>>> There are environment variables available in my system ($MPICC,
>>> $MPICXX,
>>> $MPIFC) pointing to the appropriate MPI Wrappers (mpicc, mpicxx, mpif90).
>>>
>>It is not sufficient to have an $MPICC environment variable.
You need to have 'mpicc' in the path, which is what i would recommend you doing.
>mpicc is in my $PATH. I will do it again and send the log.
Ok. Here comes the log (see [1]). As you can see while installing PyOP2 he uses gcc instead of mpicxx to compile sparsity.cpp. I compiled this file manually with mpicxx with no problems. So how can I tell him to use
mpicxx when installing PyOP2.
Thank you!
Henrik
[1]
2017-03-09 21:24:05,785 INFO Installing PyOP2/
2017-03-09 21:24:05,785 INFO Firedrake/firedrake/bin/pip install --no-binary mpi4py --no-deps -vvv -e PyOP2/
2017-03-09 21:24:15,490 DEBUG Obtaining file://Firedrake/firedrake/src/PyOP2
Running setup.py (path:Firedrake/firedrake/src/PyOP2/setup.py) egg_info for package from file://Firedrake/firedrake/src/PyOP2
Running command python setup.py egg_info
/rwthfs/rz/SW/UTIL.common/Python/2.7.12/x86_64/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'test_requires'
warnings.warn(msg)
running egg_info
creating PyOP2.egg-info
writing requirements to PyOP2.egg-info/requires.txt
writing PyOP2.egg-info/PKG-INFO
writing top-level names to PyOP2.egg-info/top_level.txt
writing dependency_links to PyOP2.egg-info/dependency_links.txt
writing manifest file 'PyOP2.egg-info/SOURCES.txt'
reading manifest file 'PyOP2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.c' under directory 'pyop2'
writing manifest file 'PyOP2.egg-info/SOURCES.txt'
Source in ./PyOP2 has version 0.13.0+295.gb12f740, which satisfies requirement PyOP2==0.13.0+295.gb12f740 from file://Firedrake/firedrake/src/PyOP2
Installing collected packages: PyOP2
Running setup.py develop for PyOP2
Running command Firedrake/firedrake/bin/python -c "import setuptools, tokenize;__file__='Firedrake/firedrake/src/PyOP2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code,
__file__, 'exec'))" develop --no-deps
/rwthfs/rz/SW/UTIL.common/Python/2.7.12/x86_64/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'test_requires'
warnings.warn(msg)
running develop
running egg_info
writing requirements to PyOP2.egg-info/requires.txt
writing PyOP2.egg-info/PKG-INFO
writing top-level names to PyOP2.egg-info/top_level.txt
writing dependency_links to PyOP2.egg-info/dependency_links.txt
reading manifest file 'PyOP2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.c' under directory 'pyop2'
writing manifest file 'PyOP2.egg-info/SOURCES.txt'
running build_ext
cythoning pyop2/sparsity.pyx to pyop2/sparsity.cpp
building 'pyop2.sparsity' extension
creating build
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/pyop2
gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipyop2 -IFiredrake/firedrake/lib/python2.7/site-packages/numpy/core/include -IFiredrake/firedrake/lib/python2.7/site-packages/petsc4py/include
-IFiredrake/firedrake/lib/python2.7/site-packages/petsc/include -I/rwthfs/rz/SW/UTIL.common/Python/2.7.12/x86_64/include/python2.7 -c pyop2/sparsity.cpp -o build/temp.linux-x86_64-2.7/pyop2/sparsity.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default]
In file included from Firedrake/firedrake/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1788:0,
from Firedrake/firedrake/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from Firedrake/firedrake/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from pyop2/sparsity.cpp:456:
Firedrake/firedrake/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 " \
^
In file included from Firedrake/firedrake/lib/python2.7/site-packages/petsc/include/petscbag.h:4:0,
from Firedrake/firedrake/lib/python2.7/site-packages/petsc/include/petsc.h:5,
from pyop2/sparsity.cpp:458:
Firedrake/firedrake/lib/python2.7/site-packages/petsc/include/petscsys.h:130:17: fatal error: mpi.h: No such file or directory
#include <mpi.h>
^
compilation terminated.
error: command 'gcc' failed with exit status 1
Cleaning up...
Command "Firedrake/firedrake/bin/python -c "import setuptools, tokenize;__file__='Firedrake/firedrake/src/PyOP2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code,
__file__, 'exec'))" develop --no-deps" failed with error code 1 in Firedrake/firedrake/src/PyOP2/
Exception information:
Traceback (most recent call last):
File "Firedrake/firedrake/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main
status = self.run(options, args)
File "Firedrake/firedrake/lib/python2.7/site-packages/pip/commands/install.py", line 342, in run
prefix=options.prefix_path,
File "Firedrake/firedrake/lib/python2.7/site-packages/pip/req/req_set.py", line 784, in install
**kwargs
File "Firedrake/firedrake/lib/python2.7/site-packages/pip/req/req_install.py", line 845, in install
install_options, global_options, prefix=prefix)
File "Firedrake/firedrake/lib/python2.7/site-packages/pip/req/req_install.py", line 1007, in install_editable
show_stdout=False)
File "Firedrake/firedrake/lib/python2.7/site-packages/pip/utils/__init__.py", line 707, in call_subprocess
% (command_desc, proc.returncode, cwd))
InstallationError: Command "Firedrake/firedrake/bin/python -c "import setuptools, tokenize;__file__='Firedrake/firedrake/src/PyOP2/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n',
'\n');f.close();exec(compile(code, __file__, 'exec'))" develop --no-deps" failed with error code 1 in Firedrake/firedrake/src/PyOP2/