It looks like that benchmark doesn't properly disable itself when you don't have hdf5 installed. You can safetly ignore it for now (just use -k with scons). On Oct 7, 2011, at 1:50 AM, Davide Baù wrote:
> I have re-run scones without the -j option. It seems that it's a problem with domino? > > Davide > >> g++ -o modules/benchmark/bin/benchmark_domino_container.o -c -isystem /usr/src/imp/imp-r11289 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wundef - >> Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop- >> optimizations -fno-signed-zeros -freciprocal-math -fassociative-math -DBOOST_ALL_NO_LIB -Ibuild/include -Ibuild/src modules/benchmark/bin/benchmark_domino_container.cpp >> modules/benchmark/bin/benchmark_domino_container.cpp: In function 'int main(int, char**)': >> modules/benchmark/bin/benchmark_domino_container.cpp:43:5: error: 'RMF' has not been declared >> modules/benchmark/bin/benchmark_domino_container.cpp:43:19: error: expected ';' before 'file' >> modules/benchmark/bin/benchmark_domino_container.cpp:45:5: error: 'RMF' has not been declared >> modules/benchmark/bin/benchmark_domino_container.cpp:45:29: error: expected ';' before 'ds' >> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: 'HDF5AssignmentContainer' was not declared in this scope >> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: template argument 1 is invalid >> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: invalid type in declaration before '(' token >> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: expected type-specifier before 'HDF5AssignmentContainer' >> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: expected ')' before 'HDF5AssignmentContainer' >> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: invalid conversion from 'int*' to 'int' >> modules/benchmark/bin/benchmark_domino_container.cpp:47:7: error: base operand of '->' is not a pointer >> modules/benchmark/bin/benchmark_domino_container.cpp:48:21: error: 'HDF5AssignmentContainer' cannot appear in a constant-expression >> modules/benchmark/bin/benchmark_domino_container.cpp:48:65: error: no matching function for call to 'benchmark_table(int&, const char [14])' >> modules/benchmark/bin/benchmark_domino_container.cpp:51:5: error: 'RMF' has not been declared >> modules/benchmark/bin/benchmark_domino_container.cpp:51:19: error: expected ';' before 'file' >> modules/benchmark/bin/benchmark_domino_container.cpp:53:5: error: 'RMF' has not been declared >> modules/benchmark/bin/benchmark_domino_container.cpp:53:29: error: expected ';' before 'ds' >> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: 'HDF5AssignmentContainer' was not declared in this scope >> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: template argument 1 is invalid >> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: invalid type in declaration before '(' token >> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: expected type-specifier before 'HDF5AssignmentContainer' >> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: expected ')' before 'HDF5AssignmentContainer' >> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: invalid conversion from 'int*' to 'int' >> modules/benchmark/bin/benchmark_domino_container.cpp:55:7: error: base operand of '->' is not a pointer >> modules/benchmark/bin/benchmark_domino_container.cpp:56:21: error: 'HDF5AssignmentContainer' cannot appear in a constant-expression >> modules/benchmark/bin/benchmark_domino_container.cpp:56:56: error: no matching function for call to 'benchmark_table(int&, const char [5])' >> modules/benchmark/bin/benchmark_domino_container.cpp:60:21: error: 'HDF5AssignmentContainer' was not declared in this scope >> modules/benchmark/bin/benchmark_domino_container.cpp:60:68: error: no matching function for call to 'benchmark_table(IMP::base::PointerIMP::domino::PackedAssignmentContainer&, const char [17])' >> modules/benchmark/bin/benchmark_domino_container.cpp:64:21: error: 'HDF5AssignmentContainer' was not declared in this scope >> modules/benchmark/bin/benchmark_domino_container.cpp:64:66: error: no matching function for call to 'benchmark_table(IMP::base::PointerIMP::domino::ListAssignmentContainer&, const char [15])' >> scons: *** [modules/benchmark/bin/benchmark_domino_container.o] Error 1 >> scons: building terminated because of errors. > > >> Enabled dependencies: CGAL, Boost.ProgramOptions, Boost.Thread, Boost >> Disabled dependencies: Bullet, HDF5, OpenCV21, ANN, Boost.FileSystem, modeller, FFTW3, GSL, OpenCV22 >> >> Enabled modules: em, kernel, scratch, domino, misc, statistics, container, saxs, system, parallel, example, benchmark, core, algebra, cgal, restrainer, example_system_local, base, atom, compatibility, display >> Disabled modules: rmf, RMF, multifit, bullet, gsl, modeller, em2d >> >> Enabled applications: saxs_tools, em_tools, foxs >> Disabled applications: rmf_tools, ligand_score, nup84, multifit, example_system, rnapii >> >> Enabled systems: Groel >> >> Errors building: >> modules/benchmark/bin/benchmark_domino_container.o > > > > <config.log> > > > On Oct 6, 2011, at 5:27 PM, Daniel Russel wrote: >> I think the linux errors are elsewhere in the output (you are probably using -j n with n>1 and so different build commands and errors are woven together). >> >> On Oct 6, 2011, at 3:49 AM, Davide Baù wrote: >> >>> You're right. I had some references to ExampleLib in a local library. That solved the issue on my Mac but not on my linux machine (updated to revision 11289 on both machines): >>> >>>> g++ -o modules/benchmark/bin/benchmark_knn -Wl,-rpath=/usr/src/imp/imp-r11289 modules/benchmark/bin/benchmark_knn.o -Lbuild/lib -L. -limp_benchmark -limp_domino -limp_display -limp_em -limp_atom -limp_con >>>> tainer -limp_core -limp_statistics -limp -limp_algebra -limp_cgal -limp_base -limp_compatibility -lCGAL -lgmp -lmpfr -lgmpxx -lboost_thread -lpthread -lmscons: *** [modules/benchmark/bin/benchmark_domino_container.o] Error 1scons: building terminated because of errors. >>> >>> I don't know if it depends on CGAL which is installed anyway. >>> Davide > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev