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

Mon Jul 17 01:27:46 PDT 2017

I'll look into the simage test later today.
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 11:47 PM, <Graeme.Winter at diamond.ac.uk> wrote:

> Good detective work Markus, probably also explains
>
> https://github.com/xia2/xia2/issues/158
>
> (I'll need you to run through this process with me real slow like, but
> good result)
>
> Cheers Graeme
>
> ________________________________________
> From: cctbxbb-bounces at phenix-online.org [cctbxbb-bounces at phenix-online.org]
> on behalf of markus.gerstel at diamond.ac.uk [markus.gerstel at diamond.ac.uk]
> Sent: 17 July 2017 07:41
> To: cctbxbb at phenix-online.org
> Subject: Re: [cctbxbb] New error appeared recently, do not know who it
> belongs to...
>
> 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@
> 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:nksau
> ter 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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