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[simuPOP-devel] SF.net SVN: simupop:[5008] trunk
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From: <bpe...@us...> - 2016-02-09 23:35:38
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Revision: 5008
http://sourceforge.net/p/simupop/code/5008
Author: bpeng2000
Date: 2016-02-09 23:35:36 +0000 (Tue, 09 Feb 2016)
Log Message:
-----------
Use pre-compiled header and static library to suppress compiling warnings from boost and reduce build time
Modified Paths:
--------------
trunk/MANIFEST.in
trunk/setup.py
trunk/simuPOP_version.py
trunk/src/genoStru.cpp
trunk/src/genoStru.h
trunk/src/migrator.cpp
trunk/src/migrator.h
trunk/src/pedigree.h
trunk/src/penetrance.h
trunk/src/population.cpp
trunk/src/population.h
trunk/src/qtrait.h
trunk/src/selector.h
trunk/src/simuPOP_cfg.h
trunk/src/utility.cpp
Modified: trunk/MANIFEST.in
===================================================================
--- trunk/MANIFEST.in 2016-01-27 15:00:33 UTC (rev 5007)
+++ trunk/MANIFEST.in 2016-02-09 23:35:36 UTC (rev 5008)
@@ -18,6 +18,7 @@
include config_linux.h
include config_mac.h
include src/simuPOP_cfg.h
+include src/boost_pch.h
include src/mutant_vector.h
include src/utility.h
include src/genoStru.h
Modified: trunk/setup.py
===================================================================
--- trunk/setup.py 2016-01-27 15:00:33 UTC (rev 5007)
+++ trunk/setup.py 2016-02-09 23:35:36 UTC (rev 5008)
@@ -41,6 +41,7 @@
"""
import os, sys, platform, shutil, glob, re, tempfile, subprocess
import distutils.sysconfig
+from distutils.ccompiler import new_compiler
from distutils.errors import CompileError
from distutils.errors import DistutilsExecError
@@ -186,6 +187,9 @@
if distutils.sysconfig.get_config_var('CC') is not None:
USE_ICC = 'icc' in distutils.sysconfig.get_config_var('CC')
+if not USE_ICC and USE_OPENMP:
+ COMMON_MACROS.append(('_GLIBCXX_PARALLEL', None))
+
# simuPOP works with these boost versions. Newer versions will be used if these
# versions are not available, and will most likely work just fine.
boost_versions = ['1_35_0', '1_36_0', '1_37_0', '1_38_0', '1_39_0', '1_40_0',
@@ -385,7 +389,7 @@
# since it is troublesome to link to external gsl library,
# I embed some GSL files with simuPOP.
-LIB_FILES = [
+GSL_LIB_FILES = [
'gsl/sys/infnan.c',
'gsl/sys/coerce.c',
'gsl/sys/fdiv.c',
@@ -470,7 +474,9 @@
'gsl/cdf/gamma.c',
'gsl/cdf/poisson.c',
'gsl/error.c'
-] + [x for x in glob.glob(os.path.join(boost_serialization_dir, '*.cpp')) if 'xml' not in x and 'binary' not in x]\
+]
+
+LIB_FILES = [x for x in glob.glob(os.path.join(boost_serialization_dir, '*.cpp')) if 'xml' not in x and 'binary' not in x]\
+ [x for x in glob.glob(os.path.join(boost_iostreams_dir, '*.cpp')) if 'bzip' not in x]\
+ glob.glob(os.path.join(boost_regex_dir, '*.cpp'))
@@ -551,32 +557,39 @@
if not os.path.isdir('build'):
os.mkdir('build')
+COMMON_MACROS = [
+ ('BOOST_UBLAS_NDEBUG', None),
+ ('_HAS_ITERATOR_DEBUGGING', 0)
+ ]
+
+if os.name == 'nt':
+ COMMON_MACROS.extend([('BOOST_ALL_NO_LIB', None),
+ ('NO_ZLIB', 0), ('NO_BZIP' , 1),
+ # this one disables a lot of warnings about VC Checked iterators.
+ #('_SCL_SECURE_NO_WARNINGS', None)
+ ])
+
MACROS = {
'std': [('SIMUPOP_MODULE', 'simuPOP_std'),
- ('_SECURE_SCL', 1), ('_HAS_ITERATOR_DEBUGGING', 0)],
+ ('_SECURE_SCL', 1)],
'op': [('SIMUPOP_MODULE', 'simuPOP_op'), ('OPTIMIZED', None),
- ('NDEBUG', None), ('BOOST_UBLAS_NDEBUG', None),
- ('_SECURE_SCL', 0), ('_HAS_ITERATOR_DEBUGGING', 0)],
+ ('NDEBUG', None), ('_SECURE_SCL', 0)],
'la': [('SIMUPOP_MODULE', 'simuPOP_la'), ('LONGALLELE', None),
- ('_SECURE_SCL', 1), ('_HAS_ITERATOR_DEBUGGING', 0)],
+ ('_SECURE_SCL', 1)],
'laop': [('SIMUPOP_MODULE', 'simuPOP_laop'), ('LONGALLELE', None),
- ('OPTIMIZED', None),('NDEBUG', None), ('BOOST_UBLAS_NDEBUG', None),
- ('_SECURE_SCL', 0), ('_HAS_ITERATOR_DEBUGGING', 0)],
+ ('OPTIMIZED', None),('NDEBUG', None), ('_SECURE_SCL', 0)],
'ba': [('SIMUPOP_MODULE', 'simuPOP_ba'), ('BINARYALLELE', None),
- ('_SECURE_SCL', 1), ('_HAS_ITERATOR_DEBUGGING', 0)],
+ ('_SECURE_SCL', 1)],
'baop': [('SIMUPOP_MODULE', 'simuPOP_baop'), ('BINARYALLELE', None),
- ('OPTIMIZED', None),('NDEBUG', None), ('BOOST_UBLAS_NDEBUG', None),
- ('_SECURE_SCL', 0), ('_HAS_ITERATOR_DEBUGGING', 0)],
+ ('OPTIMIZED', None),('NDEBUG', None), ('_SECURE_SCL', 0)],
'mu': [('SIMUPOP_MODULE', 'simuPOP_mu'), ('MUTANTALLELE', None),
- ('_SECURE_SCL', 1), ('_HAS_ITERATOR_DEBUGGING', 0)],
+ ('_SECURE_SCL', 1)],
'muop': [('SIMUPOP_MODULE', 'simuPOP_muop'), ('MUTANTALLELE', None),
- ('OPTIMIZED', None),('NDEBUG', None), ('BOOST_UBLAS_NDEBUG', None),
- ('_SECURE_SCL', 0), ('_HAS_ITERATOR_DEBUGGING', 0)],
+ ('OPTIMIZED', None),('NDEBUG', None), ('_SECURE_SCL', 0)],
'lin': [('SIMUPOP_MODULE', 'simuPOP_lin'), ('LINEAGE', None),
- ('_SECURE_SCL', 1), ('_HAS_ITERATOR_DEBUGGING', 0)],
+ ('_SECURE_SCL', 1)],
'linop': [('SIMUPOP_MODULE', 'simuPOP_linop'), ('LINEAGE', None),
- ('OPTIMIZED', None),('NDEBUG', None), ('BOOST_UBLAS_NDEBUG', None),
- ('_SECURE_SCL', 0), ('_HAS_ITERATOR_DEBUGGING', 0)],
+ ('OPTIMIZED', None),('NDEBUG', None), ('_SECURE_SCL', 0)],
}
@@ -640,7 +653,8 @@
if is_maverick():
common_extra_link_args = ['-stdlib=libstdc++']
common_extra_include_dirs = ['/usr/include/c++/4.2.1']
- common_extra_compile_args = ['-Wno-error=unused-command-line-argument-hard-error-in-future']
+ #common_extra_compile_args = ['-Wno-error=unused-command-line-argument-hard-error-in-future']
+ common_extra_compile_args = ['-Wno-error=unused-command-line-argument']
elif os.name == 'nt':
common_extra_link_args = []
common_extra_include_dirs = []
@@ -660,12 +674,18 @@
res['src'] = ['src/simuPOP_' + modu + '_wrap.cpp']
for src in SOURCE_FILES:
res['src'].append('build/%s/%s' % (modu, src))
- res['src'].extend(LIB_FILES)
+ #
+ # For some reason that I have not got a change to investigate, including GSL_LIB_FILES
+ # to LIB_FILES would lead to symbol not found and some error like that. I suspect
+ # that this is related to the order the library is linked, or some MACRO that is only
+ # used when the GSL files are compiled with simuPOP modules.
+ #
+ res['src'].extend(GSL_LIB_FILES)
# lib
if os.name == 'nt': # Windows, build zlib from source
- res['libraries'] = []
+ res['libraries'] = ['simuPOP_shared']
else:
- res['libraries'] = ['z']
+ res['libraries'] = ['z', 'simuPOP_shared']
if USE_OPENMP:
if USE_ICC:
res['libraries'].append('iomp5')
@@ -711,18 +731,8 @@
if USE_ICC:
res['extra_compile_args'].extend(['-wd981', '-wd191'])
# define_macros (deep copy)
- res['define_macros'] = [x for x in MACROS[modu]]
- res['define_macros'].extend([('SIMUPOP_VER', SIMUPOP_VER), ('SIMUPOP_REV', SIMUPOP_REV)])
- if os.name == 'nt':
- res['define_macros'].extend([('BOOST_ALL_NO_LIB', None),
- ('NO_ZLIB', 0), ('NO_BZIP' , 1),
- # this one disables a lot of warnings about VC Checked iterators.
- #('_SCL_SECURE_NO_WARNINGS', None)
- ])
- else:
- if not USE_ICC:
- if USE_OPENMP:
- res['define_macros'].append(('_GLIBCXX_PARALLEL', None))
+ res['define_macros'] = COMMON_MACROS + MACROS[modu]
+
res['undef_macros'] = []
return res
@@ -746,7 +756,40 @@
SIMUPOP_VER, SIMUPOP_REV = simuPOP_version()
# create source file for each module
MODULES = ['std', 'op', 'la', 'laop', 'ba', 'baop', 'mu', 'muop', 'lin', 'linop']
-
+ COMMON_MACROS.extend([
+ ('SIMUPOP_VER', SIMUPOP_VER),
+ ('SIMUPOP_REV', SIMUPOP_REV)
+ ])
+
+ try:
+ if os.name != 'nt' and (not os.path.isfile('src/boost_pch.h.pch') or \
+ os.path.getmtime('src/boost_pch.h.pch') > os.path.getmtime('src/boost_pch.h')):
+ c = new_compiler(verbose=1)
+ # allow compiling .h file
+ c.src_extensions.append('.hpp')
+ c.compile(['src/boost_pch.hpp'], output_dir='src',
+ include_dirs=['.', 'gsr', boost_include_dir] + common_extra_include_dirs,
+ extra_preargs = common_extra_compile_args,
+ macros=COMMON_MACROS)
+ except Exception as e:
+ # it is ok if boost_pch cannot be precompiled.
+ print('Failed to pre-compile boost headers: {}'.format(e))
+
+ try:
+ # try to get
+ print('Building a static library')
+ c = new_compiler(verbose=1)
+ # -w suppress all warnings caused by the use of boost libraries
+ objects = c.compile(LIB_FILES, extra_postargs=['-w', '-unknownnn'],
+ include_dirs=['gsl', 'gsl/specfunc', 'build', '.', boost_include_dir] + common_extra_include_dirs,
+ output_dir='build',
+ extra_preargs = common_extra_compile_args,
+ macros = COMMON_MACROS
+ )
+ c.create_static_lib(objects, "simuPOP_shared", output_dir='build')
+ except Exception as e:
+ sys.exit("Failed to build a shared supporting library: {}".format(e))
+
#
# Generate Wrapping files
#
@@ -803,7 +846,7 @@
Extension('simuPOP._gsl',
sources = GSL_FILES + ['src/gsl_wrap.c'],
include_dirs = ['gsl', 'gsl/specfunc', 'build', '.'] + common_extra_include_dirs,
- extra_compile_args = common_extra_compile_args,
+ extra_compile_args = common_extra_compile_args + ['-w'],
extra_link_args = common_extra_link_args,
)
]
Modified: trunk/simuPOP_version.py
===================================================================
--- trunk/simuPOP_version.py 2016-01-27 15:00:33 UTC (rev 5007)
+++ trunk/simuPOP_version.py 2016-02-09 23:35:36 UTC (rev 5008)
@@ -1,2 +1,2 @@
-SIMUPOP_VER="1.1.8svn"
+SIMUPOP_VER="1.1.8"
SIMUPOP_REV="5003"
Modified: trunk/src/genoStru.cpp
===================================================================
--- trunk/src/genoStru.cpp 2016-01-27 15:00:33 UTC (rev 5007)
+++ trunk/src/genoStru.cpp 2016-02-09 23:35:36 UTC (rev 5008)
@@ -25,7 +25,7 @@
#include "genoStru.h"
-#include "boost/lambda/lambda.hpp"
+#include "boost_pch.hpp"
using namespace boost::lambda;
Modified: trunk/src/genoStru.h
===================================================================
--- trunk/src/genoStru.h 2016-01-27 15:00:33 UTC (rev 5007)
+++ trunk/src/genoStru.h 2016-02-09 23:35:36 UTC (rev 5008)
@@ -34,11 +34,7 @@
#include "utility.h"
#include "simuPOP_cfg.h"
-#include <boost/serialization/vector.hpp>
-#include <boost/serialization/version.hpp>
-#include <boost/serialization/split_member.hpp>
-#include <boost/serialization/split_free.hpp>
-
+#include "boost_pch.hpp"
#include <iterator>
using std::ostream;
using std::ostream_iterator;
Modified: trunk/src/migrator.cpp
===================================================================
--- trunk/src/migrator.cpp 2016-01-27 15:00:33 UTC (rev 5007)
+++ trunk/src/migrator.cpp 2016-02-09 23:35:36 UTC (rev 5008)
@@ -26,9 +26,7 @@
#include "virtualSubPop.h"
#include "migrator.h"
-#include <boost/numeric/ublas/lu.hpp>
-#include <boost/numeric/ublas/io.hpp>
-
+#include "boost_pch.hpp"
namespace simuPOP {
Migrator::Migrator(const floatMatrix & rate, int mode, const uintList & toSubPops,
Modified: trunk/src/migrator.h
===================================================================
--- trunk/src/migrator.h 2016-01-27 15:00:33 UTC (rev 5007)
+++ trunk/src/migrator.h 2016-02-09 23:35:36 UTC (rev 5008)
@@ -33,8 +33,9 @@
#include <list>
using std::list;
-#include <boost/numeric/ublas/matrix.hpp>
+#include "boost_pch.hpp"
+
#include <iostream>
using std::cout;
using std::endl;
Modified: trunk/src/pedigree.h
===================================================================
--- trunk/src/pedigree.h 2016-01-27 15:00:33 UTC (rev 5007)
+++ trunk/src/pedigree.h 2016-02-09 23:35:36 UTC (rev 5008)
@@ -31,13 +31,7 @@
*/
#include "population.h"
-#if TR1_SUPPORT == 0
-# include <map>
-#elif TR1_SUPPORT == 1
-# include <unordered_map>
-#else
-# include <tr1/unordered_map>
-#endif
+#include "boost_pch.hpp"
namespace simuPOP {
Modified: trunk/src/penetrance.h
===================================================================
--- trunk/src/penetrance.h 2016-01-27 15:00:33 UTC (rev 5007)
+++ trunk/src/penetrance.h 2016-02-09 23:35:36 UTC (rev 5008)
@@ -32,7 +32,7 @@
#include "utility.h"
#include "operator.h"
-#include "boost/tuple/tuple.hpp"
+#include "boost_pch.hpp"
#include <numeric>
using std::min;
Modified: trunk/src/population.cpp
===================================================================
--- trunk/src/population.cpp 2016-01-27 15:00:33 UTC (rev 5007)
+++ trunk/src/population.cpp 2016-02-09 23:35:36 UTC (rev 5008)
@@ -27,9 +27,7 @@
#include "virtualSubPop.h"
// for file compression
-#include <boost/iostreams/filtering_stream.hpp>
-#include <boost/iostreams/filter/gzip.hpp>
-#include <boost/iostreams/device/file.hpp>
+#include "boost_pch.hpp"
#if PY_VERSION_HEX >= 0x03000000
# define PyInt_FromLong(x) PyLong_FromLong(x)
Modified: trunk/src/population.h
===================================================================
--- trunk/src/population.h 2016-01-27 15:00:33 UTC (rev 5007)
+++ trunk/src/population.h 2016-02-09 23:35:36 UTC (rev 5008)
@@ -46,14 +46,7 @@
#include <deque>
using std::deque;
-#include <boost/archive/text_iarchive.hpp>
-#include <boost/archive/text_oarchive.hpp>
-#include <boost/serialization/utility.hpp>
-#include <boost/serialization/vector.hpp>
-#include <boost/serialization/split_member.hpp>
-#include <boost/serialization/split_free.hpp>
-#include <boost/serialization/version.hpp>
-
+#include "boost_pch.hpp"
#include "individual.h"
#include "virtualSubPop.h"
Modified: trunk/src/qtrait.h
===================================================================
--- trunk/src/qtrait.h 2016-01-27 15:00:33 UTC (rev 5007)
+++ trunk/src/qtrait.h 2016-02-09 23:35:36 UTC (rev 5008)
@@ -32,7 +32,7 @@
#include "utility.h"
#include "operator.h"
-#include "boost/tuple/tuple.hpp"
+#include "boost_pch.hpp"
#include <numeric>
using std::min;
Modified: trunk/src/selector.h
===================================================================
--- trunk/src/selector.h 2016-01-27 15:00:33 UTC (rev 5007)
+++ trunk/src/selector.h 2016-02-09 23:35:36 UTC (rev 5008)
@@ -32,7 +32,7 @@
#include "utility.h"
#include "operator.h"
-#include "boost/tuple/tuple.hpp"
+#include "boost_pch.hpp"
#include <numeric>
using std::min;
Modified: trunk/src/simuPOP_cfg.h
===================================================================
--- trunk/src/simuPOP_cfg.h 2016-01-27 15:00:33 UTC (rev 5007)
+++ trunk/src/simuPOP_cfg.h 2016-02-09 23:35:36 UTC (rev 5008)
@@ -498,8 +498,9 @@
}
#pragma GCC system_header
-#include <boost/format.hpp>
+#include "boost_pch.hpp"
+
namespace simuPOP {
// standard library
Modified: trunk/src/utility.cpp
===================================================================
--- trunk/src/utility.cpp 2016-01-27 15:00:33 UTC (rev 5007)
+++ trunk/src/utility.cpp 2016-02-09 23:35:36 UTC (rev 5008)
@@ -52,7 +52,7 @@
using std::ifstream;
using std::ofstream;
-#include "boost/lexical_cast.hpp"
+#include "boost_pch.hpp"
// for data type lociList
#include "genoStru.h"
@@ -105,7 +105,7 @@
#include "boost/pending/lowest_bit.hpp"
using boost::lowest_bit;
-#include "boost/regex.hpp"
+
using boost::regex;
using boost::regex_match;
using boost::cmatch;
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