GenSim Simulation Program

In [1]:

    

%%bash
cd ..
qmake -project
ls -lrt


    

    




total 1392
-rw-r--r--@  1 haocheng  staff    1717 Dec 12 22:39 tools.cpp
-rw-r--r--@  1 haocheng  staff     270 Dec 12 22:39 ped.h
-rw-r--r--@  1 haocheng  staff  288416 Dec 13 21:00 libGenSim.a
-rw-r--r--@  1 haocheng  staff     918 Dec 14 00:53 popMap.h
-rw-r--r--@  1 haocheng  staff    1174 Dec 14 01:05 popMap.cpp
-rw-r--r--@  1 haocheng  staff     348 Jan  5 20:19 makeGenSim
-rw-r--r--@  1 haocheng  staff  109968 Jan  5 20:20 main.o
-rwxr-xr-x@  1 haocheng  staff  194120 Jan  5 20:20 GenSim
drwxr-xr-x@  6 haocheng  staff     204 Jan  5 20:32 data
drwxr-xr-x@ 10 haocheng  staff     340 Jan  5 21:27 ReadMe
-rw-r--r--@  1 haocheng  staff    1121 Jan  7 21:45 tools.h
-rw-r--r--@  1 haocheng  staff    1697 Jan  7 22:54 genome_info.cpp
-rw-r--r--@  1 haocheng  staff    1487 Jan  7 22:55 genome_info.h
-rw-r--r--@  1 haocheng  staff     917 Jan 10 01:33 cohort.h
-rw-r--r--@  1 haocheng  staff    4715 Jan 10 14:30 cohort.cpp
-rw-r--r--@  1 haocheng  staff    1716 Jan 10 16:06 simPop.h
-rw-r--r--@  1 haocheng  staff    8436 Jan 10 22:06 simPop.cpp
-rw-r--r--@  1 haocheng  staff     462 Jan 10 22:10 global.h
-rw-r--r--@  1 haocheng  staff     765 Jan 10 22:10 parmMap.h
-rw-r--r--@  1 haocheng  staff    1388 Jan 10 22:10 parmMap.cpp
-rw-r--r--@  1 haocheng  staff    4311 Jan 11 15:15 main.cpp
-rw-r--r--@  1 haocheng  staff    2426 Jan 11 20:01 animal_class.h
-rw-r--r--@  1 haocheng  staff   22318 Jan 11 20:13 animal_class.cpp
-rw-r--r--   1 haocheng  staff     702 Jan 11 20:17 GenSim1.4.pro

In [2]:

    

%%bash
cd ..
cat GenSim1.4.pro


    

    




######################################################################
# Automatically generated by qmake (2.01a) Sun Jan 11 20:17:33 2015
######################################################################

TEMPLATE = app
TARGET = 
DEPENDPATH += ../../gensim/GenSim1.4
INCLUDEPATH += .

# Input
HEADERS += animal_class.h \
           cohort.h \
           genome_info.h \
           global.h \
           parmMap.h \
           ped.h \
           popMap.h \
           simPop.h \
           tools.h
SOURCES += animal_class.cpp \
           cohort.cpp \
           genome_info.cpp \
           main.cpp \
           parmMap.cpp \
           popMap.cpp \
           simPop.cpp \
           tools.cpp

In [3]:

    

%%file GenSim.pro


######################################################################
# Automatically generated by qmake (2.01a) Sat Dec 13 20:11:00 2014
######################################################################

TEMPLATE = lib
CONFIG   = staticlib
TARGET = 
DEPENDPATH += .
INCLUDEPATH += . \
               /Users/erxingfangshui/Dropbox/CODE/eigen3 \
               /Users/erxingfangshui/Dropbox/CODE/boost
#QMAKE_CXXFLAGS += -std=c++11 -stdlib=libc++ -mmacosx-version-min=10.7 


# Input
HEADERS += animal_class.h \
           cohort.h \
           genome_info.h \
           global.h \
           parmMap.h \
           ped.h \
           simPop.h \
           tools.h
SOURCES += animal_class.cpp \
           cohort.cpp \
           genome_info.cpp \
           parmMap.cpp \
           simPop.cpp \
           tools.cpp


    

    




Writing GenSim.pro

In [4]:

    

%%bash
mv GenSim.pro ../


    

In [5]:

    

%%bash
cd ..
qmake -spec /anaconda/mkspecs/darwin-g++ GenSim.pro

#to use llvm , the line QMAKE_CXXFLAGS in GenSim.pro is needed.
#qmake -spec /anaconda/mkspecs/macx-llvm GenSim.pro


    

In [10]:

    

%%bash
cd ..
make


    

    




llvm-g++ -c -pipe -std=c++11 -stdlib=libc++ -mmacosx-version-min=10.7 -O2 -fPIC  -I/anaconda/mkspecs/macx-llvm -I. -I. -I../../CODE/eigen3 -I../../CODE/boost -o animal_class.o animal_class.cpp
llvm-g++ -c -pipe -std=c++11 -stdlib=libc++ -mmacosx-version-min=10.7 -O2 -fPIC  -I/anaconda/mkspecs/macx-llvm -I. -I. -I../../CODE/eigen3 -I../../CODE/boost -o cohort.o cohort.cpp
llvm-g++ -c -pipe -std=c++11 -stdlib=libc++ -mmacosx-version-min=10.7 -O2 -fPIC  -I/anaconda/mkspecs/macx-llvm -I. -I. -I../../CODE/eigen3 -I../../CODE/boost -o genome_info.o genome_info.cpp
llvm-g++ -c -pipe -std=c++11 -stdlib=libc++ -mmacosx-version-min=10.7 -O2 -fPIC  -I/anaconda/mkspecs/macx-llvm -I. -I. -I../../CODE/eigen3 -I../../CODE/boost -o parmMap.o parmMap.cpp
llvm-g++ -c -pipe -std=c++11 -stdlib=libc++ -mmacosx-version-min=10.7 -O2 -fPIC  -I/anaconda/mkspecs/macx-llvm -I. -I. -I../../CODE/eigen3 -I../../CODE/boost -o simPop.o simPop.cpp
llvm-g++ -c -pipe -std=c++11 -stdlib=libc++ -mmacosx-version-min=10.7 -O2 -fPIC  -I/anaconda/mkspecs/macx-llvm -I. -I. -I../../CODE/eigen3 -I../../CODE/boost -o tools.o tools.cpp
rm -f libGenSim.a
ar cq libGenSim.a animal_class.o cohort.o genome_info.o parmMap.o simPop.o tools.o
ranlib -s libGenSim.a

In [6]:

    

%%bash
cd ..
rm *.o *.pro
rm Makefile