dev-python:mpi4py-3.0.3:20210612-062326.log

dev-python:mpi4py-3.0.3:20210612-062326.log (text/plain), 16.21 KB, created by Toralf Förster on 2021-06-12 08:34:14 UTC

 * Package:    dev-python/mpi4py-3.0.3
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python3_9 userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox splitdebug userpriv usersandbox

>>> Unpacking source...
>>> Unpacking mpi4py-3.0.3.tar.gz to /var/tmp/portage/dev-python/mpi4py-3.0.3/work
>>> Source unpacked in /var/tmp/portage/dev-python/mpi4py-3.0.3/work
>>> Preparing source in /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3 ...
removed 'docs/source/usrman/index.rst'
removed 'docs/source/usrman/make.bat'
removed 'docs/source/usrman/intro.rst'
removed 'docs/source/usrman/abstract.txt'
removed 'docs/source/usrman/conf.py'
removed 'docs/source/usrman/mpi4py.run.rst'
removed 'docs/source/usrman/manual.rst'
removed 'docs/source/usrman/tutorial.rst'
removed 'docs/source/usrman/overview.rst'
removed 'docs/source/usrman/install.rst'
removed 'docs/source/usrman/appendix.rst'
removed 'docs/source/usrman/toctree.txt'
removed 'docs/source/usrman/mpi4py.futures.rst'
removed 'docs/source/usrman/Makefile'
removed 'docs/source/usrman/citing.rst'
removed directory 'docs/source/usrman'
removed directory 'docs/source'
 * Applying mpi4py-3.0.3-py38setup.patch ...
 [ ok ]
 * Applying mpi4py-3.0.3-py38futures.patch ...
 [ ok ]
 * Will copy sources from /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3
 * python3_9: copying to /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3 ...
 * python3_9: running distutils-r1_run_phase distutils-r1_python_compile
python3.9 setup.py build -j 3
running build
running build_src
running build_py
creating /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py
copying src/mpi4py/__init__.py -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py
copying src/mpi4py/bench.py -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py
copying src/mpi4py/__main__.py -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py
copying src/mpi4py/run.py -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py
creating /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/futures
copying src/mpi4py/futures/_base.py -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/futures
copying src/mpi4py/futures/__init__.py -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/futures
copying src/mpi4py/futures/aplus.py -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/futures
copying src/mpi4py/futures/_lib.py -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/futures
copying src/mpi4py/futures/pool.py -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/futures
copying src/mpi4py/futures/server.py -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/futures
copying src/mpi4py/futures/__main__.py -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/futures
copying src/mpi4py/libmpi.pxd -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py
copying src/mpi4py/__init__.pxd -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py
copying src/mpi4py/MPI.pxd -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py
creating /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/include
creating /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.h -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.i -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi.pxi -> /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/include/mpi4py
warning: build_py: byte-compiling is disabled, skipping.

running build_clib
MPI configuration: [mpi] from 'mpi.cfg'
MPI C compiler:    /usr/bin/mpicc
MPI C++ compiler:  /usr/bin/mpicxx
MPI F compiler:    /usr/bin/mpifort
MPI F90 compiler:  /usr/bin/mpif90
MPI F77 compiler:  /usr/bin/mpif77
checking for library 'lmpe' ...
/usr/bin/mpicc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 _configtest.o -llmpe -o _configtest
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -llmpe
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'mpe' dylib library
creating /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9
creating /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9/src
creating /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9/src/lib-pmpi
/usr/bin/mpicc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -c src/lib-pmpi/mpe.c -o /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9/src/lib-pmpi/mpe.o
creating /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/lib-pmpi
/usr/bin/mpicc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -Wl,--no-as-needed /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9/src/lib-pmpi/mpe.o -o /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/lib-pmpi/libmpe.so
checking for library 'vt-mpi' ...
/usr/bin/mpicc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 _configtest.o -lvt-mpi -o _configtest
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lvt-mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.mpi' ...
/usr/bin/mpicc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 _configtest.o -lvt.mpi -o _configtest
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lvt.mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt' dylib library
/usr/bin/mpicc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -c src/lib-pmpi/vt.c -o /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9/src/lib-pmpi/vt.o
/usr/bin/mpicc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -Wl,--no-as-needed /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9/src/lib-pmpi/vt.o -o /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/lib-pmpi/libvt.so
checking for library 'vt-mpi' ...
/usr/bin/mpicc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 _configtest.o -lvt-mpi -o _configtest
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lvt-mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.mpi' ...
/usr/bin/mpicc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 _configtest.o -lvt.mpi -o _configtest
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lvt.mpi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt-mpi' dylib library
/usr/bin/mpicc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -c src/lib-pmpi/vt-mpi.c -o /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9/src/lib-pmpi/vt-mpi.o
/usr/bin/mpicc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -Wl,--no-as-needed /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9/src/lib-pmpi/vt-mpi.o -o /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/lib-pmpi/libvt-mpi.so
checking for library 'vt-hyb' ...
/usr/bin/mpicc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 _configtest.o -lvt-hyb -o _configtest
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lvt-hyb
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.ompi' ...
/usr/bin/mpicc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -c _configtest.c -o _configtest.o
/usr/bin/mpicc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 _configtest.o -lvt.ompi -o _configtest
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lvt.ompi
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt-hyb' dylib library
/usr/bin/mpicc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -c src/lib-pmpi/vt-hyb.c -o /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9/src/lib-pmpi/vt-hyb.o
/usr/bin/mpicc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -Wl,--no-as-needed /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9/src/lib-pmpi/vt-hyb.o -o /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/lib-pmpi/libvt-hyb.so
running build_ext
MPI configuration: [mpi] from 'mpi.cfg'
MPI C compiler:    /usr/bin/mpicc
MPI C++ compiler:  /usr/bin/mpicxx
MPI F compiler:    /usr/bin/mpifort
MPI F90 compiler:  /usr/bin/mpif90
MPI F77 compiler:  /usr/bin/mpif77
checking for dlopen() availability ...
checking for header 'dlfcn.h' ...
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -I/usr/include/python3.9 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
success!
checking for library 'dl' ...
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -I/usr/include/python3.9 -c _configtest.c -o _configtest.o
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 _configtest.o -L/var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'dlopen' ...
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -I/usr/include/python3.9 -c _configtest.c -o _configtest.o
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 _configtest.o -L/var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.dl' extension
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/usr/include/python3.9 -c src/dynload.c -o /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9/src/dynload.o
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9/src/dynload.o -L/var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9 -ldl -o /var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/lib/mpi4py/dl.cpython-39-x86_64-linux-gnu.so
checking for MPI compile and link ...
/usr/bin/mpicc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -I/usr/include/python3.9 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
/usr/bin/mpicc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -I/usr/include/python3.9 -c _configtest.c -o _configtest.o
/usr/bin/mpicc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 _configtest.o -L/var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9/build/temp.linux-x86_64-3.9 -o _configtest
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpi.so: undefined reference to `MPIR_being_debugged'
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpi.so: undefined reference to `orte_data_server_uri'
collect2: error: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
error: Cannot link MPI programs. Check your configuration!!!
 * ERROR: dev-python/mpi4py-3.0.3::gentoo failed (compile phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line  127:  Called src_compile
 *   environment, line 2830:  Called distutils-r1_src_compile
 *   environment, line 1184:  Called _distutils-r1_run_foreach_impl 'distutils-r1_python_compile'
 *   environment, line  471:  Called python_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line 2506:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line 2038:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line 2036:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line  793:  Called distutils-r1_run_phase 'distutils-r1_python_compile'
 *   environment, line 1175:  Called distutils-r1_python_compile
 *   environment, line 1036:  Called esetup.py 'build' '-j' '3'
 *   environment, line 1573:  Called die
 * The specific snippet of code:
 *       "${@}" || die -n;
 * 
 * If you need support, post the output of `emerge --info '=dev-python/mpi4py-3.0.3::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=dev-python/mpi4py-3.0.3::gentoo'`.
 * The complete build log is located at '/var/log/portage/dev-python:mpi4py-3.0.3:20210612-062326.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/dev-python/mpi4py-3.0.3/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/dev-python/mpi4py-3.0.3/temp/environment'.
 * Working directory: '/var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3-python3_9'
 * S: '/var/tmp/portage/dev-python/mpi4py-3.0.3/work/mpi4py-3.0.3'