Hello,
I have limited knowledge about Xeon Phi system and I am trying to compile python, numpy and scipy using PyPhi. My system is a Ubuntu 14.04 (64x) with composer_xe_2015 and host system python is 2.7.6 (and have adopted "site.cfg" for 'composer_xe_2015'). but I encountered an error while running:
"cd numpy && PYTHONXCPREFIX=$(MIC_PY_HOME) python numpyxc.py build_clib"
... and here's what the error looks like. any idea, what I am doing wrong?
part of my log
make[1]: Leaving directory `/opt/pyphi/mic/python'
wget http://downloads.sourceforge.net/project/numpy/NumPy/1.8.1/numpy-1.8.1.tar.gz -O numpy.tgz
--2015-10-09 15:52:05-- http://downloads.sourceforge.net/project/numpy/NumPy/1.8.1/numpy-1.8.1.tar.gz
Resolving downloads.sourceforge.net (downloads.sourceforge.net)... 216.34.181.59
Connecting to downloads.sourceforge.net (downloads.sourceforge.net)|216.34.181.59|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: http://netassist.dl.sourceforge.net/project/numpy/NumPy/1.8.1/numpy-1.8.1.tar.gz [following]
--2015-10-09 15:52:06-- http://netassist.dl.sourceforge.net/project/numpy/NumPy/1.8.1/numpy-1.8.1.tar.gz
Resolving netassist.dl.sourceforge.net (netassist.dl.sourceforge.net)... 62.205.134.42, 2a01:d0:0:37::2
Connecting to netassist.dl.sourceforge.net (netassist.dl.sourceforge.net)|62.205.134.42|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3794076 (3.6M) [application/x-gzip]
Saving to: ‘numpy.tgz’
100%[================================================================================================================================================>] 3,794,076 --.-K/s in 0.03s
2015-10-09 15:52:18 (104 MB/s) - ‘numpy.tgz’ saved [3794076/3794076]
mkdir numpy
tar -xf numpy.tgz -C numpy --strip-components=1
wget https://raw.github.com/bpartridge/PyPhi/master/numpyxc.py -O numpy/numpyxc.py
--2015-10-09 15:52:18-- https://raw.github.com/bpartridge/PyPhi/master/numpyxc.py
Resolving raw.github.com (raw.github.com)... 185.31.17.133
Connecting to raw.github.com (raw.github.com)|185.31.17.133|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://raw.githubusercontent.com/bpartridge/PyPhi/master/numpyxc.py [following]
--2015-10-09 15:52:19-- https://raw.githubusercontent.com/bpartridge/PyPhi/master/numpyxc.py
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.31.17.133
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.31.17.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2602 (2.5K) [text/plain]
Saving to: ‘numpy/numpyxc.py’
100%[================================================================================================================================================>] 2,602 --.-K/s in 0s
2015-10-09 15:52:19 (482 MB/s) - ‘numpy/numpyxc.py’ saved [2602/2602]
wget https://raw.githubusercontent.com/neel9102/michack/master/PyPhi/site.cfg -O numpy/site.cfg
--2015-10-09 15:52:19-- https://raw.githubusercontent.com/neel9102/michack/master/PyPhi/site.cfg
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.31.17.133
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.31.17.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 223 [text/plain]
Saving to: ‘numpy/site.cfg’
100%[================================================================================================================================================>] 223 --.-K/s in 0s
2015-10-09 15:52:19 (45.1 MB/s) - ‘numpy/site.cfg’ saved [223/223]
wget https://raw.github.com/bpartridge/PyPhi/master/setup.cfg -O numpy/setup.cfg
--2015-10-09 15:52:19-- https://raw.github.com/bpartridge/PyPhi/master/setup.cfg
Resolving raw.github.com (raw.github.com)... 185.31.17.133
Connecting to raw.github.com (raw.github.com)|185.31.17.133|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://raw.githubusercontent.com/bpartridge/PyPhi/master/setup.cfg [following]
--2015-10-09 15:52:19-- https://raw.githubusercontent.com/bpartridge/PyPhi/master/setup.cfg
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.31.17.133
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.31.17.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 193 [text/plain]
Saving to: ‘numpy/setup.cfg’
100%[================================================================================================================================================>] 193 --.-K/s in 0s
2015-10-09 15:52:20 (38.2 MB/s) - ‘numpy/setup.cfg’ saved [193/193]
build_clib forces config.h to be created; it needs to be modified before extensions are built
cd numpy && PYTHONXCPREFIX=/opt/pyphi/mic/python/_install python numpyxc.py build_clib
/opt/pyphi/mic/numpy/setup.py
Running from numpy source directory.
/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'test_suite'
warnings.warn(msg)
/bin/sh: 1: svnversion: not found
F2PY Version 2
blas_opt_info:
blas_mkl_info:
FOUND:
libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'pthread']
library_dirs = ['/opt/intel/composer_xe_2015/mkl/lib/mic']
define_macros = [('SCIPY_MKL_H', None)]
include_dirs = ['/opt/intel/composer_xe_2015/mkl/include']
FOUND:
libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'pthread']
library_dirs = ['/opt/intel/composer_xe_2015/mkl/lib/mic']
define_macros = [('SCIPY_MKL_H', None)]
include_dirs = ['/opt/intel/composer_xe_2015/mkl/include']
/bin/sh: 1: svnversion: not found
non-existing path in 'numpy/lib': 'benchmarks'
lapack_opt_info:
openblas_info:
libraries not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
lapack_mkl_info:
mkl_info:
FOUND:
libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'pthread']
library_dirs = ['/opt/intel/composer_xe_2015/mkl/lib/mic']
define_macros = [('SCIPY_MKL_H', None)]
include_dirs = ['/opt/intel/composer_xe_2015/mkl/include']
FOUND:
libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'pthread']
library_dirs = ['/opt/intel/composer_xe_2015/mkl/lib/mic']
define_macros = [('SCIPY_MKL_H', None)]
include_dirs = ['/opt/intel/composer_xe_2015/mkl/include']
FOUND:
libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'pthread']
library_dirs = ['/opt/intel/composer_xe_2015/mkl/lib/mic']
define_macros = [('SCIPY_MKL_H', None)]
include_dirs = ['/opt/intel/composer_xe_2015/mkl/include']
/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'define_macros'
warnings.warn(msg)
running build_clib
running build_src
build_src
building py_modules sources
creating build
creating build/src.linux-x86_64-2.7
creating build/src.linux-x86_64-2.7/numpy
creating build/src.linux-x86_64-2.7/numpy/distutils
building library "npymath" sources
customize IntelMICFCompiler
Found executable /opt/intel/bin/ifort
customize IntelMICFCompiler using config
C compiler: icc -mmic -mkl -fPIC -fp-model strict -g -I/opt/pyphi/mic/python/_install/include -L/opt/pyphi/mic/python/_install/lib -L/opt/pyphi/mic/python/_install/lib/python2.7 -L/opt/pyphi/mic/python/_install/lib/python2.7/site-packages/numpy/core/lib
compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/usr/include/python2.7 -c'
icc: _configtest.c
icc: command line remark #10364: Using '-fp-model strict' forces the compiler to generate legacy floating-point instructions instead of KNC for most floating-point operations, which may impact performance. Consider using a floating-point model that allows the compiler to assume the default floating-point environment.
icc -mmic -mkl -fPIC -fp-model strict -g -I/opt/pyphi/mic/python/_install/include -L/opt/pyphi/mic/python/_install/lib -L/opt/pyphi/mic/python/_install/lib/python2.7 -L/opt/pyphi/mic/python/_install/lib/python2.7/site-packages/numpy/core/lib _configtest.o -o _configtest
icc: command line remark #10364: Using '-fp-model strict' forces the compiler to generate legacy floating-point instructions instead of KNC for most floating-point operations, which may impact performance. Consider using a floating-point model that allows the compiler to assume the default floating-point environment.
success!
removing: _configtest.c _configtest.o _configtest
C compiler: icc -mmic -mkl -fPIC -fp-model strict -g -I/opt/pyphi/mic/python/_install/include -L/opt/pyphi/mic/python/_install/lib -L/opt/pyphi/mic/python/_install/lib/python2.7 -L/opt/pyphi/mic/python/_install/lib/python2.7/site-packages/numpy/core/lib
compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/usr/include/python2.7 -c'
icc: _configtest.c
icc: command line remark #10364: Using '-fp-model strict' forces the compiler to generate legacy floating-point instructions instead of KNC for most floating-point operations, which may impact performance. Consider using a floating-point model that allows the compiler to assume the default floating-point environment.
icc -mmic -mkl -fPIC -fp-model strict -g -I/opt/pyphi/mic/python/_install/include -L/opt/pyphi/mic/python/_install/lib -L/opt/pyphi/mic/python/_install/lib/python2.7 -L/opt/pyphi/mic/python/_install/lib/python2.7/site-packages/numpy/core/lib _configtest.o -o _configtest
icc: command line remark #10364: Using '-fp-model strict' forces the compiler to generate legacy floating-point instructions instead of KNC for most floating-point operations, which may impact performance. Consider using a floating-point model that allows the compiler to assume the default floating-point environment.
success!
removing: _configtest.c _configtest.o _configtest
creating build/src.linux-x86_64-2.7/numpy/core
creating build/src.linux-x86_64-2.7/numpy/core/src
creating build/src.linux-x86_64-2.7/numpy/core/src/npymath
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/npymath/npy_math.c
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/npymath/ieee754.c
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/npymath/npy_math_complex.c
building library "npysort" sources
creating build/src.linux-x86_64-2.7/numpy/core/src/npysort
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/npysort/quicksort.c
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/npysort/mergesort.c
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/npysort/heapsort.c
creating build/src.linux-x86_64-2.7/numpy/core/src/private
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/private/npy_partition.h
adding 'build/src.linux-x86_64-2.7/numpy/core/src/private' to include_dirs.
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/npysort/selection.c
None - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/src/private/npy_partition.h']
building extension "numpy.core._dummy" sources
Generating build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h
C compiler: icc -mmic -mkl -fPIC -fp-model strict -g -I/opt/pyphi/mic/python/_install/include -L/opt/pyphi/mic/python/_install/lib -L/opt/pyphi/mic/python/_install/lib/python2.7 -L/opt/pyphi/mic/python/_install/lib/python2.7/site-packages/numpy/core/lib
compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/usr/include/python2.7 -c'
icc: _configtest.c
icc: command line remark #10364: Using '-fp-model strict' forces the compiler to generate legacy floating-point instructions instead of KNC for most floating-point operations, which may impact performance. Consider using a floating-point model that allows the compiler to assume the default floating-point environment.
In file included from /usr/include/python2.7/Python.h(8),
from _configtest.c(1):
/usr/include/python2.7/pyconfig.h(3): catastrophic error: cannot open source file "x86_64-linux-gnu/python2.7/pyconfig.h"
include <x86_64-linux-gnu/python2.7/pyconfig.h>
compilation aborted for _configtest.c (code 4)
icc: command line remark #10364: Using '-fp-model strict' forces the compiler to generate legacy floating-point instructions instead of KNC for most floating-point operations, which may impact performance. Consider using a floating-point model that allows the compiler to assume the default floating-point environment.
In file included from /usr/include/python2.7/Python.h(8),
from _configtest.c(1):
/usr/include/python2.7/pyconfig.h(3): catastrophic error: cannot open source file "x86_64-linux-gnu/python2.7/pyconfig.h"
include <x86_64-linux-gnu/python2.7/pyconfig.h>
compilation aborted for _configtest.c (code 4)
failure.
removing: _configtest.c _configtest.o
Traceback (most recent call last):
File "numpyxc.py", line 73, in
setup.setup_package()
File "/opt/pyphi/mic/numpy/setup.py", line 231, in setup_package
setup(**metadata)
File "/opt/pyphi/mic/numpy/numpy/distutils/core.py", line 169, in setup
return old_setup(**new_attr)
File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/opt/pyphi/mic/numpy/numpy/distutils/command/build_clib.py", line 63, in run
self.run_command('build_src')
File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/opt/pyphi/mic/numpy/numpy/distutils/command/build_src.py", line 153, in run
self.build_sources()
File "/opt/pyphi/mic/numpy/numpy/distutils/command/build_src.py", line 170, in build_sources
self.build_extension_sources(ext)
File "/opt/pyphi/mic/numpy/numpy/distutils/command/build_src.py", line 329, in build_extension_sources
sources = self.generate_sources(sources, ext)
File "/opt/pyphi/mic/numpy/numpy/distutils/command/build_src.py", line 386, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 428, in generate_config_h
moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
File "numpy/core/setup.py", line 42, in check_types
out = check_types(_a, *_kw)
File "numpy/core/setup.py", line 289, in check_types
"Cannot compile 'Python.h'. Perhaps you need to "
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
make: *** [numpyxc] Error 1
Hello,
I have limited knowledge about Xeon Phi system and I am trying to compile python, numpy and scipy using PyPhi. My system is a Ubuntu 14.04 (64x) with composer_xe_2015 and host system python is 2.7.6 (and have adopted "site.cfg" for 'composer_xe_2015'). but I encountered an error while running:
"cd numpy && PYTHONXCPREFIX=$(MIC_PY_HOME) python numpyxc.py build_clib"
... and here's what the error looks like. any idea, what I am doing wrong?
part of my log
make[1]: Leaving directory `/opt/pyphi/mic/python'
wget http://downloads.sourceforge.net/project/numpy/NumPy/1.8.1/numpy-1.8.1.tar.gz -O numpy.tgz
--2015-10-09 15:52:05-- http://downloads.sourceforge.net/project/numpy/NumPy/1.8.1/numpy-1.8.1.tar.gz
Resolving downloads.sourceforge.net (downloads.sourceforge.net)... 216.34.181.59
Connecting to downloads.sourceforge.net (downloads.sourceforge.net)|216.34.181.59|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: http://netassist.dl.sourceforge.net/project/numpy/NumPy/1.8.1/numpy-1.8.1.tar.gz [following]
--2015-10-09 15:52:06-- http://netassist.dl.sourceforge.net/project/numpy/NumPy/1.8.1/numpy-1.8.1.tar.gz
Resolving netassist.dl.sourceforge.net (netassist.dl.sourceforge.net)... 62.205.134.42, 2a01:d0:0:37::2
Connecting to netassist.dl.sourceforge.net (netassist.dl.sourceforge.net)|62.205.134.42|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3794076 (3.6M) [application/x-gzip]
Saving to: ‘numpy.tgz’
100%[================================================================================================================================================>] 3,794,076 --.-K/s in 0.03s
2015-10-09 15:52:18 (104 MB/s) - ‘numpy.tgz’ saved [3794076/3794076]
mkdir numpy
tar -xf numpy.tgz -C numpy --strip-components=1
wget https://raw.github.com/bpartridge/PyPhi/master/numpyxc.py -O numpy/numpyxc.py
--2015-10-09 15:52:18-- https://raw.github.com/bpartridge/PyPhi/master/numpyxc.py
Resolving raw.github.com (raw.github.com)... 185.31.17.133
Connecting to raw.github.com (raw.github.com)|185.31.17.133|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://raw.githubusercontent.com/bpartridge/PyPhi/master/numpyxc.py [following]
--2015-10-09 15:52:19-- https://raw.githubusercontent.com/bpartridge/PyPhi/master/numpyxc.py
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.31.17.133
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.31.17.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2602 (2.5K) [text/plain]
Saving to: ‘numpy/numpyxc.py’
100%[================================================================================================================================================>] 2,602 --.-K/s in 0s
2015-10-09 15:52:19 (482 MB/s) - ‘numpy/numpyxc.py’ saved [2602/2602]
wget https://raw.githubusercontent.com/neel9102/michack/master/PyPhi/site.cfg -O numpy/site.cfg
--2015-10-09 15:52:19-- https://raw.githubusercontent.com/neel9102/michack/master/PyPhi/site.cfg
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.31.17.133
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.31.17.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 223 [text/plain]
Saving to: ‘numpy/site.cfg’
100%[================================================================================================================================================>] 223 --.-K/s in 0s
2015-10-09 15:52:19 (45.1 MB/s) - ‘numpy/site.cfg’ saved [223/223]
wget https://raw.github.com/bpartridge/PyPhi/master/setup.cfg -O numpy/setup.cfg
--2015-10-09 15:52:19-- https://raw.github.com/bpartridge/PyPhi/master/setup.cfg
Resolving raw.github.com (raw.github.com)... 185.31.17.133
Connecting to raw.github.com (raw.github.com)|185.31.17.133|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://raw.githubusercontent.com/bpartridge/PyPhi/master/setup.cfg [following]
--2015-10-09 15:52:19-- https://raw.githubusercontent.com/bpartridge/PyPhi/master/setup.cfg
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.31.17.133
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.31.17.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 193 [text/plain]
Saving to: ‘numpy/setup.cfg’
100%[================================================================================================================================================>] 193 --.-K/s in 0s
2015-10-09 15:52:20 (38.2 MB/s) - ‘numpy/setup.cfg’ saved [193/193]
build_clib forces config.h to be created; it needs to be modified before extensions are built
cd numpy && PYTHONXCPREFIX=/opt/pyphi/mic/python/_install python numpyxc.py build_clib
/opt/pyphi/mic/numpy/setup.py
Running from numpy source directory.
/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'test_suite'
warnings.warn(msg)
/bin/sh: 1: svnversion: not found
F2PY Version 2
blas_opt_info:
blas_mkl_info:
FOUND:
libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'pthread']
library_dirs = ['/opt/intel/composer_xe_2015/mkl/lib/mic']
define_macros = [('SCIPY_MKL_H', None)]
include_dirs = ['/opt/intel/composer_xe_2015/mkl/include']
FOUND:
libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'pthread']
library_dirs = ['/opt/intel/composer_xe_2015/mkl/lib/mic']
define_macros = [('SCIPY_MKL_H', None)]
include_dirs = ['/opt/intel/composer_xe_2015/mkl/include']
/bin/sh: 1: svnversion: not found
non-existing path in 'numpy/lib': 'benchmarks'
lapack_opt_info:
openblas_info:
libraries not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
lapack_mkl_info:
mkl_info:
FOUND:
libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'pthread']
library_dirs = ['/opt/intel/composer_xe_2015/mkl/lib/mic']
define_macros = [('SCIPY_MKL_H', None)]
include_dirs = ['/opt/intel/composer_xe_2015/mkl/include']
FOUND:
libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'pthread']
library_dirs = ['/opt/intel/composer_xe_2015/mkl/lib/mic']
define_macros = [('SCIPY_MKL_H', None)]
include_dirs = ['/opt/intel/composer_xe_2015/mkl/include']
FOUND:
libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'pthread']
library_dirs = ['/opt/intel/composer_xe_2015/mkl/lib/mic']
define_macros = [('SCIPY_MKL_H', None)]
include_dirs = ['/opt/intel/composer_xe_2015/mkl/include']
/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'define_macros'
warnings.warn(msg)
running build_clib
running build_src
build_src
building py_modules sources
creating build
creating build/src.linux-x86_64-2.7
creating build/src.linux-x86_64-2.7/numpy
creating build/src.linux-x86_64-2.7/numpy/distutils
building library "npymath" sources
customize IntelMICFCompiler
Found executable /opt/intel/bin/ifort
customize IntelMICFCompiler using config
C compiler: icc -mmic -mkl -fPIC -fp-model strict -g -I/opt/pyphi/mic/python/_install/include -L/opt/pyphi/mic/python/_install/lib -L/opt/pyphi/mic/python/_install/lib/python2.7 -L/opt/pyphi/mic/python/_install/lib/python2.7/site-packages/numpy/core/lib
compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/usr/include/python2.7 -c'
icc: _configtest.c
icc: command line remark #10364: Using '-fp-model strict' forces the compiler to generate legacy floating-point instructions instead of KNC for most floating-point operations, which may impact performance. Consider using a floating-point model that allows the compiler to assume the default floating-point environment.
icc -mmic -mkl -fPIC -fp-model strict -g -I/opt/pyphi/mic/python/_install/include -L/opt/pyphi/mic/python/_install/lib -L/opt/pyphi/mic/python/_install/lib/python2.7 -L/opt/pyphi/mic/python/_install/lib/python2.7/site-packages/numpy/core/lib _configtest.o -o _configtest
icc: command line remark #10364: Using '-fp-model strict' forces the compiler to generate legacy floating-point instructions instead of KNC for most floating-point operations, which may impact performance. Consider using a floating-point model that allows the compiler to assume the default floating-point environment.
success!
removing: _configtest.c _configtest.o _configtest
C compiler: icc -mmic -mkl -fPIC -fp-model strict -g -I/opt/pyphi/mic/python/_install/include -L/opt/pyphi/mic/python/_install/lib -L/opt/pyphi/mic/python/_install/lib/python2.7 -L/opt/pyphi/mic/python/_install/lib/python2.7/site-packages/numpy/core/lib
compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/usr/include/python2.7 -c'
icc: _configtest.c
icc: command line remark #10364: Using '-fp-model strict' forces the compiler to generate legacy floating-point instructions instead of KNC for most floating-point operations, which may impact performance. Consider using a floating-point model that allows the compiler to assume the default floating-point environment.
icc -mmic -mkl -fPIC -fp-model strict -g -I/opt/pyphi/mic/python/_install/include -L/opt/pyphi/mic/python/_install/lib -L/opt/pyphi/mic/python/_install/lib/python2.7 -L/opt/pyphi/mic/python/_install/lib/python2.7/site-packages/numpy/core/lib _configtest.o -o _configtest
icc: command line remark #10364: Using '-fp-model strict' forces the compiler to generate legacy floating-point instructions instead of KNC for most floating-point operations, which may impact performance. Consider using a floating-point model that allows the compiler to assume the default floating-point environment.
success!
removing: _configtest.c _configtest.o _configtest
creating build/src.linux-x86_64-2.7/numpy/core
creating build/src.linux-x86_64-2.7/numpy/core/src
creating build/src.linux-x86_64-2.7/numpy/core/src/npymath
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/npymath/npy_math.c
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/npymath/ieee754.c
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/npymath/npy_math_complex.c
building library "npysort" sources
creating build/src.linux-x86_64-2.7/numpy/core/src/npysort
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/npysort/quicksort.c
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/npysort/mergesort.c
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/npysort/heapsort.c
creating build/src.linux-x86_64-2.7/numpy/core/src/private
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/private/npy_partition.h
adding 'build/src.linux-x86_64-2.7/numpy/core/src/private' to include_dirs.
conv_template:> build/src.linux-x86_64-2.7/numpy/core/src/npysort/selection.c
None - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/src/private/npy_partition.h']
building extension "numpy.core._dummy" sources
Generating build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h
C compiler: icc -mmic -mkl -fPIC -fp-model strict -g -I/opt/pyphi/mic/python/_install/include -L/opt/pyphi/mic/python/_install/lib -L/opt/pyphi/mic/python/_install/lib/python2.7 -L/opt/pyphi/mic/python/_install/lib/python2.7/site-packages/numpy/core/lib
compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/usr/include/python2.7 -c'
icc: _configtest.c
icc: command line remark #10364: Using '-fp-model strict' forces the compiler to generate legacy floating-point instructions instead of KNC for most floating-point operations, which may impact performance. Consider using a floating-point model that allows the compiler to assume the default floating-point environment.
In file included from /usr/include/python2.7/Python.h(8),
from _configtest.c(1):
/usr/include/python2.7/pyconfig.h(3): catastrophic error: cannot open source file "x86_64-linux-gnu/python2.7/pyconfig.h"
include <x86_64-linux-gnu/python2.7/pyconfig.h>
compilation aborted for _configtest.c (code 4)
icc: command line remark #10364: Using '-fp-model strict' forces the compiler to generate legacy floating-point instructions instead of KNC for most floating-point operations, which may impact performance. Consider using a floating-point model that allows the compiler to assume the default floating-point environment.
In file included from /usr/include/python2.7/Python.h(8),
from _configtest.c(1):
/usr/include/python2.7/pyconfig.h(3): catastrophic error: cannot open source file "x86_64-linux-gnu/python2.7/pyconfig.h"
include <x86_64-linux-gnu/python2.7/pyconfig.h>
compilation aborted for _configtest.c (code 4)
failure.
removing: _configtest.c _configtest.o
Traceback (most recent call last):
File "numpyxc.py", line 73, in
setup.setup_package()
File "/opt/pyphi/mic/numpy/setup.py", line 231, in setup_package
setup(**metadata)
File "/opt/pyphi/mic/numpy/numpy/distutils/core.py", line 169, in setup
return old_setup(**new_attr)
File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/opt/pyphi/mic/numpy/numpy/distutils/command/build_clib.py", line 63, in run
self.run_command('build_src')
File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/opt/pyphi/mic/numpy/numpy/distutils/command/build_src.py", line 153, in run
self.build_sources()
File "/opt/pyphi/mic/numpy/numpy/distutils/command/build_src.py", line 170, in build_sources
self.build_extension_sources(ext)
File "/opt/pyphi/mic/numpy/numpy/distutils/command/build_src.py", line 329, in build_extension_sources
sources = self.generate_sources(sources, ext)
File "/opt/pyphi/mic/numpy/numpy/distutils/command/build_src.py", line 386, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 428, in generate_config_h
moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
File "numpy/core/setup.py", line 42, in check_types
out = check_types(_a, *_kw)
File "numpy/core/setup.py", line 289, in check_types
"Cannot compile 'Python.h'. Perhaps you need to "
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
make: *** [numpyxc] Error 1