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 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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, 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: [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:cctbxbb-bounces@ phenix-online.org] 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 > 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, > 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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