[phenixbb] Cannot compile rosetta interface Centos 7 with 1.11.1

Nigel Moriarty nwmoriarty at lbl.gov
Mon Nov 7 09:39:13 PST 2016


Ludovic

Can you move to Rosetta 3.7 and let me know if it still fails?

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 Thu, Nov 3, 2016 at 9:16 AM, ludovic Pecqueur <
ludovic.pecqueur at college-de-france.fr> wrote:

> Dear Phenix developers,
>
> I installed the latest phenix version today (1.11.1-2575) on Centos 7.2
> I have rosetta_2016.13.58602
>
> When I try to compile the rosetta interface (after exporting
> PHENIX_ROSETTA_PATH), compilation fails (see end of message for errors).
>
> When I compile the rosetta interface using phenix 1.11-2567, compilation
> goes to completion without errors.
>
> If you have any idea of the change between the two versions leading to
> this issue.
>
> Thank you for your help,
>
> Ludovic.
>
> ########################
> Error message:
>
> Substituting phenix.python into build shell scripts
>   update_options.sh
>   update_ResidueType_enum_files.sh
> /usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_
> src_2016.13.58602_bundle/main/source
>
>   ~> phenix.python scons.py bin mode=release extras=python  -j 8
>
> scons: Reading SConscript files ...
> Running versioning script ... fatal: Not a git repository (or any parent
> up to mount point /usr/local)
> Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
> Done. (0.0 seconds)
> file ./options.dox being updated
> file ./full-options-list.md being updated
> Number of option files updated: 2
> Total 3657 options.
> Finished updating ResidueProperty code -- no changes needed
> Finished updating VariantType code -- no changes needed
> scons: done reading SConscript files.
> scons: Building targets ...
> g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/
> protocols/hybridization/CartesianSampler.os -c -std=c++98 -ffor-scope
> -isystem external/boost_1_55_0/ -isystem external/ -isystem
> external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic
> -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3
> -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s
> -Wno-unused-variable -Wno-unused-parameter -fPIC
> -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED
> -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG
> -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8
> -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux
> -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include
> -I/usr/local/include -Iexternal/include/python2.7
> src/protocols/hybridization/CartesianSampler.cc
> In file included from src/protocols/hybridization/
> CartesianSampler.cc:17:0:
> src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h:
> No such file or directory
>  #include "Python.h"
>                     ^
> compilation terminated.
> g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/
> protocols/cryst/cryst_movers.os -c -std=c++98 -ffor-scope -isystem
> external/boost_1_55_0/ -isystem external/ -isystem external/include/
> -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long
> -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math
> -funroll-loops -finline-functions -finline-limit=20000 -s
> -Wno-unused-variable -Wno-unused-parameter -fPIC
> -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED
> -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG
> -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8
> -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux
> -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include
> -I/usr/local/include -Iexternal/include/python2.7 src/protocols/cryst/cryst_
> movers.cc
> In file included from src/protocols/cryst/cryst_movers.cc:16:0:
> src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h:
> No such file or directory
>  #include "Python.h"
>                     ^
> compilation terminated.
> gcc -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libsqlite3.so
> -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/dbio/sqlite3/sqlite3.os
> -L/usr/lib -L/usr/local/lib -Lexternal/lib -lpython2.7 -ldl -lpthread -lutil
> g++ -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libcifparse.so
> -Wl,-rpath=/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_
> 2016.13.58602_bundle/main/source/build/external/release/
> linux/3.10/64/x86/gcc/4.8/python -Wl,-rpath=\$ORIGIN
> -Wl,-rpath=\$ORIGIN/../lib -shared build/external/release/linux/
> 3.10/64/x86/gcc/4.8/python/cifparse/BlockIO.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifDataInfo.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifExcept.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFile.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFileReadDef.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParentChild.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParserBase.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScannerBase.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifString.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DataInfo.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DicFile.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParserBase.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScannerBase.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Exceptions.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenCont.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenString.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ISTable.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ITTable.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_ptr_vector.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_vector.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ParentChild.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/
> cifparse/RcsbFile.!
>  os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbPlatform.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Serializer.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TableFile.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TTable.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParser.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScanner.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParser.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScanner.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regcomp.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regerror.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regexec.os
> build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regfree.os
> -Lexternal/lib -Lbuild/external/release/linux/3.10/64/x86/gcc/4.8/python
> -Lexternal -L/usr/lib -L/usr/local/lib -lpython2.7 -ldl -lpthread -lutil
> g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/
> scoring/cryst/PhenixInterface.os -c -std=c++98 -ffor-scope -isystem
> external/boost_1_55_0/ -isystem external/ -isystem external/include/
> -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long
> -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math
> -funroll-loops -finline-functions -finline-limit=20000 -s
> -Wno-unused-variable -Wno-unused-parameter -fPIC
> -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED
> -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG
> -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8
> -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux
> -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include
> -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/
> PhenixInterface.cc
> In file included from src/core/scoring/cryst/PhenixInterface.cc:15:0:
> src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h:
> No such file or directory
>  #include "Python.h"
>                     ^
> compilation terminated.
> g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os
> -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem
> external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall
> -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2
> -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions
> -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC
> -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED
> -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG
> -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8
> -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux
> -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include
> -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/
> XtalMLEnergy.cc
> In file included from src/core/scoring/cryst/XtalMLEnergy.cc:16:0:
> src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h:
> No such file or directory
>  #include "Python.h"
>                     ^
> compilation terminated.
> scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/
> protocols/hybridization/CartesianSampler.os] Error 1
> scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/
> protocols/cryst/cryst_movers.os] Error 1
> scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/
> scoring/cryst/PhenixInterface.os] Error 1
> scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os]
> Error 1
> scons: building terminated because of errors.
>
>
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