[petsc-users] Trouble installing petsc4py in Anaconda environment
William T Jones
w.t.jones at nasa.gov
Wed Oct 11 16:29:47 CDT 2017
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
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