[petsc-users] Trouble installing petsc4py in Anaconda environment
William T. Jones
w.t.jones at nasa.gov
Thu Oct 12 07:35:42 CDT 2017
On 10/12/17 3:43 AM, Lisandro Dalcin wrote:
> Please install the maint branch (see issue
> https://bitbucket.org/petsc/petsc4py/issues/75/)
>
> $ conda install cython # required to build the C wrapper source code
> $ pip install --no-dependencies
> https://bitbucket.org/petsc/petsc4py/get/maint.tar.gz
Thank You. Thank You! Thank You!!
I spent a day trying to fix this before emailing this list. Works like
a charm.
>
> On 12 October 2017 at 00:29, 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.
>>
>> 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
>> 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
>
>
>
--
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
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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