[cctbxbb] Molprobity / CCTBX incompatibility
Nigel Moriarty
nwmoriarty at lbl.gov
Mon Aug 12 13:51:49 PDT 2019
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
>
>
>
>
>
>
>
>
>
>
>
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