pmap is as simple as
>>> import pytraj as pt
>>> pt.pmap(pt.radgyr, traj, n_cores=4)
pytraj.parallel.mpi.pmap_mpi(func, traj, *args, **kwd)¶parallel with MPI (mpi4py)
| Parameters: | func : a function traj : pytraj.TrajectoryIterator *args, **kwd: additional arguments |
|---|
Examples
$ # create test_radgyr.py file
$ cat > test_radgyr.py <<EOF
import pytraj as pt
from mpi4py import MPI
comm = MPI.COMM_WORLD
traj = pt.iterload('tz2.nc', 'tz2.parm7')
result_arr = pt.pmap_mpi(pt.radgyr, traj, "@CA")
if comm.rank == 0:
# save data to disk to read later by pytraj.read_pickle
# pt.to_pickle(result_arr, 'output.pk')
print(result_arr)
EOF
$ # run in parallel
$ mpirun -n 4 python ./test_radgyr.py
[array([ 8.10916061, 7.7643485 , 8.09693108, ..., 9.70825678,
9.3161563 , 8.86720964]), array([ 8.82037273, 8.89008289, 9.48540176, ..., 9.29585981,
9.53138062, 9.19155977]), array([ 9.13735723, 8.94651001, 8.97810478, ..., 7.68751186,
8.31361647, 7.83763754]), array([ 7.37423766, 7.05637263, 6.52135566, ..., 6.38061648,
6.24139008, 6.48994552])]