Problems with compiling ...

[ocho]

Could you help me further? I tried different compilers with no success:

cmake -DCMAKE_BUILD_TYPE=Release .. && make
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
-- Check for working C compiler: /home/prog/gcc/gcc-7.4.0/bin/gcc
-- Check for working C compiler: /home/prog/gcc/gcc-7.4.0/bin/gcc -- 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: /home/prog/gcc/gcc-7.4.0/bin/g++
-- Check for working CXX compiler: /home/prog/gcc/gcc-7.4.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of off64_t
-- Check size of off64_t - done
-- Looking for fseeko
-- Looking for fseeko - found
-- Looking for unistd.h
-- Looking for unistd.h - found
Setting warning flags
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ms257013/bin/ra/build
Scanning dependencies of target minimap2
[  0%] Built target minimap2
Scanning dependencies of target thread_pool
[  2%] Building CXX object vendor/rala/vendor/thread_pool/CMakeFiles/thread_pool.dir/src/thread_pool.cpp.o
[  5%] Linking CXX static library lib/libthread_pool.a
[  5%] Built target thread_pool
Scanning dependencies of target zlibstatic
[  7%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/adler32.o
[ 10%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/compress.o
[ 13%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/crc32.o
[ 15%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/deflate.o
[ 18%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzclose.o
[ 21%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzlib.o
[ 23%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzread.o
[ 26%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzwrite.o
[ 28%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inflate.o
[ 31%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/infback.o
[ 34%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inftrees.o
[ 36%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inffast.o
[ 39%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/trees.o
[ 42%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/uncompr.o
[ 44%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/zutil.o
[ 47%] Linking C static library ../../lib/libz.a
[ 47%] Built target zlibstatic
Scanning dependencies of target rala
[ 50%] Building CXX object vendor/rala/CMakeFiles/rala.dir/src/graph.cpp.o
[ 52%] Building CXX object vendor/rala/CMakeFiles/rala.dir/src/main.cpp.o
[ 55%] Building CXX object vendor/rala/CMakeFiles/rala.dir/src/overlap.cpp.o
[ 57%] Building CXX object vendor/rala/CMakeFiles/rala.dir/src/pile.cpp.o
[ 60%] Building CXX object vendor/rala/CMakeFiles/rala.dir/src/sequence.cpp.o
[ 63%] Building CXX object vendor/rala/CMakeFiles/rala.dir/src/timer.cpp.o
[ 65%] Linking CXX executable bin/rala
[ 65%] Built target rala
Scanning dependencies of target edlib_static
[ 68%] Building CXX object vendor/racon/vendor/edlib/CMakeFiles/edlib_static.dir/edlib/src/edlib.cpp.o
[ 71%] Linking CXX static library ../../../../lib/libedlib_static.a
[ 71%] Built target edlib_static
Scanning dependencies of target spoa
[ 73%] Building CXX object vendor/racon/vendor/spoa/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o
[ 76%] Building CXX object vendor/racon/vendor/spoa/CMakeFiles/spoa.dir/src/graph.cpp.o
/tmp/cc3avReL.s: Assembler messages:
/tmp/cc3avReL.s:3615: Error: no such instruction: `vpbroadcastd %xmm0,%ymm0'
/tmp/cc3avReL.s:3760: Error: no such instruction: `vpbroadcastd %xmm0,%ymm0'
/tmp/cc3avReL.s:3887: Error: no such instruction: `vpbroadcastd %xmm0,%ymm0'
/tmp/cc3avReL.s:4055: Error: no such instruction: `vpbroadcastd %xmm0,%ymm0'
/tmp/cc3avReL.s:5249: Error: no such instruction: `vpbroadcastd %xmm0,%ymm0'
/tmp/cc3avReL.s:5394: Error: no such instruction: `vpbroadcastd %xmm0,%ymm0'
/tmp/cc3avReL.s:5521: Error: no such instruction: `vpbroadcastd %xmm0,%ymm0'
/tmp/cc3avReL.s:5689: Error: no such instruction: `vpbroadcastd %xmm0,%ymm0'
/tmp/cc3avReL.s:6709: Error: no such instruction: `shlx %rax,%rdi,%rax'
/tmp/cc3avReL.s:6722: Error: no such instruction: `shlx %rax,%rdi,%rax'
/tmp/cc3avReL.s:6731: Error: no such instruction: `shlx %r11,%rdi,%r11'
/tmp/cc3avReL.s:7065: Error: no such instruction: `shlx %r10,%rax,%r14'
/tmp/cc3avReL.s:7071: Error: no such instruction: `shlx %r9,%rax,%rax'
/tmp/cc3avReL.s:7137: Error: no such instruction: `vpbroadcastq %xmm1,%ymm0'
/tmp/cc3avReL.s:7201: Error: no such instruction: `shlx %rbx,%r8,%rsi'
/tmp/cc3avReL.s:7289: Error: no such instruction: `shlx %rcx,%r9,%rsi'
/tmp/cc3avReL.s:7327: Error: no such instruction: `shlx %rcx,%r9,%r8'
/tmp/cc3avReL.s:7335: Error: no such instruction: `shlx %rcx,%r9,%r8'
/tmp/cc3avReL.s:7404: Error: no such instruction: `shlx %rax,%r10,%rsi'
/tmp/cc3avReL.s:7478: Error: no such instruction: `vpbroadcastq %xmm2,%ymm0'
/tmp/cc3avReL.s:7545: Error: no such instruction: `shlx %rax,%rdi,%rsi'
/tmp/cc3avReL.s:7573: Error: no such instruction: `shlx %rax,%rsi,%rdx'
/tmp/cc3avReL.s:7582: Error: no such instruction: `shlx %rax,%rsi,%rdx'
/tmp/cc3avReL.s:7618: Error: no such instruction: `shlx %r13,%rdi,%rax'
/tmp/cc3avReL.s:7619: Error: no such instruction: `shlx %rbx,%rdi,%r8'
/tmp/cc3avReL.s:7649: Error: no such instruction: `shlx %rax,%rsi,%rcx'
/tmp/cc3avReL.s:7657: Error: no such instruction: `shlx %rax,%rsi,%rcx'
/tmp/cc3avReL.s:7691: Error: no such instruction: `shlx %rbx,%r8,%rcx'
/tmp/cc3avReL.s:7700: Error: no such instruction: `shlx %rbx,%r8,%rcx'
/tmp/cc3avReL.s:7730: Error: no such instruction: `shlx %rbx,%r8,%rsi'
/tmp/cc3avReL.s:7738: Error: no such instruction: `shlx %rbx,%r8,%rsi'
/tmp/cc3avReL.s:7761: Error: no such instruction: `shlx %rax,%rsi,%rcx'
/tmp/cc3avReL.s:7770: Error: no such instruction: `shlx %rax,%rsi,%rcx'
/tmp/cc3avReL.s:7791: Error: no such instruction: `shlx %rax,%rsi,%rcx'
/tmp/cc3avReL.s:8126: Error: no such instruction: `shlx %r9,%rbx,%r12'
/tmp/cc3avReL.s:8222: Error: no such instruction: `shlx %rbx,%rsi,%r12'
/tmp/cc3avReL.s:8535: Error: no such instruction: `shlx %rax,%r14,%r8'
/tmp/cc3avReL.s:8545: Error: no such instruction: `shlx %rax,%r14,%rdi'
/tmp/cc3avReL.s:8612: Error: no such instruction: `shlx %rax,%r14,%rax'
/tmp/cc3avReL.s:9529: Error: no such instruction: `vpbroadcastd %xmm0,%ymm0'
/tmp/cc3avReL.s:9992: Error: no such instruction: `vpbroadcastd %xmm0,%ymm0'
/tmp/cc3avReL.s:10527: Error: no such instruction: `shlx %r12,%rdx,%rdx'
/tmp/cc3avReL.s:10606: Error: no such instruction: `shlx %r11,%r10,%r9'
make[2]: *** [vendor/racon/vendor/spoa/CMakeFiles/spoa.dir/src/graph.cpp.o] Error 1
make[1]: *** [vendor/racon/vendor/spoa/CMakeFiles/spoa.dir/all] Error 2
make: *** [all] Error 2

build > export CXX=/home/prog/gcc/gcc-5.4.0/bin/g++
 build > export CC=/home/prog/gcc/gcc-5.4.0/bin/gcc
 build > cmake -DCMAKE_BUILD_TYPE=Release .. && make
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /home/prog/gcc/gcc-5.4.0/bin/gcc
-- Check for working C compiler: /home/prog/gcc/gcc-5.4.0/bin/gcc -- 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: /home/prog/gcc/gcc-5.4.0/bin/g++
-- Check for working CXX compiler: /home/prog/gcc/gcc-5.4.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of off64_t
-- Check size of off64_t - done
-- Looking for fseeko
-- Looking for fseeko - found
-- Looking for unistd.h
-- Looking for unistd.h - found
Setting warning flags
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ms257013/bin/ra/build
Scanning dependencies of target minimap2
[  0%] Built target minimap2
Scanning dependencies of target thread_pool
[  2%] Building CXX object vendor/rala/vendor/thread_pool/CMakeFiles/thread_pool.dir/src/thread_pool.cpp.o
/tmp/cc9xYZfp.s: Assembler messages:
/tmp/cc9xYZfp.s:2106: Error: no such instruction: `vinserti128 $0x1,%xmm2,%ymm1,%ymm1'
/tmp/cc9xYZfp.s:2110: Error: no such instruction: `vinserti128 $0x1,%xmm1,%ymm0,%ymm0'
make[2]: *** [vendor/rala/vendor/thread_pool/CMakeFiles/thread_pool.dir/src/thread_pool.cpp.o] Error 1
make[1]: *** [vendor/rala/vendor/thread_pool/CMakeFiles/thread_pool.dir/all] Error 2
make: *** [all] Error 2

[rvaser]

Hello,
it looks like your assembler is outdated, the compiler translated commands which are not supported by the assembler. You can try updating it or try adding -DCMAKE_CXX_FLAGS="-mno-avx2" while running cmake.

Best regards,
Robert

[ocho]

I tried your flag, something is still wrong. I tried several GCC versions 4.8.x upwards to 8.2.0.
On the other hand, on my local desktop (gcc (Ubuntu 5.4.0-6ubuntu1~16.04.11) 5.4.0 20160609) it compiles just fine. Something seems wrong with the cluster where I tried to compile it on?

 build > export CC=/home/prog/gcc/gcc-5.4.0/bin/gcc                                                                                                                                                 
 build > export CXX=/home/prog/gcc/gcc-5.4.0/bin/g++                                                                                                                                                
 build > rm -rf *                                                                                                                                                                                   
 build > cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-mno-avx2" .. && make                                                                                                                  
-- The C compiler identification is GNU 5.4.0                                                                                                                                                       
-- The CXX compiler identification is GNU 5.4.0                                                                                                                                                     
-- Check for working C compiler: /home/prog/gcc/gcc-5.4.0/bin/gcc                                                                                                                                   
-- Check for working C compiler: /home/prog/gcc/gcc-5.4.0/bin/gcc -- 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: /home/prog/gcc/gcc-5.4.0/bin/g++                                                                                                                                 
-- Check for working CXX compiler: /home/prog/gcc/gcc-5.4.0/bin/g++ -- works                                                                                                                        
-- Detecting CXX compiler ABI info                                                                                                                                                                  
-- Detecting CXX compiler ABI info - done                                                                                                                                                           
-- Detecting CXX compile features                                                                                                                                                                   
-- Detecting CXX compile features - done                                                                                                                                                            
-- Looking for sys/types.h                                                                                                                                                                          
-- Looking for sys/types.h - found                                                                                                                                                                  
-- Looking for stdint.h                                                                                                                                                                             
-- Looking for stdint.h - found                                                                                                                                                                     
-- Looking for stddef.h                                                                                                                                                                             
-- Looking for stddef.h - found                                                                                                                                                                     
-- Check size of off64_t                                                                                                                                                                            
-- Check size of off64_t - done                                                                                                                                                                     
-- Looking for fseeko                                                                                                                                                                               
-- Looking for fseeko - found                                                                                                                                                                       
-- Looking for unistd.h                                                                                                                                                                             
-- Looking for unistd.h - found                                                                                                                                                                     
Setting warning flags                                                                                                                                                                               
-- Configuring done                                                                                                                                                                                 
-- Generating done                                                                                                                                                                                  
-- Build files have been written to: /nobackup/ms/ra/build                                                                                                                                          
Scanning dependencies of target minimap2                                                                                                                                                            
[  0%] Built target minimap2                                                                                                                                                                        
Scanning dependencies of target thread_pool                                                                                                                                                         
[  2%] Building CXX object vendor/rala/vendor/thread_pool/CMakeFiles/thread_pool.dir/src/thread_pool.cpp.o                                                                                          
[  5%] Linking CXX static library lib/libthread_pool.a                                                                                                                                              
[  5%] Built target thread_pool                                                                                                                                                                     
Scanning dependencies of target zlibstatic                                                                                                                                                          
[  7%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/adler32.o                                                                                               
[ 10%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/compress.o                                                                                              
[ 13%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/crc32.o
[ 15%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/deflate.o
[ 18%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzclose.o
[ 21%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzlib.o
[ 23%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzread.o
[ 26%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzwrite.o
[ 28%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inflate.o
[ 31%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/infback.o
[ 34%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inftrees.o
[ 36%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inffast.o
[ 39%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/trees.o
[ 42%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/uncompr.o
[ 44%] Building C object vendor/rala/vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/zutil.o
[ 47%] Linking C static library ../../lib/libz.a
[ 47%] Built target zlibstatic
Scanning dependencies of target rala
[ 50%] Building CXX object vendor/rala/CMakeFiles/rala.dir/src/graph.cpp.o
[ 52%] Building CXX object vendor/rala/CMakeFiles/rala.dir/src/main.cpp.o
[ 55%] Building CXX object vendor/rala/CMakeFiles/rala.dir/src/overlap.cpp.o
[ 57%] Building CXX object vendor/rala/CMakeFiles/rala.dir/src/pile.cpp.o
[ 60%] Building CXX object vendor/rala/CMakeFiles/rala.dir/src/sequence.cpp.o
[ 63%] Building CXX object vendor/rala/CMakeFiles/rala.dir/src/timer.cpp.o
[ 65%] Linking CXX executable bin/rala
[ 65%] Built target rala
Scanning dependencies of target edlib_static
[ 68%] Building CXX object vendor/racon/vendor/edlib/CMakeFiles/edlib_static.dir/edlib/src/edlib.cpp.o
[ 71%] Linking CXX static library ../../../../lib/libedlib_static.a
[ 71%] Built target edlib_static
Scanning dependencies of target spoa
[ 73%] Building CXX object vendor/racon/vendor/spoa/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o 
[ 76%] Building CXX object vendor/racon/vendor/spoa/CMakeFiles/spoa.dir/src/graph.cpp.o
/tmp/ccnBhUn0.s: Assembler messages:
/tmp/ccnBhUn0.s:6475: Error: no such instruction: `shlx %r10,%r15,%r14'
/tmp/ccnBhUn0.s:6480: Error: no such instruction: `shlx %r9,%r15,%rax'
/tmp/ccnBhUn0.s:6620: Error: no such instruction: `shlx %rbx,%rsi,%rdx'
/tmp/ccnBhUn0.s:6638: Error: no such instruction: `shlx %rdx,%r8,%rcx'
/tmp/ccnBhUn0.s:6685: Error: no such instruction: `shlx %rbx,%rsi,%rdx'
/tmp/ccnBhUn0.s:6702: Error: no such instruction: `shlx %rdx,%r8,%rsi'
/tmp/ccnBhUn0.s:6713: Error: no such instruction: `shlx %rdx,%r8,%rsi'
/tmp/ccnBhUn0.s:6805: Error: no such instruction: `shlx %rax,%r8,%rcx'
/tmp/ccnBhUn0.s:6806: Error: no such instruction: `shlx %rsi,%r8,%r9'
/tmp/ccnBhUn0.s:6944: Error: no such instruction: `shlx %rax,%r9,%rdi'
/tmp/ccnBhUn0.s:6962: Error: no such instruction: `shlx %rax,%r8,%rdx'
/tmp/ccnBhUn0.s:7003: Error: no such instruction: `shlx %rdx,%rdi,%rax'
/tmp/ccnBhUn0.s:7004: Error: no such instruction: `shlx %rbx,%rdi,%r8'
/tmp/ccnBhUn0.s:7050: Error: no such instruction: `shlx %rax,%r9,%rdi'
/tmp/ccnBhUn0.s:7067: Error: no such instruction: `shlx %rax,%r8,%rdi'
/tmp/ccnBhUn0.s:7170: Error: no such instruction: `shlx %rbx,%rsi,%rcx'
/tmp/ccnBhUn0.s:7199: Error: no such instruction: `shlx %rbx,%rsi,%rdx'
/tmp/ccnBhUn0.s:7224: Error: no such instruction: `shlx %rax,%r8,%rdi'
/tmp/ccnBhUn0.s:7246: Error: no such instruction: `shlx %rax,%r8,%rdx'
make[2]: *** [vendor/racon/vendor/spoa/CMakeFiles/spoa.dir/src/graph.cpp.o] Error 1
make[1]: *** [vendor/racon/vendor/spoa/CMakeFiles/spoa.dir/all] Error 2
make: *** [all] Error 2

[rvaser]

Probably it is due to the outdated assembler.

[ocho]

Good news, on another node it magically worked... can't wait to examine the outcome next.