I think you may want to try build using clang instead of g++. I had the
similar problem with g++ but clang is fine.
Regards,
Wei
On Fri, Oct 28, 2016 at 6:08 AM, Gerhard Fischer
I am having some trouble setting up phenix.rosetta_refine on my Kubuntu 16.04 LTS-system.
I've been following the instructions found here: https://www.phenix-online.org/documentation/reference/rosetta_install.html
The installation/compilation of Rosetta as such (rosetta_src_2016.37.58930_bundle.tgz) worked fine, and so did installing the latest version of Phenix - here, I've tried both the binary available for download (phenix -installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6) and a self-compiled version (phenix-installer-1.11-2567-source).
But when running
rosetta.build_phenix_interface
(both with nproc=6 or no multiple processor options set), the compilation crashes at some point. This takes quite a while, and I suspect most parts get compiled, but it does not run to completion.
Any ideas? I attach the output of the error message below.
Best wishes,
Gerhard
------ stdout ---- g++ -o build/src/release/linux/4.4/64/x86/gcc/5.4/python/core/ scoring/cryst/PhenixInterface.os -c -std=c++11 -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_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/5.4 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)': src/core/scoring/cryst/PhenixInterface.cc:253:34: error: no matching function for call to 'core::pose::Pose::dump_pdb(char [256], const char [2])' pose_asu.dump_pdb( pdbout , "1" ); ^ In file included from src/core/scoring/cryst/PhenixInterface.cc:18:0: src/core/pose/Pose.hh:1518:2: note: candidate: bool core::pose::Pose::dump_pdb(const string&) const dump_pdb(std::string const & file_name) const; ^ src/core/pose/Pose.hh:1518:2: note: candidate expects 1 argument, 2 provided src/core/pose/Pose.hh:1521:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&) const dump_pdb(std::ostream & out) const; ^ src/core/pose/Pose.hh:1521:2: note: candidate expects 1 argument, 2 provided src/core/pose/Pose.hh:1525:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&, const utility::vector1<long unsigned int>&) const dump_pdb( ^ src/core/pose/Pose.hh:1525:2: note: no known conversion for argument 1 from 'char [256]' to 'std::ostream& {aka std::basic_ostream<char>&}' src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const core::pose::Pose&, std::__cxx11::string)': src/core/scoring/cryst/PhenixInterface.cc:916:34: error: no matching function for call to 'core::pose::Pose::dump_pdb(char [256], const char [2])' pose_asu.dump_pdb( buffer , "1" ); ^ In file included from src/core/scoring/cryst/PhenixInterface.cc:18:0: src/core/pose/Pose.hh:1518:2: note: candidate: bool core::pose::Pose::dump_pdb(const string&) const dump_pdb(std::string const & file_name) const; ^ src/core/pose/Pose.hh:1518:2: note: candidate expects 1 argument, 2 provided src/core/pose/Pose.hh:1521:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&) const dump_pdb(std::ostream & out) const; ^ src/core/pose/Pose.hh:1521:2: note: candidate expects 1 argument, 2 provided src/core/pose/Pose.hh:1525:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&, const utility::vector1<long unsigned int>&) const dump_pdb( ^ src/core/pose/Pose.hh:1525:2: note: no known conversion for argument 1 from 'char [256]' to 'std::ostream& {aka std::basic_ostream<char>&}' src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)': src/core/scoring/cryst/PhenixInterface.cc:244:25: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:375:13: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(".."); ^ src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const core::pose::Pose&, std::__cxx11::string)': src/core/scoring/cryst/PhenixInterface.cc:914:25: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:1080:13: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(".."); ^ src/core/scoring/cryst/PhenixInterface.cc: In member function 'std::__cxx11::string core::scoring::cryst::PhenixInterface:: calculateDensityMap(core::pose::Pose&, bool)': src/core/scoring/cryst/PhenixInterface.cc:1100:25: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:1109:13: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(".."); ^ scons: *** [build/src/release/linux/4.4/64/x86/gcc/5.4/python/core/ scoring/cryst/PhenixInterface.os] Error 1 scons: building terminated because of errors. --------- stdout end ------
-- Gerhard Fischer, PhD Postdoctoral Research Associate
University of Cambridge Department of Biochemistry 80 Tennis Court Road CB2 1GA Cambridge United Kingdom
--- This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]