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 <[email protected]> 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 [email protected] > 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
