Hi,
just to let you know that I managed to compile version 12787 on the RedHat based machine.
>From the IT department they suggested me to copy the include/internal did to the build dir: > cp -r ./modules/kernel/include/internal/ build/include/
Doing so, the code compiles. Also, in order to properly use the code via the imppy.sh script, I just needed to add "$LD_LIBRARY_PATH" at the end of the LD_LIBRARY_PATH definition.
Davide
On Feb 22, 2012, at 10:04 AM, Davide Baù wrote:
> Hi, > > I did a checkout of the last release (r12796), but I still have the same compilation error: > Errors building: > build/src/IMP.algebra.py > > Could it depend on the OS version? > >> Linking Program modules/algebra/bin/benchmark_rotate >> Building version check /project/devel/dbau/imp/imp-r12796/build/lib/IMP/algebra/_version_check.py >> Generating swig interface build/swig/IMP_algebra.i from modules/algebra/pyext/swig.i-in >> Install file: "modules/algebra/pyext/IMP_algebra_bounding_box.i" as "build/swig/IMP_algebra_bounding_box.i" >> Install file: "modules/algebra/pyext/IMP_algebra_matrix2d.i" as "build/swig/IMP_algebra_matrix2d.i" >> Install file: "modules/algebra/pyext/IMP_algebra_matrix3d.i" as "build/swig/IMP_algebra_matrix3d.i" >> Install file: "modules/algebra/pyext/IMP_algebra_spherical_coords.i" as "build/swig/IMP_algebra_spherical_coords.i" >> Install file: "modules/algebra/pyext/IMP_algebra_transformation2d.i" as "build/swig/IMP_algebra_transformation2d.i" >> Install file: "modules/algebra/pyext/IMP_algebra_transformation3d.i" as "build/swig/IMP_algebra_transformation3d.i" >> Install file: "modules/algebra/pyext/IMP_algebra_types.i" as "build/swig/IMP_algebra_types.i" >> Install file: "modules/algebra/pyext/IMP_algebra_vector.i" as "build/swig/IMP_algebra_vector.i" >> Install file: "build/swig/IMP_algebra.i" as "build/data/swig/IMP_algebra.i" >> Running swig on file build/swig/IMP_algebra.i >> /apps/SWIG/2.0.4/bin/swig -castmode -interface _IMP_algebra -DPySwigIterator=IMP_ALGEBRA_PySwigIterator -DSwigPyIterator=IMP_ALGEBRA_SwigPyIterator -python -c++ -naturalvar -fvirtual -Wextra -o /project/devel/dbau/imp/imp-r12796/build/src/IMP_algebra_wrap.cpp-in -oh /project/devel/dbau/imp/imp-r12796/build/src/IMP_algebra_wrap.h-in -Ibuild/swig -I/apps/IMP/include/ -I/apps/BOOST/1_48_0/include -I/apps/CGAL/3.9/include -I/project/devel/dbau/imp/imp-r12796/build/include -I/apps/SWIG/2.0.4/bin -DIMP_SWIG /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i >> /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i:243: Error: Template 'GridD' undefined. >> /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i:244: Error: Template 'GridD' undefined. >> /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i:245: Error: Template 'GridD' undefined. >> /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i:246: Error: Template 'GridD' undefined. >> /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i:247: Error: Template 'GridD' undefined. >> /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i:248: Error: Template 'GridD' undefined. >> /project/devel/dbau/imp/imp-r12796/build/swig/IMP_algebra.i:249: Error: Template 'GridD' undefined. >> scons: *** Error 7 >> Running swig on file build/swig/IMP_algebra.i >> scons: *** [build/src/IMP.algebra.py] Error 7 >> scons: building terminated because of errors. >> >> >> IMP configuration: >> boost ='yes' >> boostlibs ='' >> boostversion ='104800' >> boostlibsuffix ='' >> endian ='little' >> boost_filesystem ='yes' >> boost_filesystemlibs='boost_filesystem' >> google_perftools_profile='no' >> hdf5 ='no' >> boost_thread ='yes' >> boost_threadlibs ='boost_thread' >> cgal ='no' >> ann ='no' >> gsl ='no' >> fftw3 ='no' >> boost_programoptions='no' >> opencv21 ='no' >> opencv22 ='no' >> eigen3 ='no' >> cholmod ='no' >> build ='fast' >> prefix ='/usr' >> local ='True' >> pythonpath ='/project/devel/dbau/imp/imp-r12796' >> libpath ='/apps/BOOST/1_48_0/lib' >> ldlibpath ='/project/devel/dbau/imp/imp-r12796' >> swigpath ='/apps/SWIG/2.0.4/bin' >> datapath ='/project/devel/dbau/imp/imp-r12796' >> cxxcompiler ='g++' >> cxxflags='-isystem /apps/IMP/include -isystem /apps/BOOST/1_48_0/include -isystem /apps/CGAL/3.9/include -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' >> pythoncxxflags ='-isystem /apps/IMP/include -isystem /apps/BOOST/1_48_0/include -isystem /apps/CGAL/3.9/include -Wno-deprecated -Winit-self -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -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' >> bincxxflags='-isystem /apps/IMP/include -isystem /apps/BOOST/1_48_0/include -isystem /apps/CGAL/3.9/include -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' >> shliblinkflags =' -shared' >> arliblinkflags ='' >> binlinkflags ='' >> pythonlinkflags =' -shared' >> rpath ='True' >> static ='False' >> pythonsosuffix ='.so' >> pkgconfig ='True' >> path ="/apps/GCC/4.6.2/bin:/apps/PYTHON/2.7.2/bin:/apps/modules//wrappers/fortran:/apps/modules//wrappers/c++:/apps/modules//wrappers/c:/opt/mpi/mpibull2-1.3.9-18.s/bin:/opt/intel/Compiler/11.0/069/bin/intel64:/usr/kerberos/bin:/opt/cuda//bin:/usr/local/bin:/bin:/usr/bin:/home/devel/dbau/bin" >> python ="/apps/PYTHON/2.7.2/bin/python" >> >> >> Enabled dependencies: Boost.FileSystem, Boost.Thread, Boost >> Disabled dependencies: HDF5, OpenCV21, CGAL, ANN, Boost.ProgramOptions, modeller, CHOLMOD, eigen3, google_perftools_profile, FFTW3, GSL, OpenCV22 >> >> Enabled modules: em, kernel, scratch, domino, misc, fivec, statistics, container, saxs, system, parallel, example, benchmark, core, algebra, restrainer, example_system_local, base, atom, compatibility, pepdock, display >> Disabled modules: rmf, RMF, cgal, multifit, gsl, modeller, em2d, isd >> >> Enabled applications: em_tools >> Disabled applications: rmf_tools, pdb_tools, saxs_merge, saxs_tools, em3d_dock, rnapii, foxsdock, nup84, example_system, nmr_rtc, multifit_tools, em2d_dock, ligand_score, foxs >> >> Enabled systems: Groel >> >> Errors building: >> build/src/IMP.algebra.py > > > On Feb 21, 2012, at 11:11 PM, Daniel Russel wrote: > >> To fix the last problem, I would suggest removing all build and scons >> files (if you are building out or source, do "rm -rf .scon* modules >> build applications" if you are building in source, then just do "rm >> -rf .scons* build" and you are probably OK. Scons gets easily >> confused. >> >> On Tue, Feb 21, 2012 at 10:27 AM, Ben Webb ben@salilab.org wrote: >>> On 02/21/2012 08:36 AM, Davide Baů wrote: >>>> >>>> On Feb 21, 2012, at 5:23 PM, Ben Webb wrote: >>>>> >>>>> Is there a reason this machine is years out of date? (The latest >>>>> update for RHEL 5 is 5.7.) It seems entirely possible that a bug in >>>>> one of the system headers was fixed in the interim. >>>> >>>> Actually I don't know. I will contact the informatics department to >>>> ask if it is possible to update the system (unfortunately we can >>>> just "use" the cluster.) >>> >>> >>> You can point them to http://en.wikipedia.org/wiki/RHEL#Version_history >>> 5.3 has been obsolete since 5.4 was released in September 2009. >>> >>>> I got a error on the algebra module: Errors building: >>>> build/src/IMP.algebra.py. It's curious that there's a red box on the >>>> algebra module on Mac while it compiled with no errors on my Mac. >>> >>> >>> It's a different Mac (32-bit code is built on a 10.4 - Tiger - machine). >>> Chances are your machine is more similar to our Snow Leopard 64-bit build >>> machine. I've added more descriptive labels to this page, which should show >>> up tomorrow. >>> >>> ... >>>> >>>> /project/devel/dbau/imp/imp-r12787/build/swig/IMP_algebra.i:243: >>>> Error: Template 'GridD' undefined. >>>> /project/devel/dbau/imp/imp-r12787/build/swig/IMP_algebra.i:244: >>>> Error: Template 'GridD' undefined. >>>> /project/devel/dbau/imp/imp-r12787/build/swig/IMP_algebra.i:245: >>>> Error: Template 'GridD' undefined. >>>> /project/devel/dbau/imp/imp-r12787/build/swig/IMP_algebra.i:246: >>>> Error: Template 'GridD' undefined. >>>> /project/devel/dbau/imp/imp-r12787/build/swig/IMP_algebra.i:247: >>>> Error: Template 'GridD' undefined. >>>> /project/devel/dbau/imp/imp-r12787/build/swig/IMP_algebra.i:248: >>>> Error: Template 'GridD' undefined. >>>> /project/devel/dbau/imp/imp-r12787/build/swig/IMP_algebra.i:249: >>> >>> >>> Odd. The SWIG file should be parsing algebra's GridD.h header, which defines >>> that template. But Daniel did make some changes there recently - are you >>> sure you don't have a mismatch of versions somewhere (perhaps an older >>> version of GridD.h paired with a newer SWIG interface)? I'd suggest a fresh >>> checkout to be sure. >>> >>> Ben >>> -- >>> ben@salilab.org http://salilab.org/~ben/ >>> "It is a capital mistake to theorize before one has data." >>> - Sir Arthur Conan Doyle >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >