<div dir="ltr">I'll look into the simage test later today.<div>Nick</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>Nicholas K. Sauter, Ph. D.<br>Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division<div>Lawrence Berkeley National Laboratory<br>1 Cyclotron Rd., Bldg. 33R0345<br>Berkeley, CA 94720<br>(510) 486-5713<br></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Sun, Jul 16, 2017 at 11:47 PM, <span dir="ltr"><<a href="mailto:Graeme.Winter@diamond.ac.uk" target="_blank">Graeme.Winter@diamond.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Good detective work Markus, probably also explains<br>
<br>
<a href="https://github.com/xia2/xia2/issues/158" rel="noreferrer" target="_blank">https://github.com/xia2/xia2/<wbr>issues/158</a><br>
<br>
(I'll need you to run through this process with me real slow like, but good result)<br>
<br>
Cheers Graeme<br>
<br>
______________________________<wbr>__________<br>
From: <a href="mailto:cctbxbb-bounces@phenix-online.org">cctbxbb-bounces@phenix-online.<wbr>org</a> [<a href="mailto:cctbxbb-bounces@phenix-online.org">cctbxbb-bounces@phenix-<wbr>online.org</a>] on behalf of <a href="mailto:markus.gerstel@diamond.ac.uk">markus.gerstel@diamond.ac.uk</a> [<a href="mailto:markus.gerstel@diamond.ac.uk">markus.gerstel@diamond.ac.uk</a>]<br>
Sent: 17 July 2017 07:41<br>
<div class="HOEnZb"><div class="h5">To: <a href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a><br>
Subject: Re: [cctbxbb] New error appeared recently, do not know who it belongs to...<br>
<br>
It worked on my checked out revision (4eeed...), so I:<br>
<br>
$ git checkout master; git pull --rebase<br>
$ git bisect start<br>
$ git bisect bad<br>
$ git bisect good 4eeed<br>
Bisecting: 7 revisions left to test after this (roughly 3 steps)<br>
[<wbr>d80a6e66937818a4da8d65e5571c40<wbr>2868fd5c34] catch case with zero target length<br>
(make reconf, run test, test fails)<br>
<br>
$ git bisect bad<br>
Bisecting: 3 revisions left to test after this (roughly 2 steps)<br>
[<wbr>166904e0b9678f9c092464bddb7d3d<wbr>2fc12f6085] 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.<br>
(make reconf, run test, test fails)<br>
<br>
$ git bisect bad<br>
Bisecting: 1 revision left to test after this (roughly 1 step)<br>
[<wbr>050b520791887430d5ac3116040ea4<wbr>bc3877039e] remove faulty .map_data(); add .crystal_symmetry()<br>
(make reconf, run test, test succeeds)<br>
<br>
$ git bisect good<br>
Bisecting: 0 revisions left to test after this (roughly 0 steps)<br>
[<wbr>20ece6eb8f0ef6dc3298d90cf64631<wbr>59159874bc] Store all H atoms in connectivity list (also those without bond proxies).<br>
(make reconf, run test, test succeeds)<br>
<br>
$ git bisect good<br>
166904e0b9678f9c092464bddb7d3d<wbr>2fc12f6085 is the first bad commit<br>
commit 166904e0b9678f9c092464bddb7d3d<wbr>2fc12f6085<br>
Author: Nicholas Sauter <<a href="mailto:nksauter@lbl.gov">nksauter@lbl.gov</a>><br>
Date: Wed Jul 12 20:39:15 2017 -0700<br>
<br>
Longstanding formula for areaupper implements a very complicated heuristic that is not<br>
consistent with the simple explanation given on the web page. Change to the simple semantics:<br>
area limit = minimum_spot_area * spot_area_maximum_factor.<br>
<br>
:040000 040000 bf112507a50e171d9d29a4d181414c<wbr>77d8ab564c ed60de2719af6f6f75f4b07b592db1<wbr>2cac0207ae M spotfinder<br>
<br>
<br>
Thus <a href="https://github.com/cctbx/cctbx_project/commit/166904e" rel="noreferrer" target="_blank">https://github.com/cctbx/<wbr>cctbx_project/commit/166904e</a> to blame<br>
<br>
-Markus<br>
<br>
<br>
-----Original Message-----<br>
From: <a href="mailto:cctbxbb-bounces@phenix-online.org">cctbxbb-bounces@phenix-online.<wbr>org</a> [mailto:<a href="mailto:cctbxbb-bounces@phenix-online.org">cctbxbb-bounces@<wbr>phenix-online.org</a>] On Behalf Of <a href="mailto:Graeme.Winter@diamond.ac.uk">Graeme.Winter@diamond.ac.uk</a><br>
Sent: 17 July 2017 07:13<br>
To: <a href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a><br>
Subject: Re: [cctbxbb] New error appeared recently, do not know who it belongs to...<br>
<br>
Nick,<br>
<br>
I share your confusion. If I could have tracked it down to a revision I would have done…<br>
<br>
Cheers Graeme<br>
<br>
<br>
On 17 Jul 2017, at 07:07, Nicholas Sauter <<a href="mailto:nksauter@lbl.gov">nksauter@lbl.gov</a><mailto:<a href="mailto:nksauter@lbl.gov">nksau<wbr>ter@lbl.gov</a>>> wrote:<br>
<br>
that code hasn't changed in 5 years, so how can an error suddenly appear?<br>
Nick<br>
<br>
Nicholas K. Sauter, Ph. D.<br>
Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division Lawrence Berkeley National Laboratory<br>
1 Cyclotron Rd., Bldg. 33R0345<br>
Berkeley, CA 94720<br>
<a href="tel:%28510%29%20486-5713" value="+15104865713">(510) 486-5713</a><br>
<br>
On Sun, Jul 16, 2017 at 10:57 PM, <<a href="mailto:Graeme.Winter@diamond.ac.uk">Graeme.Winter@diamond.ac.uk</a><<wbr>mailto:<a href="mailto:Graeme.Winter@diamond.ac.uk">Graeme.Winter@diamond.<wbr>ac.uk</a>>> wrote:<br>
Exhibit A:<br>
<br>
libtbx.python "/Users/graeme/svn/cctbx/<wbr>modules/cctbx_project/rstbx/<wbr>simage/tst.py"<br>
rstbx.simage.explore_<wbr>completeness d_min=10 rstbx.simage.explore_<wbr>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):<br>
File "/Users/graeme/svn/cctbx/<wbr>modules/cctbx_project/rstbx/<wbr>simage/tst.py", line 273, in <module><br>
run(args=sys.argv[1:])<br>
File "/Users/graeme/svn/cctbx/<wbr>modules/cctbx_project/rstbx/<wbr>simage/tst.py", line 269, in run<br>
exercise_solver()<br>
File "/Users/graeme/svn/cctbx/<wbr>modules/cctbx_project/rstbx/<wbr>simage/tst.py", line 255, in exercise_solver<br>
"index_and_integrate=True", "multiprocessing=True"])<br>
File "/Users/graeme/svn/cctbx/<wbr>modules/cctbx_project/rstbx/<wbr>simage/tst.py", line 213, in run<br>
command=cmd, stdout_splitlines=False).<wbr>raise_if_errors().stdout_<wbr>buffer<br>
File "/Users/graeme/svn/cctbx/<wbr>modules/cctbx_project/libtbx/<wbr>easy_run.py", line 39, in raise_if_errors<br>
raise Error(msg)<br>
RuntimeError: child process stderr output:<br>
command: 'rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 index_and_integrate=True multiprocessing=True'<br>
Traceback (most recent call last):<br>
File "/Users/graeme/svn/cctbx/<wbr>build/../modules/cctbx_<wbr>project/rstbx/command_line/<a href="http://simage.solver.py" rel="noreferrer" target="_blank">sim<wbr>age.solver.py</a><<a href="http://simage.solver.py/" rel="noreferrer" target="_blank">http://simage.<wbr>solver.py/</a>>", line 5, in <module><br>
run(args=sys.argv[1:])<br>
File "/Users/graeme/svn/cctbx/<wbr>modules/cctbx_project/rstbx/<wbr>simage/solver.py", line 1161, in run<br>
return run_fresh(args)<br>
File "/Users/graeme/svn/cctbx/<wbr>modules/cctbx_project/rstbx/<wbr>simage/solver.py", line 1145, in run_fresh<br>
process(work_params, i_calc)<br>
File "/Users/graeme/svn/cctbx/<wbr>modules/cctbx_project/rstbx/<wbr>simage/solver.py", line 1088, in process<br>
process_core(work_params, i_calc.p1_anom, reindexing_assistant, image_mdls)<br>
File "/Users/graeme/svn/cctbx/<wbr>modules/cctbx_project/rstbx/<wbr>simage/solver.py", line 985, in process_core<br>
work_params, reindexing_assistant, image_mdls, usables)<br>
File "/Users/graeme/svn/cctbx/<wbr>modules/cctbx_project/rstbx/<wbr>simage/solver.py", line 883, in build_image_cluster<br>
raise RuntimeError("Insufficient connectivity between images.")<br>
RuntimeError: Insufficient connectivity between images.<br>
usr+sys time: 0.78 seconds, ticks: 777467, micro-seconds/tick: 1.003<br>
wall clock time: 6.99 seconds<br>
<br>
OS X & RHEL6<br>
<br>
Any volunteers?<br>
<br>
Cheers Graeme<br>
<br>
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</div></div></blockquote></div><br></div>