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HyPhy: Hypothesis testing using Phylogenies
http://www.hyphy.org
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Compile error #1564 persists in version 2.4.47 (Ubuntu 20.04.5) #1572

Closed mjeltsch closed 1 year ago

mjeltsch commented 1 year ago

Hi, 2.4.47 does not solve the problem for me. Same issue as previously reported.

/home/mjeltsch/Documents/Informatics/hyphy-2.5.47/src/core/matrix_mult.cpp: In function ‘void _hy_matrix_multiply_4x4x2(double, double, double*, int, bool)’: /home/mjeltsch/Documents/Informatics/hyphy-2.5.47/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/Makefile2:141: CMakeFiles/hyphy.dir/all] Error 2 make[1]: [CMakeFiles/Makefile2:391: CMakeFiles/MP.dir/rule] Error 2 make: *** [Makefile:318: MP] Error 2

I would need this asap (12 days to deadline for revision...). I guess I just need to find a newer system to install this, correct? Cheers, Michael `

spond commented 1 year ago

Dear @mjeltsch,

Bummer. Can you tell me which version of C/C++ cmake finds (just paste whatever cmake outputs when the second command in the set below)?

In the meantime, you should be able to compile by turning off avx2 extensions. Do the following (from the HyPhy directory)

rm -rf CMakeFiles CMakeCache.txt
cmake -DNOAVX=ON ./
make

Best, Sergei

mjeltsch commented 1 year ago

mjeltsch@ubuntu2004:~/Documents/Informatics/hyphy-2.5.47$ cmake -DNOAVX=ON ./ -- The C compiler identification is GNU 9.4.0 -- The CXX compiler identification is GNU 9.4.0 -- 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_SSE4_EXTENSIONS -- Performing Test HAVE_SSE4_EXTENSIONS - Success -- Performing Test HAVE_NEON_EXTENSIONS -- Performing Test HAVE_NEON_EXTENSIONS - Failed Set default compiler flags to -fsigned-char -O3 -std=c++14 -g -mno-avx -msse4.1 -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5")
-- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.68.0")
/usr/lib/x86_64-linux-gnu/libcurl.so -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found suitable version "1.2.11", minimum required is "1.2.9") -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1")
-fsigned-char -O3 -std=c++14 -g -mno-avx -msse4.1 -pthread -fopenmp -- Configuring done -- Generating done -- Build files have been written to: /home/mjeltsch/Documents/Informatics/hyphy-2.5.47

mjeltsch commented 1 year ago

The build completed successfully using your instructions! Thanks!

github-actions[bot] commented 1 year ago

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