installation error: Undefined symbols for architecture arm64

[msarrias]

Hi, when I try to compile CAFE 5 I get the following error:

g++ -std=c++11 -O3  -o bin/cafe5 -I. obj/base_model.o obj/cafexp.o obj/clade.o obj/core.o obj/easylogging++.o obj/error_model.o obj/execute.o obj/gamma.o obj/gamma_core.o obj/gene_family.o obj/gene_family_reconstructor.o obj/io.o obj/lambda.o obj/likelihood_ratio.o obj/matrix_cache.o obj/optimizer.o obj/optimizer_scorer.o obj/poisson.o obj/probability.o obj/root_equilibrium_distribution.o obj/simulator.o obj/user_data.o obj/main.o -lm
Undefined symbols for architecture arm64:
  "_omp_set_num_threads", referenced from:
      cafe5(int, char* const*) in cafexp.o
ld: symbol(s) not found for architecture arm64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [bin/cafe5] Error 1

about my computer: MacOS Big Sur (version 11.2.3), apple M1 processor.

Any help is greatly appreciated!

[benfulton]

You might try installing the OpenMP library

brew install libomp

Then run the configure and make steps again.

[msarrias]

Thank you for your reply.

I already have the libomp library installed.

[benfulton]

For some reason it didn't get picked up by the configure. Try editing the makefile manually and add

-fopenmp

to the line that starts

g++ -std=c++11 -O3 -o bin/cafe5...

[gnick18]

Just wanted to add how I fixed this problem in case others come across it in the future! In short, it has to do with directives and functions not playing nicely with the newer MacOS. But a lot of the nuance goes way over my head. This StackOverflow forum is exactly how I ended up solving it!
StackOverflow link

In short I had to add not only
-fopenmp
but the following
-Xpreprocessor -fopenmp -lomp
on every line that was calling $(LINKER). I then tested cafe5 on the example files and it appears to be working! Will update this comment if I run into more issues later on.

To see the full Makefile example with the edits here is what mine looked:

#edited Makefile
# compilers and flags
CC=g++
CXX=g++
LD=g++


CFLAGS = -std=c++11 -I. -O3 -include config.h
LINKER = $(LD) -std=c++11 -O3  -o
LFLAGS = -I.

AUX =   CHANGELOG.md configure INSTALL LICENSE Makefile.in README.md config.h.in docs/tutorial examples Test_data

# directories
SRCDIR = src
OBJDIR = obj
BINDIR = bin

# our program
TARGET = cafe5

# Default build
all: prep release

release: $(BINDIR)/$(TARGET)


SOURCES := $(wildcard $(SRCDIR)/*.cpp)
OBJECTS := $(SOURCES:$(SRCDIR)/%.cpp=$(OBJDIR)/%.o)
rm = rm -f

$(BINDIR)/$(TARGET): $(OBJECTS) $(OBJDIR)/main.o
	$(LINKER) $@ $(LFLAGS) $(OBJECTS) $(OBJDIR)/main.o -lm -Xpreprocessor -fopenmp -lomp

$(OBJECTS): $(OBJDIR)/%.o: $(SRCDIR)/%.cpp
	$(CC) $(CFLAGS) $(INCLUDES) -c $< -o $@

$(OBJDIR)/main.o: main.cpp
	$(CC) $(CFLAGS) -c $< -o $@

$(OBJDIR)/test.o: test.cpp
	$(CC) $(CFLAGS) -c $< -o $@

.PHONY: clean
clean:
	$(rm) $(OBJECTS) $(OBJDIR)/main.o

.PHONY: remove
remove: clean
	@$(rm) $(BINDIR)/$(TARGET)

#
# Debug build settings
#
DBGDIR = debug
DBG_OBJECTS := $(SOURCES:$(SRCDIR)/%.cpp=$(DBGDIR)/%.o)
DBG_CFLAGS = -std=c++11 -Wall -Werror  -g -I. -include config.h $(INCLUDES) -D_GLIBCXX_DEBUG -D_GLIBCXX_DEBUG_PEDANTIC
DBG_LINKER = $(LD) -std=c++11  -o

$(DBG_OBJECTS): $(DBGDIR)/%.o: $(SRCDIR)/%.cpp
	$(CC) $(DBG_CFLAGS) -c $< -o $@

$(DBGDIR)/main.o: main.cpp
	$(CC) $(DBG_CFLAGS) -c $< -o $@

$(DBGDIR)/$(TARGET): $(DBG_OBJECTS) $(DBGDIR)/main.o
	$(DBG_LINKER) $@ $(LFLAGS) $(DBG_OBJECTS) $(DBGDIR)/main.o -lm -Xpreprocessor -fopenmp -lomp

.PHONY: debug
debug: $(DBGDIR)/$(TARGET)

TESTDIR = test
TEST_TARGET = runtests
TEST_OBJECTS := $(SOURCES:$(SRCDIR)/%.cpp=$(TESTDIR)/%.o)
$(TEST_OBJECTS): $(TESTDIR)/%.o: $(SRCDIR)/%.cpp
	$(CC) $(DBG_CFLAGS)  $(INCLUDES) -DSILENT -c $< -o $@

$(TESTDIR)/test.o: test.cpp
	$(CC) $(DBG_CFLAGS) -c $< -o $@

$(TESTDIR)/$(TEST_TARGET): $(TEST_OBJECTS) $(TESTDIR)/test.o
	$(LINKER) $@ $(LFLAGS) $(TEST_OBJECTS) $(TESTDIR)/test.o -lm -Xpreprocessor -fopenmp -lomp

.PHONY: test
test: $(TESTDIR)/$(TEST_TARGET)

prep:
	@mkdir -p $(OBJDIR) $(BINDIR) $(TESTDIR)

.PHONY: docs
docs:
	$(MAKE) -C docs

.PHONY: dist
dist: $(AUX)
	mkdir -p distro
	tar  --transform "s,^,CAFE5/," --transform "s,docs/,," --owner=0 --group=0 -czf distro/CAFE5-5.0.0.tar.gz src test.cpp main.cpp $(AUX)

[benfulton]

Thanks, this is very helpful! I added a link to your answer to a new wiki page and will close this issue.