On 02/21/2012 08:36 AM, Davide Baù 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 Is there a reason this machine is years out of date?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
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
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
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 >
On 02/28/2012 03:14 AM, Davide Baù wrote: >> 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/
Odd that that would work, since 1) something similar is supposed to happen automatically when you build IMP anyway and 2) the problem you reported was with the algebra module, not kernel. But if it works for you...
> 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.
The "official IMP way" to do this would be to set the ldlibpath variable in config.py or on the scons command line.
Ben
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Ben Webb -
Daniel Russel -
Davide Baù