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Add MPI test application
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‎source-code/mpi4py/README.md

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@@ -21,3 +21,4 @@ C/C++ or Fortran implementations.
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1. `mpi_count.py`: count amino acids in a long sequence, distributing
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the work over processes.
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1. `large_dna.txt`: example data file to use with `mpi_count.py`.
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1. `mpifitness.py`: application to tmie various MPI communications.

‎source-code/mpi4py/mpifitness.py

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#!/usr/bin/env python
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from argparse import ArgumentParser
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from mpi4py import MPI
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import sys
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import time
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def make_msg(value, nr_bytes):
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return f'{value:08d}'*(nr_bytes//8)
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def make_float_msg(value, nr_bytes):
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return float(value)*(nr_bytes//8)
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def acknowledge(comm):
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comm.barrier()
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rank = comm.Get_rank()
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size = comm.Get_size()
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print(f'process {rank} out of {size}')
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comm.barrier()
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def pingpong(comm, nr_iters, msg_size):
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comm.barrier()
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rank = comm.Get_rank()
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size = comm.Get_size()
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for _ in range(nr_iters):
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for source in range(size):
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for dest in range(size):
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if (source != dest):
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if rank == source:
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start_time = time.time()
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comm.send(make_msg(source, msg_size), dest=dest)
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msg = comm.recv(source=dest)
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end_time = time.time()
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if msg != make_msg(dest, msg_size):
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print(f'{rank} received {msg}, expected {dest}',
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file=sys.stderr)
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comm.Abort(1)
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print(f'{rank} -> {dest} pig-pong: {end_time - start_time}')
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if rank == dest:
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start_time = time.time()
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msg = comm.recv(source=source)
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comm.send(make_msg(dest, msg_size), dest=source)
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end_time = time.time()
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if msg != make_msg(source, msg_size):
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print(f'{rank} received {msg}, expected {source}',
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file=sys.stderr)
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comm.Abort(1)
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print(f'{rank} -> {source} ping-pong: {end_time - start_time}')
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comm.barrier()
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def broadcast(comm, nr_iters, msg_size):
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comm.barrier()
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rank = comm.Get_rank()
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size = comm.Get_size()
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for _ in range(nr_iters):
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for root in range(size):
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msg = None
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if (rank == root):
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msg = make_msg(root, msg_size)
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start_time = time.time()
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msg = comm.bcast(msg, root=root)
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end_time = time.time()
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print(f'{root} -> {rank} bcast: {end_time - start_time}')
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if msg != make_msg(root, msg_size):
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print(f'{rank} received unexpected bcast message')
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comm.Abort(2)
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comm.barrier()
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def scatter(comm, nr_iters, msg_size):
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comm.barrier()
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rank = comm.Get_rank()
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size = comm.Get_size()
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for _ in range(nr_iters):
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for root in range(size):
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msg = None
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if (rank == root):
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msg = [make_msg(dest, msg_size) for dest in range(size)]
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start_time = time.time()
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msg = comm.scatter(msg, root=root)
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end_time = time.time()
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print(f'{root} -> {rank} scatter: {end_time - start_time}')
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if msg != make_msg(rank, msg_size):
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print(f'{rank} received unexpected scatter message')
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comm.Abort(2)
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comm.barrier()
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def gather(comm, nr_iters, msg_size):
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comm.barrier()
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rank = comm.Get_rank()
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size = comm.Get_size()
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for _ in range(nr_iters):
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for root in range(size):
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msg = make_msg(rank, msg_size)
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start_time = time.time()
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msg = comm.gather(msg, root=root)
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end_time = time.time()
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print(f'{root} -> {rank} gather: {end_time - start_time}')
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if (rank == root):
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if len(msg) != size:
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print(f'{rank} received unexpected gather message')
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comm.Abort(2)
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for i, msg in enumerate(msg):
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if msg != make_msg(i, msg_size):
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print(f'{rank} received unexpected gather message')
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comm.Abort(2)
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comm.barrier()
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def alltoall(comm, nr_iters, msg_size):
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comm.barrier()
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rank = comm.Get_rank()
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size = comm.Get_size()
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for _ in range(nr_iters):
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msg = [make_msg(rank, msg_size) for _ in range(size)]
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start_time = time.time()
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msg = comm.alltoall(msg)
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end_time = time.time()
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print(f'{rank} alltoall: {end_time - start_time}')
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if len(msg) != size:
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print(f'{rank} received unexpected alltoall message')
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comm.Abort(2)
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for i, msg in enumerate(msg):
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if msg != make_msg(i, msg_size):
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print(f'{rank} received unexpected alltoall message')
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comm.Abort(2)
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comm.barrier()
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def reduce(comm, nr_iters, msg_size):
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comm.barrier()
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rank = comm.Get_rank()
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size = comm.Get_size()
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for _ in range(nr_iters):
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for root in range(size):
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msg = make_float_msg(rank, msg_size)
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start_time = time.time()
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msg = comm.reduce(msg, op=MPI.SUM, root=root)
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end_time = time.time()
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print(f'{root} -> {rank} reduce: {end_time - start_time}')
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comm.barrier()
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def main():
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root = 0
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comm = MPI.COMM_WORLD
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rank = comm.Get_rank()
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if (rank == root):
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print(f'# acknowledgment')
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acknowledge(comm)
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arg_parser = ArgumentParser(description='MPI performance benchmark')
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arg_parser.add_argument('--nr_pingpongs', type=int, default=10,
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help='number of ping-pong iterations to perform')
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arg_parser.add_argument('--pingpong_size', type=int, default=8,
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help='number of bytes for ping-pong message')
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arg_parser.add_argument('--nr_bcasts', type=int, default=10,
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help='number of broadcast iteration to perform')
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arg_parser.add_argument('--bcast_size', type=int, default=8,
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help='number of bytes for broadcast message')
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arg_parser.add_argument('--nr_scatters', type=int, default=10,
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help='number of scatter iteration to perform')
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arg_parser.add_argument('--scatter_size', type=int, default=8,
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help='number of bytes for scatter message')
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arg_parser.add_argument('--nr_gathers', type=int, default=10,
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help='number of gather iteration to perform')
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arg_parser.add_argument('--gather_size', type=int, default=8,
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help='number of bytes for gather message')
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arg_parser.add_argument('--nr_alltoalls', type=int, default=10,
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help='number of alltoall iteration to perform')
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arg_parser.add_argument('--alltoall_size', type=int, default=8,
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help='number of bytes for alltoall message')
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arg_parser.add_argument('--nr_reduces', type=int, default=10,
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help='number of reduce iteration to perform')
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arg_parser.add_argument('--reduce_size', type=int, default=8,
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help='number of bytes for reduce message')
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options = arg_parser.parse_args()
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comm.barrier()
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if (rank == root):
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print(f'# {options.nr_pingpongs} ping-pong iterations, '
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f'size {options.pingpong_size}')
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comm.barrier()
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pingpong(comm, options.nr_pingpongs, options.pingpong_size)
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comm.barrier()
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if (rank == root):
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print(f'# {options.nr_bcasts} broadcast iterations, '
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f'size {options.bcast_size}')
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comm.barrier()
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broadcast(comm, options.nr_bcasts, options.bcast_size)
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comm.barrier()
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if (rank == root):
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print(f'# {options.nr_scatters} scatter iterations, '
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f'size {options.scatter_size}')
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comm.barrier()
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scatter(comm, options.nr_scatters, options.scatter_size)
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comm.barrier()
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if (rank == root):
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print(f'# {options.nr_gathers} gather iterations, '
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f'size {options.gather_size}')
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comm.barrier()
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gather(comm, options.nr_gathers, options.gather_size)
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comm.barrier()
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if (rank == root):
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print(f'# {options.nr_alltoalls} alltoall iterations, '
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f'size {options.alltoall_size}')
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comm.barrier()
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alltoall(comm, options.nr_alltoalls, options.alltoall_size)
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comm.barrier()
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if (rank == root):
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print(f'# {options.nr_reduces} reduce iterations, '
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f'size {options.reduce_size}')
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comm.barrier()
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reduce(comm, options.nr_reduces, options.reduce_size)
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comm.barrier()
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return 0
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if __name__ == '__main__':
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sys.exit(main())

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