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veg / hyphy-analyses

HyPhy standalone analyses
MIT License
38 stars 17 forks source link

fail to make #32

Open Xiaojun928 opened 1 year ago

Xiaojun928 commented 1 year ago

Hi,

Thanks for developing this great tool! After successfully running cmake ./, I got the error when running make -j MP like below. I did not find a similar issue in this repo. I really appreciate any help you can provide. 

$ make -j MP
[  0%] Building CXX object CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o
[  0%] Building CXX object CMakeFiles/hyphy.dir/src/core/alignment.cpp.o
[  4%] Building CXX object CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o
[  4%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.cpp.o
[  4%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o
[  8%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o
[  8%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o
[ 12%] Building CXX object CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o
[ 12%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o
[ 16%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o
[ 16%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o
[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o
[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o
[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o
[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/category.cpp.o
[ 24%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset.cpp.o
[ 24%] Building CXX object CMakeFiles/hyphy.dir/src/core/constant.cpp.o
[ 24%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o
[ 28%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o
[ 32%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula.cpp.o
[ 32%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o
[ 32%] Building CXX object CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o
[ 32%] Building CXX object CMakeFiles/hyphy.dir/src/core/fstring.cpp.o
[ 32%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o
[ 32%] Building CXX object CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o
[ 36%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_things.cpp.o
[ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o
[ 44%] Building CXX object CMakeFiles/hyphy.dir/src/core/list.cpp.o
[ 44%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o
[ 44%] Building CXX object CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o
[ 44%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o
[ 44%] Building CXX object CMakeFiles/hyphy.dir/src/core/matrix.cpp.o
[ 44%] Building CXX object CMakeFiles/hyphy.dir/src/core/nexus.cpp.o
[ 48%] Building CXX object CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o
[ 48%] Building CXX object CMakeFiles/hyphy.dir/src/core/operation.cpp.o
[ 52%] Building CXX object CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o
[ 52%] Building CXX object CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o
[ 56%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser2.cpp.o
[ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/site.cpp.o
[ 64%] Building CXX object CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o
[ 64%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser.cpp.o
[ 64%] Building CXX object CMakeFiles/hyphy.dir/src/core/stack.cpp.o
[ 64%] Building CXX object CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o
[ 64%] Building CXX object CMakeFiles/hyphy.dir/src/core/strings.cpp.o
[ 64%] Building CXX object CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o
[ 68%] Building CXX object CMakeFiles/hyphy.dir/src/core/topology.cpp.o
[ 68%] Building CXX object CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o
[ 68%] Building CXX object CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o
[ 68%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o
[ 72%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree.cpp.o
[ 72%] Building CXX object CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o
[ 72%] Building CXX object CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o
[ 72%] Building CXX object CMakeFiles/hyphy.dir/src/core/vector.cpp.o
[ 76%] Building CXX object CMakeFiles/hyphy.dir/src/core/variable.cpp.o
[ 76%] Building CXX object CMakeFiles/hyphy.dir/src/core/trie.cpp.o
[ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o
[ 84%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o
[ 84%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o
[ 84%] Building CXX object CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o
[ 88%] Building C object CMakeFiles/hyphy.dir/contrib/SQLite-3.8.2/sqlite3.c.o
[ 88%] Building CXX object CMakeFiles/hyphy.dir/src/new/scfg.cpp.o
[ 92%] Building CXX object CMakeFiles/hyphy.dir/src/new/bgm.cpp.o
[ 92%] Building CXX object CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o
[ 92%] Building CXX object CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o
[ 96%] Building CXX object CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o
[ 96%] Building CXX object CMakeFiles/hyphy.dir/src/mains/unix.cpp.o
/share/software/hyphy-develop/src/core/matrix_mult.cpp: In function 'void _hy_matrix_multiply_4x4x2(double*, double*, double*, int, bool)':
/share/software/hyphy-develop/src/core/matrix_mult.cpp:2622:10: error: '_mm256_set_m128d' was not declared in this scope
     A1 = _mm256_set_m128d  (_mm_loaddup_pd (A+S1), _mm_loaddup_pd (A));       // 00,00,10,10
          ^~~~~~~~~~~~~~~~
/share/software/hyphy-develop/src/core/matrix_mult.cpp:2622:10: note: suggested alternative: '_mm256_set1_pd'
     A1 = _mm256_set_m128d  (_mm_loaddup_pd (A+S1), _mm_loaddup_pd (A));       // 00,00,10,10
          ^~~~~~~~~~~~~~~~
          _mm256_set1_pd
/share/software/hyphy-develop/src/core/matrix_mult.cpp:2624:10: error: '_mm256_loadu2_m128d' was not declared in this scope
     B1 = _mm256_loadu2_m128d  (B,B);      // 00,01 x 2
          ^~~~~~~~~~~~~~~~~~~
/share/software/hyphy-develop/src/core/matrix_mult.cpp:2624:10: note: suggested alternative: '_mm256_loadu_si256'
     B1 = _mm256_loadu2_m128d  (B,B);      // 00,01 x 2
          ^~~~~~~~~~~~~~~~~~~
          _mm256_loadu_si256
make[3]: *** [CMakeFiles/hyphy.dir/build.make:524: CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[2]: *** [CMakeFiles/Makefile2:143: CMakeFiles/hyphy.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:98: CMakeFiles/MP.dir/rule] Error 2
make: *** [Makefile:179: MP] Error 2

Kind regards, Xiaojun

spond commented 1 year ago

Dear @Xiaojun928,

What C/C++ compilers are you using?

Best, Sergei

Xiaojun928 commented 1 year ago

Hi Sergei,

Thanks for your quick reply. I am using GCC (g++) as the compiler.

Best, Xiaojun

Xiaojun928 commented 1 year ago

And the version is 6.1.0

spond commented 1 year ago

Dear @Xiaojun928,

Looks like this is a GCC bug (missing intrinsics) for versions prior to version 8 (the current version is 12+). Is it possible for you to upgrade to a newer GCC version?

Best, Sergei

Xiaojun928 commented 1 year ago

Dear Sergei,

Thanks for your advice. I cannot upgrade gcc without root privilege. I also tried to install a newer one but failed. So I compiled hyphy-develop on another Ubuntu OS with a newer GCC (9.3.0), but the error persists.

 $ cmake ./
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test HAVE_AVX_EXTENSIONS
-- Performing Test HAVE_AVX_EXTENSIONS - Success
-- Performing Test HAVE_FMA3
-- Performing Test HAVE_FMA3 - Success
-- Performing Test HAVE_NEON_EXTENSIONS
-- Performing Test HAVE_NEON_EXTENSIONS - Failed
Set default compiler flags to -fsigned-char -O3 -std=c++14 -g -march=native -mtune=native -mavx2  -mfma
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Could NOT find CURL (missing: CURL_LIBRARY CURL_INCLUDE_DIR)
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found suitable version "1.2.11", minimum required is "1.2.9")
Node not installed; API documentation will not be generated
-- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS)
-- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS)
-- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND)
-- Configuring done
-- Generating done
-- Build files have been written to: /home/xiaojun/hyphy-develop
$ make -j MP
Scanning dependencies of target hyphy
[  0%] Building CXX object CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o
[  8%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.cpp.o
[  8%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o
[  8%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o
[  8%] Building CXX object CMakeFiles/hyphy.dir/src/core/alignment.cpp.o
[  8%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o
[  8%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o
[  8%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o
[  8%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o
[  8%] Building CXX object CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o
[ 12%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o
[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o
[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o
[ 12%] Building CXX object CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o
[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/category.cpp.o
[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/constant.cpp.o
[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o
[ 28%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o
[ 28%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset.cpp.o
[ 28%] Building CXX object CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o
[ 28%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula.cpp.o
[ 32%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o
[ 32%] Building CXX object CMakeFiles/hyphy.dir/src/core/fstring.cpp.o
[ 32%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o
[ 32%] Building CXX object CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o
[ 36%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_things.cpp.o
[ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o
[ 44%] Building CXX object CMakeFiles/hyphy.dir/src/core/list.cpp.o
[ 44%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o
[ 44%] Building CXX object CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o
[ 44%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o
[ 44%] Building CXX object CMakeFiles/hyphy.dir/src/core/matrix.cpp.o
[ 44%] Building CXX object CMakeFiles/hyphy.dir/src/core/nexus.cpp.o
[ 48%] Building CXX object CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o
[ 48%] Building CXX object CMakeFiles/hyphy.dir/src/core/operation.cpp.o
[ 52%] Building CXX object CMakeFiles/hyphy.dir/src/core/ntuplestorage.cpp.o
[ 56%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser2.cpp.o
[ 56%] Building CXX object CMakeFiles/hyphy.dir/src/core/parser.cpp.o
[ 56%] Building CXX object CMakeFiles/hyphy.dir/src/core/simplelist.cpp.o
[ 56%] Building CXX object CMakeFiles/hyphy.dir/src/core/stack.cpp.o
[ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/site.cpp.o
[ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/string_file_wrapper.cpp.o
[ 64%] Building CXX object CMakeFiles/hyphy.dir/src/core/string_buffer.cpp.o
[ 60%] Building CXX object CMakeFiles/hyphy.dir/src/core/polynoml.cpp.o
[ 64%] Building CXX object CMakeFiles/hyphy.dir/src/core/strings.cpp.o
[ 68%] Building CXX object CMakeFiles/hyphy.dir/src/core/time_difference.cpp.o
[ 72%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree.cpp.o
[ 72%] Building CXX object CMakeFiles/hyphy.dir/src/core/translation_table.cpp.o
[ 72%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_evaluator.cpp.o
[ 72%] Building CXX object CMakeFiles/hyphy.dir/src/core/topology.cpp.o
[ 76%] Building CXX object CMakeFiles/hyphy.dir/src/core/tree_iterator.cpp.o
[ 76%] Building CXX object CMakeFiles/hyphy.dir/src/core/trie.cpp.o
[ 76%] Building CXX object CMakeFiles/hyphy.dir/src/core/trie_iterator.cpp.o
[ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/variable.cpp.o
[ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/variablecontainer.cpp.o
[ 80%] Building CXX object CMakeFiles/hyphy.dir/src/core/vector.cpp.o
[ 84%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph.cpp.o
[ 84%] Building CXX object CMakeFiles/hyphy.dir/src/new/bayesgraph2.cpp.o
[ 84%] Building CXX object CMakeFiles/hyphy.dir/src/new/bgm2.cpp.o
[ 88%] Building CXX object CMakeFiles/hyphy.dir/src/new/scfg.cpp.o
[ 92%] Building C object CMakeFiles/hyphy.dir/contrib/SQLite-3.8.2/sqlite3.c.o
[ 92%] Building CXX object CMakeFiles/hyphy.dir/src/new/bgm.cpp.o
[ 92%] Building CXX object CMakeFiles/hyphy.dir/src/utils/hyphyunixutils.cpp.o
[ 92%] Building CXX object CMakeFiles/hyphy.dir/src/contrib/mersenne_twister.cpp.o
[ 96%] Building CXX object CMakeFiles/hyphy.dir/src/contrib/regex.cpp.o
[ 96%] Building CXX object CMakeFiles/hyphy.dir/src/mains/unix.cpp.o
/home/xiaojun/hyphy-develop/src/core/matrix_mult.cpp: In function ‘void _hy_matrix_multiply_4x4x2(double*, double*, double*, int, bool)’:
/home/xiaojun/hyphy-develop/src/core/matrix_mult.cpp:2624:10: error: ‘_mm256_loadu2_m128d’ was not declared in this scope; did you mean ‘_mm256_loadu_si256’?
 2624 |     B1 = _mm256_loadu2_m128d  (B,B);      // 00,01 x 2
      |          ^~~~~~~~~~~~~~~~~~~
      |          _mm256_loadu_si256
make[3]: *** [CMakeFiles/hyphy.dir/build.make:479: CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[2]: *** [CMakeFiles/Makefile2:84: CMakeFiles/hyphy.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:307: CMakeFiles/MP.dir/rule] Error 2
make: *** [Makefile:279: MP] Error 2

Best, Xiaojun

spond commented 1 year ago

Dear @Xiaojun928,

Try version 2.5.46 (just released). I replaced _mm256_loadu2_m128d with a different instruction that is supported by older (pre 10) GCC versions.

Best, Sergei

Xiaojun928 commented 1 year ago

Dear Sergei,

Many thanks for your help! I downloaded the latest version and complied it by following the guide here, while the same error persists for make -j MP.

Since my goal is to using modules in hyphy-analyses, I tried to build hyphy form source by following your guide here. 

git clone https://github.com/veg/hyphy.git
cd hyphy
cmake .
make install

As make -j MP was skipped this time, no error was reported. Then the modules in HyPhy standalone analyses could work now. It seems that make -j MP for hyphy-develop is not neccessary. Alternatively, building hyphy from source is enough if we want to use modules in Hyphy analyses? Please correct me if I am wrong. Thanks a lot!

Best, Xiaojun

spond commented 1 year ago

Dear @Xiaojun928,

My apologies. I managed not to commit the compilation fix to 2.5.46. It is in the develop branch now. Please give it a try

git clone https://github.com/veg/hyphy.git
cd hyphy
git checkout develop
cmake .
make install

Best, Sergei

Xiaojun928 commented 1 year ago

Dear Sergei,

Thanks a lot for your help! I tried as you suggested, but I failed to make install. Here is the log.

$ git checkout develop
Branch develop set up to track remote branch develop from origin.
Switched to a new branch 'develop'
(base) [xjwang@cl001 hyphy]$ cmake .
-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /home-user/xjwang/miniconda3/bin/x86_64-conda_cos6-linux-gnu-cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /home-user/xjwang/miniconda3/bin/x86_64-conda_cos6-linux-gnu-c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test HAVE_AVX_EXTENSIONS
-- Performing Test HAVE_AVX_EXTENSIONS - Success
-- Performing Test HAVE_FMA3
-- Performing Test HAVE_FMA3 - Success
-- Performing Test HAVE_NEON_EXTENSIONS
-- Performing Test HAVE_NEON_EXTENSIONS - Failed
Set default compiler flags to -fsigned-char -O3 -std=c++14 -g -march=native -mtune=native -mavx2  -mfma
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) 
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) 
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) 
-- Found CURL: /home-user/xjwang/miniconda3/lib/libcurl.so (found version "7.71.1")  
/home-user/xjwang/miniconda3/lib/libcurl.so
-- Found ZLIB: /home-user/xjwang/miniconda3/lib/libz.so (found suitable version "1.2.11", minimum required is "1.2.9") 
Node not installed; API documentation will not be generated
-- Found MPI_C: /home-user/xjwang/miniconda3/lib/libmpi.so (found version "3.1") 
-- Found MPI_CXX: /home-user/xjwang/miniconda3/lib/libmpi.so (found version "3.1") 
-- Found MPI: TRUE (found version "3.1")  
-fsigned-char -O3 -std=c++14 -g -march=native -mtune=native -mavx2  -mfma   -Wl,-rpath,/home-user/xjwang/miniconda3/lib -pthread NOTFOUND
-- Configuring done
-- Generating done
-- Build files have been written to: /home-user/software/hyphy
(base) [xjwang@cl001 hyphy]$ make install
Scanning dependencies of target hyphy
[  0%] Building CXX object CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o
[  0%] Building CXX object CMakeFiles/hyphy.dir/src/core/alignment.cpp.o
[  0%] Building CXX object CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o
[  5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.cpp.o
[  5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o
[  5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o
[ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o
[ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o
[ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o
[ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o
[ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o
[ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o
[ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o
[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o
[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/category.cpp.o
[ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/constant.cpp.o
[ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset.cpp.o
[ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o
[ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o
[ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o
[ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula.cpp.o
[ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o
[ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/fstring.cpp.o
[ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o
[ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_things.cpp.o
[ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o
[ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o
[ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o
[ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefuncocl.cpp.o
[ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/list.cpp.o
[ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/mathobj.cpp.o
[ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/matrix.cpp.o
[ 45%] Building CXX object CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o
/home-user/software/hyphy/src/core/matrix_mult.cpp: In function 'void _hy_matrix_multiply_4x4x2(double*, double*, double*, int, bool)':
/home-user/software/hyphy/src/core/matrix_mult.cpp:2622:10: error: '_mm256_set_m128d' was not declared in this scope
     A1 = _mm256_set_m128d  (_mm_loaddup_pd (A+S1), _mm_loaddup_pd (A));       // 00,00,10,10
          ^~~~~~~~~~~~~~~~
/home-user/software/hyphy/src/core/matrix_mult.cpp:2622:10: note: suggested alternative: '_mm256_set1_pd'
     A1 = _mm256_set_m128d  (_mm_loaddup_pd (A+S1), _mm_loaddup_pd (A));       // 00,00,10,10
          ^~~~~~~~~~~~~~~~
          _mm256_set1_pd
make[2]: *** [CMakeFiles/hyphy.dir/src/core/matrix_mult.cpp.o] Error 1
make[1]: *** [CMakeFiles/hyphy.dir/all] Error 2
make: *** [all] Error 2

Best, Xiaojun

spond commented 1 year ago

Dear @Xiaojun928,

Making progress. This is a different error. Let me look into that; just to check -- what is the GCC version for the latest error?

Best, Sergei

PS _mm256_set_m128d is supported by GCC as of version 8.1

Xiaojun928 commented 1 year ago

Dear Sergei,

The latest error was reported if using GCC 6.1.0. And make install works well if using GCC 9.3.0.

Best, Xiaojun