gpi2.md

GPI-2

##A library that implements the GASPI specification

Introduction

Programming Next Generation Supercomputers: GPI-2 is an API library for asynchronous interprocess, cross-node communication. It provides a flexible, scalable and fault tolerant interface for parallel applications.

The GPI-2 library (www.gpi-site.com/gpi2/) implements the GASPI specification (Global Address Space Programming Interface, www.gaspi.de). GASPI is a Partitioned Global Address Space (PGAS) API. It aims at scalable, flexible and failure tolerant computing in massively parallel environments.

Modules

The GPI-2, version 1.0.2 is available on Anselm via module gpi2:

    $ module load gpi2

The module sets up environment variables, required for linking and running GPI-2 enabled applications. This particular command loads the default module, which is gpi2/1.0.2

Linking

!!! Note "Note" Link with -lGPI2 -libverbs

Load the gpi2 module. Link using -lGPI2 and -libverbs switches to link your code against GPI-2. The GPI-2 requires the OFED infinband communication library ibverbs.

Compiling and linking with Intel compilers

    $ module load intel
    $ module load gpi2
    $ icc myprog.c -o myprog.x -Wl,-rpath=$LIBRARY_PATH -lGPI2 -libverbs

Compiling and linking with GNU compilers

    $ module load gcc
    $ module load gpi2
    $ gcc myprog.c -o myprog.x -Wl,-rpath=$LIBRARY_PATH -lGPI2 -libverbs

Running the GPI-2 codes

!!! Note "Note" gaspi_run starts the GPI-2 application

The gaspi_run utility is used to start and run GPI-2 applications:

    $ gaspi_run -m machinefile ./myprog.x

A machine file (machinefile) with the hostnames of nodes where the application will run, must be provided. The machinefile lists all nodes on which to run, one entry per node per process. This file may be hand created or obtained from standard $PBS_NODEFILE:

    $ cut -f1 -d"." $PBS_NODEFILE > machinefile

machinefile:

    cn79
    cn80

This machinefile will run 2 GPI-2 processes, one on node cn79 other on node cn80.

machinefle:

    cn79
    cn79
    cn80
    cn80

This machinefile will run 4 GPI-2 processes, 2 on node cn79 o 2 on node cn80.

!!! Note "Note" Use the mpiprocs to control how many GPI-2 processes will run per node

Example:

    $ qsub -A OPEN-0-0 -q qexp -l select=2:ncpus=16:mpiprocs=16 -I

This example will produce $PBS_NODEFILE with 16 entries per node.

gaspi_logger

!!! Note "Note" gaspi_logger views the output form GPI-2 application ranks

The gaspi_logger utility is used to view the output from all nodes except the master node (rank 0). The gaspi_logger is started, on another session, on the master node - the node where the gaspi_run is executed. The output of the application, when called with gaspi_printf(), will be redirected to the gaspi_logger. Other I/O routines (e.g. printf) will not.

Example

Following is an example GPI-2 enabled code:

    #include <GASPI.h>
    #include <stdlib.h>

    void success_or_exit ( const char* file, const int line, const int ec)
    {
      if (ec != GASPI_SUCCESS)
        {
          gaspi_printf ("Assertion failed in %s[%i]:%dn", file, line, ec);
          exit (1);
        }
    }

    #define ASSERT(ec) success_or_exit (__FILE__, __LINE__, ec);

    int main(int argc, char *argv[])
    {
      gaspi_rank_t rank, num;
      gaspi_return_t ret;

      /* Initialize GPI-2 */
      ASSERT( gaspi_proc_init(GASPI_BLOCK) );

      /* Get ranks information */
      ASSERT( gaspi_proc_rank(&rank) );
      ASSERT( gaspi_proc_num(&num) );

      gaspi_printf("Hello from rank %d of %dn",
               rank, num);

      /* Terminate */
      ASSERT( gaspi_proc_term(GASPI_BLOCK) );

      return 0;
    }

Load modules and compile:

    $ module load gcc gpi2
    $ gcc helloworld_gpi.c -o helloworld_gpi.x -Wl,-rpath=$LIBRARY_PATH -lGPI2 -libverbs

Submit the job and run the GPI-2 application

    $ qsub -q qexp -l select=2:ncpus=1:mpiprocs=1,place=scatter,walltime=00:05:00 -I
    qsub: waiting for job 171247.dm2 to start
    qsub: job 171247.dm2 ready

    cn79 $ module load gpi2
    cn79 $ cut -f1 -d"." $PBS_NODEFILE > machinefile
    cn79 $ gaspi_run -m machinefile ./helloworld_gpi.x
    Hello from rank 0 of 2

At the same time, in another session, you may start the gaspi logger:

    $ ssh cn79
    cn79 $ gaspi_logger
    GASPI Logger (v1.1)
    [cn80:0] Hello from rank 1 of 2

In this example, we compile the helloworld_gpi.c code using the gnu compiler (gcc) and link it to the GPI-2 and ibverbs library. The library search path is compiled in. For execution, we use the qexp queue, 2 nodes 1 core each. The GPI module must be loaded on the master compute node (in this example the cn79), gaspi_logger is used from different session to view the output of the second process.