Compilation errors for CUDA-7.5.17, Nvidia K40

[ravimanumachu]

Dear Nvbio developers,

I hope you are well. There are compilation errors with nvbio-1.1.00 and even the latest git version.

Following are the diagnostics, which I hope will help you fix the errors.

Please let me know if you need further information.

$ nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2015 NVIDIA Corporation
Built on Tue_Aug_11_14:27:32_CDT_2015
Cuda compilation tools, release 7.5, V7.5.17

$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-16) (GCC)

$ nvidia-smi -q

==============NVSMI LOG==============

Timestamp : Tue Feb 6 10:13:14 2018
Driver Version : 352.79

Attached GPUs : 1
GPU 0000:85:00.0
Product Name : Tesla K40c
Product Brand : Tesla
Display Mode : Disabled
Display Active : Disabled
Persistence Mode : Disabled
Accounting Mode : Disabled
Accounting Mode Buffer Size : 1920
Driver Model
Current : N/A
Pending : N/A
Serial Number : 0325215045418
GPU UUID : GPU-d19a0dc3-9023-218c-2911-b34bab7d6a1b
Minor Number : 0
VBIOS Version : 80.80.3E.00.02
MultiGPU Board : No
Board ID : 0x8500
Inforom Version
Image Version : 2081.0206.01.04
OEM Object : 1.1
ECC Object : 3.0
Power Management Object : N/A
GPU Operation Mode
Current : N/A
Pending : N/A
PCI
Bus : 0x85
Device : 0x00
Domain : 0x0000
Device Id : 0x102410DE
Bus Id : 0000:85:00.0
Sub System Id : 0x098310DE
GPU Link Info
PCIe Generation
Max : 3
Current : 3
Link Width
Max : 16x
Current : 16x
Bridge Chip
Type : N/A
Firmware : N/A
Replays since reset : 0
Tx Throughput : N/A
Rx Throughput : N/A
Fan Speed : 23 %
Performance State : P0
Clocks Throttle Reasons
Idle : Not Active
Applications Clocks Setting : Active
SW Power Cap : Not Active
HW Slowdown : Not Active
Unknown : Not Active
FB Memory Usage
Total : 11519 MiB
Used : 23 MiB
Free : 11496 MiB
BAR1 Memory Usage
Total : 256 MiB
Used : 2 MiB
Free : 254 MiB
Compute Mode : Default
Utilization
Gpu : 66 %
Memory : 3 %
Encoder : 0 %
Decoder : 0 %
Ecc Mode
Current : Enabled
Pending : Enabled
ECC Errors
Volatile
Single Bit
Device Memory : 0
Register File : 0
L1 Cache : 0
L2 Cache : 0
Texture Memory : 0
Total : 0
Double Bit
Device Memory : 0
Register File : 0
L1 Cache : 0
L2 Cache : 0
Texture Memory : 0
Total : 0
Aggregate
Single Bit
Device Memory : 0
Register File : 0
L1 Cache : 0
L2 Cache : 0
Texture Memory : 0
Total : 0
Double Bit
Device Memory : 0
Register File : 0
L1 Cache : 0
L2 Cache : 0
Texture Memory : 0
Total : 0
Retired Pages
Single Bit ECC : 0
Double Bit ECC : 0
Pending : No
Temperature
GPU Current Temp : 37 C
GPU Shutdown Temp : 95 C
GPU Slowdown Temp : 90 C
Power Readings
Power Management : Supported
Power Draw : 66.41 W
Power Limit : 235.00 W
Default Power Limit : 235.00 W
Enforced Power Limit : 235.00 W
Min Power Limit : 180.00 W
Max Power Limit : 235.00 W
Clocks
Graphics : 745 MHz
SM : 745 MHz
Memory : 3004 MHz
Applications Clocks
Graphics : 745 MHz
Memory : 3004 MHz
Default Applications Clocks
Graphics : 745 MHz
Memory : 3004 MHz
Max Clocks
Graphics : 875 MHz
SM : 875 MHz
Memory : 3004 MHz
Clock Policy
Auto Boost : N/A
Auto Boost Default : N/A
Processes : None

COMPILATION Problems

-- Building Release
==> Found Doxygen file for module nvbio-project
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ravi/Research/nvbio-1.1.00/build
[ 8%] Built target zlib
[ 17%] Built target zlibstatic
[ 18%] Built target crcstatic
[ 19%] Built target bamtools
Linking CXX static library libmoderngpu.a
[ 21%] Built target moderngpu
[ 39%] Built target htslib
Linking CXX static library libnvbio.a
[ 61%] Built target nvbio
...
nvbio-1.1.00/contrib/cub/block/specializations/../../block/../util_arch.cuh:178:0: warning: "CUB_PTX_PREFER_CONFLICT_OVER_PADDING" redefined [enabled by default]
#define CUB_PTX_PREFER_CONFLICT_OVER_PADDING CUB_PREFER_CONFLICT_OVER_PADDING(CUB_PTX_VERSION)
^
In file included from /usr/local/cuda/include/thrust/system/cuda/detail/cub/block/specializations/../../block/../util_type.cuh:40:0,
from /usr/local/cuda/include/thrust/system/cuda/detail/cub/block/specializations/../../block/../util_ptx.cuh:37,
from /usr/local/cuda/include/thrust/system/cuda/detail/cub/block/specializations/../../block/block_exchange.cuh:36,
from /usr/local/cuda/include/thrust/system/cuda/detail/cub/block/specializations/../../block/block_radix_sort.cuh:37,
from /usr/local/cuda/include/thrust/system/cuda/detail/cub/block/specializations/block_histogram_sort.cuh:36,
from /usr/local/cuda/include/thrust/system/cuda/detail/cub/block/block_histogram.cuh:36,
from /usr/local/cuda/include/thrust/system/cuda/detail/cub/cub.cuh:38,
from /usr/local/cuda/include/thrust/system/cuda/detail/cub.h:63,
from /usr/local/cuda/include/thrust/system/cuda/detail/detail/stable_radix_sort.inl:28,
from /usr/local/cuda/include/thrust/system/cuda/detail/detail/stable_radix_sort.h:86,
from /usr/local/cuda/include/thrust/system/cuda/detail/detail/stable_primitive_sort.inl:21,
from /usr/local/cuda/include/thrust/system/cuda/detail/detail/stable_primitive_sort.h:81,
from /usr/local/cuda/include/thrust/system/cuda/detail/sort.inl:23,
from /usr/local/cuda/include/thrust/system/cuda/detail/sort.h:59,
from /usr/local/cuda/include/thrust/system/detail/adl/sort.h:32,
from /usr/local/cuda/include/thrust/detail/sort.inl:27,
from /usr/local/cuda/include/thrust/sort.h:1361,
from /home/ravi/Research/nvbio-1.1.00/nvbio/basic/primitives.h:38,
from /home/ravi/Research/nvbio-1.1.00/nvbio/strings/wavelet_tree.h:32,
from /home/ravi/Research/nvbio-1.1.00/nvbio-test/wavelet_test.cu:34:
/usr/local/cuda/include/thrust/system/cuda/detail/cub/block/specializations/../../block/../util_arch.cuh:190:0: note: this is the location of the previous definition
#define CUB_PTX_PREFER_CONFLICT_OVER_PADDING CUB_PREFER_CONFLICT_OVER_PADDING(CUB_PTX_ARCH)
^
/home/ravi/Research/nvbio-1.1.00/nvbio/basic/iterator.h(101): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type"
detected during:
instantiation of class "nvbio::iterator_system [with iterator=nvbio::PackedStream<thrust::device_ptrnvbio::uint32, nvbio::uint8, 1U, true, nvbio::uint32>]"
/home/ravi/Research/nvbio-1.1.00/nvbio/strings/wavelet_tree.h(80): here
instantiation of class "nvbio::WaveletTree<BitStreamIterator, IndexIterator, SymbolType> [with BitStreamIterator=nvbio::PackedStream<thrust::device_ptrnvbio::uint32, nvbio::uint8, 1U, true, nvbio::uint32>, IndexIterator=thrust::detail::normal_iterator<thrust::device_ptrnvbio::uint32>, SymbolType=nvbio::uint8]"
/home/ravi/Research/nvbio-1.1.00/nvbio-test/wavelet_test.cu(106): here

/home/ravi/Research/nvbio-1.1.00/nvbio/basic/iterator.h(101): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type"
detected during:
instantiation of class "nvbio::iterator_system [with iterator=thrust::device_ptrnvbio::uint32]"
/home/ravi/Research/nvbio-1.1.00/nvbio/basic/packedstream_inl.h(1370): here
instantiation of "void nvbio::assign(IndexType, InputIterator, nvbio::PackedStream<InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType>) [with InputIterator=thrust::transform_iterator<nvbio::select_bit_functornvbio::uint8, thrust::detail::normal_iterator<thrust::device_ptrnvbio::uint8>, thrust::use_default, thrust::use_default>, InputStream=thrust::device_ptrnvbio::uint32, Symbol=nvbio::uint8, SYMBOL_SIZE_T=1U, BIG_ENDIAN_T=true, IndexType=nvbio::uint32]"
/home/ravi/Research/nvbio-1.1.00/nvbio/strings/wavelet_tree_inl.h(197): here
instantiation of "void nvbio::setup(index_type, const string_iterator &, nvbio::WaveletTreeStorage<system_tag, index_type, symbol_type> &) [with system_tag=nvbio::device_tag, string_iterator=thrust::detail::normal_iterator<thrust::device_ptrnvbio::uint8>, index_type=nvbio::uint32, symbol_type=nvbio::uint8]"
/home/ravi/Research/nvbio-1.1.00/nvbio-test/wavelet_test.cu(97): here

/home/ravi/Research/nvbio-1.1.00/nvbio/basic/iterator.h(101): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type"
detected during:
instantiation of class "nvbio::iterator_system [with iterator=nvbio::PackedStream<thrust::device_ptr, nvbio::uint8, 1U, true, nvbio::uint32>]"
/home/ravi/Research/nvbio-1.1.00/nvbio/strings/wavelet_tree.h(80): here
instantiation of class "nvbio::WaveletTree<BitStreamIterator, IndexIterator, SymbolType> [with BitStreamIterator=nvbio::PackedStream<thrust::device_ptr, nvbio::uint8, 1U, true, nvbio::uint32>, IndexIterator=thrust::detail::normal_iterator<thrust::device_ptr>, SymbolType=nvbio::uint8]"
/home/ravi/Research/nvbio-1.1.00/nvbio/strings/wavelet_tree.h(343): here
instantiation of "nvbio::WaveletTreeStorage<SystemTag, IndexType, SymbolType>::plain_view_type nvbio::plain_view(nvbio::WaveletTreeStorage<SystemTag, IndexType, SymbolType> &) [with SystemTag=nvbio::device_tag, IndexType=nvbio::uint32, SymbolType=nvbio::uint8]"
/home/ravi/Research/nvbio-1.1.00/nvbio-test/wavelet_test.cu(106): here

3 errors detected in the compilation of "/tmp/tmpxft_00004872_00000000-7_wavelet_test.cpp1.ii".
CMake Error at nvbio-test_generated_wavelet_test.cu.o.cmake:264 (message):
Error generating file
/home/ravi/Research/nvbio-1.1.00/build/nvbio-test/CMakeFiles/nvbio-test.dir//./nvbio-test_generated_wavelet_test.cu.o

make[2]: *** [nvbio-test/CMakeFiles/nvbio-test.dir/./nvbio-test_generated_wavelet_test.cu.o] Error 1
make[1]: *** [nvbio-test/CMakeFiles/nvbio-test.dir/all] Error 2

Regards
Ravi

[vmiheer]

@ravimanumachu, #13 (comment), nvbio needs cuda 6.5.
As an alternative I am looking at:
https://github.com/ngstools/nvbio
This repository "compiles".
While compiling if you get erros -zlibstatic not found,
Uncomment lines in CMakeLists.txt:
add_subdirectory(contrib/zlib-1.2.7)
add_subdirectory(contrib/htslib)

[changephilip]

@ravimanumachu, #13 (comment), nvbio needs cuda 6.5.
As an alternative I am looking at:
https://github.com/ngstools/nvbio
This repository "compiles".
While compiling if you get erros -zlibstatic not found,
Uncomment lines in CMakeLists.txt:
add_subdirectory(contrib/zlib-1.2.7)
add_subdirectory(contrib/htslib)

Hello, I met similar errors during compiling the Nvbio.
ngstools/nvbio cannot be found on the internet.
Could you provide a git patch to help me compile the program?
Thank you very much!

[vmiheer]

@changephilip, Try this: https://github.com/vmiheer/nvbio
There are commits from a user the ngstool author Tony which I won't vouch for. Please verify that code before using.
Thanking you,
+miheer.

[r-barnes]

master now permits compilation with newer versions of CUDA and GCC and incorporates a number of bug fixes. This issue can probably be closed (@foertter ).

[vmiheer]

Maybe @foertter should be in README.md as contact person? 🙂

[BlingLee]

也许应该在 README.md 作为联系人？🙂

Hello, I am having problems compiling nvbio and my cuda toolkit version is 12.1.
the following is error:
[ 66%] Building CXX object nvbio-test/CMakeFiles/nvbio-test.dir/sum_tree_test.cpp.o
/home/bling07/Downloads/nvbio/nvbio-test/nvbio-test.cpp: In function ‘int main(int, char**)’:
/home/bling07/Downloads/nvbio/nvbio-test/nvbio-test.cpp:101:9: error: reference to ‘cuda’ is ambiguous
cuda::check_error("cuda-check");
^~~~
In file included from /usr/local/cuda-12.1/include/cuda/std/version:13:0,
from /usr/local/cuda-12.1/include/cuda/std/cstddef:20,
from /usr/local/cuda-12.1/include/cuda/std/type_traits:17,
from /usr/local/cuda-12.1/include/thrust/detail/type_traits.h:27,
from /usr/local/cuda-12.1/include/thrust/detail/execute_with_allocator_fwd.h:21,
from /usr/local/cuda-12.1/include/thrust/detail/allocator_aware_execution_policy.h:20,
from /usr/local/cuda-12.1/include/thrust/system/cuda/detail/execution_policy.h:37,
from /usr/local/cuda-12.1/include/thrust/iterator/detail/device_system_tag.h:23,
from /home/bling07/Downloads/nvbio/nvbio/basic/types.h:35,
from /home/bling07/Downloads/nvbio/nvbio-test/nvbio-test.cpp:34:
/usr/local/cuda-12.1/include/cuda/std/detail/__config:183:14: note: candidates are: namespace cuda { }
namespace cuda { namespace std { inline namespace _LIBCUDACXX_CUDA_ABI_NAMESPACE {
^
/usr/local/cuda-12.1/include/cuda/std/cstddef:26:1: note: in expansion of macro ‘_LIBCUDACXX_BEGIN_NAMESPACE_STD’
_LIBCUDACXX_BEGIN_NAMESPACE_STD
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/bling07/Downloads/nvbio/nvbio-test/nvbio-test.cpp:37:0:
/home/bling07/Downloads/nvbio/nvbio/basic/cuda/arch.h:56:11: note: namespace nvbio::cuda { }
namespace cuda {
^~~~
/home/bling07/Downloads/nvbio/nvbio-test/nvbio-test.cpp:206:37: error: reference to ‘cuda’ is ambiguous
if (tests & kScan) cuda::scan_test();
^~~~
In file included from /usr/local/cuda-12.1/include/cuda/std/version:13:0,
from /usr/local/cuda-12.1/include/cuda/std/cstddef:20,
from /usr/local/cuda-12.1/include/cuda/std/type_traits:17,
from /usr/local/cuda-12.1/include/thrust/detail/type_traits.h:27,
from /usr/local/cuda-12.1/include/thrust/detail/execute_with_allocator_fwd.h:21,
from /usr/local/cuda-12.1/include/thrust/detail/allocator_aware_execution_policy.h:20,
from /usr/local/cuda-12.1/include/thrust/system/cuda/detail/execution_policy.h:37,
from /usr/local/cuda-12.1/include/thrust/iterator/detail/device_system_tag.h:23,
from /home/bling07/Downloads/nvbio/nvbio/basic/types.h:35,
from /home/bling07/Downloads/nvbio/nvbio-test/nvbio-test.cpp:34:
/usr/local/cuda-12.1/include/cuda/std/detail/__config:183:14: note: candidates are: namespace cuda { }
namespace cuda { namespace std { inline namespace _LIBCUDACXX_CUDA_ABI_NAMESPACE {
^
/usr/local/cuda-12.1/include/cuda/std/cstddef:26:1: note: in expansion of macro ‘_LIBCUDACXX_BEGIN_NAMESPACE_STD’
_LIBCUDACXX_BEGIN_NAMESPACE_STD
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/bling07/Downloads/nvbio/nvbio-test/nvbio-test.cpp:37:0:
/home/bling07/Downloads/nvbio/nvbio/basic/cuda/arch.h:56:11: note: namespace nvbio::cuda { }
namespace cuda {
^~~~
make[2]: *** [nvbio-test/CMakeFiles/nvbio-test.dir/build.make:199：nvbio-test/CMakeFiles/nvbio-test.dir/nvbio-test.cpp.o] 错误 1
make[2]: *** 正在等待未完成的任务....
make[1]: *** [CMakeFiles/Makefile2:924：nvbio-test/CMakeFiles/nvbio-test.dir/all] 错误 2
make: *** [Makefile:130：all] 错误 2