Script started on Mon 05 Mar 2012 06:55:37 PM EST [NOTE: environment variables needed to build and run from the build directory on Mirasol] bash-4.1$ ls ~alugowski/KDT kdt-0.2-beta2.tar.gz KDT_env_vars.txt bash-4.1$ cp ~alugowski/KDT/kdt-0.2-beta2.tar.gz . bash-4.1$ cat ~alugowski/KDT/KDT_env_vars.txt # for compilation export PATH=$PATH:/usr/lib64/openmpi/bin export CC=mpicxx export CXX=mpicxx # to run directly from build directory export PYTHONPATH=~/kdt-0.2/build/lib.linux-x86_64-2.6 # to make OpenMPI manage to link to itself export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib/ export LD_PRELOAD=/usr/lib64/openmpi/lib/libmpi.so bash-4.1$ # for compilation bash-4.1$ export PATH=$PATH:/usr/lib64/openmpi/bin bash-4.1$ export CC=mpicxx bash-4.1$ export CXX=mpicxx bash-4.1$ bash-4.1$ # to run directly from build directory bash-4.1$ export PYTHONPATH=~/kdt-0.2/build/lib.linux-x86_64-2.6 bash-4.1$ bash-4.1$ # to make OpenMPI manage to link to itself bash-4.1$ export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib/ bash-4.1$ export LD_PRELOAD=/usr/lib64/openmpi/lib/libmpi.so bash-4.1$ bash-4.1$ ls kdt-0.2-beta2.tar.gz kdt_env_vars.txt KDT_tutorial.txt bash-4.1$ tar -xzf kdt-0.2-beta2.tar.gz bash-4.1$ ls kdt-0.2 kdt-0.2-beta2.tar.gz kdt_env_vars.txt KDT_tutorial.txt bash-4.1$ cd kdt-0.2 bash-4.1$ ls CombBLAS examples kdt KDT_User_Guide.pdf LICENSE.txt PKG-INFO README.txt setup.py test bash-4.1$ python setup.py build Checking for Windows... No Checking for ... OK Checking for ... OK Checking for ... Not found Please install the Python development libraries. They are required to compile any Python C++ module. On most systems that just means installing the `python-dev` or `python-devel` package. attempting to continue anyway... Checking for MPI... No ERROR: MPI not found. KDT requires an MPI compiler to be used. On Linux/Unix/MacOSX: Set your preferred MPI C++ compiler in the CC and CXX environment variables. For example, in Bash: export CC=mpicxx export CXX=mpicxx (specify both CC and CXX. Distutils uses CC for compilation and CXX for linking. Both need to be specified) Remember that you must use an MPI compiler based on the same compiler used to compile Python. On most systems that is GCC (ICC should also work). On Windows: Make sure you have a compatible MPI library installed and its include path is specified. You can append an include path with the -IC:\path\to\mpi\include switch to setup.py. attempting to continue anyway... Checking for C++11: Checking for ... OK Checking for ... Not found No C++11. Checking for TR1: Checking for ... OK Checking for ... OK Checking for C99 constants... Not found, will use __STDC_CONSTANT_MACROS and __STDC_LIMIT_MACROS Checking for restrict keyword... No running build running build_py running build_ext building 'kdt._pyCombBLAS' extension mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c kdt/pyCombBLAS/pyCombBLAS.cpp -o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pyCombBLAS.o mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c kdt/pyCombBLAS/pyCombBLAS_wrap.cpp -o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pyCombBLAS_wrap.o kdt/pyCombBLAS/pyCombBLAS_wrap.cpp: In constructor ‘swig::PyObject_ptr::PyObject_ptr(PyObject*, bool)’: kdt/pyCombBLAS/pyCombBLAS_wrap.cpp:2546: warning: suggest explicit braces to avoid ambiguous ‘else’ kdt/pyCombBLAS/pyCombBLAS_wrap.cpp: In function ‘PyObject* _wrap_new_Obj1(PyObject*, PyObject*)’: kdt/pyCombBLAS/pyCombBLAS_wrap.cpp:39600: warning: ‘argv[0]’ may be used uninitialized in this function kdt/pyCombBLAS/pyCombBLAS_wrap.cpp: In function ‘PyObject* _wrap_new_Obj2(PyObject*, PyObject*)’: kdt/pyCombBLAS/pyCombBLAS_wrap.cpp:40101: warning: ‘argv[0]’ may be used uninitialized in this function kdt/pyCombBLAS/pyCombBLAS_wrap.cpp: In function ‘PyObject* _wrap_EWise_OnlyNZ(PyObject*, PyObject*)’: kdt/pyCombBLAS/pyCombBLAS_wrap.cpp:43108: warning: ‘argv[0]’ may be used uninitialized in this function mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c kdt/pyCombBLAS/pyDenseParVec.cpp -o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pyDenseParVec.o In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pyDenseParVec.h:4, from kdt/pyCombBLAS/pyDenseParVec.cpp:4: /usr/include/python2.6/pyconfig-64.h:1034:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/bits/stl_algobase.h:60, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/bits/stl_tree.h:62, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/map:60, from /usr/include/openmpi-x86_64/openmpi/ompi/mpi/cxx/mpicxx.h:36, from /usr/include/openmpi-x86_64/mpi.h:1886, from kdt/pyCombBLAS/pyDenseParVec.cpp:1: /usr/include/features.h:162:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pyDenseParVec.h:4, from kdt/pyCombBLAS/pyDenseParVec.cpp:4: /usr/include/python2.6/pyconfig-64.h:1043:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/bits/stl_algobase.h:60, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/bits/stl_tree.h:62, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/map:60, from /usr/include/openmpi-x86_64/openmpi/ompi/mpi/cxx/mpicxx.h:36, from /usr/include/openmpi-x86_64/mpi.h:1886, from kdt/pyCombBLAS/pyDenseParVec.cpp:1: /usr/include/features.h:164:1: warning: this is the location of the previous definition In file included from kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.h:269, from kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.cpp:30, from kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.h:270, from kdt/pyCombBLAS/../../CombBLAS/SpParMat.h:50, from kdt/pyCombBLAS/../../CombBLAS/CombBLAS.h:52, from kdt/pyCombBLAS/pyCombBLAS.h:10, from kdt/pyCombBLAS/pyDenseParVec.h:4, from kdt/pyCombBLAS/pyDenseParVec.cpp:4: kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp: In member function ‘void FullyDistSpVec::SaveGathered(std::ofstream&, int, HANDLER, bool) [with HANDLER = FullyDistVec::ScalarReadSaveHandler, IT = long int, NT = doubleint]’: kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.cpp:403: instantiated from ‘void FullyDistVec::SaveGathered(std::ofstream&, int, HANDLER, bool) [with HANDLER = FullyDistVec::ScalarReadSaveHandler, IT = long int, NT = doubleint]’ kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.h:97: instantiated from ‘void FullyDistVec::SaveGathered(std::ofstream&, int) [with IT = long int, NT = doubleint]’ kdt/pyCombBLAS/pyDenseParVec.cpp:53: instantiated from here kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp:654: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c kdt/pyCombBLAS/pyDenseParVecObj1.cpp -o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pyDenseParVecObj1.o In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pyDenseParVecObj1.h:4, from kdt/pyCombBLAS/pyDenseParVecObj1.cpp:4: /usr/include/python2.6/pyconfig-64.h:1034:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/bits/stl_algobase.h:60, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/bits/stl_tree.h:62, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/map:60, from /usr/include/openmpi-x86_64/openmpi/ompi/mpi/cxx/mpicxx.h:36, from /usr/include/openmpi-x86_64/mpi.h:1886, from kdt/pyCombBLAS/pyDenseParVecObj1.cpp:1: /usr/include/features.h:162:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pyDenseParVecObj1.h:4, from kdt/pyCombBLAS/pyDenseParVecObj1.cpp:4: /usr/include/python2.6/pyconfig-64.h:1043:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/bits/stl_algobase.h:60, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/bits/stl_tree.h:62, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/map:60, from /usr/include/openmpi-x86_64/openmpi/ompi/mpi/cxx/mpicxx.h:36, from /usr/include/openmpi-x86_64/mpi.h:1886, from kdt/pyCombBLAS/pyDenseParVecObj1.cpp:1: /usr/include/features.h:164:1: warning: this is the location of the previous definition In file included from kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.h:269, from kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.cpp:30, from kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.h:270, from kdt/pyCombBLAS/../../CombBLAS/SpParMat.h:50, from kdt/pyCombBLAS/../../CombBLAS/CombBLAS.h:52, from kdt/pyCombBLAS/pyCombBLAS.h:10, from kdt/pyCombBLAS/pyDenseParVecObj1.h:4, from kdt/pyCombBLAS/pyDenseParVecObj1.cpp:4: kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp: In member function ‘void FullyDistSpVec::SaveGathered(std::ofstream&, int, HANDLER, bool) [with HANDLER = Obj1ReadSaveHandlerD, IT = long int, NT = Obj1]’: kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.cpp:403: instantiated from ‘void FullyDistVec::SaveGathered(std::ofstream&, int, HANDLER, bool) [with HANDLER = Obj1ReadSaveHandlerD, IT = long int, NT = Obj1]’ kdt/pyCombBLAS/pyDenseParVecObj1.cpp:66: instantiated from here kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp:654: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c kdt/pyCombBLAS/pyDenseParVecObj2.cpp -o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pyDenseParVecObj2.o In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pyDenseParVecObj2.h:4, from kdt/pyCombBLAS/pyDenseParVecObj2.cpp:4: /usr/include/python2.6/pyconfig-64.h:1034:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/bits/stl_algobase.h:60, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/bits/stl_tree.h:62, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/map:60, from /usr/include/openmpi-x86_64/openmpi/ompi/mpi/cxx/mpicxx.h:36, from /usr/include/openmpi-x86_64/mpi.h:1886, from kdt/pyCombBLAS/pyDenseParVecObj2.cpp:1: /usr/include/features.h:162:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pyDenseParVecObj2.h:4, from kdt/pyCombBLAS/pyDenseParVecObj2.cpp:4: /usr/include/python2.6/pyconfig-64.h:1043:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/bits/stl_algobase.h:60, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/bits/stl_tree.h:62, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/map:60, from /usr/include/openmpi-x86_64/openmpi/ompi/mpi/cxx/mpicxx.h:36, from /usr/include/openmpi-x86_64/mpi.h:1886, from kdt/pyCombBLAS/pyDenseParVecObj2.cpp:1: /usr/include/features.h:164:1: warning: this is the location of the previous definition In file included from kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.h:269, from kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.cpp:30, from kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.h:270, from kdt/pyCombBLAS/../../CombBLAS/SpParMat.h:50, from kdt/pyCombBLAS/../../CombBLAS/CombBLAS.h:52, from kdt/pyCombBLAS/pyCombBLAS.h:10, from kdt/pyCombBLAS/pyDenseParVecObj2.h:4, from kdt/pyCombBLAS/pyDenseParVecObj2.cpp:4: kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp: In member function ‘void FullyDistSpVec::SaveGathered(std::ofstream&, int, HANDLER, bool) [with HANDLER = Obj2ReadSaveHandlerD, IT = long int, NT = Obj2]’: kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.cpp:403: instantiated from ‘void FullyDistVec::SaveGathered(std::ofstream&, int, HANDLER, bool) [with HANDLER = Obj2ReadSaveHandlerD, IT = long int, NT = Obj2]’ kdt/pyCombBLAS/pyDenseParVecObj2.cpp:66: instantiated from here kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp:654: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c kdt/pyCombBLAS/pySpParVec.cpp -o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pySpParVec.o In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pySpParVec.h:4, from kdt/pyCombBLAS/pySpParVec.cpp:6: /usr/include/python2.6/pyconfig-64.h:1034:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/iostream:39, from kdt/pyCombBLAS/pySpParVec.cpp:3: /usr/include/features.h:162:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pySpParVec.h:4, from kdt/pyCombBLAS/pySpParVec.cpp:6: /usr/include/python2.6/pyconfig-64.h:1043:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/iostream:39, from kdt/pyCombBLAS/pySpParVec.cpp:3: /usr/include/features.h:164:1: warning: this is the location of the previous definition In file included from kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.h:269, from kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.cpp:30, from kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.h:270, from kdt/pyCombBLAS/../../CombBLAS/SpParMat.h:50, from kdt/pyCombBLAS/../../CombBLAS/CombBLAS.h:52, from kdt/pyCombBLAS/pyCombBLAS.h:10, from kdt/pyCombBLAS/pySpParVec.h:4, from kdt/pyCombBLAS/pySpParVec.cpp:6: kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp: In member function ‘void FullyDistSpVec::DebugPrint() [with IT = long int, NT = doubleint]’: kdt/pyCombBLAS/pySpParVec.cpp:83: instantiated from here kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp:782: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp: In member function ‘void FullyDistSpVec::SaveGathered(std::ofstream&, int, HANDLER, bool) [with HANDLER = FullyDistSpVec::ScalarReadSaveHandler, IT = long int, NT = doubleint]’: kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.h:115: instantiated from ‘void FullyDistSpVec::SaveGathered(std::ofstream&, int) [with IT = long int, NT = doubleint]’ kdt/pyCombBLAS/pySpParVec.cpp:77: instantiated from here kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp:654: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c kdt/pyCombBLAS/pySpParVecObj1.cpp -o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pySpParVecObj1.o In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pySpParVecObj1.h:4, from kdt/pyCombBLAS/pySpParVecObj1.cpp:6: /usr/include/python2.6/pyconfig-64.h:1034:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/iostream:39, from kdt/pyCombBLAS/pySpParVecObj1.cpp:3: /usr/include/features.h:162:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pySpParVecObj1.h:4, from kdt/pyCombBLAS/pySpParVecObj1.cpp:6: /usr/include/python2.6/pyconfig-64.h:1043:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/iostream:39, from kdt/pyCombBLAS/pySpParVecObj1.cpp:3: /usr/include/features.h:164:1: warning: this is the location of the previous definition In file included from kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.h:269, from kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.cpp:30, from kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.h:270, from kdt/pyCombBLAS/../../CombBLAS/SpParMat.h:50, from kdt/pyCombBLAS/../../CombBLAS/CombBLAS.h:52, from kdt/pyCombBLAS/pyCombBLAS.h:10, from kdt/pyCombBLAS/pySpParVecObj1.h:4, from kdt/pyCombBLAS/pySpParVecObj1.cpp:6: kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp: In member function ‘void FullyDistSpVec::SaveGathered(std::ofstream&, int, HANDLER, bool) [with HANDLER = Obj1ReadSaveHandler, IT = long int, NT = Obj1]’: kdt/pyCombBLAS/pySpParVecObj1.cpp:102: instantiated from here kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp:654: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp: In member function ‘void FullyDistSpVec::DebugPrint() [with IT = long int, NT = Obj1]’: kdt/pyCombBLAS/pySpParVecObj1.cpp:108: instantiated from here kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp:782: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp: In member function ‘void FullyDistSpVec::DebugPrint() [with IT = long int, NT = long int]’: kdt/pyCombBLAS/pySpParVecObj1.cpp:222: instantiated from here kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp:746: warning: unused variable ‘data’ kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp:782: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c kdt/pyCombBLAS/pySpParVecObj2.cpp -o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pySpParVecObj2.o In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pySpParVecObj2.h:4, from kdt/pyCombBLAS/pySpParVecObj2.cpp:6: /usr/include/python2.6/pyconfig-64.h:1034:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/iostream:39, from kdt/pyCombBLAS/pySpParVecObj2.cpp:3: /usr/include/features.h:162:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pySpParVecObj2.h:4, from kdt/pyCombBLAS/pySpParVecObj2.cpp:6: /usr/include/python2.6/pyconfig-64.h:1043:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/iostream:39, from kdt/pyCombBLAS/pySpParVecObj2.cpp:3: /usr/include/features.h:164:1: warning: this is the location of the previous definition In file included from kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.h:269, from kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.cpp:30, from kdt/pyCombBLAS/../../CombBLAS/FullyDistVec.h:270, from kdt/pyCombBLAS/../../CombBLAS/SpParMat.h:50, from kdt/pyCombBLAS/../../CombBLAS/CombBLAS.h:52, from kdt/pyCombBLAS/pyCombBLAS.h:10, from kdt/pyCombBLAS/pySpParVecObj2.h:4, from kdt/pyCombBLAS/pySpParVecObj2.cpp:6: kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp: In member function ‘void FullyDistSpVec::SaveGathered(std::ofstream&, int, HANDLER, bool) [with HANDLER = Obj2ReadSaveHandler, IT = long int, NT = Obj2]’: kdt/pyCombBLAS/pySpParVecObj2.cpp:102: instantiated from here kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp:654: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp: In member function ‘void FullyDistSpVec::DebugPrint() [with IT = long int, NT = Obj2]’: kdt/pyCombBLAS/pySpParVecObj2.cpp:108: instantiated from here kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp:782: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp: In member function ‘void FullyDistSpVec::DebugPrint() [with IT = long int, NT = long int]’: kdt/pyCombBLAS/pySpParVecObj2.cpp:222: instantiated from here kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp:746: warning: unused variable ‘data’ kdt/pyCombBLAS/../../CombBLAS/FullyDistSpVec.cpp:782: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c kdt/pyCombBLAS/pySpParMat.cpp -o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pySpParMat.o In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pySpParMat.h:4, from kdt/pyCombBLAS/pySpParMat.cpp:2: /usr/include/python2.6/pyconfig-64.h:1034:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/iostream:39, from kdt/pyCombBLAS/pySpParMat.cpp:1: /usr/include/features.h:162:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pySpParMat.h:4, from kdt/pyCombBLAS/pySpParMat.cpp:2: /usr/include/python2.6/pyconfig-64.h:1043:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/iostream:39, from kdt/pyCombBLAS/pySpParMat.cpp:1: /usr/include/features.h:164:1: warning: this is the location of the previous definition In file included from kdt/pyCombBLAS/../../CombBLAS/DistEdgeList.h:125, from kdt/pyCombBLAS/../../CombBLAS/SpParMat.h:53, from kdt/pyCombBLAS/../../CombBLAS/CombBLAS.h:52, from kdt/pyCombBLAS/pyCombBLAS.h:10, from kdt/pyCombBLAS/pySpParMat.h:4, from kdt/pyCombBLAS/pySpParMat.cpp:2: kdt/pyCombBLAS/../../CombBLAS/DistEdgeList.cpp: In constructor ‘DistEdgeList::DistEdgeList(const char*, IT, IT) [with IT = long int]’: kdt/pyCombBLAS/pySpParMat.cpp:82: instantiated from here kdt/pyCombBLAS/../../CombBLAS/DistEdgeList.cpp:74: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result kdt/pyCombBLAS/../../CombBLAS/DistEdgeList.cpp: In constructor ‘DistEdgeList::DistEdgeList(const char*, IT, IT) [with IT = long int]’: kdt/pyCombBLAS/../../CombBLAS/DistEdgeList.cpp:74: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c kdt/pyCombBLAS/pySpParMatObj1.cpp -o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pySpParMatObj1.o In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pySpParMatObj1.h:4, from kdt/pyCombBLAS/pySpParMatObj1.cpp:2: /usr/include/python2.6/pyconfig-64.h:1034:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/iostream:39, from kdt/pyCombBLAS/pySpParMatObj1.cpp:1: /usr/include/features.h:162:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pySpParMatObj1.h:4, from kdt/pyCombBLAS/pySpParMatObj1.cpp:2: /usr/include/python2.6/pyconfig-64.h:1043:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/iostream:39, from kdt/pyCombBLAS/pySpParMatObj1.cpp:1: /usr/include/features.h:164:1: warning: this is the location of the previous definition mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c kdt/pyCombBLAS/pySpParMatObj2.cpp -o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pySpParMatObj2.o In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pySpParMatObj2.h:4, from kdt/pyCombBLAS/pySpParMatObj2.cpp:2: /usr/include/python2.6/pyconfig-64.h:1034:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/iostream:39, from kdt/pyCombBLAS/pySpParMatObj2.cpp:1: /usr/include/features.h:162:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pySpParMatObj2.h:4, from kdt/pyCombBLAS/pySpParMatObj2.cpp:2: /usr/include/python2.6/pyconfig-64.h:1043:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/iostream:39, from kdt/pyCombBLAS/pySpParMatObj2.cpp:1: /usr/include/features.h:164:1: warning: this is the location of the previous definition mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c kdt/pyCombBLAS/pySpParMatBool.cpp -o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pySpParMatBool.o In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pySpParMatBool.h:4, from kdt/pyCombBLAS/pySpParMatBool.cpp:2: /usr/include/python2.6/pyconfig-64.h:1034:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/iostream:39, from kdt/pyCombBLAS/pySpParMatBool.cpp:1: /usr/include/features.h:162:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from kdt/pyCombBLAS/pyCombBLAS.h:9, from kdt/pyCombBLAS/pySpParMatBool.h:4, from kdt/pyCombBLAS/pySpParMatBool.cpp:2: /usr/include/python2.6/pyconfig-64.h:1043:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/x86_64-redhat-linux/bits/c++config.h:1687, from /usr/lib/gcc/x86_64-redhat-linux/4.4.5/../../../../include/c++/4.4.5/iostream:39, from kdt/pyCombBLAS/pySpParMatBool.cpp:1: /usr/include/features.h:164:1: warning: this is the location of the previous definition In file included from kdt/pyCombBLAS/../../CombBLAS/SpParMat.h:300, from kdt/pyCombBLAS/../../CombBLAS/CombBLAS.h:52, from kdt/pyCombBLAS/pyCombBLAS.h:10, from kdt/pyCombBLAS/pySpParMatBool.h:4, from kdt/pyCombBLAS/pySpParMatBool.cpp:2: kdt/pyCombBLAS/../../CombBLAS/SpParMat.cpp: In member function ‘void SpParMat::ReadDistribute(const std::string&, int, bool, HANDLER, bool) [with HANDLER = SpParMat >::ScalarReadSaveHandler, IT = long int, NT = bool, DER = SpDCCols]’: kdt/pyCombBLAS/../../CombBLAS/SpParMat.cpp:2120: warning: ‘tempval’ may be used uninitialized in this function mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c kdt/pyCombBLAS/pyOperations.cpp -o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pyOperations.o mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c kdt/pyCombBLAS/pyOperationsObj.cpp -o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pyOperationsObj.o mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c CombBLAS/CommGrid.cpp -o build/temp.linux-x86_64-2.6/CombBLAS/CommGrid.o mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c CombBLAS/MPIType.cpp -o build/temp.linux-x86_64-2.6/CombBLAS/MPIType.o mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c CombBLAS/MemoryPool.cpp -o build/temp.linux-x86_64-2.6/CombBLAS/MemoryPool.o mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c CombBLAS/graph500-1.2/generator/btrd_binomial_distribution.c -o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/btrd_binomial_distribution.o CombBLAS/graph500-1.2/generator/btrd_binomial_distribution.c: In function ‘size_t btrd_binomial_distribution(size_t, double, mrg_state*)’: CombBLAS/graph500-1.2/generator/btrd_binomial_distribution.c:76: warning: comparison between signed and unsigned integer expressions mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c CombBLAS/graph500-1.2/generator/splittable_mrg.c -o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/splittable_mrg.o mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c CombBLAS/graph500-1.2/generator/mrg_transitions.c -o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/mrg_transitions.o mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c CombBLAS/graph500-1.2/generator/graph_generator.c -o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/graph_generator.o mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c CombBLAS/graph500-1.2/generator/permutation_gen.c -o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/permutation_gen.o mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c CombBLAS/graph500-1.2/generator/make_graph.c -o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/make_graph.o CombBLAS/graph500-1.2/generator/make_graph.c: In function ‘void make_graph(int, int64_t, uint64_t, uint64_t, const double*, int64_t*, int64_t**)’: CombBLAS/graph500-1.2/generator/make_graph.c:70: warning: statement has no effect mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c CombBLAS/graph500-1.2/generator/utils.c -o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/utils.o mpicxx -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DGRAPH_GENERATOR_SEQ=1 -DCOMBBLAS_TR1 -DMPICH_IGNORE_CXX_SEEK -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -Drestrict= -DNDEBUG=1 -I/usr/include/python2.6 -c CombBLAS/graph500-1.2/generator/scramble_edges.c -o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/scramble_edges.o mpicxx -pthread -shared build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pyCombBLAS.o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pyCombBLAS_wrap.o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pyDenseParVec.o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pyDenseParVecObj1.o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pyDenseParVecObj2.o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pySpParVec.o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pySpParVecObj1.o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pySpParVecObj2.o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pySpParMat.o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pySpParMatObj1.o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pySpParMatObj2.o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pySpParMatBool.o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pyOperations.o build/temp.linux-x86_64-2.6/kdt/pyCombBLAS/pyOperationsObj.o build/temp.linux-x86_64-2.6/CombBLAS/CommGrid.o build/temp.linux-x86_64-2.6/CombBLAS/MPIType.o build/temp.linux-x86_64-2.6/CombBLAS/MemoryPool.o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/btrd_binomial_distribution.o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/splittable_mrg.o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/mrg_transitions.o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/graph_generator.o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/permutation_gen.o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/make_graph.o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/utils.o build/temp.linux-x86_64-2.6/CombBLAS/graph500-1.2/generator/scramble_edges.o -L/usr/lib64 -lpython2.6 -o build/lib.linux-x86_64-2.6/kdt/_pyCombBLAS.so [NOTE: a common problem you may run into] bash-4.1$ python Python 2.6.6 (r266:84292, Apr 11 2011, 15:50:32) [GCC 4.4.4 20100726 (Red Hat 4.4.4-13)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import kdt Traceback (most recent call last): File "", line 1, in File "kdt/__init__.py", line 3, in from Util import * File "kdt/Util.py", line 1, in import pyCombBLAS as pcb File "kdt/pyCombBLAS.py", line 7, in import _pyCombBLAS ImportError: No module named _pyCombBLAS >>> [NOTE: This error is because there is a "kdt" subdirectory in the current directory so Python interprets it as the module. Simply change to any directory that does not have a "kdt" subdirectory and the error will go away.] bash-4.1$ ls build examples KDT_User_Guide.pdf PKG-INFO setup.py CombBLAS kdt LICENSE.txt README.txt test bash-4.1$ cd .. bash-4.1$ python Python 2.6.6 (r266:84292, Apr 11 2011, 15:50:32) [GCC 4.4.4 20100726 (Red Hat 4.4.4-13)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import kdt >>> s = kdt.Vec(10) >>> s length=10, sparse, [] >>> m = kdt.DiGraph.generateRMAT(10) graph_generation: 0.005591 s Generated renamed edge lists Generation took 0.00566816 seconds Warning: Using smaller indices for the matrix than DistEdgeList Local matrices are 1024-by-1024 Duplicates removed (or summed): 5703 and self-loops removed: 0 Created Sparse Matrix (with int32 local indices and values) Calculated degrees in 8.89301e-05 seconds Converted to Boolean and removed 29 loops As a whole: 1024 rows and 1024 columns and 10652 nonzeros Reductions done Intersection of colsums and rowsums found Found (and permuted) non-isolated vertices As a whole: 1024 rows and 1024 columns and 10652 nonzeros Dropped isolated vertices from input As a whole: 887 rows and 887 columns and 10652 nonzeros Symmetricized As a whole: 887 rows and 887 columns and 21304 nonzeros >>> >>> x = kdt.UFget("Pajek/CSphd") >>> x edge Mat: 1882-by-1882 (row-by-col) Mat with 1740 elements. Too many elements to print. vertex attribute Vec: length=1882, dense, [ *too many to print* ] >>> x.e 1882-by-1882 (row-by-col) Mat with 1740 elements. Too many elements to print. >>> x.v length=1882, dense, [ *too many to print* ] >>> x = kdt.DiGraph.generateRMAT(4) graph_generation: 0.000070 s Generated renamed edge lists Generation took 0.00014782 seconds Warning: Using smaller indices for the matrix than DistEdgeList Local matrices are 16-by-16 Duplicates removed (or summed): 193 and self-loops removed: 0 Created Sparse Matrix (with int32 local indices and values) Calculated degrees in 2.69413e-05 seconds Converted to Boolean and removed 5 loops As a whole: 16 rows and 16 columns and 58 nonzeros Reductions done Intersection of colsums and rowsums found Found (and permuted) non-isolated vertices As a whole: 16 rows and 16 columns and 58 nonzeros Dropped isolated vertices from input As a whole: 16 rows and 16 columns and 58 nonzeros Symmetricized As a whole: 16 rows and 16 columns and 116 nonzeros >>> x edge Mat: 16-by-16 (row-by-col) Mat with 116 elements. - 1.0 - 1.0 2.0 1.0 2.0 6.0 1.0 - - 1.0 - - - - 1.0 - - - 1.0 1.0 1.0 1.0 - - - - - - - - - - - - - 1.0 - - - - - - - - - - 1.0 - - - 2.0 6.0 3.0 18.0 2.0 - - 9.0 1.0 2.0 1.0 - 2.0 1.0 - 2.0 - 1.0 1.0 8.0 1.0 1.0 - 1.0 - - - - 1.0 1.0 1.0 6.0 1.0 - 7.0 19.0 - - - 4.0 2.0 1.0 1.0 - 2.0 1.0 - 3.0 1.0 7.0 - 21.0 3.0 - - 7.0 - 3.0 1.0 - 6.0 1.0 - 18.0 8.0 19.0 21.0 - 7.0 4.0 2.0 22.0 6.0 4.0 7.0 3.0 1.0 - - 2.0 1.0 - 3.0 7.0 - - 1.0 1.0 1.0 1.0 1.0 - - - - - 1.0 - - 4.0 - - - - - 2.0 - - - - - - - - - 2.0 1.0 - - 2.0 - - - - 1.0 - - 9.0 1.0 4.0 7.0 22.0 1.0 - 2.0 - 2.0 4.0 1.0 - - - - 1.0 - 2.0 - 6.0 1.0 - - 2.0 - - 1.0 - - - - 2.0 - 1.0 3.0 4.0 1.0 2.0 - 4.0 - - - - - - - 1.0 - 1.0 1.0 7.0 1.0 - - 1.0 1.0 - - - - - - - - - - 3.0 - - - - - - - - vertex attribute Vec: length=16, dense, [7.0, 1.0, 0.0, 13.0, 1.0, 24.0, 6.0, 157.0, 1.0, 1.0, 1.0, 35.0, 2.0, 6.0, 1.0, 0.0] >>> KeyboardInterrupt >>> bash-4.1$ cd kdt-0.2/examples/ bash-4.1$ ls [NOTE: These are some of our example programs. Not all of them are meant for public consumption, but they're included here to give you ideas if you need them. BetwCent.py and Graph500.py are good starting points, MiniWorkflow.py was used to draw our diagram for our SDM paper.] BetwCent.py GaBP_A100.py Kmeans.py MiniWorkflow.py stats.py Cluster.py Graph500_HyGraph.py mcldraw.py ModelProblemGen.py TwitterBFS.py FilteredBFS.py Graph500.py mcl.py roofline.py TwitterFilterPercent.py [NOTE: how to run Graph500 on a scale 12 graph.] bash-4.1$ python Graph500.py -s12 Generating a Graph500 RMAT graph with 2^12 vertices... graph_generation: 0.024689 s Generated renamed edge lists Generation took 0.024904 seconds Warning: Using smaller indices for the matrix than DistEdgeList Local matrices are 4096-by-4096 Duplicates removed (or summed): 16962 and self-loops removed: 0 Created Sparse Matrix (with int32 local indices and values) Calculated degrees in 0.000313997 seconds Converted to Boolean and removed 51 loops As a whole: 4096 rows and 4096 columns and 48523 nonzeros Reductions done Intersection of colsums and rowsums found Found (and permuted) non-isolated vertices As a whole: 4096 rows and 4096 columns and 48523 nonzeros Dropped isolated vertices from input As a whole: 3353 rows and 3353 columns and 48523 nonzeros Symmetricized As a whole: 3353 rows and 3353 columns and 97046 nonzeros Generation took 0.051391s. iteration 1: start=1, BFS took 0.015834s, verification took 0.000000s and not done (use -v switch), TEPS=4,138,916 iteration 2: start=2498, BFS took 0.015743s, verification took 0.000000s and not done (use -v switch), TEPS=4,162,797 iteration 3: start=567, BFS took 0.015841s, verification took 0.000000s and not done (use -v switch), TEPS=4,137,047 iteration 4: start=155, BFS took 0.015547s, verification took 0.000000s and not done (use -v switch), TEPS=4,215,272 iteration 5: start=2280, BFS took 0.015864s, verification took 0.000000s and not done (use -v switch), TEPS=4,131,078 iteration 6: start=1151, BFS took 0.015739s, verification took 0.000000s and not done (use -v switch), TEPS=4,163,869 iteration 7: start=271, BFS took 0.015652s, verification took 0.000000s and not done (use -v switch), TEPS=4,187,020 iteration 8: start=3097, BFS took 0.015497s, verification took 0.000000s and not done (use -v switch), TEPS=4,228,891 iteration 9: start=2032, BFS took 0.015178s, verification took 0.000000s and not done (use -v switch), TEPS=4,317,772 iteration 10: start=1863, BFS took 0.015244s, verification took 0.000000s and not done (use -v switch), TEPS=4,299,066 iteration 11: start=1649, BFS took 0.015766s, verification took 0.000000s and not done (use -v switch), TEPS=4,156,691 iteration 12: start=3074, BFS took 0.015743s, verification took 0.000000s and not done (use -v switch), TEPS=4,162,797 iteration 13: start=3337, BFS took 0.015730s, verification took 0.000000s and not done (use -v switch), TEPS=4,166,205 iteration 14: start=1115, BFS took 0.015581s, verification took 0.000000s and not done (use -v switch), TEPS=4,206,113 iteration 15: start=3263, BFS took 0.015223s, verification took 0.000000s and not done (use -v switch), TEPS=4,304,991 iteration 16: start=703, BFS took 0.015840s, verification took 0.000000s and not done (use -v switch), TEPS=4,137,296 Graph500 benchmark run for scale = 12 Kernel 1 time = 0.0514 seconds Kernel 2 BFS execution times min_time: 1.51779651641845703e-02 firstquartile_time: 1.55094861984252930e-02 median_time: 1.57345533370971680e-02 thirdquartile_time: 1.58169269561767578e-02 max_time: 1.58638954162597656e-02 mean_time: 1.56263709068298340e-02 stddev_time: 2.30522426874086656e-04 Kernel 2 number of edges traversed min_nedge: 6.55350000000000000e+04 firstquartile_nedge: 6.55350000000000000e+04 median_nedge: 6.55350000000000000e+04 thirdquartile_nedge: 6.55350000000000000e+04 max_nedge: 6.55350000000000000e+04 mean_nedge: 6.55350000000000000e+04 stddev_nedge: 0.00000000000000000e+00 Kernel 2 TEPS min_TEPS: 4.13107867143587116e+06 firstquartile_TEPS: 4.14336020229612011e+06 median_TEPS: 4.16503752891813172e+06 thirdquartile_TEPS: 4.22548671252108831e+06 max_TEPS: 4.31777246100438293e+06 harmonic_mean_TEPS: 4.19387203789950674e+06 harmonic_stddev_TEPS: 8.02300298184442818e+03 [NOTE: how to run Graph500 on a scale 12 graph on 4 cores. The speedup isn't that great, but it's a very small problem.] bash-4.1$ mpirun -np 4 python Graph500.py -s12 Generating a Graph500 RMAT graph with 2^12 vertices... graph_generation: 0.006166 s Generated renamed edge lists Generation took 0.00634885 seconds Warning: Using smaller indices for the matrix than DistEdgeList Local matrices are 2048-by-2048 Duplicates removed (or summed): 16962 and self-loops removed: 0 Created Sparse Matrix (with int32 local indices and values) Calculated degrees in 0.000270844 seconds Converted to Boolean and removed 51 loops As a whole: 4096 rows and 4096 columns and 48523 nonzeros Reductions done Intersection of colsums and rowsums found Found (and permuted) non-isolated vertices As a whole: 4096 rows and 4096 columns and 48523 nonzeros Dropped isolated vertices from input As a whole: 3353 rows and 3353 columns and 48523 nonzeros Symmetricized As a whole: 3353 rows and 3353 columns and 97046 nonzeros Generation took 0.026281s. iteration 1: start=1960, BFS took 0.006519s, verification took 0.000000s and not done (use -v switch), TEPS=10,053,167 iteration 2: start=2270, BFS took 0.005516s, verification took 0.000000s and not done (use -v switch), TEPS=11,880,779 iteration 3: start=1602, BFS took 0.005630s, verification took 0.000000s and not done (use -v switch), TEPS=11,640,778 iteration 4: start=1148, BFS took 0.005572s, verification took 0.000000s and not done (use -v switch), TEPS=11,761,315 iteration 5: start=836, BFS took 0.005501s, verification took 0.000000s and not done (use -v switch), TEPS=11,913,219 iteration 6: start=2813, BFS took 0.005200s, verification took 0.000000s and not done (use -v switch), TEPS=12,603,104 iteration 7: start=2240, BFS took 0.005486s, verification took 0.000000s and not done (use -v switch), TEPS=11,945,837 iteration 8: start=2110, BFS took 0.005560s, verification took 0.000000s and not done (use -v switch), TEPS=11,786,531 iteration 9: start=3007, BFS took 0.005624s, verification took 0.000000s and not done (use -v switch), TEPS=11,653,116 iteration 10: start=2551, BFS took 0.005476s, verification took 0.000000s and not done (use -v switch), TEPS=11,967,681 iteration 11: start=1562, BFS took 0.005514s, verification took 0.000000s and not done (use -v switch), TEPS=11,884,888 iteration 12: start=1799, BFS took 0.005480s, verification took 0.000000s and not done (use -v switch), TEPS=11,958,830 iteration 13: start=2281, BFS took 0.005142s, verification took 0.000000s and not done (use -v switch), TEPS=12,745,106 iteration 14: start=2071, BFS took 0.005514s, verification took 0.000000s and not done (use -v switch), TEPS=11,885,402 iteration 15: start=1552, BFS took 0.005396s, verification took 0.000000s and not done (use -v switch), TEPS=12,144,820 iteration 16: start=1590, BFS took 0.005517s, verification took 0.000000s and not done (use -v switch), TEPS=11,878,725 Graph500 benchmark run for scale = 12 Kernel 1 time = 0.0263 seconds Kernel 2 BFS execution times min_time: 5.14197349548339844e-03 firstquartile_time: 5.47701120376586914e-03 median_time: 5.51402568817138672e-03 thirdquartile_time: 5.56910037994384766e-03 max_time: 6.51884078979492188e-03 mean_time: 5.54043054580688477e-03 stddev_time: 2.92575736017034805e-04 Kernel 2 number of edges traversed min_nedge: 6.55350000000000000e+04 firstquartile_nedge: 6.55350000000000000e+04 median_nedge: 6.55350000000000000e+04 thirdquartile_nedge: 6.55350000000000000e+04 max_nedge: 6.55350000000000000e+04 mean_nedge: 6.55350000000000000e+04 stddev_nedge: 0.00000000000000000e+00 Kernel 2 TEPS min_TEPS: 1.00531677507131882e+07 firstquartile_TEPS: 1.17676198831855394e+07 median_TEPS: 1.18851459417781495e+07 thirdquartile_TEPS: 1.19654688092806879e+07 max_TEPS: 1.27451065349840038e+07 harmonic_mean_TEPS: 1.18285031205017604e+07 harmonic_stddev_TEPS: 5.67122046342805334e+04 bash-4.1$ python [NOTE: a filtering example] Python 2.6.6 (r266:84292, Apr 11 2011, 15:50:32) [GCC 4.4.4 20100726 (Red Hat 4.4.4-13)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import kdt >>> m = kdt.DiGraph.generateRMAT(4) graph_generation: 0.000067 s Generated renamed edge lists Generation took 0.000138998 seconds Warning: Using smaller indices for the matrix than DistEdgeList Local matrices are 16-by-16 Duplicates removed (or summed): 193 and self-loops removed: 0 Created Sparse Matrix (with int32 local indices and values) Calculated degrees in 2.59876e-05 seconds Converted to Boolean and removed 5 loops As a whole: 16 rows and 16 columns and 58 nonzeros Reductions done Intersection of colsums and rowsums found Found (and permuted) non-isolated vertices As a whole: 16 rows and 16 columns and 58 nonzeros Dropped isolated vertices from input As a whole: 16 rows and 16 columns and 58 nonzeros Symmetricized As a whole: 16 rows and 16 columns and 116 nonzeros >>> m edge Mat: 16-by-16 (row-by-col) Mat with 116 elements. - 2.0 1.0 1.0 - - - 8.0 1.0 - 1.0 - 2.0 1.0 1.0 - 2.0 - 1.0 1.0 - - - 6.0 1.0 - 2.0 - 1.0 - 1.0 - 1.0 1.0 - - 1.0 - 1.0 19.0 4.0 1.0 7.0 2.0 6.0 - 1.0 - 1.0 1.0 - - - - 1.0 7.0 1.0 1.0 3.0 1.0 2.0 - - 1.0 - - 1.0 - - - - - - - - - - - - - - - - - - - - 3.0 - - - - - - - - - - 1.0 1.0 - - - 4.0 4.0 - 3.0 - 2.0 2.0 - - 8.0 6.0 19.0 7.0 - 3.0 4.0 - 22.0 7.0 21.0 6.0 18.0 4.0 1.0 2.0 1.0 1.0 4.0 1.0 - - 4.0 22.0 - 1.0 7.0 2.0 9.0 - - 2.0 - - 1.0 1.0 - - - 7.0 1.0 - 1.0 1.0 1.0 - - - 1.0 2.0 7.0 3.0 - - 3.0 21.0 7.0 1.0 - - 3.0 - 1.0 - - - 2.0 1.0 - - - 6.0 2.0 1.0 - - 1.0 - - - 2.0 1.0 6.0 2.0 - - 2.0 18.0 9.0 1.0 3.0 1.0 - - - - 1.0 - - - - - 2.0 4.0 - - - - - - - - 1.0 1.0 1.0 - - - - 1.0 - - 1.0 - - - - - - - - 1.0 - - - 2.0 2.0 - - - - - - - vertex attribute Vec: length=16, dense, [1.0, 7.0, 24.0, 1.0, 0.0, 0.0, 6.0, 157.0, 35.0, 1.0, 6.0, 2.0, 13.0, 1.0, 1.0, 1.0] >>> def f(x): ... return x == 1 ... >>> m.e.addFilter(f) >>> m edge Mat: 16-by-16 (row-by-col) Mat with 54 elements. 1 filter(s) remove 62 additional elements (116 total elements stored). - - 1.0 1.0 - - - - 1.0 - 1.0 - - 1.0 1.0 - - - 1.0 1.0 - - - - 1.0 - - - 1.0 - 1.0 - 1.0 1.0 - - 1.0 - 1.0 - - 1.0 - - - - 1.0 - 1.0 1.0 - - - - 1.0 - 1.0 1.0 - 1.0 - - - 1.0 - - 1.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1.0 1.0 - - - - - - - - - - - - - - - - - - - - - - - - - - 1.0 - 1.0 1.0 - 1.0 - - - - - 1.0 - - - - - - - - 1.0 1.0 - - - - 1.0 - 1.0 1.0 1.0 - - - 1.0 - - - - - - - - 1.0 - - - - 1.0 - - - - 1.0 - - - - - 1.0 - - 1.0 - - - - 1.0 - - - - - - - 1.0 - 1.0 - - - - 1.0 - - - - - - - - - - - - - - - 1.0 1.0 1.0 - - - - 1.0 - - 1.0 - - - - - - - - 1.0 - - - - - - - - - - - - vertex attribute Vec: length=16, dense, [1.0, 7.0, 24.0, 1.0, 0.0, 0.0, 6.0, 157.0, 35.0, 1.0, 6.0, 2.0, 13.0, 1.0, 1.0, 1.0] >>> m.e.materializeFilter() >>> m.e 16-by-16 (row-by-col) Mat with 54 elements. 1 filter(s) remove 62 additional elements (116 total elements stored). - - 1.0 1.0 - - - - 1.0 - 1.0 - - 1.0 1.0 - - - 1.0 1.0 - - - - 1.0 - - - 1.0 - 1.0 - 1.0 1.0 - - 1.0 - 1.0 - - 1.0 - - - - 1.0 - 1.0 1.0 - - - - 1.0 - 1.0 1.0 - 1.0 - - - 1.0 - - 1.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1.0 1.0 - - - - - - - - - - - - - - - - - - - - - - - - - - 1.0 - 1.0 1.0 - 1.0 - - - - - 1.0 - - - - - - - - 1.0 1.0 - - - - 1.0 - 1.0 1.0 1.0 - - - 1.0 - - - - - - - - 1.0 - - - - 1.0 - - - - 1.0 - - - - - 1.0 - - 1.0 - - - - 1.0 - - - - - - - 1.0 - 1.0 - - - - 1.0 - - - - - - - - - - - - - - - 1.0 1.0 1.0 - - - - 1.0 - - 1.0 - - - - - - - - 1.0 - - - - - - - - - - - - >>> m.e._materialized 16-by-16 (row-by-col) Mat with 54 elements. - - 1.0 1.0 - - - - 1.0 - 1.0 - - 1.0 1.0 - - - 1.0 1.0 - - - - 1.0 - - - 1.0 - 1.0 - 1.0 1.0 - - 1.0 - 1.0 - - 1.0 - - - - 1.0 - 1.0 1.0 - - - - 1.0 - 1.0 1.0 - 1.0 - - - 1.0 - - 1.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1.0 1.0 - - - - - - - - - - - - - - - - - - - - - - - - - - 1.0 - 1.0 1.0 - 1.0 - - - - - 1.0 - - - - - - - - 1.0 1.0 - - - - 1.0 - 1.0 1.0 1.0 - - - 1.0 - - - - - - - - 1.0 - - - - 1.0 - - - - 1.0 - - - - - 1.0 - - 1.0 - - - - 1.0 - - - - - - - 1.0 - 1.0 - - - - 1.0 - - - - - - - - - - - - - - - 1.0 1.0 1.0 - - - - 1.0 - - 1.0 - - - - - - - - 1.0 - - - - - - - - - - - - >>> m.e.delFilter(f) >>> m edge Mat: 16-by-16 (row-by-col) Mat with 116 elements. - 2.0 1.0 1.0 - - - 8.0 1.0 - 1.0 - 2.0 1.0 1.0 - 2.0 - 1.0 1.0 - - - 6.0 1.0 - 2.0 - 1.0 - 1.0 - 1.0 1.0 - - 1.0 - 1.0 19.0 4.0 1.0 7.0 2.0 6.0 - 1.0 - 1.0 1.0 - - - - 1.0 7.0 1.0 1.0 3.0 1.0 2.0 - - 1.0 - - 1.0 - - - - - - - - - - - - - - - - - - - - 3.0 - - - - - - - - - - 1.0 1.0 - - - 4.0 4.0 - 3.0 - 2.0 2.0 - - 8.0 6.0 19.0 7.0 - 3.0 4.0 - 22.0 7.0 21.0 6.0 18.0 4.0 1.0 2.0 1.0 1.0 4.0 1.0 - - 4.0 22.0 - 1.0 7.0 2.0 9.0 - - 2.0 - - 1.0 1.0 - - - 7.0 1.0 - 1.0 1.0 1.0 - - - 1.0 2.0 7.0 3.0 - - 3.0 21.0 7.0 1.0 - - 3.0 - 1.0 - - - 2.0 1.0 - - - 6.0 2.0 1.0 - - 1.0 - - - 2.0 1.0 6.0 2.0 - - 2.0 18.0 9.0 1.0 3.0 1.0 - - - - 1.0 - - - - - 2.0 4.0 - - - - - - - - 1.0 1.0 1.0 - - - - 1.0 - - 1.0 - - - - - - - - 1.0 - - - 2.0 2.0 - - - - - - - vertex attribute Vec: length=16, dense, [1.0, 7.0, 24.0, 1.0, 0.0, 0.0, 6.0, 157.0, 35.0, 1.0, 6.0, 2.0, 13.0, 1.0, 1.0, 1.0] >>> bash-4.1$ ls BetwCent.py Graph500_HyGraph.py mcl.py stats.py Cluster.py Graph500.py MiniWorkflow.py stats.pyc FilteredBFS.py Kmeans.py ModelProblemGen.py TwitterBFS.py GaBP_A100.py mcldraw.py roofline.py TwitterFilterPercent.py bash-4.1$ cd .. bash-4.1$ ls build examples KDT_User_Guide.pdf PKG-INFO setup.py CombBLAS kdt LICENSE.txt README.txt test bash-4.1$ cd kdt/ bash-4.1$ ls [NOTE: This is where the main implementation lives. Mat and Vec are the bread-and-butter classes, DiGraph puts them together into a directed graph object, and Algorithms.py includes our algorithms that work on a DiGraph.] Algorithms.py Graph.py Mat.py pyCombBLAS.py Util.py DiGraph.py HyGraph.py multiproccheck.py pyCombBLAS.pyc Util.pyc eig.py __init__.py ObjMethods.py SpectralClustering.py Vec.py feedback.py __init__.pyc pyCombBLAS UFget.py bash-4.1$ cd pyCombBLAS bash-4.1$ ls [NOTE: This is our Python wrapper of CombBLAS] doubleint.h pyDenseParVec.cpp pyOperationsObj.h pySpParMatObj2.cpp Makefile-dist pyDenseParVec.h pyOperationsSEJITS.h pySpParMatObj2.h obj.h pyDenseParVecObj1.cpp pySemirings.h pySpParVec.cpp pyCombBLAS.cpp pyDenseParVecObj1.h pySpParMatBool.cpp pySpParVec.h pyCombBLAS.h pyDenseParVecObj2.cpp pySpParMatBool.h pySpParVecObj1.cpp pyCombBLAS.i pyDenseParVecObj2.h pySpParMat.cpp pySpParVecObj1.h pyCombBLAS_wrap.cpp pyOperations.cpp pySpParMat.h pySpParVecObj2.cpp pyCommonMatFuncs.cpp pyOperations.h pySpParMatObj1.cpp pySpParVecObj2.h pyCommonVecFuncs.cpp pyOperationsObj.cpp pySpParMatObj1.h swigpyrun.h bash-4.1$ vi obj.h [NOTE: This is where the objects that we can use for semantic graphs (i.e. vertex and edge attribute types) are defined. Important takeaways are these definitions. They can be used as the elemental types of both Mat and Vec.] class Obj1 { public: //////////////////////////////////////////////////// //////////////////////////////////////////////////// ///// USER CHANGEABLE CODE BEGIN double weight; int category; ... } class Obj2 { public: //////////////////////////////////////////////////// //////////////////////////////////////////////////// ///// USER CHANGEABLE CODE BEGIN bool follower; // default constructor sets all to zero long latest; // not assigned if no retweets happened short count; ... }