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CC=g++
CFLAGS=-O3 -c -Wall
DFLAGS=-g -Wall
LDFLAGS= -lz -lm -lpthread

KSWSOURCE=ksw.c
ALGNSOURCES=main.cpp aligner.cpp graph.cpp  readfl.cpp hash.cpp form.cpp btree.cpp conLSH.cpp
INDSOURCES=whash.cpp genhash.cpp formh.cpp conLSH.cpp

INDOBJECTS=$(INDSOURCES:.cpp=.o) $(KSWSOURCE:.c=.o)
ALGNOBJECTS=$(ALGNSOURCES:.cpp=.o) $(KSWSOURCE:.c=.o)

INDEXER=conLSH-indexer
ALIGNER=conLSH-aligner

all: $(INDSOURCES) $(ALGNSOURCES) $(KSWSOURCE) $(ALIGNER) $(INDEXER)

$(ALIGNER): $(ALGNOBJECTS)
        $(CC)  $(ALGNOBJECTS) -o $@ $(LDFLAGS)

$(INDEXER): $(INDOBJECTS)
        $(CC)  $(INDOBJECTS) readfl.o -o $@ $(LDFLAGS)

debug:
        $(CC) $(DFLAGS) $(ALGNSOURCES) $(KSWSOURCE) $(LDFLAGS)

.cpp.o:
        $(CC) $(CFLAGS) $< -o $@
.c.o:
        $(CC) $(CFLAGS) $< -o $@
clean:
        rm -rf *.o $(ALIGNER) $(INDEXER) a.out

I have the above makefile but I am getting an error

/usr/lib/gcc/i686-linux-gnu/4.8/include/emmintrin.h:31:3: error: #error "SSE2 instruction set not enabled"
 # error "SSE2 instruction set not enabled"

From what I understand and googled this is a flag for parallel computation.

I tried from other posts with the same problem to either include:

CXXFLAGS=-03 -c Wall -mfpmath=sse

OR:

set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse -msse2 -msse3")

but without any success. Can you help?

I am not sure a CXX flags is necessary because a lot of (probably) cascading errors are shown in ksw like,

ksw.c:49:2: error: ‘__m128i’ does not name a type
  __m128i *qp, *H0, *H1, *E, *Hmax;
Paramar
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  • Are you using a pure (handwritten) Makefile, or cmake? Are you in 32 or 64 bit mode? Does your CPU actually support SSE2 (check `cat /proc/cpuinfo`)? – chtz May 05 '21 at 09:15

2 Answers2

3

-msse2 is the specific option, so passing that to GCC will work, if you get your build scripts set up to actually do that. https://gcc.gnu.org/onlinedocs/gcc/x86-Options.html#x86-Options

Or better, use -march=native to enable everything your CPU has, if you're building for local use, not for distributing a binary that might have to work on an old-but-not-ancient CPU. (Of course, if you care about performance, it's weird to be building for 32-bit mode. SSE2 is baseline for x86-64. Unless your CPU is too old to support SSE2, e.g. a Pentium III. Or for example, there are embedded x86 CPUs without SSE, like AMD Geode. In that case, a binary built (successfully) with -msse2 will probably crash with an illegal instruction on such a CPU.)

-mfpmath=sse just tells GCC to use SSE for scalar FP math assuming that SSE is available; unrelated to telling GCC to assume the target CPU does support SSE2. It can be good to use it as well for performance, but it's not going to matter in getting your code to compile.

And yes, SSE1/2 intrinsic types like __m128i will only get defined when SSE is enabled, so error: ‘__m128i’ does not name a type is a clear sign that -msse wasn't enabled

If using autoconf or something, maybe use this:

./configure CPPFLAGS="-O3 -march=native -fno-math-errno"

If you have .c files as well as .cpp, set CFLAGS as well as CPPFLAGS. More options like -flto can be helpful for optimization (cross-file inlining at link time), if you get those added to your LD options. As well as any other optimization options like -ffast-math if you want to use it. Or at least -fno-trapping-math helps some, and GCC already did optimizations that violated the semantics trapping-math was supposed to provide. See this Q&A re: -fno-trapping-math -fno-math-errno being safe to use basically everywhere, even in code that depends on strict FP like Kahan summation.

Peter Cordes
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This worked for me also:

./configure CPPFLAGS="-march=native"
Justin Case
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