utils.h 2.8 KB

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  1. /*
  2. * nvbio
  3. * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
  4. *
  5. * Redistribution and use in source and binary forms, with or without
  6. * modification, are permitted provided that the following conditions are met:
  7. * * Redistributions of source code must retain the above copyright
  8. * notice, this list of conditions and the following disclaimer.
  9. * * Redistributions in binary form must reproduce the above copyright
  10. * notice, this list of conditions and the following disclaimer in the
  11. * documentation and/or other materials provided with the distribution.
  12. * * Neither the name of the NVIDIA CORPORATION nor the
  13. * names of its contributors may be used to endorse or promote products
  14. * derived from this software without specific prior written permission.
  15. *
  16. * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
  17. * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  18. * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
  19. * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY
  20. * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
  21. * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
  22. * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
  23. * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
  24. * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
  25. * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  26. */
  27. #pragma once
  28. #include <nvbio/basic/timer.h>
  29. #include <nvbio/basic/cuda/timer.h>
  30. #include <cuda_runtime.h>
  31. namespace nvbio {
  32. namespace bowtie2 {
  33. namespace cuda {
  34. inline void optional_device_synchronize()
  35. {
  36. #if DO_OPTIONAL_SYNCHRONIZE
  37. cudaDeviceSynchronize();
  38. #endif
  39. }
  40. #if DO_DEVICE_TIMING
  41. typedef nvbio::cuda::Timer DeviceTimer;
  42. #else
  43. typedef nvbio::FakeTimer DeviceTimer;
  44. #endif
  45. // convert a range from a [begin,last] representation to a [begin,end) one
  46. NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
  47. uint2 inclusive_to_exclusive(const uint2 range) { return make_uint2( range.x, range.y + 1u ); }
  48. #ifdef __CUDACC__
  49. // alloc some slots from a counter using a warp-synchronous reduction
  50. NVBIO_FORCEINLINE NVBIO_DEVICE uint32 alloc(uint32* counter, volatile uint32 *warp_broadcast)
  51. {
  52. #if USE_WARP_SYNCHRONOUS_QUEUES
  53. const uint32 mask = __ballot( true );
  54. const uint32 pop_scan = __popc( mask << (32u - warp_tid()) );
  55. const uint32 pop_count = __popc( mask );
  56. if (pop_scan == 0)
  57. *warp_broadcast = atomicAdd( counter, pop_count );
  58. return *warp_broadcast + pop_scan;
  59. #else
  60. return atomicAdd( counter, 1u );
  61. #endif
  62. }
  63. #endif // __CUDACC__
  64. } // namespace cuda
  65. } // namespace bowtie2
  66. } // namespace nvbio