Parallel Meep


Meep supports distributed-memory parallelism via MPI. This allows it to scale up from single multi-core machines to multi-node clusters and supercomputers, and to work on large problems that may not fit into the memory of one machine. Meep simulations can use hundreds of processors, if necessary. Of course, your problem must be sufficiently large in order to benefit from many processors. (Note that it is not possible to run a parallel simulation from within a notebook environment.)

Installing Parallel Meep

To build from source the parallel version of Meep, you must have a version of MPI installed on your system. For an overview, see Build From Source/MPI.

We also strongly recommend installing the HDF5 package with parallel I/O support if you are going to run with more than a few cores/processors. When building from source, HDF5 needs to be configured with the flag --enable-parallel. You may also have to set the CC environment variable to mpicc.

If you don't install HDF5 with parallel I/O support, you can still do I/O from MPI — Meep has some hacks to let it write HDF5 files using serial I/O from multiple processes, one at a time. However, this does not scale very well to many processors. Some MPI implementations have been observed to freeze under the strain of trying to write from many processes at once.

Then you just configure Meep with the flag --with-mpi. If you run the resulting Python or Scheme script, it runs on a single process; to run with multiple cores/processors you should use mpirun as described in the next section. Because you can run the parallel Meep in a single process using this approach (i.e., mpirun -np 1 python foo.py or just python foo.py, mpirun -np 1 meep foo.ctl or just meep foo.ctl), there is no need to separately compile and install the serial version of Meep.

Using Parallel Meep

The parallel version of Meep is designed to operate completely transparently: you use the same Python or Scheme script as for the serial version; the output is the same but it is just faster. In Python, the output of each process that is not the master (rank 0) is sent to devnull, and in Scheme, the special print function only prints output from the master process.

In order to run MPI programs, you typically have to use a command like mpirun with an argument to indicate how many processes you want to use. Consult your MPI documentation. For example, with many popular MPI implementations, to run with 4 processes you would use something like:

Python

mpirun -np 4 python foo.py > foo.out

Scheme

mpirun -np 4 meep foo.ctl > foo.out

There is one important requirement: every MPI process must be able to read the foo.py/foo.ctl input file or whatever your script file is called. On most systems, this is no problem, but if for some reason your MPI processes don't all have access to the local filesystem then you may need to make copies of your input file or something. This requirement also applies to HDF5 files used for input (i.e., via epsilon_input_file) or output (i.e., output_epsilon(), output_efield(), etc.). Any disruptions to the network or disk failures on individual machines which affect the network file system may cause Meep to freeze/hang.

For a potential improvement in load balancing, you can try setting split_chunks_evenly=False in the Simulation constructor. For a technical description of the load balancing features in Meep as well as some performance metrics, see arXiv:2003.04287.

In general, you cannot run Meep interactively on multiple processors.

Warning: when running a parallel PyMeep job, the failure of any one MPI process may cause the simulation to deadlock and not abort. This is due to a behavior of mpi4py. To avoid having to manually kill all the remaining processes, a simple solution is to load the mpi4py module (for versions 3.0+) on the mpirun command line:

mpirun -np 4 python -m mpi4py foo.py

Different Forms of Parallelization

Parallel Meep works by taking your simulation and dividing the cell among the MPI processes. This is the only way of parallelizing a single simulation and enables simulating very large problems.

However, there is an alternative strategy for parallelization. If you have many smaller simulations that you want to run, say for many different values of some parameter, then you can just run these as separate jobs. Such parallelization is known as embarrassingly parallel because no communication is required. Additionally, Meep provides explicit support for this mode of operation even when using a single MPI job via the meep.divide_parallel_processes(N) routine which divides N MPI processes into N equal subgroups and returns the index n (0,...,N-1) of the current group which can be used to decide which simulation to run. That is, you have one script, and the script only creates one simulation object — depending on the value of n that it receives, it will create a different simulation object (i.e., using different parameters). Only the fields from the same subgroup communicate using MPI. There is an auxiliary routine meep.merge_subgroup_data(data) which takes a NumPy array data from every process (which is identical across each subgroup) and then returns an array which is just the concatenated data from each subgroup. For an example, see python/tests/divide_mpi_processes.py in the source repository. This feature can be useful for large supercomputers which typically restrict the total number of jobs that can be executed but do not restrict the size of each job. Note that when using this feature using the Python interface, only the output of the subgroup belonging to the master process of the entire simulation is shown in the standard output. (In C++, the master process from every subgroup prints to standard output.)

Meep also supports thread-level parallelism (i.e., multi-threading) on a single, shared-memory, multi-core machine for multi-frequency near-to-far field computations. Meep does not currently use thread-level parallelism for the time stepping although this feature may be added in the future (see Issue #228).

Technical Details

When you run Meep under MPI, the following is a brief description of what is happening behind the scenes. For the most part, you shouldn't need to know this stuff. Just use the same Python/Scheme script file exactly as you would for a uniprocessor simulation.

First, every MPI process executes the Python/Scheme file in parallel. The processes communicate however, to only perform one simulation in sync with one another. In particular, the cell is divided into "chunks", one per process, to roughly equally divide the work and the memory. For additional details, see Chunks and Symmetry as well as Section 2.2 ("Grid chunks and owned points") of Computer Physics Communications, Vol. 181, pp. 687-702, 2010.

When you time-step via Python's meep.Simulation.run(until=...) or Scheme's run-until, etc., the chunks are time-stepped in parallel, communicating the values of the pixels on their boundaries with one another. In general, any Meep function that performs some collective operation over the whole cell or a large portion thereof is parallelized, including: time-stepping, HDF5 I/O, accumulation of flux spectra, and field integration via integrate_field_function (Python) or integrate-field-function (Scheme), although the results are communicated to all processes.

Computations that only involve isolated points, such as get_field_point (Python) or get-field-point (Scheme), or Harminv (Python) or harminv (Scheme) analyses, are performed by all processes redundantly. In the case of get_field_point or get-field-point, Meep figures out which process "knows" the field at the given field, and then sends the field value from that process to all other processes. This is harmless because such computations are rarely performance bottlenecks.

Although all processes execute the Python/Scheme file in parallel, print statements are ignored for all process but one (process #0). In this way, you only get one copy of the output.

Sometimes you only want an operation to take place on one process. A common use case is showing a matplotlib plot with plt.show(), or saving a file with plt.savefig(). In cases where you need to distinguish different MPI processes in your Python/Scheme file, you can use the following functions:

meep.am_master(), (meep-am-master) — Returns true if the current process is the master process (rank 0).

This can be useful for calling external I/O or visualization routines, e.g. Matplotlib plotting functions, that you only want to execute on the master process. Note that the Scheme (print) or Python print functions are already set up so that by default their output is suppressed on non-master processes.

Warning: Most Meep functions operating on the simulation (e.g. fields or structure) are "collective" operations that must be called from all processes in the same sequence — if you call them from only one process via am_master (or my_rank) checks, then they will deadlock. Code inside an am_master check should generally only call non-Meep library functions.

meep.count_processors(), (meep-count-processors) — Returns the number of processes that Meep is using in parallel.

meep.my_rank(), (meep-my-rank) — Returns the index of the process running the current file, from zero to meep.count_processors()-1.

meep.all_wait(), (meep-all-wait) — Blocks until all processes execute this statement (MPI_Barrier).

For large multicore jobs with I/O, it may be necessary to have (meep-all-wait) as the last line in the Scheme file to ensure that all processors terminate at the same point in the execution. Otherwise, one processor may finish and abruptly terminate the other processors.

Runtime Scaling on MPI Clusters

The following are benchmarking results of the total runtime vs. number of processors for a 3d OLED simulation involving Lorentzian susceptibility, Absorber, 1d PML, and DFT flux monitors for MPICH clusters of n1-standard-16 instances (8 single-threaded cores) on the Google Cloud Platform (GCP). One slot on each node is reserved for kernel tasks leaving 7 slots per node. The software stack includes Ubuntu 16.04, the Meep nightly build Conda package, elasticluster for the cluster management, and grid engine for the job scheduler. In order to reduce cache contention, process affinity is used via the mpirun option -bind-to core. Meep's simulation domain is split into equal-sized chunks (split_chunks_evenly=True). There are 13 clusters ranging in size from 2 to 14 nodes (14 to 98 processors).

As shown in the first figure below, the runtime reaches a minimum at 77 processors. The second figure shows the scaling of the ratio of the mean time spent on communication (MPI/synchronization) to the computation (time stepping and DFTs). (Timing metrics were obtained using Simulation.mean_time_spent_on.) This ratio is a measure of the parallelization efficiency. The crossover point when the parallelization efficiency becomes larger than one — the regime in which the simulation is constrained by the network bandwidth rather than the CPU clock speed — corresponds well to the minimum runtime of the first figure.

These results are not continuous because as the number of processors changes slightly (e.g., from 42 to 49), the chunk divisions can change by a lot (i.e., it can switch from splitting some chunk along the axis to along the axis) which significantly affects the runtime performance.

For a given cluster, we can also analyze the time spent by each processor on time-stepping, MPI/synchronization, and DFT. This is shown in the next figure for the case of a cluster with 35 processors (5 nodes). Because the simulation is not properly load balanced due to the equal-sized chunks, there is a large variation in the timings for different processors particularly for the DFT where there are several idle processors (i.e., chunks which do not contain any DFT pixels).

Based on these results, we plot the average of the inverse of the timings (proportional to the number of cycles per second; a "rate" quantity which can demonstrate linear scaling) for the time-stepping and DFT over the full range of cluster sizes. The time-stepping results demonstrate (approximately) linear scaling. The size of the error bars increases with the number of cluster nodes mainly due to pronounced variations in the network bandwidth; the N1 instances do not support colocation via a compact placement policy. The DFT results (which excludes those processors without any DFT pixels) seem to be oscillating around a constant. This is not surprising because the processor(s) which takes the longest time to update its DFT pixels sets an upper bound on how fast the DFT calculation for all processors can proceed. It is the presence of this unique upper bound for each cluster which is revealed by the scaling plot.

See also FAQ/Should I expect linear speedup from the parallel Meep?