Open KaiFeng007 opened 6 years ago
srechner
commented
6 years ago Yes, it looks like this has to do with a stricter policy of the g++-7 compiler included in Ubuntu 18.04. I updated the CMakeLists.txt file and added some compiler flags that should eliminate this problem. Please update and try again.
KaiFeng007
commented
6 years ago Hi, srechner,
I have updated the install code and tried twice. It worked well at the beginning, but still left one error. The compile was not completed. Any suggestions for this error? Thanks a lot!
Kai
Scanning dependencies of target toFasta
[ 5%] Building CXX object CMakeFiles/toFasta.dir/src/gerbil/toFasta.cpp.o
[ 10%] Linking CXX executable toFasta
[ 10%] Built target toFasta
[ 15%] Building NVCC (Device) object CMakeFiles/cuda_compile_1.dir/src/cuda_ds/cuda_compile_1_generated_CompressKernel.cu.o
[ 21%] Building NVCC (Device) object CMakeFiles/cuda_compile_1.dir/src/cuda_ds/cuda_compile_1_generated_AddKernel.cu.o
Scanning dependencies of target gerbil
[ 26%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o
[ 31%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/Bundle.cpp.o
[ 36%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/FastFile.cpp.o
[ 42%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/FastParser.cpp.o
[ 47%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/FastReader.cpp.o
[ 52%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/KmcWriter.cpp.o
[ 57%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/KmerDistributor.cpp.o
[ 63%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/SequenceSplitter.cpp.o
[ 68%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/SuperReader.cpp.o
[ 73%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/SuperWriter.cpp.o
[ 78%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/TempFile.cpp.o
[ 84%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/debug.cpp.o
[ 89%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/gerbil.cpp.o
[ 94%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/global.cpp.o
[100%] Linking CXX executable gerbil
CMakeFiles/gerbil.dir/src/gerbil/FastParser.cpp.o: In function gerbil::FastParser::nextPart(char*&, char*&, unsigned long const&)': FastParser.cpp:(.text+0x8fa): undefined reference toinflateReset2'
collect2: error: ld returned 1 exit status
CMakeFiles/gerbil.dir/build.make:464: recipe for target 'gerbil' failed
make[2]: [gerbil] Error 1
CMakeFiles/Makefile2:104: recipe for target 'CMakeFiles/gerbil.dir/all' failed
make[1]: [CMakeFiles/gerbil.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2
srechner
commented
6 years ago Try removing everything in the build directory and than call cmake and make again. If it still does not compile, please give us the output of the cmake command.
KaiFeng007
commented
6 years ago Yes, I tried but it still did not compile. The cmake command ran well and the make command still export same error as mentioned above.
This is the information when I call cmake command.
fengkai@ubuntu_r740:~/download/gerbil/build$ cmake ..
-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- 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
-- 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
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- system
-- thread
-- filesystem
-- regex
-- chrono
-- date_time
-- atomic
-- Found BZip2: /usr/local/lib/libbz2.a (found version "1.0.6")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Found ZLIB: /usr/local/lib/libz.a (found version "1.2.11")
-- Found CUDA: /usr/local/cuda (found version "10.0")
-- Build type: Release
-- Configuring done
-- Generating done
-- Build files have been written to: /home/fengkai/download/gerbil/build
This is the output information of the cmake command when I try to call it again.
fengkai@ubuntu_r740:~/download/gerbil/build$cmake ..
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- system
-- thread
-- filesystem
-- regex
-- chrono
-- date_time
-- atomic
-- Build type: Release
-- Configuring done
-- Generating done
-- Build files have been written to: /home/fengkai/download/gerbil/build
srechner
commented
6 years ago It seems that CMake is preferring static libraries over shared ones at your system. However, for reasons I do not understand, the static library /usr/local/lib/libz.a does not contain all functions that are included in the associated shared library. Telling CMake to use the shared library should fix the problem. Please replace the CMakeLists.txt file in the gerbil directory by the attached one and try again.
KaiFeng007
commented
6 years ago Now the compile works well. I have tried to use gerbil to test my sequence file. It works fine. Thanks for your help!
Kai
mhorlacher
commented
4 years ago I get the following error when calling make as well:
CMakeFiles/gerbil.dir/build.make:62: recipe for target 'CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o' failed
make[2]: *** [CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o] Error 1
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/gerbil.dir/all' failed
make[1]: *** [CMakeFiles/gerbil.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2This is my cmake .. output:
(bioinfo) [marc.horlacher@sepp build]$ cmake ..
-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- Check for working C compiler: /home/icb/marc.horlacher/miniconda3/envs/bioinfo/bin/x86_64-conda_cos6-linux-gnu-cc
-- Check for working C compiler: /home/icb/marc.horlacher/miniconda3/envs/bioinfo/bin/x86_64-conda_cos6-linux-gnu-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: /home/icb/marc.horlacher/miniconda3/envs/bioinfo/bin/x86_64-conda_cos6-linux-gnu-c++
-- Check for working CXX compiler: /home/icb/marc.horlacher/miniconda3/envs/bioinfo/bin/x86_64-conda_cos6-linux-gnu-c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
Boost found.
Found Boost components:
system;thread;filesystem;regex
-- Found BZip2: /home/icb/marc.horlacher/miniconda3/envs/bioinfo/lib/libbz2.so (found version "1.0.8")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Found ZLIB: /home/icb/marc.horlacher/miniconda3/envs/bioinfo/lib/libz.so (found version "1.2.11")
-- Found Threads: TRUE
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
-- Build type: Release
-- Configuring done
-- Generating done
-- Build files have been written to: /home/icb/marc.horlacher/software/gerbil/buildHere is the full output of make:
(bioinfo) [marc.horlacher@sepp build]$ make
Scanning dependencies of target gerbil
[ 5%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o
In file included from /home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/types.h:27:0,
from /home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/SyncQueue.h:25,
from /home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/FastReader.h:26,
from /home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/Application.h:26,
from /home/icb/marc.horlacher/software/gerbil/src/gerbil/Application.cpp:8:
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:50:2: error: '__syscall_slong_t' does not name a type
__syscall_slong_t _nsec;
^~~~~~~~~~~~~~~~~
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h: In constructor 'gerbil::StopWatch::StopWatch(clockid_t)':
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:54:17: error: class 'gerbil::StopWatch' does not have any field named '_nsec'
_mode(mode), _nsec(0), _sec(0) {
^~~~~
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h: In constructor 'gerbil::StopWatch::StopWatch()':
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:57:27: error: class 'gerbil::StopWatch' does not have any field named '_nsec'
_mode(CLOCK_REALTIME), _nsec(0), _sec(0) {
^~~~~
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h: In member function 'void gerbil::StopWatch::start()':
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:65:3: error: '_nsec' was not declared in this scope
_nsec = 0;
^~~~~
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:65:3: note: suggested alternative: '_sec'
_nsec = 0;
^~~~~
_sec
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h: In member function 'void gerbil::StopWatch::stop()':
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:70:3: error: '_nsec' was not declared in this scope
_nsec += _end.tv_nsec - _start.tv_nsec;
^~~~~
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:70:3: note: suggested alternative: '_sec'
_nsec += _end.tv_nsec - _start.tv_nsec;
^~~~~
_sec
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h: In member function 'void gerbil::StopWatch::hold()':
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:75:3: error: '_nsec' was not declared in this scope
_nsec += _end.tv_nsec - _start.tv_nsec;
^~~~~
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:75:3: note: suggested alternative: '_sec'
_nsec += _end.tv_nsec - _start.tv_nsec;
^~~~~
_sec
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h: In member function 'double gerbil::StopWatch::get_s()':
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:82:27: error: '_nsec' was not declared in this scope
return _sec + ((double) _nsec / 1000000000);
^~~~~
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:82:27: note: suggested alternative: '_sec'
return _sec + ((double) _nsec / 1000000000);
^~~~~
_sec
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h: At global scope:
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:100:2: error: '__syscall_slong_t' does not name a type
__syscall_slong_t _nsec;
^~~~~~~~~~~~~~~~~
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h: In constructor 'gerbil::StackStopWatch::StackStopWatch(clockid_t)':
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:105:17: error: class 'gerbil::StackStopWatch' does not have any field named '_nsec'
_mode(mode), _nsec(0), _sec(0), _inProgress(false) {
^~~~~
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h: In constructor 'gerbil::StackStopWatch::StackStopWatch()':
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:108:27: error: class 'gerbil::StackStopWatch' does not have any field named '_nsec'
_mode(CLOCK_REALTIME), _nsec(0), _sec(0), _inProgress(false) {
^~~~~
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h: In member function 'void gerbil::StackStopWatch::start()':
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:114:3: error: '_nsec' was not declared in this scope
_nsec = 0;
^~~~~
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:114:3: note: suggested alternative: '_sec'
_nsec = 0;
^~~~~
_sec
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h: In member function 'void gerbil::StackStopWatch::stop()':
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:121:3: error: '_nsec' was not declared in this scope
_nsec += _end.tv_nsec - _start.tv_nsec;
^~~~~
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:121:3: note: suggested alternative: '_sec'
_nsec += _end.tv_nsec - _start.tv_nsec;
^~~~~
_sec
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h: In member function 'void gerbil::StackStopWatch::hold()':
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:128:3: error: '_nsec' was not declared in this scope
_nsec += _end.tv_nsec - _start.tv_nsec;
^~~~~
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:128:3: note: suggested alternative: '_sec'
_nsec += _end.tv_nsec - _start.tv_nsec;
^~~~~
_sec
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h: In member function 'double gerbil::StackStopWatch::get_s()':
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:136:27: error: '_nsec' was not declared in this scope
return _sec + ((double) _nsec / 1000000000);
^~~~~
/home/icb/marc.horlacher/software/gerbil/src/gerbil/../../include/gerbil/debug.h:136:27: note: suggested alternative: '_sec'
return _sec + ((double) _nsec / 1000000000);
^~~~~
_sec
CMakeFiles/gerbil.dir/build.make:62: recipe for target 'CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o' failed
make[2]: *** [CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o] Error 1
CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/gerbil.dir/all' failed
make[1]: *** [CMakeFiles/gerbil.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2
Using the attached CMakeLists.txt file did not solve my problem.
Note: I'm working in a conda environment.
Best, M.
Hi,
I am very happy to find this excellent tool to do k-mer statistics. However, I met some problems during compiling this software. I thought the problem might be due to newer operation system version, but I am not sure.
Please check with the following messages and do me a favor.
Thanks a lot!
Kai
Scanning dependencies of target toFasta [ 5%] Building CXX object CMakeFiles/toFasta.dir/src/gerbil/toFasta.cpp.o [ 10%] Linking CXX executable toFasta [ 10%] Built target toFasta [ 15%] Building NVCC (Device) object CMakeFiles/cuda_compile_1.dir/src/cuda_ds/cuda_compile_1_generated_CompressKernel.cu.o [ 21%] Building NVCC (Device) object CMakeFiles/cuda_compile_1.dir/src/cuda_ds/cuda_compile_1_generated_AddKernel.cu.o Scanning dependencies of target gerbil [ 26%] Building CXX object CMakeFiles/gerbil.dir/src/gerbil/Application.cpp.o In file included from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable.h:25:0, from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerCountingHashTable.h:25, from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/GpuHasher.h:31, from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:28, from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/Application.h:31, from /home/fengkai/download/gerbil/src/gerbil/Application.cpp:8: /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h: In instantiation of ‘cuda_ds::internal::CountingHashTable<intsPerKey, keyBufferSize>::~CountingHashTable() [with unsigned int intsPerKey = 1; long unsigned int keyBufferSize = 262144]’: /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable.h:43:7: required from ‘gerbil::gpu::KmerCountingHashTable::KmerCountingHashTable(uint32_t, gerbil::SyncSwapQueueMPSC, uint32_t, std::__cxx11::string) [with unsigned int K = 9; uint32_t = unsigned int; std::cxx11::string = std::cxx11::basic_string]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/GpuHasher.h:97:16: required from ‘gerbil::gpu::HasherTask::HasherTask(uint8_t, gerbil::KmerDistributer , gerbil::SyncSwapQueueMPSC, gerbil::TempFile, std::cxx11::string, uint32_t) [with unsigned int K = 9; uint8_t = unsigned char; std::cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:136:26: required from ‘gerbil::KmerHasher::process_template()::<lambda()> [with unsigned int K = 9]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:23: required from ‘struct gerbil::KmerHasher::process_template() [with unsigned int K = 9]::<lambda()>’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:6: required from ‘void gerbil::KmerHasher::process_template() [with unsigned int K = 9]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:539:6: required from here
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:176:46: warning: throw will always call terminate() [-Wterminate]