rstbx test is failing without indication in test_all_parallel

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Should we enable boost threads in...

Oleg Sobolev

20 Sep 2017 20 Sep '17

6:33 p.m.

Dear colleagues, Accidentally I found out that this command: rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 index_and_integrate=True multiprocessing=True finishes with traceback. It is run as part of phenix_regression/misc/tst_rstbx.csh The second problem is that test_all_parallel script fails to detect an actual failure. It would be great if somebody who is in charge of rstbx and testing could look at this. Best regards, Oleg Sobolev.

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Graeme.Winter＠diamond.ac.uk

20 Sep 20 Sep

8:12 p.m.

New subject: rstbx test is failing without indication in test_all_parallel

Hi Oleg I've been getting a similar error for a while now: libtbx.python "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py" [FAIL] Time: 17.13 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py", line 273, in <module> run(args=sys.argv[1:]) File "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py", line 269, in run exercise_solver() File "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py", line 255, in exercise_solver "index_and_integrate=True", "multiprocessing=True"]) File "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py", line 213, in run command=cmd, stdout_splitlines=False).raise_if_errors().stdout_buffer File "/dls/science/users/gw56/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 "/dls/science/users/gw56/svn/cctbx/build/../modules/cctbx_project/rstbx/command_line/simage.solver.py", line 5, in <module> run(args=sys.argv[1:]) File "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/solver.py", line 1161, in run return run_fresh(args) File "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/solver.py", line 1145, in run_fresh process(work_params, i_calc) File "/dls/science/users/gw56/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 "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/solver.py", line 985, in process_core work_params, reindexing_assistant, image_mdls, usables) File "/dls/science/users/gw56/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. I mentioned it a few times but no one bit... However it has always (in my experience) actually been reported as an error - few months now, only this error Cheers Graeme ________________________________ From: [email protected] [[email protected]] on behalf of Oleg Sobolev [[email protected]] Sent: 20 September 2017 19:33 To: cctbx mailing list Subject: [cctbxbb] rstbx test is failing without indication in test_all_parallel Dear colleagues, Accidentally I found out that this command: rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 index_and_integrate=True multiprocessing=True finishes with traceback. It is run as part of phenix_regression/misc/tst_rstbx.csh The second problem is that test_all_parallel script fails to detect an actual failure. It would be great if somebody who is in charge of rstbx and testing could look at this. Best regards, Oleg Sobolev. -- 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

Graeme.Winter＠diamond.ac.uk

8:13 p.m.

New subject: rstbx test is failing without indication in test_all_parallel

Also OS X - below was Linux: Error: the following jobs returned non-zero exit codes or suspicious stderr output: libtbx.python "/Users/graeme/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py" [FAIL] Time: 8.92 Return code: 1 OKs: 0 Standard error: 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", 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. Please verify these tests manually. Summary: Tests run : 360 Failures : 1 Warnings (possible failures) : 0 Stderr output (discouraged) : 1 See run_tests_parallel_zlog for full output. ******************************************************************************** ERROR: 1 TEST FAILURES. PLEASE FIX BEFORE COMMITTING CODE. ******************************************************************************** ________________________________ From: Winter, Graeme (DLSLtd,RAL,LSCI) Sent: 20 September 2017 21:12 To: cctbx mailing list Subject: RE: [cctbxbb] rstbx test is failing without indication in test_all_parallel Hi Oleg I've been getting a similar error for a while now: libtbx.python "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py" [FAIL] Time: 17.13 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py", line 273, in <module> run(args=sys.argv[1:]) File "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py", line 269, in run exercise_solver() File "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py", line 255, in exercise_solver "index_and_integrate=True", "multiprocessing=True"]) File "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/tst.py", line 213, in run command=cmd, stdout_splitlines=False).raise_if_errors().stdout_buffer File "/dls/science/users/gw56/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 "/dls/science/users/gw56/svn/cctbx/build/../modules/cctbx_project/rstbx/command_line/simage.solver.py", line 5, in <module> run(args=sys.argv[1:]) File "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/solver.py", line 1161, in run return run_fresh(args) File "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/solver.py", line 1145, in run_fresh process(work_params, i_calc) File "/dls/science/users/gw56/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 "/dls/science/users/gw56/svn/cctbx/modules/cctbx_project/rstbx/simage/solver.py", line 985, in process_core work_params, reindexing_assistant, image_mdls, usables) File "/dls/science/users/gw56/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. I mentioned it a few times but no one bit... However it has always (in my experience) actually been reported as an error - few months now, only this error Cheers Graeme ________________________________ From: [email protected] [[email protected]] on behalf of Oleg Sobolev [[email protected]] Sent: 20 September 2017 19:33 To: cctbx mailing list Subject: [cctbxbb] rstbx test is failing without indication in test_all_parallel Dear colleagues, Accidentally I found out that this command: rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 index_and_integrate=True multiprocessing=True finishes with traceback. It is run as part of phenix_regression/misc/tst_rstbx.csh The second problem is that test_all_parallel script fails to detect an actual failure. It would be great if somebody who is in charge of rstbx and testing could look at this. Best regards, Oleg Sobolev. -- 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

richard.gildea＠diamond.ac.uk

22 Sep 22 Sep

11:08 a.m.

New subject: rstbx test is failing without indication in test_all_parallel

As far as I recall rstbx/simage was a research project by Ralf that hasn't been touched for over 5 years, and isn't used by any code outside of rstbx/simage. Could this code be potentially "retired" somewhere outside of cctbx? Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: [email protected] [[email protected]] on behalf of Oleg Sobolev [[email protected]] Sent: 20 September 2017 19:33 To: cctbx mailing list Subject: [cctbxbb] rstbx test is failing without indication in test_all_parallel Dear colleagues, Accidentally I found out that this command: rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 index_and_integrate=True multiprocessing=True finishes with traceback. It is run as part of phenix_regression/misc/tst_rstbx.csh The second problem is that test_all_parallel script fails to detect an actual failure. It would be great if somebody who is in charge of rstbx and testing could look at this. Best regards, Oleg Sobolev. -- 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

markus.gerstel＠diamond.ac.uk

11:22 a.m.

New subject: rstbx test is failing without indication in test_all_parallel

This appears to be true: looking through cctbx_project, dials, labelit, phenix, phenix_regression I found no references apart from the tests that sparked this thread. I would just remove it for retirement - it will be preserved in the history. -Markus ________________________________________ From: [email protected] [[email protected]] on behalf of [email protected] [[email protected]] Sent: Friday, September 22, 2017 12:08 To: [email protected] Subject: Re: [cctbxbb] rstbx test is failing without indication in test_all_parallel As far as I recall rstbx/simage was a research project by Ralf that hasn't been touched for over 5 years, and isn't used by any code outside of rstbx/simage. Could this code be potentially "retired" somewhere outside of cctbx? Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: [email protected] [[email protected]] on behalf of Oleg Sobolev [[email protected]] Sent: 20 September 2017 19:33 To: cctbx mailing list Subject: [cctbxbb] rstbx test is failing without indication in test_all_parallel Dear colleagues, Accidentally I found out that this command: rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 index_and_integrate=True multiprocessing=True finishes with traceback. It is run as part of phenix_regression/misc/tst_rstbx.csh The second problem is that test_all_parallel script fails to detect an actual failure. It would be great if somebody who is in charge of rstbx and testing could look at this. Best regards, Oleg Sobolev. -- 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] http://phenix-online.org/mailman/listinfo/cctbxbb

Aaron Brewster

2:56 p.m.

FWIW I have used it on several occasions to understand how diffraction looks for different settings. For example, when I was working on amyloids on the cspad detector I would run it like this: rstbx.simage.wx_display unit_cell=24.1460,4.8614,22.2291,90.000,107.319,90.000 wavelength=1.452514 detector.distance=111 detector.size=194.15,194.15 detector.pixels=1765,1765 ewald_proximity=0.042500 point_spread=20 Twiddle the rotx, roty and rotz. It's nifty. I don't see any reason to kill this code. -Aaron On Fri, Sep 22, 2017 at 4:22 AM, wrote:

...

This appears to be true: looking through cctbx_project, dials, labelit, phenix, phenix_regression I found no references apart from the tests that sparked this thread. I would just remove it for retirement - it will be preserved in the history.

-Markus ________________________________________ From: [email protected] [[email protected]] on behalf of [email protected] [[email protected]] Sent: Friday, September 22, 2017 12:08 To: [email protected] Subject: Re: [cctbxbb] rstbx test is failing without indication in test_all_parallel

As far as I recall rstbx/simage was a research project by Ralf that hasn't been touched for over 5 years, and isn't used by any code outside of rstbx/simage. Could this code be potentially "retired" somewhere outside of cctbx?

Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078

Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: [email protected] [[email protected]] on behalf of Oleg Sobolev [[email protected]] Sent: 20 September 2017 19:33 To: cctbx mailing list Subject: [cctbxbb] rstbx test is failing without indication in test_all_parallel

Dear colleagues,

Accidentally I found out that this command:

rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 index_and_integrate=True multiprocessing=True finishes with traceback.

It is run as part of phenix_regression/misc/tst_rstbx.csh

The second problem is that test_all_parallel script fails to detect an actual failure.

It would be great if somebody who is in charge of rstbx and testing could look at this.

Best regards, Oleg Sobolev.

-- 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] http://phenix-online.org/mailman/listinfo/cctbxbb

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Nicholas Sauter

3:49 p.m.

Agreed. This is stable, mature code. No reason to kill it. 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 Fri, Sep 22, 2017 at 7:56 AM, Aaron Brewster wrote:

...

FWIW I have used it on several occasions to understand how diffraction looks for different settings. For example, when I was working on amyloids on the cspad detector I would run it like this:

rstbx.simage.wx_display unit_cell=24.1460,4.8614,22.2291,90.000,107.319,90.000 wavelength=1.452514 detector.distance=111 detector.size=194.15,194.15 detector.pixels=1765,1765 ewald_proximity=0.042500 point_spread=20

Twiddle the rotx, roty and rotz. It's nifty.

I don't see any reason to kill this code.

-Aaron

On Fri, Sep 22, 2017 at 4:22 AM, wrote:

...
This appears to be true: looking through cctbx_project, dials, labelit, phenix, phenix_regression I found no references apart from the tests that sparked this thread. I would just remove it for retirement - it will be preserved in the history.

-Markus ________________________________________ From: [email protected] [cctbxbb-bounces@phenix-online .org] on behalf of [email protected] [ [email protected]] Sent: Friday, September 22, 2017 12:08 To: [email protected] Subject: Re: [cctbxbb] rstbx test is failing without indication in test_all_parallel

As far as I recall rstbx/simage was a research project by Ralf that hasn't been touched for over 5 years, and isn't used by any code outside of rstbx/simage. Could this code be potentially "retired" somewhere outside of cctbx?

Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078

Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: [email protected] [cctbxbb-bounces@phenix-online .org] on behalf of Oleg Sobolev [[email protected]] Sent: 20 September 2017 19:33 To: cctbx mailing list Subject: [cctbxbb] rstbx test is failing without indication in test_all_parallel

Dear colleagues,

Accidentally I found out that this command:

rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 index_and_integrate=True multiprocessing=True finishes with traceback.

It is run as part of phenix_regression/misc/tst_rstbx.csh

The second problem is that test_all_parallel script fails to detect an actual failure.

It would be great if somebody who is in charge of rstbx and testing could look at this.

Best regards, Oleg Sobolev.

-- 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] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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richard.gildea＠diamond.ac.uk

3:58 p.m.

New subject: rstbx test is failing without indication in test_all_parallel

I was unaware that the code was actually used by anyone. So does anyone know enough about the code to fix the failing test that Oleg and Graeme both complained about? Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: [email protected] [[email protected]] on behalf of Aaron Brewster [[email protected]] Sent: 22 September 2017 15:56 To: cctbx mailing list Subject: Re: [cctbxbb] rstbx test is failing without indication in test_all_parallel FWIW I have used it on several occasions to understand how diffraction looks for different settings. For example, when I was working on amyloids on the cspad detector I would run it like this: rstbx.simage.wx_display unit_cell=24.1460,4.8614,22.2291,90.000,107.319,90.000 wavelength=1.452514 detector.distance=111 detector.size=194.15,194.15 detector.pixels=1765,1765 ewald_proximity=0.042500 point_spread=20 Twiddle the rotx, roty and rotz. It's nifty. I don't see any reason to kill this code. -Aaron On Fri, Sep 22, 2017 at 4:22 AM, mailto:[email protected]> wrote: This appears to be true: looking through cctbx_project, dials, labelit, phenix, phenix_regression I found no references apart from the tests that sparked this thread. I would just remove it for retirement - it will be preserved in the history. -Markus ________________________________________ From: [email protected]mailto:[email protected] [[email protected]mailto:[email protected]] on behalf of [email protected]mailto:[email protected] [[email protected]mailto:[email protected]] Sent: Friday, September 22, 2017 12:08 To: [email protected]mailto:[email protected] Subject: Re: [cctbxbb] rstbx test is failing without indication in test_all_parallel As far as I recall rstbx/simage was a research project by Ralf that hasn't been touched for over 5 years, and isn't used by any code outside of rstbx/simage. Could this code be potentially "retired" somewhere outside of cctbx? Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078tel:%2B441235%2077%208078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: [email protected]mailto:[email protected] [[email protected]mailto:[email protected]] on behalf of Oleg Sobolev [[email protected]mailto:[email protected]] Sent: 20 September 2017 19:33 To: cctbx mailing list Subject: [cctbxbb] rstbx test is failing without indication in test_all_parallel Dear colleagues, Accidentally I found out that this command: rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 index_and_integrate=True multiprocessing=True finishes with traceback. It is run as part of phenix_regression/misc/tst_rstbx.csh The second problem is that test_all_parallel script fails to detect an actual failure. It would be great if somebody who is in charge of rstbx and testing could look at this. Best regards, Oleg Sobolev. -- 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

James Holton

4:01 p.m.

New subject: rstbx test is failing without indication in test_all_parallel

I'm no expert, but it looks to me like the test is getting something from the phenix regression repository. Maybe it is this dependency that's making it bonk? -James On 9/22/2017 8:58 AM, [email protected] wrote:

...

I was unaware that the code was actually used by anyone.

So does anyone know enough about the code to fix the failing test that Oleg and Graeme both complained about?

Cheers,

Richard

Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078

Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: [email protected] [[email protected]] on behalf of Aaron Brewster [[email protected]] Sent: 22 September 2017 15:56 To: cctbx mailing list Subject: Re: [cctbxbb] rstbx test is failing without indication in test_all_parallel

FWIW I have used it on several occasions to understand how diffraction looks for different settings. For example, when I was working on amyloids on the cspad detector I would run it like this:

rstbx.simage.wx_display unit_cell=24.1460,4.8614,22.2291,90.000,107.319,90.000 wavelength=1.452514 detector.distance=111 detector.size=194.15,194.15 detector.pixels=1765,1765 ewald_proximity=0.042500 point_spread=20

Twiddle the rotx, roty and rotz. It's nifty.

I don't see any reason to kill this code.

-Aaron

On Fri, Sep 22, 2017 at 4:22 AM, mailto:[email protected]> wrote: This appears to be true: looking through cctbx_project, dials, labelit, phenix, phenix_regression I found no references apart from the tests that sparked this thread. I would just remove it for retirement - it will be preserved in the history.

-Markus ________________________________________ From: [email protected]mailto:[email protected] [[email protected]mailto:[email protected]] on behalf of [email protected]mailto:[email protected] [[email protected]mailto:[email protected]] Sent: Friday, September 22, 2017 12:08 To: [email protected]mailto:[email protected] Subject: Re: [cctbxbb] rstbx test is failing without indication in test_all_parallel

As far as I recall rstbx/simage was a research project by Ralf that hasn't been touched for over 5 years, and isn't used by any code outside of rstbx/simage. Could this code be potentially "retired" somewhere outside of cctbx?

Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078tel:%2B441235%2077%208078

Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: [email protected]mailto:[email protected] [[email protected]mailto:[email protected]] on behalf of Oleg Sobolev [[email protected]mailto:[email protected]] Sent: 20 September 2017 19:33 To: cctbx mailing list Subject: [cctbxbb] rstbx test is failing without indication in test_all_parallel

Dear colleagues,

Accidentally I found out that this command:

rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 index_and_integrate=True multiprocessing=True finishes with traceback.

It is run as part of phenix_regression/misc/tst_rstbx.csh

The second problem is that test_all_parallel script fails to detect an actual failure.

It would be great if somebody who is in charge of rstbx and testing could look at this.

Best regards, Oleg Sobolev.

-- 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

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Nicholas Sauter

4:05 p.m.

Billy Poon has said that he will look into the matter next week. 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 Fri, Sep 22, 2017 at 8:58 AM, wrote:

...

I was unaware that the code was actually used by anyone.

So does anyone know enough about the code to fix the failing test that Oleg and Graeme both complained about?

Cheers,

Richard

Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078

Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: [email protected] [[email protected]] on behalf of Aaron Brewster [[email protected]] Sent: 22 September 2017 15:56 To: cctbx mailing list Subject: Re: [cctbxbb] rstbx test is failing without indication in test_all_parallel

FWIW I have used it on several occasions to understand how diffraction looks for different settings. For example, when I was working on amyloids on the cspad detector I would run it like this:

rstbx.simage.wx_display unit_cell=24.1460,4.8614,22.2291,90.000,107.319,90.000 wavelength=1.452514 detector.distance=111 detector.size=194.15,194.15 detector.pixels=1765,1765 ewald_proximity=0.042500 point_spread=20

Twiddle the rotx, roty and rotz. It's nifty.

I don't see any reason to kill this code.

-Aaron

On Fri, Sep 22, 2017 at 4:22 AM, > wrote: This appears to be true: looking through cctbx_project, dials, labelit, phenix, phenix_regression I found no references apart from the tests that sparked this thread. I would just remove it for retirement - it will be preserved in the history.

-Markus ________________________________________ From: [email protected] [[email protected]] on behalf of [email protected]< mailto:[email protected]> [[email protected]] Sent: Friday, September 22, 2017 12:08 To: [email protected]mailto:[email protected] Subject: Re: [cctbxbb] rstbx test is failing without indication in test_all_parallel

As far as I recall rstbx/simage was a research project by Ralf that hasn't been touched for over 5 years, and isn't used by any code outside of rstbx/simage. Could this code be potentially "retired" somewhere outside of cctbx?

Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078tel:%2B441235%2077%208078

Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: [email protected] [[email protected]] on behalf of Oleg Sobolev [[email protected] mailto:[email protected]] Sent: 20 September 2017 19:33 To: cctbx mailing list Subject: [cctbxbb] rstbx test is failing without indication in test_all_parallel

Dear colleagues,

Accidentally I found out that this command:

rstbx.simage.solver d_min=5 lattice_symmetry=P422 intensity_symmetry=P4 index_and_integrate=True multiprocessing=True finishes with traceback.

It is run as part of phenix_regression/misc/tst_rstbx.csh

The second problem is that test_all_parallel script fails to detect an actual failure.

It would be great if somebody who is in charge of rstbx and testing could look at this.

Best regards, Oleg Sobolev.

-- 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

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Aaron Brewster
Graeme.Winter＠diamond.ac.uk
James Holton
markus.gerstel＠diamond.ac.uk
Nicholas Sauter
Oleg Sobolev
richard.gildea＠diamond.ac.uk