Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Compile error on Ubuntu 18.04.1 LTS Server #10

Open
KaiFeng007 opened this issue Oct 10, 2018 · 7 comments
Open

Compile error on Ubuntu 18.04.1 LTS Server #10

KaiFeng007 opened this issue Oct 10, 2018 · 7 comments

Comments

@KaiFeng007
Copy link

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::SyncSwapQueueMPSCgerbil::KmcBundle, 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::SyncSwapQueueMPSCgerbil::KmcBundle, 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]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:176:46: note: in C++11 destructors default to noexcept
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:186:46: warning: throw will always call terminate() [-Wterminate]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:186:46: note: in C++11 destructors default to noexcept
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:198:47: warning: throw will always call terminate() [-Wterminate]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:198:47: note: in C++11 destructors default to noexcept
/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 = 2; 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::SyncSwapQueueMPSCgerbil::KmcBundle, uint32_t, std::__cxx11::string) [with unsigned int K = 16; 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::SyncSwapQueueMPSCgerbil::KmcBundle, gerbil::TempFile, std::__cxx11::string, uint32_t) [with unsigned int K = 16; 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 = 16]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:23: required from ‘struct gerbil::KmerHasher::process_template() [with unsigned int K = 16]::<lambda()>’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:6: required from ‘void gerbil::KmerHasher::process_template() [with unsigned int K = 16]’
/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]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:176:46: note: in C++11 destructors default to noexcept
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:186:46: warning: throw will always call terminate() [-Wterminate]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:186:46: note: in C++11 destructors default to noexcept
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:198:47: warning: throw will always call terminate() [-Wterminate]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:198:47: note: in C++11 destructors default to noexcept
/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 = 4; 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::SyncSwapQueueMPSCgerbil::KmcBundle, uint32_t, std::__cxx11::string) [with unsigned int K = 32; 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::SyncSwapQueueMPSCgerbil::KmcBundle, gerbil::TempFile, std::__cxx11::string, uint32_t) [with unsigned int K = 32; 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 = 32]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:23: required from ‘struct gerbil::KmerHasher::process_template() [with unsigned int K = 32]::<lambda()>’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:6: required from ‘void gerbil::KmerHasher::process_template() [with unsigned int K = 32]’
/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]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:176:46: note: in C++11 destructors default to noexcept
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:186:46: warning: throw will always call terminate() [-Wterminate]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:186:46: note: in C++11 destructors default to noexcept
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:198:47: warning: throw will always call terminate() [-Wterminate]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:198:47: note: in C++11 destructors default to noexcept
In file included from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/Bundle.h:25:0,
from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/FastReader.h:27,
from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/Application.h:26,
from /home/fengkai/download/gerbil/src/gerbil/Application.cpp:8:
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h: In instantiation of ‘constexpr const uint64_t gerbil::KMer<32, 9, 8, 2>::_c_mask’:
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h:123:7: required from ‘void gerbil::KMer<K, B, 8, C>::set(const byte* const&) [with unsigned int K = 32; unsigned int B = 9; unsigned int C = 2; gerbil::byte = unsigned char]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:363:9: required from ‘void gerbil::KmerHasher::processThreadSplit(const uint8_t&, gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >) [with unsigned int K = 32; bool NORM = true; uint8_t = unsigned char]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:107:38: required from ‘gerbil::KmerHasher::processSplit(gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >)::<lambda(const uint8_t&, gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >)> [with unsigned int K = 32; uint8_t = unsigned char]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:102:10: required from ‘struct gerbil::KmerHasher::processSplit(gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >) [with unsigned int K = 32]::<lambda(const uint8_t&, class gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle<32> >, class gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle<32> >)>’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:101:7: required from ‘void gerbil::KmerHasher::processSplit(gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >) [with unsigned int K = 32]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:162:22: required from ‘gerbil::KmerHasher::process_template()::<lambda()> [with unsigned int K = 32]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:23: required from ‘struct gerbil::KmerHasher::process_template() [with unsigned int K = 32]::<lambda()>’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:6: required from ‘void gerbil::KmerHasher::process_template() [with unsigned int K = 32]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:539:6: required from here
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h:65:58: warning: left shift count >= width of type [-Wshift-count-overflow]
static constexpr uint64_t _c_mask = 0xffffffffffffffff << _c_offset;
~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h:65:58: error: right operand of shift expression ‘(18446744073709551615 << 64)’ is >= than the precision of the left operand [-fpermissive]
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 = 6; 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::SyncSwapQueueMPSCgerbil::KmcBundle, uint32_t, std::__cxx11::string) [with unsigned int K = 64; 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::SyncSwapQueueMPSCgerbil::KmcBundle, gerbil::TempFile, std::__cxx11::string, uint32_t) [with unsigned int K = 64; 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 = 64]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:23: required from ‘struct gerbil::KmerHasher::process_template() [with unsigned int K = 64]::<lambda()>’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:6: required from ‘void gerbil::KmerHasher::process_template() [with unsigned int K = 64]’
/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]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:176:46: note: in C++11 destructors default to noexcept
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:186:46: warning: throw will always call terminate() [-Wterminate]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:186:46: note: in C++11 destructors default to noexcept
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:198:47: warning: throw will always call terminate() [-Wterminate]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:198:47: note: in C++11 destructors default to noexcept
In file included from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/Bundle.h:25:0,
from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/FastReader.h:27,
from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/Application.h:26,
from /home/fengkai/download/gerbil/src/gerbil/Application.cpp:8:
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h: In instantiation of ‘constexpr const uint64_t gerbil::KMer<64, 17, 8, 3>::_c_mask’:
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h:123:7: required from ‘void gerbil::KMer<K, B, 8, C>::set(const byte* const&) [with unsigned int K = 64; unsigned int B = 17; unsigned int C = 3; gerbil::byte = unsigned char]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:363:9: required from ‘void gerbil::KmerHasher::processThreadSplit(const uint8_t&, gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >) [with unsigned int K = 64; bool NORM = true; uint8_t = unsigned char]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:107:38: required from ‘gerbil::KmerHasher::processSplit(gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >)::<lambda(const uint8_t&, gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >)> [with unsigned int K = 64; uint8_t = unsigned char]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:102:10: required from ‘struct gerbil::KmerHasher::processSplit(gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >) [with unsigned int K = 64]::<lambda(const uint8_t&, class gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle<64> >, class gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle<64> >)>’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:101:7: required from ‘void gerbil::KmerHasher::processSplit(gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >) [with unsigned int K = 64]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:162:22: required from ‘gerbil::KmerHasher::process_template()::<lambda()> [with unsigned int K = 64]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:23: required from ‘struct gerbil::KmerHasher::process_template() [with unsigned int K = 64]::<lambda()>’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:6: required from ‘void gerbil::KmerHasher::process_template() [with unsigned int K = 64]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:539:6: required from here
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h:65:58: warning: left shift count >= width of type [-Wshift-count-overflow]
static constexpr uint64_t _c_mask = 0xffffffffffffffff << _c_offset;
~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h:65:58: error: right operand of shift expression ‘(18446744073709551615 << 64)’ is >= than the precision of the left operand [-fpermissive]
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 = 8; 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::SyncSwapQueueMPSCgerbil::KmcBundle, uint32_t, std::__cxx11::string) [with unsigned int K = 96; 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::SyncSwapQueueMPSCgerbil::KmcBundle, gerbil::TempFile, std::__cxx11::string, uint32_t) [with unsigned int K = 96; 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 = 96]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:23: required from ‘struct gerbil::KmerHasher::process_template() [with unsigned int K = 96]::<lambda()>’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:6: required from ‘void gerbil::KmerHasher::process_template() [with unsigned int K = 96]’
/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]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:176:46: note: in C++11 destructors default to noexcept
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:186:46: warning: throw will always call terminate() [-Wterminate]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:186:46: note: in C++11 destructors default to noexcept
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:198:47: warning: throw will always call terminate() [-Wterminate]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:198:47: note: in C++11 destructors default to noexcept
In file included from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/Bundle.h:25:0,
from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/FastReader.h:27,
from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/Application.h:26,
from /home/fengkai/download/gerbil/src/gerbil/Application.cpp:8:
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h: In instantiation of ‘constexpr const uint64_t gerbil::KMer<96, 25, 8, 4>::_c_mask’:
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h:123:7: required from ‘void gerbil::KMer<K, B, 8, C>::set(const byte* const&) [with unsigned int K = 96; unsigned int B = 25; unsigned int C = 4; gerbil::byte = unsigned char]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:363:9: required from ‘void gerbil::KmerHasher::processThreadSplit(const uint8_t&, gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >) [with unsigned int K = 96; bool NORM = true; uint8_t = unsigned char]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:107:38: required from ‘gerbil::KmerHasher::processSplit(gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >)::<lambda(const uint8_t&, gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >)> [with unsigned int K = 96; uint8_t = unsigned char]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:102:10: required from ‘struct gerbil::KmerHasher::processSplit(gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >) [with unsigned int K = 96]::<lambda(const uint8_t&, class gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle<96> >, class gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle<96> >)>’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:101:7: required from ‘void gerbil::KmerHasher::processSplit(gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >) [with unsigned int K = 96]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:162:22: required from ‘gerbil::KmerHasher::process_template()::<lambda()> [with unsigned int K = 96]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:23: required from ‘struct gerbil::KmerHasher::process_template() [with unsigned int K = 96]::<lambda()>’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:6: required from ‘void gerbil::KmerHasher::process_template() [with unsigned int K = 96]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:539:6: required from here
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h:65:58: warning: left shift count >= width of type [-Wshift-count-overflow]
static constexpr uint64_t _c_mask = 0xffffffffffffffff << _c_offset;
~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h:65:58: error: right operand of shift expression ‘(18446744073709551615 << 64)’ is >= than the precision of the left operand [-fpermissive]
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 = 10; 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::SyncSwapQueueMPSCgerbil::KmcBundle, uint32_t, std::__cxx11::string) [with unsigned int K = 128; 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::SyncSwapQueueMPSCgerbil::KmcBundle, gerbil::TempFile, std::__cxx11::string, uint32_t) [with unsigned int K = 128; 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 = 128]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:23: required from ‘struct gerbil::KmerHasher::process_template() [with unsigned int K = 128]::<lambda()>’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:6: required from ‘void gerbil::KmerHasher::process_template() [with unsigned int K = 128]’
/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]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:176:46: note: in C++11 destructors default to noexcept
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:186:46: warning: throw will always call terminate() [-Wterminate]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:186:46: note: in C++11 destructors default to noexcept
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:198:47: warning: throw will always call terminate() [-Wterminate]
+ std::string(cudaGetErrorString(err)));
^
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/../cuda_ds/CountingHashTable/_CountingHashTable.h:198:47: note: in C++11 destructors default to noexcept
In file included from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/Bundle.h:25:0,
from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/FastReader.h:27,
from /home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/Application.h:26,
from /home/fengkai/download/gerbil/src/gerbil/Application.cpp:8:
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h: In instantiation of ‘constexpr const uint64_t gerbil::KMer<128, 33, 8, 5>::_c_mask’:
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h:123:7: required from ‘void gerbil::KMer<K, B, 8, C>::set(const byte* const&) [with unsigned int K = 128; unsigned int B = 33; unsigned int C = 5; gerbil::byte = unsigned char]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:363:9: required from ‘void gerbil::KmerHasher::processThreadSplit(const uint8_t&, gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >) [with unsigned int K = 128; bool NORM = true; uint8_t = unsigned char]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:107:38: required from ‘gerbil::KmerHasher::processSplit(gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >)::<lambda(const uint8_t&, gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >)> [with unsigned int K = 128; uint8_t = unsigned char]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:102:10: required from ‘struct gerbil::KmerHasher::processSplit(gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >) [with unsigned int K = 128]::<lambda(const uint8_t&, class gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle<128> >, class gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle<128> >)>’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:101:7: required from ‘void gerbil::KmerHasher::processSplit(gerbil::SyncSwapQueueMPSC<gerbil::cpu::KMerBundle >, gerbil::SyncSwapQueueMPSC<gerbil::gpu::KMerBundle >) [with unsigned int K = 128]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:162:22: required from ‘gerbil::KmerHasher::process_template()::<lambda()> [with unsigned int K = 128]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:23: required from ‘struct gerbil::KmerHasher::process_template() [with unsigned int K = 128]::<lambda()>’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:120:6: required from ‘void gerbil::KmerHasher::process_template() [with unsigned int K = 128]’
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KmerHasher.h:539:6: required from here
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h:65:58: warning: left shift count >= width of type [-Wshift-count-overflow]
static constexpr uint64_t _c_mask = 0xffffffffffffffff << _c_offset;
~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/home/fengkai/download/gerbil/src/gerbil/../../include/gerbil/KMer.h:65:58: error: right operand of shift expression ‘(18446744073709551615 << 64)’ is >= than the precision of the left operand [-fpermissive]
CMakeFiles/gerbil.dir/build.make:76: 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/Makefile2:104: 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
Copy link
Collaborator

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
Copy link
Author

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 to inflateReset2'
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
Copy link
Collaborator

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
Copy link
Author

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
Copy link
Collaborator

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
Copy link
Author

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
Copy link

mhorlacher commented Jun 25, 2020 •
edited
Loading

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 2

This 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/build

Here 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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@srechner @KaiFeng007 @mhorlacher