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@lbl.gov>
Sent: Monday, August 12, 2019 5:55 PM
To: Robert Nolte <robert.t.nolte@gsk.com>
Cc: Charitha Belluru Shetty <charitha-belluru.b.shetty@gsk.com>; Christopher Williams <christopher.sci.williams@gmail.com>; cctbxbb@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 BioimagingLawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty@LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
On Mon, Aug 12, 2019 at 2:44 PM Robert Nolte <robert.t.nolte@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@lbl.gov>
Sent: Monday, August 12, 2019 4:52 PM
To: Charitha Belluru Shetty <charitha-belluru.b.shetty@gsk.com>
Cc: Christopher Williams <christopher.sci.williams@gmail.com>; cctbxbb@phenix-online.org; Robert Nolte <robert.t.nolte@gsk.com>
Subject: Re: Molprobity / CCTBX incompatibility
EXTERNAL
Does molprobity.reduce run?
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated BioimagingLawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty@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@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@lbl.gov>
Sent: Monday, August 12, 2019 4:08 PM
To: Charitha Belluru Shetty <charitha-belluru.b.shetty@gsk.com>
Cc: Christopher Williams <christopher.sci.williams@gmail.com>; cctbxbb@phenix-online.org; Robert Nolte <robert.t.nolte@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 BioimagingLawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty@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@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@gmail.com>
Sent: Monday, August 12, 2019 3:34 PM
To: Charitha Belluru Shetty <charitha-belluru.b.shetty@gsk.com>
Cc: Nigel Moriarty (nwmoriarty@lbl.gov) <nwmoriarty@lbl.gov>; cctbxbb@phenix-online.org; Robert Nolte <robert.t.nolte@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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