Update abismal to build and run on Apple M1

[melaniesilvis-epic]

Hi! I'm having an issue installing on my MacOS following the instructions, not sure what's going on but I would really appreciate any help!

• Installed all dependencies using homebrew
• downloaded abismal-3.2.2
• made build directory and config file
• failing during make with error: '_MM_HINT_T0' was not declared in this scope

(dnmtools_env) melaniesilvis@Melanie-Silvis-MacBook-Air abismal-3.2.2 % ./configure --prefix=$(pwd) \
    CXX="g++-13" \
    CPPFLAGS="-I$(brew --prefix)/include" \
    LDFLAGS="-L$(brew --prefix)/lib"
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++-13 accepts -g... yes
checking for g++-13 option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++-13... gcc3
checking whether g++-13 supports C++17 features with -std=c++17... yes
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for ar... ar
checking the archiver (ar) interface... ar
checking for ranlib... ranlib
checking for library containing hts_version... -lhts
checking for g++-13 -std=c++17 option to support OpenMP... -fopenmp
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: linking data/md5sum.txt to tests/md5sum.txt
config.status: linking data/tRex1.fa to tests/tRex1.fa
config.status: executing depfiles commands
=== configuring in src/smithlab_cpp (/Users/melaniesilvis/Documents/GitHub/abismal-3.2.2/src/smithlab_cpp)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/Users/melaniesilvis/Documents/GitHub/abismal-3.2.2'  'CXX=g++-13' 'CPPFLAGS=-I/opt/homebrew/include' 'LDFLAGS=-L/opt/homebrew/lib' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++-13 accepts -g... yes
checking for g++-13 option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++-13... gcc3
checking whether g++-13 supports C++17 features with -std=c++17... yes
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for ar... ar
checking the archiver (ar) interface... ar
checking for ranlib... ranlib
checking for zlibVersion in -lz... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands


(dnmtools_env) melaniesilvis@Melanie-Silvis-MacBook-Air abismal-3.2.2 % make
/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-recursive
Making all in src/smithlab_cpp
/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-am
depbase=`echo src/abismal.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
	g++-13 -std=c++17 -DHAVE_CONFIG_H -I.  -I ./src/smithlab_cpp -I ./src/bamxx -I/opt/homebrew/include -fopenmp -O3  -MT src/abismal.o -MD -MP -MF $depbase.Tpo -c -o src/abismal.o src/abismal.cpp &&\
	mv -f $depbase.Tpo $depbase.Po
src/abismal.cpp: In function 'void check_hits(uint32_t, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, const std::vector<unsigned int>::const_iterator&, std::vector<unsigned int>::const_iterator, result_type&)':
src/abismal.cpp:1006:18: error: '_MM_HINT_T0' was not declared in this scope
 1006 |                  _MM_HINT_T0);
      |                  ^~~~~~~~~~~
src/abismal.cpp:1005:5: error: there are no arguments to '_mm_prefetch' that depend on a template parameter, so a declaration of '_mm_prefetch' must be available [-fpermissive]
 1005 |     _mm_prefetch(&(*(genome_st + ((*(start_idx + 10) - offset) >> 4))),
      |     ^~~~~~~~~~~~
src/abismal.cpp:1005:5: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
src/abismal.cpp: In instantiation of 'void check_hits(uint32_t, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, const std::vector<unsigned int>::const_iterator&, std::vector<unsigned int>::const_iterator, result_type&) [with short unsigned int strand_code = 0; bool specific = true; result_type = se_candidates; uint32_t = unsigned int; std::vector<long unsigned int>::const_iterator = std::vector<long unsigned int>::const_iterator; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator]':
src/abismal.cpp:1188:36:   required from 'void process_seeds(uint32_t, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, genome_iterator, const Read&, const PackedRead&, result_type&) [with short unsigned int strand_code = 0; result_type = se_candidates; uint32_t = unsigned int; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator; genome_iterator = genome_four_bit_itr; Read = std::vector<unsigned char>; PackedRead = std::vector<long unsigned int>]'
src/abismal.cpp:1531:52:   required from here
src/abismal.cpp:1006:29: error: '_mm_prefetch' was not declared in this scope
 1006 |                  _MM_HINT_T0);
      |                             ^
src/abismal.cpp: In instantiation of 'void check_hits(uint32_t, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, const std::vector<unsigned int>::const_iterator&, std::vector<unsigned int>::const_iterator, result_type&) [with short unsigned int strand_code = 4096; bool specific = true; result_type = se_candidates; uint32_t = unsigned int; std::vector<long unsigned int>::const_iterator = std::vector<long unsigned int>::const_iterator; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator]':
src/abismal.cpp:1188:36:   required from 'void process_seeds(uint32_t, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, genome_iterator, const Read&, const PackedRead&, result_type&) [with short unsigned int strand_code = 4096; result_type = se_candidates; uint32_t = unsigned int; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator; genome_iterator = genome_four_bit_itr; Read = std::vector<unsigned char>; PackedRead = std::vector<long unsigned int>]'
src/abismal.cpp:1538:52:   required from here
src/abismal.cpp:1006:29: error: '_mm_prefetch' was not declared in this scope
src/abismal.cpp: In instantiation of 'void check_hits(uint32_t, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, const std::vector<unsigned int>::const_iterator&, std::vector<unsigned int>::const_iterator, result_type&) [with short unsigned int strand_code = 4112; bool specific = true; result_type = se_candidates; uint32_t = unsigned int; std::vector<long unsigned int>::const_iterator = std::vector<long unsigned int>::const_iterator; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator]':
src/abismal.cpp:1188:36:   required from 'void process_seeds(uint32_t, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, genome_iterator, const Read&, const PackedRead&, result_type&) [with short unsigned int strand_code = 4112; result_type = se_candidates; uint32_t = unsigned int; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator; genome_iterator = genome_four_bit_itr; Read = std::vector<unsigned char>; PackedRead = std::vector<long unsigned int>]'
src/abismal.cpp:1546:52:   required from here
src/abismal.cpp:1006:29: error: '_mm_prefetch' was not declared in this scope
src/abismal.cpp: In instantiation of 'void check_hits(uint32_t, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, const std::vector<unsigned int>::const_iterator&, std::vector<unsigned int>::const_iterator, result_type&) [with short unsigned int strand_code = 16; bool specific = true; result_type = se_candidates; uint32_t = unsigned int; std::vector<long unsigned int>::const_iterator = std::vector<long unsigned int>::const_iterator; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator]':
src/abismal.cpp:1188:36:   required from 'void process_seeds(uint32_t, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, genome_iterator, const Read&, const PackedRead&, result_type&) [with short unsigned int strand_code = 16; result_type = se_candidates; uint32_t = unsigned int; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator; genome_iterator = genome_four_bit_itr; Read = std::vector<unsigned char>; PackedRead = std::vector<long unsigned int>]'
src/abismal.cpp:1553:52:   required from here
src/abismal.cpp:1006:29: error: '_mm_prefetch' was not declared in this scope
src/abismal.cpp: In instantiation of 'void check_hits(uint32_t, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, const std::vector<unsigned int>::const_iterator&, std::vector<unsigned int>::const_iterator, result_type&) [with short unsigned int strand_code = 0; bool specific = true; result_type = pe_candidates; uint32_t = unsigned int; std::vector<long unsigned int>::const_iterator = std::vector<long unsigned int>::const_iterator; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator]':
src/abismal.cpp:1188:36:   required from 'void process_seeds(uint32_t, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, genome_iterator, const Read&, const PackedRead&, result_type&) [with short unsigned int strand_code = 0; result_type = pe_candidates; uint32_t = unsigned int; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator; genome_iterator = genome_four_bit_itr; Read = std::vector<unsigned char>; PackedRead = std::vector<long unsigned int>]'
src/abismal.cpp:1778:32:   required from 'bool map_fragments(uint32_t, const std::string&, const std::string&, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, genome_iterator, Read&, Read&, PackedRead&, bam_cigar_t&, bam_cigar_t&, AbismalAlignSimple&, pe_candidates&, pe_candidates&, std::vector<short int>&, se_candidates&, se_candidates&, pe_element&) [with bool cmp = false; bool swap_ends = false; short unsigned int strand_code1 = 0; short unsigned int strand_code2 = 4112; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator; genome_iterator = genome_four_bit_itr; Read = std::vector<unsigned char>; PackedRead = std::vector<long unsigned int>; bam_cigar_t = std::vector<unsigned int>; AbismalAlignSimple = AbismalAlign<simple_aln::mismatch_score, -4>]'
src/abismal.cpp:2058:52:   required from here
src/abismal.cpp:1006:29: error: '_mm_prefetch' was not declared in this scope
src/abismal.cpp: In instantiation of 'void check_hits(uint32_t, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, const std::vector<unsigned int>::const_iterator&, std::vector<unsigned int>::const_iterator, result_type&) [with short unsigned int strand_code = 4112; bool specific = true; result_type = pe_candidates; uint32_t = unsigned int; std::vector<long unsigned int>::const_iterator = std::vector<long unsigned int>::const_iterator; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator]':
src/abismal.cpp:1188:36:   required from 'void process_seeds(uint32_t, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, genome_iterator, const Read&, const PackedRead&, result_type&) [with short unsigned int strand_code = 4112; result_type = pe_candidates; uint32_t = unsigned int; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator; genome_iterator = genome_four_bit_itr; Read = std::vector<unsigned char>; PackedRead = std::vector<long unsigned int>]'
src/abismal.cpp:1787:32:   required from 'bool map_fragments(uint32_t, const std::string&, const std::string&, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, genome_iterator, Read&, Read&, PackedRead&, bam_cigar_t&, bam_cigar_t&, AbismalAlignSimple&, pe_candidates&, pe_candidates&, std::vector<short int>&, se_candidates&, se_candidates&, pe_element&) [with bool cmp = false; bool swap_ends = false; short unsigned int strand_code1 = 0; short unsigned int strand_code2 = 4112; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator; genome_iterator = genome_four_bit_itr; Read = std::vector<unsigned char>; PackedRead = std::vector<long unsigned int>; bam_cigar_t = std::vector<unsigned int>; AbismalAlignSimple = AbismalAlign<simple_aln::mismatch_score, -4>]'
src/abismal.cpp:2058:52:   required from here
src/abismal.cpp:1006:29: error: '_mm_prefetch' was not declared in this scope
src/abismal.cpp: In instantiation of 'void check_hits(uint32_t, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, const std::vector<unsigned int>::const_iterator&, std::vector<unsigned int>::const_iterator, result_type&) [with short unsigned int strand_code = 4096; bool specific = true; result_type = pe_candidates; uint32_t = unsigned int; std::vector<long unsigned int>::const_iterator = std::vector<long unsigned int>::const_iterator; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator]':
src/abismal.cpp:1188:36:   required from 'void process_seeds(uint32_t, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, genome_iterator, const Read&, const PackedRead&, result_type&) [with short unsigned int strand_code = 4096; result_type = pe_candidates; uint32_t = unsigned int; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator; genome_iterator = genome_four_bit_itr; Read = std::vector<unsigned char>; PackedRead = std::vector<long unsigned int>]'
src/abismal.cpp:1778:32:   required from 'bool map_fragments(uint32_t, const std::string&, const std::string&, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, genome_iterator, Read&, Read&, PackedRead&, bam_cigar_t&, bam_cigar_t&, AbismalAlignSimple&, pe_candidates&, pe_candidates&, std::vector<short int>&, se_candidates&, se_candidates&, pe_element&) [with bool cmp = true; bool swap_ends = true; short unsigned int strand_code1 = 4096; short unsigned int strand_code2 = 16; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator; genome_iterator = genome_four_bit_itr; Read = std::vector<unsigned char>; PackedRead = std::vector<long unsigned int>; bam_cigar_t = std::vector<unsigned int>; AbismalAlignSimple = AbismalAlign<simple_aln::mismatch_score, -4>]'
src/abismal.cpp:2066:52:   required from here
src/abismal.cpp:1006:29: error: '_mm_prefetch' was not declared in this scope
src/abismal.cpp: In instantiation of 'void check_hits(uint32_t, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, std::vector<long unsigned int>::const_iterator, const std::vector<unsigned int>::const_iterator&, std::vector<unsigned int>::const_iterator, result_type&) [with short unsigned int strand_code = 16; bool specific = true; result_type = pe_candidates; uint32_t = unsigned int; std::vector<long unsigned int>::const_iterator = std::vector<long unsigned int>::const_iterator; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator]':
src/abismal.cpp:1188:36:   required from 'void process_seeds(uint32_t, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, genome_iterator, const Read&, const PackedRead&, result_type&) [with short unsigned int strand_code = 16; result_type = pe_candidates; uint32_t = unsigned int; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator; genome_iterator = genome_four_bit_itr; Read = std::vector<unsigned char>; PackedRead = std::vector<long unsigned int>]'
src/abismal.cpp:1787:32:   required from 'bool map_fragments(uint32_t, const std::string&, const std::string&, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, std::vector<unsigned int>::const_iterator, genome_iterator, Read&, Read&, PackedRead&, bam_cigar_t&, bam_cigar_t&, AbismalAlignSimple&, pe_candidates&, pe_candidates&, std::vector<short int>&, se_candidates&, se_candidates&, pe_element&) [with bool cmp = true; bool swap_ends = true; short unsigned int strand_code1 = 4096; short unsigned int strand_code2 = 16; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::vector<unsigned int>::const_iterator = std::vector<unsigned int>::const_iterator; genome_iterator = genome_four_bit_itr; Read = std::vector<unsigned char>; PackedRead = std::vector<long unsigned int>; bam_cigar_t = std::vector<unsigned int>; AbismalAlignSimple = AbismalAlign<simple_aln::mismatch_score, -4>]'
src/abismal.cpp:2066:52:   required from here
src/abismal.cpp:1006:29: error: '_mm_prefetch' was not declared in this scope
make[2]: *** [src/abismal.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
```

[andrewdavidsmith]

@melaniesilvis-epic I think this is because of the M1 hardware. Currently abismal won't build on M1 and I can't fix it because my mac is x86. I'll get a new one probably in the next month or so and should be able to fix this. I was able to see it in action using the github runner for macos with M1. I'll update this issue accordingly.