[cctbxbb] Molprobity / CCTBX incompatibility

[Nigel Moriarty]

That is the correct directory for the general Phenix install.

@Christopher Williams <christopher.sci.williams at 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 at 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 at 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 at lbl.gov>
> *Sent:* Monday, August 19, 2019 1:08 PM
> *To:* Christopher Williams <christopher.sci.williams at gmail.com>
> *Cc:* Charitha Belluru Shetty <charitha-belluru.b.shetty at gsk.com>; Robert
> Nolte <robert.t.nolte at gsk.com>; cctbxbb at 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 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.*
>
> *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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