
The Intel Mac XDS programs also work on the Apple Silicon machines, but the libraries for e.g. reading data from Eiger detectors don't, and the native binaries are faster. | The Intel Mac XDS programs also work on the Apple Silicon machines, but the plugin libraries (see below) for e.g. reading data from Eiger detectors don't, and the native binaries are faster. | ||
Thus, change the above <code>curl</code> and <code>ln</code> commands to | Thus, change the above <code>curl</code> and <code>ln</code> commands to | ||
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# release root permissions: | # release root permissions: | ||
exit | exit | ||
As explained above, you may need | |||
sudo xattr -d com.apple.quarantine XDS-Apple_M1/* | |||
if you get a security-related popup saying that Apple cannot verify the software. | |||
If you want to process .h5 files written by Eiger detectors, use the [https://{{SERVERNAME}}/pub/mac_bin/durin-plugin-Apple-arm64.so Durin plugin for Apple ARM64 processors] (source code [https://github.com/DiamondLightSource/durin available]) or the [https://{{SERVERNAME}}/pub/mac_bin/dectris-neggia-Apple-arm64.so Dectris-Neggia plugin for Apple ARM64 processors] (source code [https://github.com/dectris/neggia available]). The latter may be faster, but does not work on data collected at Diamond Light Source. The former should in principle work for all HDF5 data. | If you want to process .h5 files written by Eiger detectors, use the [https://{{SERVERNAME}}/pub/mac_bin/durin-plugin-Apple-arm64.so Durin plugin for Apple ARM64 processors] (source code [https://github.com/DiamondLightSource/durin available]) or the [https://{{SERVERNAME}}/pub/mac_bin/dectris-neggia-Apple-arm64.so Dectris-Neggia plugin for Apple ARM64 processors] (source code [https://github.com/dectris/neggia available]). The latter may be faster, but does not work on data collected at Diamond Light Source. The former should in principle work for all HDF5 data. | ||
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... can be downloaded from https://{{SERVERNAME}}/pub/mac_bin/ . A simple way to obtain them is is to open a Terminal, and type: | ... can be downloaded from https://{{SERVERNAME}}/pub/mac_bin/ . A simple way to obtain them is is to open a Terminal, and type: | ||
sudo su | sudo su | ||
which asks for the password and gives you administrator permissions. Then, | which asks for the password and gives you administrator permissions. Then, for Intel Macs, | ||
# any folder would do; here we use /usr/local/bin/mac_bin | # any folder would do; here we use /usr/local/bin/mac_bin | ||
mkdir -p /usr/local/bin/mac_bin | mkdir -p /usr/local/bin/mac_bin | ||
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chmod +x get_folder.sh | chmod +x get_folder.sh | ||
./get_folder.sh | ./get_folder.sh | ||
For Silicon Macs, | |||
# any folder would do; here we use /usr/local/bin/mac_bin | |||
mkdir -p /usr/local/bin/mac_bin | |||
cd /usr/local/bin/mac_bin | |||
curl -O -R https://{{SERVERNAME}}/pub/mac_bin/get_folder_silicon.sh | |||
chmod +x get_folder_silicon.sh | |||
./get_folder_silicon.sh | |||
After that, release root privileges: | |||
exit | exit | ||
If you want to update the programs some time later, just run these commands again. | If you want to update the programs some time later, just run these commands again. | ||
In order to enable [[Eiger]] data processing, the <code>get_folder.sh</code> script | In order to enable [[Eiger]] data processing, the <code>get_folder.sh</code> (or <code>get_folder_silicon.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> . NOTE that the names of the native libraries for the Apple Silicon Macs ends with *-Apple-arm64.so . On Silicon Macs you can either use the Intel binaries for XDSGUI and XDS, or the Silicon binaries - the latter are recommended. You could in principle mix them but then you have to be careful with what you enter in the LIB= line of XDS.INP; and what you enter in Menu/Preferences/Paths/generic library of XDSGUI. | ||
# 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 [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> | # 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.dmg this version]; newer macOS should install [https://{{SERVERNAME}}/pub/mac_bin/XDS-Viewer-macOS10.15.dmg 10.15]. For XDSGUI, the | 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, you have a choice between the version for Intel Macs and that for Silicon Macs. Both do work on Silicon Macs, except for the plugin libraries - for these, the correct version (ending with -Apple-arm64.so) must be used together with xdsgui_mac_silicon. | |||
Lastly, it is useful (for e.g. XDSGUI) to install <code>xxdiff</code> . This used to be available from http://furius.ca/downloads/xxdiff/releases/macosx/ , but is also [https://{{SERVERNAME}}/pub/mac_bin/xxdiff-4.0b1.osx.dmg here]. I had to go to System Preferences > Security & Privacy > Privacy and add <code>xxdiff</code> to the programs with full disk access. | Lastly, it is useful (for e.g. XDSGUI) to install <code>xxdiff</code> . This used to be available from http://furius.ca/downloads/xxdiff/releases/macosx/ , but is also [https://{{SERVERNAME}}/pub/mac_bin/xxdiff-4.0b1.osx.dmg here]. I had to go to System Preferences > Security & Privacy > Privacy and add <code>xxdiff</code> to the programs with full disk access. | ||