Running the same python script using python3 or through an embedded interpreter using libpython3 gives different execution times.
$ time PYTHONPATH=. ./simple
real 0m6,201s
user 1m3,680s
sys 0m0,212s
$ time PYTHONPATH=. python3 -c 'import test; test.run()'
real 0m5,193s
user 0m53,349s
sys 0m0,164s
(removing the content of __pycache__ between runs does not seem to have an impact)
Currently, calling python3 with the script is faster; on my actual use case the factor is 1.5 faster, compared to the same script ran from within an embedded interpreter.
I would like to (1) understand where does the difference come from and (2) if it is possible to have the same performance using an embedded interpreter? (using e.g. cython is currently not an option).
Code
simple.cpp
#include <Python.h>
int main()
{
Py_Initialize();
const char* pythonScript = "import test; test.run()";
int result = PyRun_SimpleString(pythonScript);
Py_Finalize();
return result;
}
Compilation:
g++ -std=c++11 -fPIC $(python3-config --cflags) simple.cpp \
$(python3-config --ldflags) -o simple
test.py
import sys
sys.stdout = open('output.bin', 'bw')
import mandel
def run():
mandel.mandelbrot(4096)
mandel.py
Tweaked version from benchmarks-game's Mandlebrot (see License)
from contextlib import closing
from itertools import islice
from os import cpu_count
from sys import stdout
def pixels(y, n, abs):
range7 = bytearray(range(7))
pixel_bits = bytearray(128 >> pos for pos in range(8))
c1 = 2. / float(n)
c0 = -1.5 + 1j * y * c1 - 1j
x = 0
while True:
pixel = 0
c = x * c1 + c0
for pixel_bit in pixel_bits:
z = c
for _ in range7:
for _ in range7:
z = z * z + c
if abs(z) >= 2.: break
else:
pixel += pixel_bit
c += c1
yield pixel
x += 8
def compute_row(p):
y, n = p
result = bytearray(islice(pixels(y, n, abs), (n + 7) // 8))
result[-1] &= 0xff << (8 - n % 8)
return y, result
def ordered_rows(rows, n):
order = [None] * n
i = 0
j = n
while i < len(order):
if j > 0:
row = next(rows)
order[row[0]] = row
j -= 1
if order[i]:
yield order[i]
order[i] = None
i += 1
def compute_rows(n, f):
row_jobs = ((y, n) for y in range(n))
if cpu_count() < 2:
yield from map(f, row_jobs)
else:
from multiprocessing import Pool
with Pool() as pool:
unordered_rows = pool.imap_unordered(f, row_jobs)
yield from ordered_rows(unordered_rows, n)
def mandelbrot(n):
write = stdout.write
with closing(compute_rows(n, compute_row)) as rows:
write("P4\n{0} {0}\n".format(n).encode())
for row in rows:
write(row[1])
So apparently the time difference comes from either linking with libpython statically vs. dynamically. In a Makefile sitting next to python.c (from the reference implementation), the following builds a statically linked version of the interpreter:
snake: python.c
g++ \
-I/usr/include/python3.6m \
-pthread \
-specs=/usr/share/dpkg/no-pie-link.specs \
-specs=/usr/share/dpkg/no-pie-compile.specs \
\
-Wall \
-Wformat \
-Werror=format-security \
-Wno-unused-result \
-Wsign-compare \
-DNDEBUG \
-g \
-fwrapv \
-fstack-protector \
-O3 \
\
-Xlinker -export-dynamic \
-Wl,-Bsymbolic-functions \
-Wl,-z,relro \
-Wl,-O1 \
python.c \
/usr/lib/python3.6/config-3.6m-x86_64-linux-gnu/libpython3.6m.a \
-lexpat \
-lpthread \
-ldl \
-lutil \
-lexpat \
-L/usr/lib \
-lz \
-lm \
-o $#
Changing the line /usr/lib/.../libpython3.6m.a with -llibpython3.6m builds the version that ends up being slower (also need -L/usr/lib/python3.6/config-3.6m-x86_64-linux-gnu)
Epilog
The difference in speed exists but is not the full answer to my original problem; in practice the "slower" interpreter was executed under a specific LD_PRELOAD environment which changed how system time functions behaves in a way that messed up with cProfile.
Related
New at this so please bare with me. Following these instructions trying update to the latest version of Python
https://www.vultr.com/docs/update-python3-on-centos/
I get all the way to step 2.5 and get the following:
[user1#localhost Python-3.9.6]$ ./configure --enable-optimizations
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for python3.9... no
checking for python3... python3
checking for --enable-universalsdk... no
checking for --with-universal-archs... no
checking MACHDEP... "linux"
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in `/home/user1/Python-3.9.6':
configure: error: C compiler cannot create executables
See `config.log' for more details
My config.log file
## --------- ##
## Platform. ##
## --------- ##
hostname = localhost.localdomain
uname -m = x86_64
uname -r = 3.10.0-1160.76.1.el7.x86_64
uname -s = Linux
uname -v = #1 SMP Wed Aug 10 16:21:17 UTC 2022
/usr/bin/uname -p = x86_64
/bin/uname -X = unknown
/bin/arch = x86_64
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /opt/rh/devtoolset-8/root/usr/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /usr/local/sbin
PATH: /usr/sbin
PATH: /home/user1/.local/bin
PATH: /home/user1/bin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2848: checking build system type
configure:2862: result: x86_64-pc-linux-gnu
configure:2882: checking host system type
configure:2895: result: x86_64-pc-linux-gnu
configure:2925: checking for python3.9
configure:2955: result: no
configure:2925: checking for python3
configure:2941: found /usr/bin/python3
configure:2952: result: python3
configure:3046: checking for --enable-universalsdk
configure:3093: result: no
configure:3117: checking for --with-universal-archs
configure:3132: result: no
configure:3288: checking MACHDEP
configure:3339: result: "linux"
configure:3633: checking for gcc
configure:3649: found /opt/rh/devtoolset-8/root/usr/bin/gcc
configure:3660: result: gcc
configure:3889: checking for C compiler version
configure:3898: gcc --version >&5
gcc (GCC) 8.3.1 20190311 (Red Hat 8.3.1-3)
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:3909: $? = 0
configure:3898: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/opt/rh/devtoolset-8/root/usr --mandir=/opt/rh/devtoolset-8/root/usr/share/man --infodir=/opt/rh/devtoolset-8/root/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --with-default-libstdcxx-abi=gcc4-compatible --enable-plugin --enable-initfini-array --with-isl=/builddir/build/BUILD/gcc-8.3.1-20190311/obj-x86_64-redhat-linux/isl-install --disable-libmpx --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 8.3.1 20190311 (Red Hat 8.3.1-3) (GCC)
configure:3909: $? = 0
configure:3898: gcc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:3909: $? = 1
configure:3898: gcc -qversion >&5
gcc: error: unrecognized command line option '-qversion'; did you mean '--version'?
gcc: fatal error: no input files
compilation terminated.
configure:3909: $? = 1
configure:3929: checking whether the C compiler works
configure:3951: gcc conftest.c >&5
/lib/../lib64/crt1.o: file not recognized: File truncated
collect2: error: ld returned 1 exit status
configure:3955: $? = 1
configure:3993: result: no
configure: failed program was:
| /* confdefs.h */
| #define _GNU_SOURCE 1
| #define _NETBSD_SOURCE 1
| #define __BSD_VISIBLE 1
| #define _DARWIN_C_SOURCE 1
| #define _PYTHONFRAMEWORK ""
| #define _XOPEN_SOURCE 700
| #define _XOPEN_SOURCE_EXTENDED 1
| #define _POSIX_C_SOURCE 200809L
| /* end confdefs.h. */
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:3998: error: in `/home/user1/Python-3.9.6':
configure:4000: error: C compiler cannot create executables
See `config.log' for more details
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_build=x86_64-pc-linux-gnu
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
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ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_MACHDEP_set=
ac_cv_env_MACHDEP_value=
ac_cv_env_PKG_CONFIG_LIBDIR_set=
ac_cv_env_PKG_CONFIG_LIBDIR_value=
ac_cv_env_PKG_CONFIG_PATH_set=set
ac_cv_env_PKG_CONFIG_PATH_value=/opt/rh/devtoolset-8/root/usr/lib64/pkgconfig
ac_cv_env_PKG_CONFIG_set=
ac_cv_env_PKG_CONFIG_value=
ac_cv_env_PROFILE_TASK_set=
ac_cv_env_PROFILE_TASK_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_host=x86_64-pc-linux-gnu
ac_cv_prog_PYTHON_FOR_REGEN=python3
ac_cv_prog_ac_ct_CC=gcc
## ----------------- ##
## Output variables. ##
## ----------------- ##
ABIFLAGS=''
ALT_SOABI=''
AR=''
ARCH_RUN_32BIT=''
ARFLAGS=''
BASECFLAGS=''
BASECPPFLAGS=''
BINLIBDEST=''
BLDLIBRARY=''
BLDSHARED=''
BUILDEXEEXT=''
CC='gcc'
CCSHARED=''
CFLAGS=''
CFLAGSFORSHARED=''
CFLAGS_ALIASING=''
CFLAGS_NODIST=''
CONFIGURE_MACOSX_DEPLOYMENT_TARGET=''
CONFIG_ARGS=' '\''--enable-optimizations'\'' '\''PKG_CONFIG_PATH=/opt/rh/devtoolset-8/root/usr/lib64/pkgconfig'\'''
CPP=''
CPPFLAGS=''
CXX=''
DEFS=''
DEF_MAKE_ALL_RULE=''
DEF_MAKE_RULE=''
DFLAGS=''
DLINCLDIR=''
DLLLIBRARY=''
DTRACE=''
DTRACE_HEADERS=''
DTRACE_OBJS=''
DYNLOADFILE=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP=''
ENSUREPIP=''
EXEEXT=''
EXPORTSFROM=''
EXPORTSYMS=''
EXPORT_MACOSX_DEPLOYMENT_TARGET='#'
EXT_SUFFIX=''
FRAMEWORKALTINSTALLFIRST=''
FRAMEWORKALTINSTALLLAST=''
FRAMEWORKINSTALLAPPSPREFIX=''
FRAMEWORKINSTALLFIRST=''
FRAMEWORKINSTALLLAST=''
FRAMEWORKPYTHONW=''
FRAMEWORKUNIXTOOLSPREFIX='/usr/local'
GITBRANCH=''
GITTAG=''
GITVERSION=''
GNULD=''
GREP=''
HAS_GIT='no-repository'
HAVE_GETHOSTBYNAME=''
HAVE_GETHOSTBYNAME_R=''
HAVE_GETHOSTBYNAME_R_3_ARG=''
HAVE_GETHOSTBYNAME_R_5_ARG=''
HAVE_GETHOSTBYNAME_R_6_ARG=''
INSTALL_DATA=''
INSTALL_PROGRAM=''
INSTALL_SCRIPT=''
INSTSONAME=''
LDCXXSHARED=''
LDFLAGS=''
LDFLAGS_NODIST=''
LDLIBRARY=''
LDLIBRARYDIR=''
LDSHARED=''
LDVERSION=''
LIBC=''
LIBFFI_INCLUDEDIR=''
LIBM=''
LIBOBJS=''
LIBPL=''
LIBPYTHON=''
LIBRARY=''
LIBS=''
LIBTOOL_CRUFT=''
LINKCC=''
LINKFORSHARED=''
LIPO_32BIT_FLAGS=''
LIPO_INTEL64_FLAGS=''
LLVM_AR=''
LLVM_AR_FOUND=''
LLVM_PROFDATA=''
LLVM_PROF_ERR=''
LLVM_PROF_FILE=''
LLVM_PROF_FOUND=''
LLVM_PROF_MERGER=''
LN=''
LTLIBOBJS=''
MACHDEP='linux'
MACHDEP_OBJS=''
MAINCC=''
MKDIR_P=''
MULTIARCH=''
MULTIARCH_CPPFLAGS=''
NO_AS_NEEDED=''
OBJEXT=''
OPENSSL_INCLUDES=''
OPENSSL_LDFLAGS=''
OPENSSL_LIBS=''
OPT=''
OTHER_LIBTOOL_OPT=''
PACKAGE_BUGREPORT='https://bugs.python.org/'
PACKAGE_NAME='python'
PACKAGE_STRING='python 3.9'
PACKAGE_TARNAME='python'
PACKAGE_URL=''
PACKAGE_VERSION='3.9'
PATH_SEPARATOR=':'
PGO_PROF_GEN_FLAG=''
PGO_PROF_USE_FLAG=''
PKG_CONFIG=''
PKG_CONFIG_LIBDIR=''
PKG_CONFIG_PATH='/opt/rh/devtoolset-8/root/usr/lib64/pkgconfig'
PLATFORM_TRIPLET=''
PLATLIBDIR=''
PROFILE_TASK=''
PY3LIBRARY=''
PYTHONFRAMEWORK=''
PYTHONFRAMEWORKDIR='no-framework'
PYTHONFRAMEWORKIDENTIFIER='org.python.python'
PYTHONFRAMEWORKINSTALLDIR=''
PYTHONFRAMEWORKPREFIX=''
PYTHON_FOR_BUILD='./$(BUILDPYTHON) -E'
PYTHON_FOR_REGEN='python3'
PY_ENABLE_SHARED=''
READELF=''
RUNSHARED=''
SED=''
SHELL='/bin/sh'
SHLIBS=''
SHLIB_SUFFIX=''
SOABI=''
SOVERSION='1.0'
SRCDIRS=''
TCLTK_INCLUDES=''
TCLTK_LIBS=''
THREADHEADERS=''
TRUE=''
TZPATH=''
UNIVERSALSDK=''
UNIVERSAL_ARCH_FLAGS=''
VERSION='3.9'
_PYTHON_HOST_PLATFORM=''
ac_ct_AR=''
ac_ct_CC='gcc'
ac_ct_CXX=''
ac_ct_READELF=''
bindir='${exec_prefix}/bin'
build='x86_64-pc-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='pc'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='NONE'
host='x86_64-pc-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='pc'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='NONE'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
/* confdefs.h */
#define _GNU_SOURCE 1
#define _NETBSD_SOURCE 1
#define __BSD_VISIBLE 1
#define _DARWIN_C_SOURCE 1
#define _PYTHONFRAMEWORK ""
#define _XOPEN_SOURCE 700
#define _XOPEN_SOURCE_EXTENDED 1
#define _POSIX_C_SOURCE 200809L
configure: exit 77
Is there something that I need to install within my Linux (Centos 7) to get this to work?
My current Python Version is 3.6.8
My objective is to give an ECG_sample (integer) and reference of the structure as input to the C code and create a python wrapper for the same. Below is what I have attempted. The structure HRV_index actually has 5 members(4 floats and 1 integer), but I am trying the code for just one member.
gcc -c -Wall -Werror -fpic test.c
gcc -shared test.o -o test.so to create the shared library
C code:
void simple_function(int16_t ecg_wave_sample,HRV_index *HRV)
{
Filter_CurrentECG_sample(&ecg_wave_sample, &ecg_filterout); // filter out the line noise #40Hz cutoff 161 order
Calculate_HeartRate(ecg_filterout,&global_HeartRate,&npeakflag); // calculate
if(npeakflag == 1)
{
read_send_data(global_HeartRate,*HRV);
printf("NN50: %d\n",HRV->nn50);
}
}
python code:
def wrap_function(lib, funcname, restype, argtypes):
''' Simplify wrapping ctypes functions '''
func = lib.__getattr__(funcname)
func.restype = restype
func.argtypes = argtypes
return func
class HRV_index(ctypes.Structure):
#_fields_ = [('mean', ctypes.c_float), ('sdnn', ctypes.c_float),('nn50', ctypes.c_int), ('pnn50', ctypes.c_float),('rmssd', ctypes.c_float)]
_fields_ = [('nn50', ctypes.c_int)]
def __repr__(self):
return '({0})'.format( self.nn50)
if __name__ == '__main__':
# load the shared library into c types. NOTE: don't use a hard-coded path in production code, please
libc = ctypes.CDLL("./test.so")
record = wfdb.rdrecord("/home/yasaswini/hp2-notebooks/notebooks/Algorithm_testing_on_database/MIT-BIH/100", channels=[0],sampto = 1000)
ECG_samples = record.p_signal[:,0]
ECG_samples = ECG_samples * 1000
Heart_rate_array = np.zeros(len(ECG_samples),dtype = np.int32)
print("Pass by reference")
simple_function = wrap_function(libc, 'simple_function', None, [ctypes.c_int,ctypes.POINTER(HRV_index)])
a = HRV_index(0)
print("Point in python is", a)
for i in range(len(ECG_samples)):
simple_function(ECG_samples[i], a)
print("Point in python is", a)
print()
I getting this error:
Pass by reference
Point in python is (0)
Traceback (most recent call last):
File "/home/yasaswini/hp2-notebooks/notebooks/Algorithm_testing_on_database /structure_python_wrapper/test.py", line 45, in <module>
simple_function(ECG_samples[i], a)
ctypes.ArgumentError: argument 1: <class 'TypeError'>: wrong type
The ECG_sample[i] is an integer, so why is it showing wrong type error?
I am trying to use sphinx for the first time. I'm using sphinx3 because I need s3_aligner so I followed many tutorials but none of them got me a result I always get this error :
**configure: error: in `/Users/Bassem/downloads/cmusphinx/sphinxbase':
configure: error:
Could not link test program to Python. Maybe the main Python library has been
installed in some non-standard library path. If so, pass it to configure,
via the LDFLAGS environment variable.
Example: ./configure LDFLAGS="-L/usr/non-standard-path/python/lib"
============================================================================
ERROR!
You probably have to install the development version of the Python package
for your distribution. The exact name of this package varies among them.
===========================================================================**
I tried so many solution but none of them helped me out all the solutions give the same error .There is a solution for ubuntu which is python-dev for easy linking . I need something equivalent to it on mac or anything to solve me the problem
Here is my config.log:
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_build=x86_64-apple-darwin15.3.0
ac_cv_c_bigendian=no
ac_cv_c_compiler_gnu=yes
ac_cv_c_const=yes
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_LT_SYS_LIBRARY_PATH_set=
ac_cv_env_LT_SYS_LIBRARY_PATH_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_file__Users_Bassem_downloads_cmusphinx_sphinx3____sphinxbase_include_sphinxbase_prim_type_h=yes
ac_cv_file__Users_Bassem_downloads_cmusphinx_sphinx3____sphinxbase_src_libsphinxbase_libsphinxbase_la=no
ac_cv_func_bcopy=yes
ac_cv_func_memmove=yes
ac_cv_header_dlfcn_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_sphinxbase_sphinx_config_h=no
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_host=x86_64-apple-darwin15.3.0
ac_cv_objext=o
ac_cv_path_EGREP='/usr/bin/grep -E'
ac_cv_path_FGREP='/usr/bin/grep -F'
ac_cv_path_GREP=/usr/bin/grep
ac_cv_path_SED=/usr/bin/sed
ac_cv_path_install='/usr/bin/install -c'
ac_cv_path_lt_DD=/bin/dd
ac_cv_prog_AWK=awk
ac_cv_prog_CPP='gcc -E'
ac_cv_prog_ac_ct_AR=ar
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_ac_ct_DSYMUTIL=dsymutil
ac_cv_prog_ac_ct_LIPO=lipo
ac_cv_prog_ac_ct_NMEDIT=nmedit
ac_cv_prog_ac_ct_OTOOL=otool
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_ac_ct_STRIP=strip
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_make_make_set=yes
ac_cv_search_strerror='none required'
ac_cv_type_signal=void
ac_cv_type_size_t=yes
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_make_support_nested_variables=yes
am_cv_prog_cc_c_o=yes
am_cv_prog_cc_stdc=
cc_cv_attribute_visibility=yes
lt_cv_apple_cc_single_mod=yes
lt_cv_ar_at_file=no
lt_cv_deplibs_check_method=pass_all
lt_cv_file_magic_cmd='$MAGIC_CMD'
lt_cv_file_magic_test_file=
lt_cv_ld_exported_symbols_list=yes
lt_cv_ld_force_load=yes
lt_cv_ld_reload_flag=-r
lt_cv_nm_interface='BSD nm'
lt_cv_objdir=.libs
lt_cv_path_LD=/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
lt_cv_path_NM=/usr/bin/nm
lt_cv_path_mainfest_tool=no
lt_cv_prog_compiler_c_o=yes
lt_cv_prog_compiler_pic='-fno-common -DPIC'
lt_cv_prog_compiler_pic_works=yes
lt_cv_prog_compiler_rtti_exceptions=yes
lt_cv_prog_compiler_static_works=no
lt_cv_prog_gnu_ld=no
lt_cv_sharedlib_from_linklib_cmd='printf %s\n'
lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([BCDEGRST][BCDEGRST]*\)[ ][ ]*_\([_A-Za-z][_A-Za-z0-9]*\)$/\1 _\2 \2/p'\'' | sed '\''/ __gnu_lto/d'\'''
lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \(.*\) .*$/ {"\1", (void *) 0},/p'\'' -e '\''s/^[BCDEGRST][BCDEGRST]* .* \(.*\)$/ {"\1", (void *) \&\1},/p'\'''
lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \(.*\) .*$/ {"\1", (void *) 0},/p'\'' -e '\''s/^[BCDEGRST][BCDEGRST]* .* \(lib.*\)$/ {"\1", (void *) \&\1},/p'\'' -e '\''s/^[BCDEGRST][BCDEGRST]* .* \(.*\)$/ {"lib\1", (void *) \&\1},/p'\'''
lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[BCDEGRST][BCDEGRST]* .* \(.*\)$/extern char \1;/p'\'''
lt_cv_sys_global_symbol_to_import=
lt_cv_sys_max_cmd_len=196608
lt_cv_to_host_file_cmd=func_convert_file_noop
lt_cv_to_tool_file_cmd=func_convert_file_noop
lt_cv_truncate_bin='/bin/dd bs=4096 count=1'
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL} /Users/Bassem/downloads/cmusphinx/sphinx3/missing aclocal-1.15'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='$${TAR-tar}'
AM_BACKSLASH='\'
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='1'
AM_V='$(V)'
AR='ar'
AUTOCONF='${SHELL} /Users/Bassem/downloads/cmusphinx/sphinx3/missing autoconf'
AUTOHEADER='${SHELL} /Users/Bassem/downloads/cmusphinx/sphinx3/missing autoheader'
AUTOMAKE='${SHELL} /Users/Bassem/downloads/cmusphinx/sphinx3/missing automake-1.15'
AWK='awk'
CC='gcc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2 -Wall -fvisibility=hidden'
CPP='gcc -E'
CPPFLAGS='-I/Users/Bassem/downloads/cmusphinx/sphinx3/../sphinxbase/include '
CSH=''
CYGPATH_W='echo'
DEFS=''
DEPDIR='.deps'
DLLTOOL='false'
DSYMUTIL='dsymutil'
DUMPBIN=''
ECHO_C='\c'
ECHO_N=''
ECHO_T=''
EGREP='/usr/bin/grep -E'
EXEEXT=''
FGREP='/usr/bin/grep -F'
GREP='/usr/bin/grep'
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LD='/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld'
LDFLAGS=''
LIBOBJS=''
LIBS=''
LIBTOOL='$(SHELL) $(top_builddir)/libtool'
LIPO='lipo'
LN_S='ln -s'
LTLIBOBJS=''
LT_SYS_LIBRARY_PATH=''
MAKEINFO='${SHELL} /Users/Bassem/downloads/cmusphinx/sphinx3/missing makeinfo'
MANIFEST_TOOL=':'
MKDIR_P='./install-sh -c -d'
NM='/usr/bin/nm'
NMEDIT='nmedit'
OBJDUMP='false'
OBJEXT='o'
OTOOL64=':'
OTOOL='otool'
PACKAGE='sphinx3'
PACKAGE_BUGREPORT=''
PACKAGE_NAME='sphinx3'
PACKAGE_STRING='sphinx3 0.7'
PACKAGE_TARNAME='sphinx3'
PACKAGE_URL=''
PACKAGE_VERSION='0.7'
PATH_SEPARATOR=':'
PERL=''
RANLIB='ranlib'
SED='/usr/bin/sed'
SET_MAKE=''
SHELL='/bin/sh'
STRIP='strip'
VERSION='0.7'
ac_ct_AR='ar'
ac_ct_CC='gcc'
ac_ct_DUMPBIN=''
ad_backend=''
ad_files=''
ad_libs=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE=''
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__include='include'
am__isrc=''
am__leading_dot='.'
am__nodep='_no'
am__quote=''
am__tar='$${TAR-tar} chof - "$$tardir"'
am__untar='$${TAR-tar} xf -'
bindir='${exec_prefix}/bin'
build='x86_64-apple-darwin15.3.0'
build_alias=''
build_cpu='x86_64'
build_os='darwin15.3.0'
build_vendor='apple'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdata='./.DS_Store ./BN_AM_HUB96-97.doc ./BN_AM_HUB96-97.htm ./cmdhelp.txt ./doxygen.cfg ./doxygen.main ./images/rarrow.gif ./index.html ./models.html ./rarrow.gif ./s3/falign.fig ./s3/falign.gif ./s3/feat.fig ./s3/feat.gif ./s3/hypseg.txt ./s3-2.htm ./s3-2.pdf ./s3-2.ppt ./s3-2_files/buttons.gif ./s3-2_files/error.htm ./s3-2_files/filelist.xml ./s3-2_files/frame.htm ./s3-2_files/fullscreen.htm ./s3-2_files/master01.htm ./s3-2_files/master02.htm ./s3-2_files/master03.htm ./s3-2_files/master03.xml ./s3-2_files/master03_image002.gif ./s3-2_files/master03_stylesheet.css ./s3-2_files/outline.htm ./s3-2_files/pres.xml ./s3-2_files/preview.wmf ./s3-2_files/script.js ./s3-2_files/slide0001.htm ./s3-2_files/slide0001_image001.gif ./s3-2_files/slide0004.htm ./s3-2_files/slide0005.htm ./s3-2_files/slide0006.htm ./s3-2_files/slide0007.htm ./s3-2_files/slide0008.htm ./s3-2_files/slide0009.htm ./s3-2_files/slide0010.htm ./s3-2_files/slide0011.htm ./s3-2_files/slide0012.htm ./s3-2_files/slide0012_image003.gif ./s3-2_files/slide0015.htm ./s3-2_files/slide0015_image004.gif ./s3-2_files/slide0015_image005.gif ./s3-2_files/slide0015_image006.gif ./s3-2_files/slide0015_image007.gif ./s3-2_files/slide0015_image008.gif ./s3-2_files/slide0016.htm ./s3-2_files/slide0016.xml ./s3-2_files/slide0016_image009.gif ./s3-2_files/slide0016_image010.gif ./s3-2_files/slide0016_image011.gif ./s3-2_files/slide0016_image012.gif ./s3-2_files/slide0016_image013.gif ./s3-2_files/slide0016_image014.gif ./s3-2_files/slide0016_image015.gif ./s3-2_files/slide0016_image016.gif ./s3-2_files/slide0016_image017.gif ./s3-2_files/slide0016_image018.gif ./s3-2_files/slide0016_image019.gif ./s3-2_files/slide0016_image020.gif ./s3-2_files/slide0017.htm ./s3-2_files/slide0017.xml ./s3-2_files/slide0017_image021.gif ./s3-2_files/slide0017_image022.gif ./s3-2_files/slide0017_image023.gif ./s3-2_files/slide0017_image024.gif ./s3-2_files/slide0017_image025.gif ./s3-2_files/slide0017_image026.gif ./s3-2_files/slide0017_image027.gif ./s3-2_files/slide0017_image028.gif ./s3-2_files/slide0017_image029.gif ./s3-2_files/slide0017_image030.gif ./s3-2_files/slide0017_image031.gif ./s3-2_files/slide0018.htm ./s3-2_files/slide0018.xml ./s3-2_files/slide0018_image032.gif ./s3-2_files/slide0019.htm ./s3-2_files/slide0020.htm ./s3-2_files/slide0020_image033.gif ./s3-2_files/slide0021.htm ./s3-2_files/slide0021_image034.gif ./s3-2_files/slide0022.htm ./s3-2_files/slide0022_image035.gif ./s3-2_files/slide0023.htm ./s3-2_files/slide0023_image036.gif ./s3-2_files/slide0024.htm ./s3-2_files/slide0024_image037.gif ./s3-2_files/slide0026.htm ./s3-2_files/slide0026_image038.gif ./s3-2_files/slide0027.htm ./s3-2_files/slide0028.htm ./s3-2_files/slide0028_image039.gif ./s3-2_files/slide0029.htm ./s3-2_files/slide0029.xml ./s3-2_files/slide0029_image040.gif ./s3-2_files/slide0030.htm ./s3-2_files/slide0030.xml ./s3-2_files/slide0030_image041.gif ./s3-2_files/slide0031.htm ./s3-2_files/slide0031_image042.gif ./s3-2_files/slide0032.htm ./s3-2_files/slide0032_image043.gif ./s3-2_files/slide0033.htm ./s3-2_files/slide0034.htm ./s3-2_files/slide0034_image044.gif ./s3-2_files/slide0035.htm ./s3-2_files/slide0035_image045.gif ./s3-2_files/slide0036.htm ./s3-2_files/slide0036_image046.gif ./s3-2_files/slide0037.htm ./s3-2_files/slide0037_image047.gif ./s3-2_files/slide0038.htm ./s3-2_files/slide0038_image048.gif ./s3-2_files/slide0039.htm ./s3-2_files/slide0040.htm ./s3-2_files/slide0041.htm ./s3-4.pdf ./s3-4.ppt ./s3-5.ppt ./s3-6.ppt ./s3_codewalk.html ./s3_description.html ./s3_fe_spec.pdf ./s3_overview.html ./sphinx3.3-6.ppt ./sphinx3.4.code.tracing ./sphinx3.5_refactoring.note ./sphinxman_FAQ.html ./sphinxman_manual.html ./sphinxman_misc.html'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
epdata='./chan3-dither.cepview ./chan3-logspec.cepview ./chan3.cepview ./chan3.logspec ./chan3.mfc ./chan3.raw ./ep.mdef ./ep.result ./means ./mixture_weights ./variances'
exec_prefix='NONE'
hmmdata='./8gau.6000sen.quant ./feat.params ./mdef ./means ./mixture_weights ./mllr_matrices ./test-align-mllr.out ./test-conf.confhypseg ./test.align.mllr.out ./test.align.out ./test.align.phseg ./test.align.wdseg ./test.allphone.allp ./test.allphone.match ./test.allphone.matchseg ./test.allphone.mllr.allp ./test.allphone.mllr.match ./test.allphone.mllr.matchseg ./test.allphone.phone_tg.allp ./test.allphone.phone_tg.match ./test.allphone.phone_tg.matchseg ./test.allphone.phone_tg.mllr.allp ./test.allphone.phone_tg.mllr.match ./test.allphone.phone_tg.mllr.matchseg ./test.dp.hyp ./test.dp.ref ./test.dp.simple.log ./test.mode1369.dump ./test.subvq ./transition_matrices ./variances'
host='x86_64-apple-darwin15.3.0'
host_alias=''
host_cpu='x86_64'
host_os='darwin15.3.0'
host_vendor='apple'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /Users/Bassem/downloads/cmusphinx/sphinx3/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
lmdata='./README ./align.correct ./an4.cls.probdef ./an4.ctl ./an4.ctl.platform_independent ./an4.ctl_lm ./an4.dict ./an4.phone.dict ./an4.phonelist ./an4.tg.phone.arpa ./an4.tg.phone.arpa.DMP ./an4.tg.phone.arpa.FST ./an4.tg.phone.arpa.FST.SYM ./an4.tg.phone.arpa.lm_convert ./an4.ug.cls.lm ./an4.ug.cls.lm.DMP ./an4.ug.cls.lmctl ./an4.ug.fsg ./an4.ug.lm ./an4.ug.lm.DMP ./an4.ug.lm.FST ./an4.ug.lm.FST.SYM ./an4.ug.lm.lm_convert ./args.an4 ./args.an4.test ./args.an4.test.cls ./args.an4.test.fsg ./args.an4.test.mllr ./args.an4.test.win32 ./filler.dict ./pittsburgh.bigendian.mfc ./pittsburgh.bigendian.raw ./pittsburgh.lat.gz ./pittsburgh.littleendian.abcd ./pittsburgh.littleendian.mfc ./pittsburgh.littleendian.raw ./pittsburgh.littleendian.slf ./pittsburgh.nbest'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
mkdir_p='$(MKDIR_P)'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='NONE'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sphinxbase='/Users/Bassem/downloads/cmusphinx/sphinx3/../sphinxbase'
sysconfdir='${prefix}/etc'
target_alias=''
tidigitsdata='./cepstra/man/man.ah.111a.mfc ./cepstra/man/man.ah.1b.mfc ./cepstra/man/man.ah.2934za.mfc ./cepstra/man/man.ah.35oa.mfc ./cepstra/man/man.ah.3oa.mfc ./cepstra/man/man.ah.4625a.mfc ./cepstra/man/man.ah.588zza.mfc ./cepstra/man/man.ah.63a.mfc ./cepstra/man/man.ah.6o838a.mfc ./cepstra/man/man.ah.75913a.mfc ./cepstra/man/man.ah.844o1a.mfc ./cepstra/man/man.ah.8b.mfc ./cepstra/man/man.ah.9b.mfc ./cepstra/man/man.ah.o789a.mfc ./cepstra/man/man.ah.z4548a.mfc ./cepstra/man/man.ah.zb.mfc ./cepstra/woman/woman.ak.1b.mfc ./cepstra/woman/woman.ak.276317oa.mfc ./cepstra/woman/woman.ak.334a.mfc ./cepstra/woman/woman.ak.3z3z9a.mfc ./cepstra/woman/woman.ak.48z66zza.mfc ./cepstra/woman/woman.ak.532a.mfc ./cepstra/woman/woman.ak.5z874a.mfc ./cepstra/woman/woman.ak.6728za.mfc ./cepstra/woman/woman.ak.75a.mfc ./cepstra/woman/woman.ak.84983a.mfc ./cepstra/woman/woman.ak.8a.mfc ./cepstra/woman/woman.ak.99731a.mfc ./cepstra/woman/woman.ak.o69a.mfc ./cepstra/woman/woman.ak.ooa.mfc ./cepstra/woman/woman.ak.za.mfc ./dictionary ./fillerdict ./test.2.digits.fsg ./test.digits.fsg ./test.iso.digits.fsg ./tidigits.length.1.regression ./tidigits.length.1.result ./tidigits.length.2.regression ./tidigits.length.2.result ./tidigits.length.arb.regression ./tidigits.length.arb.result ./wd_dependent_phone.cd_continuous_8gau/mdef ./wd_dependent_phone.cd_continuous_8gau/means ./wd_dependent_phone.cd_continuous_8gau/mixture_weights ./wd_dependent_phone.cd_continuous_8gau/transition_matrices ./wd_dependent_phone.cd_continuous_8gau/variances'
## ----------- ##
## confdefs.h. ##
## ----------- ##
/* confdefs.h */
#define PACKAGE_NAME "sphinx3"
#define PACKAGE_TARNAME "sphinx3"
#define PACKAGE_VERSION "0.7"
#define PACKAGE_STRING "sphinx3 0.7"
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define STDC_HEADERS 1
#define HAVE_MEMMOVE 1
#define HAVE_BCOPY 1
#define RETSIGTYPE void
#define HAVE_DLFCN_H 1
#define LT_OBJDIR ".libs/"
#define HAVE_ATTRIBUTE_VISIBILITY 1
configure: exit 1
I have a project with many subdirectories and types of files (python, c++, configuration files, images, etc).
When I use SCons env.Package like this:
env.Package(
NAME = 'isid',
VERSION = '1.0',
PACKAGEVERSION = '11',
PACKAGETYPE = 'rpm',
LICENSE = 'gpl',
SUMMARY = 'just a test',
DESCRIPTION = 'the most test app in the world',
X_RPM_GROUP = 'Application/isid',
SOURCE_URL = 'http://isid.com/versions/isid-1.0.11.tar.gz',
)
I get everything in isid-1.0.11.tar.gz except for the h files.
This automatically leads to build errors in ./isid-1.0.11 that stops rpmbuild from running.
EDIT
My project is split into few subdirectories.
In each I have SConscript that starts with these lines, or similar, depending on the includes it needs:
# import all variables
Import('*')
include = Dir([
'../inc/',
])
local_env = env.Clone( CPPPATH = include )
SConstruct just defines the variables and calls SConscript() on each subdirectory.
The call to Package is done in SConstruct, so I guess SCons indeed does not know the dependencies.
snippet of
# scons --tree=prune:
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
scons: `.' is up to date.
+-.
+-SConstruct
+-correlator
| +-correlator/SConscript
| +-correlator/collector
| +-correlator/correlation_command
| | +-correlator/correlation_command/app_command_device.cpp
| | +-correlator/correlation_command/app_command_device.h
| | +-correlator/correlation_command/app_command_device.o
| | | +-correlator/correlation_command/app_command_device.cpp
| | | +-correlator/correlation_command/app_command_device.h
| | | +-correlator/entity/entity.h
| | | +-infra/inc/app_command/app_command.h
| | | +-/bin/g++
| | +-correlator/correlation_command/app_command_event.cpp
| | +-correlator/correlation_command/app_command_event.h
EDIT #2
Here is a complete, minimal, example that produces the same problem.
To reproduce the problem, run:
scons pack=1.0 ver=1
files:
SConstruct.
app1/SConscript
app1/main.cpp
app1/inc.h
Listing
SConstruct
1
2 # main file
3
4 env = Environment(tools=['default', 'packaging'])
5
6 Export( 'env' )
7
8 flags = [
9 '-Wall',
10 '-Werror',
11 '-g',
12 '-ggdb3',
13 '-gdwarf-2',
14 '-std=c++11',
15 ]
16
17 env.Append( CPPFLAGS = flags )
18
19
20 scripts = []
21
22 Sapp1 = 'app1/SConscript'
23 scripts.append( Sapp1 )
24
25
26 env.SConscript( scripts )
27
28 pack = ARGUMENTS.get('pack', '')
29 ver = ARGUMENTS.get('ver', '99' )
30 if pack:
31 env.Package(
32 NAME = 'app1',
33 VERSION = pack,
34 PACKAGEVERSION = ver,
35 PACKAGETYPE = 'rpm',
36 LICENSE = 'private',
37 SUMMARY = 'exampe app #1',
38 DESCRIPTION = 'the most powerfull exampe #1',
39 X_RPM_GROUP = 'Application/app1',
40 SOURCE_URL = 'http://example.com/1/app1-1.0.1.tar.gz',
41 )
42
app1/SConscript
1
2 # import all variables
3 Import('*')
4
5 # add specific include directory
6
7 include = Dir( [
8 '.',
9 ])
10
11 local_env = env.Clone( CPPPATH = include )
12
13 # define sources
14 sources = [
15 'main.cpp',
16 ]
17
18 libs = [
19 ]
20
21 main_name = 'app1',
22
23 main_obj = local_env.Program( target = main_name, source = sources, LIBS = libs )
24
25 # install
26 install_dir = '/opt/rf/app1'
27 install_files = [ main_obj ]
28
29 local_env.Install( dir = install_dir, source = install_files )
30 local_env.Command( install_dir, install_files, "chown -R rf:rfids $TARGET" )
31
32
33 local_env.Alias( 'install', install_dir )
app1/main.cpp
1
2 #include "inc.h"
3
4
5 int main()
6 {
7 int l = g;
8
9 return l;
10 }
app1/inc.h
1
2 int g = 100;
output:
# scons pack=1.0 ver=1
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
g++ -o app1/main.o -c -Wall -Werror -g -ggdb3 -gdwarf-2 -std=c++11 -Iapp1 app1/main.cpp
g++ -o app1/app1 app1/main.o
LC_ALL=C rpmbuild -ta /home/ran/work/rpmexample/app1-1.0.1.tar.gz
scons: *** [app1-1.0-1.src.rpm] app1-1.0-1.src.rpm: Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.wU9lDZ
+ umask 022
+ cd /home/ran/work/rpmexample/rpmtemp/BUILD
+ '[' -n /home/ran/work/rpmexample/rpmtemp/BUILDROOT/app1-1.0-1.x86_64 -a /home/ran/work/rpmexample/rpmtemp/BUILDROOT/app1-1.0-1.x86_64 '!=' / ']'
+ rm -rf /home/ran/work/rpmexample/rpmtemp/BUILDROOT/app1-1.0-1.x86_64
+ cd /home/ran/work/rpmexample/rpmtemp/BUILD
+ rm -rf app1-1.0
+ /usr/bin/gzip -dc /home/ran/work/rpmexample/app1-1.0.1.tar.gz
+ /usr/bin/tar -xf -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd app1-1.0
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.gVaX4j
+ umask 022
+ cd /home/ran/work/rpmexample/rpmtemp/BUILD
+ cd app1-1.0
+ '[' '!' -e /home/ran/work/rpmexample/rpmtemp/BUILDROOT/app1-1.0-1.x86_64 -a /home/ran/work/rpmexample/rpmtemp/BUILDROOT/app1-1.0-1.x86_64 '!=' / ']'
+ mkdir /home/ran/work/rpmexample/rpmtemp/BUILDROOT/app1-1.0-1.x86_64
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.JWAdxE
+ umask 022
+ cd /home/ran/work/rpmexample/rpmtemp/BUILD
+ '[' /home/ran/work/rpmexample/rpmtemp/BUILDROOT/app1-1.0-1.x86_64 '!=' / ']'
+ rm -rf /home/ran/work/rpmexample/rpmtemp/BUILDROOT/app1-1.0-1.x86_64
++ dirname /home/ran/work/rpmexample/rpmtemp/BUILDROOT/app1-1.0-1.x86_64
+ mkdir -p /home/ran/work/rpmexample/rpmtemp/BUILDROOT
+ mkdir /home/ran/work/rpmexample/rpmtemp/BUILDROOT/app1-1.0-1.x86_64
+ cd app1-1.0
+ scons --install-sandbox=/home/ran/work/rpmexample/rpmtemp/BUILDROOT/app1-1.0-1.x86_64 /home/ran/work/rpmexample/rpmtemp/BUILDROOT/app1-1.0-1.x86_64
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
g++ -o app1/main.o -c -Wall -Werror -g -ggdb3 -gdwarf-2 -std=c++11 -Iapp1 app1/main.cpp
app1/main.cpp:2:17: fatal error: inc.h: No such file or directory
#include "inc.h"
^
compilation terminated.
scons: *** [app1/main.o] Error 1
scons: building terminated because of errors.
error: Bad exit status from /var/tmp/rpm-tmp.JWAdxE (%install)
RPM build errors:
Bad exit status from /var/tmp/rpm-tmp.JWAdxE (%install)
scons: building terminated because of errors.
When trying to port a Python code to cython, I get the following linker error message:
cls ~/workspace/Prototypes/PLPcython $ python3 setup.py build_ext --inplace
running build_ext
cythoning src/graph.pyx to src/graph.c
cythoning src/community.pyx to src/community.c
building 'PLPcython' extension
creating build
creating build/temp.macosx-10.8-x86_64-3.3
creating build/temp.macosx-10.8-x86_64-3.3/src
cc -Wno-unused-result -fno-common -dynamic -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -I/usr/local/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python3/3.3.0/Frameworks/Python.framework/Versions/3.3/include/python3.3m -c src/graph.c -o build/temp.macosx-10.8-x86_64-3.3/src/graph.o
cc -Wno-unused-result -fno-common -dynamic -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -I/usr/local/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python3/3.3.0/Frameworks/Python.framework/Versions/3.3/include/python3.3m -c src/community.c -o build/temp.macosx-10.8-x86_64-3.3/src/community.o
src/community.c:1414:19: warning: expression result unused [-Wunused-value]
PyObject_INIT(o, t);
~~~~~~~~~~~~~~^~~~~
/usr/local/Cellar/python3/3.3.0/Frameworks/Python.framework/Versions/3.3/include/python3.3m/objimpl.h:163:69: note: expanded from macro 'PyObject_INIT'
( Py_TYPE(op) = (typeobj), _Py_NewReference((PyObject *)(op)), (op) )
^
1 warning generated.
cc -bundle -undefined dynamic_lookup -L/usr/local/lib -L/usr/local/opt/sqlite/lib build/temp.macosx-10.8-x86_64-3.3/src/graph.o build/temp.macosx-10.8-x86_64-3.3/src/community.o -o /Users/cls/workspace/Prototypes/PLPcython/PLPcython.so
duplicate symbol _PyInit_PLPcython in:
build/temp.macosx-10.8-x86_64-3.3/src/graph.o
build/temp.macosx-10.8-x86_64-3.3/src/community.o
duplicate symbol ___pyx_module_is_main_PLPcython in:
build/temp.macosx-10.8-x86_64-3.3/src/graph.o
build/temp.macosx-10.8-x86_64-3.3/src/community.o
ld: 2 duplicate symbols for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'cc' failed with exit status 1
Apparently duplicate symbols are produced. What is _PyInit_* and ___pyx_module_is_main_?
These are the two source files I try to cythonize: graph.pyx
class Graph:
def __init__(self, n=0):
self.n = n
self.m = 0
self.z = n # max node id
self.adja = [[] for i in range(self.z)]
self.deg = [0 for i in range(self.z)]
def maxNodeId(self):
return self.z
def numberOfNodes(self):
return self.n
def numberOfEdges(self):
return self.m
def addEdge(self, u, v):
if (u == v):
self.adja[u].append(v)
self.deg[u] += 1
else:
self.adja[u].append(v)
self.adja[v].append(u)
self.deg[u] += 1
self.deg[v] += 1
self.m += 1
def hasEdge(self, u, v):
for w in self.adja[u]:
if w == v:
return True
return False
def degree(self, u):
return self.deg[u]
def forNodes(self, handle):
# assumtion: all nodes exist
for u in range(self.z):
handle(u)
def forEdges(self, handle):
for u in range(self.z):
for v in self.adja[u]:
if v <= u:
handle(u, v)
def forNeighborsOf(self, u, handle):
for v in self.adja[u]:
handle(v)
and community.pyx
def numberOfCommunities(zeta, G):
labels = set()
for label in zeta:
if label is not None:
labels.add(label)
return len(labels)
def coverage(zeta, G):
intra = 0
inter = 0
m = G.numberOfEdges()
def scan(u, v):
nonlocal intra
nonlocal inter
if zeta[u] == zeta[v]:
intra += 1
else:
inter += 1
G.forEdges(scan)
print("intra-community edges: ", intra)
print("inter-community edges: ",inter)
assert (inter + intra == m)
coverage = intra / m
return coverage
I believe Cython only supports the compilation of a single source file to a single module. So either you compile your two files as two separate modules or you use the include statement (http://docs.cython.org/src/userguide/language_basics.html#the-include-statement) to combine them in a single source file.