$ /RADTree --help
Compute a sum of distributed double values
Usage:
RADTree [OPTION...]
--allreduce Use MPI_Allreduce to compute the sum
--baseline Gather numbers on a single rank and use
std::accumulate
--tree Use the distributed binary tree scheme to compute
the sum (default: true)
-f, --file arg File name of the binary psllh file
-r, --repetitions arg Repeat the calculation at most n times (default:
18446744073709551615)
-d, --duration arg Run the calculation for at least n seconds.
(default: 0)
-h, --help Display this help message
RADTree allows summation of per-site log-likelihood files (psllh, binpsllh).
There are three methods of calculation:
- Allreduce. The summands are scattered across the cluster, accumulated locally and then reduced into a global sum. Since the order of summation depends on the cluster size, this method yields different results on different clusters.
- Baseline. This is a simple variant used to compare performance of the tree summation. It simply gathers all summands on a single rank, accumulates them locally and broadcasts the result.
- Tree. The summands are distributed across the cluster. The summation order is given through a binary tree, with each leaf corresponding to a summand. The ranks reduce the sums locally in the given order and exchange intermediary results where necessary. After the whole sum has been computed as root of the tree, rank 0 broadcasts it to the other ranks.
cmake -DBUILD_TESTS=ON -DBUILD_BENCHMARKS=ON -B build -S .
make -C build./build/test/tests # Run unit tests of C++ code
python3 test/reproducibility_test.py # Run reproducibility tests./build/benchmarks/benchmark # Run microbenchmarks
python3 benchmarks/benchmark.py # Run large benchmark on different datasetsThis will generate a sqlite database under benchmarks/results.db.