Known Issues in 20230614 autoPROC release:

Introduction

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

ID23-2@ESRF writing incorrect meta-data into HDF5 master.h5 files

As of 3rd May 2023 (and most likely before and after that date), *_master.h5 files created at beamline ID23-2 of ESRF contain incorrect meta-data: hte omega axis is described as (-1,0,0) when it should be (0,1,0).

Beamline staff is aware of that but are currently unable to correct this (this will possible happen sometime in summer). A user has therefore two options: 

    process XdsFormatSpecificJiffyOverwrite=no autoPROC_XdsKeyword_ROTATION_AXIS="0 1 0" ...
    fix_omega.py some_master.h5

Both solutions should provide you with correct autoPROC processing - even if we slightly prefer the second solution (since archiving the dataset and revisiting it in a few years time becomes easier). Of course, the best/proper solution is a fix directly at the beamline so that correct meta-data is available within those HDF5 files.

imginfo warnings for Eiger/HDF5 data

We've had reports about warning messages of the form 

img2xds >>>
img2xds >>>   >>> imginfo >>> Extracted from file ./HDF5_1/imginfo.log :
img2xds >>>   >>> imginfo >>>
img2xds >>>   >>> imginfo >>> WARNING: expected unit "degree" for item "/entry/sample/goniometer/omega_range_total" - but found unit "A<88>^B" (length=6)!!
img2xds >>>   >>> imginfo >>>
img2xds >>>

that we are currently investigating. The underlying cause is a change in string encoding of the "units" attribute for specific items (like "degree" etc). We are not 100% sure yet if that is due to some local configuration or a change in the SIMPLON software.

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 ...