[petsc-users] Trouble installing petsc4py in Anaconda environment

Matthew Knepley knepley at gmail.com
Wed Oct 11 18:06:58 CDT 2017 

On Wed, Oct 11, 2017 at 5:29 PM, William T Jones <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
>
> 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


> 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-bu
> ild-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/mye
> nv/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0,
>
>                    from /home/login/anaconda2/envs/mye
> nv/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
>
>                    from /home/login/anaconda2/envs/mye
> nv/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/anacond
> a2/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-bu
> ild-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/mye
> nv/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/mye
> nv/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0,
>
>                      from /home/login/anaconda2/envs/mye
> nv/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
>
>                      from /home/login/anaconda2/envs/mye
> nv/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/anacond
> a2/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
>     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
>                                                     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/>
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