[petsc-users] Trouble installing petsc4py in Anaconda environment
Lisandro Dalcin
dalcinl at gmail.com
Thu Oct 12 02:43:39 CDT 2017
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
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
--
Lisandro Dalcin
============
Research Scientist
Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
Extreme Computing Research Center (ECRC)
King Abdullah University of Science and Technology (KAUST)
http://ecrc.kaust.edu.sa/
4700 King Abdullah University of Science and Technology
al-Khawarizmi Bldg (Bldg 1), Office # 0109
Thuwal 23955-6900, Kingdom of Saudi Arabia
http://www.kaust.edu.sa
Office Phone: +966 12 808-0459
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