MPI for Python provides an object oriented approach to message passing which grounds on the standard MPI-2 C++ bindings. The interface was designed with focus in translating MPI syntax and semantics of standard MPI-2 bindings for C++ to Python. Any user of the standard C/C++ MPI bindings should be able to use this module without need of learning a new interface.
Communicating Python Objects and Array Data¶
The Python standard library supports different mechanisms for data persistence. Many of them rely on disk storage, but pickling and marshaling can also work with memory buffers.
pickle (slower, written in pure Python) and
(faster, written in C) modules provide user-extensible facilities to
serialize generic Python objects using ASCII or binary formats. The
marshal module provides facilities to serialize built-in Python
objects using a binary format specific to Python, but independent of
machine architecture issues.
MPI for Python can communicate any built-in or user-defined Python object taking advantage of the features provided by the mod:pickle module. These facilities will be routinely used to build binary representations of objects to communicate (at sending processes), and restoring them back (at receiving processes).
Although simple and general, the serialization approach (i.e., pickling and unpickling) previously discussed imposes important overheads in memory as well as processor usage, especially in the scenario of objects with large memory footprints being communicated. Pickling generic Python objects, ranging from primitive or container built-in types to user-defined classes, necessarily requires computer resources. Processing is also needed for dispatching the appropriate serialization method (that depends on the type of the object) and doing the actual packing. Additional memory is always needed, and if its total amount is not known a priori, many reallocations can occur. Indeed, in the case of large numeric arrays, this is certainly unacceptable and precludes communication of objects occupying half or more of the available memory resources.
MPI for Python supports direct communication of any object exporting the single-segment buffer interface. This interface is a standard Python mechanism provided by some types (e.g., strings and numeric arrays), allowing access in the C side to a contiguous memory buffer (i.e., address and length) containing the relevant data. This feature, in conjunction with the capability of constructing user-defined MPI datatypes describing complicated memory layouts, enables the implementation of many algorithms involving multidimensional numeric arrays (e.g., image processing, fast Fourier transforms, finite difference schemes on structured Cartesian grids) directly in Python, with negligible overhead, and almost as fast as compiled Fortran, C, or C++ codes.
In MPI for Python,
Comm is the base class of
are sublcasses of the
Comm class. The
Is_intra(), provided for convenience, it is not part
of the MPI specification) is defined for communicator objects and can
be used to determine the particular communicator class.
The two predefined intracommunicator instances are available:
COMM_WORLD. From them, new
communicators can be created as needed.
The number of processes in a communicator and the calling process rank
can be respectively obtained with methods
Get_rank(). The associated process group can be retrieved from a
communicator by calling the
Get_group() method, which returns an
instance of the
Group class. Set operations with
Group objects like like
Difference() are fully supported, as well as the creation of new
communicators from these groups using
New communicator instances can be obtained with the
Comm objects, the
Intercomm objects, and
Intercomm objects respectively.
Virtual topologies (
Distgraphcomm classes, being them specializations of
Intracomm class) are fully supported. New instances can be
obtained from intracommunicator instances with factory methods
Point to point communication is a fundamental capability of message passing systems. This mechanism enables the transmission of data between a pair of processes, one side sending, the other receiving.
MPI provides a set of send and receive functions allowing the communication of typed data with an associated tag. The type information enables the conversion of data representation from one architecture to another in the case of heterogeneous computing environments; additionally, it allows the representation of non-contiguous data layouts and user-defined datatypes, thus avoiding the overhead of (otherwise unavoidable) packing/unpacking operations. The tag information allows selectivity of messages at the receiving end.
MPI provides basic send and receive functions that are blocking. These functions block the caller until the data buffers involved in the communication can be safely reused by the application program.
In MPI for Python, the
Sendrecv() methods of communicator objects provide support for
blocking point-to-point communications within
Intercomm instances. These methods can communicate memory
buffers. The variants
can communicate generic Python objects.
On many systems, performance can be significantly increased by overlapping communication and computation. This is particularly true on systems where communication can be executed autonomously by an intelligent, dedicated communication controller.
MPI provides nonblocking send and receive functions. They allow the possible overlap of communication and computation. Non-blocking communication always come in two parts: posting functions, which begin the requested operation; and test-for-completion functions, which allow to discover whether the requested operation has completed.
In MPI for Python, the
Irecv() methods of
Comm class initiate a send and receive operation
respectively. These methods return a
uniquely identifying the started operation. Its completion can be
managed using the
methods of the
Request class. The management of
Request objects and associated memory buffers involved in
communication requires a careful, rather low-level coordination. Users
must ensure that objects exposing their memory buffers are not
accessed at the Python level while they are involved in nonblocking
Often a communication with the same argument list is repeatedly executed within an inner loop. In such cases, communication can be further optimized by using persistent communication, a particular case of nonblocking communication allowing the reduction of the overhead between processes and communication controllers. Furthermore , this kind of optimization can also alleviate the extra call overheads associated to interpreted, dynamic languages like Python.
In MPI for Python, the
methods of the
Comm class create a persistent request for a
send and receive operation respectively. These methods return an
instance of the
Prequest class, a subclass of the
Request class. The actual communication can be effectively
started using the
Start() method, and its completion can be
managed as previously described.
Collective communications allow the transmittal of data between multiple processes of a group simultaneously. The syntax and semantics of collective functions is consistent with point-to-point communication. Collective functions communicate typed data, but messages are not paired with an associated tag; selectivity of messages is implied in the calling order. Additionally, collective functions come in blocking versions only.
The more commonly used collective communication operations are the following.
- Barrier synchronization across all group members.
- Global communication functions
- Broadcast data from one member to all members of a group.
- Gather data from all members to one member of a group.
- Scatter data from one member to all members of a group.
- Global reduction operations such as sum, maximum, minimum, etc.
MPI for Python provides support for almost all collective
calls. Unfortunately, the
methods are currently unimplemented.
In MPI for Python, the
Alltoall() methods of
Comm instances provide support for collective communications
of memory buffers. The variants
alltoall() can communicate
generic Python objects. The vector variants (which can communicate
different amounts of data to each process)
Alltoallv() are also
supported, they can only communicate objects exposing memory buffers.
Global reduction operations on memory buffers are accessible through
methods. The variants
exscan() can communicate generic Python objects; however,
the actual required reduction computations are performed sequentially
at some process. All the predefined (i.e.,
MAX, etc.) reduction operations can be
Dynamic Process Management¶
In the context of the MPI-1 specification, a parallel application is static; that is, no processes can be added to or deleted from a running application after it has been started. Fortunately, this limitation was addressed in MPI-2. The new specification added a process management model providing a basic interface between an application and external resources and process managers.
This MPI-2 extension can be really useful, especially for sequential applications built on top of parallel modules, or parallel applications with a client/server model. The MPI-2 process model provides a mechanism to create new processes and establish communication between them and the existing MPI application. It also provides mechanisms to establish communication between two existing MPI applications, even when one did not start the other.
In MPI for Python, new independent process groups can be created
by calling the
Spawn() method within an intracommunicator (i.e.,
Intracomm instance). This call returns a new
intercommunicator (i.e., an
Intercomm instance) at the parent
process group. The child process group can retrieve the matching
intercommunicator by calling the
Get_parent() (class) method
defined in the
Comm class. At each side, the new
intercommunicator can be used to perform point to point and collective
communications between the parent and child groups of processes.
Alternatively, disjoint groups of processes can establish
communication using a client/server approach. Any server application
must first call the
Open_port() function to open a port and
Publish_name() function to publish a provided service, and
next call the
Accept() method within an
instance. Any client applications can first find a published
service by calling the
Lookup_name() function, which returns
the port where a server can be contacted; and next call the
Connect() method within an
Intracomm instance. Both
Connect() methods return an
Intercomm instance. When connection between client/server
processes is no longer needed, all of them must cooperatively call the
Disconnect() method of the
Comm class. Additionally,
server applications should release resources by calling the
One-sided communications (also called Remote Memory Access, RMA) supplements the traditional two-sided, send/receive based MPI communication model with a one-sided, put/get based interface. One-sided communication that can take advantage of the capabilities of highly specialized network hardware. Additionally, this extension lowers latency and software overhead in applications written using a shared-memory-like paradigm.
The MPI specification revolves around the use of objects called windows; they intuitively specify regions of a process’s memory that have been made available for remote read and write operations. The published memory blocks can be accessed through three functions for put (remote send), get (remote write), and accumulate (remote update or reduction) data items. A much larger number of functions support different synchronization styles; the semantics of these synchronization operations are fairly complex.
In MPI for Python, one-sided operations are available by using
instances of the
Win class. New window objects are
created by calling the
Create() method at all processes within a
communicator and specifying a memory buffer . When a window instance
is no longer needed, the
Free() method should be called.
The three one-sided MPI operations for remote write, read and
reduction are available through calling the methods
Accumulate() respectively within a
Win instance. These methods need an integer rank identifying
the target process and an integer offset relative the base address of
the remote memory block being accessed.
The one-sided operations read, write, and reduction are implicitly
nonblocking, and must be synchronized by using two primary modes.
Active target synchronization requires the origin process to call the
Complete() methods at the origin process, and
target process cooperates by calling the
methods. There is also a collective variant provided by the
Fence() method. Passive target synchronization is more lenient,
only the origin process calls the
methods. Locks are used to protect remote accesses to the locked
remote window and to protect local load/store accesses to a locked
The POSIX standard provides a model of a widely portable file system. However, the optimization needed for parallel input/output cannot be achieved with this generic interface. In order to ensure efficiency and scalability, the underlying parallel input/output system must provide a high-level interface supporting partitioning of file data among processes and a collective interface supporting complete transfers of global data structures between process memories and files. Additionally, further efficiencies can be gained via support for asynchronous input/output, strided accesses to data, and control over physical file layout on storage devices. This scenario motivated the inclusion in the MPI-2 standard of a custom interface in order to support more elaborated parallel input/output operations.
The MPI specification for parallel input/output revolves around the use objects called files. As defined by MPI, files are not just contiguous byte streams. Instead, they are regarded as ordered collections of typed data items. MPI supports sequential or random access to any integral set of these items. Furthermore, files are opened collectively by a group of processes.
The common patterns for accessing a shared file (broadcast, scatter, gather, reduction) is expressed by using user-defined datatypes. Compared to the communication patterns of point-to-point and collective communications, this approach has the advantage of added flexibility and expressiveness. Data access operations (read and write) are defined for different kinds of positioning (using explicit offsets, individual file pointers, and shared file pointers), coordination (non-collective and collective), and synchronism (blocking, nonblocking, and split collective with begin/end phases).
In MPI for Python, all MPI input/output operations are performed
through instances of the
File class. File handles are
obtained by calling the
Open() method at all processes within a
communicator and providing a file name and the intended access mode.
After use, they must be closed by calling the
Files even can be deleted by calling method
After creation, files are typically associated with a per-process
view. The view defines the current set of data visible and
accessible from an open file as an ordered set of elementary
datatypes. This data layout can be set and queried with the
Get_view() methods respectively.
Actual input/output operations are achieved by many methods combining read and write calls with different behavior regarding positioning, coordination, and synchronism. Summing up, MPI for Python provides the thirty (30) methods defined in MPI-2 for reading from or writing to files using explicit offsets or file pointers (individual or shared), in blocking or nonblocking and collective or noncollective versions.
Initialization and Exit¶
Finalize() provide MPI initialization and finalization
respectively. Module functions
Is_finalized() provide the respective tests for initialization
actually called when you import the
MPI module from the
mpi4py package, but only if MPI is not already
initialized. In such case, calling
from Python is expected to generate an MPI error, and in turn an
exception will be raised.
MPI_Finalize() is registered (by using Python
Py_AtExit()) for being automatically
called when Python processes exit, but only if
actually initialized Therefore, there is no need to call
Finalize() from Python to ensure MPI finalization.
- The MPI version number can be retrieved from module function
Get_version(). It returns a two-integer tuple
Get_processor_name()function can be used to access the processor name.
- The values of predefined attributes attached to the world
communicator can be obtained by calling the
Get_attr()method within the
MPI timer functionalities are available through the
In order facilitate handle sharing with other Python modules
interfacing MPI-based parallel libraries, the predefined MPI error
ERRORS_ARE_FATAL can be
assigned to and retrieved from communicators, windows and files using
When the predefined error handler
ERRORS_RETURN is set,
errors returned from MPI calls within Python code will raise an
instance of the exception class
Exception, which is a subclass
of the standard Python exception
After import, mpi4py overrides the default MPI rules governing
inheritance of error handlers. The
handler is set in the predefined
COMM_WORLD communicators, as well as any new
File instance created
through mpi4py. If you ever pass such handles to C/C++/Fortran
library code, it is recommended to set the
ERRORS_ARE_FATAL error handler on them to ensure MPI
errors do not pass silently.
from mpi4py.MPI import * will cause a name
clashing with standard Python
Exception base class.