install problem

[istv01]

I'm trying to install the latest pyem on a RHEL7 system. I get the following error:

pip install git+https://github.com/asarnow/pyem
Collecting git+https://github.com/asarnow/pyem
Cloning https://github.com/asarnow/pyem to /tmp/pip-req-build-bNGQwH
Requirement already satisfied (use --upgrade to upgrade): pyem==0.3 from git+https://github.com/asarnow/pyem in ./EMAN2/lib/python2.7/site-packages/pyem-0.3-py2.7.egg
Requirement already satisfied: future in ./EMAN2/lib/python2.7/site-packages (from pyem==0.3) (0.16.0)
Requirement already satisfied: numba in ./EMAN2/lib/python2.7/site-packages (from pyem==0.3) (0.40.1)
Requirement already satisfied: numpy in ./EMAN2/lib/python2.7/site-packages (from pyem==0.3) (1.9.3)
Requirement already satisfied: scipy in ./EMAN2/lib/python2.7/site-packages (from pyem==0.3) (1.0.0)
Requirement already satisfied: matplotlib in ./EMAN2/lib/python2.7/site-packages (from pyem==0.3) (1.4.3)
Requirement already satisfied: seaborn in ./EMAN2/lib/python2.7/site-packages (from pyem==0.3) (0.9.0)
Requirement already satisfied: pandas in ./EMAN2/lib/python2.7/site-packages (from pyem==0.3) (0.22.0)
Requirement already satisfied: pathos in ./EMAN2/lib/python2.7/site-packages (from pyem==0.3) (0.2.2.1)
Collecting pyfftw (from pyem==0.3)
Using cached https://files.pythonhosted.org/packages/c2/2e/b25edc6960fc837e915eb1b38e5f0e3013e32e90aff14a1d0f4556b3d145/pyFFTW-0.10.4.tar.gz
Requirement already satisfied: singledispatch in ./EMAN2/lib/python2.7/site-packages (from numba->pyem==0.3) (3.4.0.3)
Requirement already satisfied: enum34 in ./EMAN2/lib/python2.7/site-packages (from numba->pyem==0.3) (1.1.6)
Requirement already satisfied: funcsigs in ./EMAN2/lib/python2.7/site-packages (from numba->pyem==0.3) (1.0.2)
Requirement already satisfied: llvmlite>=0.25.0dev0 in ./EMAN2/lib/python2.7/site-packages (from numba->pyem==0.3) (0.25.0)
Requirement already satisfied: six>=1.4 in ./EMAN2/lib/python2.7/site-packages (from matplotlib->pyem==0.3) (1.10.0)
Requirement already satisfied: python-dateutil in ./EMAN2/lib/python2.7/site-packages (from matplotlib->pyem==0.3) (2.6.1)
Requirement already satisfied: pytz in ./EMAN2/lib/python2.7/site-packages (from matplotlib->pyem==0.3) (2017.2)
Requirement already satisfied: pyparsing>=1.5.6 in ./EMAN2/lib/python2.7/site-packages (from matplotlib->pyem==0.3) (2.0.3)
Requirement already satisfied: nose>=0.11.1 in ./EMAN2/lib/python2.7/site-packages (from matplotlib->pyem==0.3) (1.3.7)
Collecting mock (from matplotlib->pyem==0.3)
Using cached https://files.pythonhosted.org/packages/e6/35/f187bdf23be87092bd0f1200d43d23076cee4d0dec109f195173fd3ebc79/mock-2.0.0-py2.py3-none-any.whl
Requirement already satisfied: dill>=0.2.8.2 in ./EMAN2/lib/python2.7/site-packages (from pathos->pyem==0.3) (0.2.8.2)
Requirement already satisfied: ppft>=1.6.4.8 in ./EMAN2/lib/python2.7/site-packages (from pathos->pyem==0.3) (1.6.4.8)
Requirement already satisfied: multiprocess>=0.70.6.1 in ./EMAN2/lib/python2.7/site-packages (from pathos->pyem==0.3) (0.70.6.1)
Requirement already satisfied: pox>=0.2.4 in ./EMAN2/lib/python2.7/site-packages (from pathos->pyem==0.3) (0.2.4)
Collecting pbr>=0.11 (from mock->matplotlib->pyem==0.3)
Using cached https://files.pythonhosted.org/packages/01/0a/1e81639e7ed6aa51554ab05827984d07885d6873e612a97268ab3d80c73f/pbr-4.3.0-py2.py3-none-any.whl
Building wheels for collected packages: pyem, pyfftw
Running setup.py bdist_wheel for pyem ... done
Stored in directory: /tmp/pip-ephem-wheel-cache-8s0TU6/wheels/cd/76/2c/0c50f235945adaaf47111c47856feb4dd796b5bfbf03fd7785
Running setup.py bdist_wheel for pyfftw ... error
Complete output from command /progs/EMAN2/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-install-Us0CBA/pyfftw/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/pip-wheel-eqq5Qf --python-tag cp27:
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/pyfftw
copying pyfftw/version.py -> build/lib.linux-x86_64-2.7/pyfftw
copying pyfftw/init.py -> build/lib.linux-x86_64-2.7/pyfftw
creating build/lib.linux-x86_64-2.7/pyfftw/builders
copying pyfftw/builders/_utils.py -> build/lib.linux-x86_64-2.7/pyfftw/builders
copying pyfftw/builders/init.py -> build/lib.linux-x86_64-2.7/pyfftw/builders
copying pyfftw/builders/builders.py -> build/lib.linux-x86_64-2.7/pyfftw/builders
creating build/lib.linux-x86_64-2.7/pyfftw/interfaces
copying pyfftw/interfaces/cache.py -> build/lib.linux-x86_64-2.7/pyfftw/interfaces
copying pyfftw/interfaces/scipy_fftpack.py -> build/lib.linux-x86_64-2.7/pyfftw/interfaces
copying pyfftw/interfaces/_utils.py -> build/lib.linux-x86_64-2.7/pyfftw/interfaces
copying pyfftw/interfaces/init.py -> build/lib.linux-x86_64-2.7/pyfftw/interfaces
copying pyfftw/interfaces/numpy_fft.py -> build/lib.linux-x86_64-2.7/pyfftw/interfaces
running build_ext
building 'pyfftw.pyfftw' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/tmp
creating build/temp.linux-x86_64-2.7/tmp/pip-install-Us0CBA
creating build/temp.linux-x86_64-2.7/tmp/pip-install-Us0CBA/pyfftw
creating build/temp.linux-x86_64-2.7/tmp/pip-install-Us0CBA/pyfftw/pyfftw
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-install-Us0CBA/pyfftw/include -I/tmp/pip-install-Us0CBA/pyfftw/pyfftw -I/progs/EMAN2/lib/python2.7/site-packages/numpy/core/include -I/progs/EMAN2/include/python2.7 -c /tmp/pip-install-Us0CBA/pyfftw/pyfftw/pyfftw.c -o build/temp.linux-x86_64-2.7/tmp/pip-install-Us0CBA/pyfftw/pyfftw/pyfftw.o
In file included from /progs/EMAN2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
from /progs/EMAN2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /progs/EMAN2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /tmp/pip-install-Us0CBA/pyfftw/pyfftw/pyfftw.c:268:
/progs/EMAN2/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 "
^
/tmp/pip-install-Us0CBA/pyfftw/pyfftw/pyfftw.c:272:19: fatal error: fftw3.h: No such file or directory
#include "fftw3.h"
^
compilation terminated.
error: command 'gcc' failed with exit status 1

---

Failed building wheel for pyfftw
Running setup.py clean for pyfftw
Successfully built pyem
Failed to build pyfftw
Installing collected packages: pyfftw, pbr, mock
Running setup.py install for pyfftw ... error
Complete output from command /progs/EMAN2/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-install-Us0CBA/pyfftw/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-record-KeDpa7/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
running build_ext
building 'pyfftw.pyfftw' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/tmp
creating build/temp.linux-x86_64-2.7/tmp/pip-install-Us0CBA
creating build/temp.linux-x86_64-2.7/tmp/pip-install-Us0CBA/pyfftw
creating build/temp.linux-x86_64-2.7/tmp/pip-install-Us0CBA/pyfftw/pyfftw
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-install-Us0CBA/pyfftw/include -I/tmp/pip-install-Us0CBA/pyfftw/pyfftw -I/progs/EMAN2/lib/python2.7/site-packages/numpy/core/include -I/progs/EMAN2/include/python2.7 -c /tmp/pip-install-Us0CBA/pyfftw/pyfftw/pyfftw.c -o build/temp.linux-x86_64-2.7/tmp/pip-install-Us0CBA/pyfftw/pyfftw/pyfftw.o
In file included from /progs/EMAN2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
from /progs/EMAN2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /progs/EMAN2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /tmp/pip-install-Us0CBA/pyfftw/pyfftw/pyfftw.c:268:
/progs/EMAN2/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 "
^
/tmp/pip-install-Us0CBA/pyfftw/pyfftw/pyfftw.c:272:19: fatal error: fftw3.h: No such file or directory
#include "fftw3.h"
^
compilation terminated.
error: command 'gcc' failed with exit status 1

----------------------------------------

Command "/progs/EMAN2/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-install-Us0CBA/pyfftw/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-record-KeDpa7/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-Us0CBA/pyfftw/

[asarnow]

1. FFTW is not installed. Install (with yum/dnf) fftw and fftw-devel packages (search fftw to make sure the names are right).
2. Using the EMAN2 python is not recommended. In current EMAN2, you only need to put EMAN2/bin directory at the end of your PATH. You can use the system Python, but miniconda is recommended (see wiki).
3. If you make a git clone, and install using pip install -e then you can update seamlessly just by using git pull.