Make failing

[claczny]

Hi,

I just tried do build the latest commit

$ git rev-parse HEAD
42fb5b4f2ff825b2339a8e7b254ec400e822130c

but received the following error:

$ make
  AR       libdeflate.a
  CXX      programs/gunzip.o
In file included from programs/../lib/deflate_decompress.hpp:61:0,
                 from programs/../lib/gzip_decompress.hpp:40,
                 from programs/gunzip.cpp:28:
programs/../lib/input_stream.hpp: In member function ‘bool InputStream::set_position_bits(size_t)’:
programs/../lib/input_stream.hpp:233:16: warning: declaration of ‘bits’ shadows a member of ‘InputStream’ [-Wshadow]
         size_t bits  = bit_pos & 7;
                ^~~~
programs/../lib/input_stream.hpp:282:39: note: shadowed declaration is here
     template<typename T = uint32_t> T bits(bitbuf_size_t n = 8 * sizeof(T)) const
                                       ^~~~
In file included from programs/../lib/deflate_decompress.hpp:58:0,
                 from programs/../lib/gzip_decompress.hpp:40,
                 from programs/gunzip.cpp:28:
programs/../lib/memory.hpp: In instantiation of ‘unique_span<T, D>::unique_span() [with T = unsigned char; D = lock_releaser<std::mutex>]’:
programs/../lib/deflate_decompress.hpp:946:42:   required from here
programs/../lib/memory.hpp:227:21: error: no matching function for call to ‘lock_releaser<std::mutex>::lock_releaser()’
       , _end(nullptr)
                     ^
programs/../lib/memory.hpp:436:39: note: candidate: lock_releaser<std::mutex>::lock_releaser(std::unique_lock<std::mutex>::mutex_type&)
     using std::unique_lock<Lockable>::unique_lock;
                                       ^~~~~~~~~~~
programs/../lib/memory.hpp:436:39: note:   candidate expects 1 argument, 0 provided
programs/../lib/memory.hpp:436:39: note: candidate: lock_releaser<std::mutex>::lock_releaser(std::unique_lock<std::mutex>::mutex_type&, std::defer_lock_t)
programs/../lib/memory.hpp:436:39: note:   candidate expects 2 arguments, 0 provided
programs/../lib/memory.hpp:436:39: note: candidate: lock_releaser<std::mutex>::lock_releaser(std::unique_lock<std::mutex>::mutex_type&, std::try_to_lock_t)
programs/../lib/memory.hpp:436:39: note:   candidate expects 2 arguments, 0 provided
programs/../lib/memory.hpp:436:39: note: candidate: lock_releaser<std::mutex>::lock_releaser(std::unique_lock<std::mutex>::mutex_type&, std::adopt_lock_t)
programs/../lib/memory.hpp:436:39: note:   candidate expects 2 arguments, 0 provided
programs/../lib/memory.hpp:436:39: note: candidate: template<class _Clock, class _Duration> lock_releaser<std::mutex>::lock_releaser(std::unique_lock<std::mutex>::mutex_type&, const std::chrono::time_point<_Clock, _Duration1>&)
programs/../lib/memory.hpp:436:39: note:   template argument deduction/substitution failed:
programs/../lib/memory.hpp:227:21: note:   candidate expects 2 arguments, 0 provided
       , _end(nullptr)
                     ^
programs/../lib/memory.hpp:436:39: note: candidate: template<class _Rep, class _Period> lock_releaser<std::mutex>::lock_releaser(std::unique_lock<std::mutex>::mutex_type&, const std::chrono::duration<_Rep1, _Period1>&)
     using std::unique_lock<Lockable>::unique_lock;
                                       ^~~~~~~~~~~
programs/../lib/memory.hpp:436:39: note:   template argument deduction/substitution failed:
programs/../lib/memory.hpp:227:21: note:   candidate expects 2 arguments, 0 provided
       , _end(nullptr)
                     ^
programs/../lib/memory.hpp:438:5: note: candidate: lock_releaser<Lockable>::lock_releaser(std::unique_lock<_Mutex>&&) [with Lockable = std::mutex]
     lock_releaser(std::unique_lock<Lockable>&& lock) noexcept
     ^~~~~~~~~~~~~
programs/../lib/memory.hpp:438:5: note:   candidate expects 1 argument, 0 provided
programs/../lib/memory.hpp:434:49: note: candidate: lock_releaser<std::mutex>::lock_releaser(lock_releaser<std::mutex>&&)
 template<typename Lockable = std::mutex> struct lock_releaser : private std::unique_lock<Lockable>
                                                 ^~~~~~~~~~~~~
programs/../lib/memory.hpp:434:49: note:   candidate expects 1 argument, 0 provided
make: *** [programs/gunzip.o] Error 1

My compiler:

$ g++ --version
g++ (GCC) 6.4.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Not sure what I missed here.

Thank you for your input on this issue!

Best,

Cedric

[Piezoid]

Thanks for the report.
It should be fixed in master.

It's a suitability in constructor inheritance with older version of GCC. Not sure what happened exactly...

[Piezoid]

Is the problem solved on your side ?
(closing for now, assuming it's resolved)

[claczny]

Yes, I could compile and run the bigger_benchmarck.sh.
Thank you for the quick fix!

On our uni.lu HPC on a node with 28 cores, I got 255 MB/s (decompressing with pugz) and 2154 MB/s (counting lines with pugz).

Nice tool :)

[Piezoid]

Thanks !

Yes it shows how costly in wall time it is to synchronize threads for output. I think this could be improved.

[rchikhi]

Also of note, for things like a FASTQ parser, such a costly synchronization won't be necessary.