August 2019 - cctbxbb - phenix-online.org

CCTBX documentation questionnaire
by Dorothee Liebschner 14 Jan '20

14 Jan '20

Hi everyone, During this year's ECM computing school, it came up that the CCTBX does not have a lot of documentation. This seems to be a major reason why people don't use it, even if they would like to employ the libraries. We would like to find out which parts of the CCTBX are the most interesting for users. We certainly cannot provide extensive documentation for the entire toolbox, but we can see what we can do once we know the main areas of interest. So if you were in the situation of wanting to use the CCTBX but decided to stay away from it because the documentation was non-existent or obscure, please let us know by filling out the questionnaire below (it's anonymous): questionnaire CCTBX documentation <https://forms.gle/9RawJFfHyEvhCVVP7> Best wishes, Dorothee -- Project Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Re: [cctbxbb] cctbx.python readline issue
by Mooers, Blaine H.M. (HSC) 24 Aug '19

24 Aug '19

In response to Wolfram Tempel's trouble with backspace in interactive sessions, I found the same problem with backspace in interactive sessions in cctbx.python version 1723 on Mac OS 10.14.6. I solved the problem by installing readline with pip using the command below (I did not try using conda) and sourcing the again $HOME/local/cctbx-dev-1723/cctbx_env.sh. $HOME/local/cctbx-dev-1723/build/bin/libtbx.pip install --upgrade readline Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of cctbxbb-request(a)phenix-online.org [cctbxbb-request(a)phenix-online.org] Sent: Saturday, August 24, 2019 2:00 PM To: cctbxbb(a)phenix-online.org Subject: [EXTERNAL] cctbxbb Digest, Vol 125, Issue 22 Send cctbxbb mailing list submissions to cctbxbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… or, via email, send a message with subject or body 'help' to cctbxbb-request(a)phenix-online.org You can reach the person managing the list at cctbxbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of cctbxbb digest..." Today's Topics: 1. interactive cctbx.python backspace behavior (on linux) (wtempel) 2. Re: some thoughts on cctbx and pip (Billy Poon) 3. Re: interactive cctbx.python backspace behavior (on linux) (Billy Poon) 4. Re: interactive cctbx.python backspace behavior (on linux) (Billy Poon) 5. Re: some thoughts on cctbx and pip (Tristan Croll) ---------------------------------------------------------------------- Message: 1 Date: Fri, 23 Aug 2019 15:54:09 -0400 From: wtempel <wtempel(a)gmail.com> To: cctbxbb(a)phenix-online.org Subject: [cctbxbb] interactive cctbx.python backspace behavior (on linux) Message-ID: <CAGjFzmBj3m_Uez1Siz6HPrjxAdOJqSczO-udnJo7C2W5Od4Q8A(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi, Currently, cctbx.python behaves like described in this stackoverflow post: https://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_ques… . I am missing the convenience of backspace delete, which is available on /usr/bin/python interactive sessions. Could that feature be added during compilation of the pre-built cctbx distributions? Regards. Wolfram Tempel

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interactive cctbx.python backspace behavior (on linux)
by wtempel 23 Aug '19

23 Aug '19

Hi, Currently, cctbx.python behaves like described in this stackoverflow post: https://stackoverflow.com/questions/893053/seeing-escape-characters-when-pr…. I am missing the convenience of backspace delete, which is available on /usr/bin/python interactive sessions. Could that feature be added during compilation of the pre-built cctbx distributions? Regards. Wolfram Tempel

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cls parameter
by Graeme.Winter＠Diamond.ac.uk 22 Aug '19

22 Aug '19

Folks, For reading shelxl .res files I need to define a cls parameter - it is not _used_ for anything though - so 0 works fine e.g. from iotbx import shelx import sys s = shelx.cctbx_xray_structure_from(0, filename=sys.argv[1]) will work fine. I based this on the documentation at https://cci.lbl.gov/cctbx_docs/iotbx/iotbx.shelx.html What have I missed? Thanks 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

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Re: [cctbxbb] Molprobity / CCTBX incompatibility
by Nigel Moriarty 19 Aug '19

19 Aug '19

That is the correct directory for the general Phenix install. @Christopher Williams <christopher.sci.williams(a)gmail.com> Does the script run bootstrap.py from the current directory or does it cd elsewhere. I have noticed that accessing the repos at Duke can be a problem but I just did so the servers are fine. I still think the "running the install script with bootstrap.py in the current directory" could still be the problem. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging 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 On Mon, Aug 19, 2019 at 10:49 AM Charitha Belluru Shetty < charitha-belluru.b.shetty(a)gsk.com> wrote: > Hi Nigel, > > > > Can you please let us know which directory? Since the Molprobity directory > is not created after running > > *. install_via_bootstrap.sh 10* > > > > The steps to install ideally would be as below: > > ./install_via_bootstrap.sh 4 > > cd/molprobity > > ./setup.sh > > > > > > But in our case “modules” directory got created. > > > > -bash-4.2$ ls -l > > total 131 > > -rw-r--r-- 1 cbs72396 appmgmt 90799 Aug 14 18:26 bootstrap.py > > -rw-r--r-- 1 cbs72396 appmgmt 82015 Aug 16 13:38 bootstrap.pyc > > -rw-r--r-- 1 cbs72396 appmgmt 1817 Aug 14 14:03 install_via_bootstrap.sh > > drwxr-sr-x 12 cbs72396 appmgmt 22 Aug 16 13:38 modules > > > > -bash-4.2$ ls -l modules > > total 2913 > > drwxr-xr-x 11 cbs72396 appmgmt 17 Nov 27 2012 annlib > > drwxr-sr-x 8 cbs72396 appmgmt 15 Aug 16 13:38 annlib_adaptbx > > -rw-r--r-- 1 cbs72396 appmgmt 519563 Aug 16 05:13 annlib.gz > > drwxr-sr-x 5 cbs72396 appmgmt 6 Aug 16 13:38 boost > > drwxr-sr-x 20 cbs72396 appmgmt 48 Aug 16 13:38 cbflib > > drwxr-xr-x 5 cbs72396 appmgmt 6 Oct 30 2013 ccp4io > > drwxr-xr-x 5 cbs72396 appmgmt 30 May 19 17:56 ccp4io_adaptbx > > -rw-r--r-- 1 cbs72396 appmgmt 208764 Aug 16 05:13 ccp4io_adaptbx.gz > > -rw-r--r-- 1 cbs72396 appmgmt 1417443 Aug 16 05:13 ccp4io.gz > > drwxr-sr-x 38 cbs72396 appmgmt 45 Aug 16 13:38 cctbx_project > > drwxr-sr-x 5 cbs72396 appmgmt 5 Aug 16 13:37 chem_data > > drwxrwxr-x 4 cbs72396 appmgmt 15 Sep 18 2017 scons > > -rw-r--r-- 1 cbs72396 appmgmt 636186 Aug 16 05:13 scons.gz > > drwxr-xr-x 4 cbs72396 appmgmt 11 Aug 19 2009 tntbx > > -rw-r--r-- 1 cbs72396 appmgmt 38909 Aug 16 05:13 tntbx.gz > > > > Best Regards, > > Charitha Shetty > > > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 19, 2019 1:08 PM > *To:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Cc:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com>; Robert > Nolte <robert.t.nolte(a)gsk.com>; cctbxbb(a)phenix-online.org > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Sorry guy, I was on holidays and the maintenance was a problem. > > > > Try putting the bootstrap.py in the directory that the command is being > run. > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > 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 > > > > > > On Fri, Aug 16, 2019 at 7:27 PM Christopher Williams < > christopher.sci.williams(a)gmail.com> wrote: > > Hmm. Nigel, I may need some of your expertise here. It looks like > there's a consistent problem with svn checkouts. > > > > "git clone" operations seem to have been successful, so it probably isn't > a matter of GitHub being down. Especially since the svn checkout of geostd > from Sourceforge also failed. > > > > Do you know if your system has problems with svn? Our svn checkouts > generally take this form: " svn co > https://github.com/rlabduke/MolProbity.git/trunk molprobity > --non-interactive --trust-server-cert " Is there perhaps a security > issue with the --trust-server-cert flag? > > > > I believe that the cci machines at Berkeley are under maintenance until > Sunday, so there are other reasons the script won't work until then. > > > > Good luck, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > > > On Fri, Aug 16, 2019 at 5:45 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Christopher, > > > > I ran the installer script twice and this is what I got… > > > > *When I ran it first time, only the modules directory was created* > > bash-4.2$ *. install_via_bootstrap.sh 10* > > ++++++++++ creating build directories ... > > svn: E000110: Unable to connect to a repository at URL 'svn:// > svn.code.sf.net/p/geostd/code/trunk' > > svn: E000110: Can't read from connection: Connection timed out > > svn: E175002: Unable to connect to a repository at URL ' > https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_rotame… > ' > > svn: E175002: OPTIONS of ' > https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_rotame…': > SSL handshake failed: SSL socket read failed (https://github.com) > > svn: E175002: Unable to connect to a repository at URL ' > https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_ramach… > ' > > svn: E175002: OPTIONS of ' > https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_ramach…': > SSL handshake failed: SSL socket read failed (https://github.com) > > svn: E175002: Unable to connect to a repository at URL ' > https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_cablam… > ' > > svn: E175002: OPTIONS of ' > https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_cablam…': > SSL handshake failed: SSL socket read failed (https://github.com) > > svn: E175002: Unable to connect to a repository at URL ' > https://github.com/cctbx/cctbx_project.git/trunk/libtbx/auto_build/bootstra… > ' > > svn: E175002: OPTIONS of ' > https://github.com/cctbx/cctbx_project.git/trunk/libtbx/auto_build/bootstra…': > SSL handshake failed: SSL socket read failed (https://github.com) > > python: can't open file 'bootstrap.py': [Errno 2] No such file or directory > > -bash: build/setpaths.sh: No such file or directory > > python: can't open file > 'modules/chem_data/cablam_data/rebuild_cablam_cache.py': [Errno 2] No such > file or directory > > ++++++++++ MolProbity configure.sh finished. > > ++++++++++ Run molprobity/setup.sh to complete installation. > > -bash-4.2$ > > > > -bash-4.2$ pwd > > /hpc/apps/current/molprobity/v4.4.app > > -bash-4.2$ ls -l > > total 31 > > *-rw-r--r-- 1 cbs72396 appmgmt 1817 Aug 14 14:03 install_via_bootstrap.sh* > > *drwxr-sr-x 3 cbs72396 appmgmt 3 Aug 15 17:58 modules* > > > > > > *Second time when I ran..bootstap.py and bootstrap.pyc was crated and the > modules directory…* > > > > -bash-4.2$ *. install_via_bootstrap.sh 4* > > ++++++++++ creating build directories ... > > > > > > svn: E000110: Unable to connect to a repository at URL 'svn:// > svn.code.sf.net/p/geostd/code/trunk' > > svn: E000110: Can't read from connection: Connection timed out > > Performing actions: hot update base build > > Installing base packages using: > > python modules/cctbx_project/libtbx/auto_build/install_conda.py > --builder=molprobity --install_conda > > ===== Downloading http://cci.lbl.gov/repositories/annlib.gz: 0.5 MB > > [0%.........20%.........40%.........60%.........80%.........100%] > > ===== Running in modules: extracting files from annlib.gz > > ===== Downloading http://cci.lbl.gov/repositories/scons.gz: 0.6 MB > > [0%.........20%.........40%.........60%.........80%.........100%] > > ===== Running in modules: extracting files from scons.gz > > ===== Downloading http://cci.lbl.gov/repositories/ccp4io.gz: 1.4 MB > > [0%.........20%.........40%.........60%.........80%.........100%] > > ===== Running in modules: extracting files from ccp4io.gz > > ===== Running in modules: git clone --recursive > https://github.com/cctbx/boost.git boost --progress --verbose > > Cloning into 'boost'... > > POST git-upload-pack (942 bytes) > > remote: Enumerating objects: 27664, done. > > remote: Total 27664 (delta 0), reused 0 (delta 0), pack-reused 27664 > > Receiving objects: 100% (27664/27664), 20.47 MiB | 14.72 MiB/s, done. > > Resolving deltas: 100% (15913/15913), done. > > Checking out files: 100% (14245/14245), done. > > setting branch master to rebase > > ===== Running in modules/boost: git rev-parse HEAD > > 72edfa007c73dd3dd01f5530205f7ca14cda7420 > > ===== Running in modules: git clone --recursive > https://github.com/yayahjb/cbflib.git cbflib --progress --verbose > > Cloning into 'cbflib'... > > POST git-upload-pack (gzip 2442 to 1233 bytes) > > remote: Enumerating objects: 7463, done. > > remote: Total 7463 (delta 0), reused 0 (delta 0), pack-reused 7463 > > Receiving objects: 100% (7463/7463), 24.84 MiB | 13.21 MiB/s, done. > > Resolving deltas: 100% (5380/5380), done. > > setting branch master to rebase > > ===== Running in modules/cbflib: git rev-parse HEAD > > 611f21bbef81c5104954aaab9b72e4e55ec3e70d > > ===== Running in modules: git clone --recursive > https://github.com/cctbx/cctbx_project.git cctbx_project --progress > --verbose > > Cloning into 'cctbx_project'... > > POST git-upload-pack (gzip 1842 to 958 bytes) > > remote: Enumerating objects: 61, done. > > remote: Counting objects: 100% (61/61), done. > > remote: Compressing objects: 100% (52/52), done. > > remote: Total 243691 (delta 14), reused 22 (delta 9), pack-reused 243630 > > Receiving objects: 100% (243691/243691), 91.05 MiB | 14.77 MiB/s, done. > > Resolving deltas: 100% (192566/192566), done. > > Checking out files: 100% (6173/6173), done. > > setting branch master to rebase > > ===== Running in modules/cctbx_project: git rev-parse HEAD > > bd3139c85312f5f43009e1eb31baa34f41734fbb > > ===== Downloading http://cci.lbl.gov/repositories/ccp4io_adaptbx.gz: > 203.9 kB > > [0%.........20%.........40%.........60%.........80%.........100%] > > ===== Running in modules: extracting files from ccp4io_adaptbx.gz > > ===== Running in modules: git clone --recursive > https://github.com/cctbx/annlib_adaptbx.git annlib_adaptbx --progress > --verbose > > Cloning into 'annlib_adaptbx'... > > POST git-upload-pack (842 bytes) > > remote: Enumerating objects: 175, done. > > remote: Total 175 (delta 0), reused 0 (delta 0), pack-reused 175 > > Receiving objects: 100% (175/175), 162.09 KiB | 0 bytes/s, done. > > Resolving deltas: 100% (77/77), done. > > setting branch master to rebase > > ===== Running in modules/annlib_adaptbx: git rev-parse HEAD > > 3ca66b2dd77eacd7524f915fce0705ac0764b46f > > ===== Downloading http://cci.lbl.gov/repositories/tntbx.gz: 38.0 kB > > [0%.........20%.........40%.........60%.........80%.........100%] > > ===== Running in modules: extracting files from tntbx.gz > > ===== Running in .: svn co > https://github.com/rlabduke/MolProbity.git/trunk molprobity > --non-interactive --trust-server-cert > > svn: E175002: Unable to connect to a repository at URL ' > https://github.com/rlabduke/MolProbity.git/trunk' > > svn: E175002: OPTIONS of 'https://github.com/rlabduke/MolProbity.git/trunk': > SSL handshake failed: SSL socket read failed (https://github.com) > > Process failed with return code 1 > > -bash: build/setpaths.sh: No such file or directory > > Traceback (most recent call last): > > File "modules/chem_data/cablam_data/rebuild_cablam_cache.py", line 2, in > <module> > > import libtbx.load_env > > ImportError: No module named libtbx.load_env > > ++++++++++ MolProbity configure.sh finished. > > ++++++++++ Run molprobity/setup.sh to complete installation. > > -bash-4.2$ > > -bash-4.2$ > > *-bash-4.2$ ls -l* > > *total 131* > > *-rw-r--r-- 1 cbs72396 appmgmt 90799 Aug 14 18:26 bootstrap.py* > > *-rw-r--r-- 1 cbs72396 appmgmt 82015 Aug 16 13:38 bootstrap.pyc* > > *-rw-r--r-- 1 cbs72396 appmgmt 1817 Aug 14 14:03 > install_via_bootstrap.sh* > > *drwxr-sr-x 12 cbs72396 appmgmt 22 Aug 16 13:38 modules* > > > > > > Best Regards, > > Charitha Shetty > > > > *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Sent:* Wednesday, August 14, 2019 2:23 PM > *To:* Robert Nolte <robert.t.nolte(a)gsk.com> > *Cc:* Nigel Moriarty <nwmoriarty(a)lbl.gov>; Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com>; cctbxbb(a)phenix-online.org > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Hi All, > > > > Okay looks like the new installer works. It uses the conda mode of the > cctbx bootstrap builder for everything except chem_data, which it builds on > its own. > > > > Get the new installer from our GitHub here: > > svn --quiet --non-interactive --trust-server-cert export > https://github.com/rlabduke/MolProbity.git/trunk/install_via_bootstrap.sh > > > > Place it in the dir where you want to install MolProbity, then run it. > > . install_via_bootstrap.sh > > The script optionally accepts a single integer argument to set the number > of processors that the bootstrap builder will use. > > . install_via_bootstrap.sh 4 > > > > When this is complete, cd to the molprobity dir it created and run > setup.sh, as usual. > > > > Good luck, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > > > On Wed, Aug 14, 2019 at 1:33 PM Christopher Williams < > christopher.sci.williams(a)gmail.com> wrote: > > Hi Bob, > > > > I am currently doing one more test build to make sure that the new > installer works. It looks promising. > > > > Regards, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > On Wed, Aug 14, 2019 at 11:17 AM Robert Nolte <robert.t.nolte(a)gsk.com> > wrote: > > Folks, > > Any progress on sorting out our issue, or cleaning up the installer? > > Bob > > > > > > *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Sent:* Monday, August 12, 2019 7:48 PM > *To:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Cc:* Robert Nolte <robert.t.nolte(a)gsk.com>; Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com>; cctbxbb(a)phenix-online.org > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > The dispatcher should be using both phenix.reduce and molprobity.reduce > interchangeably in all cases. Ditto for all the validations that > MolProbity runs like phenix.rotalyze/molprobity.rotalyze. > > > > My current install of MolProbity is successfully accessing Reduce via > phenix.reduce, so I don't *think* this is the issue. > > > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > On Mon, Aug 12, 2019 at 6:07 PM Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: > > But maybe the installation of cctbx has molprobity.reduce and not > phenix.reduce so if that is the case we can change the script to look for > molprobity.reduce instead of phenix.reduce. > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > 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 > > > > > > On Mon, Aug 12, 2019 at 2:58 PM Robert Nolte <robert.t.nolte(a)gsk.com> > wrote: > > According to the log file when I just tried to run it, it is phenix.reduce > that it can’t find. > > Bob > > > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 5:55 PM > *To:* Robert Nolte <robert.t.nolte(a)gsk.com> > *Cc:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com>; > Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > I'm just trying to find out if, at the command line, whether it is > phenix.reduce or molprobity.reduce. Charitha just needs to type one or the > other to see what happens. > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > 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 > > > > > > On Mon, Aug 12, 2019 at 2:44 PM Robert Nolte <robert.t.nolte(a)gsk.com> > wrote: > > Nigel, > > Currently it is not running. This was working from the scratch > install last week. I am not sure what is going on now. > > Bob > > > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 4:52 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Does molprobity.reduce run? > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > 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 > > > > > > On Mon, Aug 12, 2019 at 1:14 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Nigel, > > > > I hit the send button too soon..Ignore my previous email 😊 > > > > -bash-4.2$ source setpaths.sh > > -bash-4.2$ > > -bash-4.2$ env |grep -i reduce > > -bash-4.2$ > > > > So the “setpath.sh” has the below contents… > > > > $ cat /hpc/apps/current/molprobity/v4.4.app/MolProbity/build/setpaths.sh > > # THIS IS AN AUTOMATICALLY GENERATED FILE. > > # DO NOT EDIT! CHANGES WILL BE LOST. > > ocwd="`pwd`" > > if [ -n "$LIBTBX_BUILD_RELOCATION_HINT" ]; then > > cd "$LIBTBX_BUILD_RELOCATION_HINT" > > LIBTBX_BUILD_RELOCATION_HINT= > > export LIBTBX_BUILD_RELOCATION_HINT > > elif [ -n "$BASH_SOURCE" ]; then > > LIBTBX_BUILD=`dirname "$BASH_SOURCE[0]"` > > cd "$LIBTBX_BUILD" > > else > > cd "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > fi > > LIBTBX_BUILD=`pwd -P` > > export LIBTBX_BUILD > > LIBTBX_OPATH="$PATH" > > export LIBTBX_OPATH > > PATH="$LIBTBX_BUILD/bin:$PATH" > > export PATH > > cd "$ocwd" > > ocwd= > > alias libtbx.setpaths_all=". \"$LIBTBX_BUILD/setpaths_all.sh\"" > > alias libtbx.unsetpaths=". \"$LIBTBX_BUILD/unsetpaths.sh\"" > > if [ -n "$LIBTBX_OPATH" ]; then > > LIBTBX_TMPVAL="$LIBTBX_OPATH" > > else > > LIBTBX_TMPVAL= > > fi > > export LIBTBX_TMPVAL > > PATH=`libtbx.path_utility prepend LIBTBX_TMPVAL "$LIBTBX_BUILD/bin" < > /dev/null` > > export PATH > > if [ "$PATH" = "L_I_B_T_B_X_E_M_P_T_Y" ]; then unset PATH; fi > > LIBTBX_TMPVAL= > > LIBTBX_OPATH= > > LIBTBX_BUILD= > > > > > > Best Regards, > > Charitha Shetty > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 4:08 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Once you source the setpaths.sh file in the build directory do you have > phenix.reduce or molprobity.reduce? > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > 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 > > > > > > On Mon, Aug 12, 2019 at 12:43 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Christopher/ Nigel, > > > > Thank you for your quick reply. > > > > The build process was completed without any error. Pasting few of the > lines from it… > > > > > > ===== Running in build: rebuild rotarama > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rota8000-cys.data -> rota8000-cys.pickle: converting ... done. > > rota8000-asp.data -> rota8000-asp.pickle: converting ... done. > > rota8000-ser.data -> rota8000-ser.pickle: converting ... done. > > rota8000-gln.data -> rota8000-gln.pickle: converting ... done. > > rota8000-ile.data -> rota8000-ile.pickle: converting ... done. > > rota8000-pro.data -> rota8000-pro.pickle: converting ... done. > > rota8000-lys.data -> rota8000-lys.pickle: converting ... done. > > rota8000-thr.data -> rota8000-thr.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: converting ... done. > > rota8000-glu.data -> rota8000-glu.pickle: converting ... done. > > rota8000-met.data -> rota8000-met.pickle: converting ... done. > > rota8000-his.data -> rota8000-his.pickle: converting ... done. > > rota8000-leu.data -> rota8000-leu.pickle: converting ... done. > > rota8000-arg.data -> rota8000-arg.pickle: converting ... done. > > rota8000-trp.data -> rota8000-trp.pickle: converting ... done. > > rota8000-asn.data -> rota8000-asn.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: already up to date. > > rota8000-val.data -> rota8000-val.pickle: converting ... done. > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rama8000-ileval-nopreP.data -> rama8000-ileval-nopreP.pickle: converting > ... done. > > rama8000-gly-sym.data -> rama8000-gly-sym.pickle: converting ... done. > > rama8000-cispro.data -> rama8000-cispro.pickle: converting ... done. > > rama8000-general-noGPIVpreP.data -> rama8000-general-noGPIVpreP.pickle: > converting ... done. > > rama8000-transpro.data -> rama8000-transpro.pickle: converting ... done. > > rama8000-prepro-noGP.data -> rama8000-prepro-noGP.pickle: converting ... > done. > > u+s,u,s: 10.06 9.83 0.23 > > ===== Running in .: libtbx.refresh > > Python: 2.7.16 > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/bin/python2.7" > > Compiler: default > > Build mode: release > > Warning level: 0 > > Precompiled Headers: False > > Static libraries: False > > Static exe: False > > Scan Boost headers: False > > Write full flex_fwd.h files: False > > Build Boost.Python extensions: True > > Define BOOST_PYTHON_NO_PY_SIGNATURES: False > > Define BOOST_PYTHON_BOOL_INT_STRICT: True > > Enable OpenMP if possible: False > > Boost threads enabled: True > > Enable CUDA: False > > Use conda: False > > Use opt_resources if available: False > > Use environment flags: False > > Enable C++11: False > > Python3 migration warning policy: None > > command_version_suffix: None > > Relocatable paths anchored at: > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/build > > Top-down list of all modules involved: > > mmtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx" > > iotbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx" > > ccp4io+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io_adaptbx" > > smtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx" > > ucif > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/ucif" > > cctbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx" > > scitbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx" > > fable > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable" > > omptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/omptbx" > > boost+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/boost" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx" > > tbxx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/tbxx" > > chiltbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/chiltbx" > > libtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx" > > Creating files in build directory: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > dispatcher_include_template.sh > > dispatcher_head.sh > > setpaths.sh > > setpaths.csh > > setpaths_all.sh > > setpaths_all.csh > > setpaths_debug.sh > > unsetpaths.sh > > setpaths_debug.csh > > unsetpaths.csh > > SConstruct > > Makefile > > run_tests.csh > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py" > > Generating C++ header files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family/boost_python" > > Using fable to convert scitbx/lbfgs.f > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py" > > Generating C++ files in: > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/cctbx/eltbx" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/cctbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/smtbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py" > > Using fable to convert iotbx/pdb/hybrid_36_f.f > > Writing: iotbx/pdb/hybrid_36_fem.cpp > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py" > > Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/exe_dev" > > Regenerating module files in > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/pango not present, > could not regenerate pango files > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/gtk-2.0 not > present, could not regenerate gdk-pixbuf.loaders > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/fonts not present, > could not rebuild fonts > > generating index.theme file > > Done. > > > > *Bootstrap success: build* > > *++++++++++ MolProbity configure.sh finished.* > > > > > > > > [tm375568@uptus060-3 MolProbity]$ ./setup.sh > > ++++++++++ creating directories ... > > ++++++++++ setting permisions ... > > *Couldn't get a file descriptor referring to the console **à I assume > this can be ignored. * > > [tm375568@uptus060-3 MolProbity]$ > > > > Best Regards, > > Charitha Shetty > > > > *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Sent:* Monday, August 12, 2019 3:34 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Nigel Moriarty (nwmoriarty(a)lbl.gov) <nwmoriarty(a)lbl.gov>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Hmm. It looks like Reduce and/or Probe has failed to install correctly. > Most likely an early call to Reduce has resulted in an empty file, which is > then passed into other programs, resulting in error messages. > > > > The configure script ran a build process. Do you know if that process > finished successfully or if it ended with errors? If the build exited > early, it may have never reached the part where Reduce gets compiled. Some > dependencies have changed, and I have been having trouble with my own > builds lately. > > > > It is also possible that there was just a network hiccup that prevented > something from downloading correctly, and a second attempt will work. > > > > I am working on a new configure/install script for more consistent > handling of dependencies. Hopefully it will be ready in about a day. > > > > Good luck, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > > > > > > > > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* >

1 0

Re: [cctbxbb] Molprobity / CCTBX incompatibility
by Nigel Moriarty 19 Aug '19

19 Aug '19

Sorry guy, I was on holidays and the maintenance was a problem. Try putting the bootstrap.py in the directory that the command is being run. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging 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 On Fri, Aug 16, 2019 at 7:27 PM Christopher Williams < christopher.sci.williams(a)gmail.com> wrote: > Hmm. Nigel, I may need some of your expertise here. It looks like > there's a consistent problem with svn checkouts. > > "git clone" operations seem to have been successful, so it probably isn't > a matter of GitHub being down. Especially since the svn checkout of geostd > from Sourceforge also failed. > > Do you know if your system has problems with svn? Our svn checkouts > generally take this form: " svn co > https://github.com/rlabduke/MolProbity.git/trunk molprobity > --non-interactive --trust-server-cert " Is there perhaps a security > issue with the --trust-server-cert flag? > > I believe that the cci machines at Berkeley are under maintenance until > Sunday, so there are other reasons the script won't work until then. > > Good luck, > -Christopher Williams > ---Richardson Lab, Duke University > > > On Fri, Aug 16, 2019 at 5:45 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > >> Hi Christopher, >> >> >> >> I ran the installer script twice and this is what I got… >> >> >> >> *When I ran it first time, only the modules directory was created* >> >> bash-4.2$ *. install_via_bootstrap.sh 10* >> >> ++++++++++ creating build directories ... >> >> svn: E000110: Unable to connect to a repository at URL 'svn:// >> svn.code.sf.net/p/geostd/code/trunk' >> >> svn: E000110: Can't read from connection: Connection timed out >> >> svn: E175002: Unable to connect to a repository at URL ' >> https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_rotame… >> ' >> >> svn: E175002: OPTIONS of ' >> https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_rotame…': >> SSL handshake failed: SSL socket read failed (https://github.com) >> >> svn: E175002: Unable to connect to a repository at URL ' >> https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_ramach… >> ' >> >> svn: E175002: OPTIONS of ' >> https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_ramach…': >> SSL handshake failed: SSL socket read failed (https://github.com) >> >> svn: E175002: Unable to connect to a repository at URL ' >> https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_cablam… >> ' >> >> svn: E175002: OPTIONS of ' >> https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_cablam…': >> SSL handshake failed: SSL socket read failed (https://github.com) >> >> svn: E175002: Unable to connect to a repository at URL ' >> https://github.com/cctbx/cctbx_project.git/trunk/libtbx/auto_build/bootstra… >> ' >> >> svn: E175002: OPTIONS of ' >> https://github.com/cctbx/cctbx_project.git/trunk/libtbx/auto_build/bootstra…': >> SSL handshake failed: SSL socket read failed (https://github.com) >> >> python: can't open file 'bootstrap.py': [Errno 2] No such file or >> directory >> >> -bash: build/setpaths.sh: No such file or directory >> >> python: can't open file >> 'modules/chem_data/cablam_data/rebuild_cablam_cache.py': [Errno 2] No such >> file or directory >> >> ++++++++++ MolProbity configure.sh finished. >> >> ++++++++++ Run molprobity/setup.sh to complete installation. >> >> -bash-4.2$ >> >> >> >> -bash-4.2$ pwd >> >> /hpc/apps/current/molprobity/v4.4.app >> >> -bash-4.2$ ls -l >> >> total 31 >> >> *-rw-r--r-- 1 cbs72396 appmgmt 1817 Aug 14 14:03 >> install_via_bootstrap.sh* >> >> *drwxr-sr-x 3 cbs72396 appmgmt 3 Aug 15 17:58 modules* >> >> >> >> >> >> *Second time when I ran..bootstap.py and bootstrap.pyc was crated and the >> modules directory…* >> >> >> >> -bash-4.2$ *. install_via_bootstrap.sh 4* >> >> ++++++++++ creating build directories ... >> >> >> >> >> >> svn: E000110: Unable to connect to a repository at URL 'svn:// >> svn.code.sf.net/p/geostd/code/trunk' >> >> svn: E000110: Can't read from connection: Connection timed out >> >> Performing actions: hot update base build >> >> Installing base packages using: >> >> python modules/cctbx_project/libtbx/auto_build/install_conda.py >> --builder=molprobity --install_conda >> >> ===== Downloading http://cci.lbl.gov/repositories/annlib.gz: 0.5 MB >> >> [0%.........20%.........40%.........60%.........80%.........100%] >> >> ===== Running in modules: extracting files from annlib.gz >> >> ===== Downloading http://cci.lbl.gov/repositories/scons.gz: 0.6 MB >> >> [0%.........20%.........40%.........60%.........80%.........100%] >> >> ===== Running in modules: extracting files from scons.gz >> >> ===== Downloading http://cci.lbl.gov/repositories/ccp4io.gz: 1.4 MB >> >> [0%.........20%.........40%.........60%.........80%.........100%] >> >> ===== Running in modules: extracting files from ccp4io.gz >> >> ===== Running in modules: git clone --recursive >> https://github.com/cctbx/boost.git boost --progress --verbose >> >> Cloning into 'boost'... >> >> POST git-upload-pack (942 bytes) >> >> remote: Enumerating objects: 27664, done. >> >> remote: Total 27664 (delta 0), reused 0 (delta 0), pack-reused 27664 >> >> Receiving objects: 100% (27664/27664), 20.47 MiB | 14.72 MiB/s, done. >> >> Resolving deltas: 100% (15913/15913), done. >> >> Checking out files: 100% (14245/14245), done. >> >> setting branch master to rebase >> >> ===== Running in modules/boost: git rev-parse HEAD >> >> 72edfa007c73dd3dd01f5530205f7ca14cda7420 >> >> ===== Running in modules: git clone --recursive >> https://github.com/yayahjb/cbflib.git cbflib --progress --verbose >> >> Cloning into 'cbflib'... >> >> POST git-upload-pack (gzip 2442 to 1233 bytes) >> >> remote: Enumerating objects: 7463, done. >> >> remote: Total 7463 (delta 0), reused 0 (delta 0), pack-reused 7463 >> >> Receiving objects: 100% (7463/7463), 24.84 MiB | 13.21 MiB/s, done. >> >> Resolving deltas: 100% (5380/5380), done. >> >> setting branch master to rebase >> >> ===== Running in modules/cbflib: git rev-parse HEAD >> >> 611f21bbef81c5104954aaab9b72e4e55ec3e70d >> >> ===== Running in modules: git clone --recursive >> https://github.com/cctbx/cctbx_project.git cctbx_project --progress >> --verbose >> >> Cloning into 'cctbx_project'... >> >> POST git-upload-pack (gzip 1842 to 958 bytes) >> >> remote: Enumerating objects: 61, done. >> >> remote: Counting objects: 100% (61/61), done. >> >> remote: Compressing objects: 100% (52/52), done. >> >> remote: Total 243691 (delta 14), reused 22 (delta 9), pack-reused 243630 >> >> Receiving objects: 100% (243691/243691), 91.05 MiB | 14.77 MiB/s, done. >> >> Resolving deltas: 100% (192566/192566), done. >> >> Checking out files: 100% (6173/6173), done. >> >> setting branch master to rebase >> >> ===== Running in modules/cctbx_project: git rev-parse HEAD >> >> bd3139c85312f5f43009e1eb31baa34f41734fbb >> >> ===== Downloading http://cci.lbl.gov/repositories/ccp4io_adaptbx.gz: >> 203.9 kB >> >> [0%.........20%.........40%.........60%.........80%.........100%] >> >> ===== Running in modules: extracting files from ccp4io_adaptbx.gz >> >> ===== Running in modules: git clone --recursive >> https://github.com/cctbx/annlib_adaptbx.git annlib_adaptbx --progress >> --verbose >> >> Cloning into 'annlib_adaptbx'... >> >> POST git-upload-pack (842 bytes) >> >> remote: Enumerating objects: 175, done. >> >> remote: Total 175 (delta 0), reused 0 (delta 0), pack-reused 175 >> >> Receiving objects: 100% (175/175), 162.09 KiB | 0 bytes/s, done. >> >> Resolving deltas: 100% (77/77), done. >> >> setting branch master to rebase >> >> ===== Running in modules/annlib_adaptbx: git rev-parse HEAD >> >> 3ca66b2dd77eacd7524f915fce0705ac0764b46f >> >> ===== Downloading http://cci.lbl.gov/repositories/tntbx.gz: 38.0 kB >> >> [0%.........20%.........40%.........60%.........80%.........100%] >> >> ===== Running in modules: extracting files from tntbx.gz >> >> ===== Running in .: svn co >> https://github.com/rlabduke/MolProbity.git/trunk molprobity >> --non-interactive --trust-server-cert >> >> svn: E175002: Unable to connect to a repository at URL ' >> https://github.com/rlabduke/MolProbity.git/trunk' >> >> svn: E175002: OPTIONS of ' >> https://github.com/rlabduke/MolProbity.git/trunk': SSL handshake failed: >> SSL socket read failed (https://github.com) >> >> Process failed with return code 1 >> >> -bash: build/setpaths.sh: No such file or directory >> >> Traceback (most recent call last): >> >> File "modules/chem_data/cablam_data/rebuild_cablam_cache.py", line 2, >> in <module> >> >> import libtbx.load_env >> >> ImportError: No module named libtbx.load_env >> >> ++++++++++ MolProbity configure.sh finished. >> >> ++++++++++ Run molprobity/setup.sh to complete installation. >> >> -bash-4.2$ >> >> -bash-4.2$ >> >> *-bash-4.2$ ls -l* >> >> *total 131* >> >> *-rw-r--r-- 1 cbs72396 appmgmt 90799 Aug 14 18:26 bootstrap.py* >> >> *-rw-r--r-- 1 cbs72396 appmgmt 82015 Aug 16 13:38 bootstrap.pyc* >> >> *-rw-r--r-- 1 cbs72396 appmgmt 1817 Aug 14 14:03 >> install_via_bootstrap.sh* >> >> *drwxr-sr-x 12 cbs72396 appmgmt 22 Aug 16 13:38 modules* >> >> >> >> >> >> Best Regards, >> >> Charitha Shetty >> >> >> >> *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> >> *Sent:* Wednesday, August 14, 2019 2:23 PM >> *To:* Robert Nolte <robert.t.nolte(a)gsk.com> >> *Cc:* Nigel Moriarty <nwmoriarty(a)lbl.gov>; Charitha Belluru Shetty < >> charitha-belluru.b.shetty(a)gsk.com>; cctbxbb(a)phenix-online.org >> *Subject:* Re: Molprobity / CCTBX incompatibility >> >> >> >> *EXTERNAL* >> >> Hi All, >> >> >> >> Okay looks like the new installer works. It uses the conda mode of the >> cctbx bootstrap builder for everything except chem_data, which it builds on >> its own. >> >> >> >> Get the new installer from our GitHub here: >> >> svn --quiet --non-interactive --trust-server-cert export >> https://github.com/rlabduke/MolProbity.git/trunk/install_via_bootstrap.sh >> >> >> >> Place it in the dir where you want to install MolProbity, then run it. >> >> . install_via_bootstrap.sh >> >> The script optionally accepts a single integer argument to set the number >> of processors that the bootstrap builder will use. >> >> . install_via_bootstrap.sh 4 >> >> >> >> When this is complete, cd to the molprobity dir it created and run >> setup.sh, as usual. >> >> >> >> Good luck, >> >> -Christopher Williams >> >> ---Richardson Lab, Duke University >> >> >> >> >> >> On Wed, Aug 14, 2019 at 1:33 PM Christopher Williams < >> christopher.sci.williams(a)gmail.com> wrote: >> >> Hi Bob, >> >> >> >> I am currently doing one more test build to make sure that the new >> installer works. It looks promising. >> >> >> >> Regards, >> >> -Christopher Williams >> >> ---Richardson Lab, Duke University >> >> >> >> On Wed, Aug 14, 2019 at 11:17 AM Robert Nolte <robert.t.nolte(a)gsk.com> >> wrote: >> >> Folks, >> >> Any progress on sorting out our issue, or cleaning up the installer? >> >> Bob >> >> >> >> >> >> *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> >> *Sent:* Monday, August 12, 2019 7:48 PM >> *To:* Nigel Moriarty <nwmoriarty(a)lbl.gov> >> *Cc:* Robert Nolte <robert.t.nolte(a)gsk.com>; Charitha Belluru Shetty < >> charitha-belluru.b.shetty(a)gsk.com>; cctbxbb(a)phenix-online.org >> *Subject:* Re: Molprobity / CCTBX incompatibility >> >> >> >> *EXTERNAL* >> >> The dispatcher should be using both phenix.reduce and molprobity.reduce >> interchangeably in all cases. Ditto for all the validations that >> MolProbity runs like phenix.rotalyze/molprobity.rotalyze. >> >> >> >> My current install of MolProbity is successfully accessing Reduce via >> phenix.reduce, so I don't *think* this is the issue. >> >> >> >> -Christopher Williams >> >> ---Richardson Lab, Duke University >> >> >> >> On Mon, Aug 12, 2019 at 6:07 PM Nigel Moriarty <nwmoriarty(a)lbl.gov> >> wrote: >> >> But maybe the installation of cctbx has molprobity.reduce and not >> phenix.reduce so if that is the case we can change the script to look for >> molprobity.reduce instead of phenix.reduce. >> >> >> Cheers >> >> >> >> Nigel >> >> >> >> --- >> >> Nigel W. Moriarty >> Building 33R0349, Molecular Biophysics and Integrated Bioimaging >> >> 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 >> >> >> >> >> >> On Mon, Aug 12, 2019 at 2:58 PM Robert Nolte <robert.t.nolte(a)gsk.com> >> wrote: >> >> According to the log file when I just tried to run it, it is >> phenix.reduce that it can’t find. >> >> Bob >> >> >> >> >> >> *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> >> *Sent:* Monday, August 12, 2019 5:55 PM >> *To:* Robert Nolte <robert.t.nolte(a)gsk.com> >> *Cc:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com>; >> Christopher Williams <christopher.sci.williams(a)gmail.com>; >> cctbxbb(a)phenix-online.org >> *Subject:* Re: Molprobity / CCTBX incompatibility >> >> >> >> *EXTERNAL* >> >> I'm just trying to find out if, at the command line, whether it is >> phenix.reduce or molprobity.reduce. Charitha just needs to type one or the >> other to see what happens. >> >> >> Cheers >> >> >> >> Nigel >> >> >> >> --- >> >> Nigel W. Moriarty >> Building 33R0349, Molecular Biophysics and Integrated Bioimaging >> >> 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 >> >> >> >> >> >> On Mon, Aug 12, 2019 at 2:44 PM Robert Nolte <robert.t.nolte(a)gsk.com> >> wrote: >> >> Nigel, >> >> Currently it is not running. This was working from the scratch >> install last week. I am not sure what is going on now. >> >> Bob >> >> >> >> >> >> *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> >> *Sent:* Monday, August 12, 2019 4:52 PM >> *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> >> *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; >> cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> >> *Subject:* Re: Molprobity / CCTBX incompatibility >> >> >> >> *EXTERNAL* >> >> Does molprobity.reduce run? >> >> >> Cheers >> >> >> >> Nigel >> >> >> >> --- >> >> Nigel W. Moriarty >> Building 33R0349, Molecular Biophysics and Integrated Bioimaging >> >> 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 >> >> >> >> >> >> On Mon, Aug 12, 2019 at 1:14 PM Charitha Belluru Shetty < >> charitha-belluru.b.shetty(a)gsk.com> wrote: >> >> Hi Nigel, >> >> >> >> I hit the send button too soon..Ignore my previous email 😊 >> >> >> >> -bash-4.2$ source setpaths.sh >> >> -bash-4.2$ >> >> -bash-4.2$ env |grep -i reduce >> >> -bash-4.2$ >> >> >> >> So the “setpath.sh” has the below contents… >> >> >> >> $ cat /hpc/apps/current/molprobity/v4.4.app/MolProbity/build/setpaths.sh >> >> # THIS IS AN AUTOMATICALLY GENERATED FILE. >> >> # DO NOT EDIT! CHANGES WILL BE LOST. >> >> ocwd="`pwd`" >> >> if [ -n "$LIBTBX_BUILD_RELOCATION_HINT" ]; then >> >> cd "$LIBTBX_BUILD_RELOCATION_HINT" >> >> LIBTBX_BUILD_RELOCATION_HINT= >> >> export LIBTBX_BUILD_RELOCATION_HINT >> >> elif [ -n "$BASH_SOURCE" ]; then >> >> LIBTBX_BUILD=`dirname "$BASH_SOURCE[0]"` >> >> cd "$LIBTBX_BUILD" >> >> else >> >> cd "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" >> >> fi >> >> LIBTBX_BUILD=`pwd -P` >> >> export LIBTBX_BUILD >> >> LIBTBX_OPATH="$PATH" >> >> export LIBTBX_OPATH >> >> PATH="$LIBTBX_BUILD/bin:$PATH" >> >> export PATH >> >> cd "$ocwd" >> >> ocwd= >> >> alias libtbx.setpaths_all=". \"$LIBTBX_BUILD/setpaths_all.sh\"" >> >> alias libtbx.unsetpaths=". \"$LIBTBX_BUILD/unsetpaths.sh\"" >> >> if [ -n "$LIBTBX_OPATH" ]; then >> >> LIBTBX_TMPVAL="$LIBTBX_OPATH" >> >> else >> >> LIBTBX_TMPVAL= >> >> fi >> >> export LIBTBX_TMPVAL >> >> PATH=`libtbx.path_utility prepend LIBTBX_TMPVAL "$LIBTBX_BUILD/bin" < >> /dev/null` >> >> export PATH >> >> if [ "$PATH" = "L_I_B_T_B_X_E_M_P_T_Y" ]; then unset PATH; fi >> >> LIBTBX_TMPVAL= >> >> LIBTBX_OPATH= >> >> LIBTBX_BUILD= >> >> >> >> >> >> Best Regards, >> >> Charitha Shetty >> >> >> >> *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> >> *Sent:* Monday, August 12, 2019 4:08 PM >> *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> >> *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; >> cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> >> *Subject:* Re: Molprobity / CCTBX incompatibility >> >> >> >> *EXTERNAL* >> >> Once you source the setpaths.sh file in the build directory do you have >> phenix.reduce or molprobity.reduce? >> >> Cheers >> >> >> >> Nigel >> >> >> >> --- >> >> Nigel W. Moriarty >> Building 33R0349, Molecular Biophysics and Integrated Bioimaging >> >> 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 >> >> >> >> >> >> On Mon, Aug 12, 2019 at 12:43 PM Charitha Belluru Shetty < >> charitha-belluru.b.shetty(a)gsk.com> wrote: >> >> Hi Christopher/ Nigel, >> >> >> >> Thank you for your quick reply. >> >> >> >> The build process was completed without any error. Pasting few of the >> lines from it… >> >> >> >> >> >> ===== Running in build: rebuild rotarama >> >> Processing data files in >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": >> >> rota8000-cys.data -> rota8000-cys.pickle: converting ... done. >> >> rota8000-asp.data -> rota8000-asp.pickle: converting ... done. >> >> rota8000-ser.data -> rota8000-ser.pickle: converting ... done. >> >> rota8000-gln.data -> rota8000-gln.pickle: converting ... done. >> >> rota8000-ile.data -> rota8000-ile.pickle: converting ... done. >> >> rota8000-pro.data -> rota8000-pro.pickle: converting ... done. >> >> rota8000-lys.data -> rota8000-lys.pickle: converting ... done. >> >> rota8000-thr.data -> rota8000-thr.pickle: converting ... done. >> >> rota8000-phetyr.data -> rota8000-phetyr.pickle: converting ... done. >> >> rota8000-glu.data -> rota8000-glu.pickle: converting ... done. >> >> rota8000-met.data -> rota8000-met.pickle: converting ... done. >> >> rota8000-his.data -> rota8000-his.pickle: converting ... done. >> >> rota8000-leu.data -> rota8000-leu.pickle: converting ... done. >> >> rota8000-arg.data -> rota8000-arg.pickle: converting ... done. >> >> rota8000-trp.data -> rota8000-trp.pickle: converting ... done. >> >> rota8000-asn.data -> rota8000-asn.pickle: converting ... done. >> >> rota8000-phetyr.data -> rota8000-phetyr.pickle: already up to date. >> >> rota8000-val.data -> rota8000-val.pickle: converting ... done. >> >> Processing data files in >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": >> >> rama8000-ileval-nopreP.data -> rama8000-ileval-nopreP.pickle: >> converting ... done. >> >> rama8000-gly-sym.data -> rama8000-gly-sym.pickle: converting ... done. >> >> rama8000-cispro.data -> rama8000-cispro.pickle: converting ... done. >> >> rama8000-general-noGPIVpreP.data -> rama8000-general-noGPIVpreP.pickle: >> converting ... done. >> >> rama8000-transpro.data -> rama8000-transpro.pickle: converting ... done. >> >> rama8000-prepro-noGP.data -> rama8000-prepro-noGP.pickle: converting >> ... done. >> >> u+s,u,s: 10.06 9.83 0.23 >> >> ===== Running in .: libtbx.refresh >> >> Python: 2.7.16 >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/bin/python2.7" >> >> Compiler: default >> >> Build mode: release >> >> Warning level: 0 >> >> Precompiled Headers: False >> >> Static libraries: False >> >> Static exe: False >> >> Scan Boost headers: False >> >> Write full flex_fwd.h files: False >> >> Build Boost.Python extensions: True >> >> Define BOOST_PYTHON_NO_PY_SIGNATURES: False >> >> Define BOOST_PYTHON_BOOL_INT_STRICT: True >> >> Enable OpenMP if possible: False >> >> Boost threads enabled: True >> >> Enable CUDA: False >> >> Use conda: False >> >> Use opt_resources if available: False >> >> Use environment flags: False >> >> Enable C++11: False >> >> Python3 migration warning policy: None >> >> command_version_suffix: None >> >> Relocatable paths anchored at: >> /hpc/apps/2018/molprobity/v4.4.app/MolProbity/build >> >> Top-down list of all modules involved: >> >> mmtbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx" >> >> iotbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx" >> >> ccp4io+adaptbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io" >> >> >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io_adaptbx" >> >> smtbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx" >> >> ucif >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/ucif" >> >> cctbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx" >> >> scitbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx" >> >> fable >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable" >> >> omptbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/omptbx" >> >> boost+adaptbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/boost" >> >> >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx" >> >> tbxx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/tbxx" >> >> chiltbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/chiltbx" >> >> libtbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx" >> >> Creating files in build directory: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" >> >> dispatcher_include_template.sh >> >> dispatcher_head.sh >> >> setpaths.sh >> >> setpaths.csh >> >> setpaths_all.sh >> >> setpaths_all.csh >> >> setpaths_debug.sh >> >> unsetpaths.sh >> >> setpaths_debug.csh >> >> unsetpaths.csh >> >> SConstruct >> >> Makefile >> >> run_tests.csh >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py" >> >> Generating C++ header files in: >> >> >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family" >> >> Generating C++ files in: >> >> >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family/boost_python" >> >> Using fable to convert scitbx/lbfgs.f >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py" >> >> Generating C++ files in: >> >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/cctbx/eltbx" >> >> Generating C++ files in: >> >> >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/cctbx/boost_python" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py" >> >> Generating C++ files in: >> >> >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/smtbx/boost_python" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py" >> >> Using fable to convert iotbx/pdb/hybrid_36_f.f >> >> Writing: iotbx/pdb/hybrid_36_fem.cpp >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py" >> >> Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/exe_dev" >> >> Regenerating module files in >> /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base >> >> /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/pango not present, >> could not regenerate pango files >> >> /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/gtk-2.0 not >> present, could not regenerate gdk-pixbuf.loaders >> >> /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/fonts not present, >> could not rebuild fonts >> >> generating index.theme file >> >> Done. >> >> >> >> *Bootstrap success: build* >> >> *++++++++++ MolProbity configure.sh finished.* >> >> >> >> >> >> >> >> [tm375568@uptus060-3 MolProbity]$ ./setup.sh >> >> ++++++++++ creating directories ... >> >> ++++++++++ setting permisions ... >> >> *Couldn't get a file descriptor referring to the console **à I assume >> this can be ignored. * >> >> [tm375568@uptus060-3 MolProbity]$ >> >> >> >> Best Regards, >> >> Charitha Shetty >> >> >> >> *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> >> *Sent:* Monday, August 12, 2019 3:34 PM >> *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> >> *Cc:* Nigel Moriarty (nwmoriarty(a)lbl.gov) <nwmoriarty(a)lbl.gov>; >> cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> >> *Subject:* Re: Molprobity / CCTBX incompatibility >> >> >> >> *EXTERNAL* >> >> Hmm. It looks like Reduce and/or Probe has failed to install correctly. >> Most likely an early call to Reduce has resulted in an empty file, which is >> then passed into other programs, resulting in error messages. >> >> >> >> The configure script ran a build process. Do you know if that process >> finished successfully or if it ended with errors? If the build exited >> early, it may have never reached the part where Reduce gets compiled. Some >> dependencies have changed, and I have been having trouble with my own >> builds lately. >> >> >> >> It is also possible that there was just a network hiccup that prevented >> something from downloading correctly, and a second attempt will work. >> >> >> >> I am working on a new configure/install script for more consistent >> handling of dependencies. Hopefully it will be ready in about a day. >> >> >> >> Good luck, >> >> -Christopher Williams >> >> ---Richardson Lab, Duke University >> >> >> >> >> >> >> >> >> >> >> >> *GSK monitors email communications sent to and from GSK in order to >> protect GSK, our employees, customers, suppliers and business partners, >> from cyber threats and loss of GSK Information. GSK monitoring is conducted >> with appropriate confidentiality controls and in accordance with local laws >> and after appropriate consultation.* >> >> *GSK monitors email communications sent to and from GSK in order to >> protect GSK, our employees, customers, suppliers and business partners, >> from cyber threats and loss of GSK Information. GSK monitoring is conducted >> with appropriate confidentiality controls and in accordance with local laws >> and after appropriate consultation.* >> >> *GSK monitors email communications sent to and from GSK in order to >> protect GSK, our employees, customers, suppliers and business partners, >> from cyber threats and loss of GSK Information. GSK monitoring is conducted >> with appropriate confidentiality controls and in accordance with local laws >> and after appropriate consultation.* >> >> *GSK monitors email communications sent to and from GSK in order to >> protect GSK, our employees, customers, suppliers and business partners, >> from cyber threats and loss of GSK Information. GSK monitoring is conducted >> with appropriate confidentiality controls and in accordance with local laws >> and after appropriate consultation.* >> >> *GSK monitors email communications sent to and from GSK in order to >> protect GSK, our employees, customers, suppliers and business partners, >> from cyber threats and loss of GSK Information. GSK monitoring is conducted >> with appropriate confidentiality controls and in accordance with local laws >> and after appropriate consultation.* >> >> *GSK monitors email communications sent to and from GSK in order to >> protect GSK, our employees, customers, suppliers and business partners, >> from cyber threats and loss of GSK Information. GSK monitoring is conducted >> with appropriate confidentiality controls and in accordance with local laws >> and after appropriate consultation.* >> >

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Berkeley Server Downtime (8/16 - 8/18)
by Billy Poon 18 Aug '19

18 Aug '19

Dear all, On Friday, August 16, our servers will be shut down starting at 4:00 pm Pacific for scheduled maintenance in our building. We expect that the servers will be available by 10:00 am Pacific on Sunday (8/18) at the latest. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

1 1

Disruptive and counterproductive comments
by Graeme.Winter＠Diamond.ac.uk 17 Aug '19

17 Aug '19

Deliberately starting a new thread My thinking was that this was feedback on why users find it hard getting started on cctbx. I had assumed, incorrectly as it turns out, that on the developer list a wider discussion was appropriate. This was not meant as criticism, rather direct feedback from talking to potential users at diamond. However I sense that it was not welcome so I’ll keep my thoughts to myself. I’m obviously aware of the work Billy and co are doing to help the situation with conda, but I’m not aware of the longer term intentions for this. Anyhow, sorry for interfering Best wishes 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

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Re: [cctbxbb] CCTBX documentation questionnaire
by ben.williams＠diamond.ac.uk 16 Aug '19

16 Aug '19

Dear Dorothee, Is there a reason for only allowing a single choice of library in the questionnaire? I've wanted to use several components from across the CCTBX project and would like my response to reflect that. I'm sure there are probably others in the same boat. Many thanks, Ben — Ben Williams Post-doctoral research associate Scientific Software Diamond Light Source On 15 Aug 2019 20:05, Dorothee Liebschner <dcliebschner(a)lbl.gov> wrote: Hi everyone, During this year's ECM computing school, it came up that the CCTBX does not have a lot of documentation. This seems to be a major reason why people don't use it, even if they would like to employ the libraries. We would like to find out which parts of the CCTBX are the most interesting for users. We certainly cannot provide extensive documentation for the entire toolbox, but we can see what we can do once we know the main areas of interest. So if you were in the situation of wanting to use the CCTBX but decided to stay away from it because the documentation was non-existent or obscure, please let us know by filling out the questionnaire below (it's anonymous): questionnaire CCTBX documentation<https://forms.gle/9RawJFfHyEvhCVVP7> Best wishes, Dorothee -- Project Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org<https://phenix-online.org/> -- 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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cctbx azure pipelines skipping tests if clutter
by richard.gildea＠diamond.ac.uk 14 Aug '19

14 Aug '19

Hi, I noticed that the cctbx azure pipelines run libtbx.find_clutter as part of the Python "syntax" jobs, and if they find any "clutter", then the pipeline immediately fails and doesn't run any further tests (e.g. https://dev.azure.com/cctbx/cctbx_project/_build/results?buildId=374). This raises the following questions: 1) Why skip running tests just because "clutter" has been found? 2) Why run libtbx.find_clutter as part of the "syntax" job, as strictly speaking trailing whitespaces, unused imports etc, aren't syntax issues? 3) If finding clutter is so important, why not add an optional pre-commit hook to help prevent "clutter" ever being committed in the first place? 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 -- 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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