4.5. Communication patterns¶
This page describes various inter-processor communication operations provided by LAMMPS, mostly in the core Comm class. These are operations for common tasks implemented using MPI library calls. They are used by other classes to perform communication of different kinds. These operations are useful to know about when writing new code for LAMMPS that needs to communicate data between processors.
4.5.1. Owned and ghost atoms¶
As described on the parallel partitioning algorithms page, LAMMPS spatially decomposes the simulation domain, either in a brick or tiled manner. Each processor (MPI task) owns atoms within its subdomain and additionally stores ghost atoms within a cutoff distance of its subdomain.
Forward and reverse communication¶
As described on the parallel communication algorithms page, the most common communication operations are first, forward communication which sends owned atom information from each processor to nearby processors to store with their ghost atoms. The need to do this communication arises when data from the owned atoms is updated (e.g. their positions) and this updated information needs to be copied to the corresponding ghost atoms.
And second, reverse communication, which sends ghost atom information from each processor to the owning processor to accumulate (sum) the values with the corresponding owned atoms. The need for this arises when data is computed and also stored with ghost atoms (e.g. forces when using a “half” neighbor list) and thus those terms need to be added to their corresponding atoms on the process where they are “owned” atoms. Please note, that with the newton off setting this does not happen and the neighbor lists are constructed so that these interactions are computed on both MPI processes containing one of the atoms and only the data pertaining to the local atom is stored.
The time-integration classes in LAMMPS invoke these operations each timestep via the forward_comm() and reverse_comm() methods in the Comm class. Which per-atom data is communicated depends on the currently used atom style and whether comm_modify vel setting is “no” (default) or “yes”.
Similarly, Pair style classes can invoke the forward_comm(this)
and reverse_comm(this) methods in the Comm class to perform the
same operations on per-atom data that is generated and stored within
the pair style class. Note that this function requires passing the
this pointer as the first argument to enable the Comm class to
call the “pack” and “unpack” functions discussed below. An example of
the use of these functions are many-body pair styles like the
embedded-atom method (EAM) which compute intermediate values in the
first part of the compute() function that need to be stored by both
owned and ghost atoms for the second part of the force computation.
The Comm class methods perform the MPI communication for buffers of
per-atom data. They “call back” to the Pair class, so it can pack
or unpack the buffer with data the Pair class owns. There are 4
such methods that the Pair class must define, assuming it uses both
forward and reverse communication:
The arguments to these methods include the buffer and a list of atoms
to pack or unpack. The Pair class also must set the comm_forward
and comm_reverse variables, which store the number of values stored
in the communication buffers for each operation. This means, if
desired, it can choose to store multiple per-atom values in the
buffer, and they will be communicated together to minimize
communication overhead. The communication buffers are defined vectors
double values. To correctly store integers that may be
64-bit (bigint, tagint, imageint) in the buffer, you need to use the
ubuf union construct.
The Fix, Compute, and Dump classes can also invoke the same kind of forward and reverse communication operations using the same Comm class methods. Likewise, the same pack/unpack methods and comm_forward/comm_reverse variables must be defined by the calling Fix, Compute, or Dump class.
For Fix classes, there is an optional second argument to the forward_comm() and reverse_comm() call which can be used when the fix performs multiple modes of communication, with different numbers of values per atom. The fix should set the comm_forward and comm_reverse variables to the maximum value, but can invoke the communication for a particular mode with a smaller value. For this to work, the pack_forward_comm(), etc methods typically use a class member variable to choose which values to pack/unpack into/from the buffer.
Finally, for reverse communications in Fix classes there is also the reverse_comm_variable() method that allows the communication to have a different amount of data per-atom. It invokes these corresponding callback methods:
which have extra arguments to specify the amount of data stored in the buffer for each atom.
4.5.2. Higher level communication¶
There are also several higher-level communication operations provided in LAMMPS which work for either brick or tiled decompositions. They may be useful for a new class to invoke if it requires more sophisticated communication than the forward and reverse methods provide. The 3 communication operations described here are
You can invoke these grep command in the LAMMPS src directory, to see a list of classes that invoke the 3 operations.
grep "\->ring" *.cpp */*.cpp
grep "irregular\->" *.cpp
grep "\->rendezvous" *.cpp */*.cpp
The ring operation is invoked via the ring() method in the Comm class.
Each processor first creates a buffer with a list of values, typically associated with a subset of the atoms it owns. Now think of the P processors as connected to each other in a ring. Each processor M sends data to the next M+1 processor. It receives data from the preceding M-1 processor. The ring is periodic so that the last processor sends to the first processor, and the first processor receives from the last processor.
Invoking the ring() method passes each processor’s buffer in P steps around the ring. At each step a callback method, provided as an argument to ring(), in the caller is invoked. This allows each processor to examine the data buffer provided by every other processor. It may extract values needed by its atoms from the buffers, or it may alter placeholder values in the buffer. In the latter case, when the ring operation is complete, each processor can examine its original buffer to extract modified values.
Note that the ring operation is similar to an MPI_Alltoall() operation, where every processor effectively sends and receives data to every other processor. The difference is that the ring operation does it one step at a time, so the total volume of data does not need to be stored by every processor. However, the ring operation is also less efficient than MPI_Alltoall() because of the P stages required. So it is typically only suitable for small data buffers and occasional operations that are not time-critical.
The irregular operation is provided by the Irregular class. What LAMMPS terms irregular communication is when each processor knows what data it needs to send to what processor, but does not know what processors are sending it data. An example is when load-balancing is performed and each processor needs to send some of its atoms to new processors.
The Irregular class provides 5 high-level methods useful in this context:
For the create_data() method, each processor specifies a list of N datums to send, each to a specified processor. Internally, the method creates efficient data structures for performing the communication. The exchange_data() method triggers the communication to be performed. Each processor provides the vector of N datums to send, and the size of each datum. All datums must be the same size.
The create_atom() and exchange_atom() methods are similar, except that the size of each datum can be different. Typically, this is used to communicate atoms, each with a variable amount of per-atom data, to other processors.
The migrate_atoms() method is a convenience wrapper on the create_atom() and exchange_atom() methods to simplify communication of all the per-atom data associated with an atom so that the atom can effectively migrate to a new owning processor. It is similar to the exchange() method in the Comm class invoked when atoms move to neighboring processors (in the regular or tiled decomposition) during timestepping, except that it allows atoms to have moved arbitrarily long distances and still be properly communicated to a new owning processor.
Finally, the rendezvous operation is invoked via the rendezvous() method in the Comm class. Depending on how much communication is needed and how many processors a LAMMPS simulation is running on, it can be a much more efficient choice than the ring() method. It uses the irregular operation internally once or twice to do its communication. The rendezvous algorithm is described in detail in (Plimpton), including some LAMMPS use cases.
For the rendezvous() method, each processor specifies a list of N datums to send and which processor to send each of them to. Internally, this communication is performed as an irregular operation. The received datums are returned to the caller via invocation of callback function, provided as an argument to rendezvous(). The caller can then process the received datums and (optionally) assemble a new list of datums to communicate to a new list of specific processors. When the callback function exits, the rendezvous() method performs a second irregular communication on the new list of datums.
Examples in LAMMPS of use of the rendezvous operation are the fix rigid/small and fix shake commands (for one-time identification of the rigid body atom clusters) and the identification of special_bond 1-2, 1-3 and 1-4 neighbors within molecules. See the special_bonds command for context.
(Plimpton) Plimpton and Knight, JPDC, 147, 184-195 (2021).