[cctbxbb] Molprobity / CCTBX incompatibility

Nigel Moriarty nwmoriarty at lbl.gov
Mon Aug 12 15:07:15 PDT 2019


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.*
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20190812/32ea461b/attachment-0001.htm>


More information about the cctbxbb mailing list