Created attachment 406825 [details] preprocessed sources Description of problem: While compiling RDkit (http://rdkit.org/), a boost based project I am getting an internal compiler error. As requested by the message, I'm attaching here the .out file Last part of error message: /home/ric/MIDB/rdkit_070415/Code/GraphMol/Wrap/EditableMol.cpp:114: instantiated from here /home/ric/boost/include/boost/type_traits/detail/cv_traits_impl.hpp:37: internal compiler error: in make_rtl_for_nonlocal_decl, at cp/decl.c:5067 Please submit a full bug report, with preprocessed source if appropriate. See <URL:http://bugzilla.redhat.com/bugzilla> for instructions. Preprocessed source stored into /tmp/ccqsYSQx.out file, please attach this to your bugreport. make[2]: *** [Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o] Error 1 make[1]: *** [Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all] Error 2
This seems to be http://gcc.gnu.org/PR33094, which is even applied on redhat/gcc-4_1-branch, but not on redhat/gcc-4_1-fc6 branch RHEL5 gcc is based on. The patch is backportable to RHEL5 and is not risky.
Thanks Jakub for looking into this. I suggest you also check bug 503565 and bug 508735 as they reference the same make_rtl_for_nonlocal_decl function so maybe you can close three with one patch ;)
Created attachment 415636 [details] Preprocessed source Hi, I tried to compile pycuda: # /usr/bin/python setup.py build Scanning installed packages Setuptools installation detected at /usr/local/pycuda Non-egg installation Removing elements out of the way... Already patched. /usr/local/pycuda/setuptools-0.6c9-py2.6.egg-info already patched. Extracting in /tmp/tmpBOz-Wu Now working in /tmp/tmpBOz-Wu/distribute-0.6.4 Building a Distribute egg in /usr/local/pycuda /usr/local/pycuda/setuptools-0.6c9-py2.4.egg-info already exists /usr/local/boost /boost/ python .hpp /usr/local/boost/stage/lib / lib boost_python .so /usr/local/boost/stage/lib / lib boost_thread .so /usr/local/cuda /bin/ nvcc /usr/local/cuda/include / cuda .h /usr/local/cuda/lib / lib cuda .so /usr/local/cuda/lib / lib cuda .dylib /usr/local/cuda/lib / lib cuda .lib /usr/local/cuda/lib / cuda .so /usr/local/cuda/lib / cuda .dylib /usr/local/cuda/lib / cuda .lib /usr/local/cuda/lib / cuda .so /usr/local/cuda/lib / cuda .dylib /usr/local/cuda/lib / cuda .lib /usr/local/cuda/lib / cuda .so /usr/local/cuda/lib / cuda .dylib /usr/local/cuda/lib / cuda .lib *** Cannot find CUDA driver library. Checked locations: /usr/local/cuda/lib/libcuda.so /usr/local/cuda/lib/libcuda.dylib /usr/local/cuda/lib/libcuda.lib /usr/local/cuda/lib/cuda.so /usr/local/cuda/lib/cuda.dylib /usr/local/cuda/lib/cuda.lib /usr/local/cuda/lib/cuda.so /usr/local/cuda/lib/cuda.dylib /usr/local/cuda/lib/cuda.lib /usr/local/cuda/lib/cuda.so /usr/local/cuda/lib/cuda.dylib /usr/local/cuda/lib/cuda.lib *** Note that this may not be a problem as this component is often installed system-wide. /usr/lib64/python2.4/distutils/dist.py:236: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) running build running build_py running build_ext building '_driver' extension gcc -pthread -fno-strict-aliasing -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -O3 -DNDEBUG -fPIC -Isrc/cpp -I/usr/local/boost -I/usr/local/cuda/include -I/usr/lib64/python2.4/site-packages/numpy/core/include -I/usr/include/python2.4 -c src/wrapper/mempool.cpp -o build/temp.linux-x86_64-2.4/src/wrapper/mempool.o src/cpp/mempool.hpp: In instantiation of ‘pycuda::memory_pool<<unnamed>::device_allocator>’: src/wrapper/mempool.cpp:85: instantiated from ‘<unnamed>::context_dependent_memory_pool<<unnamed>::device_allocator>’ src/cpp/mempool.hpp:284: instantiated from ‘pycuda::pooled_allocation<<unnamed>::context_dependent_memory_pool<<unnamed>::device_allocator> >’ src/wrapper/mempool.cpp:100: instantiated from here src/cpp/mempool.hpp:48: warning: ‘class pycuda::memory_pool<<unnamed>::device_allocator>’ has virtual functions but non-virtual destructor src/wrapper/mempool.cpp: In instantiation of ‘<unnamed>::context_dependent_memory_pool<<unnamed>::device_allocator>’: src/cpp/mempool.hpp:284: instantiated from ‘pycuda::pooled_allocation<<unnamed>::context_dependent_memory_pool<<unnamed>::device_allocator> >’ src/wrapper/me . . . /usr/local/boost/boost/type_traits/is_volatile.hpp:52: instantiated from ‘boost::is_volatile<<unnamed>::pooled_host_allocation>’ /usr/local/boost/boost/type_traits/remove_const.hpp:54: instantiated from ‘boost::detail::remove_const_impl<<unnamed>::pooled_host_allocation>’ /usr/local/boost/boost/type_traits/remove_const.hpp:61: instantiated from ‘boost::remove_const<<unnamed>::pooled_host_allocation>’ /usr/local/boost/boost/python/object/pointer_holder.hpp:127: instantiated from ‘void* boost::python::objects::pointer_holder<Pointer, Value>::holds(boost::python::type_info, bool) [with Pointer = std::auto_ptr<<unnamed>::pooled_host_allocation>, Value = <unnamed>::pooled_host_allocation]’ src/wrapper/mempool.cpp:278: instantiated from here /usr/local/boost/boost/type_traits/detail/cv_traits_impl.hpp:38: internal compiler error: in make_rtl_for_nonlocal_decl, at cp/decl.c:5067 Please submit a full bug report, with preprocessed source if appropriate. See <URL:http://bugzilla.redhat.com/bugzilla> for instructions. Preprocessed source stored into /tmp/cccT6FJK.out file, please attach this to your bugreport. error: command 'gcc' failed with exit status 1 gcc -v Using built-in specs. Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux Thread model: posix gcc version 4.1.2 20080704 (Red Hat 4.1.2-46)
*** Bug 597380 has been marked as a duplicate of this bug. ***
In gcc-4.1.2-49.el5
An advisory has been issued which should help the problem described in this bug report. This report is therefore being closed with a resolution of ERRATA. For more information on therefore solution and/or where to find the updated files, please follow the link below. You may reopen this bug report if the solution does not work for you. http://rhn.redhat.com/errata/RHSA-2011-0025.html