[cctbxbb] Molprobity / CCTBX incompatibility
Nigel Moriarty
nwmoriarty at lbl.gov
Mon Aug 19 10:07:42 PDT 2019
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 at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
On Fri, Aug 16, 2019 at 7:27 PM Christopher Williams <
christopher.sci.williams at 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 at 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_rotamer_pct_contour_grids
>> '
>>
>> svn: E175002: OPTIONS of '
>> https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_rotamer_pct_contour_grids':
>> 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_ramachandran_pct_contour_grids
>> '
>>
>> svn: E175002: OPTIONS of '
>> https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_ramachandran_pct_contour_grids':
>> 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_pct_contour_grids
>> '
>>
>> svn: E175002: OPTIONS of '
>> https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_cablam_pct_contour_grids':
>> 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/bootstrap.py
>> '
>>
>> svn: E175002: OPTIONS of '
>> https://github.com/cctbx/cctbx_project.git/trunk/libtbx/auto_build/bootstrap.py':
>> 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 at gmail.com>
>> *Sent:* Wednesday, August 14, 2019 2:23 PM
>> *To:* Robert Nolte <robert.t.nolte at gsk.com>
>> *Cc:* Nigel Moriarty <nwmoriarty at lbl.gov>; Charitha Belluru Shetty <
>> charitha-belluru.b.shetty at gsk.com>; cctbxbb at 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 at 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 at gsk.com>
>> wrote:
>>
>> Folks,
>>
>> Any progress on sorting out our issue, or cleaning up the installer?
>>
>> Bob
>>
>>
>>
>>
>>
>> *From:* Christopher Williams <christopher.sci.williams at gmail.com>
>> *Sent:* Monday, August 12, 2019 7:48 PM
>> *To:* Nigel Moriarty <nwmoriarty at lbl.gov>
>> *Cc:* Robert Nolte <robert.t.nolte at gsk.com>; Charitha Belluru Shetty <
>> charitha-belluru.b.shetty at gsk.com>; cctbxbb at 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 at 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 at LBL.gov
>> Fax : 510-486-5909 Web : CCI.LBL.gov
>>
>>
>>
>>
>>
>> On Mon, Aug 12, 2019 at 2:58 PM Robert Nolte <robert.t.nolte at 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 at lbl.gov>
>> *Sent:* Monday, August 12, 2019 5:55 PM
>> *To:* Robert Nolte <robert.t.nolte at gsk.com>
>> *Cc:* Charitha Belluru Shetty <charitha-belluru.b.shetty at gsk.com>;
>> Christopher Williams <christopher.sci.williams at gmail.com>;
>> cctbxbb at 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 at LBL.gov
>> Fax : 510-486-5909 Web : CCI.LBL.gov
>>
>>
>>
>>
>>
>> On Mon, Aug 12, 2019 at 2:44 PM Robert Nolte <robert.t.nolte at 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 at lbl.gov>
>> *Sent:* Monday, August 12, 2019 4:52 PM
>> *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty at gsk.com>
>> *Cc:* Christopher Williams <christopher.sci.williams at gmail.com>;
>> cctbxbb at phenix-online.org; Robert Nolte <robert.t.nolte at 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 at 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 at 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 at lbl.gov>
>> *Sent:* Monday, August 12, 2019 4:08 PM
>> *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty at gsk.com>
>> *Cc:* Christopher Williams <christopher.sci.williams at gmail.com>;
>> cctbxbb at phenix-online.org; Robert Nolte <robert.t.nolte at 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 at 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 at 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 at 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 at uptus060-3 MolProbity]$
>>
>>
>>
>> Best Regards,
>>
>> Charitha Shetty
>>
>>
>>
>> *From:* Christopher Williams <christopher.sci.williams at gmail.com>
>> *Sent:* Monday, August 12, 2019 3:34 PM
>> *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty at gsk.com>
>> *Cc:* Nigel Moriarty (nwmoriarty at lbl.gov) <nwmoriarty at lbl.gov>;
>> cctbxbb at phenix-online.org; Robert Nolte <robert.t.nolte at 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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