On Wed, Oct 11, 2017 at 10:13 PM, William T. Jones <[email protected]> wrote:
> On 10/11/17 7:06 PM, Matthew Knepley wrote: > >> On Wed, Oct 11, 2017 at 5:29 PM, William T Jones <[email protected] >> <mailto:[email protected]>> wrote: >> >> I have created an Anaconda Pytyoh 2.7 environment on an SGI-ICE >> machine and included cython, numpy=1.12, scipy, and mpi4py (based >> SGI-MPT). While petsc installs fine with: >> >> % PETSC_CONFIGURE_OPTIONS="--download-fblaslapack=1" pip install >> https://bitbucket.org/petsc/petsc/get/maint.tar.gz >> <https://bitbucket.org/petsc/petsc/get/maint.tar.gz> >> >> I cannot get petsc4py to build/install. I am attempting with: >> >> % export >> PETSC_DIR=${PREFIX}/envs/myenv/lib/python2.7/site-packages/petsc >> % pip install --no-dependencies petsc4py >> >> Note, I am using "--no-dependencies" because I want to leave numpy >> at 1.12 and do not want it to be upgraded. Either way I get the >> output below. It appears that the link command has been corrupted >> with the addition of the "gcc" command in the middle of the link >> command. >> >> >> /vendor/sgi/mpt/2.14r19/bin/mpicc is being called. Does this actually >> work? I would suspect it of calling 'gcc' >> >> > Matt, Thanks for the response. > > Yes, `/vendor/sgi/mpt/2.14r19/bin/mpicc` is a compiler wrapper that > ultimately calls gcc. The problem is that in the middle of the link line > there is an extraneous "...-fstack-protector -g -O gcc -pthread -shared > -B...". From the error message, it is this embedded "gcc" that is the > problem. > > I cannot see where petsc4py gets its compiler and linker commands. It > would appear that they come from petsc. I would not have that interpretation. This is because the build outputs the Petsc information underneath PETSC_ARCH and it shows the compiler and linker given to it. Neither has 'gcc' in it. You could grep the files in $PETSC_DIR/$PETSC_ARCH/lib/petsc/conf for 'gcc', but i suspect it will not be there. Thanks, Matt > Again, it appears that the link line is being constructed > inappropriately. > > Matt >> >> Any help is appreciated, >> >> >> % pip install --no-dependencies petsc4py >> Collecting petsc4py >> Using cached petsc4py-3.8.0.tar.gz >> Building wheels for collected packages: petsc4py >> Running setup.py bdist_wheel for petsc4py ... error >> Complete output from command >> /home/login/anaconda2/envs/myenv/bin/python -u -c "import >> setuptools, >> tokenize;__file__='/tmp/pip-build-v6lDIk/petsc4py/setup.py'; >> f=getattr(tokenize, >> 'open', open)(__file__);code=f.read().replace('\r\n', >> '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel >> -d /tmp/tmpD2KqLjpip-wheel- --python-tag cp27: >> running bdist_wheel >> running build >> running build_src >> running build_py >> creating build >> creating build/lib.linux-x86_64-2.7 >> creating build/lib.linux-x86_64-2.7/petsc4py >> copying src/PETSc.py -> build/lib.linux-x86_64-2.7/petsc4py >> copying src/__init__.py -> build/lib.linux-x86_64-2.7/petsc4py >> copying src/__main__.py -> build/lib.linux-x86_64-2.7/petsc4py >> creating build/lib.linux-x86_64-2.7/petsc4py/lib >> copying src/lib/__init__.py -> >> build/lib.linux-x86_64-2.7/petsc4py/lib >> creating build/lib.linux-x86_64-2.7/petsc4py/include >> creating build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/petsc4py.PETSc.h -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/numpy.h -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/petsc4py.PETSc_api.h -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/petsc4py.h -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/petsc4py.i -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/__init__.pxd -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/PETSc.pxd -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/__init__.pyx -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/PETSc.pxd -> build/lib.linux-x86_64-2.7/petsc4py >> copying src/lib/petsc.cfg -> build/lib.linux-x86_64-2.7/pet >> sc4py/lib >> running build_ext >> PETSC_DIR: >> /home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/petsc >> PETSC_ARCH: >> version: 3.8.0 release >> integer-size: 32-bit >> scalar-type: real >> precision: double >> language: CONLY >> compiler: /vendor/sgi/mpt/2.14r19/bin/mpicc >> linker: /vendor/sgi/mpt/2.14r19/bin/mpicc >> building 'PETSc' extension >> creating build/temp.linux-x86_64-2.7 >> creating build/temp.linux-x86_64-2.7/src >> /vendor/sgi/mpt/2.14r19/bin/mpicc -pthread -B >> /home/login/anaconda2/envs/myenv/compiler_compat -fPIC -Wall >> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >> -fstack-protector -g -O -fPIC -fno-strict-aliasing -g -O2 -DNDEBUG >> -g -fwrapv -O3 -Wall >> -DPETSC_DIR=/home/login/anaconda2/envs/myenv/lib/python2.7/ >> site-packages/petsc >> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packag >> es/petsc/include >> -Isrc/include >> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packag >> es/numpy/core/include >> -I/home/login/anaconda2/envs/myenv/include/python2.7 -c src/PETSc.c >> -o build/temp.linux-x86_64-2.7/src/PETSc.o >> In file included from >> /home/login/anaconda2/envs/myenv/lib/python2.7/site-packages >> /numpy/core/include/numpy/ndarraytypes.h:1788:0, >> >> from >> /home/login/anaconda2/envs/myenv/lib/python2.7/site-packages >> /numpy/core/include/numpy/ndarrayobject.h:18, >> >> from >> /home/login/anaconda2/envs/myenv/lib/python2.7/site-packages >> /numpy/core/include/numpy/arrayobject.h:4, >> >> from src/include/petsc4py/numpy.h:11, >> from src/petsc4py.PETSc.c:519, >> from src/PETSc.c:3: >> >> /home/login/anaconda2/envs/myenv/lib/python2.7/site-packages >> /numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: >> warning: #warning "Using deprecated NumPy API, disable it by " >> "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] >> #warning "Using deprecated NumPy API, disable it by " \ >> ^ >> /vendor/sgi/mpt/2.14r19/bin/mpicc -pthread -B >> /home/login/anaconda2/envs/myenv/compiler_compat -fPIC -Wall >> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >> -fstack-protector -g -O -fPIC -fno-strict-aliasing -g -O2 -DNDEBUG >> -g -fwrapv -O3 -Wall >> -DPETSC_DIR=/home/login/anaconda2/envs/myenv/lib/python2.7/ >> site-packages/petsc >> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packag >> es/petsc/include >> -Isrc/include >> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packag >> es/numpy/core/include >> -I/home/login/anaconda2/envs/myenv/include/python2.7 -c >> src/libpetsc4py.c -o build/temp.linux-x86_64-2.7/src/libpetsc4py.o >> /vendor/sgi/mpt/2.14r19/bin/mpicc -pthread -B >> /home/login/anaconda2/envs/myenv/compiler_compat -fPIC -Wall >> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >> -fstack-protector -g -O gcc -pthread -shared -B >> /home/login/anaconda2/envs/myenv/compiler_compat >> -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall >> -L/home/login/anaconda2/envs/myenv/lib >> -Wl,-rpath=/home/login/anaconda2/envs/myenv/lib -Wl,--no-as-needed >> -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/src/PETSc.o >> build/temp.linux-x86_64-2.7/src/libpetsc4py.o >> -L/home/login/anaconda2/envs/myenv/lib/python2.7/site-packag >> es/petsc/lib >> -L/home/login/anaconda2/envs/myenv/lib >> -Wl,-rpath,/home/login/anaconda2/envs/myenv/lib/python2.7/ >> site-packages/petsc/lib >> -Wl,-rpath,/home/login/anaconda2/envs/myenv/lib -lpetsc -lpython2.7 >> -o build/lib.linux-x86_64-2.7/petsc4py/lib/PETSc.so >> gcc: error: gcc: No such file or directory >> error: command '/vendor/sgi/mpt/2.14r19/bin/mpicc' failed with >> exit status 1 >> >> >> ---------------------------------------- >> Failed building wheel for petsc4py >> Running setup.py clean for petsc4py >> Failed to build petsc4py >> Installing collected packages: petsc4py >> Running setup.py install for petsc4py ... error >> Complete output from command >> /home/login/anaconda2/envs/myenv/bin/python -u -c "import >> setuptools, >> tokenize;__file__='/tmp/pip-build-v6lDIk/petsc4py/setup.py'; >> f=getattr(tokenize, >> 'open', open)(__file__);code=f.read().replace('\r\n', >> '\n');f.close();exec(compile(code, __file__, 'exec'))" install >> --record /tmp/pip-d6NYW8-record/install-record.txt >> --single-version-externally-managed --compile: >> running install >> running build >> running build_src >> running build_py >> creating build >> creating build/lib.linux-x86_64-2.7 >> creating build/lib.linux-x86_64-2.7/petsc4py >> copying src/PETSc.py -> build/lib.linux-x86_64-2.7/petsc4py >> copying src/__init__.py -> build/lib.linux-x86_64-2.7/petsc4py >> copying src/__main__.py -> build/lib.linux-x86_64-2.7/petsc4py >> creating build/lib.linux-x86_64-2.7/petsc4py/lib >> copying src/lib/__init__.py -> >> build/lib.linux-x86_64-2.7/petsc4py/lib >> creating build/lib.linux-x86_64-2.7/petsc4py/include >> creating build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/petsc4py.PETSc.h -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/numpy.h -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/petsc4py.PETSc_api.h -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/petsc4py.h -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/petsc4py.i -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/__init__.pxd -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/PETSc.pxd -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/include/petsc4py/__init__.pyx -> >> build/lib.linux-x86_64-2.7/petsc4py/include/petsc4py >> copying src/PETSc.pxd -> build/lib.linux-x86_64-2.7/petsc4py >> copying src/lib/petsc.cfg -> >> build/lib.linux-x86_64-2.7/petsc4py/lib >> running build_ext >> PETSC_DIR: >> /home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/petsc >> PETSC_ARCH: >> version: 3.8.0 release >> integer-size: 32-bit >> scalar-type: real >> precision: double >> language: CONLY >> compiler: /vendor/sgi/mpt/2.14r19/bin/mpicc >> linker: /vendor/sgi/mpt/2.14r19/bin/mpicc >> building 'PETSc' extension >> creating build/temp.linux-x86_64-2.7 >> creating build/temp.linux-x86_64-2.7/src >> /vendor/sgi/mpt/2.14r19/bin/mpicc -pthread -B >> /home/login/anaconda2/envs/myenv/compiler_compat -fPIC -Wall >> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >> -fstack-protector -g -O -fPIC -fno-strict-aliasing -g -O2 -DNDEBUG >> -g -fwrapv -O3 -Wall >> -DPETSC_DIR=/home/login/anaconda2/envs/myenv/lib/python2.7/ >> site-packages/petsc >> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packag >> es/petsc/include >> -Isrc/include >> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packag >> es/numpy/core/include >> -I/home/login/anaconda2/envs/myenv/include/python2.7 -c src/PETSc.c >> -o build/temp.linux-x86_64-2.7/src/PETSc.o >> In file included from >> /home/login/anaconda2/envs/myenv/lib/python2.7/site-packages >> /numpy/core/include/numpy/ndarraytypes.h:1788:0, >> >> from >> /home/login/anaconda2/envs/myenv/lib/python2.7/site-packages >> /numpy/core/include/numpy/ndarrayobject.h:18, >> >> from >> /home/login/anaconda2/envs/myenv/lib/python2.7/site-packages >> /numpy/core/include/numpy/arrayobject.h:4, >> >> from src/include/petsc4py/numpy.h:11, >> from src/petsc4py.PETSc.c:519, >> from src/PETSc.c:3: >> >> /home/login/anaconda2/envs/myenv/lib/python2.7/site-packages >> /numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: >> warning: #warning "Using deprecated NumPy API, disable it by " >> "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] >> #warning "Using deprecated NumPy API, disable it by " \ >> ^ >> /vendor/sgi/mpt/2.14r19/bin/mpicc -pthread -B >> /home/login/anaconda2/envs/myenv/compiler_compat -fPIC -Wall >> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >> -fstack-protector -g -O -fPIC -fno-strict-aliasing -g -O2 -DNDEBUG >> -g -fwrapv -O3 -Wall >> -DPETSC_DIR=/home/login/anaconda2/envs/myenv/lib/python2.7/ >> site-packages/petsc >> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packag >> es/petsc/include >> -Isrc/include >> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packag >> es/numpy/core/include >> -I/home/login/anaconda2/envs/myenv/include/python2.7 -c >> src/libpetsc4py.c -o build/temp.linux-x86_64-2.7/src/libpetsc4py.o >> /vendor/sgi/mpt/2.14r19/bin/mpicc -pthread -B >> /home/login/anaconda2/envs/myenv/compiler_compat -fPIC -Wall >> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >> -fstack-protector -g -O gcc -pthread -shared -B >> /home/login/anaconda2/envs/myenv/compiler_compat >> -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall >> -L/home/login/anaconda2/envs/myenv/lib >> -Wl,-rpath=/home/login/anaconda2/envs/myenv/lib -Wl,--no-as-needed >> -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/src/PETSc.o >> build/temp.linux-x86_64-2.7/src/libpetsc4py.o >> -L/home/login/anaconda2/envs/myenv/lib/python2.7/site-packag >> es/petsc/lib >> -L/home/login/anaconda2/envs/myenv/lib >> -Wl,-rpath,/home/login/anaconda2/envs/myenv/lib/python2.7/ >> site-packages/petsc/lib >> -Wl,-rpath,/home/login/anaconda2/envs/myenv/lib -lpetsc -lpython2.7 >> -o build/lib.linux-x86_64-2.7/petsc4py/lib/PETSc.so >> gcc: error: gcc: No such file or directory >> error: command '/vendor/sgi/mpt/2.14r19/bin/mpicc' failed with >> exit status 1 >> >> ---------------------------------------- >> Command "/home/login/anaconda2/envs/myenv/bin/python -u -c "import >> setuptools, >> tokenize;__file__='/tmp/pip-build-v6lDIk/petsc4py/setup.py'; >> f=getattr(tokenize, >> 'open', open)(__file__);code=f.read().replace('\r\n', >> '\n');f.close();exec(compile(code, __file__, 'exec'))" install >> --record /tmp/pip-d6NYW8-record/install-record.txt >> --single-version-externally-managed --compile" failed with error >> code 1 in /tmp/pip-build-v6lDIk/petsc4py/ >> >> >> -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= >> -=-=-=-=-=-=- >> >> Bill Jones [email protected] <mailto:[email protected]> >> Mail Stop 128 Computational AeroSciences >> Branch >> 15 Langley Boulevard Research >> Directorate >> NASA Langley Research Center Building 1268, Room >> 1044 >> Hampton, VA 23681-2199 Phone +1 757 >> 864-5318 <tel:%2B1%20757%20864-5318> >> Fax +1 757 >> 864-8816 <tel:%2B1%20757%20864-8816> >> http://fun3d.larc.nasa.gov >> >> >> >> >> -- >> What most experimenters take for granted before they begin their >> experiments is infinitely more interesting than any results to which their >> experiments lead. >> -- Norbert Wiener >> >> https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/> >> > > -- > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > > Bill Jones [email protected] > Mail Stop 128 Computational AeroSciences Branch > 15 Langley Boulevard Research Directorate > NASA Langley Research Center Building 1268, Room 1060 > Hampton, VA 23681-2199 Phone +1 757 864-5318 > Fax +1 757 864-8816 > http://fun3d.larc.nasa.gov > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
