Re: [IMP-dev] Problem compiling IMP trunk on a Mac with Lion

[Daniel Russel <>]

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::Pointer<IMP::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::Pointer<IMP::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
> 
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