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HemePure

Build dependencies before attempting to build HemePure.

DEPENDENCIES

  1. Create dep/build/.
  2. In dep/build/ run ccmake -B. -H../' or 'ccmake ...
  3. Configure using CMake.
  4. Run make in dep/build/.

SOURCE

  1. Create src/build/.
  2. In src/build/ run ccmake -B. -H../ or ccmake ...
  3. Configure using CMake.
  4. Run make in src/build/.

CASES

  • Two simple examples are included:
    • pressure-driven flow in a pipe.
    • pressure-driven flow in a wye joint (provided at two resolutions).
  • Run with: mpirun -np xx <HemePure binary> -in input.xml.
  • Case should run with the default build options.
  • Ensure that you are running with enough MPI ranks to satisfy HEMELB_READING_GROUP_SIZE.

DEVELOPMENT

A few parts of the code are under heavy development.

Although the current version of ALL has been fully incorporated, ALL itself is undergoing development. As a result, it is likely that the implementation in src/geometry/decomposition/BasicDecomposition.cc (in the function BasicDecomposition::DecomposeBlock()) will need to be modified. Once development is complete, ALL should be enabled through cmake. After rotation of the geometry (necessary for ALL decomposition), HemeLB and ALL interact through

points.push_back(p);

where

#ifdef HEMELB_USE_GMYPLUS
	ALL_Point<double> p(3,block_coords,blockWeights.at(blockNumber));
#else
	ALL_Point<double> p(3,block_coords,1);
#endif

This is dependant on block weighting (included in .gmy+ files). To use BasicDecomposition::DecomposeBlock(), uncomment the call in GeometryReader.cc. Note, geometry rotation is necessary so that layers of sites and partition boundary surfaces are not parallel. Rotation is performed in BasicDecomposition::RotateAndAllocate.

The new shared memory implementation (found in GeometryReader.cc) only shares principalProcForEachBlock. Further savings can be achieved by sharing other common variables, e.g. blockInformation. Also note that only the MPI_WIN_UNIFIED memory model is supported (see https://www.mpi-forum.org/docs/mpi-3.1/mpi31-report/node278.htm#Node278). If the machine in use does not support this, it will not be possible to use this implementation. EPCC ARCHER seems to have issues with the current implementation. Further investigation is necessary.

Verification checks have yet to be reintroduced following conversion of sequential containers std::vector to associative containers std::unordered_map. Checks are performed during loading and decomposition. They are currently commented out and disabled at compile time. Cross-reference with master branch of HemeLB. Checks will need to be rewritten.

NOTES

  • Compilation of some dependencies is disabled:
    • CppUnit: compilation of unit tests is disabled.
  • This version of HemePure is in continuous development - some features are in testing.
  • Disable optimised decomposition for memory-intensive runs. ParMETIS is resource hungry.