I run macOS Big Sur (v. 11.4) and I am trying to do Fisher analysis by using fishchips (https://github.com/xzackli/fishchips-public.git). In order to do so, I need to use CLASS (https://github.com/lesgourg/class_public.git). Following the instructions here, Class requires using make to allow us to use classy. When I initially run make, I get the error: clang: error: unsupported option '-fopenmp'. After reading here, I changed the OMPFLAG in my makefile from OMPFLAG = -fopenmp to OMPFLAG = -Xpreprocessor -fopenmp and now I get the error:
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see
invocation)
make: *** [class] Error 1.
I am confused about how to solve this. Here is a copy of my current makefile if it helps:
#Some Makefile for CLASS.
#Julien Lesgourgues, 28.11.2011
#Nils Schöneberg, Matteo Lucca, 27.02.2019
MDIR := $(shell pwd)
WRKDIR = $(MDIR)/build
.base:
if ! [ -e $(WRKDIR) ]; then mkdir $(WRKDIR) ; mkdir $(WRKDIR)/lib; fi;
touch build/.base
vpath %.c source:tools:main:test
vpath %.o build
vpath .base build
########################################################
###### LINES TO ADAPT TO YOUR PLATEFORM ################
########################################################
# your C compiler:
CC = gcc
#CC = icc
#CC = pgcc
# your tool for creating static libraries:
AR = ar rv
# Your python interpreter.
# In order to use Python 3, you can manually
# substitute python3 to python in the line below, or you can simply
# add a compilation option on the terminal command line:
# "PYTHON=python3 make all" (Thanks to Marius Millea for python3 compatibility)
PYTHON ?= python
# your optimization flag
OPTFLAG = -O3
#OPTFLAG = -Ofast -ffast-math #-march=native
#OPTFLAG = -fast
# your openmp flag (comment for compiling without openmp)
OMPFLAG = -Xpreprocessor -fopenmp
#OMPFLAG = -mp -mp=nonuma -mp=allcores -g
#OMPFLAG = -openmp
# all other compilation flags
CCFLAG = -g -fPIC
LDFLAG = -g -fPIC
# leave blank to compile without HyRec, or put path to HyRec directory
# (with no slash at the end: e.g. "external/RecfastCLASS")
HYREC = external/HyRec2020
RECFAST = external/RecfastCLASS
HEATING = external/heating
########################################################
###### IN PRINCIPLE THE REST SHOULD BE LEFT UNCHANGED ##
########################################################
# pass current working directory to the code
CCFLAG += -D__CLASSDIR__='"$(MDIR)"'
# where to find include files *.h
INCLUDES = -I../include
HEADERFILES = $(wildcard ./include/*.h)
# automatically add external programs if needed. First, initialize to blank.
EXTERNAL =
vpath %.c $(RECFAST)
#CCFLAG += -DRECFAST
INCLUDES += -I../$(RECFAST)
EXTERNAL += wrap_recfast.o
HEADERFILES += $(wildcard ./$(RECFAST)/*.h)
vpath %.c $(HEATING)
#CCFLAG += -DHEATING
INCLUDES += -I../$(HEATING)
EXTERNAL += injection.o noninjection.o
HEADERFILES += $(wildcard ./$(HEATING)/*.h)
# update flags for including HyRec
ifneq ($(HYREC),)
vpath %.c $(HYREC)
CCFLAG += -DHYREC
#LDFLAGS += -DHYREC
INCLUDES += -I../$(HYREC)
EXTERNAL += hyrectools.o helium.o hydrogen.o history.o wrap_hyrec.o energy_injection.o
HEADERFILES += $(wildcard ./$(HYREC)/*.h)
endif
%.o: %.c .base $(HEADERFILES)
cd $(WRKDIR);$(CC) $(OPTFLAG) $(OMPFLAG) $(CCFLAG) $(INCLUDES) -c ../$< -o $*.o
TOOLS = growTable.o dei_rkck.o sparse.o evolver_rkck.o evolver_ndf15.o arrays.o parser.o quadrature.o hyperspherical.o common.o trigonometric_integrals.o
SOURCE = input.o background.o thermodynamics.o perturbations.o primordial.o fourier.o transfer.o harmonic.o lensing.o distortions.o
INPUT = input.o
PRECISION = precision.o
BACKGROUND = background.o
THERMO = thermodynamics.o
PERTURBATIONS = perturbations.o
TRANSFER = transfer.o
PRIMORDIAL = primordial.o
HARMONIC = harmonic.o
FOURIER = fourier.o
LENSING = lensing.o
DISTORTIONS = distortions.o
OUTPUT = output.o
CLASS = class.o
TEST_LOOPS = test_loops.o
TEST_LOOPS_OMP = test_loops_omp.o
TEST_HARMONIC = test_harmonic.o
TEST_TRANSFER = test_transfer.o
TEST_FOURIER = test_fourier.o
TEST_PERTURBATIONS = test_perturbations.o
TEST_THERMODYNAMICS = test_thermodynamics.o
TEST_BACKGROUND = test_background.o
TEST_HYPERSPHERICAL = test_hyperspherical.o
C_TOOLS = $(addprefix tools/, $(addsuffix .c,$(basename $(TOOLS))))
C_SOURCE = $(addprefix source/, $(addsuffix .c,$(basename $(SOURCE) $(OUTPUT))))
C_TEST = $(addprefix test/, $(addsuffix .c,$(basename $(TEST_DEGENERACY) $(TEST_LOOPS) $(TEST_TRANSFER) $(TEST_FOURIER) $(TEST_PERTURBATIONS) $(TEST_THERMODYNAMICS))))
C_MAIN = $(addprefix main/, $(addsuffix .c,$(basename $(CLASS))))
C_ALL = $(C_MAIN) $(C_TOOLS) $(C_SOURCE)
H_ALL = $(addprefix include/, common.h svnversion.h $(addsuffix .h, $(basename $(notdir $(C_ALL)))))
PRE_ALL = cl_ref.pre clt_permille.pre
INI_ALL = explanatory.ini lcdm.ini
MISC_FILES = Makefile CPU psd_FD_single.dat myselection.dat myevolution.dat README bbn/sBBN.dat external_Pk/* cpp
PYTHON_FILES = python/classy.pyx python/setup.py python/cclassy.pxd python/test_class.py
all: class libclass.a classy
libclass.a: $(TOOLS) $(SOURCE) $(EXTERNAL)
$(AR) $@ $(addprefix build/, $(TOOLS) $(SOURCE) $(EXTERNAL))
class: $(TOOLS) $(SOURCE) $(EXTERNAL) $(OUTPUT) $(CLASS)
$(CC) $(OPTFLAG) $(OMPFLAG) $(LDFLAG) -o class $(addprefix build/,$(notdir $^)) -lm
test_loops: $(TOOLS) $(SOURCE) $(EXTERNAL) $(OUTPUT) $(TEST_LOOPS)
$(CC) $(OPTFLAG) $(OMPFLAG) $(LDFLAG) -o $@ $(addprefix build/,$(notdir $^)) -lm
test_loops_omp: $(TOOLS) $(SOURCE) $(EXTERNAL) $(OUTPUT) $(TEST_LOOPS_OMP)
$(CC) $(OPTFLAG) $(OMPFLAG) $(LDFLAG) -o $@ $(addprefix build/,$(notdir $^)) -lm
test_harmonic: $(TOOLS) $(SOURCE) $(EXTERNAL) $(TEST_HARMONIC)
$(CC) $(OPTFLAG) $(OMPFLAG) $(LDFLAG) -o $@ $(addprefix build/,$(notdir $^)) -lm
test_transfer: $(TOOLS) $(SOURCE) $(EXTERNAL) $(TEST_TRANSFER)
$(CC) $(OPTFLAG) $(OMPFLAG) $(LDFLAG) -o $@ $(addprefix build/,$(notdir $^)) -lm
test_fourier: $(TOOLS) $(SOURCE) $(EXTERNAL) $(TEST_FOURIER)
$(CC) $(OPTFLAG) $(OMPFLAG) $(LDFLAG) -o $@ $(addprefix build/,$(notdir $^)) -lm
test_perturbations: $(TOOLS) $(SOURCE) $(EXTERNAL) $(TEST_PERTURBATIONS)
$(CC) $(OPTFLAG) $(OMPFLAG) $(LDFLAG) -o $@ $(addprefix build/,$(notdir $^)) -lm
test_thermodynamics: $(TOOLS) $(SOURCE) $(EXTERNAL) $(TEST_THERMODYNAMICS)
$(CC) $(OPTFLAG) $(OMPFLAG) $(LDFLAG) -o $@ $(addprefix build/,$(notdir $^)) -lm
test_background: $(TOOLS) $(SOURCE) $(EXTERNAL) $(TEST_BACKGROUND)
$(CC) $(OPTFLAG) $(OMPFLAG) $(LDFLAG) -o $@ $(addprefix build/,$(notdir $^)) -lm
test_hyperspherical: $(TOOLS) $(TEST_HYPERSPHERICAL)
$(CC) $(OPTFLAG) $(OMPFLAG) $(LDFLAG) -o test_hyperspherical $(addprefix build/,$(notdir $^)) -lm
tar: $(C_ALL) $(C_TEST) $(H_ALL) $(PRE_ALL) $(INI_ALL) $(MISC_FILES) $(HYREC) $(PYTHON_FILES)
tar czvf class.tar.gz $(C_ALL) $(H_ALL) $(PRE_ALL) $(INI_ALL) $(MISC_FILES) $(HYREC) $(PYTHON_FILES)
classy: libclass.a python/classy.pyx python/cclassy.pxd
ifdef OMPFLAG
cp python/setup.py python/autosetup.py
else
grep -v "lgomp" python/setup.py > python/autosetup.py
endif
cd python; export CC=$(CC); $(PYTHON) autosetup.py install || $(PYTHON) autosetup.py install --user
rm python/autosetup.py
clean: .base
rm -rf $(WRKDIR);
rm -f libclass.a
rm -f $(MDIR)/python/classy.c
rm -rf $(MDIR)/python/build
rm -f python/autosetup.py
