Known Issues in 20211020 autoPROC release:


Introduction

Please also check the autoPROC home page and the news page for updates and snapshot releases.


Bruker Photon-II data in imgCIF/CBF format

The same issue as in previous versions (going back to 2017) still seems to exist. At least we haven't had any feedback to the contrary.

Please note that native SFRM formatted datasets should be fully supported in autoPROC.


Odd GPX2 behaviour on MacOS 10.15

We've had reports from users about some unexpected GPX2 pop-up windows appearing on MacOS 10.15 (this apparently didn't happen on previous 10.X versions). We are trying to recreate and analyse this, but in the meantime you can set the parameter autoPROC_CreateGpxPictures to "no" which will switch the generation of diffraction image pictures completely off. This can be done via an environment variable


  setenv autoPROC_CreateGpxPictures "no"            # csh/tcsh
    - or -
  export autoPROC_CreateGpxPictures="no"            # bash/sh

or on the autoPROC command-line


  process autoPROC_CreateGpxPictures="no" ...

You can still check processing and predictions using GPX2 via the created gpx.sh scripts (see standard output).


Potentially slow Gnuplot on CentOS8

With previous releases, we've seen some long execution times for autoPROC on CentOS8 due to the distributed Gnuplot binary taking a surprisingly long time. This should be fixed with this release, but if you still experience slowdowns, we would recommend the installation of an OS-specific version of Gnuplot on those systems.

As root, run

    yum install gnuplot

or (if you don't need a GUI for Gnuplot)

    yum install gnuplot-nox

and as software installer run

    echo "setenv BDG_TOOL_GNUPLOT \"/usr/bin/gnuplot\"" >> $autoPROC_home/setup_local.csh
    echo "export BDG_TOOL_GNUPLOT=\"/usr/bin/gnuplot\"" >> $autoPROC_home/setup_local.sh

The setting of the environment variable BDG_TOOL_GNUPLOT will ensure the use of the newly installed OS-version of "gnuplot".

Remember that CentOS8 will reach end-of-life on December 31, 2021, while CentOS7 is still supported til June 30th, 2024!


Gnuplot on Fedora 34

We've had reports (thanks to M. Peligro) that the STARANISO 2D plots are not generated correctly when running on a Fedora 34 Workstation system and using our supplied Gnuplot binary. This can be fixed by installing Gnuplot directly on the operating system level and then running autoPROC via

  process gnuplot=/usr/bin/gnuplot ...
 

Running autoPROC/XDS on Apple/Silicon (M1) fixed/supported in 20220603 release

See also:

If the XDS binary used by autoPROC (e.g. picked up from the users PATH or set explicitely via "process xds=/where/ever/XDS-Apple_M1/xds_par ...") is the "arm64" binary, the processing of HDF5 files will require a different plugin from the ones distributed with autoPROC itself, which are for the Intel chip.

  • Find out what type of XDS binary you are using via something like
      type xds_par
      file /where/ever/XDS-Apple_M1/xds_par
      file `which xds_par`
  • If this reports "Mach-O 64-bit executable x86_64" you are running the Intel executable and no further action is required
  • If this reports "Mach-O 64-bit executable arm64" you are running the arm (Apple Silicon) executable
  • Unpack this via
      unzip plugins-arm64.zip
      ls -l `pwd`/plugins-arm64/*.so
  • Run autoPROC with explicitely setting the plugin location, something like
      process autoPROC_XdsKeyword_LIB=/where/ever/plugins-arm64/durin-plugin.so ...

The next release of autoPROC will have automatic support for this.