July 2015 - cctbxbb - phenix-online.org

dependency on phenix
by Roger Martin 26 Jan '16

26 Jan '16

Hi, looking through http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/minimi… shows at line 61 from phenix.refinement import weight_xray_chem and http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/occupa… line 134 Is weight_xray_chem.py code that could move to cctbx? (cctbx_project/mmtbx/refinement/weight_xray_chem.py) Are there other cross dependencies?

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cctbx developers: sf outage has lead to local corruption of your cctbx_project
by Aaron Brewster 27 Jul '15

27 Jul '15

Hi folks, because of the recent parallel commits to the cctbx repository due to the sourceforge outage, you will likely need to move your old cctbx_project directory aside and check it out fresh again. The 'too long didn't read' version of this email is you need to do this or several files will remain out of sync. This email only applies to developers or users who use svn directly. How to proceed: $ cd <your sources/modules directory> $ mv cctbx_project cctbx_project.old $ svn co https://svn.code.sf.net/p/cctbx/code/trunk cctbx_project If you have local edits in your cctbx_project directory, you'll need to copy them over to your new folder. More detail for those interested. The following example illustrates the problem: [phenix-src/cctbx_project/scitbx/lstbx]$ svn update [phenix-src/cctbx_project/scitbx/lstbx]$ svn status According to svn, this directory is up to date [phenix-src/cctbx_project/scitbx/lstbx]$ svn info normal_equations.h Path: normal_equations.h Name: normal_equations.h URL: https://svn.code.sf.net/p/cctbx/code/trunk/scitbx/lstbx/normal_equations.h Repository Root: https://svn.code.sf.net/p/cctbx/code Repository UUID: 3c1a6239-ac2c-0410-bc49-92500e444112 Revision: 22630 Node Kind: file Schedule: normal Last Changed Author: luc_j_bourhis Last Changed Rev: 15039 Last Changed Date: 2012-03-12 10:03:05 -0700 (Mon, 12 Mar 2012) Text Last Updated: 2015-07-27 10:24:16 -0700 (Mon, 27 Jul 2015) Checksum: ec2e555a9ad1d2553bb37bc04f677ef5 Note the revision number is 22630, and it lists the last revision for this file as 15039. After I move my directory aside and re-check out the directory: [phenix-src/cctbx_project/scitbx/lstbx]$ svn info normal_equations.h Path: normal_equations.h Name: normal_equations.h URL: https://svn.code.sf.net/p/cctbx/code/trunk/scitbx/lstbx/normal_equations.h Repository Root: https://svn.code.sf.net/p/cctbx/code Repository UUID: 3c1a6239-ac2c-0410-bc49-92500e444112 Revision: 22630 Node Kind: file Schedule: normal Last Changed Author: nksauter Last Changed Rev: 22624 Last Changed Date: 2015-07-25 17:16:55 -0700 (Sat, 25 Jul 2015) Text Last Updated: 2015-07-27 10:46:36 -0700 (Mon, 27 Jul 2015) Checksum: e5e5e623ecdde362afadf321d37b2c5e The correct revision is now retrieved. Thanks, -Aaron

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Re: [cctbxbb] git on BuildBot machines
by markus.gerstel＠diamond.ac.uk 26 Jul '15

26 Jul '15

Hi Aaron, Is there some documentation about the buildbot objects I could use to figure out a sensible way to determine whether git is available? I could of course just do try-run-catch... -Markus On 26 Jul 2015 16:35, Aaron Brewster <asbrewster(a)lbl.gov> wrote: Moving the cctbx_project directory to cctbx_project.old forced svn to get the latest version from scratch so buildbot at LBL has no versioning issues like Jenkins at Diamond does. Further, svn update on my local sources got the latest version, so I'm inclined to agree with Markus that that's a Jenkins issue. I installed git on the build nodes at LBL to accommodate the changes to bootstrap.py, however reconfig.sh still fails. This new line from r22623 and r22626 is the culprit: git_available = self.shell(command=['git', '--version'], haltOnFailure=False, quiet=True, silent=True).run() == 0 While this clearly works on Jenkins, when ran by buildbot, self.shell() is returning a buildbot shell object instead of a Builder shell object, so the .run call fails (not implemented). I'm out of time until this afternoon to look deeper. I've left the build bot server running using r22622 of bootstrap.py for now. -Aaron On Sun, Jul 26, 2015 at 7:00 AM, Nigel Moriarty <nwmoriarty(a)lbl.gov<mailto:[email protected]>> wrote: Aaron Recent changes to include git in bootstrap.py have broken the buildbot master (won't start) because git is not available on the VM. I don't have time before I fly to ACA, so please install git when you can. One reason I was hoping to see the buildbot website was because it has an interface to see all the commits to cctbx. This is likely on the buildbot master in some other format. It may be useful that I just moved the old cctbx_project to cctbx_project.old on all the builds. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov<http://CCI.LBL.gov> _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/cctbxbb -- 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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lost cctbx commits
by Aaron Brewster 26 Jul '15

26 Jul '15

Hi folks, after more investigation I now agree we have parallel commits. The following commits have been lost, all done on July 15th: nwmoriatry: r22622 phyy-nx: r22623-4 tmmclark: r22625 olegsobolev, r22626-7, r22629 alyubimov: r22628 These revisions number have been reused by svn and are no longer valid. The authors should recommit their changes. -Aaron

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git on BuildBot machines
by Nigel Moriarty 26 Jul '15

26 Jul '15

Aaron Recent changes to include git in bootstrap.py have broken the buildbot master (won't start) because git is not available on the VM. I don't have time before I fly to ACA, so please install git when you can. One reason I was hoping to see the buildbot website was because it has an interface to see all the commits to cctbx. This is likely on the buildbot master in some other format. It may be useful that I just moved the old cctbx_project to cctbx_project.old on all the builds. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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SVN is back on SourceForge
by Nigel Moriarty 26 Jul '15

26 Jul '15

Folks The return of SVN on SF has caused a few problems on the BuildBot but I moved the cctbx_project directory and forced some builds. I'm hoping things will progress but will check later tonight. There have been some strange error messages causing some emails to be send but I'm hoping things will settle soon. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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console
by Nigel Moriarty 26 Jul '15

26 Jul '15

I reverted the version of bootstrap.py on cci-vm-6 and got the attached console GUI. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Re: [cctbxbb] after SourceForge awakens
by Graeme.Winter＠diamond.ac.uk 22 Jul '15

22 Jul '15

Hi Nigel We're thinking along the same lines moving xia2 across first then maybe dials, depending on how people feel. Moving all of it across in the longer term would work well. Thanks Graeme On 20 Jul 2015 20:42, Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: Folks I have not read the emails regarding the current SourceForge situation. However, we had been planning to move to github in the near future. SF has been very reliable so I don't think it was too much of pain given the long use we've had from them. It does, however, come at a time when we are trying to get out a major release of Phenix. To that end, it would be helpful if any commits were bug fixes only to minimise the risk of breaking to the codebase. We will be actively evaluating the options regarding to github after Phenix 1.10 is safely away... Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov<http://CCI.LBL.gov> -- 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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after SourceForge awakens
by Nigel Moriarty 20 Jul '15

20 Jul '15

Folks I have not read the emails regarding the current SourceForge situation. However, we had been planning to move to github in the near future. SF has been very reliable so I don't think it was too much of pain given the long use we've had from them. It does, however, come at a time when we are trying to get out a major release of Phenix. To that end, it would be helpful if any commits were bug fixes only to minimise the risk of breaking to the codebase. We will be actively evaluating the options regarding to github after Phenix 1.10 is safely away... Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Re: [cctbxbb] List usage
by Graeme.Winter＠diamond.ac.uk 20 Jul '15

20 Jul '15

Hi Nigel Sensible however unknowable in advance that this is the behaviour & also who is on list! Sorry Graeme On 20 Jul 2015 18:13, Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: Folks To those of you on the cctbx list (and even those not), as moderator I have received over a dozen requests from the server. One cause of the problem is non-members posting to a members-only list. This is usually caused by people including the ccbx list in a long list of recipients. This leads to another problem. The list complains about too many recipients. I'm sure that some of the discussion regarding the current SourceForge situation has been garbled as a result. There is an easy solution. When sending to the list, include only the list in the recipients. Anybody who is interested should subscribe to the list. Non members such as David Waterman should be encouraged to join the list. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov<http://CCI.LBL.gov> -- 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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