mpi4all 1.1.1.dev1

MPI4All: An MPI Binding Generator

Overview

This package provides a Python script to parse and generate bindings for Message Passing Interface (MPI) standard. The parser analyzes the MPI headers and generates a specification file with the defined macros, functions and types. The specification file is different for each version and implementation of MPI, the file can be stored to generate binding without using the parser.

We can currently generate bindings for Java and Go. Java makes use of Foreign Linker API and Foreign Memory Access API so the performance is significantly better than Java Native Interface (JNI) implementations. Go use cgo, so MPI headers are needed to compile. More languages may be added in the future, feel free to make a pull request.

The objective of the project is to create efficient bindings for MPI automatically. The project will never become an object oriented interface like mpi4py, although an equivalent library could be built using our bindings.

MPI4All has been built in the field of the IgnisHPC project for MPI usage.

Install

You can install MPI4All using pip:

$ pip install mpi4all

Dependencies

• Python 3.8+

• An MPI implementation, Java requires building shared/dynamic libraries.

Tested with:

• MPICH: 3.1.4, 3.2.1, 3.3.2, 3.4.3, 4.0, 4.1

• Open MPI: 4.0.7, 4.1.4, 5.0.0rc12

Examples

MPI4All

MPI4All can generate the bindings for Java and Go with the default MPI library installed in the system:

$ mpi4all --go --java

or using a specification file:

$ mpi4all --load mpich-4.0.json --go --java

Specification files can be generated with --dump or downloaded from the releases section.

Java

External functions cannot use data inside java heap. The example shows how to use ByteBuffer.allocateDirect and Arena to allocate memory outside the java heap.

import java.lang.foreign.*;
import java.nio.ByteBuffer;
import java.nio.IntBuffer;

import org.mpi.Mpi;

public class Main {
    public static void main(String[] args) throws Throwable {
        Mpi.MPI_Init(Mpi.C_pointer.NULL.cast(), Mpi.MPI_ARGVS_NULL);

        int rank;
        int size;

        // When the buffer is interpreted by the MPI function, the native order must be used.
        // If the MPI function only sends or receives the buffer, the order is indifferent.
        ByteBuffer buffer = ByteBuffer.allocateDirect(Mpi.C_int.byteSize()).order(ByteOrder.nativeOrder());

        Mpi.MPI_Comm_rank(Mpi.MPI_COMM_WORLD, new Mpi.C_pointer<>(MemorySegment.ofBuffer(buffer)));
        rank = buffer.get(0);
        try (Arena arena = Arena.ofConfined()) {// Using confined arena
            Mpi.C_int c_size = Mpi.C_int.alloc(arena);
            Mpi.MPI_Comm_size(Mpi.MPI_COMM_WORLD, c_size.pointer(arena));
            size = c_size.get();
        }

        buffer = ByteBuffer.allocateDirect(Mpi.C_int.byteSize() * size);

        Mpi.C_int c_rank = Mpi.C_int.alloc(); // Using auto gc arena
        c_rank.set(rank);
        Mpi.MPI_Allgather(c_rank.pointer().cast(), 1, Mpi.MPI_INT,
                new Mpi.C_pointer<>(MemorySegment.ofBuffer(buffer)), 1, Mpi.MPI_INT, Mpi.MPI_COMM_WORLD);


        for (int i = 0; i < size; i++) {
            if (i != buffer.get(i)) {
                throw new RuntimeException("Allgather error");
            }
        }


        Mpi.MPI_Finalize();
    }
}

GO

C_int and int data types are usually aliases but it is preferable to use C_int to avoid surprises. Functions with void * arguments use usafe.pointer instead, you can use the auxiliary functions mpi.P and mpi.PA to convert variables and array respectively to usafe.pointer. All other pointers are converted to their equivalents in Go, &var or &array[0] is sufficient to send the memory address.

package main

import "mpi"

func main() {
    if err := mpi.MPI_Init(nil, nil); err != nil {
        panic(err)
    }

    var rank mpi.C_int
    var size mpi.C_int

    if err := mpi.MPI_Comm_rank(mpi.MPI_COMM_WORLD, &rank); err != nil {
        panic(err)
    }

    if err := mpi.MPI_Comm_size(mpi.MPI_COMM_WORLD, &size); err != nil {
        panic(err)
    }

    result := make([]mpi.C_int, int(size))

    if err := mpi.MPI_Allgather(mpi.P(&rank), 1, mpi.MPI_INT,
        mpi.PA(&result), mpi.C_int(len(result)), mpi.MPI_INT, mpi.MPI_COMM_WORLD); err != nil {
        panic(err)
    }

    for i := 0; i < int(size); i++ {
        if i != int(result[i]) {
            panic("Allgather error")
        }
    }

    if err := mpi.MPI_Finalize(); err != nil {
        panic(err)
    }

}

Usage

usage: mpi4all [-h] [--out path] [--log lvl] [--cc path] [--cxx path]
               [--exclude str [str ...]] [--enable-fortran] [--no-arg-names]
               [--dump path] [--load path] [--cache path] [--go]
               [--no-generic] [--go-package name] [--go-out name] [--java]
               [--java-package name] [--java-class name] [--java-out name]
               [--java-lib-name name] [--java-lib-out name] [--version]

A script to generate mpi bindings

options:
  -h, --help            show this help message and exit
  --out path            Output folder, by default is working directory
  --log lvl             Log level, default error
  --version             show program's version number and exit

Mpi parser arguments:
  --cc path             MPI C compiler, by default uses the 'mpicc' in PATH
  --cxx path            MPI C++ compiler, by default uses the 'mpic++' in PATH
  --exclude str [str ...]
                        Exclude functions and macros that match with any
                        pattern
  --enable-fortran      Parse MPI Fortran functions, which are disabled by
                        default, to avoid linking errors if they are not
                        available
  --no-arg-names        Use xi as the parameter name in MPI functions
  --dump path           Dump parser output as json file, - for stdout
  --load path           Don't use a parser and load info from a JSON file, -
                        for stdin
  --cache path          Make --dump if the file does not exist and --load
                        otherwise

Go builder arguments:
  --go                  Enable Go generator
  --no-generic          Disable utility functions that require go 1.18+
  --go-package name     Go package name, default mpi
  --go-out name         Go output directory, by default <out>

Java builder arguments:
  --java                Enable Java 21 generator
  --java-package name   Java package name, default org.mpi
  --java-class name     Java class name, default Mpi
  --java-out name       Java output directory, default <out>
  --java-lib-name name  Java C library name without any extension, default
                        mpi4alljava
  --java-lib-out name   Java output directory for C library, default <java-
                        out>/<java-lib-name>