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: [email protected] [[email protected]] on behalf of [email protected] [[email protected]]
Sent: 17 July 2017 07:41
To: [email protected]
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
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: [email protected] [mailto:[email protected]] On Behalf Of [email protected]
Sent: 17 July 2017 07:13
To: [email protected]
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 mailto:[email protected]> 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, mailto:[email protected]> 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.pyhttp://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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