.github/OpenMP_mac.md

In snlab-ch/goldfish: Statistical Network Models for Dynamic Network Data

Installing OpenMP on Mac OSX

In some cases, you may get an error that does not allow installation of goldfish from source on Mac OSX versions, including under R 4.0.0. The error may relate to compiling the parts of goldfish that are written in C++, or whether OpenMP (for parallelisation) can be found. To install OpenMP, follow these steps:

1. Install homebrew via the terminal. Homebrew allows you to easily install software.
2. Install the latest version of gcc via the terminal command brew install gcc.
3. Check what version of gcc you have with: brew list --versions gcc
4. Go to ~/.R and open the file Makevars. Add the following code to that file:

CC=/usr/local/bin/gcc-10
CXX=/usr/local/bin/g++-10
CXX1X=/usr/local/bin/g++-10
CXX11=/usr/local/bin/g++-10
SHLIB_CXXLD=/usr/local/bin/g++-10
FC=/usr/local/bin/gfortran-10
F77=/usr/local/bin/gfortran-10
MAKE=make -j8

SHLIB_OPENMP_CFLAGS=-fopenmp
SHLIB_OPENMP_CXXFLAGS=-fopenmp
SHLIB_OPENMP_FCFLAGS=-fopenmp
SHLIB_OPENMP_FFLAGS=-fopenmp

If you do not have version 10 of gcc, replace all the 10s in the code above with your version number.

1. Go to /Library/Frameworks/R.framework/Resources/etc/ and open the file Makeconf. Here you need to add the library path to SHLIB_LIBADD:

SHLIB_LIBADD = -L/usr/local/lib

1. Installing goldfish from source should work now. Otherwise get in contact with the developer team.

Update for M1, M2, ... machines

If you are using an M1, M2, ... machine, you could follow the previous instructions to install a gcc compiler and setting up the compilers for R. Thanks to @eugeniagilpa, here there is an alternative version of the Makevars file that should work for M1, M2, ... machines:

XCBASE:=$(shell xcrun --show-sdk-path)
GCCBASE:=$(shell brew --prefix gcc)
GETTEXT:=$(shell brew --prefix gettext)

CC=$(GCCBASE)/bin/gcc-13
CXX=$(GCCBASE)/bin/g++-13
CXX11=$(GCCBASE)/bin/g++-13
CXX14=$(GCCBASE)/bin/g++-13
CXX17=$(GCCBASE)/bin/g++-13 
CXX20=$(GCCBASE)/bin/g++-13
CXX23=$(GCCBASE)/bin/g++-13
SHLIB_CXXLD=$(GCCBASE)/bin/g++-13
FC=$(GCCBASE)/bin/gfortran
F77=$(GCCBASE)/bin/gfortran
FLIBS=-L/$(GCCBASE)/lib/gcc/13/ -lm -lgfortran

CPPFLAGS=-isystem "$(GCCBASE)/include" -isysroot "$(XCBASE)"
LDFLAGS=-L"$(GCCBASE)/lib" -L"$(GETTEXT)/lib" --sysroot="$(XCBASE)"

MAKE=make -j8

SHLIB_OPENMP_CFLAGS=-fopenmp
SHLIB_OPENMP_CXXFLAGS=-fopenmp
SHLIB_OPENMP_FCFLAGS=-fopenmp 
SHLIB_OPENMP_FFLAGS=-fopenmp 

SHLIB_CXXLDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CXXFLAGS) $(CXXPICFLAGS) $(LTO_LD)
SHLIB_CXX11LDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CXX11FLAGS) $(CXX11PICFLAGS) $(LTO_LD)
SHLIB_CXX14LDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CXX14FLAGS) $(CXX14PICFLAGS) $(LTO_LD)
SHLIB_CXX17LDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CXX17FLAGS) $(CXX17PICFLAGS) $(LTO_LD)
SHLIB_CXX20LDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CXX20FLAGS) $(CXX20PICFLAGS) $(LTO_LD)
SHLIB_CXX23LDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CXX23FLAGS) $(CXX23PICFLAGS) $(LTO_LD)

SHLIB_FCLDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(FCFLAGS) $(FPICFLAGS)
SHLIB_LDFLAGS = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CFLAGS) $(CPICFLAGS) $(LTO_LD)
SHLIB_LDFLAGS_R = -dynamiclib -Wl,-ld_classic,-headerpad_max_install_names -undefined dynamic_lookup $(CFLAGS) $(CPICFLAGS) $(LTO_LD)

In step 5 the path to the library should be:

SHLIB_LIBADD = -L/opt/homebrew/opt/gfortran/lib

Please share feedback on which of these work (shortcuts or unnecessary parts) and we will update the installation guide accordingly.

snlab-ch/goldfish documentation built on Sept. 5, 2024, 10:13 a.m.