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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 Baà 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 <> wrote:
>>> On 02/21/2012 08:36 AM, Davide BaÅ 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
>>> --
>>> http://salilab.org/~ben/
>>> "It is a capital mistake to theorize before one has data."
>>> - Sir Arthur Conan Doyle
>>> _______________________________________________
>>> IMP-dev mailing list
>>>
>>> https://salilab.org/mailman/listinfo/imp-dev
>>
>> _______________________________________________
>> IMP-dev mailing list
>>
>> https://salilab.org/mailman/listinfo/imp-dev
>