sempwn
commented
2 years ago It's been a while since I've looked over this code. Try compiling with the following MakeFile and calling using the below Python method:
OBJS := timer.o randomseed.o
# Provide any options and flags for the compiler here
CFLAGS = -Wall -O3
# Set name of final executable file here
EXENAME = timer
# If you are linking to external libraries, provide them here
LIBS = -lgsl -lgslcblas -lfftw3 -lm
# If there are libraries with non-standard paths, provide the paths here
LIBDIR = -L$(HOME)/lib
# If there are header files with non-standard paths, provide the paths here
INCLDIR = -I. -I$(HOME)/include
default:$(EXENAME)
# link to generate executable file
$(EXENAME): $(OBJS)
g++ $(LIBDIR) $(OBJS) $(LIBS) -o $(EXENAME)
# pull in dependency info for *existing* .o files
-include $(OBJS:.o=.d)
# compile and generate dependency info
%.o: %.cpp
gcc -c $(CFLAGS) $(INCLDIR) $*.cpp -o $*.o
gcc -MM $(CFLAGS) $(INCLDIR) $*.cpp > $*.d
# remove compilation products
clean:
rm -f $(EXENAME) *.o *.ddef runSimNoInput(filename='test3.txt',finalDistribution=True,mfDistribution=False,allDistribution=False,index=0,model_path=''):
''' use for parrellisation as does not change the parameter file. '''
'''run model '''
if finalDistribution:
args = str(yrs) + " " + str(n) + " " + str(filename) + " " + str(index)
else:
args = str(120.0) + " " + str(n) + " " + str(filename) + " " + str(index)
cmd = model_path+'timer'
ccmd = cmd + " " + args
subprocess.call(ccmd,shell=True)
'''import data '''
outtm = np.loadtxt(model_path + filename)
wp = (outtm[0::6,:]+outtm[0::6,:])>0
w = outtm[0::6,:]+outtm[0::6,:]
mfp = outtm[2::6,:]>1.0
mf = outtm[2::6,:]
ages = outtm[-2,:]/12.0
if finalDistribution:
wp = wp[-1,:]
mfp = mfp[-1,:]
mf = mf[-1,:]
os.remove(filename)
ts = np.concatenate((np.linspace(0,100,100),np.linspace(100,120,120)))
if mfDistribution:
return ts, mfp, wp, ages, mf
elif allDistribution:
return ts, mfp, wp, ages, mf, w
else:
return ts, mfp, wp, ages
sdwfrost
I've tried to run the code after compiling as follows - any help would be appreciated.
Windows:
Ubuntu:
Running without command line options gives the following output and error: