Problem in proteinsw_qp.cu file

[mmmovania]

I think there is a typo in this source file https://github.com/NVlabs/nvbio/blob/master/examples/proteinsw/proteinsw_qp.cu
Line 214 is this
nvbio::make_concatenated_string_set(n_strings, thrust::make_constant_iterator<nvbio::uint32>(0), (const nvbio::uint32*)raw_pointer(d_pattern_offsets)),

which gives me the following errors in VisualStudio2013

1> E:\Codes\GeneSequence\TestnvBio\TestnvBio>"C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\bin\nvcc.exe" -gencode=arch=compute_20,code=\"sm_20,compute_20\" --use-local-env --cl-version 2013 -ccbin "C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\bin" -IE:\Libraries\nvbio -I"E:\Libraries\cub-1.4.1" -I"C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\include" -I"C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\include" -G --keep-dir Debug -maxrregcount=0 --machine 32 --compile -cudart static -g -DNOMINMAX -DWIN32 -D_DEBUG -D_CONSOLE -D_MBCS -Xcompiler "/EHsc /W3 /nologo /Od /Zi /RTC1 /MDd " -o Debug\proteinsw_qp.cu.obj "E:\Codes\GeneSequence\TestnvBio\TestnvBio\proteinsw_qp.cu" 1>E:\Libraries\nvbio\nvbio/strings/string_traits.h(42): error : class "thrust::constant_iterator<nvbio::uint32, thrust::use_default, thrust::use_default>" has no member "SYMBOL_SIZE" 1>E:\Libraries\nvbio\nvbio/strings/string_traits.h(46): error : class "thrust::constant_iterator<nvbio::uint32, thrust::use_default, thrust::use_default>" has no member "index_type" 1>E:\Libraries\nvbio\nvbio/strings/string_traits.h(47): error : class "thrust::constant_iterator<nvbio::uint32, thrust::use_default, thrust::use_default>" has no member "iterator" 1>E:\Libraries\nvbio\nvbio/strings/string_traits.h(48): error : class "thrust::constant_iterator<nvbio::uint32, thrust::use_default, thrust::use_default>" has no member "const_iterator" 1>E:\Libraries\nvbio\nvbio/strings/string_traits.h(49): error : class "thrust::constant_iterator<nvbio::uint32, thrust::use_default, thrust::use_default>" has no member "forward_iterator" 1>E:\Libraries\nvbio\nvbio/alignment/gotoh/gotoh_inl.h(1308): error : no instance of function template "nvbio::vectorized_string_load" matches the argument list 1>E:\Libraries\nvbio\nvbio/alignment/gotoh/gotoh_inl.h(1308): error : no instance of function template "nvbio::vectorized_string_load" matches the argument list 1> proteinsw_qp.cu

Solution

Change line 214 to this
nvbio::make_concatenated_string_set(n_strings, (const nvbio::uint8*)raw_pointer(d_pattern_strings), (const nvbio::uint32*)raw_pointer(d_pattern_offsets)),

Is this correction fine?

[jpantaleoni]

Yes, it looks fine - I'll take a look!
On Jun 11, 2015 10:17 AM, "Muhammad Mobeen Movania" <
[email protected]> wrote:

I think there is a typo in this source file
https://github.com/NVlabs/nvbio/blob/master/examples/proteinsw/proteinsw_qp.cu
Line 214 is this
nvbio::make_concatenated_string_set(n_strings,
thrust::make_constant_iteratornvbio::uint32(0), (const
nvbio::uint32*)raw_pointer(d_pattern_offsets)),

which gives me the following errors in VisualStudio2013

1> E:\Codes\GeneSequence\TestnvBio\TestnvBio>"C:\Program Files\NVIDIA GPU
Computing Toolkit\CUDA\v6.5\bin\nvcc.exe"
-gencode=arch=compute_20,code="sm_20,compute_20" --use-local-env
--cl-version 2013 -ccbin "C:\Program Files (x86)\Microsoft Visual Studio
12.0\VC\bin" -IE:\Libraries\nvbio -I"E:\Libraries\cub-1.4.1" -I"C:\Program
Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\include" -I"C:\Program
Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\include" -G --keep-dir Debug
-maxrregcount=0 --machine 32 --compile -cudart static -g -DNOMINMAX -DWIN32
-D_DEBUG -D_CONSOLE -D_MBCS -Xcompiler "/EHsc /W3 /nologo /Od /Zi /RTC1
/MDd " -o Debug\proteinsw_qp.cu.obj
"E:\Codes\GeneSequence\TestnvBio\TestnvBio\proteinsw_qp.cu"
1>E:\Libraries\nvbio\nvbio/strings/string_traits.h(42): error : class
"thrust::constant_iterator<nvbio::uint32, thrust::use_default,
thrust::use_default>" has no member "SYMBOL_SIZE"
1>E:\Libraries\nvbio\nvbio/strings/string_traits.h(46): error : class
"thrust::constant_iterator<nvbio::uint32, thrust::use_default,
thrust::use_default>" has no member "index_type"
1>E:\Libraries\nvbio\nvbio/strings/string_traits.h(47): error : class
"thrust::constant_iterator<nvbio::uint32, thrust::use_default,
thrust::use_default>" has no member "iterator"
1>E:\Libraries\nvbio\nvbio/strings/string_traits.h(48): error : class
"thrust::constant_iterator<nvbio::uint32, thrust::use_default,
thrust::use_default>" has no member "const_iterator"
1>E:\Libraries\nvbio\nvbio/strings/string_traits.h(49): error : class
"thrust::constant_iterator<nvbio::uint32, thrust::use_default,
thrust::use_default>" has no member "forward_iterator"
1>E:\Libraries\nvbio\nvbio/alignment/gotoh/gotoh_inl.h(1308): error : no
instance of function template "nvbio::vectorized_string_load" matches the
argument list
1>E:\Libraries\nvbio\nvbio/alignment/gotoh/gotoh_inl.h(1308): error : no
instance of function template "nvbio::vectorized_string_load" matches the
argument list
1> proteinsw_qp.cu
Solution

Change line 214 to this
nvbio::make_concatenated_string_set(n_strings, (const
nvbio::uint8_)raw_pointer(d_pattern_strings), (const
nvbio::uint32_)raw_pointer(d_pattern_offsets)),

Is this correction fine?

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