[petsc-users] Trouble installing petsc4py in Anaconda environment
William T. Jones
w.t.jones at nasa.gov
Wed Oct 11 21:13:20 CDT 2017
On 10/11/17 7:06 PM, Matthew Knepley wrote:
> On Wed, Oct 11, 2017 at 5:29 PM, William T Jones <w.t.jones at nasa.gov
> <mailto:w.t.jones at nasa.gov>> 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. 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/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-packages/petsc/include
> -Isrc/include
> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/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-packages/petsc/include
> -Isrc/include
> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/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-packages/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-packages/petsc/include
> -Isrc/include
> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/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-packages/petsc/include
> -Isrc/include
> -I/home/login/anaconda2/envs/myenv/lib/python2.7/site-packages/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-packages/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 W.T.JONES at NASA.GOV <mailto:W.T.JONES at NASA.GOV>
> 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 W.T.JONES at NASA.GOV
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
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