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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
271 stars 49 forks source link

racon install #72

Closed Ruby2018 closed 6 years ago

Ruby2018 commented 6 years ago

I tried to install racon-v1.3.0 on the Linux cluster with gcc version 5.3.0 and the cmake version 3.9.3. I got the following errors with make, would you help me check the problem? Thanks

Scanning dependencies of target edlib_static [ 3%] Building CXX object vendor/edlib/CMakeFiles/edlib_static.dir/edlib/src/edlib.cpp.o [ 6%] Linking CXX static library ../../lib/libedlib_static.a [ 6%] Built target edlib_static Scanning dependencies of target zlibstatic [ 9%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/adler32.o [ 12%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/compress.o [ 16%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/crc32.o [ 19%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/deflate.o [ 22%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzclose.o [ 25%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzlib.o [ 29%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzread.o [ 32%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzwrite.o [ 35%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inflate.o [ 38%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/infback.o [ 41%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inftrees.o [ 45%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inffast.o [ 48%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/trees.o [ 51%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/uncompr.o [ 54%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/zutil.o [ 58%] Linking C static library ../../lib/libz.a [ 58%] Built target zlibstatic Scanning dependencies of target spoa [ 61%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o [ 64%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/graph.cpp.o /tmp/ccYssBBl.s: Assembler messages: /tmp/ccYssBBl.s:5841: Error: no such instruction: vpbroadcastd %xmm0,%ymm0' /tmp/ccYssBBl.s:5989: Error: no such instruction:vpbroadcastd %xmm0,%ymm0' /tmp/ccYssBBl.s:6099: Error: no such instruction: vpbroadcastd %xmm0,%ymm0' /tmp/ccYssBBl.s:6289: Error: no such instruction:vpbroadcastd %xmm0,%ymm0' /tmp/ccYssBBl.s:6540: Error: no such instruction: shlx %r9,%r15,%rax' /tmp/ccYssBBl.s:6552: Error: no such instruction:shlx %r10,%r15,%r14' /tmp/ccYssBBl.s:6645: Error: no such instruction: vpbroadcastq %xmm1,%ymm0' /tmp/ccYssBBl.s:6679: Error: no such instruction:shlx %rbx,%rsi,%rdx' /tmp/ccYssBBl.s:6697: Error: no such instruction: shlx %rdx,%r8,%rcx' /tmp/ccYssBBl.s:6744: Error: no such instruction:shlx %rbx,%rsi,%rdx' /tmp/ccYssBBl.s:6761: Error: no such instruction: shlx %rdx,%r8,%rsi' /tmp/ccYssBBl.s:6772: Error: no such instruction:shlx %rdx,%r8,%rsi' /tmp/ccYssBBl.s:6864: Error: no such instruction: shlx %rax,%r8,%rcx' /tmp/ccYssBBl.s:6865: Error: no such instruction:shlx %rsi,%r8,%r9' /tmp/ccYssBBl.s:6969: Error: no such instruction: vpbroadcastq %xmm2,%ymm0' /tmp/ccYssBBl.s:7003: Error: no such instruction:shlx %rax,%r9,%rdi' /tmp/ccYssBBl.s:7021: Error: no such instruction: shlx %rax,%r8,%rdx' /tmp/ccYssBBl.s:7062: Error: no such instruction:shlx %rdx,%rdi,%rax' /tmp/ccYssBBl.s:7063: Error: no such instruction: shlx %rbx,%rdi,%r8' /tmp/ccYssBBl.s:7109: Error: no such instruction:shlx %rax,%r9,%rdi' /tmp/ccYssBBl.s:7126: Error: no such instruction: shlx %rax,%r8,%rdi' /tmp/ccYssBBl.s:7229: Error: no such instruction:shlx %rbx,%rsi,%rcx' /tmp/ccYssBBl.s:7258: Error: no such instruction: shlx %rbx,%rsi,%rdx' /tmp/ccYssBBl.s:7283: Error: no such instruction:shlx %rax,%r8,%rdi' /tmp/ccYssBBl.s:7305: Error: no such instruction: shlx %rax,%r8,%rdx' /tmp/ccYssBBl.s:7887: Error: no such instruction:vpbroadcastd %xmm0,%ymm0' /tmp/ccYssBBl.s:8035: Error: no such instruction: vpbroadcastd %xmm0,%ymm0' /tmp/ccYssBBl.s:8145: Error: no such instruction:vpbroadcastd %xmm0,%ymm0' /tmp/ccYssBBl.s:8335: Error: no such instruction: vpbroadcastd %xmm0,%ymm0' /tmp/ccYssBBl.s:11075: Error: no such instruction:vpbroadcastd %xmm0,%ymm0' /tmp/ccYssBBl.s:11501: Error: no such instruction: `vpbroadcastd %xmm0,%ymm0' make[2]: [vendor/spoa/CMakeFiles/spoa.dir/src/graph.cpp.o] Error 1 make[1]: [vendor/spoa/CMakeFiles/spoa.dir/all] Error 2 make: *** [all] Error 2

rvaser commented 6 years ago

Hello, it seems that the assembler is either out of date or it is in disagreement with the compiler regarding AVX2 instructions. You can try and add -mno-avx to vendor/spoa/CMakeLists.txt at the end of CMAKE_CXX_FLAGS at line 8 or update the assembler or check whether another compiler works.

Best regards, Robert

Ruby2018 commented 6 years ago

Thanks Robert: Thanks for pointing the location of CMakeLists.txt, I knew it could be the problem of my compiler, and should related to the set up of CMAKE_CXX_FLAGS, couldn't find the location.

Now I set up line8 in both files of "vendor/spoa/CMakeLists.txt" and "vendor/thread_pool/CMakeLists.txt", with "-march=corei7", it seems compiling successfully.

Thanks for the help. Best