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soedinglab / CCMpred

Protein Residue-Residue Contacts from Correlated Mutations predicted quickly and accurately.
http://www.ncbi.nlm.nih.gov/pubmed/25064567
GNU Affero General Public License v3.0
107 stars 25 forks source link

Libmsgpack issue #4

Closed fsimkovic closed 8 years ago

fsimkovic commented 8 years ago

Just to open a new thread for this issue.

I've installed the libmsgpack library files with apt-get install libmsgpack-dev on Ubuntu 16.04 LTS. Running cmake again and make gives me the following outputs.

Any suggested fix @sseemayer?

$> cmake .
"cmake" '.'
+ cmake .
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- 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
-- Found these msgpack libs: /usr/lib/libmsgpack.so
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") 
-- Found LibJansson: /usr/lib/x86_64-linux-gnu/libjansson.so  
-- Found LibUUID: /usr/lib/x86_64-linux-gnu/libuuid.so  
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp  
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Found CUDA: /usr (found version "7.5") 
-- Found Curses: /usr/lib/x86_64-linux-gnu/libcurses.so  
-- Configuring done
-- Generating done
-- Build files have been written to: /opt/CCMpred
"make"
+ make
[  5%] Building NVCC (Device) object lib/libconjugrad/CMakeFiles/conjugrad.dir/src/conjugrad_generated_conjugrad_kernels.cu.o
ptxas info    : 0 bytes gmem
ptxas info    : Compiling entry function '_Z12vecdot_interPfS_S_i' for 'sm_20'
ptxas info    : Function properties for _Z12vecdot_interPfS_S_i
    0 bytes stack frame, 0 bytes spill stores, 0 bytes spill loads
ptxas info    : Used 14 registers, 60 bytes cmem[0]
ptxas info    : Function properties for _Z14warp_reductionPVfi
    0 bytes stack frame, 0 bytes spill stores, 0 bytes spill loads
ptxas info    : Compiling entry function '_Z12initialize_sPfS_i' for 'sm_20'
ptxas info    : Function properties for _Z12initialize_sPfS_i
    0 bytes stack frame, 0 bytes spill stores, 0 bytes spill loads
ptxas info    : Used 9 registers, 52 bytes cmem[0]
ptxas info    : Compiling entry function '_Z13sum_reductionPfS_i' for 'sm_20'
ptxas info    : Function properties for _Z13sum_reductionPfS_i
    0 bytes stack frame, 0 bytes spill stores, 0 bytes spill loads
ptxas info    : Used 12 registers, 52 bytes cmem[0]
ptxas info    : Compiling entry function '_Z8update_xPfS_ffi' for 'sm_20'
ptxas info    : Function properties for _Z8update_xPfS_ffi
    0 bytes stack frame, 0 bytes spill stores, 0 bytes spill loads
ptxas info    : Used 11 registers, 60 bytes cmem[0]
ptxas info    : Function properties for _Z22sum_reduction_functionPVfi
    0 bytes stack frame, 0 bytes spill stores, 0 bytes spill loads
ptxas info    : Compiling entry function '_Z8update_sPfS_fi' for 'sm_20'
ptxas info    : Function properties for _Z8update_sPfS_fi
    0 bytes stack frame, 0 bytes spill stores, 0 bytes spill loads
ptxas info    : Used 10 registers, 56 bytes cmem[0]
Scanning dependencies of target conjugrad
[ 10%] Building C object lib/libconjugrad/CMakeFiles/conjugrad.dir/src/conjugrad.c.o
[ 15%] Building C object lib/libconjugrad/CMakeFiles/conjugrad.dir/src/debug.c.o
[ 21%] Building C object lib/libconjugrad/CMakeFiles/conjugrad.dir/src/arithmetic_ansi.c.o
[ 26%] Building C object lib/libconjugrad/CMakeFiles/conjugrad.dir/src/conjugrad_cuda.c.o
[ 31%] Linking CXX static library libconjugrad.a
[ 31%] Built target conjugrad
[ 36%] Building NVCC (Device) object CMakeFiles/cuda_compile.dir/src/cuda_compile_generated_evaluate_cuda_kernels.cu.o
Scanning dependencies of target ccmpred
[ 42%] Building C object CMakeFiles/ccmpred.dir/src/ccmpred.c.o
[ 47%] Building C object CMakeFiles/ccmpred.dir/src/sequence.c.o
/opt/CCMpred/src/sequence.c: In function ‘read_msa’:
/opt/CCMpred/src/sequence.c:73:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(buf, SEQ_BUFFER, f);
   ^
[ 52%] Building C object CMakeFiles/ccmpred.dir/src/util.c.o
[ 57%] Building C object CMakeFiles/ccmpred.dir/src/io.c.o
/opt/CCMpred/src/io.c: In function ‘write_raw_msgpack’:
/opt/CCMpred/src/io.c:126:2: warning: implicit declaration of function ‘msgpack_pack_str’ [-Wimplicit-function-declaration]
  msgpack_pack_str(pk, 6);
  ^
/opt/CCMpred/src/io.c:127:2: warning: implicit declaration of function ‘msgpack_pack_str_body’ [-Wimplicit-function-declaration]
  msgpack_pack_str_body(pk, "format", 6);
  ^
/opt/CCMpred/src/io.c: In function ‘read_raw’:
/opt/CCMpred/src/io.c:72:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, 8192, f);
   ^
/opt/CCMpred/src/io.c:81:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    fgets(line, 8192, f);
    ^
/opt/CCMpred/src/io.c:87:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, 8192, f);
     ^
[ 63%] Building C object CMakeFiles/ccmpred.dir/src/evaluate_cpu.c.o
[ 68%] Building C object CMakeFiles/ccmpred.dir/src/parseopt.c.o
[ 73%] Building C object CMakeFiles/ccmpred.dir/src/reweighting.c.o
[ 78%] Building C object CMakeFiles/ccmpred.dir/src/numdif.c.o
[ 84%] Building C object CMakeFiles/ccmpred.dir/src/meta.c.o
/opt/CCMpred/src/meta.c: In function ‘json_object_to_msgpack’:
/opt/CCMpred/src/meta.c:88:3: warning: implicit declaration of function ‘msgpack_pack_str’ [-Wimplicit-function-declaration]
   msgpack_pack_str(pk, strlen(key));
   ^
/opt/CCMpred/src/meta.c:89:3: warning: implicit declaration of function ‘msgpack_pack_str_body’ [-Wimplicit-function-declaration]
   msgpack_pack_str_body(pk, key, strlen(key));
   ^
[ 89%] Building C object CMakeFiles/ccmpred.dir/src/evaluate_cpu_omp.c.o
[ 94%] Building C object CMakeFiles/ccmpred.dir/src/evaluate_cuda.c.o
[100%] Linking C executable bin/ccmpred
CMakeFiles/ccmpred.dir/src/io.c.o: In function `write_raw_msgpack':
/opt/CCMpred/src/io.c:126: undefined reference to `msgpack_pack_str'
/opt/CCMpred/src/io.c:127: undefined reference to `msgpack_pack_str_body'
/opt/CCMpred/src/io.c:128: undefined reference to `msgpack_pack_str'
/opt/CCMpred/src/io.c:129: undefined reference to `msgpack_pack_str_body'
/opt/CCMpred/src/io.c:131: undefined reference to `msgpack_pack_str'
/opt/CCMpred/src/io.c:132: undefined reference to `msgpack_pack_str_body'
/opt/CCMpred/src/io.c:135: undefined reference to `msgpack_pack_str'
/opt/CCMpred/src/io.c:136: undefined reference to `msgpack_pack_str_body'
/opt/CCMpred/src/io.c:148: undefined reference to `msgpack_pack_str'
/opt/CCMpred/src/io.c:149: undefined reference to `msgpack_pack_str_body'
/opt/CCMpred/src/io.c:160: undefined reference to `msgpack_pack_str'
/opt/CCMpred/src/io.c:161: undefined reference to `msgpack_pack_str_body'
/opt/CCMpred/src/io.c:165: undefined reference to `msgpack_pack_str'
/opt/CCMpred/src/io.c:166: undefined reference to `msgpack_pack_str_body'
/opt/CCMpred/src/io.c:169: undefined reference to `msgpack_pack_str'
/opt/CCMpred/src/io.c:170: undefined reference to `msgpack_pack_str_body'
/opt/CCMpred/src/io.c:173: undefined reference to `msgpack_pack_str'
/opt/CCMpred/src/io.c:174: undefined reference to `msgpack_pack_str_body'
CMakeFiles/ccmpred.dir/src/meta.c.o: In function `json_string_to_msgpack':
/opt/CCMpred/src/meta.c:107: undefined reference to `msgpack_pack_str'
/opt/CCMpred/src/meta.c:107: undefined reference to `msgpack_pack_str'
/opt/CCMpred/src/meta.c:108: undefined reference to `msgpack_pack_str_body'
CMakeFiles/ccmpred.dir/src/meta.c.o: In function `json_object_to_msgpack':
/opt/CCMpred/src/meta.c:88: undefined reference to `msgpack_pack_str'
/opt/CCMpred/src/meta.c:89: undefined reference to `msgpack_pack_str_body'
CMakeFiles/ccmpred.dir/src/meta.c.o: In function `json_string_to_msgpack':
/opt/CCMpred/src/meta.c:107: undefined reference to `msgpack_pack_str'
/opt/CCMpred/src/meta.c:108: undefined reference to `msgpack_pack_str_body'
CMakeFiles/ccmpred.dir/src/meta.c.o: In function `meta_write_msgpack':
/opt/CCMpred/src/meta.c:158: undefined reference to `msgpack_pack_str'
/opt/CCMpred/src/meta.c:159: undefined reference to `msgpack_pack_str_body'
CMakeFiles/ccmpred.dir/src/meta.c.o: In function `json_string_to_msgpack':
/opt/CCMpred/src/meta.c:107: undefined reference to `msgpack_pack_str'
/opt/CCMpred/src/meta.c:108: undefined reference to `msgpack_pack_str_body'
/opt/CCMpred/src/meta.c:108: undefined reference to `msgpack_pack_str_body'
collect2: error: ld returned 1 exit status
CMakeFiles/ccmpred.dir/build.make:368: recipe for target 'bin/ccmpred' failed
make[2]: *** [bin/ccmpred] Error 1
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/ccmpred.dir/all' failed
make[1]: *** [CMakeFiles/ccmpred.dir/all] Error 2
Makefile:149: recipe for target 'all' failed
make: *** [all] Error 2
sseemayer commented 8 years ago

MessagePack had an API change for string type names. The errors indicate that you're trying to compile CCMpred with an outdated MessagePack library.

fsimkovic commented 8 years ago

Which version number is required? I am currently using version 0.5.7-3ubuntu1.

sseemayer commented 8 years ago

Any version > 1.0 should be fine.

fsimkovic commented 8 years ago

Thanks for the Merge.