Working with MPI

Distributed memory parallelism in Tamaas is implemented with MPI. Due to the bottleneck role of the fast-Fourier transform in Tamaas’ core routines, the data layout of Tamaas is that of FFTW. Tamaas is somewhat affected by limitations of FFTW, and MPI only works on systems with a 2D boundary, i.e. basic_2d, surface_2d and volume_2d model types (which are the most important anyways, since rough contact mechanics can yield different scaling laws in 1D).

MPI support in Tamaas is still experimental, but the following parts are tested:

  • Rough surface generation

  • Surface statistics computation

  • Elastic normal contact

  • Elastic-plastic contact (with DFSANECXXSolver)

  • Dumping models with H5Dumper and NetCDFDumper.

Tip

One can look at examples/plasticity.py for a full example of an elastic-plastic contact simulation that can run in MPI.

Transparent MPI context

Some parts of Tamaas work transparently with MPI and no additional work or logic is needed.

Warning

MPI_Init() is automatically called when importing the tamaas module in Python. While this works transparently most of the time, in some situations, e.g. in Singularity containers, the program can hang if tamaas is imported first. It is therefore advised to run from mpi4py import MPI before import tamaas to avoid issues.

Creating a model

The following snippet creates a model whose global shape is [16, 2048, 2048]:

import tamaas as tm

model = tm.Model(tm.model_type.volume_2d,
                 [0.1, 1, 1], [16, 2048, 2048])
print(model.shape, model.global_shape)

Running this code with mpirun -np 3 will print the following (not necessarily in this order):

[16, 683, 2048] [16, 2048, 2048]
[16, 682, 2048] [16, 2048, 2048]
[16, 683, 2048] [16, 2048, 2048]

Note that the partitioning occurs on the x dimension of the model (see below for more information on the data layout imposed by FFTW).

Creating a rough surface

Similarly, rough surface generators expect a global shape and return the partionned data:

iso = tm.Isopowerlaw2D()
iso.q0, iso.q1, iso.q2, iso.hurst = 4, 4, 32, .5
gen = tm.SurfaceGeneratorRandomPhase2D([2048, 2048])
gen.spectrum = iso

surface = gen.buildSurface()
print(surface.shape, tm.mpi.global_shape(surface.shape))

With mpirun -np 3 this should print:

(682, 2048) [2048, 2048]
(683, 2048) [2048, 2048]
(683, 2048) [2048, 2048]

Handling partitioning edge cases

Under certain conditions, FFTW may assign to one or more processes a size of zero to the x dimension of the model. If that happens, the surface generator will raise a runtime error, which causes a deadlock because it does not exit the processes with zero data. The correct way to handle this edge case is:

from mpi4py import MPI

try:
    gen = tm.SurfaceGeneratorRandomPhase2D([128, 128])
except RuntimeError as e:
    print(e)
    MPI.COMM_WORLD.Abort(1)

This will correctly kill all processes. Alternatively, os._exit() can be used, but one should avoid sys.exit(), as it kills the process by raising an exception, which still results in a deadlock.

Computing statistics

With a model’s data distributed among independent process, computing global properties, like the true contact area, must be done in a collective fashion. This is transparently handled by the Statistics class, e.g. with:

contact = tm.Statistics2D.contact(model.traction)

This gives the correct contact fraction, whereas something like np.mean(model.traction > 0) will give a different result on each processor.

Nonlinear solvers

The only nonlinear solver (for plastic contact) that works with MPI is DFSANECXXSolver, which is a C++ implementation of DFSANESolver that works in an MPI context.

Note

Scipy and Numpy use optimized BLAS routines for array operations, while Tamaas does not, which results in serial performance of the C++ implementation of the DF-SANE algorithm being lower than the Scipy version.

Dumping models

The only dumpers that properly works in MPI are the H5Dumper and NetCDFDumper. Output is then as simple as:

from tamaas.dumpers import H5Dumper

H5Dumper('output', all_fields=True) << model

This is useful for doing post-processing separately from the main simulation: the post-processing can then be done in serial.

MPI convenience methods

Not every use case can be handled transparently, but although adapting existing scripts to work in an MPI context can require some work, especially if said scripts rely on numpy and scipy for pre- and post-processing (e.g. constructing a parabolic surface for hertzian contact, computing the total contact area), the module mpi provides some convenience functions to make that task easier. The functions mpi.scatter and mpi.gather can be used to scatter/gather 2D data using the partitioning scheme expected from FFTW (see figure below). The functions mpi.rank and mpi.size are used to determine the local process rank and the total number of processes respectively.

If finer control is needed, the function mpi.local_shape gives the 2D shape of the local data if given the global 2D shape (its counterpart mpi.global_shape does the exact opposite), while mpi.local_offset gives the offset of the local data in the global \(x\) dimension. These two functions mirror FFTW’s own data distribution functions.

_images/mpi_data_distribution.png

2D Data distribution scheme from FFTW. N0 and N1 are the number of points in the \(x\) and \(y\) directions respectively. The array local_N0, indexed by the process rank, give the local size of the \(x\) dimension. The local_offset function gives the offset in \(x\) for each process rank.

The mpi module also contains a function sequential whose return value is meant to be used as a context manager. Within the sequential context the default communicator is MPI_COMM_SELF instead of MPI_COMM_WORLD.

For other MPI functionality not covered by Tamaas that may be required, one can use mpi4py, which in conjunction with the methods in mpi should handle just about any use case.