[cctbxbb] New error appeared recently, do not know who it belongs to...

markus.gerstel at diamond.ac.uk markus.gerstel at diamond.ac.uk
Sun Jul 16 23:41:12 PDT 2017


It worked on my checked out revision (4eeed...), so I:

$ git checkout master; git pull --rebase
$ git bisect start
$ git bisect bad
$ git bisect good 4eeed
Bisecting: 7 revisions left to test after this (roughly 3 steps)
[d80a6e66937818a4da8d65e5571c402868fd5c34] catch case with zero target length
(make reconf, run test, test fails)

$ git bisect bad
Bisecting: 3 revisions left to test after this (roughly 2 steps)
[166904e0b9678f9c092464bddb7d3d2fc12f6085] Longstanding formula for areaupper implements a very complicated heuristic that is not consistent with the simple explanation given on the web page.  Change to the simple semantics: area limit = minimum_spot_area * spot_area_maximum_factor.
(make reconf, run test, test fails)

$ git bisect bad
Bisecting: 1 revision left to test after this (roughly 1 step)
[050b520791887430d5ac3116040ea4bc3877039e] remove faulty .map_data(); add .crystal_symmetry()
(make reconf, run test, test succeeds)

$ git bisect good
Bisecting: 0 revisions left to test after this (roughly 0 steps)
[20ece6eb8f0ef6dc3298d90cf6463159159874bc] Store all H atoms in connectivity list (also those without bond proxies).
(make reconf, run test, test succeeds)

$ git bisect good
166904e0b9678f9c092464bddb7d3d2fc12f6085 is the first bad commit
commit 166904e0b9678f9c092464bddb7d3d2fc12f6085
Author: Nicholas Sauter <nksauter at lbl.gov>
Date:   Wed Jul 12 20:39:15 2017 -0700

    Longstanding formula for areaupper implements a very complicated heuristic that is not
    consistent with the simple explanation given on the web page.  Change to the simple semantics:
    area limit = minimum_spot_area * spot_area_maximum_factor.

:040000 040000 bf112507a50e171d9d29a4d181414c77d8ab564c ed60de2719af6f6f75f4b07b592db12cac0207ae M	spotfinder


Thus https://github.com/cctbx/cctbx_project/commit/166904e to blame

-Markus


-----Original Message-----
From: cctbxbb-bounces at phenix-online.org [mailto:cctbxbb-bounces at phenix-online.org] On Behalf Of Graeme.Winter at diamond.ac.uk
Sent: 17 July 2017 07:13
To: cctbxbb at phenix-online.org
Subject: Re: [cctbxbb] New error appeared recently, do not know who it belongs to...

Nick,

I share your confusion. If I could have tracked it down to a revision I would have done…

Cheers Graeme


On 17 Jul 2017, at 07:07, Nicholas Sauter <nksauter at lbl.gov<mailto:nksauter at lbl.gov>> wrote:

that code hasn't changed in 5 years, so how can an error suddenly appear?
Nick

Nicholas K. Sauter, Ph. D.
Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720
(510) 486-5713

On Sun, Jul 16, 2017 at 10:57 PM, <Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk>> wrote:
Exhibit A:

libtbx.python "/Users/graeme/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py"
rstbx.simage.explore_completeness d_min=10 rstbx.simage.explore_completeness d_min=10 intensity_symmetry=P4 use_symmetry=True multiprocessing=True rstbx.simage.solver d_min=5 rstbx.simage.solver d_min=5 lattice_symmetry=R32:R intensity_symmetry=R3:R rstbx.simage.solver d_min=5 lattice_symmetry=R32:R intensity_symmetry=P1 rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 index_and_integrate=True multiprocessing=True Traceback (most recent call last):
  File "/Users/graeme/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py", line 273, in <module>
    run(args=sys.argv[1:])
  File "/Users/graeme/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py", line 269, in run
    exercise_solver()
  File "/Users/graeme/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py", line 255, in exercise_solver
    "index_and_integrate=True", "multiprocessing=True"])
  File "/Users/graeme/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py", line 213, in run
    command=cmd, stdout_splitlines=False).raise_if_errors().stdout_buffer
  File "/Users/graeme/svn/cctbx/modules/cctbx_project/libtbx/easy_run.py", line 39, in raise_if_errors
    raise Error(msg)
RuntimeError: child process stderr output:
  command: 'rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 index_and_integrate=True multiprocessing=True'
  Traceback (most recent call last):
    File "/Users/graeme/svn/cctbx/build/../modules/cctbx_project/rstbx/command_line/simage.solver.py<http://simage.solver.py/>", line 5, in <module>
      run(args=sys.argv[1:])
    File "/Users/graeme/svn/cctbx/modules/cctbx_project/rstbx/simage/solver.py", line 1161, in run
      return run_fresh(args)
    File "/Users/graeme/svn/cctbx/modules/cctbx_project/rstbx/simage/solver.py", line 1145, in run_fresh
      process(work_params, i_calc)
    File "/Users/graeme/svn/cctbx/modules/cctbx_project/rstbx/simage/solver.py", line 1088, in process
      process_core(work_params, i_calc.p1_anom, reindexing_assistant, image_mdls)
    File "/Users/graeme/svn/cctbx/modules/cctbx_project/rstbx/simage/solver.py", line 985, in process_core
      work_params, reindexing_assistant, image_mdls, usables)
    File "/Users/graeme/svn/cctbx/modules/cctbx_project/rstbx/simage/solver.py", line 883, in build_image_cluster
      raise RuntimeError("Insufficient connectivity between images.")
  RuntimeError: Insufficient connectivity between images.
usr+sys time: 0.78 seconds, ticks: 777467, micro-seconds/tick: 1.003
wall clock time: 6.99 seconds

OS X & RHEL6

Any volunteers?

Cheers Graeme

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