DIALS core meeting 2023-11-30

Previous Actions

• ND: PR to remove std::string support for messagepack from dials code
• ND Investigate getting psana tests running on the DIALS xfel-regression testing
• ND or DW: Cannot view reciprocal lattice using dials.reciprocal_lattice_viewer #2443
  • Probably needs someone to dig into windows gltbx behaviour, or at least work out where issue lies
  • Reports from CCP4 workshop that people are having issue on latest ubuntu
  • David reproduced the problem which is progress…
• ND: Investigate using stable-nightly conda builds of cctbx (e.g. cctbx tests) longer term

Agenda

small cell serialtbx

https://github.com/dials/dials/pull/2477 - small cell code did not make it into serialtbx yet.

• Previously:
  • AB: Did small cell xfel recently. Had sequences indexer success over stills.
    • Ran sweeps indexer. Many bad indexing solutions, suspect differences down to index assignment tolerance at 0.3 hkl by default
    • Can still move code into serial toolbox, but don’t think best end solution is obvious yet
  • Dan experience using new small cell algorithm - does index a lot of “nonsense” when you give it an incorrect unit cell, so went back to small_cell_process command line tool. Now need to dig into why it claims to work when it didn’t (yay false positive debug) - on the whole good step in right direction. Work continues.
• Time needs to be applied.

dials.cosym finds the right operator but puts it wrongly

• dials#2486
• Draft PR at https://github.com/dials/dials/pull/2497
• Pulled in other problems that need to be worked through
• Potential fix opened a large box of problems
• GW believes needs a rethink and a rewrite and patching is essentially impossible
• GW and DP to discuss on 27th
  • Met! DP has made some progress but had other obligations
• Recent attempt… regression test pass but Takanori’s case still fails
• We are back where we started, but with a better understanding of the problem and some belief that what we are doing is correct => the issue is perhaps somewhere else
• DP to continue on the quest
• JBE Solved!
  • For some symmetries, lattice/space group symmetries were misapplied
  • PR: https://github.com/dials/dials/pull/2548
  • Merge!

Build fails on latest ventura

• https://github.com/dials/dials/issues/2522
• GW to update from 13.3 to 13.6 to try this out
• ND Looked but could not replicate, need to reinvestigate with more of user’s environment
  • ND: Follow up
  • GW: Also had a quick look, missing exe_dev

Reports of build failures on RHEL8

• JBE noticed some CI tests started to fail on linux / bootstrap but not regular linux
• Should we think about moving the default to a cmake build (DP notes this would diverge further from the XFEL regression tests)
• JBE to test clean bootstrap in RHEL8 (ws448)
  • Now Working
  • ND planning to move DIALS to prebuilt CCTBX

Starting January DLS Loan of RSE

• We have someone who can do some work for 6 months on the actual codebase, refactoring, tidying etc. with a view to future optimisation

Add support for Pilatus 4

• GW has data, has promised to ensure works - apropos to this the current issue is
• Pls can has review on https://github.com/cctbx/dxtbx/pull/663
  • DECTRIS fixed a bug that inverted order
  • Now Merged

Removing setting batch offset when creating imagesets

• https://github.com/cctbx/dxtbx/pull/662
• We no longer need the batch offset => we can just remove it after changes by DGW
• Much testing and reviews please
• DP also to test via XFEL-regression
• JBE holding off for more testing

Changes to retain unindexed reflections in indexers (mainly stills)

• https://github.com/dials/dials/pull/2545

AOB?

Optimisation Post

• DLS Hiring someone to work on performance optimisation
• A position on the DIALS grant hiring soon

XFEL CI

• MPI backend changes has caused test failures due to output changes
• Finding HDF5 mpi installed even when not requested
• Some fixes to check imports ready to add to XFEL CI

JBE Demos

• Demoing structural changes to indexing/retaining unindexed images
• Very exciting!

Next meeting

Thursday, December 14th, 4pm (GMT), 8am (PST)