18. Jupyter Notebook Setup¶
To use Bodo with Jupyter Notebook, install
in your Bodo Conda environment:
conda install jupyter ipyparallel mpi4py -c conda-forge
Create an MPI profile for IPython:
ipython profile create --parallel --profile=mpi
and add the following line:
c.IPClusterEngines.engine_launcher_class = 'MPIEngineSetLauncher'
Start the Jupyter notebook in your Bodo Conda environment:
Go to IPython Clusters tab and select the
number of engines (i.e., cores) you’d like to use and click Start next to the
mpi profile. Alternatively, you can use
ipcluster start -n 4 --profile=mpi
in a terminal to start the engines. Initialization of the engines can take several seconds.
Now start a new notebook and run this code in a cell to setup the environment:
import ipyparallel as ipp c = ipp.Client(profile='mpi') view = c[:] view.activate() view.block = True # equivalent to running with %%px --block # Set the working directory: import os view["cwd"] = os.getcwd() %px cd $cwd
This should complete without any errors. An error may appear if the cluster is not initialized yet (usually NoEnginesRegistered). In this case, just wait a few seconds and try again.
You can now run Bodo functions on the execution engines
using ipyparallel hooks such as
and the work will be distributed
across the engines. For example, run this code in a cell:
%%px import bodo import numpy as np import time @bodo.jit def calc_pi(n): t1 = time.time() x = 2 * np.random.ranf(n) - 1 y = 2 * np.random.ranf(n) - 1 pi = 4 * np.sum(x**2 + y**2 < 1) / n print("Execution time:", time.time()-t1, "\nresult:", pi) calc_pi(2 * 10**8)
If you wish to run across multiple nodes, you can add the following to ipcluster_config.py:
c.MPILauncher.mpi_args = ["-machinefile", "path_to_file/machinefile"]
where machinefile (or hostfile) is a file with the hostnames of available nodes that MPI can use. More information about machinefiles can be found here.
It is important to note that other MPI systems and launchers (such as QSUB/PBS) may use a different user interface for the allocation of computational nodes.