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Installation instructions

Installation of XDSAPP3

After downloading the file xdsapp3v1-yyyy-mm-dd.tar.gz in the directory of your choice, run the command
   tar -zxf xdsapp3v1-yyyy-mm-dd.tar.gz
A new directory will be created, containing 17 files:

  • eiger2cbf.py
  • generate_XDS.INP
  • logo_hzb.gif
  • messages.py
  • mp_xdsconv_job.py
  • myutils.py
  • plotting3.py
  • README
  • signals.py
  • XDS_from_H5.py
  • xdsapp3_gui.py
  • xdsapp3_help.html
  • xdsapp3_help.txt
  • xdsapp3.1.py
  • xdsenv.py
  • xdsit.py

Create an alias "xdsapp3" or "xdsapp" pointing to the file xdsapp3.1.py for easy use of the program.

Installation of the GUI components

Read carefully the README file for installation instructions.

The instructions are provided for x86_64 architecture and have been tested by us with the specified operating systems. They may not work with different or older systems. Please note that we can not provide solutions for all operating systems.
Before starting the installation, ensure that your OS and package management software are up to date.
You can check the installation of packages by using the search command of your package manager (e.g. yum search pyqt5). The packages for your architecture will be listed.

Isolated environment with Anaconda

If you like not to touch your Linux or MacOS installation, it is possible to run XDSAPP3 in an isolated Python environment with Anaconda. To do so, install the "Individual Edition" from the anaconda.com home page. During the installation, chose not to modify your shell  startup script. Instead, create a file named xdsapp3.sh or similar with content:

example tcsh:

#!/bin/tcsh
# setup PATH to python3
set path_stored="$PATH"
setenv PATH /path/to/anaconda3/bin:$PATH
# to avoid OMP crash of XDS (Linux only)
setenv KMP_INIT_AT_FORK FALSE
# start xdsapp3
python /path/to/xdsapp3/xdsapp3.1.py $argv:q
#restore PATH
setenv PATH $path_stored

example bash:

#!/bin/bash
# setup PATH to python3
set path_stored="$PATH"
export PATH=/path/to/anaconda3/bin:$PATH
# to avoid OMP crash of XDS (Linux only)
export KMP_INIT_AT_FORK=FALSE
# start xdsapp3
python /path/to/xdsapp3/xdsapp3.1.py $@
#restore PATH
export PATH $path_stored

Linux specific

There seems to be a bug in a multiprocessing library, which causes to crash xds_par (the parallel processing version of xds). A workaround is to set the environment variable KMP_INIT_AT_FORK to FALSE, e.g:
bash: export KMP_INIT_AT_FORK=FALSE
tcsh: setenv KMP_INIT_AT_FORK FALSE

macOS

macOS 10.13 (High Sierra)

Install Xcode including the Command Line Tools
install Qt5, PyQt5, and Python3, and Matplotlib:
with Anaconda3 (everything is included)
or
homebrew:
(this requires the previous installation of Xcode)
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
Then the rest of the packages can be easily installed:
brew install qt (will install Qt5)
brew install pyqt
Copy the line
export PYTHONPATH=/usr/local/lib/python3.7/site-packages:$PYTHONPATH
into your ~/.bashrc or ~/.bash_profile file (for the bash shell) for
future uses of XDSAPP3.

install hdf5 with e.g.
brew install hdf5

 

MacOS 10.15 (Catalina) , 11.1 (Big Sur)

See MacOS 10.13. In addition:

On macOS Catalina many of the programs used by XDSAPP3 will not run
immediately because they were not written by an "identified developer".
Try this:
* delete a possible quarantine attribute: >xattr -d com.apple.quarantine program
* start a program from the command line, there will be a message
* open System Preferences
* go to Security & Privacy and select the General tab
* click the button "Open Anyway"
* run the program again and acknowledge the pop-up message

(For the adventurous:
in terminal, activate a hidden option in Security & Privacy:
sudo spctl --master-disable
This will show a "Anywhere" button in the General tab. To revert it
sudo spctl --master-enable
Be aware of the risk to install malware, if you leave this option active.


On macOS Catalina make sure you have PyQt 5.12.3 installed, PyQt 5.9.2 will crash when opening a file selection dialog.

On macOS Catalina sometimes the XDSAPP3 GUI will not respond, click in the desktop and then back to the GUI.